BIS2C. Biodiversity and the Tree of Life. 2014. L15. FungiJonathan Eisen
This document contains slides from a lecture about fungi. It discusses fungi's role in mutualistic relationships like lichens and mycorrhizae. It also covers fungi's importance in areas like food production, medicine, industry, and ecosystems. Fungi play key roles in decomposition, nutrient cycling, and as a source of antibiotics. The lecture provides examples of many fungi and their functions, highlighting the diversity and impacts of fungi.
BIS2C. Biodiversity and the Tree of Life. 2014. L14. FungiJonathan Eisen
The document is a set of lecture slides about fungi. It discusses several types of fungi, including microsporidia, chytrids, zygospore fungi, glomeromycota, and dikarya. It provides details on the characteristics, life cycles, and evolution of these groups. It specifically examines the life cycles of sac fungi, noting they have a haploid stage, form a dikaryotic mycelium through plasmogamy, undergo karyogamy and meiosis within ascocarps to produce haploid ascospores.
The document summarizes the immune system's defense against pathogens. It discusses:
1) Non-specific immunity/innate immunity which provides first and second lines of defense through barriers like skin and mucous membranes, and responses like phagocytosis, inflammation, fever, and interferon.
2) Specific immunity/acquired immunity provides a third line of defense and has humoral immunity through antibodies and cell-mediated immunity with T cells.
3) The immune system defends against pathogens through non-specific innate responses and acquired specific responses utilizing organs, lymphocytes, and processes like phagocytosis and inflammation.
This document provides information about bacteria and archaea. It discusses the structure and characteristics of bacteria, including their cell shapes, arrangements, staining properties, and metabolisms. It describes how bacteria reproduce through binary fission and genetic transfer. It also discusses endospores and provides examples of pathogenic bacteria. The document concludes by describing archaea and how they are classified based on the extreme conditions they can survive in.
This document summarizes a study on the effects of copper-infused socks. 56 patients with various foot conditions like erythema, burning, itching, and scaling were observed while wearing the copper socks. For erythema, 51 patients improved and 22 resolved completely within an average of 9 days. A follow up study of 22 patients found that 19 maintained improvement or resolution after 36 days on average, while 3 reverted or did not improve. The copper socks showed promising results in reducing common foot conditions.
This document discusses the history and properties of copper as an antimicrobial agent. It summarizes that copper has been used for thousands of years by ancient Greeks, Phoenicians, and American pioneers to purify water and prevent diseases. While copper has been used for a long time, no microorganism has evolved resistance to it. Studies show that copper has potent biocidal effects against bacteria, fungi, viruses, and other microbes through damaging cellular components. Copper is also essential for human health. The document reviews several clinical studies that demonstrate the effectiveness of copper-infused fabrics, filters, and socks in reducing microbial growth and treating skin infections.
Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the microbial diversity of permafrost. Explain how the greatest diversity of Archaea exist in cold environments.
2. Describe the two main Archaeal phyla, and describe example species.
3. Explain how climate change is affecting permafrost and microbial diversity.
BIS2C. Biodiversity and the Tree of Life. 2014. L15. FungiJonathan Eisen
This document contains slides from a lecture about fungi. It discusses fungi's role in mutualistic relationships like lichens and mycorrhizae. It also covers fungi's importance in areas like food production, medicine, industry, and ecosystems. Fungi play key roles in decomposition, nutrient cycling, and as a source of antibiotics. The lecture provides examples of many fungi and their functions, highlighting the diversity and impacts of fungi.
BIS2C. Biodiversity and the Tree of Life. 2014. L14. FungiJonathan Eisen
The document is a set of lecture slides about fungi. It discusses several types of fungi, including microsporidia, chytrids, zygospore fungi, glomeromycota, and dikarya. It provides details on the characteristics, life cycles, and evolution of these groups. It specifically examines the life cycles of sac fungi, noting they have a haploid stage, form a dikaryotic mycelium through plasmogamy, undergo karyogamy and meiosis within ascocarps to produce haploid ascospores.
The document summarizes the immune system's defense against pathogens. It discusses:
1) Non-specific immunity/innate immunity which provides first and second lines of defense through barriers like skin and mucous membranes, and responses like phagocytosis, inflammation, fever, and interferon.
2) Specific immunity/acquired immunity provides a third line of defense and has humoral immunity through antibodies and cell-mediated immunity with T cells.
3) The immune system defends against pathogens through non-specific innate responses and acquired specific responses utilizing organs, lymphocytes, and processes like phagocytosis and inflammation.
This document provides information about bacteria and archaea. It discusses the structure and characteristics of bacteria, including their cell shapes, arrangements, staining properties, and metabolisms. It describes how bacteria reproduce through binary fission and genetic transfer. It also discusses endospores and provides examples of pathogenic bacteria. The document concludes by describing archaea and how they are classified based on the extreme conditions they can survive in.
This document summarizes a study on the effects of copper-infused socks. 56 patients with various foot conditions like erythema, burning, itching, and scaling were observed while wearing the copper socks. For erythema, 51 patients improved and 22 resolved completely within an average of 9 days. A follow up study of 22 patients found that 19 maintained improvement or resolution after 36 days on average, while 3 reverted or did not improve. The copper socks showed promising results in reducing common foot conditions.
This document discusses the history and properties of copper as an antimicrobial agent. It summarizes that copper has been used for thousands of years by ancient Greeks, Phoenicians, and American pioneers to purify water and prevent diseases. While copper has been used for a long time, no microorganism has evolved resistance to it. Studies show that copper has potent biocidal effects against bacteria, fungi, viruses, and other microbes through damaging cellular components. Copper is also essential for human health. The document reviews several clinical studies that demonstrate the effectiveness of copper-infused fabrics, filters, and socks in reducing microbial growth and treating skin infections.
Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the microbial diversity of permafrost. Explain how the greatest diversity of Archaea exist in cold environments.
2. Describe the two main Archaeal phyla, and describe example species.
3. Explain how climate change is affecting permafrost and microbial diversity.
The document discusses the contributions of several important scientists to the field of microbiology, including:
- Antonie van Leeuwenhoek, known as "the Father of Microbiology", who was the first to observe microbes using single-lensed microscopes of his own design.
- Francesco Redi who demonstrated that maggots come from fly eggs, challenging the theory of spontaneous generation.
- Louis Pasteur who developed the germ theory of disease and pioneered pasteurization.
- Robert Koch who isolated the bacteria that cause anthrax, tuberculosis, and cholera and established the Koch's postulates to define causative relationships between microbes and diseases.
This document provides an overview of medical microbiology for medical graduates. It discusses what medical microbiology is, the importance of studying it, and some key concepts. Some highlights include how microorganisms are classified, the contributions of early scientists like Leeuwenhoek and Pasteur, Koch's postulates for determining causative agents of disease, and the different types of microorganisms including bacteria, viruses, fungi and parasites that can cause human illness. The document emphasizes understanding microbial classification, pathogenesis and treatment of infectious diseases.
Bacteria and viruses are among the smallest organisms. Bacteria are classified as prokaryotes and have different shapes. They lack membrane-bound organelles and a nucleus. Bacteria reproduce through binary fission and can form spores. They are useful in food production and decay of organic matter but some cause diseases. Viruses are not living cells and are much smaller than bacteria. They contain genetic material surrounded by a protein coat and reproduce by infecting host cells.
This document discusses the classification of microorganisms. It describes the three domain system proposed by Carl Woese which divides organisms into Archaea, Bacteria and Eukarya. It then provides details on the characteristics of fungi, algae, protozoa, viruses and bacteria; and discusses methods used to identify bacteria including biochemical tests and serological tests.
This document provides an overview of bacteria. It begins by defining bacteria and discussing their discovery. It then covers the characteristics of bacteria, including their size, shape, reproduction methods, and habitats. The document also summarizes methods of classifying bacteria based on morphology, oxygen needs, staining properties, heat tolerance, and pathogenicity. Finally, it outlines the structure of bacteria and discusses both the beneficial and harmful effects of bacteria.
This document provides information about bacteria. It describes bacteria as among the smallest living organisms that usually band together in colonies and can be autotrophic or heterotrophic. It discusses their basic shapes of rod, round, or spiral and their structures including cell walls, flagella, pili, and capsules. The document also covers how some bacteria move and feed, their importance in industry and nutrient cycles, and how certain bacteria can cause harmful diseases. It emphasizes the need to wash hands and properly store and cook food to avoid pathogenic bacteria.
Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophileJosé Luis Moreno Garvayo
Thermus aquaticus is a newly isolated thermophilic bacterium that is widespread in aquatic thermal environments. It is a non-sporulating, nonmotile rod that forms yellow pigmentation and large spheres. Isolates have been obtained from hot springs in Yellowstone National Park and California between 40-79°C, as well as from man-made thermal habitats like hot tap water distant from natural springs. The organism is an aerobic obligate with optimal growth at 70°C and generation time of 50 minutes.
There are more bacteria on Earth than all other living things combined. Bacteria come in three main shapes - bacilli, cocci, and spirilla - which help them in different ways. All bacteria are single-celled prokaryotes that reproduce through binary fission and do not have nuclei. Some bacteria form protective endospores that allow them to survive in harsh environments. The two kingdoms of bacteria are Eubacteria and Archaebacteria, which contain the oldest and most diverse forms of life and can be found in extreme habitats.
Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
The document describes the bombardier beetle, classified as Brachinus tenuicollis. It has a unique defense mechanism where it produces and sprays boiling water from its abdomen at predators through a chemical reaction. The beetles grow up to 5cm long, reproduce sexually, and females can lay dozens to hundreds of eggs. Internally, bombardier beetles have organ systems that help them move and function compared to less complex invertebrates.
Classification of Microorganisms
1. Whittaker Five Kingdom Classification
2. Three Domain System of Classification
Groups of Microorganisms
1.Bacteria
2. Virus
3. Fungi
4. Algae
5. Protozoa
1. Microbes play important roles in ecosystems by recycling nutrients and driving biochemical processes like the nitrogen cycle. Bacteria and archaea are involved in nitrogen fixation, nitrification, and denitrification.
2. Sewage treatment harnesses microbes to break down organic waste through aerobic and anaerobic digestion. Biofilms and microbial communities in trickling filters and reed beds lower the biological oxygen demand and remove nutrients from sewage water.
3. Anaerobic digestion by methanogenic archaea produces methane from organic materials like sewage sludge. The process occurs in three stages carried out by different microbial communities that convert waste to methane via intermediate products.
High school biology lesson on bacteria. Covers morphology, metabolism, reproduction, and usefulness of bacteria. Also included, an activity that teaches students the morphology of bacteria. To complete the activity, the teacher should provide each student with 2 poker chips (preferably each should be a different color), one side marked with a sticker. The side with the sticker is the dominant allele, the blank side is the recessive allele. The students must recall how traits are inherited and how organisms express dominant or recessive traits to draw each of their bacteria cells.
This document summarizes a lecture on how different parts of genomes and cells can have different evolutionary histories. It discusses how endosymbiosis led to the origins of mitochondria and chloroplasts from ancient bacteria. Phylogenetic analysis of mitochondrial and chloroplast genes supports a single origin for each from ancient endosymbiotic events, though some lineages have since lost these organelles. The distribution and trees of chloroplasts and mitochondria do not always match the nuclear genome tree.
The document discusses the contributions of several important scientists to the field of microbiology, including:
- Antonie van Leeuwenhoek, known as "the Father of Microbiology", who was the first to observe microbes using single-lensed microscopes of his own design.
- Francesco Redi who demonstrated that maggots come from fly eggs, challenging the theory of spontaneous generation.
- Louis Pasteur who developed the germ theory of disease and pioneered pasteurization.
- Robert Koch who isolated the bacteria that cause anthrax, tuberculosis, and cholera and established the Koch's postulates to define causative relationships between microbes and diseases.
This document provides an overview of medical microbiology for medical graduates. It discusses what medical microbiology is, the importance of studying it, and some key concepts. Some highlights include how microorganisms are classified, the contributions of early scientists like Leeuwenhoek and Pasteur, Koch's postulates for determining causative agents of disease, and the different types of microorganisms including bacteria, viruses, fungi and parasites that can cause human illness. The document emphasizes understanding microbial classification, pathogenesis and treatment of infectious diseases.
Bacteria and viruses are among the smallest organisms. Bacteria are classified as prokaryotes and have different shapes. They lack membrane-bound organelles and a nucleus. Bacteria reproduce through binary fission and can form spores. They are useful in food production and decay of organic matter but some cause diseases. Viruses are not living cells and are much smaller than bacteria. They contain genetic material surrounded by a protein coat and reproduce by infecting host cells.
This document discusses the classification of microorganisms. It describes the three domain system proposed by Carl Woese which divides organisms into Archaea, Bacteria and Eukarya. It then provides details on the characteristics of fungi, algae, protozoa, viruses and bacteria; and discusses methods used to identify bacteria including biochemical tests and serological tests.
This document provides an overview of bacteria. It begins by defining bacteria and discussing their discovery. It then covers the characteristics of bacteria, including their size, shape, reproduction methods, and habitats. The document also summarizes methods of classifying bacteria based on morphology, oxygen needs, staining properties, heat tolerance, and pathogenicity. Finally, it outlines the structure of bacteria and discusses both the beneficial and harmful effects of bacteria.
This document provides information about bacteria. It describes bacteria as among the smallest living organisms that usually band together in colonies and can be autotrophic or heterotrophic. It discusses their basic shapes of rod, round, or spiral and their structures including cell walls, flagella, pili, and capsules. The document also covers how some bacteria move and feed, their importance in industry and nutrient cycles, and how certain bacteria can cause harmful diseases. It emphasizes the need to wash hands and properly store and cook food to avoid pathogenic bacteria.
Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophileJosé Luis Moreno Garvayo
Thermus aquaticus is a newly isolated thermophilic bacterium that is widespread in aquatic thermal environments. It is a non-sporulating, nonmotile rod that forms yellow pigmentation and large spheres. Isolates have been obtained from hot springs in Yellowstone National Park and California between 40-79°C, as well as from man-made thermal habitats like hot tap water distant from natural springs. The organism is an aerobic obligate with optimal growth at 70°C and generation time of 50 minutes.
There are more bacteria on Earth than all other living things combined. Bacteria come in three main shapes - bacilli, cocci, and spirilla - which help them in different ways. All bacteria are single-celled prokaryotes that reproduce through binary fission and do not have nuclei. Some bacteria form protective endospores that allow them to survive in harsh environments. The two kingdoms of bacteria are Eubacteria and Archaebacteria, which contain the oldest and most diverse forms of life and can be found in extreme habitats.
Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
The document describes the bombardier beetle, classified as Brachinus tenuicollis. It has a unique defense mechanism where it produces and sprays boiling water from its abdomen at predators through a chemical reaction. The beetles grow up to 5cm long, reproduce sexually, and females can lay dozens to hundreds of eggs. Internally, bombardier beetles have organ systems that help them move and function compared to less complex invertebrates.
Classification of Microorganisms
1. Whittaker Five Kingdom Classification
2. Three Domain System of Classification
Groups of Microorganisms
1.Bacteria
2. Virus
3. Fungi
4. Algae
5. Protozoa
1. Microbes play important roles in ecosystems by recycling nutrients and driving biochemical processes like the nitrogen cycle. Bacteria and archaea are involved in nitrogen fixation, nitrification, and denitrification.
2. Sewage treatment harnesses microbes to break down organic waste through aerobic and anaerobic digestion. Biofilms and microbial communities in trickling filters and reed beds lower the biological oxygen demand and remove nutrients from sewage water.
3. Anaerobic digestion by methanogenic archaea produces methane from organic materials like sewage sludge. The process occurs in three stages carried out by different microbial communities that convert waste to methane via intermediate products.
High school biology lesson on bacteria. Covers morphology, metabolism, reproduction, and usefulness of bacteria. Also included, an activity that teaches students the morphology of bacteria. To complete the activity, the teacher should provide each student with 2 poker chips (preferably each should be a different color), one side marked with a sticker. The side with the sticker is the dominant allele, the blank side is the recessive allele. The students must recall how traits are inherited and how organisms express dominant or recessive traits to draw each of their bacteria cells.
This document summarizes a lecture on how different parts of genomes and cells can have different evolutionary histories. It discusses how endosymbiosis led to the origins of mitochondria and chloroplasts from ancient bacteria. Phylogenetic analysis of mitochondrial and chloroplast genes supports a single origin for each from ancient endosymbiotic events, though some lineages have since lost these organelles. The distribution and trees of chloroplasts and mitochondria do not always match the nuclear genome tree.
This document contains slides from a lecture on Opisthokonts. The lecture covers the key groups within the Opisthokonts, including fungi, animals, and choanoflagellates. It discusses shared derived traits of the opisthokont clade, as well as derived features of fungi, such as their absorptive heterotrophic nutrition. The slides also mention the relevance of studying opisthokonts and fungi to understanding human diseases and developing antifungal drugs.
This document contains slides from a lecture on triploblasts and protostomes, focusing on ecdysozoans. It discusses the key features of arthropods like segmentation, exoskeletons, and compound eyes. It then covers the major arthropod groups including trilobites, crustaceans, myriapods, chelicerates, and hexapods. For each group, it highlights some representative types and their characteristics. The slides include diagrams and photos to illustrate arthropod anatomy and diversity.
This document contains slides from a lecture on triploblasts and lophotrochozoans. It discusses the key features of lophotrochozoans like their lophophore and trochophore larval stages. Major groups within the lophotrochozoans are discussed like mollusks and annelids. Examples of mollusks like cephalopods are described in more detail, highlighting characteristics like their advanced vision and ability to change appearance. Annelid examples discussed include pogonophorans that live at hydrothermal vents and rely on bacterial symbionts for nutrition.
This document contains lecture slides about diploblastic animals. It discusses the key characteristics of diploblasts, including ctenophores, placozoans, and cnidarians. Cnidarians are described in more detail, including their features like cnidae and nematocysts. Examples of cnidarians discussed include corals, which form a symbiosis with dinoflagellates, and box jellies, whose sting can be deadly. The document also addresses the number of endosymbiotic events in the evolution of dinoflagellate chloroplasts.
This document contains slides from a lecture on animal diversity and the phylum Ecdysozoa. It discusses key features of ecdysozoans like molting and their cuticle. It focuses on nematodes, highlighting features like their thick cuticle and use of C. elegans as a model organism. The document also covers tardigrades, their ability to enter a dormant state during drying, and their widespread distribution. The slides provide summaries of content and examples to illustrate concepts from the lecture.
This document contains slides from a lecture on chordates and vertebrate evolution. The slides cover topics like the phylogeny of chordates and vertebrates, innovations in vertebrate evolution like jaws and limbs, and examples of key vertebrate groups like lampreys and hagfish. The document emphasizes how scientists use comparative biology and phylogenetic trees to study relationships between organisms and infer ancestral traits.
BIS2C: Lecture 35: Symbioses Across the Tree of LifeJonathan Eisen
This document outlines a lecture on interactions across the tree of life. It discusses how the course is organized based on the tree of life and phylogeny. It provides examples of symbiotic relationships between organisms, such as the relationship between the Xylella fastidiosa bacterium, grapes, and the glassy-winged sharpshooter vector. It also describes the complex coevolution between plants and the insects that feed on them, and how insects have adapted to overcome plant defenses by developing symbiotic relationships with microbes.
The document contains slides from a lecture on fungi. It discusses the evolution of fungi and their diversity of forms. It covers fungal reproduction, life styles including parasitic, mutualistic and saprobic, and various uses of fungi in food, industry and pharmaceuticals. It provides examples of important mutualistic fungi like mycorrhizae and lichens. It also discusses the discovery of penicillin from the fungus Penicillium notatum.
The document is a set of slides for a lecture on deuterostomes, specifically echinoderms and hemichordates. It includes a phylogenetic tree of animals showing the relationships between major groups like sponges, cnidarians, protostomes, deuterostomes. It also notes some of the key innovations along the branches, such as the development of multicellularity and tissues in the common ancestor of all animals.
This document contains slides from a lecture on the Tree of Life. It discusses how the Tree of Life can be rooted using gene trees of elongation factors. The overall structure is generally considered to have three domains - Bacteria, Archaea, and Eukaryota. Within each domain there is diversity in form, function, and phylogeny. The slides explore how molecular evidence has led to competing proposals about the rooting and relationships between the three domains.
The document is a set of slides for a lecture on the Tree of Life. It discusses evidence that all life on Earth is related, including universal traits like the genetic code and cell structure. It covers historical models of the Tree of Life from Darwin to the modern understanding based on Carl Woese's work comparing rRNA sequences. Woese's RNA-based tree supported the division of life into Bacteria, Archaea, and Eukarya domains, reflecting a more complex early evolution than previously thought.
The document summarizes a lecture on the human microbiome. It discusses how humans are colonized by vast numbers of microbes, forming complex microbial ecosystems. There is enormous variation in microbiome composition both within and between individuals, and this variation is associated with health states and phenotypes. Research has identified some possible causes of microbiome variation and suggests it may be possible to alter or restore microbiome composition.
The document discusses a lecture on microbial diversity. It notes that the tree of life is mostly microbial, diverse methods exist to study microbial diversity, and most microbial diversity remains poorly characterized. Sequencing methods like rRNA and metagenomic sequencing have improved understanding of microbial phylogeny but much diversity remains unknown.
This document contains slides from a lecture on chordates. It discusses the key characteristics of chordates like the notochord and dorsal hollow nerve cord. It covers the three major chordate groups: lancelets, tunicates, and vertebrates. Lancelets retain many chordate features throughout life. Tunicates resemble chordates as larvae but undergo metamorphosis and lose most features as adults. Many slides show examples of symbiosis in chordates and other animals.
DNA-based methods for bioaerosol analysisjordanpeccia
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
This document discusses methods for analyzing microbial diversity in soil without culturing. It notes that while culturing methods have provided access to some microbes, they represent only about 1% of soil microbes due to physiological constraints. Molecular methods like 16S rRNA gene sequencing reveal far greater phylogenetic diversity in soil. The document reviews various culture-independent methods like DNA-DNA hybridization, PCR amplification, and gene expression cloning that provide insights into the phylogenetic and functional diversity of uncultured soil microbes, opening possibilities for discovering novel products. It suggests both culturable and unculturable microbes likely contribute to untapped natural product resources.
Physical conditions for bacterial culturingNizadSultana
Here is presentation of how physical conditions like temperature PH and other factors affect bacterial growth. Culturing conditions for bacterial which factors are important for bacterial growth what we take in consideration for bacterial growth
1. The document discusses the evolution of eukaryotic cells from prokaryotic cells between 1-1.5 billion years ago. Two main theories for this evolution are the infolding theory and endosymbiotic theory.
2. The endosymbiotic theory proposes that smaller photosynthetic and heterotrophic prokaryotes entered larger prokaryotic host cells, forming cellular organelles like chloroplasts and mitochondria.
3. Bacteria are classified into domains, with Eubacteria and Archaebacteria being the two main kingdoms. Bacteria have distinct cell structures like cell walls, flagella, and pili that allow further classification. Gram staining is also used
UNIT 6 Fermentation technology, Fermenters, Study of Media, types of fermenta...Shyam Bass
UNIT-6 6th Sem B.Pharma Pharmaceutical Biotechnology-
Following slides include-
Fermentation technology and biotechnological products :
Fermentation methods and general requirements
Study of media
Equipment
Sterilization methods
Aeration process
Stirring
large scale production fermenter design and its various controls
BY- SHYAM BASS
1. An incubator provides optimal conditions like temperature, humidity, and gas levels for microbial growth. It maintains these conditions through heating/cooling cycles and insulation.
2. A Bunsen burner is a gas-fueled open flame tool used commonly for sterilization and heating in medical laboratories.
3. Pipettes are used to precisely transfer small volumes of liquids and include manual, disposable, Pasteur, and micropipettes ranging from milliliters to microliters. Micropipettes accurately measure volumes in the microliter range for molecular biology applications.
Refrigeration is a technique used for preserving food in low temperatures. This procedure slow down or stop most bacteria from dividing and thereby multiplying, but do not kill them.
This chapter discusses the requirements for microbial growth, including physical factors like temperature, pH, and osmotic pressure as well as chemical requirements like carbon, nitrogen, and oxygen. It also covers culture media that can be used to grow microbes in the lab, including nutrient broth, selective media, and differential media. The chapter describes how to obtain pure cultures using the streak plate method and calculates microbial generation time. It outlines the phases of a bacterial growth curve, including the lag, exponential, stationary, and death phases.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
Extremophiles are microorganisms that thrive in extreme environments such as high temperatures, acidic or alkaline conditions, and high salt concentrations. They have unique enzymes that allow them to survive in these harsh conditions. These enzymes, called extremozymes, have potential applications in industries like food production and manufacturing that require enzymes to function under extreme conditions. For example, thermophilic bacteria provide heat-resistant enzymes for processes like PCR that use high temperatures. Extremophiles may also help scientists understand how life could exist in other extreme environments like those found on other planets.
Extremophiles are microorganisms that thrive in extreme environments such as high temperatures, acidic or alkaline conditions, and high salt concentrations. They have unique enzymes that allow them to survive in these harsh conditions. These enzymes, called extremozymes, have potential applications in industries like food production and manufacturing that require enzymes to function under extreme conditions. For example, thermophilic bacteria provide heat-resistant enzymes for processes like PCR that use high temperatures. Extremophiles may also help scientists understand how life could exist in extreme environments on other planets.
This document provides instructions for home canning of various foods. It discusses selecting high quality fresh produce for canning and proper storage. Canning methods depend on whether the food is acidic or low-acid. Acidic foods can be water bath canned while low-acid foods require pressure canning to reach higher temperatures needed to destroy bacteria spores. Precise following of approved canning recipes and procedures is important for safety, including proper headspace, processing times and sealing of jars. Altitude adjustments may be needed for processing times. The document provides various tips and resources for safe home canning.
Preparation of plant tissue culture media,types and SterilizationSubhas Picheli
The document discusses preparation of plant tissue culture media, types of media, and sterilization techniques. It covers:
- Types of media including Murashige and Skoog, White's Medium, and Gamborg Medium.
- Steps for preparing media including making stock solutions, adding ingredients, adjusting pH, dispensing, and autoclaving.
- Sources of contamination and methods for sterilizing glassware, equipment, media, explants, and the environment using techniques like autoclaving, dry heat, filtration, and surface sterilization.
This document discusses various methods for preserving microorganisms, including freeze-drying, cryopreservation, periodic transfer to fresh media, saline suspension, and the oil overlay method. It also describes DNA and RNA, DNA replication, recombinant DNA technology, and the distribution of microorganisms in different environments such as soil, air, water, and indoor and outdoor settings.
Fermentation is the process of breaking down organic matter into smaller components with enzymes from microbes. There are aerobic, anaerobic, and facultative anaerobic fermentation types. Penicillin fermentation is an example of aerobic fermentation using Penicillium fungi. Deep aerated submerged fermentation is commonly used for large-scale penicillin production and involves agitation, aeration, and feeding of precursors and nutrients to maximize penicillin yield over 5-7 days of fermentation. The penicillin product is recovered through filtration, extraction, crystallization, and drying steps.
This document provides instructions for an experiment to demonstrate diffusion and the effect of temperature on the rate of diffusion. Students will use three containers of water with different temperatures (cold, medium, hot) and add food coloring to observe how quickly it spreads through the water. They will record the initial temperatures and time it takes for uniform coloring. The objectives are to observe diffusion and recognize how temperature relates to diffusion rate. Analysis questions ask students to define diffusion based on observations, explain how temperature affects diffusion, and why a warm body is advantageous for living things.
Midterm Lad Report 7
Midterm Lab Report
Introduction
Cellular respiration refers to all the metabolic processes and chemical reactions that take place in living organisms, particularly at the cellular level. These processes focus on the extraction of energy from nutrients. It is also responsible for converting the biochemical energy into 'adenosine triphosphate' (ATP) by the breakdown of sugars in the cells (Bennet 58). Cellular respiration is also responsible for the process by which cells release chemical energy required for conducting cellular activities. The reactions and processes facilitate the release of waste products from the cells. This experiment seeks to conduct a study of the processes and reactions involved during cellular respiration. The experiment will include several activities, such as having a study on the amount of Carbon dioxide produced during the experiment.
The number of levels of the growth of a yeast medium as a dependent variable will also be monitored during the experiment. There are other several independent variables associated with the experiment. These independent variables include sugar and temperature, among others, and their role in the experiment were also monitored. The experiment design involved the use of airtight balloons capped over reaction chambers that were used to collect the Carbon dioxide produced during the experiment. The reaction chambers contained sugars and yeast medium, which facilitated the reactions. Thermometers and pH scale were used to monitor the changes in temperature and acidity levels during the experiment. The paper involves a lab design that institute steps such as arranging the bottles used on the experiment. Notably, a proper arrangement to make sure that all the carbon dioxide released during the respiration process is well tapped in the bottles for correct lab results
Methodology
The actual procedure for experimenting involved taking measurements and recording of all observations made during the experiment. For accurate results, measures were taken three times, and a mean measurement was calculated and recorded. Winzler asserts that the mean obtained from the measurements should be used to calculate the standard deviation, which in turn facilitated the calculation of uncertainty (276). Below are the steps for conducting the experiment. It is essential to read the instructions carefully safety and accuracy during the experiment. Notably, all the lab and experiment results were well observed and thus making sure that there are limited errors in the whole process.
Consequently, all the steps required in the lab report were also clearly followed to help in getting the correct data and even not to affect the whole experiment process. The experiment involved setting the apparatus as per the set standard and the requirement. As per this concept, all the apparatus were set in a proper way to avoid vague results. Notably, to get the correct measurement and results, it is import.
Midterm Lad Report 7
Midterm Lab Report
Introduction
Cellular respiration refers to all the metabolic processes and chemical reactions that take place in living organisms, particularly at the cellular level. These processes focus on the extraction of energy from nutrients. It is also responsible for converting the biochemical energy into 'adenosine triphosphate' (ATP) by the breakdown of sugars in the cells (Bennet 58). Cellular respiration is also responsible for the process by which cells release chemical energy required for conducting cellular activities. The reactions and processes facilitate the release of waste products from the cells. This experiment seeks to conduct a study of the processes and reactions involved during cellular respiration. The experiment will include several activities, such as having a study on the amount of Carbon dioxide produced during the experiment.
The number of levels of the growth of a yeast medium as a dependent variable will also be monitored during the experiment. There are other several independent variables associated with the experiment. These independent variables include sugar and temperature, among others, and their role in the experiment were also monitored. The experiment design involved the use of airtight balloons capped over reaction chambers that were used to collect the Carbon dioxide produced during the experiment. The reaction chambers contained sugars and yeast medium, which facilitated the reactions. Thermometers and pH scale were used to monitor the changes in temperature and acidity levels during the experiment. The paper involves a lab design that institute steps such as arranging the bottles used on the experiment. Notably, a proper arrangement to make sure that all the carbon dioxide released during the respiration process is well tapped in the bottles for correct lab results
Methodology
The actual procedure for experimenting involved taking measurements and recording of all observations made during the experiment. For accurate results, measures were taken three times, and a mean measurement was calculated and recorded. Winzler asserts that the mean obtained from the measurements should be used to calculate the standard deviation, which in turn facilitated the calculation of uncertainty (276). Below are the steps for conducting the experiment. It is essential to read the instructions carefully safety and accuracy during the experiment. Notably, all the lab and experiment results were well observed and thus making sure that there are limited errors in the whole process.
Consequently, all the steps required in the lab report were also clearly followed to help in getting the correct data and even not to affect the whole experiment process. The experiment involved setting the apparatus as per the set standard and the requirement. As per this concept, all the apparatus were set in a proper way to avoid vague results. Notably, to get the correct measurement and results, it is import.
This document defines fermentation and fermenter. It then describes the key components of a fermenter:
1) The vessel, which is designed to carry out fermentation under aseptic and controlled environmental conditions. Vessels come in small-scale laboratory or large-scale industrial sizes.
2) An impeller that provides mixing for oxygen transfer, heat transfer, and maintaining a uniform environment.
3) A sparger that introduces air into the medium through small holes.
4) Baffles that prevent vortexes and improve aeration.
5) Devices for controlling temperature, as fermentation generates or requires heat.
6) Sensors and controls for maintaining the optimal pH for microbial growth
This document discusses scaling up animal cell and microbial production processes from small to large scale. Key points include:
1. Maintaining optimal physiological conditions as processes are scaled up from small to large bioreactors.
2. Factors that must be considered when scaling up include the fermentor/bioreactor system, agitation, pH, temperature, and dissolved oxygen levels.
3. Scaling up usually occurs gradually in 10x increments from 1L to 10,000L bioreactors. Limiting factors include oxygen supply, shear damage from mixing, and toxic metabolite build up.
Similar to BiS2C: Lecture 11: Microbial Growth and Functions (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Talk by Jonathan Eisen for LAMG2022 meetingJonathan Eisen
The document discusses the history of the Lake Arrowhead Microbial Genomes (LAMG) conference. It reveals that LAMG2020 was cancelled due to a secret plan by organizers who formed an "anti-karyote society" that hates eukaryotes. The meeting was to be renamed the "Big, Large, Enormous" meeting of the Lake Arrowhead Big Large Enormous Anti-Karyote Society. The document also hints that several past LAMG speakers have made cryptic comments indicating involvement in a conspiracy surrounding the conference.
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Phylogenetic and Phylogenomic Approaches to the Study of Microbes and Microbi...Jonathan Eisen
The document discusses Jonathan Eisen's work as a microbiology professor at UC Davis. It provides an overview of his research topics, which include microbial phylogenomics and evolvability, phylogenetic methods and tools, and using phylogenomics to study microbial communities and interactions between microbes and hosts under stress. The document also acknowledges collaborators and funding sources for Eisen's research over the years.
This document summarizes a class on detecting, quantifying, and tracking variations of SARS-CoV-2 RNA from COVID-19 samples. It discusses using quantitative RT-PCR (qRT-PCR) to detect and measure viral RNA levels in samples. Sequencing is used to identify variations in the viral genome over time, and online tools like Nextstrain allow viewing the evolution and global transmission of variants. Genotyping assays are also described that can rapidly screen samples for known single nucleotide variations during PCR.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 8 - COVID RNA DetectionJonathan Eisen
This document summarizes a class on SARS-CoV-2 RNA detection, quantification, and variation. It discusses how qRT-PCR is used to detect and quantify the virus by amplifying and detecting viral RNA. It also covers sequencing to identify variants, how variants evolve over time, and genotyping assays that can screen samples for known single nucleotide variations. Nextstrain and other online tools are presented that use sequencing data to analyze viral phylogenies, track variant distributions globally, and visualize genetic variations across the SARS-CoV-2 genome.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms for those who already suffer from conditions like depression and anxiety.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 5 - COVID VaccinesJonathan Eisen
The document discusses a class on COVID-19 vaccines. It covers topics like vaccine development, current candidates, delivery challenges, and comparisons between vaccines. Moderna and Pfizer mRNA vaccines are highlighted as being similar but having some differences in mRNA region, nanoparticle structure/synthesis, dosage amount, and storage temperature requirements. Other vaccines discussed include Novavax using spike protein nanoparticles, and AstraZeneca and Johnson & Johnson using DNA for spike protein delivered by a modified virus.
EVE198 Winter2020 Class 9 - COVID TransmissionJonathan Eisen
This document discusses modes of SARS-CoV-2 transmission including droplets, aerosols, and surfaces. It emphasizes that surfaces are not as big a risk as initially thought. It provides guidance on limiting transmission from different modes such as distancing, masks, washing hands, cleaning surfaces, and improving ventilation. The focus in 2021 is on droplets and aerosols rather than surfaces.
EVE198 Fall2020 "Covid Mass Testing" Class 8 VaccinesJonathan Eisen
This document discusses a class on vaccines for COVID-19. It covers topics like vaccine development, current candidate vaccines, challenges with vaccine distribution, and how vaccines are being assessed for safety, effectiveness, costs and production feasibility. Over 100 vaccine candidates are in development using platforms like DNA, RNA, viral vectors and inactivated viruses. Efforts like Operation Warp Speed are coordinating development of nucleic acid, viral vector and protein subunit vaccines. Distribution challenges include vaccine production, storage and logistics, number of doses required, and overcoming vaccine nationalism and hesitancy.
EVE198 Fall2020 "Covid Mass Testing" Class 2: Viruses, COIVD and TestingJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Fall2020 "Covid Mass Testing" Class 1 IntroductionJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 11:
Microbial Growth and Functions
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1
2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Where we are going and where we have been
• Previous Lecture:
!10: Not a Tree
• Current Lecture:
!11: Microbial Growth and Functions
• Next Lecture:
!12: Symbiosis
2
3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• What are the ranges of conditions in which
life on Earth lives?
• What are the ranges of conditions in which
life on Earth prefers to live?
• What are the key ways that living systems
acquire carbon and energy?
3
4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Key Concepts and Topics
• Culturing
• Extremophily
!Thermophiles
!Halophiles
• Trophies
• Oxygen
• More on organelles
4
5. Culturing
• Culturing (or cultivation) is the growth of microorganisms
in controlled or defined conditions.
• A pure culture (which is the ideal if possible) is one in
which only one type of microbe is present
!5
6. General approach to culturing
! Collect sample
! Make an environment with specific growth conditions
" Energy
" Electrons
" Carbon
" Other conditions (e.g., O2, temperature, salt, etc)
! Dilution/passaging until one obtains a “pure” sample
with just a single clone
!6
11. Examples of Benefits of Culturing:
• Allows one to connect processes and properties to single
types of organisms
• Enhances ability to do experiments from genetics, to
physiology to genomics
• Provides possibility of large volumes of uniform material
for study
• Can supplement appearance based classification with
other types of data.
!11
15. Figure 26.14 What Is the Highest Temperature Compatible with Life?
!15
Some prokaryotes can survive at temperatures above the 120°C
threshold of sterilization.
1. Seal samples of unidentified, iron-reducing, thermal vent prokaryotes in tubes with a medium
containing Fe3+ as an electron acceptor. Control tubes contain Fe3+ but no organisms.
2. Hold both tubes in a sterilizer at 121°C for 10 hours. if the iron-reducing organisms are metabolically
active, they will reduce the Fe3+ to Fe2+ (as magnetite, which can be detected with a magnet).
Archaea of “Strain 121” can survive at temperatures above the
previously defined sterilization limit.
16. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
17. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
18. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
19. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
1 2 3 4
60° 70° 80° 90°
3h 3h 3h 3h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time
23. Optimal growth temperature (OGT) for Different Species
!21
A > B >> E
Mesophile Optimum at 15-45 °C
Thermophile Optimum at 45-80°C
Hyperthermophile Optimum at > 80°C
24. Hug et al 2016
!22
Hug et al. 2016 Tree of Life
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
25. Hug et al 2016
!24
Thermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios
that would account for this
pattern of presence of
thermophily across the
Tree of Life?
26. Thermophile Adaptations
!30
Stresses of High
Temperature
Examples of common
adaptations
Denatures proteins, RNA
and DNA
Make proteins more
stable
Speeds up reactions Slow down enzyme rates
Liquifies membranes Decrease fluidity of
membranes
27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Example 1: Extreme Halophiles
31
28. Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
29. Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
30. Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
31. Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
1 2 3 4
1M 2M 3M 4M
3h 3h 3h 3h
32. Growth vs. Time
Plot Growth vs. Time for Each Condition
!33
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
1M 2M 3M 4M
Time Elapsed
DensityofGrowth
35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigments – very visible
• Have been found at
pH up to 11.5.
• Unusual adaptations
to high salt,
desiccation
• Many have
bacteriorhodopsin
which uses energy of
light to synthesize ATP
(photoheterotrophs)
36
36. Hug et al 2016
!38
Extreme Halophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios
that would account for this
pattern of presence of
halophily across the Tree
of Life?
37. • Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
Halophile adaptations
!39
H20
38. • Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
• Halophile adaptations
! Increased osmolarity inside cell
" Proteins
" Carbohydrates
" Salts
! Membrane pumps
! Desiccation resistance
Halophile adaptations
!40
H20
H20
39. • Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
• Halophile adaptations
! Increased osmolarity inside cell
" Proteins
" Carbohydrates
" Salts - only done in extremely halophilic archaea
! Membrane pumps
! Desiccation resistance
Halophile adaptations
!42
High internal salt requires ALL cellular components to be
adapted to salt, charge. For example, all proteins must
change surface charge and other properties.
40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Uses of extremophiles
!43
Type of
environment
Examples Example of
mechanism of
survival
Practical Uses
High temp
(thermophiles)
Deep sea vents,
hotsprings
Amino acid
changes
Heat stable
enzymes
Low temp
(psychrophile)
Antarctic ocean,
glaciers
Antifreeze
proteins
Enhancing cold
tolerance of crops
High pressure
(barophile)
Deep sea vents,
hotsprings
Solute changes Industrial processes
High salt
(halophiles
Evaporating
pools
Incr. internal
osmolarity
Soy sauce
production
High pH
(alkaliphiles)
Soda lakes Transporters Detergents
Low pH
(acidophiles)
Mine tailings Transporters Bioremediation
Desiccation
(xerophiles)
Deserts Spore formation Freeze-drying
additives
High radiation
(radiophiles)
Nuclear reactor
waste sites
Absorption,
repair damage
Bioremediation,
space travel
41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Novozymes in Davis
44
43. Incredible diversity in forms of nutrition in bacteria and archaea
• Bacteria and archaea exhibit incredible diversity in how
they obtain nutrition (i.e., the processes by which an
they assimilates chemicals and energy and uses them for
growth)
• Generally referred to with the suffix “trophy”
• Origin: Greek -trophiā, from trophē, from trephein, to
nourish.
• Examples:
! autotrophy
! chemotrophy
! phototrophy
! heterotrophy
!46
44. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Three main components to “trophy”
45. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• E. coli • Chemo organo hetero trophy
• Chemo hetero trophy
46. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Humans? • Chemo organo hetero trophy
• Chemo hetero trophy
47. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Cyanobacteria • Photo litho auto trophy
• Photo auto trophy
48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
αProteo
Genome
Bacterial cell envelope
Cell
membrane
Genome
A Symbiosis with a Proteobacterium
49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
52
αProteo
Cell
membrane
Genome
Genome
Bacterial cell envelope
50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Does This Provide Host?
53
51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis with Free Living Cyanobacterium
54
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano
52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
55
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano
53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Does This Provide Host?
56
54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
57
55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotrophy and
chemoheterolithotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
58
56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotrophy and
chemoheterolithotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: A, B and C
59
57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Growth vs. Oxygen
60
Aerobes vs. Anaerobes
Microbes differ in their use and tolerance of oxygen.
1. Aerobes- Require oxygen
2. Anaerobes- Vary in their tolerance/ use of oxygen
Obligate anaerobes – oxygen is toxic.
Aerotolerant anaerobes – can’t
use oxygen, but are not
damaged by it.
Facultative anaerobes – don’t need
oxygen, but use it when available.
64. Simple Model Showing Some Diversification within Eukaryotes
67
A2 E1 PBT E2 B2 B3 B4A1 A3
65. 68
Suppose we built
phylogenetic trees
with different genes
from each of these
species
A2 E1 PBT E2 B2 B3 B4A1 A3
Simple Model Showing Some Diversification within Eukaryotes
66. Gene Set 1
69
A2 E1 PBT E2 B2 B3 B4A1 A3
Some Genes with
Show This Pattern
with Eukaryotes
Sister to TACK
67. Gene Set 2: Organellar Genes
70
A2 E1 PBT E2 B2 B3 B4A1 A3
Some Genes with Show
Alternative Pattern With
“Eukaryotes” Branching
within Bacteria
74. Mitochondrial Genes
78
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
The topology of the tree within
Eukaryotes is the same
regardless of which genes.
They differ in where
eukaryotes placed in the tree.
75. Another Symbioses - with a CB - Cyanobacterium
79
Archaea T PBEukaryotes CB B3 B4
77. 81
Continued Evolution - Diversification of Plants
Archaea T PBE1 CB B3 B4E2 Plants
Suppose we built
phylogenetic trees
with different genes
from each of these
species