Metabolic flux analysis
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Combined with stable isotopes and sensitive detection of advanced analytical methods, metabolic flux pathway analysis offers mechanism details.
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Proteome analysis
Proteome analysis studies the array of proteins expressed in a biological system under particular conditions. It can help understand cellular pathways and biological processes by characterizing protein complexes. Proteome analysis is also used to discover disease biomarkers for diagnostics and drug development by identifying protein expression changes. Key developments driving the field include improvements to 2D electrophoresis for separating proteins, mass spectrometry for analyzing separated proteins, and bioinformatics tools for searching protein databases. Common steps in proteome analysis involve separating proteins, digesting them into peptides, and identifying peptides and proteins using mass spectrometry techniques like MALDI-TOF-MS and ESI-Q-IT-MS.
Primary culture and cell line
Introduction
Primary Culture
Steps In Primary Culture
Isolation Of Tissue
Dissection And/Or Disaggregation
Types Of Primary Culture
Primary Explant Culture
Enzymatic Disaggregation
Mechanical Disaggregation
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Simply describe the yeast tow hybrid,where you can find definition ,principle,procedure,advantages and disadvantages .
immobilized cell reactor
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Sequence alignment
This document discusses different types of sequence alignment methods used in bioinformatics to identify similarities between DNA, RNA, and protein sequences. It describes global and local alignment, which aim to identify conserved regions across entire or local subsequences. Pairwise alignment methods like dot matrix, dynamic programming, and word methods are used to compare two sequences. Multiple sequence alignment extends this to three or more sequences, using progressive, iterative, or dynamic programming approaches to infer evolutionary relationships.
Metabolic engineering
Metabolic engineering involves redirecting enzymatic reactions in an organism to produce new compounds or improve existing ones. It focuses on intermediates or products like starch, vitamins, amino acids. Successful approaches introduce new pathways, like producing provitamin A in rice. Rate-limiting steps and multi-level modifications are important. Unexpected results can occur. Commercialization requires safety characterization. Goals include overproducing desired compounds, underproducing unwanted ones, and novel compounds. Engineering targets pathways for carbohydrates, amino acids, lipids, alkaloids, terpenoids and more. Important examples include high-lysine plants, nutritionally-improved cottonseed oil, and Golden Rice which produces beta-carotene in rice
Cell culture based vaccines
This document discusses cell culture based vaccine production. It begins by introducing different types of vaccines and traditional egg-based vaccine production methods and their limitations. It then describes the importance and advantages of cell culture based methods, including types of cells used. The key steps of the cell culture based production process are outlined, including strain selection, bulk production, purification, virus inactivation, formulation, quality control testing, and lot release. Specific cell culture based vaccines for influenza, rabies, dengue, and Ebola are discussed. The conclusion emphasizes the potential for cell culture to replace egg-based methods by producing vaccines faster and in larger quantities to meet global demand.
Bioreactor control system
This document discusses bioreactor control systems. It describes different types of control systems including manual control, automatic control, two-position controllers, proportional control, integral control, and derivative control. It explains that automatic control systems use four basic components: a measuring element, controller, final control element, and the process to be controlled. The document also summarizes different combinations of control methods, such as proportional plus integral control and proportional plus integral plus derivative control.
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Proteome analysis
Proteome analysis studies the array of proteins expressed in a biological system under particular conditions. It can help understand cellular pathways and biological processes by characterizing protein complexes. Proteome analysis is also used to discover disease biomarkers for diagnostics and drug development by identifying protein expression changes. Key developments driving the field include improvements to 2D electrophoresis for separating proteins, mass spectrometry for analyzing separated proteins, and bioinformatics tools for searching protein databases. Common steps in proteome analysis involve separating proteins, digesting them into peptides, and identifying peptides and proteins using mass spectrometry techniques like MALDI-TOF-MS and ESI-Q-IT-MS.
Primary culture and cell line
Introduction
Primary Culture
Steps In Primary Culture
Isolation Of Tissue
Dissection And/Or Disaggregation
Types Of Primary Culture
Primary Explant Culture
Enzymatic Disaggregation
Mechanical Disaggregation
Cell Line( Finite & Continuous)
Naming A Cell Line
Choosing A Cell Line
Maintenance Of Cell Line
Conclusion
reference
YEAST TWO HYBRID SYSTEM
Simply describe the yeast tow hybrid,where you can find definition ,principle,procedure,advantages and disadvantages .
immobilized cell reactor
This document discusses different methods for immobilizing whole cells, including perfusion bioreactors and biofilm formation. Perfusion bioreactors culture cells continuously over long periods by feeding fresh media and removing waste, while various separation methods like hollow fiber membranes or centrifuges keep cells in the bioreactor. Perfusion offers advantages like improved product quality, smaller reactor size, and lower costs compared to traditional fed-batch systems. The document also covers immobilizing cells through entrapment in polymers, attachment to surfaces, or passive biofilm formation on supports.
Sequence alignment
This document discusses different types of sequence alignment methods used in bioinformatics to identify similarities between DNA, RNA, and protein sequences. It describes global and local alignment, which aim to identify conserved regions across entire or local subsequences. Pairwise alignment methods like dot matrix, dynamic programming, and word methods are used to compare two sequences. Multiple sequence alignment extends this to three or more sequences, using progressive, iterative, or dynamic programming approaches to infer evolutionary relationships.
Metabolic engineering
Metabolic engineering involves redirecting enzymatic reactions in an organism to produce new compounds or improve existing ones. It focuses on intermediates or products like starch, vitamins, amino acids. Successful approaches introduce new pathways, like producing provitamin A in rice. Rate-limiting steps and multi-level modifications are important. Unexpected results can occur. Commercialization requires safety characterization. Goals include overproducing desired compounds, underproducing unwanted ones, and novel compounds. Engineering targets pathways for carbohydrates, amino acids, lipids, alkaloids, terpenoids and more. Important examples include high-lysine plants, nutritionally-improved cottonseed oil, and Golden Rice which produces beta-carotene in rice
Cell culture based vaccines
This document discusses cell culture based vaccine production. It begins by introducing different types of vaccines and traditional egg-based vaccine production methods and their limitations. It then describes the importance and advantages of cell culture based methods, including types of cells used. The key steps of the cell culture based production process are outlined, including strain selection, bulk production, purification, virus inactivation, formulation, quality control testing, and lot release. Specific cell culture based vaccines for influenza, rabies, dengue, and Ebola are discussed. The conclusion emphasizes the potential for cell culture to replace egg-based methods by producing vaccines faster and in larger quantities to meet global demand.
Bioreactor control system
This document discusses bioreactor control systems. It describes different types of control systems including manual control, automatic control, two-position controllers, proportional control, integral control, and derivative control. It explains that automatic control systems use four basic components: a measuring element, controller, final control element, and the process to be controlled. The document also summarizes different combinations of control methods, such as proportional plus integral control and proportional plus integral plus derivative control.
MULTIPLE SEQUENCE ALIGNMENT
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Methylases
This document discusses methylases, which are enzymes that add methyl groups to DNA. Specifically:
- Methylases transfer methyl groups from S-adenosylmethionine to adenine or cytosine bases within their recognition sequence on DNA. This methylation protects the DNA from restriction endonucleases.
- The methylase and restriction enzyme of a bacterial species together form the restriction-modification system, with the methylase protecting the host DNA.
- Methylases are of interest because methylation of some restriction enzyme recognition sites protects the DNA from being cleaved by that enzyme. This allows study of DNA isolated from strains expressing common methylases like Dam or Dcm.
Growth kinetics
Microbial Kinetics in Batch Culture
Culture system containing a limited amount of nutrient, which is inoculated with the microorganism. Cells grow until some component is exhausted or until the environment changes so as to inhibit growth. Biomass concentration defined in terms of cell dry weight measurements (g/l) or total cell number (cells/ml).
Lineweaver-Burke Equation.....We remember the Monod Equation
Invert…
The equation now has the form of a straight line with intercept.
Y = MX + C
By plotting as a function of
You get a straight line, where the slope is , and the y–axis intercept is .
Product Yield Coefficient
Maintenance:
Cells use energy and raw materials for two functions, production of new cells and the maintenance of existing cells. In general, consumption of materials for maintenance is small w.r.t. the amount of materials used in the synthesis of new biomass.
Generally it is assumed that the use of materials for maintenance is proportional to the amount of cells present.
Clustal
Clustal Omega is a fast and scalable program for multiple sequence alignment. It begins by producing pairwise alignments using a word-based heuristic method. It then clusters the sequences using a modified mBed distance method and k-means clustering. Finally, it generates the multiple sequence alignment using the HHAlign package, which aligns profile HMMs built from the sequences. Clustal Omega is widely considered one of the fastest online multiple sequence alignment tools.
Catalytic antibodies
Catalytic antibodies (abzymes) are monoclonal antibodies that exhibit enzymatic activity. They are produced by immunizing animals with transition state analogs that mimic the intermediate of chemical reactions. Abzymes function like enzymes by binding and stabilizing the transition state, lowering the activation energy of reactions and catalyzing them. Potential applications of abzymes include treating cancer, HIV, drug detoxification, controlling obesity, and targeting unwanted protein-protein interactions. One example is an abzyme that catalytically destroys the CD4 binding site on HIV, rendering the virus inert.
Metagenomics and it’s applications
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
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This document discusses various mechanisms for transforming and transfecting cells, including prokaryotic, eukaryotic, plant, and fungal cells. It describes the history of bacterial transformation and mechanisms such as natural competence, artificial competence using calcium chloride or electroporation, and lipofection. For eukaryotic transfection, it discusses lipofection, dendrimers, and nucleofection. It also outlines various mechanisms for transforming plants, including Agrobacterium, electroporation, viral transformation, and particle bombardment.
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History
Why are the transgenic animals being produced
Transgenic mice
Mice: as model organism
Methods of creation of transgenic mice
knock-out mice
Application of transgenic mice
Conclusion
References
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Protein-protein interactions are important for many biological processes. There are various types of interactions depending on their composition and duration. Methods to study interactions include yeast two-hybrid, co-immunoprecipitation, affinity chromatography, and chromatin immunoprecipitation. Databases such as IntAct and MINT provide repositories for protein interaction data.
Cell disruption methods
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Metabolic engineering
This document discusses metabolic engineering and summarizes key points about manipulating metabolic pathways in organisms. Metabolic engineering involves genetically modifying organisms to modulate their metabolism and produce desired products. It can be done by directly manipulating genes encoding enzymes in pathways or indirectly altering regulatory pathways. The document outlines several approaches to metabolic engineering, including overexpressing rate-limiting enzymes, inhibiting competing pathways, and expressing heterologous genes from other organisms. It also summarizes applications of metabolic engineering for producing amino acids, antibiotics, and manipulating plant metabolism to create foods with improved nutrients or biofuel properties.
Functional proteomics, methods and tools
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Secondary protein structure prediction
Secondary structure prediction tools analyze a protein's amino acid sequence to predict its 3D structure and function. These tools use various methods like Chou-Fasman, GOR, neural networks, and hidden Markov models to identify alpha helices and beta sheets based on characteristics like residue propensity values, sequence homology, and patterns in windows of amino acids. Accurate prediction of secondary structure is important for determining a protein's tertiary structure and biological role.
Multiple sequence alignment
Multiple sequence alignment (MSA) aligns three or more biological sequences, like proteins or nucleic acids, to infer homology and evolutionary relationships. There are three main methods - dynamic programming computes an optimal alignment but has high runtime; progressive alignment first does pairwise alignments and adds sequences; iterative alignment successively improves approximations without pairwise alignments. Popular tools for MSA include Clustal W, MAFFT, MUSCLE, and T-Coffee. MSA helps detect similarities, conserved motifs, and structural homologies between sequences.
Cell culture based vaccine
Cell culture based vaccine??
Cell cultures involve growing cells in a culture dish, often with a supportive growth medium. A primary cell culture consists of cells taken directly from living tissue, and may contain multiple types of cells such as fibroblasts, epithelial, and endothelial cells.
In the United States, 10 different vaccines for chicken pox, hepatitis A, polio, rabies, and rubella are cultured on aborted tissue from two fetal cell lines known as WI-38 and MRC-5. These vaccines are chicken pox, hep-A, hep-A, hep-A/hep-B, polio, rabies, rubella, measles/rubella, mumps/rubella, and MMR II (measles/mumps/rubella).
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Cell disruption is the process of breaking open cell walls to extract intracellular fluid and components without damaging them. The goal is an effective disruption while keeping products active. Methods include mechanical techniques like bead beating, blending, and homogenization which use physical force. Non-mechanical techniques involve freeze-thawing, osmotic shock, chemicals, enzymes, or electricity to disrupt cell walls and membranes in different ways. The optimal method depends on cell type and desired outcome.
Comparative genomics
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what is scale up ?
Lab scale, Pilot scale, Industrial scale
Bioreactor scale up process
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Sequence alig Sequence Alignment Pairwise alignment:-
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
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This document discusses multiple sequence alignment techniques. It begins with definitions of key terms like homology, similarity, and conservation. It then describes pairwise alignment and its applications. The rest of the document focuses on multiple sequence alignment methods like progressive alignment, iterative refinement, tree alignment, star alignment, and using genetic algorithms. It provides examples and explanations of popular multiple sequence alignment tools like Clustal W and T-Coffee.
Methylases
This document discusses methylases, which are enzymes that add methyl groups to DNA. Specifically:
- Methylases transfer methyl groups from S-adenosylmethionine to adenine or cytosine bases within their recognition sequence on DNA. This methylation protects the DNA from restriction endonucleases.
- The methylase and restriction enzyme of a bacterial species together form the restriction-modification system, with the methylase protecting the host DNA.
- Methylases are of interest because methylation of some restriction enzyme recognition sites protects the DNA from being cleaved by that enzyme. This allows study of DNA isolated from strains expressing common methylases like Dam or Dcm.
Growth kinetics
Microbial Kinetics in Batch Culture
Culture system containing a limited amount of nutrient, which is inoculated with the microorganism. Cells grow until some component is exhausted or until the environment changes so as to inhibit growth. Biomass concentration defined in terms of cell dry weight measurements (g/l) or total cell number (cells/ml).
Lineweaver-Burke Equation.....We remember the Monod Equation
Invert…
The equation now has the form of a straight line with intercept.
Y = MX + C
By plotting as a function of
You get a straight line, where the slope is , and the y–axis intercept is .
Product Yield Coefficient
Maintenance:
Cells use energy and raw materials for two functions, production of new cells and the maintenance of existing cells. In general, consumption of materials for maintenance is small w.r.t. the amount of materials used in the synthesis of new biomass.
Generally it is assumed that the use of materials for maintenance is proportional to the amount of cells present.
Clustal
Clustal Omega is a fast and scalable program for multiple sequence alignment. It begins by producing pairwise alignments using a word-based heuristic method. It then clusters the sequences using a modified mBed distance method and k-means clustering. Finally, it generates the multiple sequence alignment using the HHAlign package, which aligns profile HMMs built from the sequences. Clustal Omega is widely considered one of the fastest online multiple sequence alignment tools.
Catalytic antibodies
Catalytic antibodies (abzymes) are monoclonal antibodies that exhibit enzymatic activity. They are produced by immunizing animals with transition state analogs that mimic the intermediate of chemical reactions. Abzymes function like enzymes by binding and stabilizing the transition state, lowering the activation energy of reactions and catalyzing them. Potential applications of abzymes include treating cancer, HIV, drug detoxification, controlling obesity, and targeting unwanted protein-protein interactions. One example is an abzyme that catalytically destroys the CD4 binding site on HIV, rendering the virus inert.
Metagenomics and it’s applications
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Transformation and transfection
This document discusses various mechanisms for transforming and transfecting cells, including prokaryotic, eukaryotic, plant, and fungal cells. It describes the history of bacterial transformation and mechanisms such as natural competence, artificial competence using calcium chloride or electroporation, and lipofection. For eukaryotic transfection, it discusses lipofection, dendrimers, and nucleofection. It also outlines various mechanisms for transforming plants, including Agrobacterium, electroporation, viral transformation, and particle bombardment.
Transgenic mice
Introduction
Definition
History
Why are the transgenic animals being produced
Transgenic mice
Mice: as model organism
Methods of creation of transgenic mice
knock-out mice
Application of transgenic mice
Conclusion
References
Protein protein interaction
Protein-protein interactions are important for many biological processes. There are various types of interactions depending on their composition and duration. Methods to study interactions include yeast two-hybrid, co-immunoprecipitation, affinity chromatography, and chromatin immunoprecipitation. Databases such as IntAct and MINT provide repositories for protein interaction data.
Cell disruption methods
This document discusses various methods for cell disruption to release intracellular products, including physical methods like ultrasonication, osmotic shock, heat shock, and high pressure homogenization. It also covers chemical methods using alkalis, organic solvents, and detergents, as well as enzymatic methods using lysozyme. Several factors influence the effectiveness of these disruption techniques.
Metabolic engineering
This document discusses metabolic engineering and summarizes key points about manipulating metabolic pathways in organisms. Metabolic engineering involves genetically modifying organisms to modulate their metabolism and produce desired products. It can be done by directly manipulating genes encoding enzymes in pathways or indirectly altering regulatory pathways. The document outlines several approaches to metabolic engineering, including overexpressing rate-limiting enzymes, inhibiting competing pathways, and expressing heterologous genes from other organisms. It also summarizes applications of metabolic engineering for producing amino acids, antibiotics, and manipulating plant metabolism to create foods with improved nutrients or biofuel properties.
Functional proteomics, methods and tools
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Secondary protein structure prediction
Secondary structure prediction tools analyze a protein's amino acid sequence to predict its 3D structure and function. These tools use various methods like Chou-Fasman, GOR, neural networks, and hidden Markov models to identify alpha helices and beta sheets based on characteristics like residue propensity values, sequence homology, and patterns in windows of amino acids. Accurate prediction of secondary structure is important for determining a protein's tertiary structure and biological role.
Multiple sequence alignment
Multiple sequence alignment (MSA) aligns three or more biological sequences, like proteins or nucleic acids, to infer homology and evolutionary relationships. There are three main methods - dynamic programming computes an optimal alignment but has high runtime; progressive alignment first does pairwise alignments and adds sequences; iterative alignment successively improves approximations without pairwise alignments. Popular tools for MSA include Clustal W, MAFFT, MUSCLE, and T-Coffee. MSA helps detect similarities, conserved motifs, and structural homologies between sequences.
Cell culture based vaccine
Cell culture based vaccine??
Cell cultures involve growing cells in a culture dish, often with a supportive growth medium. A primary cell culture consists of cells taken directly from living tissue, and may contain multiple types of cells such as fibroblasts, epithelial, and endothelial cells.
In the United States, 10 different vaccines for chicken pox, hepatitis A, polio, rabies, and rubella are cultured on aborted tissue from two fetal cell lines known as WI-38 and MRC-5. These vaccines are chicken pox, hep-A, hep-A, hep-A/hep-B, polio, rabies, rubella, measles/rubella, mumps/rubella, and MMR II (measles/mumps/rubella).
Cell disruption
Cell disruption is the process of breaking open cell walls to extract intracellular fluid and components without damaging them. The goal is an effective disruption while keeping products active. Methods include mechanical techniques like bead beating, blending, and homogenization which use physical force. Non-mechanical techniques involve freeze-thawing, osmotic shock, chemicals, enzymes, or electricity to disrupt cell walls and membranes in different ways. The optimal method depends on cell type and desired outcome.
Comparative genomics
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
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what is scale up ?
Lab scale, Pilot scale, Industrial scale
Bioreactor scale up process
Upstream process
Lecture 3 bioprocess control
This document discusses bioprocess control for cell cultivation systems. It covers various parameters that are measured for control, including cell inputs and outputs, substrate levels, oxygen, carbon dioxide, temperature, pH, dissolved oxygen, and foam. Sensors used for online measurement of these parameters in bioreactors are also outlined. The document then describes basic feedback loops and controllers for bioprocess control, including PID and model predictive control. It concludes with an overview of using a supervisory control and data acquisition (SCADA) system connected over Ethernet for monitoring and controlling bioreactor systems.
Sequence alig Sequence Alignment Pairwise alignment:-
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
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Sequence alig Sequence Alignment Pairwise alignment:-
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Metabolomics aims to quantify all metabolites in a cellular system. The challenges are chemical complexity and heterogeneity of metabolites, dynamic range of measurements, and throughput. Metabolites can be analyzed using spectroscopy and mass spectrometry coupled with gas or liquid chromatography. NMR provides information on metabolites directly from biofluids with little sample preparation. GC-MS and LC-MS are commonly used, with LC-MS measuring a broader range of primary and secondary metabolites. Data integration and identification of specific metabolites remain challenges.
Metabolomics-II.pdf
Introduction to proteomics, techniques to study proteomics such as protein electrophoresis, chromatography and mass spectrometry and protein database analysis, case studies derived from scientific literature including comparisons between healthy and diseased tissues, new approaches to analyse metabolic pathways, comprehensive analysis of protein-protein interactions in different cell types.
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The interplay between liver metabolising enzymes and transporters is a complex process. To address this, Ms. Neuhoff together with other experts in the field published a white paper on the mechanistic framework for in vitro–in vivo extrapolation of liver membrane transporters and their interplay with liver metabolizing enzymes. Read more about the methods used and conclusions in the whitepaper below: "A Mechanistic Framework for In Vitro–In Vivo Extrapolation of Liver Membrane Transporters: Prediction of Drug–Drug Interaction Between Rosuvastatin and Cyclosporine": http://bit.ly/Slideshare_NeuhoffWP
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On the basis of the experimental data we suggest that the differences discovered in certain amino acids concentrations in blood plasma, red blood cells and tumors are criteria in early diagnostics of primary cancerous growth as well as in estimation of the efficacy of specific cancer treatment. Clinical studies on biological fluids and tumors of 1,495 patients with cancer of the mammary gland, lungs, prostate, ovaries, bladder or digestive tract showed significant changes in physiological concentrations of amino acids which either directly or indirectly regulate processes of antitumor response, oncogenesis, immunogenesis and apoptosis were shown. Our strategy of application of amino acids as medicinal preparations includes a targeted effect on the functional and metabolic relationships which are changed in specific pathology through the effect on the regulatory mechanisms of intermediate metabolic reactions, limiting stages of metabolic flows, utilization of energy substrates and transport systems restricting the processes of amino acids pool formation. The creation methodology of pathogenetic compositions of amino acids and their derivatives on the basis of their physiological concentration for practical application of their regulatory effects in oncology was discussed.Intern Report
Tushar Singh Soam submitted a project report on systematically evaluating methods for integrating transcriptome data into kinetic models of metabolic pathways. The report describes:
1) Using a cancer glycolysis model as a base model to integrate transcriptomics data and evaluate the methodology. Comparing in vivo and in silico steady states showed the model predicted metabolite concentrations with over 80% accuracy.
2) Integrating gene expression data from various sources transformed the cancer model into one representing a normal cell, and comparing metabolite levels to a human database achieved 70% accuracy.
3) Analysis found inter-level data integration can provide erroneous results and should be avoided until data are compatible at the respective level. The project evaluated approaches
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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.
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Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
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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.
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https://ashpc.eu/
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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.
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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 skillsRecently uploaded (20)
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8.Isolation of pure cultures and preservation of cultures.pdf
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ESR spectroscopy in liquid food and beverages.pptx
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Cytokines and their role in immune regulation.pptx
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bordetella pertussis.................................ppt
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Metabolic flux analysis
- 1. metabolic flux analysis • As one of the fundamentals of metabolic engineering, metabolic flux analysis (MFA) has been widely used to quantify intracellular metabolic fluxes in wild type and engineered mutant type over the past three decades. It is an experimental fluxomics widely used to examine production and consumption rates of metabolites in a biological system. • Combined with stable isotopes and sensitive detection of advanced analytical methods, metabolic flux pathway analysis offers mechanism details. With the help of stable isotopes like 2H. 13C and 15N, flux analysis offers unique opportunity for establishing metabolic routes unambiguously and determining the generation and consumption rates of metabolites. Cells or animal models are supplied with 2H, 13C or 15N isotope-labeled substrates and the formed isotope-labeled metabolites can be analyzed to derive detailed information about pathways and fluxes. Because flux analysis can offer detailed information about metabolomics pathway, it is of great interest to do metabolite flux analysis on different pathways.
- 2. • Variations in metabolic pathway fluxes that result from genetic or environmental effects can be quantified through MFA. The MFA result will give clues to the regulation of metabolic pathways and may provides insights into new targets for further metabolic engineering. Various methods of MFA are available, such as stoichiometric MFA, dynamic metabolic flux analysis, isotopic non-stationary metabolic flux analysis. Each method has its own advantages and limitations. Among these approaches, 13C-based metabolic flux analysis has been developed as a standard tool and has been widely used for quantitative pathway characterization of diverse biological systems. To implement 13C-based metabolic flux analysis properly, it is of great importance to understand the underlying mathematical and computational modeling fundamentals and analytical measurements.
- 3. • If the various metabolic pathways inside the cell are regarded as highways, MFA is similar to drafting a traffic report describing the flow across these highways and how they change in response to detour or roadblock. By comparing flux maps obtained under different experimental conditions or in the presence of targeted genetic mutation provides a functional readout on the comprehensive impact of these perturbations have on cell metabolism, which is crucial for understanding how metabolic pathways are regulated in normal cells—and how they become out of order in diseased cells. Furthermore, it enables us to point out crucial metabolic points that can be manipulated to enhance production rates or to restore unhealthy cells to normal metabolic function. • Herein, Creative proteomics develops a novel metabolic flux analysis platform. What is important is that this platform allows for the determination of control structure and regulation network of the metabolic pathway. Our approach is composed of several integrated quantitative methodologies, including a detailed computational dynamic model accounting for regulatory interactions. This analytical platform is widely applicable to any metabolic system that can be depicted by kinetic modeling. The advantage of our platform is that it includes regulatory information crucial for understanding dynamic systems. For example, in response to energy demand, heart is constantly changing. The platform is a good choice to account for time-dependent behavior of heart function. The application of this platform could also give insight into mechanisms underlying cardiac contractile disorder.