This document discusses various aspects of metabolomics. It defines metabolomics as the comprehensive study of small molecule metabolites in biological systems. It discusses the differences between targeted and untargeted metabolomics approaches. It also addresses experimental design considerations for metabolomics studies, including the importance of randomizing samples, keeping sample preparation simple, and organizing metadata and raw data. Minimum reporting standards are outlined for sampling protocols, extraction procedures, chromatography separation methods, and mass spectrometry parameters.
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.
Publication - Alternative Surfactants for Improved Efficiency of In Situ Tryp...Nathan Marshall
This document summarizes a study investigating the use of alternative surfactants to improve the efficiency of in situ tryptic proteolysis of fingermarks. The study tested a range of non-ionic and anionic surfactants individually and in combination, including MEGA-8, OcGlu, OcThio, DDM, and RapiGest SF. Data demonstrated that higher percentages of MEGA-8 as well as combinations of detergents resulted in more peptide peaks detected from fingermarks. RapiGest SF, normally used for solution digestions, was also shown to improve in situ proteolysis. Similar results were observed on rat brain tissue sections. Overall, the study indicates that surfactants can enhance the efficiency
GenoMass is software that analyzes LC-MS/MS data to identify the exact location of adducts in modified oligonucleotides. It utilizes a client-server architecture and "reversed pseudo-combinatorial" approach. The document demonstrates GenoMass' ability to correctly identify monoadducted positional isomers of an oligonucleotide modified with N-acetoxy-N-acetyl-2-aminofluorene and N-hydroxy-4-aminobiphenyl through analysis of LC-MS/MS data using a monolithic poly(styrene divinylbenzene) column coupled to an ion trap mass spectrometer.
This document summarizes research on sortase enzymes. Sortases are bacterial transpeptidase enzymes that covalently attach secreted proteins to the bacterial cell wall. They play important roles in virulence and pathogenesis. The document discusses various classes of sortases, their mechanisms of action, roles in antibiotic resistance and biofilm formation. It also outlines applications of sortases in areas like vaccine development, drug targeting, and protein immobilization. Overall, the document provides an overview of the sortase enzyme family and their significance in microbial physiology and disease.
The document discusses metabolomics data analysis and issues for biostatistics. It describes the metabolomics pipeline from experimental design and data acquisition to statistical analysis and biological interpretation. Key aspects covered include data preprocessing methods, exploratory and supervised multivariate analysis, and biological interpretation tools like metabolic network inference and pathway analysis. Specific statistical challenges in metabolomics like handling non-detects and exploring variable importance are also addressed.
Foodomics - the application of advanced omics technologies to understand the molecular and genetics level in food and correleate with nutrition and authenticationn purposes. (getnet)
Collagen hybridizing peptides (CHPs) can preferentially target denatured collagen strands and have applications in diagnostics, drug delivery, and regenerative medicine. While triple helical CHPs have high serum stability, monomeric CHPs that can bind denatured collagen have yet to be tested for serum stability. This study finds that monomeric CHPs containing the (GPO)n collagen motif are resistant to endopeptidase activity but subject to exopeptidase degradation. N-terminal modification of monomeric CHPs suppresses this degradation, resulting in high serum stability comparable to triple helical CHPs. An IR680-labeled CHP conjugate used for in vivo imaging showed similar tissue binding patterns
This document discusses various aspects of metabolomics. It defines metabolomics as the comprehensive study of small molecule metabolites in biological systems. It discusses the differences between targeted and untargeted metabolomics approaches. It also addresses experimental design considerations for metabolomics studies, including the importance of randomizing samples, keeping sample preparation simple, and organizing metadata and raw data. Minimum reporting standards are outlined for sampling protocols, extraction procedures, chromatography separation methods, and mass spectrometry parameters.
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.
Publication - Alternative Surfactants for Improved Efficiency of In Situ Tryp...Nathan Marshall
This document summarizes a study investigating the use of alternative surfactants to improve the efficiency of in situ tryptic proteolysis of fingermarks. The study tested a range of non-ionic and anionic surfactants individually and in combination, including MEGA-8, OcGlu, OcThio, DDM, and RapiGest SF. Data demonstrated that higher percentages of MEGA-8 as well as combinations of detergents resulted in more peptide peaks detected from fingermarks. RapiGest SF, normally used for solution digestions, was also shown to improve in situ proteolysis. Similar results were observed on rat brain tissue sections. Overall, the study indicates that surfactants can enhance the efficiency
GenoMass is software that analyzes LC-MS/MS data to identify the exact location of adducts in modified oligonucleotides. It utilizes a client-server architecture and "reversed pseudo-combinatorial" approach. The document demonstrates GenoMass' ability to correctly identify monoadducted positional isomers of an oligonucleotide modified with N-acetoxy-N-acetyl-2-aminofluorene and N-hydroxy-4-aminobiphenyl through analysis of LC-MS/MS data using a monolithic poly(styrene divinylbenzene) column coupled to an ion trap mass spectrometer.
This document summarizes research on sortase enzymes. Sortases are bacterial transpeptidase enzymes that covalently attach secreted proteins to the bacterial cell wall. They play important roles in virulence and pathogenesis. The document discusses various classes of sortases, their mechanisms of action, roles in antibiotic resistance and biofilm formation. It also outlines applications of sortases in areas like vaccine development, drug targeting, and protein immobilization. Overall, the document provides an overview of the sortase enzyme family and their significance in microbial physiology and disease.
The document discusses metabolomics data analysis and issues for biostatistics. It describes the metabolomics pipeline from experimental design and data acquisition to statistical analysis and biological interpretation. Key aspects covered include data preprocessing methods, exploratory and supervised multivariate analysis, and biological interpretation tools like metabolic network inference and pathway analysis. Specific statistical challenges in metabolomics like handling non-detects and exploring variable importance are also addressed.
Foodomics - the application of advanced omics technologies to understand the molecular and genetics level in food and correleate with nutrition and authenticationn purposes. (getnet)
Collagen hybridizing peptides (CHPs) can preferentially target denatured collagen strands and have applications in diagnostics, drug delivery, and regenerative medicine. While triple helical CHPs have high serum stability, monomeric CHPs that can bind denatured collagen have yet to be tested for serum stability. This study finds that monomeric CHPs containing the (GPO)n collagen motif are resistant to endopeptidase activity but subject to exopeptidase degradation. N-terminal modification of monomeric CHPs suppresses this degradation, resulting in high serum stability comparable to triple helical CHPs. An IR680-labeled CHP conjugate used for in vivo imaging showed similar tissue binding patterns
Proteome-wide covalent ligand discovery in native biological systemsMegha Majumder
The document describes a new method for finding drug candidates that bind to specific proteins called isoTOP-ABPP. It involves applying small molecule fragments that covalently bind to cysteine amino acids on proteins. This allows researchers to detect which proteins the fragments bind to. They tested a library of these fragments on cancer cell proteins and found they bound to over 750 cysteines on more than 600 proteins, including some previously considered undruggable. Further experiments showed some fragments could selectively target and inhibit certain proteins like IDH1/2 and label inactive pro-forms of proteins like caspase-8, but not the active forms.
METABOLOMICS is the systematic study of the small molecular metabolites in a cell, tissue, biofluid, or cell culture media that are the tangible result of cellular processes or responses to an environmental stress.
1) The document summarizes research optimizing the amplification of three osteoblast gene markers (BMP2, OPN, and RUNX2) from human stem cells in exfoliated deciduous teeth (SHED) using reverse transcriptase PCR (RT-PCR).
2) Through several trials adjusting annealing temperature, time, and other PCR parameters, the researchers obtained a single clear band at the expected size on agarose gel for each gene marker.
3) The optimum PCR conditions identified for each gene were: BMP2 at 61.9°C, OPN at 63.2°C, and RUNX2 at 63.6°C.
This document provides an overview of plant proteomics techniques, including 2D gel electrophoresis, mass spectrometry, and software analysis. 2D gel electrophoresis separates proteins by isoelectric focusing based on pH in the first dimension, followed by SDS-PAGE based on size in the second dimension. Spots are visualized, excised, digested, and identified using mass spectrometry. Software performs matching, detection, quantitation, and annotation of protein spots across gels to identify differentially expressed proteins.
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
Sample Final Report_ Extraction of CYP microsomesEric Sudar
This document describes a proposed method to extract microsomes containing cytochrome P450 (CYP) enzymes from human liver homogenate using super-paramagnetic microspheres coated with anti-CYP2D6 antibodies. Current extraction methods require expensive centrifugation equipment not available in most forensic labs. The method aims to overcome viscosity issues when recovering the magnetic beads from liver homogenate. Bovine serum albumin is coupled to beads to determine the amount of protein coupled to the bead surface, as a proxy for quantifying antibody binding. The recovered beads will be analyzed by liquid chromatography-mass spectrometry and flow cytometry to assess anti-CYP2D6 IgG binding to CYP2D6.
The document summarizes the identification and characterization of an antimicrobial protein from the mucus of the stingray Potamotrygon cf. henlei. Through solid-phase extraction and chromatographic purification, a 16072.8 Da protein was isolated that showed antimicrobial activity against bacteria and yeast without hemolytic activity. Mass spectrometry and Edman degradation identified the protein as similar to the beta-chain of hemoglobin. Effects of the novel antimicrobial protein on the microcirculation were also evaluated. This represents the first description of a bioactive polypeptide isolated from stingray mucus.
Protein microarrays, ICAT, and HPLC protein purificationRaul Soto
The document discusses the Isotope-Coded Affinity Tag (ICAT) method for protein quantification and identification. ICAT uses chemical labeling reagents that specifically label cysteine residues. There are 4 main steps: 1) Lyse and label protein samples from two states with light and heavy ICAT tags, 2) Mix and proteolyze samples to generate peptide fragments, some tagged, 3) Isolate tagged fragments using avidin affinity chromatography, 4) Analyze isolated peptides using mass spectrometry to identify and quantify proteins between the two states. ICAT allows accurate quantification of complex protein mixtures.
The document discusses synthetic antiauxins that inhibit auxin biosynthesis. It identifies aminoethoxyvinylglycine (AVG) as the strongest synthetic antiauxin that reduces endogenous auxin (IAA) levels in both monocots and dicots. AVG directly inhibits auxin biosynthesis by blocking tryptophan aminotransferase, a key enzyme in the pathway. However, different antiauxins showed varying effects in different plant organs and species, indicating diversity in auxin biosynthesis pathways. The results provide new insights into regulating auxin biosynthesis through inhibition.
Focus on aggregation: types, causes, characterization, and impactKBI Biopharma
This document discusses protein aggregation, including types and sizes of aggregates, mechanisms of aggregation, and challenges in characterization. It summarizes sedimentation velocity and field-flow fractionation as useful analytical methods to cross-check size exclusion chromatography for characterizing aggregates. Sedimentation velocity can resolve multiple aggregate peaks but requires expertise, while field-flow fractionation has less surface interaction but high method development. No single method detects all aggregate types.
This document summarizes research purifying and characterizing a novel antioxidant peptide from the hard-shelled mussel Mytilus coruscus. Enzymatic hydrolysis was used to generate hydrolysates from M. coruscus, which were screened for antioxidant activity. The papain hydrolysate showed the highest free radical scavenging activity. Further purification using chromatography yielded a novel 10 amino acid peptide. In vitro and in vivo assays found the peptide to have potent antioxidant effects, inhibiting oxidative stress markers and enhancing antioxidant enzyme activity in mice. This is the first report of an antioxidant peptide from M. coruscus with potential anti-inflammatory properties.
This document discusses protein adducts as biomarkers of exposure to alkylating agents. It begins by introducing protein adducts and globin adducts specifically as surrogate biomarkers for DNA adducts. The document then details a research plan to test the hypothesis that globin adducts undergo degradation, producing free amino acid adducts that are excreted in urine and could serve as non-invasive biomarkers of exposure. Initial results are presented demonstrating the successful synthesis of model amino acid adducts and detection of some administered adducts and their metabolites in rat urine. Further research is planned to study the fate of native globin adducts in vivo.
Metabolomics is often described as the study of “the complete set of low molecular weight intermediates, which are context dependent, varying according to the physiology, developmental or pathological state of the cell, tissue, organ or organism”. In fact, metabolomics is a new term for an old science in which classical biochemical concepts are investigated. New and unique to the current research that is being conducted is the combination with genomics information and full system biology. In this refocus we will discuss the challenges in today's metabolomics research and how to address them
This document summarizes a study that explored using an aqueous two-phase system (ATPS) composed of polyethylene glycol (PEG) and sodium citrate to purify lectin from Canavalia grandiflora seeds. A 24 full factorial design was used to study how four factors (PEG molar mass, PEG concentration, pH, and citrate concentration) affected the partitioning of the lectin ConGF. The results showed that ConGF preferentially partitioned to the PEG-rich top phase. A system of 20% PEG 400 and 20% citrate at pH 6 allowed recovery of ConGF with an 8.67 partitioning coefficient and 104% yield, demonstrating the efficiency of this ATPS for pur
This document summarizes research aiming to understand the functional connection between a magnesium ion (Mg2+) and aspartate 101 (D101) in the active site of alkaline phosphatase (AP), which are separated by over 7 angstroms. The researchers used site-directed mutagenesis to design mutants potentially disrupting a pathway between these residues. Mutants were expressed in E. coli and purified to measure reaction rates. Preliminary data suggests redundancy between Mg2+ and D101 occurs through residue D51, potentially connecting them. The researchers tested this model by mutating D51 and measuring effects on redundancy between Mg2+ and D101. Understanding these interactions provides insight into AP's catalytic strategy and enzyme mechanisms more broadly.
1) The document discusses using NMR spectroscopy to analyze the metabolic profiles of clam mantle tissue and cultured lung epithelial cells. Spectra of extracts from different regions of clam mantle and control vs. cigarette smoke-exposed cells were obtained.
2) Glyceraldehyde and glucose levels were able to be quantified and showed differences between tissue and cell types. Glyceraldehyde levels suggested cigarette smoke exposure induced distress in lung cells.
3) Further identification of metabolites was needed using additional database comparisons to fully characterize the metabolic profiles obtained via NMR spectroscopy. Improvements were also needed in cell and tissue collection methods to better preserve metabolite levels.
This document discusses advances in protein technology. It defines different types of proteins like plant-derived, animal-derived, and microbial proteins. It describes the functions of proteins in the body like growth, enzymatic reactions, hormone regulation, fluid balance, and more. It also discusses characteristics of proteins like amino acid composition, size, shape, charge, solubility, and stability. Methods for purifying and characterizing proteins like chromatography and mass spectrometry are also summarized.
High Throughput Screening for Glycogen and PolyglucosanBen Decker
This document discusses high throughput screening (HTS) for identifying compounds that modulate glycogen and polyglucosan. HTS uses robotics, liquid handling devices, and detectors to quickly test thousands of compounds. The researcher has prepared an assay to observe changes in glycogen quality and quantity using limited digestion and staining. Mouse fibroblasts with genetic defects resulting in low glycogen branching enzyme activity and no polyglucosan are being used. Currently, 1700 FDA-approved compounds are being tested in triplicates using an automated assay to identify potential modulators of glycogen and polyglucosan pathways.
Plant metabolomics allows for comprehensive analysis of small molecule metabolites in plants. Key techniques used in plant metabolomics include nuclear magnetic resonance spectroscopy (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and direct analysis in real time-mass spectrometry (DART-MS). These techniques provide global profiling of metabolites and structural information to further understand plant physiology and metabolism.
This document discusses materials and methods used in a study involving the chemical fipronil and zinc. Twenty male albino rats were divided into four groups of five rats each: a control group, a zinc group that received zinc supplementation, a fipronil group exposed to the insecticide fipronil, and a combination group exposed to both zinc and fipronil. Biochemical assays were conducted to assess oxidative stress markers like superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, glutathione, lipid peroxidation, and total protein in the rats. Chemicals used including fipronil and zinc sulfate were obtained from reputable suppliers. Kits for the biochemical assays were purchased from a diagnostic
Proteomics of small proteins from plant tissuesExpedeon
Small genes and the proteins that they encode can play important biological roles including signaling, development, and mediation of plant-microbe interactions in organisms ranging from bacteria to plants to mammals (Frith et al.; Basrai et al.; Galindo et al.; Hemm et al. 2008, 2010; Kastenmeyer et al.). However, genes that encode proteins containing <100 residues are difficult to identify reliably solely by DNA sequence analysis (Dinger et al.)
Proteome-wide covalent ligand discovery in native biological systemsMegha Majumder
The document describes a new method for finding drug candidates that bind to specific proteins called isoTOP-ABPP. It involves applying small molecule fragments that covalently bind to cysteine amino acids on proteins. This allows researchers to detect which proteins the fragments bind to. They tested a library of these fragments on cancer cell proteins and found they bound to over 750 cysteines on more than 600 proteins, including some previously considered undruggable. Further experiments showed some fragments could selectively target and inhibit certain proteins like IDH1/2 and label inactive pro-forms of proteins like caspase-8, but not the active forms.
METABOLOMICS is the systematic study of the small molecular metabolites in a cell, tissue, biofluid, or cell culture media that are the tangible result of cellular processes or responses to an environmental stress.
1) The document summarizes research optimizing the amplification of three osteoblast gene markers (BMP2, OPN, and RUNX2) from human stem cells in exfoliated deciduous teeth (SHED) using reverse transcriptase PCR (RT-PCR).
2) Through several trials adjusting annealing temperature, time, and other PCR parameters, the researchers obtained a single clear band at the expected size on agarose gel for each gene marker.
3) The optimum PCR conditions identified for each gene were: BMP2 at 61.9°C, OPN at 63.2°C, and RUNX2 at 63.6°C.
This document provides an overview of plant proteomics techniques, including 2D gel electrophoresis, mass spectrometry, and software analysis. 2D gel electrophoresis separates proteins by isoelectric focusing based on pH in the first dimension, followed by SDS-PAGE based on size in the second dimension. Spots are visualized, excised, digested, and identified using mass spectrometry. Software performs matching, detection, quantitation, and annotation of protein spots across gels to identify differentially expressed proteins.
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
Sample Final Report_ Extraction of CYP microsomesEric Sudar
This document describes a proposed method to extract microsomes containing cytochrome P450 (CYP) enzymes from human liver homogenate using super-paramagnetic microspheres coated with anti-CYP2D6 antibodies. Current extraction methods require expensive centrifugation equipment not available in most forensic labs. The method aims to overcome viscosity issues when recovering the magnetic beads from liver homogenate. Bovine serum albumin is coupled to beads to determine the amount of protein coupled to the bead surface, as a proxy for quantifying antibody binding. The recovered beads will be analyzed by liquid chromatography-mass spectrometry and flow cytometry to assess anti-CYP2D6 IgG binding to CYP2D6.
The document summarizes the identification and characterization of an antimicrobial protein from the mucus of the stingray Potamotrygon cf. henlei. Through solid-phase extraction and chromatographic purification, a 16072.8 Da protein was isolated that showed antimicrobial activity against bacteria and yeast without hemolytic activity. Mass spectrometry and Edman degradation identified the protein as similar to the beta-chain of hemoglobin. Effects of the novel antimicrobial protein on the microcirculation were also evaluated. This represents the first description of a bioactive polypeptide isolated from stingray mucus.
Protein microarrays, ICAT, and HPLC protein purificationRaul Soto
The document discusses the Isotope-Coded Affinity Tag (ICAT) method for protein quantification and identification. ICAT uses chemical labeling reagents that specifically label cysteine residues. There are 4 main steps: 1) Lyse and label protein samples from two states with light and heavy ICAT tags, 2) Mix and proteolyze samples to generate peptide fragments, some tagged, 3) Isolate tagged fragments using avidin affinity chromatography, 4) Analyze isolated peptides using mass spectrometry to identify and quantify proteins between the two states. ICAT allows accurate quantification of complex protein mixtures.
The document discusses synthetic antiauxins that inhibit auxin biosynthesis. It identifies aminoethoxyvinylglycine (AVG) as the strongest synthetic antiauxin that reduces endogenous auxin (IAA) levels in both monocots and dicots. AVG directly inhibits auxin biosynthesis by blocking tryptophan aminotransferase, a key enzyme in the pathway. However, different antiauxins showed varying effects in different plant organs and species, indicating diversity in auxin biosynthesis pathways. The results provide new insights into regulating auxin biosynthesis through inhibition.
Focus on aggregation: types, causes, characterization, and impactKBI Biopharma
This document discusses protein aggregation, including types and sizes of aggregates, mechanisms of aggregation, and challenges in characterization. It summarizes sedimentation velocity and field-flow fractionation as useful analytical methods to cross-check size exclusion chromatography for characterizing aggregates. Sedimentation velocity can resolve multiple aggregate peaks but requires expertise, while field-flow fractionation has less surface interaction but high method development. No single method detects all aggregate types.
This document summarizes research purifying and characterizing a novel antioxidant peptide from the hard-shelled mussel Mytilus coruscus. Enzymatic hydrolysis was used to generate hydrolysates from M. coruscus, which were screened for antioxidant activity. The papain hydrolysate showed the highest free radical scavenging activity. Further purification using chromatography yielded a novel 10 amino acid peptide. In vitro and in vivo assays found the peptide to have potent antioxidant effects, inhibiting oxidative stress markers and enhancing antioxidant enzyme activity in mice. This is the first report of an antioxidant peptide from M. coruscus with potential anti-inflammatory properties.
This document discusses protein adducts as biomarkers of exposure to alkylating agents. It begins by introducing protein adducts and globin adducts specifically as surrogate biomarkers for DNA adducts. The document then details a research plan to test the hypothesis that globin adducts undergo degradation, producing free amino acid adducts that are excreted in urine and could serve as non-invasive biomarkers of exposure. Initial results are presented demonstrating the successful synthesis of model amino acid adducts and detection of some administered adducts and their metabolites in rat urine. Further research is planned to study the fate of native globin adducts in vivo.
Metabolomics is often described as the study of “the complete set of low molecular weight intermediates, which are context dependent, varying according to the physiology, developmental or pathological state of the cell, tissue, organ or organism”. In fact, metabolomics is a new term for an old science in which classical biochemical concepts are investigated. New and unique to the current research that is being conducted is the combination with genomics information and full system biology. In this refocus we will discuss the challenges in today's metabolomics research and how to address them
This document summarizes a study that explored using an aqueous two-phase system (ATPS) composed of polyethylene glycol (PEG) and sodium citrate to purify lectin from Canavalia grandiflora seeds. A 24 full factorial design was used to study how four factors (PEG molar mass, PEG concentration, pH, and citrate concentration) affected the partitioning of the lectin ConGF. The results showed that ConGF preferentially partitioned to the PEG-rich top phase. A system of 20% PEG 400 and 20% citrate at pH 6 allowed recovery of ConGF with an 8.67 partitioning coefficient and 104% yield, demonstrating the efficiency of this ATPS for pur
This document summarizes research aiming to understand the functional connection between a magnesium ion (Mg2+) and aspartate 101 (D101) in the active site of alkaline phosphatase (AP), which are separated by over 7 angstroms. The researchers used site-directed mutagenesis to design mutants potentially disrupting a pathway between these residues. Mutants were expressed in E. coli and purified to measure reaction rates. Preliminary data suggests redundancy between Mg2+ and D101 occurs through residue D51, potentially connecting them. The researchers tested this model by mutating D51 and measuring effects on redundancy between Mg2+ and D101. Understanding these interactions provides insight into AP's catalytic strategy and enzyme mechanisms more broadly.
1) The document discusses using NMR spectroscopy to analyze the metabolic profiles of clam mantle tissue and cultured lung epithelial cells. Spectra of extracts from different regions of clam mantle and control vs. cigarette smoke-exposed cells were obtained.
2) Glyceraldehyde and glucose levels were able to be quantified and showed differences between tissue and cell types. Glyceraldehyde levels suggested cigarette smoke exposure induced distress in lung cells.
3) Further identification of metabolites was needed using additional database comparisons to fully characterize the metabolic profiles obtained via NMR spectroscopy. Improvements were also needed in cell and tissue collection methods to better preserve metabolite levels.
This document discusses advances in protein technology. It defines different types of proteins like plant-derived, animal-derived, and microbial proteins. It describes the functions of proteins in the body like growth, enzymatic reactions, hormone regulation, fluid balance, and more. It also discusses characteristics of proteins like amino acid composition, size, shape, charge, solubility, and stability. Methods for purifying and characterizing proteins like chromatography and mass spectrometry are also summarized.
High Throughput Screening for Glycogen and PolyglucosanBen Decker
This document discusses high throughput screening (HTS) for identifying compounds that modulate glycogen and polyglucosan. HTS uses robotics, liquid handling devices, and detectors to quickly test thousands of compounds. The researcher has prepared an assay to observe changes in glycogen quality and quantity using limited digestion and staining. Mouse fibroblasts with genetic defects resulting in low glycogen branching enzyme activity and no polyglucosan are being used. Currently, 1700 FDA-approved compounds are being tested in triplicates using an automated assay to identify potential modulators of glycogen and polyglucosan pathways.
Plant metabolomics allows for comprehensive analysis of small molecule metabolites in plants. Key techniques used in plant metabolomics include nuclear magnetic resonance spectroscopy (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and direct analysis in real time-mass spectrometry (DART-MS). These techniques provide global profiling of metabolites and structural information to further understand plant physiology and metabolism.
This document discusses materials and methods used in a study involving the chemical fipronil and zinc. Twenty male albino rats were divided into four groups of five rats each: a control group, a zinc group that received zinc supplementation, a fipronil group exposed to the insecticide fipronil, and a combination group exposed to both zinc and fipronil. Biochemical assays were conducted to assess oxidative stress markers like superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, glutathione, lipid peroxidation, and total protein in the rats. Chemicals used including fipronil and zinc sulfate were obtained from reputable suppliers. Kits for the biochemical assays were purchased from a diagnostic
Proteomics of small proteins from plant tissuesExpedeon
Small genes and the proteins that they encode can play important biological roles including signaling, development, and mediation of plant-microbe interactions in organisms ranging from bacteria to plants to mammals (Frith et al.; Basrai et al.; Galindo et al.; Hemm et al. 2008, 2010; Kastenmeyer et al.). However, genes that encode proteins containing <100 residues are difficult to identify reliably solely by DNA sequence analysis (Dinger et al.)
This document describes the development of a novel fluorescent protein-based sensor for detecting 2-oxoglutarate (2OG) levels in living cells. The sensor, termed mOGsor, was created by inserting the 2OG-binding domain GAF from the NifA protein into yellow fluorescent protein (YFP). mOGsor exhibits increased fluorescence intensity upon binding to 2OG in a concentration-dependent manner. Testing showed mOGsor has high specificity for 2OG and fast kinetics. Using mOGsor, the authors were able to monitor real-time changes in 2OG levels in E. coli cells under different nutrient conditions. mOGsor represents an improvement over previous FRET-based 2OG sensors by providing a
This document summarizes a study examining the toxicity and antioxidant activity of two extracts from the brown seaweed Fucus vesiculosus. Both extracts were found to lack relevant toxic effects in acute and 4-week toxicity tests in rats. The extracts exhibited antioxidant activity in non-cellular systems by reducing oxidative stress and scavenging free radicals. They also showed antioxidant effects in activated macrophages and in the plasma and erythrocytes of rats treated with the extracts for 4 weeks, indicating their compounds may be absorbed and act as antioxidants in vivo. The findings support the view that daily consumption of one extract could benefit humans by reducing oxidative stress.
Optimization of experimental protocols for cellular lysisExpedeon
In this project, we have compared existing sample preparation methods for proteomics studies against newly developed FASP method and our in-house developed SDS-TCA protocol. For our
preliminary studies, we have chosen a very well characterized soil microbe Pseudomonas putida.
This study analyzed G proteins, proteomics, glycomics and metabolomics in plants grown under protected agriculture. Protein profiles showed variation between phenological stages, and western blot detected G protein subunits of 37, 46, and 57 kDa. Two-dimensional electrophoresis identified a 57 kDa protein with a pI of 5.9. Phloem sap proteins also detected G protein subunits of 28, 67 kDa between stages. Sugar analysis found glucose, fructose and sucrose varied between stages, with neutral sugars dominated by glucose, galactose and mannose. The Lightbourn Biochemical Model was applied to integrate results and propose bionanotechnology and biodynamic nutrition for high agricultural competitiveness and sustainability
This document summarizes a seminar on using Caco-2 monolayers to study transport across the intestinal barrier. The Caco-2 cell line spontaneously differentiates into enterocytes that form a polarized monolayer mimicking intestinal absorption. Key aspects covered include Caco-2 cell culture and characterization, permeability assays to measure transport, and applications in drug development. Validation is done using reference compounds to classify drug absorption. Considerations for biological factors and analytical methods are also discussed.
A visual chip-based coimmunoprecipitation technique for analysis of protein–p...Qing Chen
This document describes a visual chip-based coimmunoprecipitation (vChip-coIP) technique for analyzing protein-protein interactions. Key points:
1. The technique combines advantages of antibody microarrays, traditional coIP, and silver enhancement detection. Antibodies are spotted onto slides to capture interacting protein pairs from cell lysates.
2. Interactions are detected using a biotinylated antibody, colloidal gold-labeled streptavidin, and silver enhancement. This makes interaction signals visible without further processing.
3. The technique is shown to be simple, cost-effective, and efficient for comprehensive study of protein-protein interactions using small amounts of crude cell lysate.
JBEI Research Highlights Slides - October 2022SaraHarmon4
This document summarizes three research articles from the Office of Biological and Environmental Research.
The first article describes an approach to engineer permeability in microfluidic compartments, enabling sustained multi-cycle protein production in a cell-free system and enhanced environmental fitness for bacteria-enclosing compartments.
The second article examines carbon metabolism in soil by tracking stable isotope enrichment of metabolites from various carbon sources, finding profiles varied more by source than time and corresponded to differences in active microbial populations.
The third article compares performance of parallel microbiomes cultivated on sorghum, finding actinobacteria differentiated outcomes and network reconstructions revealed enzyme-linked processing stages.
Research Inventy : International Journal of Engineering and Scienceresearchinventy
Research Inventy : International Journal of Engineering and Science is published by the group of young academic and industrial researchers with 12 Issues per year. It is an online as well as print version open access journal that provides rapid publication (monthly) of articles in all areas of the subject such as: civil, mechanical, chemical, electronic and computer engineering as well as production and information technology. The Journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence. Papers will be published by rapid process within 20 days after acceptance and peer review process takes only 7 days. All articles published in Research Inventy will be peer-reviewed.
Exploring the Versatility of Micro-flow Technology – From Peptide Biomarkers ...Waters Corporation
Presenter: Corey D. Broeckling, Ph.D., Associate Director, Proteomics and Metabolomics Facility, Joint Assistant Professor, Colorado State University
Microfluidic technology offers multiple advantages including ease of use, robustness and sensitivity. Coupled with a tandem quadrupole mass spectrometer (such as the Xevo TQ-S) we can create an optimal and versatile “middle ground” platform in which these advantages can be exploited for both small molecule and peptide quantitative applications. For example, most small molecule applications are performed using standard flow chromatography (in the range of 600-100 L/min) consuming a high level of both solvent and sample which increases the cost (both fiscally and environmentally). The use of microfluidic technology for these small molecule applications can reduce solvent consumption by upwards of 150-fold and can significantly increase on-column sensitivity, thus reducing sample consumption. Conversely, quantitative peptide assays are almost exclusively performed using nanoscale chromatography (~400 nL/min) to achieve the required sensitivity for detection of these low abundance molecules within a complex matrix (e.g. serum, urine, etc.). We have found that the use of microfluidic technology for peptide quantitation yields the same or better sensitivity when compared to a nanoscale platform and has the additional, very significant advantages of ease of use, robustness, and improved chromatographic resolution (e.g. peak capacity). Thus, with a single analytical platform we can perform quantitative analysis for a wide range of compounds spanning from lipids/metabolites to peptides. One application in which the technology has struggled is the analysis of compounds in negative ionization mode. This limitation has been overcome in the development of a next generation microfluidic device that incorporates post-column addition of isopropanol to improve ionization and spray stability in negative mode applications. With this new capability we can now perform quantitative experiments in negative mode or with polarity switching.
This presentation was given at the 11th International Conference of the Metabolomics Society (Metabolomics 2015, #metsoc2015 on Twitter), June 29, 2015, in San Francisco.
In Vitro Cell Tests for Functional FoodInstitut Kurz
The relationship between the food we eat and our health is
clear. In the constant search for healthier foods rich in
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2013 - Correlating exoenzyme activities, operacional parameters, cellular viability and EPS in a MBR
1. Correlating exoenzyme activities, operational parameters,
cell viability and EPS in a membrane bioreactor treating
domestic wastewater
828
I. Amorós1, C. Grañana1, L. Borrás2, E. Zuriaga-Agustí3, A. Zornoza1 and J.L. Alonso1
1Instituto
INTRODUCTION
Universitario de Ingeniería del Agua y Medio Ambiente, (IIAMA). Universitat Politècnica de València, Spain (e-mail: jalonso@ihdr.upv.es)
2Departamento de Ingeniería Química, Universitat de València, 46100 Burjassot, Valencia, Spain
3Instituto de Seguridad Industrial, Radiofísica y Medioambiental (ISIRYM), Universitat Politècnica de València, Spain
Membrane biorreactors (MBR )systems are based on the combination of the activated sludge system and membrane technologies to separate the particulate material from water,
avoiding the need of a secondary clarifier. The main operational problem in MBRs is the membrane fouling or biofouling.
Equalization Tank
CAS
Aeration Tank
Secondary clarifier
MBR
Effluent Tank
Effluent
Water
Wastewater
Equalization Tank
Effluent Tank
Effluent
Water
Wastewater
Activated Sludge
Activated Sludge
Figure 1. Scheme of Activated Sludge and MBR treatments
Bacteria present in the biomass of an activated sludge system produce sticky compounds
denominated extracellular polymeric substances (EPS) which result from active bacterial secretion,
shed from the cell surface or cell lysis and mediate their adhesion to surfaces as the submerged
membrane module. After long time filtration of wastewater, both accumulation of EPS and amount of
microbial populations reach to maximum, which also indicate the minimum permeating capacity of a
membrane module. EPS are mainly polysaccharides, proteins, nucleic acids and lipids. Recent
studies point to EPS as the main cause of membrane fouling. Relationships between them and
operational parameters as potential foulants have been determined. Enzymatic activity is involved in
the degradation of biopolymers and cell viability gives information about cells damaged.
MATERIALS AND METHODS
Figure 2. Biofouling
Sludge Samples from a MBR treating domestic wastewater (316 m3) have been analysed for Exoenzymatic activities (β-glucuronidase and phosphatase), protein, carbohydrates
and cell viability. After that statistical analyses were carried out by using Canonical correspondance analyses (CCA), a method of direct gradient analysis.
• β-glucuronidase and phosphatase: Determined by fluorogenic substrate (ELF 97) which yields and insoluble fluorescent precipitate upon cleavage the enzyme. The spatial
distribution of enzymatic activity in whole flocs are detected by epifluorescence microscopy and quantification by using an optimization of Matlab®.
• EPS: were extracted by chemical extraction with cation exchange resin (CER) and later analyses with BCA (proteins) and anthrone (carbohydrates).
• Cell viability: Kit Backlight and fluorescence microscopy.
Table 1. Operating parameters and influent characteristics
Operational parameters and physicho-chemicals parameters were supplied by the treatment plant.
RESULTS
Range
Standard
deviation
1004
180-2326
814
HRT
56.9
47.1-65.7
6.4
OLR
0.014
0.01-0.02
0.004
mg·L-1
MLSS
9853
8232-11648
1259
mg·L-1
MLVSS
7626
6127-8796
1006.407
°C
Tr
22.0
18.3-28.4
4.0409
%
%MLVSS
77.3
74.1-80.5
2.3
pH_inf
8.1
8-8.4
0.1
mg·L-1
BOD5_inf
234
180-290
37
Parameters
Units
Excess sludge
production
Hydraulic retention time
Kg·d-1
ESP
h
Kg BOD/kg
MLVSS day
Organic loading rate
Acronym Average
Mixed liquor suspended
solids
Mixed liquor volatile
suspended solids
Temperature in reactor
Percentage of Mixed
liquor volatile
suspended solids
pH in influent
Biological oxygen
demand in influent
Chemical oxygen
demand in influent
Conductivity in influent
Figure 5. Cell viability
Figure 4. Quantification of enzymatic activity
(Matlab)
Enzymatic Activity
mg·L-1
COD_inf
521
371-636
85
µS/cm
Cond_inf
2780
2680-2830
58
Total nitrogen in influent
Total bacteria
mg l-1
TN_inf
69.6
60.1-79.7
6.2
Figure 3. Enzymatic activity
50
5
40
Phosphatase
3
30
2
20
1
10
0
0
1
2
3
4
5
6
7
8
9
10
11
12
13
Sample
Figure 6. EPS vs glucoronidase and phosphatase
activity
EPS (mg/g VSS)
% Activity
Carbohydrates
% Exoenzimatic Activity
Glucuronidase
4
Proteins
4
40
Glucoronidase
Phosphatase
30
3
20
2
10
1
0
0
1
2
3
4
5
6
7
8
9
10
11
12
13
Sample
Figure 7. Proteins and carbohydrates vs
glucoronidase and phosphatase activity
Proteins (mg BSA/g SVS)
Carbohydrates (mg Glucose/gVSS)
EPS
0,8
0,6
0,6
0,4
0,4
Tr
0,2
0
OLR
-0,2
-0,4
0,2
Phosphatase
HRT
EPS Carbohydrates
Cell viability
MLSS
Proteins
MLVSS
Glucuronidase
%MLVSS
ESP
-0,6
TP_inf
TN_inf
cond_inf
F2 (14,00 %)
50
F2 (21,10 %)
5
EPS
Proteins
Phosphatase
Cell viability
pH_inf
carbohydrates
Glucuronidase
0
-0,2
-0,4
BOD5_inf
COD_inf
-0,6
-0,8
-1
-1,4 -1,2 -1 -0,8 -0,6 -0,4 -0,2
-0,8
0
0,2 0,4 0,6 0,8
1
1,2 1,4
-1
-0,8
-0,6
-0,4
-0,2
0,2
0,4
0,6
0,8
1
F1 (77,43 %)
F1 (73,60 %)
Figure 8. Biplot Cell viability, EPS,
exoenzimatic activities - Operational
parameters (axes F1 y F2: 94,71%)
0
Figure 9. Biplot Cell viability, EPS,
exoenzimatic activities – Influent pysicochemical parameters (axes F1 y F2: 91,43%)
Results showed that 94% of cells from the MBR were viable and only 6% of the cells were damaged. CCA results revealed the relationships between exoenzymatic activities, cell
viability and EPS with the operational parameters and wastewater influent characteristics. Phosphatase was correlated with high levels of hydraulic retention time (HRT), while βglucuronidase was related with excess sludge production (ESP). Bioreactor temperature (Tr) correlated negatively with β- gucuronidase and phosphatase in agreement with other
works. Results of biplot analysis of influent water showed an inverse relationship between the concentration of total phosphorus (TP) and the phosphatase and β-gucuronidase
exoenzimatic activities. The increase in the availability of C in the influent might have contribute negatively to the phosphatase activity.
CONCLUSIONS
Studies on the interacting biological, chemical and physical phenomena in MBRs and innovative techniques to determine processes can contribute to a better knowledge of
biofouling and might lead to more robust MBRs operation.
ACKNOWLEDGEMENTS: This work was supported by grant no. ALI CGL2011-29231-C05-01 from the Spanish Ministry of Economy and Competitiveness.