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Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design 3rd Edition Shijie Liu

Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design 3rd Edition Shijie Liu Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design 3rd Edition Shijie Liu Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design 3rd Edition Shijie Liu

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Shijie Liu Professor Chemical Engineering SUNY ESF Syracuse NY, United States Bioprocess Engineering Kinetics, Sustainability, and Reactor Design Third Edition
Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2020 Elsevier B.V. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, in- cluding photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our ar- rangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understand- ing, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any infor- mation, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-0-12-821012-3 For information on all Elsevier publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Joe Hayton Acquisitions Editor: Kostas Marinakis Editorial Project Manager: Liz Heijkoop Production Project Manager: Omer Mukthar Designer: Mark Rogers Typeset by Thomson Digital
Bioprocess Engineering. http://dx.doi.org/10.1016/B978-0-12-821012-3.00001-4 Copyright © 2020 Elsevier B.V. All rights reserved. 1 1.1 Biological cycle Fig. 1.1 illustrates the natural biological processes occurring on Earth. Living systems consist of plants, animals, and mi- croorganisms. Sunlight is used by plants to convert CO2 and H2O into carbohydrates and other organic matter, releasing O2. Animals consume plant matter, converting plant materials into animal cells, and using the chemical energy from oxidizing plant matter into CO2 and H2O (H2O also serves as a key substrate for animals), finishing the cycle. Microorganisms further convert dead animal and/or plant biomass into other form of organic substances fertilizing the growth of plants, releasing CO2 and H2O, and the cycle is repeated. Energy from the Sun is used to form molecules and organisms that we call life. Ma- terials or matter participating in the biological cycle are renewable so long as the cycle is maintained. Bioprocess engineers manipulate and make use of this cycle by designing processes to make desired products, either by training microorganisms, plants, and animals, or via direct chemical conversions. The reactor is the heart of any chemical and/or biochemical processes. With reactors, bioprocesses turn inexpensive sus- tainably renewable chemicals such as carbohydrates, into valuable ones that humans need. As such, bioprocesses are chemi- cal processes that use biological substrates and/or catalysts. While not limited to such, we tend to refer to bioprocesses as (1) biologically converting inexpensive “chemicals” or materials into valuable chemicals or materials; and (2) manipulating biological organisms to serve as “catalyst” for conversion or production of products that human need. Bioprocess engineers are the only people technically trained to understand, design, and efficiently handle bioreactors. Bioprocess engineering ensures that a favorable sustainable state or predictable outcome of a bioprocess is achieved. This is equivalent to saying that bioprocess engineers are engineers with, differentiating from other engineers, training in biological sciences, especially quantitative and analytical biological sciences, and green chemistry. If one thinks of science as a dream, engineering is making the dream a reality. The maturing of Chemical Engineer- ing to a major discipline and as one of the very few well-defined disciplines in the 1950s has led to the ease in the mass production of commodity chemicals and completely changed the economics or value structure of materials and chemicals, thanks to the vastly available what were then “waste” and “toxic” materials—fossil resources. Food and materials can be manufactured from the cheap fossil materials. Our living standards improved significantly. Today, chemical reactors and chemical processes are not built by trial-and-error, but by design. The performance of a chemical reactor can be predicted, not just found to happen that way; the differences between large and small reactors are largely solved. Once a dream for the visional pioneers, it can now be achieved at ease. Fossil chemical and energy sources have provided much of our needs for advancing and maintaining the living standards of today. With the dwindling of fossil resources, we are facing yet an- other value structure change. The dream has been shifted to realizing a society that is built upon renewable and sustainable resources. Fossil sources will no longer be abundant for human use. Sustainability becomes the primary concern. Who is going to make this dream come true? Chapter 1 What is bioprocess engineering? Chapter outline 1.1 Biological cycle 1 1.2 Bioprocess engineering applications 2 1.3 Scales: living organism and manufacturing 3 1.4 Green chemistry 4 1.5 Sustainability 5 1.6 Biorefinery 5 1.7 Biotechnology and bioprocess engineering 8 1.8 Mathematics, biology, and engineering 9 1.9 The story of penicillin: the dawn of bioprocess engineering 9 1.10 Bioprocesses: regulatory constraints 12 1.11 The pillars of bioprocess kinetics and systems engineering 13 1.12 Summary 14 Problems 14 References 14 Further readings 15
2 Bioprocess Engineering  On a somewhat different scale, we can now manipulate life at its most basic level: the genetic. For thousands of years people have practiced genetic engineering at the level of selection and breeding, or directed evolution. But now it can be done in a purposeful, predetermined manner with the molecular-level manipulation of DNA, at a quantum leap level (as compared with directed evolution) or by design. We now have tools to probe the mysteries of life in a way unimaginable prior to the 1970s. With this intellectual revolution emerges new visions and new hopes: new medicines, semisynthetic organs, abundant and nutritious foods, computers based on biological molecules rather than silicon chips, organisms to degrade pollutants and clean up decades of unintentional damage to the environment, zero harmful chemical leakage to the environment while producing a wide array of consumer products, and revolutionized industrial processes. Our aim of comfortable living standards is ever higher. Without hard work, these dreams will remain merely dreams. Engineers will play an essential role in converting these visions into reality. Biosystems are very complex and beautifully constructed, but they must obey the rules of chemistry and physics and they are susceptible to engineering analysis. Living cells are predictable, and processes to use them can be methodically constructed on commercial scales. There lies a great task—analysis, design, and control of biosystems to the greater benefit of a sustainable humanity. This is the job of the bioprocess engineer. This text is organized such that you can learn bioprocess engineering from the principles. To limit the scope of the text, we have left out the product purification technologies, while focusing on the production generation or biotransformations. We attempt to bridge molecular level understandings to industrial applications. It is our hope that this will help you to strengthen your desire and ability to participate in the intellectual revolution and to make an important contribution to the human society. 1.2 Bioprocess engineering applications In a narrow sense, all human activities are centered around humans. In terms of human needs, bioprocess engineers deal from the production and application of biomaterials, to health defense, biologics development, and production, including gene therapy (manufacturing process), to the production of food and fuel as illustrated in Fig. 1.2. In all these applications, fundamentally, molecular interaction and/or (bio-) transformation governs the production and/or protection processes. A biologic drug is a product produced from a living organism or containing component(s) of living organisms. Biologics include recombinant proteins, tissues, genes, allergens, cells, blood components, blood, and vaccines. Biologics are used to treat numerous disease and conditions on humans. The transformation from chemicals to biologics, the functions or interac- tions of a biologic with human body, pharmacology, and the design of the biologic are subject areas of bioprocess engineering. Gene therapy is an experimental technique that uses genes to treat or prevent disease. This technique has the potential to allow doctors to treat a disorder by inserting a gene into a patient’s cells instead of using drugs or surgery. Researchers are testing several approaches to gene therapy, including: l Replacing a mutated gene that causes disease with a healthy copy of the gene. l Inactivating, or “knocking out,” a mutated gene that is functioning improperly. l Introducing a new gene into the body to help fight a disease. Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types of cancer, and certain viral infections), the technique remains risky and is still under study to make sure that it will be safe and effective. Gene therapy is currently being tested only for diseases that have no other cures. Cell therapy is the therapy in which cellular material is injected, grafted, or implanted into a patient; this generally means intact, living cells. For example, T cells capable of fighting cancer cells via cell-mediated immunity may be injected in the course of immunotherapy. FIGURE 1.1 The natural biological processes.
What is bioprocess engineering? Chapter | 1 3 Cell therapy originated in the 19th century when scientists experimented by injecting animal material in an attempt to prevent and treat illness. Although such attempts produced no positive benefit, further research found in the mid 20th century that human cells could be used to help prevent the human body rejecting transplanted organs, leading in time to successful bone-marrow transplantation Chimeric antigen receptor (CAR)-modified T cell therapy, for example, has proven to be effective for patients with B cell hematological malignancies. Challenges remain in how to scale out the production of CAR T cells under current good manufacturing procedure (cGMP) in an efficient, effective manner. Currently as a mostly autologous cell-based therapy, the CAR-T cell manufacturing process represents a completely different manufacturing model from traditional biologics. One of the challenges of this largely personalized medicine is the development of efficient technologies and cost-effective clinical manufacturing platforms to support the later-stage clinical trials toward commercialization. Substantial efforts have been placed on the upstream for gene transduction and cell expansion. Apart from health defense and/or biologics, commodity products production is crucial for the human society. Food, fuels, and materials fill in the basic needs. 1.3 Scales: living organism and manufacturing Bioprocess engineering deals with a variable scale, from the molecular level at research to process operation in a factory at manufacturing level. In health applications, this translates to medical research at the most fundamental level of enzyme/ protein to human health professionals at overall health. Fig. 1.3 shows side-side the comparison from a “traditional” chemi- cal engineering view on the left to the “health” engineering on the right. The function of a protein or an enzyme within human cells is important for the overall health of human. When or if any changes to the protein or a foreign protein invades a human cell, the physiology will change, causing a domino effect/ change to far-reaching cells. Regulating the protein and enzyme functions can also be effected with ligands or chemicals. The molecular interactions are key to the overall health of humans. FIGURE 1.2 The applications of bioprocess engineering centered around humanity needs. FIGURE 1.3 A comparison of the chemical engineering (left) with processes in a complex living organism: human body. The bottom is at the microscopic scale where molecular interactions are examined, whereas at the top the factory as a whole is considered.
4 Bioprocess Engineering  1.4 Green chemistry Green chemistry, also called sustainable chemistry, is a philosophy of chemical research and engineering that encourages the design of products and processes that minimize the use and generation of hazardous substances while maximizing the efficiency of the desired product generation. Whereas environmental chemistry is the chemistry of the natural environment, and of pollutant chemicals in nature, green chemistry seeks to reduce and prevent pollution at its source. In 1990, the Pol- lution Prevention Act was passed in the United States. This act helped create a modus operandi for dealing with pollution in an original and innovative way. It aims to avoid problems before they happen. Examples of green chemistry starts with the choice of solvent for a process—water, carbon dioxide, dry media, and non-volatile (ionic) liquids, which are some of the excellent choices. These solvents are not harmful to the environment as either emission can easily be avoided or they are ubiquous in nature. Paul Anastas, then of the United States Environmental Protection Agency, and John C. Warner developed 12 principles of green chemistry, which help to explain what the definition means in practice. The principles cover such concepts as— (1) the design of processes to maximize the amount of (all) raw material that ends up in the product; (2) the use of safe, environment-benign substances, including solvents, whenever possible; (3) the design of energy efficient processes; and (4) the best form of waste disposal: not to create it in the first place. The 12 principles are: 1. It is better to prevent waste than to treat or clean up waste after it is formed. 2. Synthetic methods should be designed to maximize “atom efficiency.” 3. Wherever practicable, synthetic methodologies should be designed to use and generate substances that possess little or no toxicity to human health and the environment. 4. Chemical products should be designed to preserve efficacy of function while reducing toxicity. 5. The use of auxiliary substances (e.g., solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used. 6. Energy requirements should be recognized for their environmental and economic impacts and should be minimized. Synthetic methods should be conducted at ambient temperature and pressure. 7. A raw material or feedstock should be renewable rather than depleting wherever technically and economically practicable. 8. Reduce derivatives—Unnecessary derivatization (blocking group, protection/ deprotection, temporary modification) should be avoided whenever possible. 9. Catalytic reagents (as selective as possible) are superior to stoichiometric reagents. 10. Chemical products should be designed so that at the end of their function they do not persist in the environment and break down into innocuous degradation products. 11. Analytical methodologies need to be further developed to allow for real-time, in-process monitoring and control prior to the formation of hazardous substances. 12. Substances and the form of a substance used in a chemical process should be chosen to minimize potential for chemi- cal accidents, including releases, explosions, and fires. One example of green chemistry achievements is the polylactic acid (or PLA). In 2002, Cargill Dow (now NatureWorks) won the Greener Reaction Conditions Award for their improved polylactic acid polymerization process. Lactic acid is pro- duced by fermenting corn and converted to lactide, the cyclic dimmer ester of lactic acid using an efficient, tin-catalyzed cyclization. The L,L-lactide enantiomers is isolated by distillation and polymerized in the melt to make a crystallizable polymer, which has use in many applications including textiles and apparel, cutlery, and food packaging. Wal-Mart has announced that it is using/will use PLA for its produce packaging. The NatureWorks PLA process substitutes renewable materials for petroleum feedstocks, does not require the use of hazardous organic solvents typical in other PLA processes, and results in a high-quality polymer that is recyclable and compostable. Understanding the concept of green chemistry holds a special position for bioprocess engineers. Processes we design and operate must have minimal potential environmental impacts while optimized for maximum benefit. Basic steps for green chemistry that are what bioprocess engineering do include: 1. Developing products and processes based on renewable resources, such as plant biomass; 2. Design processes that bypass dangerous/toxic-chemical intermediates; 3. Design processes that avoid dangerous/toxic solvent use; 4. Reducing chemical processing steps, but demands high efficiency; 5. Promoting biochemical processes to reduce chemical processing steps or toxic chemical utilization; 6. Design milder (closer to atmosphere temperature and pressure) processes and multiple product recovery routes;
What is bioprocess engineering? Chapter | 1 5 7. Bypassing chemical equilibrium with innovative reactor design, and biocatalysis, rather than adding intermediate steps. 8. Avoid production of unwanted products other than H2O and CO2. 1.5 Sustainability Sustainability is the capacity to endure or maintain at the longest timescale permissible. In other words, sustainability is the ability to maintain continuum. In ecology, the word describes how biological systems remain diverse and productive over time. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. For humans, sustainabil- ity is the potential for long-term maintenance of well-being, which has environmental, economic, and social dimensions. Healthy ecosystems and environments provide vital goods and services to humans and other organisms. Utilization and release of substances at a rate that is harmonious with a steady state nature is the key for sustainability. This naturally leads to a carrying capacity for each substance or species with which humans interact. The sustainable state can be influenced by (process conditions or) how we interact with nature. There are two major ways of reducing negative human impact and en- hancing ecosystem services. The first is environmental management; this approach is based largely on information gained from earth science, environmental science, and conservation biology. The second approach is management of human con- sumption of resources, which is based largely on information gained from economics. Practice of both of these major steps can ensure a more favorable sustainable state to be evolved into. Sustainability interfaces with economics through the social and ecological consequences of economic activity. Sus- tainable economics involves ecological economics where social, cultural, health-related, and monetary/financial aspects are integrated. Moving toward sustainability is also a social challenge that entails international and national law, urban planning and transport, local and individual lifestyles and ethical consumerism. Ways of living more sustainably can take many forms from reorganizing living conditions (e.g., ecovillages, eco-municipalities, and sustainable cities), reapprais- ing economic sectors (permaculture, green building, sustainable agriculture), or work practices (sustainable architecture), using science to develop new technologies (green technologies, renewable energy), to adjustments in individual lifestyles that conserve natural resources. These exercises reduce our reliance or demand on disturbing the environment. To make all these concepts come to light, bioprocess engineers will be at the forefront of developing and implementing the technologies needed. On a grand scale, maintaining renewability or looking for a favorable predictable steady state on everything we touch or interact is the key to sustainability (Fig. 1.4). This falls right in the arena of bioprocess engineering. Are you ready for the challenge of designing processes that meets sustainability demands? 1.6 Biorefinery On a grand scale, sustainability is the basis of nature. Enforcing sustainability at the time scale of humanity is an insurance of our way of life to continue. Prior to the 1900s, agriculture and forestry were the predominant sources of raw materi- als for energy, food and a wide range of everyday commodities, and the human civilization depended almost entirely on renewable materials. Humanity was restricted by the sustainable supply inefficiently harvested from the biomass, which drew energy from the sun. The industrial revolution has brought a leap in the human civilization. Mass production of goods by machines dominates our daily life. The industrial revolution was brought to mature by the development of combustion FIGURE 1.4 Change of sustainable state owing to human interruption.
6 Bioprocess Engineering  engines and subsequent development of fossil energy and chemical industry. Besides the more than doubling of useful bio- mass production/harvest, mankind has increasingly tapped into the large fossil-energy reserves. At first the fossil chemicals were regarded as waste and thus any use was welcomed. It soon became the cheapest chemical and energy sources for the industrial revolution. As a result, our living standards have seen a leap. There is no turning back to the primitive way of life in the past. However, fossil energy and chemical sources are depleting despite the cyclic price change of energy and com- modity materials. There is a critical need to change the current industry and human civilization to a sustainable manner, assuring that our way of life today continues on the path of improvement after the depletion of fossil sources. Our way of life exists only if sustainability is maintained on a time scale no longer than our life span. Biorefinery is concept in analogous to a petroleum refinery whereby a raw material feed (in this case plant ligocellulosic biomass instead of petroleum) is refined to a potpourri of products (on demand). In a biorefinery, lignocellulosic biomass is converted to chemicals, materials, and energy that runs on the human civilization, replacing the needs of petroleum, coal, natural gas, and other non-renewable energy and chemical sources. Lignocellulosic biomass is renewable as shown in Fig. 1.1, in that plant synthesizes chemicals by drawing energy from the sun and, carbon dioxide and water from the environment, while releasing oxygen. Combustion of biomass releases energy, carbon dioxide, and water. Therefore, biore- finery plays a key role in ensuring the cycle of biomass production and consumption included satisfying human needs for energy and chemicals. A biorefinery integrates a variety of conversion processes to produce multiple product streams such as transportation liquid fuels, steam/heat, electricity, and chemicals from lignocellulosic biomass. Biorefinery has been identified as the most promising route to the creation of a sustainable bio-based economy. Biorefinery is a collection of the essential technologies to transform biological raw materials into a range of industrially useful intermediates. By producing multiple products, a biorefinery maximizes the value derived from a lignocellulosic biomass feedstock. A biorefinery could produce one or more low-volume, high-value chemical products together with a low-value, high-volume liquid transportation fuel, while generating electricity and process heat for its own use and/or export. Fig. 1.5 shows a schematic of various biorefinery processes. There are at least three steps in converting woody biomass: pretreatment; cracking or rendering biomass to intermediate molecules; and conversion (of the intermediate molecules to desired products). There are three major categories or approaches in pretreatment—systematical disassembling processes; pyrolysis and gasification processes. In systematical disassembling processes, the lignocellulosic biomass is commonly disassembled to individual components systematically for optimal conversions that followed. The basic approach is based on a systematical disassembling and conversion to desired chemicals. This pretreatment method and the rout of conversion FIGURE 1.5 A schematic of various biorefinery processes. (With permission from: Liu, S., 2015. A synergetic pretreatment technology for woody biomass conversion. Appl. Ener. 144, 114–128).
What is bioprocess engineering? Chapter | 1 7 followed depend heavily on separation and/or physical fractionation of the intermediates as well as the final desired prod- ucts. Pyrolysis applies heat and some oxygen (or none) to render the biomass to liquid, while gasification renders the bio- mass to syngas. Biological conversions are preferred over chemical conversions due to their selectivity or green chemistry concepts. However, owing to the complexity of the lignocellulosic biomass, a multitude of biological processes is required for optimal operations. The biological reactions are also very slow and thus require larger facility foot prints. Especially following the gasification, bioconversion is in the “primitive” stage of development. Pyrolysis resembles more closely to the refinery whereby the products can be controlled in a more systematical man- ner. It may be classified as systematical disassembling as well. However, there are restrictions on the type of products the process can produce. Gasification as shown in Fig. 1.5 is at the extreme side of conversion technology, whereby the lignocellulosic biomass is disassembled to the basic building block for hydrocarbons: H2 and CO, and then reassembled to desired products as desired. The final products can be more easily tailored from syngas or CO + H2. For example, Fisher-Tropsch process can turn CO + H2 into higher alcohol, alkenes, and many other products. Syn gas (together with air: mixture of N2 and O2) is also the starting point for ammonia synthesis, from which nitrogen fertilizers and many other products are produced. However, all thermochemical processes suffer from selectivity. During the disassembling process, “coke” or “carbon” is produced especially at high temperatures and thus reduces the conversion efficiency, if H2 and CO are the desired intermediates. Thermal-chemical processes are generally considered less “green” than biological and other sequential disassembling processes due to their severe operating conditions, poor selectivity or byproducts generation, and thermodynamic restrictions. The promise of a biorefinery to supply the products human needs is shown in Fig. 1.6 for the various examples of build- ing blocks or platform chemicals that sugar (a specific example of glucose) can produce, besides the very basic building blocks of CO and H2. For example, glucose can be fermented to ethanol by yeast and bacteria anaerobically, and lactic acid can be produced by lacto bacteria. As shown in Fig. 1.6, each arrow radiates from the glucose in the center represents a route of biotransformation (or fermentation) by default, whereas chemical transformations are shown with labeled arrows. For example, glucose can be dehydrated to 5-hydroxymethylfurfural catalyzed with an acid, which can be further decomposed to levulinic acid by hydration. All these chemicals shown in Fig. 1.6 are examples of important platform (or intermediate) chemicals, as well as commodity chemicals. For example, ethanol is well known for its use as a liquid transportation fuel. FIGURE 1.6 The platform of chemicals derived from glucose (the molecule in the center of the diagram). Most of these chemicals are produced via fermentation (or biotransformation), while a few of them are produced via chemical reaction (or chemical transformation) as indicated.
8 Bioprocess Engineering  Ethanol can be dehydrated to ethylene, which is the monomer for polyethylene, or dehydrognated and dehydrated to make 1,3-butadiene, monomer for the synthetic rubber. Ethanol can also be employed to produce higher alcohols and alkenes. Are you prepared to be at the forefront of developing, designing and operating these processes for the sustainability and comfortability in humanity? 1.7 Biotechnology and bioprocess engineering Biotechnology is the use or development of methods of direct genetic manipulation for a socially desirable goal. Such a goal might be the production of a particular chemical, but it may also involve the production of better plants or seeds, gene ther- apy, or the use of specially designed organisms to degrade wastes. The key element is the use of sophisticated techniques outside the cell for genetic manipulation. Biotechnology is applied biology; it bridges biology to bioprocess engineering, just like applied chemistry or chemical technology bridges chemistry to chemical engineering. Many terms have been used to describe engineers working with biotechnology. The two terms that are considered general—Biological engineering and Bioengineering come from the two major fields of applications that require deep understanding of biology—agriculture and medicine. Bioengineering is a broad title including work on industrial, medi- cal and agricultural systems; its practitioners include agricultural, electrical, mechanical, industrial, environmental, and chemical engineers, and others. As such, Bioenegineering is not a well-defined term and usually it refers to biotechnology applications that are not easily categorized or in medical fields. Biological Engineering stems from engineering of biology which is also a general term. However, the term biological engineering is initially used by agricultural engineers for the engineering applications to or manipulation of plants and animals and is thus specific. For example, the Institute of Bio- logical Engineering (IBE) has a base in, although not limited to, agricultural engineering. ABET (Accreditation Board for Engineering and Technology, Inc.) brands Biological Engineering together with Agricultural Engineering when accredit- ing BS (Bachelor of Science) and MS (Master of Science) in engineering and technology educational programs. On the other hand, the Society for Biological Engineers was created within American Institute of Chemical Engineers. Therefore, biological engineering is also regarded as a not well defined term and can at times refer to biotechnology applications in agricultural fields. Biochemical engineering has usually meant the extension of chemical engineering principles to systems using a biological catalyst to bring about desired chemical transformations. It is often subdivided into bioreaction engineer- ing and bioseparations. Biomedical engineering has traditionally been considered totally separate from biochemical engi- neering, although the boundary between the two is increasingly vague, particularly in the areas of cell surface receptors and animal cell culture. Another relevant term is biomolecular engineering, which has been defined by the National Institutes of Health as “... research at the interface of biology and chemical engineering and is focused at the molecular level.” In all, a strong background in quantitative analysis, kinetic/dynamic behaviors, and equilibrium behaviors are strongly desirable. Increasingly, these biorelated engineering fields have become inter-related, although the names are restricting. Bioprocess engineering is a broader and at the same time a narrower field than the commonly used terms referred ear- lier—biological engineering, biochemical engineering, biomedical engineering, and biomolecular engineering. Bioprocess Engineering is a profession than spans all the bio-related engineering fields as mentioned earlier. It is a profession that has emerged to stand alone, as compared to the interdisciplinary profession once it was. Unlike the term bioengineering, the term biorpocess engineering is specific and well-defined. Bioprocess engineering emphasizes the engineering and sciences of industrial processes that are biobased—(1) biomass feedstock conversion for a sustainable society or biorefinery; (2) biocatalysis based processing; and (3) manipulation of micro-organisms for a sustainable and socially desirable goal. Bio- process engineering is not product-based nor is substrate-based. Therefore, bioprocess engineering deals with biological and chemical processes involved in all areas, not just for a particular substrate or species (of feedstock or intermediate), outcome or product. Thus, bioprocess engineering intercepts chemical, mechanical, electrical, environmental, medical, and industrial engineering fields, applying the principles to designing and analysis of processes based on using living cells or subcomponents of such cells, as well as non-living matters. Bioprocess engineering deals with both micro-scale (cellular/ molecular) and large-scale (systemwide / industrial) designs and analyses. Science and engineering of processes converting biomass materials to chemicals, materials, and energy are therefore part of bioprocess engineering by extension. Predict- ing and modeling system behaviors, detailed equipment and process design, sensor development, control algorithms, and manufacturing or operating strategies are just some of the challenges facing bioprocess engineers. At the heart of bioprocess engineering lays the process kinetics, reactor design and analysis for biosystems, which forms the basis for this text. We will focus primarily on the kinetics, dynamics, and reaction engineering involved in the bioprocess engineering. A key component is the application of engineering principles to systems containing biological catalysts and/or biomass as feedstock, but with an emphasis on those systems making use of biotechnology and green chemistry. The rapidly increasing ability to determine the complete sequence of genes in an organism offers new opportunities for bioprocess engineers in the design and monitoring of bioprocesses. The cell, itself, is now a designable component of the overall process.
What is bioprocess engineering? Chapter | 1 9 For practitioners working in the bioprocess engineering, some of journals and periodicals provide the latest develop- ments in the field. Here we name a few: l Biochemical Engineering Journal l Journal of Biological Engineering l Journal of Biomass Conversion and Biorefinery l Journal of Bioprocess Engineering and Biorefinery l Journal of Bioprocess and Bioystems Engineering l Journal of Biotechnology l Journal of Biotechnology Advances l Journal of Biotechnology and Bioprocess Engineering 1.8 Mathematics, biology, and engineering Mathematical modeling holds the key for engineers. Physics at its fundamental level examines forces and motion; one can view it as applied mathematics. In turn, chemistry examines molecules and their interactions. Since physics examines the motions of atoms, nuclei and electrons, at the basis of molecules, one can view chemistry as applied physics. This directly connects chemistry to mathematics at a fundamental level. Indeed, most physicists and chemists rely extensively on math- ematical modeling. While one can view biology as applied chemistry through the connection of chemicals and molecules, the fundamental trainings of biologists today and engineers are distinctly different. In the development of knowledge in the life sciences, unlike chemistry and physics, mathematical theories and quantitative methods (except statistics) have played a secondary role. Most progress has been due to improvements in experimental tools. Results are qualitative and descrip- tive models are formulated and tested. Consequently, biologists often have incomplete backgrounds in mathematics but are very strong with respect to laboratory tools and, more importantly, with respect to the interpretation of laboratory data from complex systems. Engineers usually possess a very good background in the physical and mathematical sciences. Often a theory leads to mathematical formulations, and the validity of the theory is tested by comparing predicted responses to those in experi- ments. Quantitative models and approaches, even to complex systems, are strengths. Biologists are usually better at the formation of testable hypotheses, experimental design, and data interpretation from complex systems. At the dawn of the biotechnology era, engineers were typically unfamiliar with the experimental techniques and strategies used by life scien- tists. However, today bioprocess engineers have entered even more sophisticated experimental techniques and strategies in life sciences (than biologists) due to the understanding and progress in the prediction and modeling of living cells. The well-groundedness in mathematical modeling gives bioprocess engineers an edge and responsibility in enforcing sustainability demands. In practice, the sustainable (or steady) state can be different from what we know today or when no human interruption is imposed. The sustainable state could even be fluctuating with a noticeable degree. Engineers hold great responsibility to convincing environmentalists and the public what to expect by accurately predicting the dynamic outcomes without speculating on the potential dramatic changes ahead. The skills of the engineer and of the life scientist are complementary. To convert the promises of molecular biology into new processes to make new products requires the integration of these skills. To function at this level, the engineer needs a solid understanding of biology and its experimental tools. In this book, we provide sufficient biological background for you to understand the chapters on applying engineering principles to biosystems. However, if you are serious about becoming a bioprocess engineer, it is desirable if you had taken courses in microbiology, biochemistry, and cell biology, as you would appreciate more of the engineering principles in this text. 1.9 The story of penicillin: the dawn of bioprocess engineering Penicillin is an antibiotic of significant importance. The familiar story of penicillin was well-presented by Kargi & Shuler in their text “Bioprocess Engineering – Basic Concepts.” As you would expect, the discovery of the chemical was acci- dental and the production of the chemical is elaborate. In September 1928, Alexander Fleming at St. Mary’s Hospital in London was trying to isolate the bacterium, Staphylococcus aureus, which causes boils. The technique in use was to grow the bacterium on the surface of a nutrient solution. One Friday, the basement window was accidently left open overnight. The experiments were carried out in the basement and one of the dishes had been contaminated inadvertently with a foreign particle. Normally, such a contaminated plate would be tossed out. However, Fleming noticed that no bacteria grew near the invading substance. Fleming’s genius was to realize that this observation was meaningful and not a “failed” experiment. Fleming recognized that the cell killing must be due to an antibacterial agent. He recovered the foreign particle and found that it was a common
10 Bioprocess Engineering  mold of the Penicillium genus (later identified as Penicillium notatum). Fleming nurtured the mold to grow and, using the crude extraction methods then available, managed to obtain a tiny quantity of secreted material. He then demonstrated that this material had powerful antimicrobial properties and named the product penicillin. Fleming carefully preserved the cul- ture, but the discovery lay essentially dormant for over a decade. World War II provided the impetus to resurrect the discovery. Sulfa drugs have a rather restricted range of activity, and an antibiotic with minimal side effects and broader applicability was desperately needed. In 1939, Howard Florey and Ernst Chain of Oxford decided to build on Fleming’s observations. Norman Heatley played the key role in producing sufficient material for Chain and Florey to test the effectiveness of penicillin. Heatley, trained as a biochemist, performed as a bioprocess engineer. He developed an assay to monitor the amount of penicillin made so as to determine the kinetics of the fermentation, developed a culture technique that could be implemented easily, and devised a novel back-extraction process to recover the very delicate product. After months of immense effort, they produced enough penicillin to treat some laboratory animals. Eighteen months after starting on the project, they began to treat a London policeman for a blood infection. The penicil- lin worked wonders initially and brought the patient to the point of recovery. Most unfortunately, the supply of penicillin was exhausted and the man relapsed and died. Nonetheless, Florey and Chain had demonstrated the great potential for penicillin, if it could be made in sufficient amount. To make large amounts of penicillin would require a process, and for such a process development, engineers would be needed, in addition to microbial physiologists and other life scientists. The war further complicated the situation. Great Britain’s industrial facilities were already totally devoted to the war. Florey and his associates approached pharmaceutical firms in the United States to persuade them to develop the capacity to produce penicillin, since the United States was not at war at that time. Many companies and government laboratories, assisted by many universities, took up the challenge. Particularly prominent were Merck, Pfizer, Squibb, and the USDA Northern Regional Research Laboratory in Peoria, Illinois. The first efforts with fermentation were modest. A large effort went into attempts to chemically synthesize penicillin. This effort involved hundreds of chemists. Consequently, many companies were at first reluctant to commit to the fermenta- tion process, beyond the pilot-plant stage. It was thought that the pilot-plant fermentation system could produce sufficient penicillin to meet the needs of clinical testing, but large-scale production would soon be done by chemical synthesis. At that time, US companies had achieved a great deal of success with chemical synthesis of other drugs, which gave the com- panies a great deal of control over the drug’s production. The chemical synthesis of penicillin proved to be exceedingly difficult (It was accomplished in the 1950s, and the synthesis route is still not competitive with fermentation). However, in 1940 fermentation for the production of a pharmaceutical was an unproved approach, and most companies were betting on chemical synthesis to ultimately dominate. The early clinical successes were so dramatic that in 1943 the War Production Board appointed A. L. Elder to coordinate the activities of producers to greatly increase the supply of penicillin. The fermentation route was chosen. As Elder recalls, “I was ridiculed by some of my closest scientific friends for allowing myself to become associated with what obviously was to be a flop-namely, the commercial production of penicillin by a fermentation process” (from Elder, 1970). The problems facing the fermentation process were indeed very formidable. The problem was typical of most new fermentation processes: a valuable product made at very low levels. The low rate of production per unit volume would necessitate very large and inefficient reactors, and the low concentration (titer) made product recovery and purification very difficult. In 1939 the final concentration in a typical penicillin fermentation broth was one part per million (ca. 0.001 g/L); gold is more plentiful in sea water. Furthermore, penicillin is a fragile and unstable product, which places significant constraints on the approaches used for recovery and purification. Life scientists at the Northern Regional Research Laboratory made many major contributions to the penicillin program. One was the development of a corn steep liquor-lactose based medium. Andrew J. Moyer succeeded to increase productiv- ity about 10-fold with this medium in November 26, 1941. A worldwide search by the laboratory for better producer strains of Penicillium led to the isolation of a Penicillium chrysogenum strain. This strain, isolated from a moldy cantaloupe at a Peoria fruit market, proved superior to hundreds of other isolates tested. Its progeny have been used in almost all commer- cial penicillin fermentations. The other hurdle was to decide on a manufacturing process. One method involved the growth of the mold on the surface of moist bran. This bran method was discarded because of difficulties in temperature control, sterilization, and equipment size. The surface method involved growth of the mold on top of a quiescent medium. The surface method used a variety of containers, including milk bottles, and the term “bottle plant” indicated such a manufacturing technique. The surface meth- od gave relatively high yields, but had a long-growing cycle and was very labor intensive. The first manufacturing plants were bottle plants because the method worked and could be implemented quickly. However, it was clear that the surface method would not meet the full need for penicillin. If the goal of the War Production Board was met by bottle plants, it was
What is bioprocess engineering? Chapter | 1 11 estimated that the necessary bottles would fill a row stretching from New York City to San Francisco. Engineers generally favored a submerged tank process. The submerged process presented challenges in terms of both mold physiology and in tank design and operation. Large volumes of absolutely clean, oil- and dirt-free sterile air were required. What were then very large agitators were required, and the mechanical seal for the agitator shaft had to be designed to prevent the entry of organisms. Even today, problems of oxygen supply and heat removal are important constraints on antibiotic fermenter design. Contamination by foreign organisms could degrade the product as fast as it was formed, consume nutrients before they were converted to penicillin, or produce toxins. In addition to these challenges in reactor design, there were similar hurdles in product recovery and purification. The very fragile nature of penicillin required the development of special techniques. A combination of pH shifts and rapid liquid-liquid extraction proved useful. Soon processes using tanks of about 10,000 gal were built. Pfizer completed in less than 6 months the first plant for commercial production of penicillin by submerged fermentation (Hobby, 1985). The plant had 14 tanks each of 7000-gal capacity. By a combination of good luck and hard work, the United States had the capacity by the end of World War II to produce enough penicillin for almost 100,000 patients per year. A schematic of the process is shown in Fig. 1.7. This accomplishment required a high level of multidisciplinary work. For example, Merck realized that men who un- derstood both engineering and biology were not available. Merck assigned a chemical engineer and microbiologist together to each aspect of the problem. They planned, executed, and analyzed the experimental program jointly, “almost as if they were one man” (see the chapter by Silcox in Elder, 1970). Progress with penicillin fermentation has continued, as has the need for the interaction of biologists and engineers. From 1939 to now, the yield of penicillin has gone from 0.001 g/L to over 50 g/L of fermentation broth. Progress has involved better understanding of mold physiology, metabolic pathways, penicillin structure, methods of mutation, and selection of mold genetics, process control, and reactor design. Before the penicillin process, almost no chemical engineers sought specialized training in the life sciences. With the advent of modem antibiotics, the concept of the bioprocess engineering was born. The penicillin process also established a paradigm for bioprocess development and biochemical engineering. This paradigm still guides much of our profession’s FIGURE 1.7 Schematic of penicillin production process.
12 Bioprocess Engineering  thinking. The mindset of bioprocess engineers was cast by the penicillin experience. It is for this reason that we have fo- cused on the penicillin story, rather than on an example for production of a protein from a genetically engineered organism. Although many parallels can be made between the penicillin process and our efforts to use recombinant DNA, no similar paradigm has yet emerged from our experience with genetically engineered cells. We must continually reexamine the preju­ dices the field has inherited from the penicillin experience. It is you, the student, who will best be able to challenge these prejudices. 1.10 Bioprocesses: regulatory constraints To be an effective in bioprocess engineering, you must understand the regulatory climate in which many bioprocess engi- neers work. The US FDA (Food and Drug Administration) and its equivalents in other countries must insure the safety and efficacy of food and medicines. For bioprocess engineers working in the pharmaceutical industry the primary concern is not reduction of manufacturing cost (although that is still a very desirable goal), but the production of a product of consistently high quality in amounts to satisfy the medical needs of the population. Consider briefly the process by which a drug obtains FDA approval. A typical drug undergoes 6–7 years of development from the discovery stage through preclinical testing in animals. To legally test the drug in humans in the United States, an Investigational New Drug (IND) designation must be issued by FDA. Biologics such as vaccines and recombinant protein drugs are generally approved by FDA via a Biologic License Application (BLA). There are five phases of trials before a new drug is placed on market after its discovery: Phase 0: Human microdosing studies (1–3 years). This is a designation for the exploratory, first-in-human trials conducted within the regulations of US-FDA 2006 Guidance on Exploratory Investigational New Drug studies. Phase I: First stage testing in human subjects. Normally, a small group of (20–80) of healthy volunteers is selected. Safety, tolerability, pharmacokinetics, and pharmacodynamics of the drug are evaluated. This phase usually lasts about 1 year. Different types of types of trials in this phase are Single Ascending Dose (SAD), Multiple Ascending Dose (MAD), and Food Effect trials. Phase II: clinical trials (about 2 years). After determining the initial safety and pharmacological parameters, this trial on a larger group of 100–300 patients and volunteers is performed. This trial is designed to assess the efficacy (i.e., does it help the patient) as well as further determining which side effects exist. Sometimes, Phase IIA is designed to determine the dos- ing requirements and Phase IIB is designed to determine the efficacy of the drug. If the drug fails to meet the established standards of the trials, further development of the new drug is usually stopped. Phase III: clinical trials (about 3 years) with 300–3000 (or more) patients. Since individuals vary in body chemistry, it is important to test the range of responses in terms of both side effects and efficacy by using a representative cross section of the population. Randomized controlled multicenter trials on large patient groups are conducted to determine the effective- ness of the drug. This phase of the clinic trials is very expensive, time-consuming, and difficult to design and run, espe- cially in therapies for chronic medical conditions. It is common practice that certain Phase III trials will continue while the regulatory submission is pending at the appropriate regulatory agency. This allows patients to continue to receive possibly lifesaving drugs until the drug us available in the market for distribution. These trials also provide additional safety data and support for marketing claims for the drug. Data from clinical trials is presented to the FDA for review (2 months to 3 years). The review document presented to FDA clearly show the trial results combined with description of the methods and results of human and animal studies, manufacturing procedures, formulation details, and shelf life. If the clinical trials are well designed and demonstrated statistically significant improvements in health with acceptable side effects, the drug is likely to be approved. Phase IV: Postmarketing surveillance trial. Continue safety surveillance (pharmacovigilance) and technical support of a drug after receiving permission to be put on the market. The whole discovery-through-approval process takes 5–10 years for a conventional small molecule drug, and 12–15 years for a new biological drug to make it to the market. It takes about $800–$2000 million to send a new drug to the market. Only one in ten drugs that enter human clinical trials receives approval. Recent FDA reforms have decreased the time to obtain approval for life-saving drugs in treatment of diseases such as cancer and AIDS, but the overall process is still lengthy. This process greatly affects a bioprocess engineer. FDA approval is for the product and the process together. There have been tragic examples where a small process change has allowed a toxic trace compound to form or become incorporated in the final product, resulting in severe side effects, including death. Thus, process changes may require new clinical trials to test the safety of the resulting product. Since clinical trials are very expensive, process improvements are made under a limited set of circumstances. Even during clinical trials it is difficult to make major process changes.
What is bioprocess engineering? Chapter | 1 13 Drugs sold on the market or used in clinical trials must come from facilities that are certified as GMP or cGMP and must follow the appropriate Code of Federal Regulations (CFR). GMP stands for (current) good manufacturing practice. GMP concerns the actual manufacturing facility design and layout, the equipment and procedures, training of production person- nel, control of process inputs (e.g., raw materials and cultures), and handling of product. The plant layout and design must prevent contamination of the product, and dictate the flow of material, personnel, and air. Equipment and procedures must be validated. Procedures include not only operation of a piece of equipment, but also cleaning and sterilization. Computer software used to monitor and control the process must be validated. Off-line assays done in laboratories must satisfy good laboratory practice (GLP). Procedures are documented by SOPs (standard operating procedures). The GMP guidelines stress the need for documented procedures to validate performance. “Process validation is estab- lishing documented evidence which provides a high degree of assurance that a specific process will consistently produce a product meeting its predetermined specifications and quality characteristics” and “There shall be written procedures for production and process-control to assure that products have the identity, strength, quality, and purity they purport or are represented to possess.” The actual process of validation is often complex, particularly when a whole facility design is considered. The FDA pro- vides extensive information and guidelines which are updated regularly. If students become involved in biomanufacturing for pharmaceuticals, they will need to consult these sources. However, certain key concepts do not change. These concepts are written documentation, consistency of procedures, consistency of product, and demonstrable measures of product qual- ity, particularly purity, and safety. These tasks are demanding and require careful attention to detail. Bioprocess engineers will often find that much of their effort will be to satisfy these regulatory requirements. The key point is that process changes cannot be made without considering their considerable regulatory impact. 1.11 The pillars of bioprocess kinetics and systems engineering As a profession, bioprocess engineers must be well-versed in thermodynamics, transport phenomena, colloids, biosepara- tions, microbiology, bioprocess kinetics and systems engineering, and process simulation and design. This text deals with the core of bioprocess engineering. Unlike earlier texts in this subject area, this text integrates bioprocess engineering prin- ciples, in particular bioprocess kinetics and transformation or reaction engineering principles together. Chemical reaction engineering is not a pre-requisite before taking on this text. Fig. 1.6 shows the pillars of this text. The sustainability on this pillar is narrowly defined as having the net benefit to the human society and/or benign environmental effects. As shown in Fig. 1.8, the fundamental knowledge of engineering science you will learn or expect in this text is among the “pillars”: mass balance, rate expression, stoichiometry, cell metabolism, yield factor, energy balance, mass FIGURE 1.8 The pillars of bioprocess kinetics and system engineering.
14 Bioprocess Engineering  transfer, cost, and profit analyses. These engineering science fundamentals form the basis or foundation for the design and performance analysis of reactors and /or fermenters. In turn, process kinetic data analysis, biocatalyst design and selection can be learned from the reactor performance, and applied to the design and performance analysis of reactors and/or bioprocess systems. Process stability usually stems from multiplicity of the process, which controls the product quality and consistency. Finally, the design and control of bioprocess systems must obey the greater law of nature: sustainability. 1.12 Summary Sustainability and green chemistry are important to the practice of bioprocess engineers. Biorefinery is a desired approach to provide the products of human needs, putting the human needs into the biological cycle. Both biotransformation and chemical transformations are important to biorefinery. Genetic manipulations and biotransformation are important to the bioprocess engineering profession. Because of the fundamental impact genetic manipulation and biotransformation can have on the cycle of life, ethics and regulations are critical to the practice of bioprocess engineers. It is the intention that this text can be used as a senior and/or graduate text for bioprocess engineering students. It may also be served as a reference and/or graduate text for chemical kinetics, chemical reactor analysis, and bioprocess systems engineering. In the same time, we have inserted materials, more advanced analysis or complex systems in the text as an extension to the introductory material. It is our aim that this text can serve equally as a reference or resource for further research or development. Problems 1.1. How bioprocess engineering affects the overall health of humans? 1.2. Why are renewable materials preferred? 1.3. What is green chemistry? 1.4. What is sustainability? 1.5. What is a biorefinery? 1.6. Why is ethanol an important platform chemical? 1.7. An uninformed researcher is questioning the sustainability of biomass cultivation and utilization, arguing that fertil- izer and fuels for heavy machinery must be produced with fossil energy and thus not renewable. Research into the basis of the arguments and dismiss the notion of unsustainable biomass use. 1.8. What is GMP and how does it relate to the regulatory process for pharmaceuticals? 1.9. When the FDA approves a process, it requires validation of the process. Explain what validation means in the FDA context. 1.10. Why does the FDA approve the process and product together? 1.11. What is biotransformation? What is chemical transformation? References D. History of Penicillin Elder, A.L. (Ed.), 1970. The History of Penicillin Production, Chem. Eng. Prog. Symp. Ser. 66 (#100). American Institute of Chemical Engineers, New York. Hobby, G.L., 1985. Penicillin. Meeting the Challenge. Yale University Press, New Haven, CT.
What is bioprocess engineering? Chapter | 1 15 Further readings A. Green Chemistry Anatas, P.C., Warner, J.C., 1998. Green Chemistry: Theory and Practice. Oxford University Press, New York. Linthorst JA, 2010. An overview: origins and development of green chemistry. Found. Chem. 12 (1), 55–68. Wilson M, Schwarzman M. 2009. Toward a New U.S. Chemicals Policy: Rebuilding the Foundation to Advance New Science, Green Chemistry, and Environmental Health. Environ Health Perspect. 117 (8) 1202–1209 and A358. www.epa.gov/greenchemistry/. B. Sustainability Adams, W.M., Jeanrenaud, S.J., 2008. Transition to Sustainability: Towards a Humane and Diverse World. IUCN, Gland, Switzerland, 108 pp. Atkinson, G., Dietz, S., Neumayer, E., 2007. Handbook of Sustainable Development. Edward Elgar, Cheltenham. Blackburn, W.R., 2007. The Sustainability Handbook. Earthscan, London. Blewitt, J., 2008. Understanding Sustainable Development. Earthscan, London. Costanza, R., Graumlich, L.J., Steffen, W. (Eds.), 2007. Sustainability or Collapse? An Integrated History and Future of People on Earth. MIT Press, Cambridge, MA. Norton, B., 2005. Sustainability, A Philosophy of Adaptive Ecosystem Management. The University of Chicago Press, Chicago. Soederbaum, P., 2008. Understanding Sustainability Economics. Earthscan, London. C. Biorefinery Liu, S., Lu, H., Hu, R., Shupe, A., Lin, L., Liang, L., 2012. A sustainable woody biomass biorefinery. J. Biotech. Adv. 30 (4), 785–810, http://dx.doi. org/10.1016/j.biotechadv.2012.01.013. FitzPatrick, M., Champagne, P., Cunningham, M.F., Whitney, R.A., 2010. A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products”. Bioresour. Technol. 101 (23), 8915–8922. Kaparaju, P., Serrano, M., Thomsen, A.B., Kongjan, P., Angelidaki, I., 2009. Bioethanol, biohydrogen and biogas production from wheat straw in a bio- refinery concept”. Bioresour. Technol. 100 (9), 2562–2568. Koutinas, A.A., Arifeen, N., Wang, R., Webb, C., 2007. Cereal-based biorefinery development: Integrated enzyme production for cereal flour hydrolysis”. Biotechn. Bioeng. 97 (1), 61–72. Liu, S., Amidon, T.E., Francis, R.C., Ramarao, B.V., Lai, Y.-Z., Scott, G.M., 2006. From forest biomass to chemicals and energy: biorefinery initiative in New York. Ind. Biotech. 2 (2), 113–120. Ohara, H., 2003. Biorefinery. App. Micobiol. and Biotechn. 62 (5–6), 474–477. D. History of Penicillin Moberg, C.L., 1991. Penicillin’s Forgotten Man: Norman Heatley. Science 253, 734–735. Mateles, R.I. (Ed.), 1998. Penicillin, A Paradigm for Biotechnology. Candida Corp., Chicago, IL. Sheehan, J.C., 1982. The Enchanted Ring. The Untold Story of Penicillin. MIT Press, Cambridge, MA. E. Regulatory Issues Currey, B., Klemic, P.A., 2008. A New Phase in Pharmaceutical Regulation. DRI Drug and Medical Device and Product Liability Committee. O’Melveny & Myers LLP, PL California, United States. Durfor, C.N., Andscribner, C.L., 1992. An FDA perspective of manufacturing changes for products in human use. Ann. NY Acad. Sci. 665, 356–363. Naglak, T.J., Keith, M.G., Omstead, D.R., 1994. Validation of fermentation processes. Biopharm 7, 28–36. Reisman, H.B., 1993. Problems in scale-up of biotechnology production processes. Crit. Rev. Biotechnol. 13, 195–253. Wechsler, J. Science and Safety. Magazine: Pharmaceutial Excutive – Washington Report, Oct., 2009. http://www.FDA.gov. http://www.FDAreview.org/approval_process.
Bioprocess Engineering. http://dx.doi.org/10.1016/B978-0-12-821012-3.00002-6 Copyright © 2020 Elsevier B.V. All rights reserved. 17 Bioprocess engineers seek chemicals and materials for human needs in a sustainable manner. It is the chemicals and materials from biological origin that can sustain the needs of humans. Microorganism also provides a tool for bioprocess engineers to manipulate the chemicals and materials so that they can meet the needs of humanity. Therefore we shall first review some of the biological basics to learn how living organisms (more specific: microorganisms) function and what their important chemicals and materials are. 2.1 Cells and organisms The cell is the basic structural and functional unit of all known living organisms. Cells are to living organisms as like atoms are to molecules. It is the smallest unit of life that is classified as a living thing, and so is often called the building block of life. Some organisms, such as most bacteria, are unicellular (consist of a single cell). Most single cell organisms are microscopic in size and not visible to (human by) naked eyes, which are commonly called microorganisms. However, some unicellular protists and bacteria are macroscopic and visible to the naked eye. For example, Xenophyophores, protozoans of the phylum Foraminifera, are the largest examples known, with Syringammina fragilissima achieving a diameter of up to 20 cm (7.9 inches). The largest bacterium is Thiomargarita namibiensis, reaching a diameter of up to 0.75 mm. Other organisms, such as humans, are multicellular. (Humans have an estimated 100 trillion or 1014 cells; a typical cell size is 10 µm; a typical cell mass is 1 nanogram.) The largest known cell is an unfertilized ostrich egg cell. An average ostrich egg is an oval about 15 cm × 13 cm and weighs 1.4 kg. In 1835, before modern cell theory was developed, Jan Evangelista Purkyně observed small “granules” while looking at plant tissue through a microscope. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells. Each cell is at least somewhat self-contained and self-maintaining: it can take in nutrients, convert these nutrients into energy, carry out specialized functions, and reproduce as necessary. Each cell stores its own set of instructions for carrying out each of these activities. Chapter 2 An overview of biological basics Chapter outline 2.1 Cells and organisms 17 2.1.1 Microbial diversity 18 2.1.2 How cells are named 18 2.1.3 Prokaryotes 20 2.1.4 Eukaryotes 23 2.2 Viruses 27 2.3 Prions 30 2.4 Stem cell 30 2.5 Cell chemistry 31 2.5.1 Amino acids and proteins 32 2.5.2 Monosaccharides 37 2.5.3 Disaccharides 42 2.5.4 Polysaccharides 42 2.5.5 Phytic acid and inositol 46 2.5.6 Chitin and chitosan 48 2.5.7 Lignin 48 2.5.8 Lipids, fats, and steroids 50 2.5.9 Nucleic acids, RNA, and DNA 52 2.6 Cell feed 57 2.6.1 Macronutrients 58 2.6.2 Micronutrients 60 2.6.3 Growth media 61 2.7 Non earthly/unnatural biological agents 61 2.8 Summary 62 Problems 63 References 64 Further readings 64
18 Bioprocess Engineering  2.1.1 Microbial diversity Life is very tenacious and can exist in extreme environments. Living cells can be found almost anywhere that water is in the liquid state. The right temperature, pH, and moisture levels vary from one organism to another. Some cells can grow at −20°C (in a brine to prevent freezing), while others can grow at 120°C (where water is under high enough pressure to prevent boiling). Cells that grow best at low temperatures (below 20°C) are usually called psychrophiles, while those with temperature optima in the range of 20–50°C are mesophiles. Organisms that grow best at temperatures greater than 50°C are thermophiles. Many organisms have pH optima far from neutrality; some prefer in an environment with a pH value down to 1 or 2, while others may grow well at pH 9. Some organisms can grow at both low pH values and high temperatures. Although most organisms can grow only with the presence of liquid water, others can grow on barely moist solid sur- faces or in solutions with high salt concentrations. Some cells require oxygen for growth and metabolism. Such organisms can be termed aerobic. Other organisms are inhibited by the presence of oxygen and grow only anaerobically. Some organisms can switch metabolic pathways to allow them to grow under either circumstance. Such organisms are facultative. Often, organisms can grow in environments with almost no obvious source of nutrients. Some cyanobacteria (formerly called blue-green algae) can grow in an environment with only a little moisture and a few dissolved minerals. These bacteria are photosynthetic and can convert CO2 from the atmosphere into the organic compounds (e.g., sugars) necessary for life. They can also convert N2 into NH3 for use in making the essential building blocks of life. + → + CO (cabondioxude) H O(water) CH O(sugar) O (oxygen) 2 2 2 2 (2.1) + → + N 3H O 2NH 3/2O 2 2 3 2 (2.2) Cyanobacteria are important in colonizing nutrient-deficient environments. Organisms from these extreme environments (extremophiles) often provide humanity with important tools for processes to make useful chemicals and medicinals. They are also key to the maintenance of natural cycles and can be used in the recovery of metals from low-grade ores or in the desulfurization of coal or other fuels. The fact that organisms can develop a capacity to exist and multiply in almost any environment on Earth is extremely useful. Not only do organisms occupy a wide variety of habitats, but they also come in a wide range of sizes and shapes. Spheri- cal, cylindrical, ellipsoidal, spiral, and pleomorphic cells exist. Special names are used to describe the shape of bacteria. A cell with a spherical or elliptical shape is often called a coccus (plural, cocci); a cylindrical cell is a rod or bacillus (plural, bacilli); a spiral-shaped cell is a spirillum (plural, spirilla). Some cells may change shape in response to changes in their local environment. Pleomophic cells take on at least two different forms or shapes during their life cycle. Thus organisms can be found in the most extreme environments and have evolved a wondrous array of shapes, sizes, and metabolic capabilities. This great diversity provides the engineer with an immense variety of potential tools. We have barely begun to learn how to manipulate these tools. 2.1.2 How cells are named The naming of cells is complicated by the large variety of organisms. A systematic approach to classifying these organ- isms is an essential aid to their intelligent use. Taxonomy is the development of approaches to organize and summarize our knowledge about the variety of organisms that exist. Although knowledge of taxonomy may seem remote from the needs of an engineer, it is necessary for efficient communication among engineers and scientists working with living cells. Tax- onomy can also play a critical role in patent litigation involving bioprocesses. While taxonomy is concerned with approaches to classification, nomenclature refers to the actual naming of organ- isms. For microorganisms we use a dual name (binary nomenclature). The names are given in Latin or are Latinized. A genus is a group of related species, while a species includes organisms that are sufficiently alike to reproduce. A common well-documented gut organism is Escherichia coli. Escherichia is the genus and coli the species. When writing a report or paper, it is common practice to give the full name when the organism is first mentioned, but to abbreviate the genus to the first letter in subsequent discussion, for example, E. coli. Although organisms that belong to the same species all share the same major characteristics, there are subtle and often technologically important variations within species. A strain of E. coli used in one laboratory may differ from that used in another. Thus various strains and substrains are designated by the addition of letters and numbers. For example, E. coli fBr5 will differ in growth and physiological properties from E. coli K01.
An overview of biological basics Chapter | 2 19 Now that we know how to name organisms, we could consider broader classification up to the level of kingdoms. There is no universal agreement on how to classify microorganisms at this level. Such classification is rather arbitrary and need not concern us. However, we must be aware that there are two primary cell types: eukaryotic and prokaryotic. The primary difference between them is the presence or absence of a membrane around the cell’s genetic information. Prokaryotes have a simple structure with a single chromosome (Fig. 2.1). Prokaryotic cells have no nuclear membrane and no organelles (such as mitochondria and endoplasmic reticulum). Eukaryotes have a more complex internal structure, with more than one chromosome (DNA molecule) in the nucleus. Eukaryotic cells have a true nuclear membrane and may contain a variety of specialized organelles such as mitochondria, endoplasmic reticulum and Golgi apparatus (Fig. 2.2). A detailed compare-son of prokaryotes and eukaryotes is presented in Table 2.1. Structural differences between prokaryotes and eukaryotes are discussed later. Evidence suggests that a common or universal ancestor gave rise to three distinctive branches of life: eukaryotes, eu- bacteria (or “true” bacteria), and archaebacteria. Table 2.2 summarizes some of the distinctive features of these groups. The ability to sequence the genes of whole organisms will have a great impact on our understanding of how these families evolved and are related. The cellular organisms summarized in Table 2.2 are free-living organisms and are all DNA based. Viruses cannot be classified under any of these categories, as they are not independent (or free-living) organisms. Still, viruses are all nucleic FIGURE 2.1 A schematic of a typical prokaryotic cell. FIGURE 2.2 A schematic of a typical eukaryotic cell.
20 Bioprocess Engineering  acid (either DNA or RNA) based. Prions, on the other hand, are not even nucleic acid based. These rather simple “organ- isms” play important roles in Bioprocess Engineering and thus we will discuss hem separately. 2.1.3 Prokaryotes The sizes of most prokaryotes vary from 0.5–3 µm in equivalent radius. Different species have different shapes, such as spherical or coccus (e.g., Staphylococci), cylindrical or bacillus (E. coli), or spiral or spirillum (Rhodospirillum). Prokary- otic cells grow rapidly, with typical doubling times of half an hour to several hours. Also, prokaryotes can utilize a variety of nutrients as carbon sources, including carbohydrates, hydrocarbons, proteins, and CO2. 2.1.3.1 Eubacteria The eubacteria can be divided into several different groups. One distinction is based on the gram stain (developed by Hans Christian Gram in 1884). The staining procedure first requires fixing the cells by heating. The basic dye, crystal violet, is added; all bacteria will stain purple. Next, iodine is added, followed by the addition of ethanol. Gram-positive cells re- main purple, while Gram-negative cells become colorless. Finally, counterstaining with safranin leaves Gram-positive cells purple, while Gram-negative cells turn red. Cell reactions to the gram stain reveal intrinsic differences in the structure of the cell envelope. TABLE 2.1 A comparison of prokaryotes with eukaryotes. Characteristic Prokaryotes Eukaryotes Genome No. of DNA molecules DNA in organelles DNA observed as chromosomes Nuclear membrane Mitotic and meiotic division of the nucleus Formation of partial diploid One No No No No Yes More than one Yes Yes Yes Yes No Organelles Mitochondria Endoplasmic reticulum Golgi apparatus Photosynthetic apparatus Flagella No No No Chromosomes Single protein, simple structure Yes Yes Yes Chloroplasts Complex structure, with microtubules Spores Heat resistance Endospores High Endo- and exospores Low Source: Millis, N.F., 1985, in: Moo-Young, M. (Ed.), Comprehensive Biotechnology, vol. I, Elsevier Science. TABLE 2.2 Primary subdivisions of cellular organisms that have been recognized. Group Cell morphology Properties Constituent groups Eukaryotes Eukaryotic Multicellular; extensive differentiation of cells and tissues Unicellular, coenocytic, or mycelial; little or no tissue differentiation Plants (seed plants, ferns, mosses) Animals (vertebrates, invertebrates) Protists (algae, fungi, protozoa, slime moulds) Eubacteria Prokaryotic Cell chemistry similar to eukaryotes Most bacteria Archaea Prokaryotic Distinctive cell chemistry Crenarchaeota (sulfolobus, therofilum, thermopteus, pyrobaculum, haloquadratum walsbyi) Nanoarchaeota Euryarchaeota (methanogens, halophiles, therrno- acidophiles) Korarchaeota
An overview of biological basics Chapter | 2 21 A typical Gram-negative cell is E. coli. It has an outer membrane supported by a thin peptidoglycan layer, as shown in Fig. 2.3. Peptidoglycan is a complex polysaccharide with amino acids and forms a structure somewhat analogous to a chain- link fence. A second membrane (the inner or cytoplasmic membrane) exists and is separated from the outer membrane by the periplasmic space. The cytoplasmic membrane contains about 50% protein, 30% lipids, and 20% carbohydrates. The cell envelope serves to retain important cellular compounds and to preferentially exclude undesirable compounds in the environment. the loss of membrane integrity leads to cell lysis (cells breaking open) and cell death. The cell envelope is crucial to the transport of selected material in and out of the cell. A typical Gram-positive cell is Bacillus subtilis. Gram-positive cells do not have an outer membrane. Rather, they have a very thick, rigid cell wall with multiple layers of peptidoglycan. Gram-positive cells also contain teichoic acids covalently bonded to the peptidoglycan. Because Gram-positive bacteria have only a cytoplasmic membrane, they are better suited to excretion of proteins. Excretion is technologically advantageous when the protein is a desired product. Some bacteria are neither Gram-positive nor Gram-negative. For example, Mycoplasma has no cell walls. These bac- teria are important not only clinically (e.g., primary atypical pneumonia), but also because they commonly contaminate media used industrially for animal cell culture. Actinomycetes are bacteria, but morphologically resemble molds with their long and highly branched hyphae. How- ever, the lack of a nuclear membrane and the composition of the cell wall require classification as bacteria. Actinomycetes are important sources of antibiotics. Certain Actinomycetes possess amylolytic and cellulolytic enzymes and are effective in the enzymatic hydrolysis of starch and cellulose. Actinomyces, Thermomonospora, and Streptomyces are examples of genera belonging to this group. Other distinctions within the eubacteria can be made based on cellular nutrition and energy metabolism. One important example is photosynthesis. Cyanobacteria (formerly called blue-green algae) have chlorophyll and fix CO2 into sugars. An- oxygenic photosynthetic bacteria (the purple and green bacteria) have light-gathering pigments called bacteriochlorophyll. Unlike true photosynthesis, the purple and green bacteria do not obtain reduction energy from the splitting of water and do not form oxygen. When stained properly, the area occupied by a prokaryotic cell’s DNA can be easily seen. Prokaryotes may also have other visible structures when viewed under the microscope, such as ribosomes, storage granules, spores, and volutins. Ribosomes are the site of protein synthesis. A typical bacterial cell contains approximately 10,000 ribosomes per cell, although this number can vary greatly with growth rate. The size of a typical ribosome is 10–20 nm and consists of ap- proximately 63% RNA and 37% protein. Storage granules (which are not present in every bacterium) can be used as a source of key metabolites and often contain polysaccharides, lipids, and sulfur granules. The sizes of storage granules vary between 0.5 µm and 1 µm. Some bacteria make intracellular spores (often called endospores in bacteria). Bacterial spores are produced as a resistance to adverse conditions such as high temperature, radiation, and toxic chemicals. The usual con- centration is 1 spore per cell, with a spore size of about 1 µm. Spores can germinate under favorable growth conditions to yield actively growing bacteria. FIGURE 2.3 Schematic of a typical Gram-negative bacterium (A) and its enlarged section of the membrane (B). A Gram-positive cell is similar, except that it has no outer membrane, its peptidoglycan layer is thicker, and the chemical composition of the cell wall differs significantly from the outer envelope of the Gram-negative cell.
22 Bioprocess Engineering  Volutin is another granular intracellular structure, made of inorganic polymetaphosphates, which is present in some species. Some photosynthetic bacteria, such as Rhodospirilium, have chromatophores that are large inclusion bodies (50– 100 nm) utilized in photosynthesis for the absorption of light. Extracellular products can adhere to or become incorporated within the surface of the cell. Certain bacteria have a coat- ing or outside cell wall called capsule, which is usually a polysaccharide, or sometimes a polypeptide. Extracellular poly- mers are important to biofilm formation and response to environmental challenges (e.g., viruses). Table 2.3 summarizes the architecture of most bacteria. 2.1.3.2 Archaebacteria Under the microscope archaebacteria appear to be nearly identical to eubacteria. However, these cells differ greatly at the molecular level. In many ways the archaebacteria are as similar to the eukaryotes as they are to the eubacteria. Some ex- amples of differences between archaebacteria and eubacteria are as follows: 1. archaebacteria have no peptidoglycan; 2. nucleotide sequences in ribosomal RNA are similar within the archaebacteria but distinctly different from those of eu- bacteria; 3. the lipid composition of the cytoplasmic membrane is very different for the two groups. TABLE 2.3 Characteristics of various components of bacteria. Part Size Composition and comments Slime layer Microcapsule 5–10 nm Protein-polysaccharide-lipid complex responsible for the specific antigens of enteric bacteria and other species. Capsule 0.5–2.0 µm Mainly polysaccharides (e.g., Streptococcus); sometimes polypeptides (e.g., Bacillus antracis). Slime Indefinite Mainly polysaccharides (e.g., Leuconostoc); sometimes polypeptides (e.g., Bacillus subtilis). Cell wall Gram-positive species 10–20 nm Confers shape and rigidity upon the cell. In total, 20% dry weight of the cell. Consists mainly of macromolecules of a mixed polymer of N-acetyl muramicpeptide, teichoic acids, and polysaccharides. Gram-negative species 10–20 nm Consists mostly of a protein-polysaccharide-lipid complex with a small amount of the mu- ramic polymer. Cell membrane 5–10 nm Semipermeable barrier to nutrients. In total, 5%–10% dry weight of the cell, consisting of 50% protein, 28% lipid, and 15%– 20% carbohydrate in a double-layered membrane. Flagellum 10–20 nm by 4–12 µm Protein of the myosin-keratin-fibrinogen class, MW of 40,000. Arises from the cell membrane and is responsible for motility. Pilus (fimbria) 5–10 nm by 0.5–2.0 µm Rigid protein projections from the cell. Especially long ones are formed by Escherichia coli. Inclusions Spore 1.0–1.5 µm by 1.6–2.0 µm One spore is formed per cell intracellularly. Spores show great resistance to heat, dryness, and antibacterial agents. Storage granule 0.5–2.0 µm Glycogenlike, sulfur, or lipid granules may be found in some species. Chromatophore 50–100 nm Organelles in photosynthetic species. Rhodospirillum rubrum contains about 6000 per cell. Ribosome 10–30 nm Organelles for synthesis of protein. About 10,000 ribosomes per cell. They contain 63% RNA and 37% protein. Volutin 0.5–1.0 µm Inorganic polymetaphosphates that stain metachromatically. Nuclear material Composed of DNA that functions genetically as if the genes were arranged linearly on a single endless chromosome, but that appears by light microscopy as irregular patches with no nuclear membrane or distinguishable chromosomes. Autoradiography confirms the linear arrangement of DNA and suggests a MW of at least 109 . Source: Aiba, S., Humphrey, A.E., Millis, N. F., 1973, Biochemical Engineering, second ed. University of Tokyo Press, Tokyo.
An overview of biological basics Chapter | 2 23 Archaebacteria usually live in extreme environments and possess unusual metabolism. Methanogens, which are meth- ane-producing bacteria, belong to this group, as well as thermoacidophiles, which can grow at high temperatures and low pH values. Halobacteria, which can live only in very strong salt solutions, are also members of this group. These organisms are important sources for catalytically active proteins (enzymes) with novel properties. 2.1.4 Eukaryotes Fungi (yeasts and molds), algae, protozoa, and animal and plant cells constitute the eukaryotes. Eukaryotes are five to ten times larger than prokaryotes in diameter (e.g., yeast about 5 µm, animal cells about 10 µm, and plants about 20 µm). Eukaryotes have a true nucleus and a number of cellular organelles inside the cytoplasm. Fig. 2.4 is a schematic of two typical eukaryotic cells. In cell wall and cell membrane structure, eukaryotes are similar to prokaryotes. The plasma membrane is made of proteins and phospholipids that form a bilayer structure. Major proteins of the membrane are hydrophobic and are embedded in the phospholipid matrix. One major difference is the presence of sterols in the cytoplasmic membrane of eukaryotes. Sterols strengthen the structure and make the membrane less flexible. The cell wall of eukaryotic cells shows considerable variations. Some eukaryotes have a peptidoglycan layer in their cell wall; some have polysaccharides and cellulose (e.g., algae). The plant cell wall is composed of cellulose fibers embedded in pectin aggregates, which impart strength to the cell wall. Animal cells do not have a cell wall but only a cytoplasmic membrane. For this reason, animal cells are very shear-sensitive and fragile. This factor significantly complicates the design of large-scale bioreactors for animal cells. The nucleus of eukaryotic cells contains chromosomes as nuclear material (DNA molecules with some closely associ- ated small proteins), surrounded by a membrane. The nuclear membrane consists of a pair of concentric and porous mem- branes. The nucleolus is an area in the nucleus that stains differently and is the site of ribosome synthesis. Many chromo- somes contain small amounts of RNA and basic proteins called histones attached to the DNA. Each chromosome contains a single linear DNA molecule on which the histones are attached. Cell division (asexual) in eukaryotes involves several major steps: DNA synthesis, nuclear division, cell division, and cell separation. Sexual reproduction in eukaryotic cells involves the conjugation of two cells called gametes (egg and sperm cells). The single cell formed from the conjugation of gametes is called a zygote. The zygote has twice as many chromosomes as the gamete. Gametes are haploid cells, while zygotes are diploid. For humans, a haploid cell contains 23 chromosomes, and diploid cells have 46 chromosomes. The cell-division cycle (asexual reproduction) in a eukaryotic cell is depicted in Fig. 2.5. The cell-division cycle is divided into four phases. The M phase consists of mitosis where the nucleus divides, and cy- tokinesis where the cell splits into separate daughter cells. All of the phases between one M phase and the next are known collectively as interphase. The interphase is divided into three phases: Gl, S, and G2.The cell increases in size during the interphase. In the S phase, the cell replicates its nuclear DNA. There are key checkpoints in the cycle when the cell machin- ery must commit to entry to the next phase. Checkpoints exist for entry into the S and M phases and exit from the M phase. Cells may also be in a G0 state, which is a resting state without growth. FIGURE 2.4 Schematics of the two primary types of higher eukaryotic cells. Neither sketch is complete, but each summarizes the principal differ- ences and similarities of such cells.
24 Bioprocess Engineering  Mitochondria are the powerhouses of an eukaryotic cell, where respiration and oxidative phosphorylation take place. Mitochondria have a nearly cylindrical shape 1 µm in diameter and 2–3 µm in length.A typical structure of a mitochondrion is shown in Fig. 2.6. The external membrane is made of a phospholipid bilayer with proteins embedded in the lipid matrix. Mitochondria contain a complex system of inner membranes called cristae. A gel-like matrix containing large amounts of protein fills the space inside the cristae. Some enzymes of oxidative respiration are bound to the cristae. A mitochondrion has its own DNA and protein-synthesizing machinery and reproduces independently. The endoplasmic reticulum is a complex, convoluted membrane system leading from the cell membrane into the cell. The rough endoplasmic reticulum contains ribosomes on the inner surfaces and is the site of protein synthesis and modifica- tions of protein structure after synthesis. The smooth endoplasmic reticulum is more involved with lipid synthesis. Lysosomes are very small membrane-bound particles that contain and release digestive enzymes. Lysosomes contrib- ute to the digestion of nutrients and invading substances. Peroxisomes are similar to lysosomes in their structure, but not in function. Peroxisomes carry out oxidative reactions that produce hydrogen peroxide. Glyoxysomes are also very small membrane-bound particles that contain the enzymes of the glyoxylate cycle. FIGURE 2.5 Schematic of cell division cycle in a eukaryote. (see text for details.) FIGURE 2.6 Diagram of a mitochondrion.
An overview of biological basics Chapter | 2 25 Golgi bodies are very small particles composed of membrane aggregates and are responsible for the secretion of certain proteins. Golgi bodies are sites where proteins are modified by the addition of various sugars in a process called glycosyl- ation. Such modifications are important to protein function in the body. Vacuoles are membrane-bound organelles of low density and are responsible for food digestion, osmotic regulation, and waste product storage. Vacuoles may occupy a large fraction of the cell volume (up to 90% in plant cells). Chloroplasts are relatively large green organelles containing chlorophyll that are responsible for photosynthesis in photo- synthetic eukaryotes, such as algae and plant cells. Every chloroplast contains an outer membrane and a large number of inner membranes called thylakoids. Chlorophyll molecules are associated with thylakoids, which have a regular membrane struc- ture with lipid bilayers. Chloroplasts are autonomous units containing their own DNA and protein-synthesizing machinery. Certain prokaryotic and eukaryotic organisms contain flagella—long, filamentous structures that are attached to one end of the cell and are responsible for the motion of the cell. Eukaryotic flagella contain two central fibers surrounded by eighteen peripheral fibers, which exist in duplets. These fibers are arranged in a tube structure called a microtubule and are composed of proteins called tubulin. The whole fiber assembly is embedded in an organic matrix and is surrounded by a membrane. The cytoskeleton (in eukaryotic cells) refers to filaments that provide an internal framework to organize the cell’s in- ternal activities and control its shape. These filaments are critical to cell movement, transduction of mechanical forces into biological responses, and separation of chromosomes into the two daughter cells during cell division. Three types of fibers are present: actin filaments, intermediate filaments, and microtubules. Cilia are structures similar to flagella, but are shorter and numerous. Only one group of protozoa, called ciliates, con- tains cilia. Paramecium species contain nearly 104 cilia per cell. Ciliated organisms move much faster than flagellated ones. This completes our summary of eukaryotic cell structure. Now let us turn our attention to the microscopic eukaryotes. Fungi are heterotrophs, which are widespread in nature. Fungal cells are larger than bacterial cells, and their typical internal structures, such as the nucleus and vacuoles, can be seen easily with a light microscope. Two major groups of fungi are yeasts and molds. Yeasts are single small cells of 5–10-µm size.Yeast cells are usually spherical, cylindrical, or oval.Yeasts can reproduce by asexual or sexual means. Asexual reproduction is by either budding or fission. In budding, a small bud cell forms on the cell, which gradually enlarges and separates from the mother cell. Asexual reproduction by fission is similar to that of bacteria. Only a few species of yeast can reproduce by fission. In fission, cells grow to a certain size and divide into two equal cells. Sexual reproduction of yeasts involves the formation of a zygote (a diploid cell) from the fusion of two haploid cells, each having a single set of chromosomes. The nucleus of the diploid cells divides several times to form ascospores. Each ascospore eventually becomes a new haploid cell and may reproduce by budding and fission. The life cycle of a typi- cal yeast cell is presented in Fig. 2.7. The classification of yeasts is based on reproductive modes (e.g., budding or fission) and the nutritional requirements of cells. The most widely used yeast, Saccharomyces cerevisiae, is used in alcohol formation under anaerobic conditions (e.g., in wine, beer and whiskey making) and also for baker’s yeast production under aerobic conditions. FIGURE 2.7 Cell-division cycle of a typical yeast, Saccharomyces cerevisiae.
26 Bioprocess Engineering  Molds are filamentous fungi and have a mycelial structure. The mycelium is a highly branched system of tubes that contains mobile cytoplasm with many nuclei. Long, thin filaments on the mycelium are called hyphae. Certain branches of mycelium may grow in the air, and asexual spores called conidia are formed on these aerial branches. Conidia are nearly spherical in structure and are often pigmented. Some molds reproduce by sexual means and form sexual spores. These spores provide resistance against heat, freezing, drying, and some chemical agents. Both sexual and asexual spores of molds can germinate and form new hyphae. Fig. 2.8 describes the structure and asexual reproduction of molds. Molds usually form long, highly branched cells and easily grow on moist, solid nutrient surfaces. The typical size of a filamentous mold is 5–20 µm. When grown in submerged culture, molds often form cell aggregates and pellets. The typical size of a mold pellet varies between 50 µm and 1 mm, depending on the type of mold and growth conditions. Pellet forma- tion can cause some nutrient-transfer (mainly oxygen) problems inside the pellet. However, pellet formation reduces broth viscosity, which can improve bulk oxygen transfer. On the basis of their mode of sexual reproduction, fungi are grouped in four classes. 1. The phycomycetes are algalike fungi; however, they do not possess chlorophyll and cannot photosynthesize. Aquatic and terrestrial molds belong to this category. 2. The ascomycetes form sexual spores called ascospores, which are contained within a sac (a capsule structure). Some molds of the genera Neurospora and Aspergillus and yeasts belong to this category. 3. The basidiomycetes reproduce by basidiospores, which are extended from the stalks of specialized cells called the basidia. Mushrooms are basidiomycetes. 4. The deuteromycetes (Fungi imperfecti) cannot reproduce by sexual means. Only asexually reproducing molds belong to this category. Some pathogenic fungi, such as Trichophyton, which causes athlete’s foot, belong to the deuteromycetes. Molds are used for the production of citric acid (Aspergillus niger) and many antibiotics, such as penicillin (Penicillium chrysogenum). Mold fermentations make up a large fraction of the fermentation industry. Algae are usually unicellular organisms, although some plantlike multicellular structures are present in marine waters. Algae can be divided into five groups: Rhodophyta (red algae), Phaeophyta (brown algae), Chlorophyta (green algae), Cyanophyta (blue-green algae), and Bacillariophyta (golden-brown algae). Fig. 2.9 shows a drawing of typical green algae. The largest alga is the giant kelp, which can grow over sixty meters long. All algae are photosynthetic and contain chloroplasts, which normally impart a green color to the organisms. The chloroplasts are the sites of chlorophyll pigments and are responsible for photosynthesis. A typical unicellular alga is 10–30 µm in size. Multicellular algae sometimes form a branched or unbranched filamentous structure. Some algae contain silica or calcium carbonate in their cell wall. Diatoms containing silica in their cell wall are used as filter aids in industry. Some algae, such as Chlorella, Scenedesmus, Spirul- lina, and Dunaliella, are used for wastewater treatment while producing single-cell proteins. Certain gelling agents such as agar and alginic acid are obtained from marine algae and seaweeds. Many algae have been proposed for biofuel production. Protozoa are unicellular, motile, relatively large (1–50 mm) eukaryotic cells that lack cell walls. Protozoa usually obtain food by ingesting other small organisms, such as bacteria, or other food particles. Protozoa are usually uninucleate and FIGURE 2.8 Structure and asexual reproduction of molds.
An overview of biological basics Chapter | 2 27 reproduce by sexual or asexual means. They are classified on the basis of their motion. The amoebae move through ame- boid motion, whereby the cytoplasm of the cell flows forward to form a pseudopodium (false foot), and the rest of the cell flows toward this lobe. The flagellates move using their flagella. Trypanosomes move by flagella and cause a number of dis- eases in humans. The ciliates move through motion of a large number of small appendages on the cell surface called cilia. The sporozoans are nonmotile and contain members that are human and animal parasites. These protozoa do not engulf food particles, but absorb dissolved food components through their membranes. Protozoa cause some diseases, such as ma- laria and dysentery. Protozoa may have a beneficial role in removing bacteria in biological wastewater treatment processes. 2.2 Viruses Viruses are very small and are obligate parasites of other cells, such as bacterial, yeast, plant, and animal cells. Viruses cannot capture or store free energy and are not functionally active except when inside their host cells. The sizes of viruses vary from 30 to 200 nm. Viruses contain either DNA (DNA viruses) or RNA (RNA viruses) as genetic material. DNA stands for deoxyribo- nucleic acid, and RNA is ribonucleic acid; we will soon discuss DNA and RNA molecules in more detail. In free-living cells, all genetic information is contained in the DNA, whereas viruses can use either RNA or DNA to encode such information. This nu- clear material is covered by a protein coat called a capsid. Some viruses have an outer envelope of a lipoprotein and some do not. Almost all cell types are susceptible to viral infections. Viruses infecting bacteria are called bacteriophages. The most common type of bacteriophage has a hexagonal head, tail, and tail fibers as shown in Fig. 2.10. Bacteriophages attach to the cell wall of a host cell with tail fibers, alter the cell wall of the host cell, and inject the viral nuclear material into the host cell. Fig. 2.11 describes the attachment of a virus onto a host cell. Bacteriophage nucleic acids reproduce inside the host cells to produce more phages. At a certain stage of viral reproduction, host cells lysis or break apart and the new phages are released, which can infect new host cells. This mode of reproduction of viruses is called the lytic cycle. In some cases, phage DNA may be incorporated into the host DNA, and the host may continue to multiply in this state, which is called the lysogenic cycle. Viruses are the cause of many diseases, and antiviral agents are important targets for drug discovery. However, viruses are also important to bioprocess technology. For example, a phage attack on an E. coli fermentation to make a recombinant protein product can be extremely destructive, causing the loss of the whole culture in vessels of many thousands of liters. However, phages can be used as agents to move desired genetic material into E. coli. Modified animal viruses can be used as vectors to genetically engineer animal cells to produce proteins from recombinant DNA technology. In some cases a killed virus preparation can be used as a vaccine. Genetic engineering allows the production of virus-like units that are empty shells; the shell is the capsid and all nucleic acid is removed. Such units can be used as vaccines without fear of viral FIGURE 2.9 A sketch of green algae. Source: “Siphoneae”, Ernst Haecket, Kunstformen der Natur, 1904.
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314 Ancesteal Records and Porteaits BALL Colonel Willla.m Ball, of Lancaster County, Va., was the progenitor of the Virffinia Balls (see pp. 134-137). His granddaughter Esther, the daughter of Colonel Joseph and Elizabeth (Rogers or Romney) Ball, married .RawROMNBY leigh Chinn, and was the mother of Ann Chinn, who married Martin Sherman, whose daughter Mary married Henry Tapscott. BAKER A descendant of the house of Norfolk, through the Howard family, Judith Wood, who married John Baker, was the daughter of Peter Wood and Susanna Howard, his wife, who was the daughter of Sir WUliam and Lady Judith Howard, of Howard Hall, Eng. Their daughter, Susanna Howard Baker, married, first, John Wood, and second, James Tapscott. THOMPSON In 1774, at the age of eighteen, John Thompson came to America. He joined the Revolutionary army, serving in Captain Watson's company in a Pennsylvania regiment, fought in the battles of Long Island and Trenton, and crossed the Delaware with Washington. He settled after the war in Nelson County, Va., where he died in 1828. He married Rebecca Edwards, the daughter of Lucas Powell, and his wife, Rebecca Edwards. The sixth of his seven children was Judge Lucas
The text on this page is estimated to be only 22.82% accurate Judge I.ucas Powell Thompson Judith Wood Wife of John Baker Sarah Coles Hull Wife of Henry Trowbridge
Ancestbal Recoeds and Poetraits 315 Powell Thompson. At the age of eighteen, after a walking tour through Spain, he returned to Virginia, where he studied and graduated in law, his license hearing the names of three of the most emiuent men of that State, Archibald Stuart, Hugh Holmes, and Briscoe Baldwin, Judges of the Supreme Court of Virginia, and by a coincidence all cousins of his wife. In a few years he was elected Judge of the Circuit Court of Augusta, Albemarle, Nelson, Amherst, and Rockbridge counties, succeeding Chief Justice Marshall, being the youngest man who had ever held this position, and after Chief Justice Marshall, admitted to be the most learned jurist in Virginia. He held his position during the Civil War, and was still kept in it by the Federal government during the stormy reconstruction days. By the advice of General Robert E. Lee, he took the oath of allegiance, and after the war, though refusing to " soil the ermine of the office " by runmng for the position he had held before, was elected to it again, one vote only being cast against him. Judge Thompson was the originator of the idea of sending a commission, during the Civil War, to meet Mr. Lincoln in the interests of peace, a suggestion which was accepted, Hon. Alexander H. H. Stuart, of Staunton, one of President Fillmore's cabinet, being chosen to represent Virginia. Judge Thompson married Susanna Caroline, the daughter of James and Susanna Howard (Baker) Tapscott. Issue : two sons and six daughters. The sons, as follows: The eldest, Lucas Powell, died s. p. The second, John Baker, became professor at Kenyon College, Cambria, Ohio, before he was twenty-one, and President of St. John's College, Arkansas, when only twenty-three years old. When the Civil War broke
316 Ancestbal Recobds and Poetbaits out he commanded a regiment of boys from his cpllege, officered by their professors. As Lieutenant-Colonel, on his twenty-seventh birthday, he led a charge at the (Battle of Shiloh, and the spot where he fell, mortally wounded, is one of the cycloramic features of the battle. Wounded unto death he was carried from the field still shouting encouragement to his men. His name is on a tablet in the rotunda at the University of Virginia, erected to the memory of the alumni who fought in the Civil War. The daughters were known as the " Six lovely Virginia sisters." Margaret, married Dr. Paul J. Carrington, of Virginia. Caroline, Eleanor Stuart, and Mary Carter, married, respectively, three brothers, Charles, Robert Harper Goodloe, and John Lee Carroll (the latter then governor, lineal descendants of Charles Carroll, the signer) . Alice Louise. The second daughter, Susanna Rebecca, married Robert Hull, of New York and Baltimore. Their daughter is: Amy Eleanor E. Hull, Member of Chapter I., The Colonial Dames of America.
The text on this page is estimated to be only 22.67% accurate Robert Hull From a miniature Susanna Rebecca Thompson Wife of Robert Hull Old clock with picture of the Indians meeting Gov. Winthrop Old pitcher with portrait of Capt. Isaac Hull and frigate Constitution
Ancestral Recobds and Portraits 317 XXI KUHN Among the eighteenth century families that were swept into Pennsylvania, on the flood tide of the remarkable German emigration, were the Kuhns, whose ancestor, John Kuhn, was a magistrate of Berwangen, near the Black Forest, Germany, and died previous to November 30, 1676. His son, George Martin Kuhn, was assistant jurat of the Court of Furfield, a village on the Neckar, in the province of Wiirtemburg. He married Barbara, the daughter of Friedrich Ponmes, a Justice of the Peace, and had six children. Their second child, John Christopher Kuhn, was born December 16, 1684, and died in 1754. He continued to reside in Furfeld, in the beautiful valley of the Neckar, until 1719, when he removed to Hutten. He had married Margaret, the daughter of the late Marx Reichss, a citizen of Sernum. The Kuhn family embarked on the ship Hope of London, Rotterdam being the port of departure, Daniel Reed, Master. They arrived in Philadelphia, August 28, 1733, with their three children, Adam Simon, aged nineteen; Eva Barbara, aged thirteen, and Anna Maria, aged nine. The list of passengers of the Hope is preserved at Harrisburg, Pa. The family settled in the present Berks County, Pa., and the father was naturalized March 28, 1747. He was living in that section, in Maiden Creek township, when he died. Adam Simon Kuhn^ the eldest child and only son, was born in Furfeld, Germany, December 26, 1713, and died January 23, 1780. He was naturalized, April 8, 1744, in Lancaster Coimty, Pa. A man of bright nat 
318 Ancesteal Recokds and Portraits ural parts, liberally educated, he bjecame a physician and settled in Lancaster, where he was considered a very skillful, attentive and successful practitioner. He also became conspicuous in public affairs in his new home. From 1749 to 1753 he was Chief Burgess of Lancaster. During the French and Indian War he took an active part in the defence of his neighborhood. He was commissioned a Justice of the Lancaster County Courts 1752, 1761, 1764 and 1770 ; a member of the committee of Observation and Correspondence, December 15, 1774, and served as a delegate to the Provincial Convention held at Philadelphia, January 23, 1775. A memorial tablet was erected to him in Trinity Church, Lancaster. Of him it has been said, " He was the principal and almost the only person who was concerned for the promotion of classical learning amongst the youth of that community." He married, December 11, 1740, Anna Maria Sabina, the daughter of John Jacob and Eva Rosina Schrack. She was born at sea October 26, 1717, and died in Lancaster, Pa., 1799. They had eight children, viz.: Adam, John, Johann Frederick, Daniel, Peter, Maria Sabina, John Jacob, Hannah, Eve. The eldest son, Adam John Kuhn, was bom November 17, 1741. He decided upon the medical profession as his life work, in which he eventually gained worldwide distinction. Having sailed for Europe 1761, he began the study of medicine and botany in January, 1762, at the University of Upsala, Sweden, under the celebrated Linnaeus. He continued there until 1764, when he entered the University of Edinburgh, graduating in 1767. While at Upsala he was a member of the family of Professor Linnaeus, who, in a letter still preserved in the family said: " Your son of great promise, and endowed with most engaging manners, arrived
Ancestrax, Recoeds and Portraits 319 here," and writing a year later, said, " You have ventured to send your beloved son to a foreign country, he is unwearied in his studies, lives in a most temperated and correct manner — he long since began to taste the sweets of science, therefore I congratulate you and myself on this your son, and I have never known any one more correct in his deportment or superior in application." After taking his degree in Edinburgh 1767, Dr. Adam Kuhn made a tour of France, Holland and Germany, returning to Philadelphia 1768, when he was at once appointed professor of Materia Medica and Botany in the College of Philadelphia. He was chosen one of the physicians of the newly organized society for inoculating the poor for small-pox in 1774, and May, 1775, was named as one of the physicians to the Pennsylvania Hosj)ital, resigning in 1798. Upon the establishment of the Philadelphia Dispensary, 1786, fop the relief of the poor. Dr. Kuhn was selected as consultant physician. In 1787, the College of Physicians, was founded and he was one of its charter members, becoming its president 1808, holding the office at the time of his death. In 1789 he was called to the Chair of Theory and Practice in the University of Pennsylvania, and when the college and university were united 1792, was chosen to the professorship of Physic. At the outbreak of the Revolution he was commissioned surgeon and physician of the continental service July 8, 1776, and served until 1777. He resided for some time in St. Croix, West Indies, where he married. May 14, 1780, Elizabeth, the daughter of Isaac and Mary Carroll ( Nanton) Hartman, and the widow of Franie Markoe. She was born August 20, 1755, and died February 25, 1791. Dr. Kuhn died intestate, leaving a
320 Ancestral Recoeds and Poetraits large fortune to his three children, Hartman, Charles and William. The second son, Charles Kuhn, was born April 12, 1785, and died September 22, 1842. He was graduated from the University of Pennsylvania 1802. He married, July 28, 1808, Elizabeth Hestia, the daughter of Benjamin and Elizabeth (Kortright) Yard. She was born January 24, 1788, and died March 12, 1870.^ Issue, eight children, viz.: Cornelius, Elizabeth, Hartman (who married his cousin, Mary Kuhn), Emily, WilUam, Edward, and a second Edward. HARRISON Their fifth child, Emily Kuhn, married Samuel Thompson Harrison, of the Maryland Harrisons. Their son, Charles Kuhn Harrison, married Louisa Triplett, the daughter of Boiling Walker and Ann (Triplett) Haxall, and their daughter, Ann Triplett Hareison, married George Somerville Jackson. HARRISON-CAILE John Caile Hareison, son of Christopher and 1 Authentic Family Papers.
Ancestbal Recohds and Poeteaits 321 Mary (Caile) Harrison, married his cousin, Mary, the daughter of Hall Caile and his wife, Elizabeth Haskins, the granddaughter of Goveet Loockeeman II. Their son. Hall Harrison, married Elizabeth, the daughter of Robert and Elizabeth (Thompson) Gait. Their son, Samuel Thompson Harrison, married Emily, the daughter of Charles Kuhn, whose son, Charles Kuhn Harrison, married Louisa Triplett Hawaii. LOOCKERMAN-WOOLFORD-DENWOOD Goveet Loockeemans I., married, second, Marritje Jansen. Jacob Loockeeman, married Helen Ketin. Goveet Loockeeman II., married Sarah, the daughter of RoGEE WooLEOED, and his wife Mary, the daughter of Levin Denwood I. Their ygungest daughter, Mary Loockerman, married Thomas Haskins, whose daughter, Elizabeth, married Hall Caile. (See pp. 56-79 for Harrison, Caile, Loockerman, Woolford and Denwood families.) HAXALL ■ The first known ancestor of the Haxall family of .Virginia, John Haxall, of Exning, England, was born 1681 and died September 17, 1751. His son, William Haxall, bom 1724, and died March, 1787, was one of the leading men of Exning, being churchwarden and collector of the vicar's tithes, and overseer of the poor. He married Catherine Newton, of Bristol, England, who died at " Whitehall," a large house still standing in Exning. Issue, six children, viz. : George, William, Joseph, Henry, John, Philip. The youngest son, Philip HaxaU, was born April
322 Ajncesteai, Records akd Porteaits 10, 1770, and died December 26, 1831. He emigrated to Petersburg, Va., 1786, where he was vestryman of Old Bristol Parish,* He moved to Richmond, Va., in June, 1809, and established the Haxall Mills. He married, July 20, 1801, Clara, the daughter of Robert and Ehzabeth (Starke) Walker, of Kingston, Dinwiddie County, Va. She was bom July 9, 1780, and died March 29, 1857. Issue, nine children, viz.: Robert Walker, Richard Barton, Elizabeth, Harriet, William, Henry, Mary Bell, Philip Augustus, BoUins Walker, David Walker, EUzabeth. The seventh child of the colonist. Boiling Walker HaxallJ^ born July 13, 1815, and died Jime 26, 1885, married, December 30, 1845, Anne, the daughter of John Richards and Louisa (Stone) Triplett, and their daughter, Louisa Triplett, married Charles Kuhn Harrison. HAXALIi TRIPLETT* The first of this name to settle in Virginia, Francis Triplett, who died 1700, went to Richmond County. He patented one thousand and fifty acres of land in Rappahannock County 1666. He was a nephew of 2 Bristol Parish Records. Hayden's Genealogies. 3 The name of Haxall is believed to be extinct in England, and it only exists in this country in the descendants of Plulip and Clara (Walker) HaxalL *A genealogy of this family will be published in the Virgima Aist. Mag. by Rev. Arnold Harris Hord, of Germantown, Penn.
Ancestbal Recobds and Portraits 323 Rev. Thomas Triplett, Dean of Westminster Abbey, whose monmnent is in the Poets' Corner of the Abbey. The Dean is described in some very old books as of London and the son of a gentleman. A son of Francis, the colonist, William Triplett, was a resident of King George's County, and a land deed bearing date November 6, 1733, is on record in Spottsylvania County; his will was dated December 3, 1738. He married Isabella, the daughter of Captain Lyman Miller, whose will was proved in Rappahannock County May 22, 1684. Captain Miller was a noted shipbuilder and a large landoAvner.' Their son, Francis Triplett II., owned estates in Westmoreland and King George's Counties; his will was proved March 5, 1767. His wife's name was Mildred . Their fifth and youngest son, Daniel Triplett, was born May 8, 1753, and married, January 1, 1777, Elizabeth, the daughter of John and Susannah (Coleman) Richards. She was born May 22, 1760. Their son, John Richards Triplett, was bom January 29, 1785, and died October 2, 1843. He married, May 19, 1813, his cousin, Louisa Richards Stone, and resided in Norfolk, Va. Their daughter, Anne, married Boiling Walker Hawaii. RICHARDS Abms: Sable a chevron between three fieur-de-Us or. The son of William Byrd Richkrds, John Richards, was born in England, January 27, 1734, and died September 13, 1785.® He married, January 1, 1754, Susannah, the daughter of Robert Coleman, of Goochland B Bruce's Economic Hist, of Va. Vol. II, p. 439. B Family Papers.
324 Ancestbal Records and Pokteaits County, She died April 15, 1778. Had twelve children, viz.: Patty, James, Elizabeth, Triplett, Susannah, Payne, Sarah, John, WiUiam, Mildred, who married WilKam Scandreth Stone November 10, 1787; Fanny, Catherine. The third child, Elizabeth, was bom May 22, 1760, and married, January 1, 1777, Daniel Triplett, whose son, John Richards, married Louisa Richards, the daughter of Mildred and William Scandreth Stone. WALKER The first of the name in Virginia, Captain David Walker, lived in Dinwiddle Coimty. Family records say that " he was a man of large means, for years Presiding Magistrate, a position that was only held by men of the highest education and wealth. He was Senior Warden of Bristol Parish, later a Warden of Bath Parish.'' His son, Robert Walker, of Kingston, Va., was born October 10, 1729, and married, 1745, Elizabeth^ the daughter of William and Mary (BoUing) Starke. Had ten children, viz.: Robert, Richard, David, Boiling, Freeman, Starke, Louisa, Martha, Mary, and Clara, who married Philip Haxall. Their son, Boiling Walker Haaiall, married Anne Triplett. STARKE Asms: Aawre, a chevron between three acorns in chief or. Chest: A bull's head erased or, distilling drops of blood proper. Motto: Fortiorum Portia Facta. The Starkes came to America from Scotland, the first mentioned being Dr. Richard Starke, of York County, Va. It becomes a matter of interest to identify this gentleman, of whom very little is remembered, beyond Tibid.
Ancestral Recobds and Poethaits 325 ' his interesting connection with our earliest American law books. In the records of York County is mentioned a Dr. Richard Starke, who died in 1704, leaving a wife Rebecca, and the following children: William, Richard, James, Catrine, and Mary Harris. In 1774, there was printed, at Wilhamsburg, by Alexander Purdie and John Dixson, a book entitled " The Office and Authority of a Justice of the Peace, explained and digested under proper titles," to which are added full and correct precedents of all kinds of process necessary to be used by magistrates, in which also the duties of sheriffs and other public officers are properly discussed. The greater part of the book was written by Dr. Richard Starke, whose death prevented its completion. His friends prevailed upon some benevolent gentlemen of the law to finish the work. Colonel William Starke, his eldest son, was a prominent man in York County, Va. He was Justice of the Peace in 1730 and other years, and Colonel of the County Militia. He built and gave Starke's Free School. He married Mary, the daughter of Robert and Anne (Cocke) Boiling, and there is a marriage contract on record between William and Mary, 1713. Their daughter, Elizabeth, married Robert Walker.* ROLLING The Boilings are of very ancient origin. Robert Boiling, Esq., in the reign of Edward IV., resided at Boiling Hall, near Bradford, in Yorkshire, England, where many generations of his ancestors in the enjoyment of private life had lived, and where he died 1485, He was buried in the family vault of the church at Bradford. It is probable that his family had been bene8 Willicmi and Mary Quar.
326 Ancestral Records and Portraits factors of that church, or had even bviilt it, since their coat-of-arms alone are engraved upon it. Boiling Hall passed in succession to the families of Tristram BoUing and Sir Richard Tempest, the latter marrying Rosamond, the daughter and heiress of Tristram. Robert Rolling, son of John and Mary, of the Boilings of "Boiling Hall," near Bradford, of All Hallows, Barking Parish, Tower Street, London, was the first of the name who settled in Virginia, arriving there October 2, 1660. He was bom December 26, 1646, and died July 17, 1709. He lived at " Kippax," sometimes called " Farmingdate," served as a Burgess 1704, and took a prominent part in the aiFairs of the colony. The BolUng family were deeply interested in the church in Virginia, and have been represented in the Vestry of Old Bristol Parish in every generation.® Robert Boiling married, first, 1675, Jane, the daughter of Thomas Rolfe and the granddaughter of Pocahontas; second, 1681, Anne, the daughter of Colonel John Stith. Issue, second wife, seven children, viz. : Robert, Stith, Edward, Anne, Doury, Thomas, and Agnes. Robert Rolling II. was born January 25, 1682, and died 1749. He was also prominent in the ajBfairs of his county; Surveyor of Charles City County 1714; Justice of the Peace, and a member of the House of Burgesses 1723, 1726 and 1730. He married, January 27, 1706, Anne, the daughter of Richard and Anne (Bowler) Cocke. They had eight children, viz. : Elizabeth, Anne, Lucy, Jane, Martha, Susanna, Robert, and Mary, who married William Starke. STITH Colonel John Stith was the first of this family in t Bristol Pariah; Va. Hist. Mag., and William and Mary Quar,
Ancestbal Recokds and Portraits 327 Virginia. He had a grant of land in Charles CityCounty 1663; was a practicing lawyer 1680; member of the House of Burgesses 1685 to 1692 and 1693, and Sheriif 1691. His known children are: Drury, John, ahd Anne, who married Robert BoUing I. Their son, Robert Bolling II., married Anne Cocke, whose daughter, Mary, married William Starke. COCKE Abms: Argent two lions passant sable crowned or a fesse sable between two talbots passant. Richard Cocke (1600-1665), the original ancestor of the Cockes of Virginia, emigrated from Leeds, England, about 1630, and settled at Milvert Hills. With him, came Captain Francis West, his sister having married Robert West, son of Lord de la Warr, and settled in Henrico County, Va. Richard Cocke was a prominent merchant in London, and several of his family were connected with the Royal households of Mary, Elizabeth, and James I., and the Cocke family was connected with the Wests, Percy Lord Chandos, the Berkeley family. Sir Hugh Poynty, and Lord Wentworth. In the Committee of Safety of Surry County, Va., 1776, there were five Cockes: Colonel Allen, Colonel John, John Jr., J. H., and Colonel Lemuel Cocke. The Cocke family sat in nearly every session of the Virginia House of Burgesses. Richard Cocke took a leading part in the affairs of the colony, serving as a Burgess 1632, 1644, and 1654. He was also a member of the " Grand Assembly of Virginia." His nephew, Captain Cocke, of London, is well known by his intimacy with Samuel Pepys, and is often mentioned in his
328 Ancestbal Records and Poeteaits celebrated diary. Richard Cocke married Mary, the daughter of Walter Aston, and had a large family. Richard Cocke II., third son of .the colonist, was born 1639, and died 1705. He took an active part in the affairs of Virginia, being a civil officer of Henrico County 1680; Justice of the Peace 1714, and Burgess. He married, 1675, Ann Bowler, and their daughter, Anne Cocke, married Robert Rolling, Jr., whose 'daughter, Mary Boiling, married William Starke. ASTON Abms: Argemt a fesae sable in chief three lozenges of the last. Crest: A hull's head, cowped sable. Walter Aston (the grandson of Sir Walter Aston, of Longdon, Stafford County, England, who was knighted 1560), was born July 9, 1584, and died August 13, 1639, and is buried at " Westover," The family came to America 1626, and August 12 of that year Walter Aston patented one thousand and forty acres of land near Shirley Hundred, two hundred acres of which were known as " Causey's Care," purchased in 1634 from John Causey (being the same land patented by Nathaniel Causey, who came in with the first supply, 1608. All of this property became part of William Byrd's celebrated "Westover"), Walter Aston represented Shirley Hundred in the House of Burgesses 1629 to 1630 and Causey's Care 1632 to 1633. He was a Justice of the Peace, and Lieutenant- Colonel of the Militia.'" His first wife's name is mentioned in land patents as being Warboe or Narboe, and his second wife's name was Hannah, who married after his death Colonel Edward Hill. Children: Susannah, Walter, 10 William and Mary Quar.
Ancestral Recoeds and Poetbaits 329 EHzabeth, and Mary, who married Richard Cocke. From them the line descends as follows: Richard Cocke II., married Ann Bowler. Anne Cocke, married Robert Rolling II. Mary Boiling, married William Starke. Elizabeth Starke, married Robert Walker. Clara Walker, married Philip Haxall. Boiling Walker Hawaii, married Anne Triplett. Louisa Triplett Haxall, married Charles Kuhn Harrison, whose daughter is: Anne Triplett Harrison Jackson, Member of Chapter I„ The Colonial Dames of America.
330 Ancestral Recoeds and Portraits XXII SWAN Scottish records, of the year 1599, contain the name of William Swan, a Burgess of Dumfrieg, who died in January, 1603, leaving a widow, Helen Anderson, and four children, viz.: Andrew, William, Alison, and Helen. The eldest child, Andrew Swan, married, before 1607, Janet, who was a daughter of Herbert Ranyng (who died in 1601), and Janet Davidson, his wife, and a granddaughter of another Herbert Ranyng (who died 1587) , and Malie Kirkpatrick, his wife. The elder Ranyng was Provost of Dumfries, 1572; member of the Parliament of Scotland the same year, and Commissioner for Dimifries, in the Convention of Royal Burghs, 1578. The younger Ranyng, was Provost of Dumfries, 1586, 1591 to 1592, and was frequently Bailie. A son of Andrew and Janet (Ranyng) Swan, was John, living in the year 1626. Of the same family was James Swan, a merchant of Dumfries, who died May 24, 1760. His son Robert, born 1720, a partner in the house of Nelson, Carlyle & Company, of Glasgow, resided at Annapolis, Md., as the American representative of the firm, and died there unmarried May 4, 1764. The larger part of his estate he left by will to his nephew, John Swan, the eldest son of his brother John, of Cocketfield, viz.: Major John Swan, who was baptized in Torthorwald Parish, November 27, 1750, and came to Maryland in the year 1766, as the heir of his uncle's estate.
The text on this page is estimated to be only 5.65% accurate ■1 1 ^^m'^-^] ^^^^^^^^^H ^^M ^^^^ I ■1 Py ' 1 9^ iJ Elizabeth Maxwell Wife of Maj. John Swan Maj. Joiix Swan James Swan Elizametli Doxnell AVife of James Swan
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Bioprocess Engineering: Kinetics, Sustainability, and Reactor Design 3rd Edition Shijie Liu

  • 1.
    Bioprocess Engineering: Kinetics, Sustainability,and Reactor Design 3rd Edition Shijie Liu install download https://textbookfull.com/product/bioprocess-engineering-kinetics- sustainability-and-reactor-design-3rd-edition-shijie-liu/ Download more ebook instantly today - get yours now at textbookfull.com
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  • 5.
    Shijie Liu Professor Chemical Engineering SUNYESF Syracuse NY, United States Bioprocess Engineering Kinetics, Sustainability, and Reactor Design Third Edition
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    Elsevier Radarweg 29, POBox 211, 1000 AE Amsterdam, Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2020 Elsevier B.V. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, in- cluding photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our ar- rangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understand- ing, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any infor- mation, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-0-12-821012-3 For information on all Elsevier publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Joe Hayton Acquisitions Editor: Kostas Marinakis Editorial Project Manager: Liz Heijkoop Production Project Manager: Omer Mukthar Designer: Mark Rogers Typeset by Thomson Digital
  • 7.
    Bioprocess Engineering. http://dx.doi.org/10.1016/B978-0-12-821012-3.00001-4 Copyright© 2020 Elsevier B.V. All rights reserved. 1 1.1 Biological cycle Fig. 1.1 illustrates the natural biological processes occurring on Earth. Living systems consist of plants, animals, and mi- croorganisms. Sunlight is used by plants to convert CO2 and H2O into carbohydrates and other organic matter, releasing O2. Animals consume plant matter, converting plant materials into animal cells, and using the chemical energy from oxidizing plant matter into CO2 and H2O (H2O also serves as a key substrate for animals), finishing the cycle. Microorganisms further convert dead animal and/or plant biomass into other form of organic substances fertilizing the growth of plants, releasing CO2 and H2O, and the cycle is repeated. Energy from the Sun is used to form molecules and organisms that we call life. Ma- terials or matter participating in the biological cycle are renewable so long as the cycle is maintained. Bioprocess engineers manipulate and make use of this cycle by designing processes to make desired products, either by training microorganisms, plants, and animals, or via direct chemical conversions. The reactor is the heart of any chemical and/or biochemical processes. With reactors, bioprocesses turn inexpensive sus- tainably renewable chemicals such as carbohydrates, into valuable ones that humans need. As such, bioprocesses are chemi- cal processes that use biological substrates and/or catalysts. While not limited to such, we tend to refer to bioprocesses as (1) biologically converting inexpensive “chemicals” or materials into valuable chemicals or materials; and (2) manipulating biological organisms to serve as “catalyst” for conversion or production of products that human need. Bioprocess engineers are the only people technically trained to understand, design, and efficiently handle bioreactors. Bioprocess engineering ensures that a favorable sustainable state or predictable outcome of a bioprocess is achieved. This is equivalent to saying that bioprocess engineers are engineers with, differentiating from other engineers, training in biological sciences, especially quantitative and analytical biological sciences, and green chemistry. If one thinks of science as a dream, engineering is making the dream a reality. The maturing of Chemical Engineer- ing to a major discipline and as one of the very few well-defined disciplines in the 1950s has led to the ease in the mass production of commodity chemicals and completely changed the economics or value structure of materials and chemicals, thanks to the vastly available what were then “waste” and “toxic” materials—fossil resources. Food and materials can be manufactured from the cheap fossil materials. Our living standards improved significantly. Today, chemical reactors and chemical processes are not built by trial-and-error, but by design. The performance of a chemical reactor can be predicted, not just found to happen that way; the differences between large and small reactors are largely solved. Once a dream for the visional pioneers, it can now be achieved at ease. Fossil chemical and energy sources have provided much of our needs for advancing and maintaining the living standards of today. With the dwindling of fossil resources, we are facing yet an- other value structure change. The dream has been shifted to realizing a society that is built upon renewable and sustainable resources. Fossil sources will no longer be abundant for human use. Sustainability becomes the primary concern. Who is going to make this dream come true? Chapter 1 What is bioprocess engineering? Chapter outline 1.1 Biological cycle 1 1.2 Bioprocess engineering applications 2 1.3 Scales: living organism and manufacturing 3 1.4 Green chemistry 4 1.5 Sustainability 5 1.6 Biorefinery 5 1.7 Biotechnology and bioprocess engineering 8 1.8 Mathematics, biology, and engineering 9 1.9 The story of penicillin: the dawn of bioprocess engineering 9 1.10 Bioprocesses: regulatory constraints 12 1.11 The pillars of bioprocess kinetics and systems engineering 13 1.12 Summary 14 Problems 14 References 14 Further readings 15
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    2 Bioprocess Engineering  Ona somewhat different scale, we can now manipulate life at its most basic level: the genetic. For thousands of years people have practiced genetic engineering at the level of selection and breeding, or directed evolution. But now it can be done in a purposeful, predetermined manner with the molecular-level manipulation of DNA, at a quantum leap level (as compared with directed evolution) or by design. We now have tools to probe the mysteries of life in a way unimaginable prior to the 1970s. With this intellectual revolution emerges new visions and new hopes: new medicines, semisynthetic organs, abundant and nutritious foods, computers based on biological molecules rather than silicon chips, organisms to degrade pollutants and clean up decades of unintentional damage to the environment, zero harmful chemical leakage to the environment while producing a wide array of consumer products, and revolutionized industrial processes. Our aim of comfortable living standards is ever higher. Without hard work, these dreams will remain merely dreams. Engineers will play an essential role in converting these visions into reality. Biosystems are very complex and beautifully constructed, but they must obey the rules of chemistry and physics and they are susceptible to engineering analysis. Living cells are predictable, and processes to use them can be methodically constructed on commercial scales. There lies a great task—analysis, design, and control of biosystems to the greater benefit of a sustainable humanity. This is the job of the bioprocess engineer. This text is organized such that you can learn bioprocess engineering from the principles. To limit the scope of the text, we have left out the product purification technologies, while focusing on the production generation or biotransformations. We attempt to bridge molecular level understandings to industrial applications. It is our hope that this will help you to strengthen your desire and ability to participate in the intellectual revolution and to make an important contribution to the human society. 1.2 Bioprocess engineering applications In a narrow sense, all human activities are centered around humans. In terms of human needs, bioprocess engineers deal from the production and application of biomaterials, to health defense, biologics development, and production, including gene therapy (manufacturing process), to the production of food and fuel as illustrated in Fig. 1.2. In all these applications, fundamentally, molecular interaction and/or (bio-) transformation governs the production and/or protection processes. A biologic drug is a product produced from a living organism or containing component(s) of living organisms. Biologics include recombinant proteins, tissues, genes, allergens, cells, blood components, blood, and vaccines. Biologics are used to treat numerous disease and conditions on humans. The transformation from chemicals to biologics, the functions or interac- tions of a biologic with human body, pharmacology, and the design of the biologic are subject areas of bioprocess engineering. Gene therapy is an experimental technique that uses genes to treat or prevent disease. This technique has the potential to allow doctors to treat a disorder by inserting a gene into a patient’s cells instead of using drugs or surgery. Researchers are testing several approaches to gene therapy, including: l Replacing a mutated gene that causes disease with a healthy copy of the gene. l Inactivating, or “knocking out,” a mutated gene that is functioning improperly. l Introducing a new gene into the body to help fight a disease. Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types of cancer, and certain viral infections), the technique remains risky and is still under study to make sure that it will be safe and effective. Gene therapy is currently being tested only for diseases that have no other cures. Cell therapy is the therapy in which cellular material is injected, grafted, or implanted into a patient; this generally means intact, living cells. For example, T cells capable of fighting cancer cells via cell-mediated immunity may be injected in the course of immunotherapy. FIGURE 1.1 The natural biological processes.
  • 9.
    What is bioprocessengineering? Chapter | 1 3 Cell therapy originated in the 19th century when scientists experimented by injecting animal material in an attempt to prevent and treat illness. Although such attempts produced no positive benefit, further research found in the mid 20th century that human cells could be used to help prevent the human body rejecting transplanted organs, leading in time to successful bone-marrow transplantation Chimeric antigen receptor (CAR)-modified T cell therapy, for example, has proven to be effective for patients with B cell hematological malignancies. Challenges remain in how to scale out the production of CAR T cells under current good manufacturing procedure (cGMP) in an efficient, effective manner. Currently as a mostly autologous cell-based therapy, the CAR-T cell manufacturing process represents a completely different manufacturing model from traditional biologics. One of the challenges of this largely personalized medicine is the development of efficient technologies and cost-effective clinical manufacturing platforms to support the later-stage clinical trials toward commercialization. Substantial efforts have been placed on the upstream for gene transduction and cell expansion. Apart from health defense and/or biologics, commodity products production is crucial for the human society. Food, fuels, and materials fill in the basic needs. 1.3 Scales: living organism and manufacturing Bioprocess engineering deals with a variable scale, from the molecular level at research to process operation in a factory at manufacturing level. In health applications, this translates to medical research at the most fundamental level of enzyme/ protein to human health professionals at overall health. Fig. 1.3 shows side-side the comparison from a “traditional” chemi- cal engineering view on the left to the “health” engineering on the right. The function of a protein or an enzyme within human cells is important for the overall health of human. When or if any changes to the protein or a foreign protein invades a human cell, the physiology will change, causing a domino effect/ change to far-reaching cells. Regulating the protein and enzyme functions can also be effected with ligands or chemicals. The molecular interactions are key to the overall health of humans. FIGURE 1.2 The applications of bioprocess engineering centered around humanity needs. FIGURE 1.3 A comparison of the chemical engineering (left) with processes in a complex living organism: human body. The bottom is at the microscopic scale where molecular interactions are examined, whereas at the top the factory as a whole is considered.
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    4 Bioprocess Engineering  1.4Green chemistry Green chemistry, also called sustainable chemistry, is a philosophy of chemical research and engineering that encourages the design of products and processes that minimize the use and generation of hazardous substances while maximizing the efficiency of the desired product generation. Whereas environmental chemistry is the chemistry of the natural environment, and of pollutant chemicals in nature, green chemistry seeks to reduce and prevent pollution at its source. In 1990, the Pol- lution Prevention Act was passed in the United States. This act helped create a modus operandi for dealing with pollution in an original and innovative way. It aims to avoid problems before they happen. Examples of green chemistry starts with the choice of solvent for a process—water, carbon dioxide, dry media, and non-volatile (ionic) liquids, which are some of the excellent choices. These solvents are not harmful to the environment as either emission can easily be avoided or they are ubiquous in nature. Paul Anastas, then of the United States Environmental Protection Agency, and John C. Warner developed 12 principles of green chemistry, which help to explain what the definition means in practice. The principles cover such concepts as— (1) the design of processes to maximize the amount of (all) raw material that ends up in the product; (2) the use of safe, environment-benign substances, including solvents, whenever possible; (3) the design of energy efficient processes; and (4) the best form of waste disposal: not to create it in the first place. The 12 principles are: 1. It is better to prevent waste than to treat or clean up waste after it is formed. 2. Synthetic methods should be designed to maximize “atom efficiency.” 3. Wherever practicable, synthetic methodologies should be designed to use and generate substances that possess little or no toxicity to human health and the environment. 4. Chemical products should be designed to preserve efficacy of function while reducing toxicity. 5. The use of auxiliary substances (e.g., solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used. 6. Energy requirements should be recognized for their environmental and economic impacts and should be minimized. Synthetic methods should be conducted at ambient temperature and pressure. 7. A raw material or feedstock should be renewable rather than depleting wherever technically and economically practicable. 8. Reduce derivatives—Unnecessary derivatization (blocking group, protection/ deprotection, temporary modification) should be avoided whenever possible. 9. Catalytic reagents (as selective as possible) are superior to stoichiometric reagents. 10. Chemical products should be designed so that at the end of their function they do not persist in the environment and break down into innocuous degradation products. 11. Analytical methodologies need to be further developed to allow for real-time, in-process monitoring and control prior to the formation of hazardous substances. 12. Substances and the form of a substance used in a chemical process should be chosen to minimize potential for chemi- cal accidents, including releases, explosions, and fires. One example of green chemistry achievements is the polylactic acid (or PLA). In 2002, Cargill Dow (now NatureWorks) won the Greener Reaction Conditions Award for their improved polylactic acid polymerization process. Lactic acid is pro- duced by fermenting corn and converted to lactide, the cyclic dimmer ester of lactic acid using an efficient, tin-catalyzed cyclization. The L,L-lactide enantiomers is isolated by distillation and polymerized in the melt to make a crystallizable polymer, which has use in many applications including textiles and apparel, cutlery, and food packaging. Wal-Mart has announced that it is using/will use PLA for its produce packaging. The NatureWorks PLA process substitutes renewable materials for petroleum feedstocks, does not require the use of hazardous organic solvents typical in other PLA processes, and results in a high-quality polymer that is recyclable and compostable. Understanding the concept of green chemistry holds a special position for bioprocess engineers. Processes we design and operate must have minimal potential environmental impacts while optimized for maximum benefit. Basic steps for green chemistry that are what bioprocess engineering do include: 1. Developing products and processes based on renewable resources, such as plant biomass; 2. Design processes that bypass dangerous/toxic-chemical intermediates; 3. Design processes that avoid dangerous/toxic solvent use; 4. Reducing chemical processing steps, but demands high efficiency; 5. Promoting biochemical processes to reduce chemical processing steps or toxic chemical utilization; 6. Design milder (closer to atmosphere temperature and pressure) processes and multiple product recovery routes;
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    What is bioprocessengineering? Chapter | 1 5 7. Bypassing chemical equilibrium with innovative reactor design, and biocatalysis, rather than adding intermediate steps. 8. Avoid production of unwanted products other than H2O and CO2. 1.5 Sustainability Sustainability is the capacity to endure or maintain at the longest timescale permissible. In other words, sustainability is the ability to maintain continuum. In ecology, the word describes how biological systems remain diverse and productive over time. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. For humans, sustainabil- ity is the potential for long-term maintenance of well-being, which has environmental, economic, and social dimensions. Healthy ecosystems and environments provide vital goods and services to humans and other organisms. Utilization and release of substances at a rate that is harmonious with a steady state nature is the key for sustainability. This naturally leads to a carrying capacity for each substance or species with which humans interact. The sustainable state can be influenced by (process conditions or) how we interact with nature. There are two major ways of reducing negative human impact and en- hancing ecosystem services. The first is environmental management; this approach is based largely on information gained from earth science, environmental science, and conservation biology. The second approach is management of human con- sumption of resources, which is based largely on information gained from economics. Practice of both of these major steps can ensure a more favorable sustainable state to be evolved into. Sustainability interfaces with economics through the social and ecological consequences of economic activity. Sus- tainable economics involves ecological economics where social, cultural, health-related, and monetary/financial aspects are integrated. Moving toward sustainability is also a social challenge that entails international and national law, urban planning and transport, local and individual lifestyles and ethical consumerism. Ways of living more sustainably can take many forms from reorganizing living conditions (e.g., ecovillages, eco-municipalities, and sustainable cities), reapprais- ing economic sectors (permaculture, green building, sustainable agriculture), or work practices (sustainable architecture), using science to develop new technologies (green technologies, renewable energy), to adjustments in individual lifestyles that conserve natural resources. These exercises reduce our reliance or demand on disturbing the environment. To make all these concepts come to light, bioprocess engineers will be at the forefront of developing and implementing the technologies needed. On a grand scale, maintaining renewability or looking for a favorable predictable steady state on everything we touch or interact is the key to sustainability (Fig. 1.4). This falls right in the arena of bioprocess engineering. Are you ready for the challenge of designing processes that meets sustainability demands? 1.6 Biorefinery On a grand scale, sustainability is the basis of nature. Enforcing sustainability at the time scale of humanity is an insurance of our way of life to continue. Prior to the 1900s, agriculture and forestry were the predominant sources of raw materi- als for energy, food and a wide range of everyday commodities, and the human civilization depended almost entirely on renewable materials. Humanity was restricted by the sustainable supply inefficiently harvested from the biomass, which drew energy from the sun. The industrial revolution has brought a leap in the human civilization. Mass production of goods by machines dominates our daily life. The industrial revolution was brought to mature by the development of combustion FIGURE 1.4 Change of sustainable state owing to human interruption.
  • 12.
    6 Bioprocess Engineering  enginesand subsequent development of fossil energy and chemical industry. Besides the more than doubling of useful bio- mass production/harvest, mankind has increasingly tapped into the large fossil-energy reserves. At first the fossil chemicals were regarded as waste and thus any use was welcomed. It soon became the cheapest chemical and energy sources for the industrial revolution. As a result, our living standards have seen a leap. There is no turning back to the primitive way of life in the past. However, fossil energy and chemical sources are depleting despite the cyclic price change of energy and com- modity materials. There is a critical need to change the current industry and human civilization to a sustainable manner, assuring that our way of life today continues on the path of improvement after the depletion of fossil sources. Our way of life exists only if sustainability is maintained on a time scale no longer than our life span. Biorefinery is concept in analogous to a petroleum refinery whereby a raw material feed (in this case plant ligocellulosic biomass instead of petroleum) is refined to a potpourri of products (on demand). In a biorefinery, lignocellulosic biomass is converted to chemicals, materials, and energy that runs on the human civilization, replacing the needs of petroleum, coal, natural gas, and other non-renewable energy and chemical sources. Lignocellulosic biomass is renewable as shown in Fig. 1.1, in that plant synthesizes chemicals by drawing energy from the sun and, carbon dioxide and water from the environment, while releasing oxygen. Combustion of biomass releases energy, carbon dioxide, and water. Therefore, biore- finery plays a key role in ensuring the cycle of biomass production and consumption included satisfying human needs for energy and chemicals. A biorefinery integrates a variety of conversion processes to produce multiple product streams such as transportation liquid fuels, steam/heat, electricity, and chemicals from lignocellulosic biomass. Biorefinery has been identified as the most promising route to the creation of a sustainable bio-based economy. Biorefinery is a collection of the essential technologies to transform biological raw materials into a range of industrially useful intermediates. By producing multiple products, a biorefinery maximizes the value derived from a lignocellulosic biomass feedstock. A biorefinery could produce one or more low-volume, high-value chemical products together with a low-value, high-volume liquid transportation fuel, while generating electricity and process heat for its own use and/or export. Fig. 1.5 shows a schematic of various biorefinery processes. There are at least three steps in converting woody biomass: pretreatment; cracking or rendering biomass to intermediate molecules; and conversion (of the intermediate molecules to desired products). There are three major categories or approaches in pretreatment—systematical disassembling processes; pyrolysis and gasification processes. In systematical disassembling processes, the lignocellulosic biomass is commonly disassembled to individual components systematically for optimal conversions that followed. The basic approach is based on a systematical disassembling and conversion to desired chemicals. This pretreatment method and the rout of conversion FIGURE 1.5 A schematic of various biorefinery processes. (With permission from: Liu, S., 2015. A synergetic pretreatment technology for woody biomass conversion. Appl. Ener. 144, 114–128).
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    What is bioprocessengineering? Chapter | 1 7 followed depend heavily on separation and/or physical fractionation of the intermediates as well as the final desired prod- ucts. Pyrolysis applies heat and some oxygen (or none) to render the biomass to liquid, while gasification renders the bio- mass to syngas. Biological conversions are preferred over chemical conversions due to their selectivity or green chemistry concepts. However, owing to the complexity of the lignocellulosic biomass, a multitude of biological processes is required for optimal operations. The biological reactions are also very slow and thus require larger facility foot prints. Especially following the gasification, bioconversion is in the “primitive” stage of development. Pyrolysis resembles more closely to the refinery whereby the products can be controlled in a more systematical man- ner. It may be classified as systematical disassembling as well. However, there are restrictions on the type of products the process can produce. Gasification as shown in Fig. 1.5 is at the extreme side of conversion technology, whereby the lignocellulosic biomass is disassembled to the basic building block for hydrocarbons: H2 and CO, and then reassembled to desired products as desired. The final products can be more easily tailored from syngas or CO + H2. For example, Fisher-Tropsch process can turn CO + H2 into higher alcohol, alkenes, and many other products. Syn gas (together with air: mixture of N2 and O2) is also the starting point for ammonia synthesis, from which nitrogen fertilizers and many other products are produced. However, all thermochemical processes suffer from selectivity. During the disassembling process, “coke” or “carbon” is produced especially at high temperatures and thus reduces the conversion efficiency, if H2 and CO are the desired intermediates. Thermal-chemical processes are generally considered less “green” than biological and other sequential disassembling processes due to their severe operating conditions, poor selectivity or byproducts generation, and thermodynamic restrictions. The promise of a biorefinery to supply the products human needs is shown in Fig. 1.6 for the various examples of build- ing blocks or platform chemicals that sugar (a specific example of glucose) can produce, besides the very basic building blocks of CO and H2. For example, glucose can be fermented to ethanol by yeast and bacteria anaerobically, and lactic acid can be produced by lacto bacteria. As shown in Fig. 1.6, each arrow radiates from the glucose in the center represents a route of biotransformation (or fermentation) by default, whereas chemical transformations are shown with labeled arrows. For example, glucose can be dehydrated to 5-hydroxymethylfurfural catalyzed with an acid, which can be further decomposed to levulinic acid by hydration. All these chemicals shown in Fig. 1.6 are examples of important platform (or intermediate) chemicals, as well as commodity chemicals. For example, ethanol is well known for its use as a liquid transportation fuel. FIGURE 1.6 The platform of chemicals derived from glucose (the molecule in the center of the diagram). Most of these chemicals are produced via fermentation (or biotransformation), while a few of them are produced via chemical reaction (or chemical transformation) as indicated.
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    8 Bioprocess Engineering  Ethanolcan be dehydrated to ethylene, which is the monomer for polyethylene, or dehydrognated and dehydrated to make 1,3-butadiene, monomer for the synthetic rubber. Ethanol can also be employed to produce higher alcohols and alkenes. Are you prepared to be at the forefront of developing, designing and operating these processes for the sustainability and comfortability in humanity? 1.7 Biotechnology and bioprocess engineering Biotechnology is the use or development of methods of direct genetic manipulation for a socially desirable goal. Such a goal might be the production of a particular chemical, but it may also involve the production of better plants or seeds, gene ther- apy, or the use of specially designed organisms to degrade wastes. The key element is the use of sophisticated techniques outside the cell for genetic manipulation. Biotechnology is applied biology; it bridges biology to bioprocess engineering, just like applied chemistry or chemical technology bridges chemistry to chemical engineering. Many terms have been used to describe engineers working with biotechnology. The two terms that are considered general—Biological engineering and Bioengineering come from the two major fields of applications that require deep understanding of biology—agriculture and medicine. Bioengineering is a broad title including work on industrial, medi- cal and agricultural systems; its practitioners include agricultural, electrical, mechanical, industrial, environmental, and chemical engineers, and others. As such, Bioenegineering is not a well-defined term and usually it refers to biotechnology applications that are not easily categorized or in medical fields. Biological Engineering stems from engineering of biology which is also a general term. However, the term biological engineering is initially used by agricultural engineers for the engineering applications to or manipulation of plants and animals and is thus specific. For example, the Institute of Bio- logical Engineering (IBE) has a base in, although not limited to, agricultural engineering. ABET (Accreditation Board for Engineering and Technology, Inc.) brands Biological Engineering together with Agricultural Engineering when accredit- ing BS (Bachelor of Science) and MS (Master of Science) in engineering and technology educational programs. On the other hand, the Society for Biological Engineers was created within American Institute of Chemical Engineers. Therefore, biological engineering is also regarded as a not well defined term and can at times refer to biotechnology applications in agricultural fields. Biochemical engineering has usually meant the extension of chemical engineering principles to systems using a biological catalyst to bring about desired chemical transformations. It is often subdivided into bioreaction engineer- ing and bioseparations. Biomedical engineering has traditionally been considered totally separate from biochemical engi- neering, although the boundary between the two is increasingly vague, particularly in the areas of cell surface receptors and animal cell culture. Another relevant term is biomolecular engineering, which has been defined by the National Institutes of Health as “... research at the interface of biology and chemical engineering and is focused at the molecular level.” In all, a strong background in quantitative analysis, kinetic/dynamic behaviors, and equilibrium behaviors are strongly desirable. Increasingly, these biorelated engineering fields have become inter-related, although the names are restricting. Bioprocess engineering is a broader and at the same time a narrower field than the commonly used terms referred ear- lier—biological engineering, biochemical engineering, biomedical engineering, and biomolecular engineering. Bioprocess Engineering is a profession than spans all the bio-related engineering fields as mentioned earlier. It is a profession that has emerged to stand alone, as compared to the interdisciplinary profession once it was. Unlike the term bioengineering, the term biorpocess engineering is specific and well-defined. Bioprocess engineering emphasizes the engineering and sciences of industrial processes that are biobased—(1) biomass feedstock conversion for a sustainable society or biorefinery; (2) biocatalysis based processing; and (3) manipulation of micro-organisms for a sustainable and socially desirable goal. Bio- process engineering is not product-based nor is substrate-based. Therefore, bioprocess engineering deals with biological and chemical processes involved in all areas, not just for a particular substrate or species (of feedstock or intermediate), outcome or product. Thus, bioprocess engineering intercepts chemical, mechanical, electrical, environmental, medical, and industrial engineering fields, applying the principles to designing and analysis of processes based on using living cells or subcomponents of such cells, as well as non-living matters. Bioprocess engineering deals with both micro-scale (cellular/ molecular) and large-scale (systemwide / industrial) designs and analyses. Science and engineering of processes converting biomass materials to chemicals, materials, and energy are therefore part of bioprocess engineering by extension. Predict- ing and modeling system behaviors, detailed equipment and process design, sensor development, control algorithms, and manufacturing or operating strategies are just some of the challenges facing bioprocess engineers. At the heart of bioprocess engineering lays the process kinetics, reactor design and analysis for biosystems, which forms the basis for this text. We will focus primarily on the kinetics, dynamics, and reaction engineering involved in the bioprocess engineering. A key component is the application of engineering principles to systems containing biological catalysts and/or biomass as feedstock, but with an emphasis on those systems making use of biotechnology and green chemistry. The rapidly increasing ability to determine the complete sequence of genes in an organism offers new opportunities for bioprocess engineers in the design and monitoring of bioprocesses. The cell, itself, is now a designable component of the overall process.
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    What is bioprocessengineering? Chapter | 1 9 For practitioners working in the bioprocess engineering, some of journals and periodicals provide the latest develop- ments in the field. Here we name a few: l Biochemical Engineering Journal l Journal of Biological Engineering l Journal of Biomass Conversion and Biorefinery l Journal of Bioprocess Engineering and Biorefinery l Journal of Bioprocess and Bioystems Engineering l Journal of Biotechnology l Journal of Biotechnology Advances l Journal of Biotechnology and Bioprocess Engineering 1.8 Mathematics, biology, and engineering Mathematical modeling holds the key for engineers. Physics at its fundamental level examines forces and motion; one can view it as applied mathematics. In turn, chemistry examines molecules and their interactions. Since physics examines the motions of atoms, nuclei and electrons, at the basis of molecules, one can view chemistry as applied physics. This directly connects chemistry to mathematics at a fundamental level. Indeed, most physicists and chemists rely extensively on math- ematical modeling. While one can view biology as applied chemistry through the connection of chemicals and molecules, the fundamental trainings of biologists today and engineers are distinctly different. In the development of knowledge in the life sciences, unlike chemistry and physics, mathematical theories and quantitative methods (except statistics) have played a secondary role. Most progress has been due to improvements in experimental tools. Results are qualitative and descrip- tive models are formulated and tested. Consequently, biologists often have incomplete backgrounds in mathematics but are very strong with respect to laboratory tools and, more importantly, with respect to the interpretation of laboratory data from complex systems. Engineers usually possess a very good background in the physical and mathematical sciences. Often a theory leads to mathematical formulations, and the validity of the theory is tested by comparing predicted responses to those in experi- ments. Quantitative models and approaches, even to complex systems, are strengths. Biologists are usually better at the formation of testable hypotheses, experimental design, and data interpretation from complex systems. At the dawn of the biotechnology era, engineers were typically unfamiliar with the experimental techniques and strategies used by life scien- tists. However, today bioprocess engineers have entered even more sophisticated experimental techniques and strategies in life sciences (than biologists) due to the understanding and progress in the prediction and modeling of living cells. The well-groundedness in mathematical modeling gives bioprocess engineers an edge and responsibility in enforcing sustainability demands. In practice, the sustainable (or steady) state can be different from what we know today or when no human interruption is imposed. The sustainable state could even be fluctuating with a noticeable degree. Engineers hold great responsibility to convincing environmentalists and the public what to expect by accurately predicting the dynamic outcomes without speculating on the potential dramatic changes ahead. The skills of the engineer and of the life scientist are complementary. To convert the promises of molecular biology into new processes to make new products requires the integration of these skills. To function at this level, the engineer needs a solid understanding of biology and its experimental tools. In this book, we provide sufficient biological background for you to understand the chapters on applying engineering principles to biosystems. However, if you are serious about becoming a bioprocess engineer, it is desirable if you had taken courses in microbiology, biochemistry, and cell biology, as you would appreciate more of the engineering principles in this text. 1.9 The story of penicillin: the dawn of bioprocess engineering Penicillin is an antibiotic of significant importance. The familiar story of penicillin was well-presented by Kargi & Shuler in their text “Bioprocess Engineering – Basic Concepts.” As you would expect, the discovery of the chemical was acci- dental and the production of the chemical is elaborate. In September 1928, Alexander Fleming at St. Mary’s Hospital in London was trying to isolate the bacterium, Staphylococcus aureus, which causes boils. The technique in use was to grow the bacterium on the surface of a nutrient solution. One Friday, the basement window was accidently left open overnight. The experiments were carried out in the basement and one of the dishes had been contaminated inadvertently with a foreign particle. Normally, such a contaminated plate would be tossed out. However, Fleming noticed that no bacteria grew near the invading substance. Fleming’s genius was to realize that this observation was meaningful and not a “failed” experiment. Fleming recognized that the cell killing must be due to an antibacterial agent. He recovered the foreign particle and found that it was a common
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    10 Bioprocess Engineering  moldof the Penicillium genus (later identified as Penicillium notatum). Fleming nurtured the mold to grow and, using the crude extraction methods then available, managed to obtain a tiny quantity of secreted material. He then demonstrated that this material had powerful antimicrobial properties and named the product penicillin. Fleming carefully preserved the cul- ture, but the discovery lay essentially dormant for over a decade. World War II provided the impetus to resurrect the discovery. Sulfa drugs have a rather restricted range of activity, and an antibiotic with minimal side effects and broader applicability was desperately needed. In 1939, Howard Florey and Ernst Chain of Oxford decided to build on Fleming’s observations. Norman Heatley played the key role in producing sufficient material for Chain and Florey to test the effectiveness of penicillin. Heatley, trained as a biochemist, performed as a bioprocess engineer. He developed an assay to monitor the amount of penicillin made so as to determine the kinetics of the fermentation, developed a culture technique that could be implemented easily, and devised a novel back-extraction process to recover the very delicate product. After months of immense effort, they produced enough penicillin to treat some laboratory animals. Eighteen months after starting on the project, they began to treat a London policeman for a blood infection. The penicil- lin worked wonders initially and brought the patient to the point of recovery. Most unfortunately, the supply of penicillin was exhausted and the man relapsed and died. Nonetheless, Florey and Chain had demonstrated the great potential for penicillin, if it could be made in sufficient amount. To make large amounts of penicillin would require a process, and for such a process development, engineers would be needed, in addition to microbial physiologists and other life scientists. The war further complicated the situation. Great Britain’s industrial facilities were already totally devoted to the war. Florey and his associates approached pharmaceutical firms in the United States to persuade them to develop the capacity to produce penicillin, since the United States was not at war at that time. Many companies and government laboratories, assisted by many universities, took up the challenge. Particularly prominent were Merck, Pfizer, Squibb, and the USDA Northern Regional Research Laboratory in Peoria, Illinois. The first efforts with fermentation were modest. A large effort went into attempts to chemically synthesize penicillin. This effort involved hundreds of chemists. Consequently, many companies were at first reluctant to commit to the fermenta- tion process, beyond the pilot-plant stage. It was thought that the pilot-plant fermentation system could produce sufficient penicillin to meet the needs of clinical testing, but large-scale production would soon be done by chemical synthesis. At that time, US companies had achieved a great deal of success with chemical synthesis of other drugs, which gave the com- panies a great deal of control over the drug’s production. The chemical synthesis of penicillin proved to be exceedingly difficult (It was accomplished in the 1950s, and the synthesis route is still not competitive with fermentation). However, in 1940 fermentation for the production of a pharmaceutical was an unproved approach, and most companies were betting on chemical synthesis to ultimately dominate. The early clinical successes were so dramatic that in 1943 the War Production Board appointed A. L. Elder to coordinate the activities of producers to greatly increase the supply of penicillin. The fermentation route was chosen. As Elder recalls, “I was ridiculed by some of my closest scientific friends for allowing myself to become associated with what obviously was to be a flop-namely, the commercial production of penicillin by a fermentation process” (from Elder, 1970). The problems facing the fermentation process were indeed very formidable. The problem was typical of most new fermentation processes: a valuable product made at very low levels. The low rate of production per unit volume would necessitate very large and inefficient reactors, and the low concentration (titer) made product recovery and purification very difficult. In 1939 the final concentration in a typical penicillin fermentation broth was one part per million (ca. 0.001 g/L); gold is more plentiful in sea water. Furthermore, penicillin is a fragile and unstable product, which places significant constraints on the approaches used for recovery and purification. Life scientists at the Northern Regional Research Laboratory made many major contributions to the penicillin program. One was the development of a corn steep liquor-lactose based medium. Andrew J. Moyer succeeded to increase productiv- ity about 10-fold with this medium in November 26, 1941. A worldwide search by the laboratory for better producer strains of Penicillium led to the isolation of a Penicillium chrysogenum strain. This strain, isolated from a moldy cantaloupe at a Peoria fruit market, proved superior to hundreds of other isolates tested. Its progeny have been used in almost all commer- cial penicillin fermentations. The other hurdle was to decide on a manufacturing process. One method involved the growth of the mold on the surface of moist bran. This bran method was discarded because of difficulties in temperature control, sterilization, and equipment size. The surface method involved growth of the mold on top of a quiescent medium. The surface method used a variety of containers, including milk bottles, and the term “bottle plant” indicated such a manufacturing technique. The surface meth- od gave relatively high yields, but had a long-growing cycle and was very labor intensive. The first manufacturing plants were bottle plants because the method worked and could be implemented quickly. However, it was clear that the surface method would not meet the full need for penicillin. If the goal of the War Production Board was met by bottle plants, it was
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    What is bioprocessengineering? Chapter | 1 11 estimated that the necessary bottles would fill a row stretching from New York City to San Francisco. Engineers generally favored a submerged tank process. The submerged process presented challenges in terms of both mold physiology and in tank design and operation. Large volumes of absolutely clean, oil- and dirt-free sterile air were required. What were then very large agitators were required, and the mechanical seal for the agitator shaft had to be designed to prevent the entry of organisms. Even today, problems of oxygen supply and heat removal are important constraints on antibiotic fermenter design. Contamination by foreign organisms could degrade the product as fast as it was formed, consume nutrients before they were converted to penicillin, or produce toxins. In addition to these challenges in reactor design, there were similar hurdles in product recovery and purification. The very fragile nature of penicillin required the development of special techniques. A combination of pH shifts and rapid liquid-liquid extraction proved useful. Soon processes using tanks of about 10,000 gal were built. Pfizer completed in less than 6 months the first plant for commercial production of penicillin by submerged fermentation (Hobby, 1985). The plant had 14 tanks each of 7000-gal capacity. By a combination of good luck and hard work, the United States had the capacity by the end of World War II to produce enough penicillin for almost 100,000 patients per year. A schematic of the process is shown in Fig. 1.7. This accomplishment required a high level of multidisciplinary work. For example, Merck realized that men who un- derstood both engineering and biology were not available. Merck assigned a chemical engineer and microbiologist together to each aspect of the problem. They planned, executed, and analyzed the experimental program jointly, “almost as if they were one man” (see the chapter by Silcox in Elder, 1970). Progress with penicillin fermentation has continued, as has the need for the interaction of biologists and engineers. From 1939 to now, the yield of penicillin has gone from 0.001 g/L to over 50 g/L of fermentation broth. Progress has involved better understanding of mold physiology, metabolic pathways, penicillin structure, methods of mutation, and selection of mold genetics, process control, and reactor design. Before the penicillin process, almost no chemical engineers sought specialized training in the life sciences. With the advent of modem antibiotics, the concept of the bioprocess engineering was born. The penicillin process also established a paradigm for bioprocess development and biochemical engineering. This paradigm still guides much of our profession’s FIGURE 1.7 Schematic of penicillin production process.
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    12 Bioprocess Engineering  thinking.The mindset of bioprocess engineers was cast by the penicillin experience. It is for this reason that we have fo- cused on the penicillin story, rather than on an example for production of a protein from a genetically engineered organism. Although many parallels can be made between the penicillin process and our efforts to use recombinant DNA, no similar paradigm has yet emerged from our experience with genetically engineered cells. We must continually reexamine the preju­ dices the field has inherited from the penicillin experience. It is you, the student, who will best be able to challenge these prejudices. 1.10 Bioprocesses: regulatory constraints To be an effective in bioprocess engineering, you must understand the regulatory climate in which many bioprocess engi- neers work. The US FDA (Food and Drug Administration) and its equivalents in other countries must insure the safety and efficacy of food and medicines. For bioprocess engineers working in the pharmaceutical industry the primary concern is not reduction of manufacturing cost (although that is still a very desirable goal), but the production of a product of consistently high quality in amounts to satisfy the medical needs of the population. Consider briefly the process by which a drug obtains FDA approval. A typical drug undergoes 6–7 years of development from the discovery stage through preclinical testing in animals. To legally test the drug in humans in the United States, an Investigational New Drug (IND) designation must be issued by FDA. Biologics such as vaccines and recombinant protein drugs are generally approved by FDA via a Biologic License Application (BLA). There are five phases of trials before a new drug is placed on market after its discovery: Phase 0: Human microdosing studies (1–3 years). This is a designation for the exploratory, first-in-human trials conducted within the regulations of US-FDA 2006 Guidance on Exploratory Investigational New Drug studies. Phase I: First stage testing in human subjects. Normally, a small group of (20–80) of healthy volunteers is selected. Safety, tolerability, pharmacokinetics, and pharmacodynamics of the drug are evaluated. This phase usually lasts about 1 year. Different types of types of trials in this phase are Single Ascending Dose (SAD), Multiple Ascending Dose (MAD), and Food Effect trials. Phase II: clinical trials (about 2 years). After determining the initial safety and pharmacological parameters, this trial on a larger group of 100–300 patients and volunteers is performed. This trial is designed to assess the efficacy (i.e., does it help the patient) as well as further determining which side effects exist. Sometimes, Phase IIA is designed to determine the dos- ing requirements and Phase IIB is designed to determine the efficacy of the drug. If the drug fails to meet the established standards of the trials, further development of the new drug is usually stopped. Phase III: clinical trials (about 3 years) with 300–3000 (or more) patients. Since individuals vary in body chemistry, it is important to test the range of responses in terms of both side effects and efficacy by using a representative cross section of the population. Randomized controlled multicenter trials on large patient groups are conducted to determine the effective- ness of the drug. This phase of the clinic trials is very expensive, time-consuming, and difficult to design and run, espe- cially in therapies for chronic medical conditions. It is common practice that certain Phase III trials will continue while the regulatory submission is pending at the appropriate regulatory agency. This allows patients to continue to receive possibly lifesaving drugs until the drug us available in the market for distribution. These trials also provide additional safety data and support for marketing claims for the drug. Data from clinical trials is presented to the FDA for review (2 months to 3 years). The review document presented to FDA clearly show the trial results combined with description of the methods and results of human and animal studies, manufacturing procedures, formulation details, and shelf life. If the clinical trials are well designed and demonstrated statistically significant improvements in health with acceptable side effects, the drug is likely to be approved. Phase IV: Postmarketing surveillance trial. Continue safety surveillance (pharmacovigilance) and technical support of a drug after receiving permission to be put on the market. The whole discovery-through-approval process takes 5–10 years for a conventional small molecule drug, and 12–15 years for a new biological drug to make it to the market. It takes about $800–$2000 million to send a new drug to the market. Only one in ten drugs that enter human clinical trials receives approval. Recent FDA reforms have decreased the time to obtain approval for life-saving drugs in treatment of diseases such as cancer and AIDS, but the overall process is still lengthy. This process greatly affects a bioprocess engineer. FDA approval is for the product and the process together. There have been tragic examples where a small process change has allowed a toxic trace compound to form or become incorporated in the final product, resulting in severe side effects, including death. Thus, process changes may require new clinical trials to test the safety of the resulting product. Since clinical trials are very expensive, process improvements are made under a limited set of circumstances. Even during clinical trials it is difficult to make major process changes.
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    What is bioprocessengineering? Chapter | 1 13 Drugs sold on the market or used in clinical trials must come from facilities that are certified as GMP or cGMP and must follow the appropriate Code of Federal Regulations (CFR). GMP stands for (current) good manufacturing practice. GMP concerns the actual manufacturing facility design and layout, the equipment and procedures, training of production person- nel, control of process inputs (e.g., raw materials and cultures), and handling of product. The plant layout and design must prevent contamination of the product, and dictate the flow of material, personnel, and air. Equipment and procedures must be validated. Procedures include not only operation of a piece of equipment, but also cleaning and sterilization. Computer software used to monitor and control the process must be validated. Off-line assays done in laboratories must satisfy good laboratory practice (GLP). Procedures are documented by SOPs (standard operating procedures). The GMP guidelines stress the need for documented procedures to validate performance. “Process validation is estab- lishing documented evidence which provides a high degree of assurance that a specific process will consistently produce a product meeting its predetermined specifications and quality characteristics” and “There shall be written procedures for production and process-control to assure that products have the identity, strength, quality, and purity they purport or are represented to possess.” The actual process of validation is often complex, particularly when a whole facility design is considered. The FDA pro- vides extensive information and guidelines which are updated regularly. If students become involved in biomanufacturing for pharmaceuticals, they will need to consult these sources. However, certain key concepts do not change. These concepts are written documentation, consistency of procedures, consistency of product, and demonstrable measures of product qual- ity, particularly purity, and safety. These tasks are demanding and require careful attention to detail. Bioprocess engineers will often find that much of their effort will be to satisfy these regulatory requirements. The key point is that process changes cannot be made without considering their considerable regulatory impact. 1.11 The pillars of bioprocess kinetics and systems engineering As a profession, bioprocess engineers must be well-versed in thermodynamics, transport phenomena, colloids, biosepara- tions, microbiology, bioprocess kinetics and systems engineering, and process simulation and design. This text deals with the core of bioprocess engineering. Unlike earlier texts in this subject area, this text integrates bioprocess engineering prin- ciples, in particular bioprocess kinetics and transformation or reaction engineering principles together. Chemical reaction engineering is not a pre-requisite before taking on this text. Fig. 1.6 shows the pillars of this text. The sustainability on this pillar is narrowly defined as having the net benefit to the human society and/or benign environmental effects. As shown in Fig. 1.8, the fundamental knowledge of engineering science you will learn or expect in this text is among the “pillars”: mass balance, rate expression, stoichiometry, cell metabolism, yield factor, energy balance, mass FIGURE 1.8 The pillars of bioprocess kinetics and system engineering.
  • 20.
    14 Bioprocess Engineering  transfer,cost, and profit analyses. These engineering science fundamentals form the basis or foundation for the design and performance analysis of reactors and /or fermenters. In turn, process kinetic data analysis, biocatalyst design and selection can be learned from the reactor performance, and applied to the design and performance analysis of reactors and/or bioprocess systems. Process stability usually stems from multiplicity of the process, which controls the product quality and consistency. Finally, the design and control of bioprocess systems must obey the greater law of nature: sustainability. 1.12 Summary Sustainability and green chemistry are important to the practice of bioprocess engineers. Biorefinery is a desired approach to provide the products of human needs, putting the human needs into the biological cycle. Both biotransformation and chemical transformations are important to biorefinery. Genetic manipulations and biotransformation are important to the bioprocess engineering profession. Because of the fundamental impact genetic manipulation and biotransformation can have on the cycle of life, ethics and regulations are critical to the practice of bioprocess engineers. It is the intention that this text can be used as a senior and/or graduate text for bioprocess engineering students. It may also be served as a reference and/or graduate text for chemical kinetics, chemical reactor analysis, and bioprocess systems engineering. In the same time, we have inserted materials, more advanced analysis or complex systems in the text as an extension to the introductory material. It is our aim that this text can serve equally as a reference or resource for further research or development. Problems 1.1. How bioprocess engineering affects the overall health of humans? 1.2. Why are renewable materials preferred? 1.3. What is green chemistry? 1.4. What is sustainability? 1.5. What is a biorefinery? 1.6. Why is ethanol an important platform chemical? 1.7. An uninformed researcher is questioning the sustainability of biomass cultivation and utilization, arguing that fertil- izer and fuels for heavy machinery must be produced with fossil energy and thus not renewable. Research into the basis of the arguments and dismiss the notion of unsustainable biomass use. 1.8. What is GMP and how does it relate to the regulatory process for pharmaceuticals? 1.9. When the FDA approves a process, it requires validation of the process. Explain what validation means in the FDA context. 1.10. Why does the FDA approve the process and product together? 1.11. What is biotransformation? What is chemical transformation? References D. History of Penicillin Elder, A.L. (Ed.), 1970. The History of Penicillin Production, Chem. Eng. Prog. Symp. Ser. 66 (#100). American Institute of Chemical Engineers, New York. Hobby, G.L., 1985. Penicillin. Meeting the Challenge. Yale University Press, New Haven, CT.
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    What is bioprocessengineering? Chapter | 1 15 Further readings A. Green Chemistry Anatas, P.C., Warner, J.C., 1998. Green Chemistry: Theory and Practice. Oxford University Press, New York. Linthorst JA, 2010. An overview: origins and development of green chemistry. Found. Chem. 12 (1), 55–68. Wilson M, Schwarzman M. 2009. Toward a New U.S. Chemicals Policy: Rebuilding the Foundation to Advance New Science, Green Chemistry, and Environmental Health. Environ Health Perspect. 117 (8) 1202–1209 and A358. www.epa.gov/greenchemistry/. B. Sustainability Adams, W.M., Jeanrenaud, S.J., 2008. Transition to Sustainability: Towards a Humane and Diverse World. IUCN, Gland, Switzerland, 108 pp. Atkinson, G., Dietz, S., Neumayer, E., 2007. Handbook of Sustainable Development. Edward Elgar, Cheltenham. Blackburn, W.R., 2007. The Sustainability Handbook. Earthscan, London. Blewitt, J., 2008. Understanding Sustainable Development. Earthscan, London. Costanza, R., Graumlich, L.J., Steffen, W. (Eds.), 2007. Sustainability or Collapse? An Integrated History and Future of People on Earth. MIT Press, Cambridge, MA. Norton, B., 2005. Sustainability, A Philosophy of Adaptive Ecosystem Management. The University of Chicago Press, Chicago. Soederbaum, P., 2008. Understanding Sustainability Economics. Earthscan, London. C. Biorefinery Liu, S., Lu, H., Hu, R., Shupe, A., Lin, L., Liang, L., 2012. A sustainable woody biomass biorefinery. J. Biotech. Adv. 30 (4), 785–810, http://dx.doi. org/10.1016/j.biotechadv.2012.01.013. FitzPatrick, M., Champagne, P., Cunningham, M.F., Whitney, R.A., 2010. A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products”. Bioresour. Technol. 101 (23), 8915–8922. Kaparaju, P., Serrano, M., Thomsen, A.B., Kongjan, P., Angelidaki, I., 2009. Bioethanol, biohydrogen and biogas production from wheat straw in a bio- refinery concept”. Bioresour. Technol. 100 (9), 2562–2568. Koutinas, A.A., Arifeen, N., Wang, R., Webb, C., 2007. Cereal-based biorefinery development: Integrated enzyme production for cereal flour hydrolysis”. Biotechn. Bioeng. 97 (1), 61–72. Liu, S., Amidon, T.E., Francis, R.C., Ramarao, B.V., Lai, Y.-Z., Scott, G.M., 2006. From forest biomass to chemicals and energy: biorefinery initiative in New York. Ind. Biotech. 2 (2), 113–120. Ohara, H., 2003. Biorefinery. App. Micobiol. and Biotechn. 62 (5–6), 474–477. D. History of Penicillin Moberg, C.L., 1991. Penicillin’s Forgotten Man: Norman Heatley. Science 253, 734–735. Mateles, R.I. (Ed.), 1998. Penicillin, A Paradigm for Biotechnology. Candida Corp., Chicago, IL. Sheehan, J.C., 1982. The Enchanted Ring. The Untold Story of Penicillin. MIT Press, Cambridge, MA. E. Regulatory Issues Currey, B., Klemic, P.A., 2008. A New Phase in Pharmaceutical Regulation. DRI Drug and Medical Device and Product Liability Committee. O’Melveny & Myers LLP, PL California, United States. Durfor, C.N., Andscribner, C.L., 1992. An FDA perspective of manufacturing changes for products in human use. Ann. NY Acad. Sci. 665, 356–363. Naglak, T.J., Keith, M.G., Omstead, D.R., 1994. Validation of fermentation processes. Biopharm 7, 28–36. Reisman, H.B., 1993. Problems in scale-up of biotechnology production processes. Crit. Rev. Biotechnol. 13, 195–253. Wechsler, J. Science and Safety. Magazine: Pharmaceutial Excutive – Washington Report, Oct., 2009. http://www.FDA.gov. http://www.FDAreview.org/approval_process.
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    Bioprocess Engineering. http://dx.doi.org/10.1016/B978-0-12-821012-3.00002-6 Copyright© 2020 Elsevier B.V. All rights reserved. 17 Bioprocess engineers seek chemicals and materials for human needs in a sustainable manner. It is the chemicals and materials from biological origin that can sustain the needs of humans. Microorganism also provides a tool for bioprocess engineers to manipulate the chemicals and materials so that they can meet the needs of humanity. Therefore we shall first review some of the biological basics to learn how living organisms (more specific: microorganisms) function and what their important chemicals and materials are. 2.1 Cells and organisms The cell is the basic structural and functional unit of all known living organisms. Cells are to living organisms as like atoms are to molecules. It is the smallest unit of life that is classified as a living thing, and so is often called the building block of life. Some organisms, such as most bacteria, are unicellular (consist of a single cell). Most single cell organisms are microscopic in size and not visible to (human by) naked eyes, which are commonly called microorganisms. However, some unicellular protists and bacteria are macroscopic and visible to the naked eye. For example, Xenophyophores, protozoans of the phylum Foraminifera, are the largest examples known, with Syringammina fragilissima achieving a diameter of up to 20 cm (7.9 inches). The largest bacterium is Thiomargarita namibiensis, reaching a diameter of up to 0.75 mm. Other organisms, such as humans, are multicellular. (Humans have an estimated 100 trillion or 1014 cells; a typical cell size is 10 µm; a typical cell mass is 1 nanogram.) The largest known cell is an unfertilized ostrich egg cell. An average ostrich egg is an oval about 15 cm × 13 cm and weighs 1.4 kg. In 1835, before modern cell theory was developed, Jan Evangelista Purkyně observed small “granules” while looking at plant tissue through a microscope. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells. Each cell is at least somewhat self-contained and self-maintaining: it can take in nutrients, convert these nutrients into energy, carry out specialized functions, and reproduce as necessary. Each cell stores its own set of instructions for carrying out each of these activities. Chapter 2 An overview of biological basics Chapter outline 2.1 Cells and organisms 17 2.1.1 Microbial diversity 18 2.1.2 How cells are named 18 2.1.3 Prokaryotes 20 2.1.4 Eukaryotes 23 2.2 Viruses 27 2.3 Prions 30 2.4 Stem cell 30 2.5 Cell chemistry 31 2.5.1 Amino acids and proteins 32 2.5.2 Monosaccharides 37 2.5.3 Disaccharides 42 2.5.4 Polysaccharides 42 2.5.5 Phytic acid and inositol 46 2.5.6 Chitin and chitosan 48 2.5.7 Lignin 48 2.5.8 Lipids, fats, and steroids 50 2.5.9 Nucleic acids, RNA, and DNA 52 2.6 Cell feed 57 2.6.1 Macronutrients 58 2.6.2 Micronutrients 60 2.6.3 Growth media 61 2.7 Non earthly/unnatural biological agents 61 2.8 Summary 62 Problems 63 References 64 Further readings 64
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    18 Bioprocess Engineering  2.1.1Microbial diversity Life is very tenacious and can exist in extreme environments. Living cells can be found almost anywhere that water is in the liquid state. The right temperature, pH, and moisture levels vary from one organism to another. Some cells can grow at −20°C (in a brine to prevent freezing), while others can grow at 120°C (where water is under high enough pressure to prevent boiling). Cells that grow best at low temperatures (below 20°C) are usually called psychrophiles, while those with temperature optima in the range of 20–50°C are mesophiles. Organisms that grow best at temperatures greater than 50°C are thermophiles. Many organisms have pH optima far from neutrality; some prefer in an environment with a pH value down to 1 or 2, while others may grow well at pH 9. Some organisms can grow at both low pH values and high temperatures. Although most organisms can grow only with the presence of liquid water, others can grow on barely moist solid sur- faces or in solutions with high salt concentrations. Some cells require oxygen for growth and metabolism. Such organisms can be termed aerobic. Other organisms are inhibited by the presence of oxygen and grow only anaerobically. Some organisms can switch metabolic pathways to allow them to grow under either circumstance. Such organisms are facultative. Often, organisms can grow in environments with almost no obvious source of nutrients. Some cyanobacteria (formerly called blue-green algae) can grow in an environment with only a little moisture and a few dissolved minerals. These bacteria are photosynthetic and can convert CO2 from the atmosphere into the organic compounds (e.g., sugars) necessary for life. They can also convert N2 into NH3 for use in making the essential building blocks of life. + → + CO (cabondioxude) H O(water) CH O(sugar) O (oxygen) 2 2 2 2 (2.1) + → + N 3H O 2NH 3/2O 2 2 3 2 (2.2) Cyanobacteria are important in colonizing nutrient-deficient environments. Organisms from these extreme environments (extremophiles) often provide humanity with important tools for processes to make useful chemicals and medicinals. They are also key to the maintenance of natural cycles and can be used in the recovery of metals from low-grade ores or in the desulfurization of coal or other fuels. The fact that organisms can develop a capacity to exist and multiply in almost any environment on Earth is extremely useful. Not only do organisms occupy a wide variety of habitats, but they also come in a wide range of sizes and shapes. Spheri- cal, cylindrical, ellipsoidal, spiral, and pleomorphic cells exist. Special names are used to describe the shape of bacteria. A cell with a spherical or elliptical shape is often called a coccus (plural, cocci); a cylindrical cell is a rod or bacillus (plural, bacilli); a spiral-shaped cell is a spirillum (plural, spirilla). Some cells may change shape in response to changes in their local environment. Pleomophic cells take on at least two different forms or shapes during their life cycle. Thus organisms can be found in the most extreme environments and have evolved a wondrous array of shapes, sizes, and metabolic capabilities. This great diversity provides the engineer with an immense variety of potential tools. We have barely begun to learn how to manipulate these tools. 2.1.2 How cells are named The naming of cells is complicated by the large variety of organisms. A systematic approach to classifying these organ- isms is an essential aid to their intelligent use. Taxonomy is the development of approaches to organize and summarize our knowledge about the variety of organisms that exist. Although knowledge of taxonomy may seem remote from the needs of an engineer, it is necessary for efficient communication among engineers and scientists working with living cells. Tax- onomy can also play a critical role in patent litigation involving bioprocesses. While taxonomy is concerned with approaches to classification, nomenclature refers to the actual naming of organ- isms. For microorganisms we use a dual name (binary nomenclature). The names are given in Latin or are Latinized. A genus is a group of related species, while a species includes organisms that are sufficiently alike to reproduce. A common well-documented gut organism is Escherichia coli. Escherichia is the genus and coli the species. When writing a report or paper, it is common practice to give the full name when the organism is first mentioned, but to abbreviate the genus to the first letter in subsequent discussion, for example, E. coli. Although organisms that belong to the same species all share the same major characteristics, there are subtle and often technologically important variations within species. A strain of E. coli used in one laboratory may differ from that used in another. Thus various strains and substrains are designated by the addition of letters and numbers. For example, E. coli fBr5 will differ in growth and physiological properties from E. coli K01.
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    An overview ofbiological basics Chapter | 2 19 Now that we know how to name organisms, we could consider broader classification up to the level of kingdoms. There is no universal agreement on how to classify microorganisms at this level. Such classification is rather arbitrary and need not concern us. However, we must be aware that there are two primary cell types: eukaryotic and prokaryotic. The primary difference between them is the presence or absence of a membrane around the cell’s genetic information. Prokaryotes have a simple structure with a single chromosome (Fig. 2.1). Prokaryotic cells have no nuclear membrane and no organelles (such as mitochondria and endoplasmic reticulum). Eukaryotes have a more complex internal structure, with more than one chromosome (DNA molecule) in the nucleus. Eukaryotic cells have a true nuclear membrane and may contain a variety of specialized organelles such as mitochondria, endoplasmic reticulum and Golgi apparatus (Fig. 2.2). A detailed compare-son of prokaryotes and eukaryotes is presented in Table 2.1. Structural differences between prokaryotes and eukaryotes are discussed later. Evidence suggests that a common or universal ancestor gave rise to three distinctive branches of life: eukaryotes, eu- bacteria (or “true” bacteria), and archaebacteria. Table 2.2 summarizes some of the distinctive features of these groups. The ability to sequence the genes of whole organisms will have a great impact on our understanding of how these families evolved and are related. The cellular organisms summarized in Table 2.2 are free-living organisms and are all DNA based. Viruses cannot be classified under any of these categories, as they are not independent (or free-living) organisms. Still, viruses are all nucleic FIGURE 2.1 A schematic of a typical prokaryotic cell. FIGURE 2.2 A schematic of a typical eukaryotic cell.
  • 25.
    20 Bioprocess Engineering  acid(either DNA or RNA) based. Prions, on the other hand, are not even nucleic acid based. These rather simple “organ- isms” play important roles in Bioprocess Engineering and thus we will discuss hem separately. 2.1.3 Prokaryotes The sizes of most prokaryotes vary from 0.5–3 µm in equivalent radius. Different species have different shapes, such as spherical or coccus (e.g., Staphylococci), cylindrical or bacillus (E. coli), or spiral or spirillum (Rhodospirillum). Prokary- otic cells grow rapidly, with typical doubling times of half an hour to several hours. Also, prokaryotes can utilize a variety of nutrients as carbon sources, including carbohydrates, hydrocarbons, proteins, and CO2. 2.1.3.1 Eubacteria The eubacteria can be divided into several different groups. One distinction is based on the gram stain (developed by Hans Christian Gram in 1884). The staining procedure first requires fixing the cells by heating. The basic dye, crystal violet, is added; all bacteria will stain purple. Next, iodine is added, followed by the addition of ethanol. Gram-positive cells re- main purple, while Gram-negative cells become colorless. Finally, counterstaining with safranin leaves Gram-positive cells purple, while Gram-negative cells turn red. Cell reactions to the gram stain reveal intrinsic differences in the structure of the cell envelope. TABLE 2.1 A comparison of prokaryotes with eukaryotes. Characteristic Prokaryotes Eukaryotes Genome No. of DNA molecules DNA in organelles DNA observed as chromosomes Nuclear membrane Mitotic and meiotic division of the nucleus Formation of partial diploid One No No No No Yes More than one Yes Yes Yes Yes No Organelles Mitochondria Endoplasmic reticulum Golgi apparatus Photosynthetic apparatus Flagella No No No Chromosomes Single protein, simple structure Yes Yes Yes Chloroplasts Complex structure, with microtubules Spores Heat resistance Endospores High Endo- and exospores Low Source: Millis, N.F., 1985, in: Moo-Young, M. (Ed.), Comprehensive Biotechnology, vol. I, Elsevier Science. TABLE 2.2 Primary subdivisions of cellular organisms that have been recognized. Group Cell morphology Properties Constituent groups Eukaryotes Eukaryotic Multicellular; extensive differentiation of cells and tissues Unicellular, coenocytic, or mycelial; little or no tissue differentiation Plants (seed plants, ferns, mosses) Animals (vertebrates, invertebrates) Protists (algae, fungi, protozoa, slime moulds) Eubacteria Prokaryotic Cell chemistry similar to eukaryotes Most bacteria Archaea Prokaryotic Distinctive cell chemistry Crenarchaeota (sulfolobus, therofilum, thermopteus, pyrobaculum, haloquadratum walsbyi) Nanoarchaeota Euryarchaeota (methanogens, halophiles, therrno- acidophiles) Korarchaeota
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    An overview ofbiological basics Chapter | 2 21 A typical Gram-negative cell is E. coli. It has an outer membrane supported by a thin peptidoglycan layer, as shown in Fig. 2.3. Peptidoglycan is a complex polysaccharide with amino acids and forms a structure somewhat analogous to a chain- link fence. A second membrane (the inner or cytoplasmic membrane) exists and is separated from the outer membrane by the periplasmic space. The cytoplasmic membrane contains about 50% protein, 30% lipids, and 20% carbohydrates. The cell envelope serves to retain important cellular compounds and to preferentially exclude undesirable compounds in the environment. the loss of membrane integrity leads to cell lysis (cells breaking open) and cell death. The cell envelope is crucial to the transport of selected material in and out of the cell. A typical Gram-positive cell is Bacillus subtilis. Gram-positive cells do not have an outer membrane. Rather, they have a very thick, rigid cell wall with multiple layers of peptidoglycan. Gram-positive cells also contain teichoic acids covalently bonded to the peptidoglycan. Because Gram-positive bacteria have only a cytoplasmic membrane, they are better suited to excretion of proteins. Excretion is technologically advantageous when the protein is a desired product. Some bacteria are neither Gram-positive nor Gram-negative. For example, Mycoplasma has no cell walls. These bac- teria are important not only clinically (e.g., primary atypical pneumonia), but also because they commonly contaminate media used industrially for animal cell culture. Actinomycetes are bacteria, but morphologically resemble molds with their long and highly branched hyphae. How- ever, the lack of a nuclear membrane and the composition of the cell wall require classification as bacteria. Actinomycetes are important sources of antibiotics. Certain Actinomycetes possess amylolytic and cellulolytic enzymes and are effective in the enzymatic hydrolysis of starch and cellulose. Actinomyces, Thermomonospora, and Streptomyces are examples of genera belonging to this group. Other distinctions within the eubacteria can be made based on cellular nutrition and energy metabolism. One important example is photosynthesis. Cyanobacteria (formerly called blue-green algae) have chlorophyll and fix CO2 into sugars. An- oxygenic photosynthetic bacteria (the purple and green bacteria) have light-gathering pigments called bacteriochlorophyll. Unlike true photosynthesis, the purple and green bacteria do not obtain reduction energy from the splitting of water and do not form oxygen. When stained properly, the area occupied by a prokaryotic cell’s DNA can be easily seen. Prokaryotes may also have other visible structures when viewed under the microscope, such as ribosomes, storage granules, spores, and volutins. Ribosomes are the site of protein synthesis. A typical bacterial cell contains approximately 10,000 ribosomes per cell, although this number can vary greatly with growth rate. The size of a typical ribosome is 10–20 nm and consists of ap- proximately 63% RNA and 37% protein. Storage granules (which are not present in every bacterium) can be used as a source of key metabolites and often contain polysaccharides, lipids, and sulfur granules. The sizes of storage granules vary between 0.5 µm and 1 µm. Some bacteria make intracellular spores (often called endospores in bacteria). Bacterial spores are produced as a resistance to adverse conditions such as high temperature, radiation, and toxic chemicals. The usual con- centration is 1 spore per cell, with a spore size of about 1 µm. Spores can germinate under favorable growth conditions to yield actively growing bacteria. FIGURE 2.3 Schematic of a typical Gram-negative bacterium (A) and its enlarged section of the membrane (B). A Gram-positive cell is similar, except that it has no outer membrane, its peptidoglycan layer is thicker, and the chemical composition of the cell wall differs significantly from the outer envelope of the Gram-negative cell.
  • 27.
    22 Bioprocess Engineering  Volutinis another granular intracellular structure, made of inorganic polymetaphosphates, which is present in some species. Some photosynthetic bacteria, such as Rhodospirilium, have chromatophores that are large inclusion bodies (50– 100 nm) utilized in photosynthesis for the absorption of light. Extracellular products can adhere to or become incorporated within the surface of the cell. Certain bacteria have a coat- ing or outside cell wall called capsule, which is usually a polysaccharide, or sometimes a polypeptide. Extracellular poly- mers are important to biofilm formation and response to environmental challenges (e.g., viruses). Table 2.3 summarizes the architecture of most bacteria. 2.1.3.2 Archaebacteria Under the microscope archaebacteria appear to be nearly identical to eubacteria. However, these cells differ greatly at the molecular level. In many ways the archaebacteria are as similar to the eukaryotes as they are to the eubacteria. Some ex- amples of differences between archaebacteria and eubacteria are as follows: 1. archaebacteria have no peptidoglycan; 2. nucleotide sequences in ribosomal RNA are similar within the archaebacteria but distinctly different from those of eu- bacteria; 3. the lipid composition of the cytoplasmic membrane is very different for the two groups. TABLE 2.3 Characteristics of various components of bacteria. Part Size Composition and comments Slime layer Microcapsule 5–10 nm Protein-polysaccharide-lipid complex responsible for the specific antigens of enteric bacteria and other species. Capsule 0.5–2.0 µm Mainly polysaccharides (e.g., Streptococcus); sometimes polypeptides (e.g., Bacillus antracis). Slime Indefinite Mainly polysaccharides (e.g., Leuconostoc); sometimes polypeptides (e.g., Bacillus subtilis). Cell wall Gram-positive species 10–20 nm Confers shape and rigidity upon the cell. In total, 20% dry weight of the cell. Consists mainly of macromolecules of a mixed polymer of N-acetyl muramicpeptide, teichoic acids, and polysaccharides. Gram-negative species 10–20 nm Consists mostly of a protein-polysaccharide-lipid complex with a small amount of the mu- ramic polymer. Cell membrane 5–10 nm Semipermeable barrier to nutrients. In total, 5%–10% dry weight of the cell, consisting of 50% protein, 28% lipid, and 15%– 20% carbohydrate in a double-layered membrane. Flagellum 10–20 nm by 4–12 µm Protein of the myosin-keratin-fibrinogen class, MW of 40,000. Arises from the cell membrane and is responsible for motility. Pilus (fimbria) 5–10 nm by 0.5–2.0 µm Rigid protein projections from the cell. Especially long ones are formed by Escherichia coli. Inclusions Spore 1.0–1.5 µm by 1.6–2.0 µm One spore is formed per cell intracellularly. Spores show great resistance to heat, dryness, and antibacterial agents. Storage granule 0.5–2.0 µm Glycogenlike, sulfur, or lipid granules may be found in some species. Chromatophore 50–100 nm Organelles in photosynthetic species. Rhodospirillum rubrum contains about 6000 per cell. Ribosome 10–30 nm Organelles for synthesis of protein. About 10,000 ribosomes per cell. They contain 63% RNA and 37% protein. Volutin 0.5–1.0 µm Inorganic polymetaphosphates that stain metachromatically. Nuclear material Composed of DNA that functions genetically as if the genes were arranged linearly on a single endless chromosome, but that appears by light microscopy as irregular patches with no nuclear membrane or distinguishable chromosomes. Autoradiography confirms the linear arrangement of DNA and suggests a MW of at least 109 . Source: Aiba, S., Humphrey, A.E., Millis, N. F., 1973, Biochemical Engineering, second ed. University of Tokyo Press, Tokyo.
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    An overview ofbiological basics Chapter | 2 23 Archaebacteria usually live in extreme environments and possess unusual metabolism. Methanogens, which are meth- ane-producing bacteria, belong to this group, as well as thermoacidophiles, which can grow at high temperatures and low pH values. Halobacteria, which can live only in very strong salt solutions, are also members of this group. These organisms are important sources for catalytically active proteins (enzymes) with novel properties. 2.1.4 Eukaryotes Fungi (yeasts and molds), algae, protozoa, and animal and plant cells constitute the eukaryotes. Eukaryotes are five to ten times larger than prokaryotes in diameter (e.g., yeast about 5 µm, animal cells about 10 µm, and plants about 20 µm). Eukaryotes have a true nucleus and a number of cellular organelles inside the cytoplasm. Fig. 2.4 is a schematic of two typical eukaryotic cells. In cell wall and cell membrane structure, eukaryotes are similar to prokaryotes. The plasma membrane is made of proteins and phospholipids that form a bilayer structure. Major proteins of the membrane are hydrophobic and are embedded in the phospholipid matrix. One major difference is the presence of sterols in the cytoplasmic membrane of eukaryotes. Sterols strengthen the structure and make the membrane less flexible. The cell wall of eukaryotic cells shows considerable variations. Some eukaryotes have a peptidoglycan layer in their cell wall; some have polysaccharides and cellulose (e.g., algae). The plant cell wall is composed of cellulose fibers embedded in pectin aggregates, which impart strength to the cell wall. Animal cells do not have a cell wall but only a cytoplasmic membrane. For this reason, animal cells are very shear-sensitive and fragile. This factor significantly complicates the design of large-scale bioreactors for animal cells. The nucleus of eukaryotic cells contains chromosomes as nuclear material (DNA molecules with some closely associ- ated small proteins), surrounded by a membrane. The nuclear membrane consists of a pair of concentric and porous mem- branes. The nucleolus is an area in the nucleus that stains differently and is the site of ribosome synthesis. Many chromo- somes contain small amounts of RNA and basic proteins called histones attached to the DNA. Each chromosome contains a single linear DNA molecule on which the histones are attached. Cell division (asexual) in eukaryotes involves several major steps: DNA synthesis, nuclear division, cell division, and cell separation. Sexual reproduction in eukaryotic cells involves the conjugation of two cells called gametes (egg and sperm cells). The single cell formed from the conjugation of gametes is called a zygote. The zygote has twice as many chromosomes as the gamete. Gametes are haploid cells, while zygotes are diploid. For humans, a haploid cell contains 23 chromosomes, and diploid cells have 46 chromosomes. The cell-division cycle (asexual reproduction) in a eukaryotic cell is depicted in Fig. 2.5. The cell-division cycle is divided into four phases. The M phase consists of mitosis where the nucleus divides, and cy- tokinesis where the cell splits into separate daughter cells. All of the phases between one M phase and the next are known collectively as interphase. The interphase is divided into three phases: Gl, S, and G2.The cell increases in size during the interphase. In the S phase, the cell replicates its nuclear DNA. There are key checkpoints in the cycle when the cell machin- ery must commit to entry to the next phase. Checkpoints exist for entry into the S and M phases and exit from the M phase. Cells may also be in a G0 state, which is a resting state without growth. FIGURE 2.4 Schematics of the two primary types of higher eukaryotic cells. Neither sketch is complete, but each summarizes the principal differ- ences and similarities of such cells.
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    24 Bioprocess Engineering  Mitochondriaare the powerhouses of an eukaryotic cell, where respiration and oxidative phosphorylation take place. Mitochondria have a nearly cylindrical shape 1 µm in diameter and 2–3 µm in length.A typical structure of a mitochondrion is shown in Fig. 2.6. The external membrane is made of a phospholipid bilayer with proteins embedded in the lipid matrix. Mitochondria contain a complex system of inner membranes called cristae. A gel-like matrix containing large amounts of protein fills the space inside the cristae. Some enzymes of oxidative respiration are bound to the cristae. A mitochondrion has its own DNA and protein-synthesizing machinery and reproduces independently. The endoplasmic reticulum is a complex, convoluted membrane system leading from the cell membrane into the cell. The rough endoplasmic reticulum contains ribosomes on the inner surfaces and is the site of protein synthesis and modifica- tions of protein structure after synthesis. The smooth endoplasmic reticulum is more involved with lipid synthesis. Lysosomes are very small membrane-bound particles that contain and release digestive enzymes. Lysosomes contrib- ute to the digestion of nutrients and invading substances. Peroxisomes are similar to lysosomes in their structure, but not in function. Peroxisomes carry out oxidative reactions that produce hydrogen peroxide. Glyoxysomes are also very small membrane-bound particles that contain the enzymes of the glyoxylate cycle. FIGURE 2.5 Schematic of cell division cycle in a eukaryote. (see text for details.) FIGURE 2.6 Diagram of a mitochondrion.
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    An overview ofbiological basics Chapter | 2 25 Golgi bodies are very small particles composed of membrane aggregates and are responsible for the secretion of certain proteins. Golgi bodies are sites where proteins are modified by the addition of various sugars in a process called glycosyl- ation. Such modifications are important to protein function in the body. Vacuoles are membrane-bound organelles of low density and are responsible for food digestion, osmotic regulation, and waste product storage. Vacuoles may occupy a large fraction of the cell volume (up to 90% in plant cells). Chloroplasts are relatively large green organelles containing chlorophyll that are responsible for photosynthesis in photo- synthetic eukaryotes, such as algae and plant cells. Every chloroplast contains an outer membrane and a large number of inner membranes called thylakoids. Chlorophyll molecules are associated with thylakoids, which have a regular membrane struc- ture with lipid bilayers. Chloroplasts are autonomous units containing their own DNA and protein-synthesizing machinery. Certain prokaryotic and eukaryotic organisms contain flagella—long, filamentous structures that are attached to one end of the cell and are responsible for the motion of the cell. Eukaryotic flagella contain two central fibers surrounded by eighteen peripheral fibers, which exist in duplets. These fibers are arranged in a tube structure called a microtubule and are composed of proteins called tubulin. The whole fiber assembly is embedded in an organic matrix and is surrounded by a membrane. The cytoskeleton (in eukaryotic cells) refers to filaments that provide an internal framework to organize the cell’s in- ternal activities and control its shape. These filaments are critical to cell movement, transduction of mechanical forces into biological responses, and separation of chromosomes into the two daughter cells during cell division. Three types of fibers are present: actin filaments, intermediate filaments, and microtubules. Cilia are structures similar to flagella, but are shorter and numerous. Only one group of protozoa, called ciliates, con- tains cilia. Paramecium species contain nearly 104 cilia per cell. Ciliated organisms move much faster than flagellated ones. This completes our summary of eukaryotic cell structure. Now let us turn our attention to the microscopic eukaryotes. Fungi are heterotrophs, which are widespread in nature. Fungal cells are larger than bacterial cells, and their typical internal structures, such as the nucleus and vacuoles, can be seen easily with a light microscope. Two major groups of fungi are yeasts and molds. Yeasts are single small cells of 5–10-µm size.Yeast cells are usually spherical, cylindrical, or oval.Yeasts can reproduce by asexual or sexual means. Asexual reproduction is by either budding or fission. In budding, a small bud cell forms on the cell, which gradually enlarges and separates from the mother cell. Asexual reproduction by fission is similar to that of bacteria. Only a few species of yeast can reproduce by fission. In fission, cells grow to a certain size and divide into two equal cells. Sexual reproduction of yeasts involves the formation of a zygote (a diploid cell) from the fusion of two haploid cells, each having a single set of chromosomes. The nucleus of the diploid cells divides several times to form ascospores. Each ascospore eventually becomes a new haploid cell and may reproduce by budding and fission. The life cycle of a typi- cal yeast cell is presented in Fig. 2.7. The classification of yeasts is based on reproductive modes (e.g., budding or fission) and the nutritional requirements of cells. The most widely used yeast, Saccharomyces cerevisiae, is used in alcohol formation under anaerobic conditions (e.g., in wine, beer and whiskey making) and also for baker’s yeast production under aerobic conditions. FIGURE 2.7 Cell-division cycle of a typical yeast, Saccharomyces cerevisiae.
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    26 Bioprocess Engineering  Moldsare filamentous fungi and have a mycelial structure. The mycelium is a highly branched system of tubes that contains mobile cytoplasm with many nuclei. Long, thin filaments on the mycelium are called hyphae. Certain branches of mycelium may grow in the air, and asexual spores called conidia are formed on these aerial branches. Conidia are nearly spherical in structure and are often pigmented. Some molds reproduce by sexual means and form sexual spores. These spores provide resistance against heat, freezing, drying, and some chemical agents. Both sexual and asexual spores of molds can germinate and form new hyphae. Fig. 2.8 describes the structure and asexual reproduction of molds. Molds usually form long, highly branched cells and easily grow on moist, solid nutrient surfaces. The typical size of a filamentous mold is 5–20 µm. When grown in submerged culture, molds often form cell aggregates and pellets. The typical size of a mold pellet varies between 50 µm and 1 mm, depending on the type of mold and growth conditions. Pellet forma- tion can cause some nutrient-transfer (mainly oxygen) problems inside the pellet. However, pellet formation reduces broth viscosity, which can improve bulk oxygen transfer. On the basis of their mode of sexual reproduction, fungi are grouped in four classes. 1. The phycomycetes are algalike fungi; however, they do not possess chlorophyll and cannot photosynthesize. Aquatic and terrestrial molds belong to this category. 2. The ascomycetes form sexual spores called ascospores, which are contained within a sac (a capsule structure). Some molds of the genera Neurospora and Aspergillus and yeasts belong to this category. 3. The basidiomycetes reproduce by basidiospores, which are extended from the stalks of specialized cells called the basidia. Mushrooms are basidiomycetes. 4. The deuteromycetes (Fungi imperfecti) cannot reproduce by sexual means. Only asexually reproducing molds belong to this category. Some pathogenic fungi, such as Trichophyton, which causes athlete’s foot, belong to the deuteromycetes. Molds are used for the production of citric acid (Aspergillus niger) and many antibiotics, such as penicillin (Penicillium chrysogenum). Mold fermentations make up a large fraction of the fermentation industry. Algae are usually unicellular organisms, although some plantlike multicellular structures are present in marine waters. Algae can be divided into five groups: Rhodophyta (red algae), Phaeophyta (brown algae), Chlorophyta (green algae), Cyanophyta (blue-green algae), and Bacillariophyta (golden-brown algae). Fig. 2.9 shows a drawing of typical green algae. The largest alga is the giant kelp, which can grow over sixty meters long. All algae are photosynthetic and contain chloroplasts, which normally impart a green color to the organisms. The chloroplasts are the sites of chlorophyll pigments and are responsible for photosynthesis. A typical unicellular alga is 10–30 µm in size. Multicellular algae sometimes form a branched or unbranched filamentous structure. Some algae contain silica or calcium carbonate in their cell wall. Diatoms containing silica in their cell wall are used as filter aids in industry. Some algae, such as Chlorella, Scenedesmus, Spirul- lina, and Dunaliella, are used for wastewater treatment while producing single-cell proteins. Certain gelling agents such as agar and alginic acid are obtained from marine algae and seaweeds. Many algae have been proposed for biofuel production. Protozoa are unicellular, motile, relatively large (1–50 mm) eukaryotic cells that lack cell walls. Protozoa usually obtain food by ingesting other small organisms, such as bacteria, or other food particles. Protozoa are usually uninucleate and FIGURE 2.8 Structure and asexual reproduction of molds.
  • 32.
    An overview ofbiological basics Chapter | 2 27 reproduce by sexual or asexual means. They are classified on the basis of their motion. The amoebae move through ame- boid motion, whereby the cytoplasm of the cell flows forward to form a pseudopodium (false foot), and the rest of the cell flows toward this lobe. The flagellates move using their flagella. Trypanosomes move by flagella and cause a number of dis- eases in humans. The ciliates move through motion of a large number of small appendages on the cell surface called cilia. The sporozoans are nonmotile and contain members that are human and animal parasites. These protozoa do not engulf food particles, but absorb dissolved food components through their membranes. Protozoa cause some diseases, such as ma- laria and dysentery. Protozoa may have a beneficial role in removing bacteria in biological wastewater treatment processes. 2.2 Viruses Viruses are very small and are obligate parasites of other cells, such as bacterial, yeast, plant, and animal cells. Viruses cannot capture or store free energy and are not functionally active except when inside their host cells. The sizes of viruses vary from 30 to 200 nm. Viruses contain either DNA (DNA viruses) or RNA (RNA viruses) as genetic material. DNA stands for deoxyribo- nucleic acid, and RNA is ribonucleic acid; we will soon discuss DNA and RNA molecules in more detail. In free-living cells, all genetic information is contained in the DNA, whereas viruses can use either RNA or DNA to encode such information. This nu- clear material is covered by a protein coat called a capsid. Some viruses have an outer envelope of a lipoprotein and some do not. Almost all cell types are susceptible to viral infections. Viruses infecting bacteria are called bacteriophages. The most common type of bacteriophage has a hexagonal head, tail, and tail fibers as shown in Fig. 2.10. Bacteriophages attach to the cell wall of a host cell with tail fibers, alter the cell wall of the host cell, and inject the viral nuclear material into the host cell. Fig. 2.11 describes the attachment of a virus onto a host cell. Bacteriophage nucleic acids reproduce inside the host cells to produce more phages. At a certain stage of viral reproduction, host cells lysis or break apart and the new phages are released, which can infect new host cells. This mode of reproduction of viruses is called the lytic cycle. In some cases, phage DNA may be incorporated into the host DNA, and the host may continue to multiply in this state, which is called the lysogenic cycle. Viruses are the cause of many diseases, and antiviral agents are important targets for drug discovery. However, viruses are also important to bioprocess technology. For example, a phage attack on an E. coli fermentation to make a recombinant protein product can be extremely destructive, causing the loss of the whole culture in vessels of many thousands of liters. However, phages can be used as agents to move desired genetic material into E. coli. Modified animal viruses can be used as vectors to genetically engineer animal cells to produce proteins from recombinant DNA technology. In some cases a killed virus preparation can be used as a vaccine. Genetic engineering allows the production of virus-like units that are empty shells; the shell is the capsid and all nucleic acid is removed. Such units can be used as vaccines without fear of viral FIGURE 2.9 A sketch of green algae. Source: “Siphoneae”, Ernst Haecket, Kunstformen der Natur, 1904.
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    Discovering Diverse ContentThrough Random Scribd Documents
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    314 Ancesteal Recordsand Porteaits BALL Colonel Willla.m Ball, of Lancaster County, Va., was the progenitor of the Virffinia Balls (see pp. 134-137). His granddaughter Esther, the daughter of Colonel Joseph and Elizabeth (Rogers or Romney) Ball, married .RawROMNBY leigh Chinn, and was the mother of Ann Chinn, who married Martin Sherman, whose daughter Mary married Henry Tapscott. BAKER A descendant of the house of Norfolk, through the Howard family, Judith Wood, who married John Baker, was the daughter of Peter Wood and Susanna Howard, his wife, who was the daughter of Sir WUliam and Lady Judith Howard, of Howard Hall, Eng. Their daughter, Susanna Howard Baker, married, first, John Wood, and second, James Tapscott. THOMPSON In 1774, at the age of eighteen, John Thompson came to America. He joined the Revolutionary army, serving in Captain Watson's company in a Pennsylvania regiment, fought in the battles of Long Island and Trenton, and crossed the Delaware with Washington. He settled after the war in Nelson County, Va., where he died in 1828. He married Rebecca Edwards, the daughter of Lucas Powell, and his wife, Rebecca Edwards. The sixth of his seven children was Judge Lucas
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    The text onthis page is estimated to be only 22.82% accurate Judge I.ucas Powell Thompson Judith Wood Wife of John Baker Sarah Coles Hull Wife of Henry Trowbridge
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    Ancestbal Recoeds andPoetraits 315 Powell Thompson. At the age of eighteen, after a walking tour through Spain, he returned to Virginia, where he studied and graduated in law, his license hearing the names of three of the most emiuent men of that State, Archibald Stuart, Hugh Holmes, and Briscoe Baldwin, Judges of the Supreme Court of Virginia, and by a coincidence all cousins of his wife. In a few years he was elected Judge of the Circuit Court of Augusta, Albemarle, Nelson, Amherst, and Rockbridge counties, succeeding Chief Justice Marshall, being the youngest man who had ever held this position, and after Chief Justice Marshall, admitted to be the most learned jurist in Virginia. He held his position during the Civil War, and was still kept in it by the Federal government during the stormy reconstruction days. By the advice of General Robert E. Lee, he took the oath of allegiance, and after the war, though refusing to " soil the ermine of the office " by runmng for the position he had held before, was elected to it again, one vote only being cast against him. Judge Thompson was the originator of the idea of sending a commission, during the Civil War, to meet Mr. Lincoln in the interests of peace, a suggestion which was accepted, Hon. Alexander H. H. Stuart, of Staunton, one of President Fillmore's cabinet, being chosen to represent Virginia. Judge Thompson married Susanna Caroline, the daughter of James and Susanna Howard (Baker) Tapscott. Issue : two sons and six daughters. The sons, as follows: The eldest, Lucas Powell, died s. p. The second, John Baker, became professor at Kenyon College, Cambria, Ohio, before he was twenty-one, and President of St. John's College, Arkansas, when only twenty-three years old. When the Civil War broke
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    316 Ancestbal Recobdsand Poetbaits out he commanded a regiment of boys from his cpllege, officered by their professors. As Lieutenant-Colonel, on his twenty-seventh birthday, he led a charge at the (Battle of Shiloh, and the spot where he fell, mortally wounded, is one of the cycloramic features of the battle. Wounded unto death he was carried from the field still shouting encouragement to his men. His name is on a tablet in the rotunda at the University of Virginia, erected to the memory of the alumni who fought in the Civil War. The daughters were known as the " Six lovely Virginia sisters." Margaret, married Dr. Paul J. Carrington, of Virginia. Caroline, Eleanor Stuart, and Mary Carter, married, respectively, three brothers, Charles, Robert Harper Goodloe, and John Lee Carroll (the latter then governor, lineal descendants of Charles Carroll, the signer) . Alice Louise. The second daughter, Susanna Rebecca, married Robert Hull, of New York and Baltimore. Their daughter is: Amy Eleanor E. Hull, Member of Chapter I., The Colonial Dames of America.
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    The text onthis page is estimated to be only 22.67% accurate Robert Hull From a miniature Susanna Rebecca Thompson Wife of Robert Hull Old clock with picture of the Indians meeting Gov. Winthrop Old pitcher with portrait of Capt. Isaac Hull and frigate Constitution
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    Ancestral Recobds andPortraits 317 XXI KUHN Among the eighteenth century families that were swept into Pennsylvania, on the flood tide of the remarkable German emigration, were the Kuhns, whose ancestor, John Kuhn, was a magistrate of Berwangen, near the Black Forest, Germany, and died previous to November 30, 1676. His son, George Martin Kuhn, was assistant jurat of the Court of Furfield, a village on the Neckar, in the province of Wiirtemburg. He married Barbara, the daughter of Friedrich Ponmes, a Justice of the Peace, and had six children. Their second child, John Christopher Kuhn, was born December 16, 1684, and died in 1754. He continued to reside in Furfeld, in the beautiful valley of the Neckar, until 1719, when he removed to Hutten. He had married Margaret, the daughter of the late Marx Reichss, a citizen of Sernum. The Kuhn family embarked on the ship Hope of London, Rotterdam being the port of departure, Daniel Reed, Master. They arrived in Philadelphia, August 28, 1733, with their three children, Adam Simon, aged nineteen; Eva Barbara, aged thirteen, and Anna Maria, aged nine. The list of passengers of the Hope is preserved at Harrisburg, Pa. The family settled in the present Berks County, Pa., and the father was naturalized March 28, 1747. He was living in that section, in Maiden Creek township, when he died. Adam Simon Kuhn^ the eldest child and only son, was born in Furfeld, Germany, December 26, 1713, and died January 23, 1780. He was naturalized, April 8, 1744, in Lancaster Coimty, Pa. A man of bright nat 
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    318 Ancesteal Recokdsand Portraits ural parts, liberally educated, he bjecame a physician and settled in Lancaster, where he was considered a very skillful, attentive and successful practitioner. He also became conspicuous in public affairs in his new home. From 1749 to 1753 he was Chief Burgess of Lancaster. During the French and Indian War he took an active part in the defence of his neighborhood. He was commissioned a Justice of the Lancaster County Courts 1752, 1761, 1764 and 1770 ; a member of the committee of Observation and Correspondence, December 15, 1774, and served as a delegate to the Provincial Convention held at Philadelphia, January 23, 1775. A memorial tablet was erected to him in Trinity Church, Lancaster. Of him it has been said, " He was the principal and almost the only person who was concerned for the promotion of classical learning amongst the youth of that community." He married, December 11, 1740, Anna Maria Sabina, the daughter of John Jacob and Eva Rosina Schrack. She was born at sea October 26, 1717, and died in Lancaster, Pa., 1799. They had eight children, viz.: Adam, John, Johann Frederick, Daniel, Peter, Maria Sabina, John Jacob, Hannah, Eve. The eldest son, Adam John Kuhn, was bom November 17, 1741. He decided upon the medical profession as his life work, in which he eventually gained worldwide distinction. Having sailed for Europe 1761, he began the study of medicine and botany in January, 1762, at the University of Upsala, Sweden, under the celebrated Linnaeus. He continued there until 1764, when he entered the University of Edinburgh, graduating in 1767. While at Upsala he was a member of the family of Professor Linnaeus, who, in a letter still preserved in the family said: " Your son of great promise, and endowed with most engaging manners, arrived
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    Ancestrax, Recoeds andPortraits 319 here," and writing a year later, said, " You have ventured to send your beloved son to a foreign country, he is unwearied in his studies, lives in a most temperated and correct manner — he long since began to taste the sweets of science, therefore I congratulate you and myself on this your son, and I have never known any one more correct in his deportment or superior in application." After taking his degree in Edinburgh 1767, Dr. Adam Kuhn made a tour of France, Holland and Germany, returning to Philadelphia 1768, when he was at once appointed professor of Materia Medica and Botany in the College of Philadelphia. He was chosen one of the physicians of the newly organized society for inoculating the poor for small-pox in 1774, and May, 1775, was named as one of the physicians to the Pennsylvania Hosj)ital, resigning in 1798. Upon the establishment of the Philadelphia Dispensary, 1786, fop the relief of the poor. Dr. Kuhn was selected as consultant physician. In 1787, the College of Physicians, was founded and he was one of its charter members, becoming its president 1808, holding the office at the time of his death. In 1789 he was called to the Chair of Theory and Practice in the University of Pennsylvania, and when the college and university were united 1792, was chosen to the professorship of Physic. At the outbreak of the Revolution he was commissioned surgeon and physician of the continental service July 8, 1776, and served until 1777. He resided for some time in St. Croix, West Indies, where he married. May 14, 1780, Elizabeth, the daughter of Isaac and Mary Carroll ( Nanton) Hartman, and the widow of Franie Markoe. She was born August 20, 1755, and died February 25, 1791. Dr. Kuhn died intestate, leaving a
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    320 Ancestral Recoedsand Poetraits large fortune to his three children, Hartman, Charles and William. The second son, Charles Kuhn, was born April 12, 1785, and died September 22, 1842. He was graduated from the University of Pennsylvania 1802. He married, July 28, 1808, Elizabeth Hestia, the daughter of Benjamin and Elizabeth (Kortright) Yard. She was born January 24, 1788, and died March 12, 1870.^ Issue, eight children, viz.: Cornelius, Elizabeth, Hartman (who married his cousin, Mary Kuhn), Emily, WilUam, Edward, and a second Edward. HARRISON Their fifth child, Emily Kuhn, married Samuel Thompson Harrison, of the Maryland Harrisons. Their son, Charles Kuhn Harrison, married Louisa Triplett, the daughter of Boiling Walker and Ann (Triplett) Haxall, and their daughter, Ann Triplett Hareison, married George Somerville Jackson. HARRISON-CAILE John Caile Hareison, son of Christopher and 1 Authentic Family Papers.
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    Ancestbal Recohds andPoeteaits 321 Mary (Caile) Harrison, married his cousin, Mary, the daughter of Hall Caile and his wife, Elizabeth Haskins, the granddaughter of Goveet Loockeeman II. Their son. Hall Harrison, married Elizabeth, the daughter of Robert and Elizabeth (Thompson) Gait. Their son, Samuel Thompson Harrison, married Emily, the daughter of Charles Kuhn, whose son, Charles Kuhn Harrison, married Louisa Triplett Hawaii. LOOCKERMAN-WOOLFORD-DENWOOD Goveet Loockeemans I., married, second, Marritje Jansen. Jacob Loockeeman, married Helen Ketin. Goveet Loockeeman II., married Sarah, the daughter of RoGEE WooLEOED, and his wife Mary, the daughter of Levin Denwood I. Their ygungest daughter, Mary Loockerman, married Thomas Haskins, whose daughter, Elizabeth, married Hall Caile. (See pp. 56-79 for Harrison, Caile, Loockerman, Woolford and Denwood families.) HAXALL ■ The first known ancestor of the Haxall family of .Virginia, John Haxall, of Exning, England, was born 1681 and died September 17, 1751. His son, William Haxall, bom 1724, and died March, 1787, was one of the leading men of Exning, being churchwarden and collector of the vicar's tithes, and overseer of the poor. He married Catherine Newton, of Bristol, England, who died at " Whitehall," a large house still standing in Exning. Issue, six children, viz. : George, William, Joseph, Henry, John, Philip. The youngest son, Philip HaxaU, was born April
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    322 Ajncesteai, Recordsakd Porteaits 10, 1770, and died December 26, 1831. He emigrated to Petersburg, Va., 1786, where he was vestryman of Old Bristol Parish,* He moved to Richmond, Va., in June, 1809, and established the Haxall Mills. He married, July 20, 1801, Clara, the daughter of Robert and Ehzabeth (Starke) Walker, of Kingston, Dinwiddie County, Va. She was bom July 9, 1780, and died March 29, 1857. Issue, nine children, viz.: Robert Walker, Richard Barton, Elizabeth, Harriet, William, Henry, Mary Bell, Philip Augustus, BoUins Walker, David Walker, EUzabeth. The seventh child of the colonist. Boiling Walker HaxallJ^ born July 13, 1815, and died Jime 26, 1885, married, December 30, 1845, Anne, the daughter of John Richards and Louisa (Stone) Triplett, and their daughter, Louisa Triplett, married Charles Kuhn Harrison. HAXALIi TRIPLETT* The first of this name to settle in Virginia, Francis Triplett, who died 1700, went to Richmond County. He patented one thousand and fifty acres of land in Rappahannock County 1666. He was a nephew of 2 Bristol Parish Records. Hayden's Genealogies. 3 The name of Haxall is believed to be extinct in England, and it only exists in this country in the descendants of Plulip and Clara (Walker) HaxalL *A genealogy of this family will be published in the Virgima Aist. Mag. by Rev. Arnold Harris Hord, of Germantown, Penn.
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    Ancestbal Recobds andPortraits 323 Rev. Thomas Triplett, Dean of Westminster Abbey, whose monmnent is in the Poets' Corner of the Abbey. The Dean is described in some very old books as of London and the son of a gentleman. A son of Francis, the colonist, William Triplett, was a resident of King George's County, and a land deed bearing date November 6, 1733, is on record in Spottsylvania County; his will was dated December 3, 1738. He married Isabella, the daughter of Captain Lyman Miller, whose will was proved in Rappahannock County May 22, 1684. Captain Miller was a noted shipbuilder and a large landoAvner.' Their son, Francis Triplett II., owned estates in Westmoreland and King George's Counties; his will was proved March 5, 1767. His wife's name was Mildred . Their fifth and youngest son, Daniel Triplett, was born May 8, 1753, and married, January 1, 1777, Elizabeth, the daughter of John and Susannah (Coleman) Richards. She was born May 22, 1760. Their son, John Richards Triplett, was bom January 29, 1785, and died October 2, 1843. He married, May 19, 1813, his cousin, Louisa Richards Stone, and resided in Norfolk, Va. Their daughter, Anne, married Boiling Walker Hawaii. RICHARDS Abms: Sable a chevron between three fieur-de-Us or. The son of William Byrd Richkrds, John Richards, was born in England, January 27, 1734, and died September 13, 1785.® He married, January 1, 1754, Susannah, the daughter of Robert Coleman, of Goochland B Bruce's Economic Hist, of Va. Vol. II, p. 439. B Family Papers.
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    324 Ancestbal Recordsand Pokteaits County, She died April 15, 1778. Had twelve children, viz.: Patty, James, Elizabeth, Triplett, Susannah, Payne, Sarah, John, WiUiam, Mildred, who married WilKam Scandreth Stone November 10, 1787; Fanny, Catherine. The third child, Elizabeth, was bom May 22, 1760, and married, January 1, 1777, Daniel Triplett, whose son, John Richards, married Louisa Richards, the daughter of Mildred and William Scandreth Stone. WALKER The first of the name in Virginia, Captain David Walker, lived in Dinwiddle Coimty. Family records say that " he was a man of large means, for years Presiding Magistrate, a position that was only held by men of the highest education and wealth. He was Senior Warden of Bristol Parish, later a Warden of Bath Parish.'' His son, Robert Walker, of Kingston, Va., was born October 10, 1729, and married, 1745, Elizabeth^ the daughter of William and Mary (BoUing) Starke. Had ten children, viz.: Robert, Richard, David, Boiling, Freeman, Starke, Louisa, Martha, Mary, and Clara, who married Philip Haxall. Their son, Boiling Walker Haaiall, married Anne Triplett. STARKE Asms: Aawre, a chevron between three acorns in chief or. Chest: A bull's head erased or, distilling drops of blood proper. Motto: Fortiorum Portia Facta. The Starkes came to America from Scotland, the first mentioned being Dr. Richard Starke, of York County, Va. It becomes a matter of interest to identify this gentleman, of whom very little is remembered, beyond Tibid.
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    Ancestral Recobds andPoethaits 325 ' his interesting connection with our earliest American law books. In the records of York County is mentioned a Dr. Richard Starke, who died in 1704, leaving a wife Rebecca, and the following children: William, Richard, James, Catrine, and Mary Harris. In 1774, there was printed, at Wilhamsburg, by Alexander Purdie and John Dixson, a book entitled " The Office and Authority of a Justice of the Peace, explained and digested under proper titles," to which are added full and correct precedents of all kinds of process necessary to be used by magistrates, in which also the duties of sheriffs and other public officers are properly discussed. The greater part of the book was written by Dr. Richard Starke, whose death prevented its completion. His friends prevailed upon some benevolent gentlemen of the law to finish the work. Colonel William Starke, his eldest son, was a prominent man in York County, Va. He was Justice of the Peace in 1730 and other years, and Colonel of the County Militia. He built and gave Starke's Free School. He married Mary, the daughter of Robert and Anne (Cocke) Boiling, and there is a marriage contract on record between William and Mary, 1713. Their daughter, Elizabeth, married Robert Walker.* ROLLING The Boilings are of very ancient origin. Robert Boiling, Esq., in the reign of Edward IV., resided at Boiling Hall, near Bradford, in Yorkshire, England, where many generations of his ancestors in the enjoyment of private life had lived, and where he died 1485, He was buried in the family vault of the church at Bradford. It is probable that his family had been bene8 Willicmi and Mary Quar.
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    326 Ancestral Recordsand Portraits factors of that church, or had even bviilt it, since their coat-of-arms alone are engraved upon it. Boiling Hall passed in succession to the families of Tristram BoUing and Sir Richard Tempest, the latter marrying Rosamond, the daughter and heiress of Tristram. Robert Rolling, son of John and Mary, of the Boilings of "Boiling Hall," near Bradford, of All Hallows, Barking Parish, Tower Street, London, was the first of the name who settled in Virginia, arriving there October 2, 1660. He was bom December 26, 1646, and died July 17, 1709. He lived at " Kippax," sometimes called " Farmingdate," served as a Burgess 1704, and took a prominent part in the aiFairs of the colony. The BolUng family were deeply interested in the church in Virginia, and have been represented in the Vestry of Old Bristol Parish in every generation.® Robert Boiling married, first, 1675, Jane, the daughter of Thomas Rolfe and the granddaughter of Pocahontas; second, 1681, Anne, the daughter of Colonel John Stith. Issue, second wife, seven children, viz. : Robert, Stith, Edward, Anne, Doury, Thomas, and Agnes. Robert Rolling II. was born January 25, 1682, and died 1749. He was also prominent in the ajBfairs of his county; Surveyor of Charles City County 1714; Justice of the Peace, and a member of the House of Burgesses 1723, 1726 and 1730. He married, January 27, 1706, Anne, the daughter of Richard and Anne (Bowler) Cocke. They had eight children, viz. : Elizabeth, Anne, Lucy, Jane, Martha, Susanna, Robert, and Mary, who married William Starke. STITH Colonel John Stith was the first of this family in t Bristol Pariah; Va. Hist. Mag., and William and Mary Quar,
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    Ancestbal Recokds andPortraits 327 Virginia. He had a grant of land in Charles CityCounty 1663; was a practicing lawyer 1680; member of the House of Burgesses 1685 to 1692 and 1693, and Sheriif 1691. His known children are: Drury, John, ahd Anne, who married Robert BoUing I. Their son, Robert Bolling II., married Anne Cocke, whose daughter, Mary, married William Starke. COCKE Abms: Argent two lions passant sable crowned or a fesse sable between two talbots passant. Richard Cocke (1600-1665), the original ancestor of the Cockes of Virginia, emigrated from Leeds, England, about 1630, and settled at Milvert Hills. With him, came Captain Francis West, his sister having married Robert West, son of Lord de la Warr, and settled in Henrico County, Va. Richard Cocke was a prominent merchant in London, and several of his family were connected with the Royal households of Mary, Elizabeth, and James I., and the Cocke family was connected with the Wests, Percy Lord Chandos, the Berkeley family. Sir Hugh Poynty, and Lord Wentworth. In the Committee of Safety of Surry County, Va., 1776, there were five Cockes: Colonel Allen, Colonel John, John Jr., J. H., and Colonel Lemuel Cocke. The Cocke family sat in nearly every session of the Virginia House of Burgesses. Richard Cocke took a leading part in the affairs of the colony, serving as a Burgess 1632, 1644, and 1654. He was also a member of the " Grand Assembly of Virginia." His nephew, Captain Cocke, of London, is well known by his intimacy with Samuel Pepys, and is often mentioned in his
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    328 Ancestbal Recordsand Poeteaits celebrated diary. Richard Cocke married Mary, the daughter of Walter Aston, and had a large family. Richard Cocke II., third son of .the colonist, was born 1639, and died 1705. He took an active part in the affairs of Virginia, being a civil officer of Henrico County 1680; Justice of the Peace 1714, and Burgess. He married, 1675, Ann Bowler, and their daughter, Anne Cocke, married Robert Rolling, Jr., whose 'daughter, Mary Boiling, married William Starke. ASTON Abms: Argemt a fesae sable in chief three lozenges of the last. Crest: A hull's head, cowped sable. Walter Aston (the grandson of Sir Walter Aston, of Longdon, Stafford County, England, who was knighted 1560), was born July 9, 1584, and died August 13, 1639, and is buried at " Westover," The family came to America 1626, and August 12 of that year Walter Aston patented one thousand and forty acres of land near Shirley Hundred, two hundred acres of which were known as " Causey's Care," purchased in 1634 from John Causey (being the same land patented by Nathaniel Causey, who came in with the first supply, 1608. All of this property became part of William Byrd's celebrated "Westover"), Walter Aston represented Shirley Hundred in the House of Burgesses 1629 to 1630 and Causey's Care 1632 to 1633. He was a Justice of the Peace, and Lieutenant- Colonel of the Militia.'" His first wife's name is mentioned in land patents as being Warboe or Narboe, and his second wife's name was Hannah, who married after his death Colonel Edward Hill. Children: Susannah, Walter, 10 William and Mary Quar.
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    Ancestral Recoeds andPoetbaits 329 EHzabeth, and Mary, who married Richard Cocke. From them the line descends as follows: Richard Cocke II., married Ann Bowler. Anne Cocke, married Robert Rolling II. Mary Boiling, married William Starke. Elizabeth Starke, married Robert Walker. Clara Walker, married Philip Haxall. Boiling Walker Hawaii, married Anne Triplett. Louisa Triplett Haxall, married Charles Kuhn Harrison, whose daughter is: Anne Triplett Harrison Jackson, Member of Chapter I„ The Colonial Dames of America.
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    330 Ancestral Recoedsand Portraits XXII SWAN Scottish records, of the year 1599, contain the name of William Swan, a Burgess of Dumfrieg, who died in January, 1603, leaving a widow, Helen Anderson, and four children, viz.: Andrew, William, Alison, and Helen. The eldest child, Andrew Swan, married, before 1607, Janet, who was a daughter of Herbert Ranyng (who died in 1601), and Janet Davidson, his wife, and a granddaughter of another Herbert Ranyng (who died 1587) , and Malie Kirkpatrick, his wife. The elder Ranyng was Provost of Dumfries, 1572; member of the Parliament of Scotland the same year, and Commissioner for Dimifries, in the Convention of Royal Burghs, 1578. The younger Ranyng, was Provost of Dumfries, 1586, 1591 to 1592, and was frequently Bailie. A son of Andrew and Janet (Ranyng) Swan, was John, living in the year 1626. Of the same family was James Swan, a merchant of Dumfries, who died May 24, 1760. His son Robert, born 1720, a partner in the house of Nelson, Carlyle & Company, of Glasgow, resided at Annapolis, Md., as the American representative of the firm, and died there unmarried May 4, 1764. The larger part of his estate he left by will to his nephew, John Swan, the eldest son of his brother John, of Cocketfield, viz.: Major John Swan, who was baptized in Torthorwald Parish, November 27, 1750, and came to Maryland in the year 1766, as the heir of his uncle's estate.
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    The text onthis page is estimated to be only 5.65% accurate ■1 1 ^^m'^-^] ^^^^^^^^^H ^^M ^^^^ I ■1 Py ' 1 9^ iJ Elizabeth Maxwell Wife of Maj. John Swan Maj. Joiix Swan James Swan Elizametli Doxnell AVife of James Swan
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