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.
Plant metabolomics is the study of small molecule metabolites within plants. It is influenced by both genetic and environmental factors. Metabolomics can help understand plant phenotype, development, physiology, and stress responses. Modern platforms for plant metabolomics use techniques like gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy to detect and quantify metabolites in plant extracts. GC-MS allows for non-targeted profiling while NMR is non-destructive and useful for quantification. Metabolite fingerprinting and profiling are used to identify markers of genetic or environmental disturbances by comparing metabolic states of plants under different conditions. Plant metabolomics has applications in understanding plant diseases, stress responses, and secondary metabolites of therapeutic importance.
Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome.
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms.
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.
Metabolomics is the scientific study of chemical processes involving metabolites, which are small molecule intermediates and products of metabolism. It uses sophisticated analytical technologies like gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy to identify and quantify the complete set of metabolites in a biological sample. This emerging field combines analytical chemistry and statistics to comprehensively study an organism's metabolic profile and extract information that can be applied to areas like drug assessment, clinical toxicology, and nutrition.
Metabolomics For Plant Improvement : Status And ProspectsSandeep Gunalan
This document discusses metabolomics, which is the study of metabolites in organisms. It describes key terms like metabolome and different omics approaches. Metabolomics deals with identifying and quantifying small molecules like peptides, amino acids, and organic acids. It is important for understanding genetic improvement and crop performance under stress. Different extraction and analytical techniques are used like LC-MS and NMR. Case studies show how metabolomics identified compounds related to thrips resistance in chili and changes in flavonoids, polyamines and alkaloids during pollen development in tomatoes under heat stress. Limitations and prospects of metabolomics in discovering biomarkers and beneficial compounds are also covered.
This document discusses secondary metabolites produced by plants. It notes that nearly 70-80% of the world's population relies on herbal medicines. Secondary metabolites are phytochemicals not directly involved in plant metabolism and include pharmaceuticals, flavors, fragrances and more. Producing these compounds through plant cell cultures allows control over production conditions and quality. Key advantages of this method include production according to market demands, independence from environmental factors, consistent quality, ease of product recovery, and ability to produce novel compounds. The document outlines various strategies for optimizing secondary metabolite production in plant cell cultures, including selection of high-yielding cell lines, culture conditions, addition of precursors, use of elicitors, biotransformation, and downstream
Metabolomics is the systematic study of small molecule metabolites in a biological system. It involves identifying and quantifying metabolites on a large scale to investigate the biochemical processes and phenotype of cells, tissues or organisms. Some key points are:
- Metabolomics studies the metabolome, which is the complete set of small molecule metabolites present under certain conditions.
- It provides insights into cellular processes by capturing the biochemical activity and state through metabolic profiling or fingerprinting.
- Metabolomics has applications in fields like biomarker discovery, personalized medicine, agriculture and food/environmental testing.
Transcriptome analysis is the study of the set of all RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNAs produced in a population of cells. The transcriptome can vary between different cell types, body parts, and environmental conditions. Transcriptomics aims to catalogue all transcript species and quantify changing expression levels during development and in different conditions. The two main techniques are DNA microarrays and RNA sequencing. Microarrays involve fluorescent labeling and hybridization of samples to probe arrays, while RNA sequencing replaces hybridization with sequencing of individual cDNAs produced from target RNA.
Plant metabolomics is the study of small molecule metabolites within plants. It is influenced by both genetic and environmental factors. Metabolomics can help understand plant phenotype, development, physiology, and stress responses. Modern platforms for plant metabolomics use techniques like gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy to detect and quantify metabolites in plant extracts. GC-MS allows for non-targeted profiling while NMR is non-destructive and useful for quantification. Metabolite fingerprinting and profiling are used to identify markers of genetic or environmental disturbances by comparing metabolic states of plants under different conditions. Plant metabolomics has applications in understanding plant diseases, stress responses, and secondary metabolites of therapeutic importance.
Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome.
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms.
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.
Metabolomics is the scientific study of chemical processes involving metabolites, which are small molecule intermediates and products of metabolism. It uses sophisticated analytical technologies like gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy to identify and quantify the complete set of metabolites in a biological sample. This emerging field combines analytical chemistry and statistics to comprehensively study an organism's metabolic profile and extract information that can be applied to areas like drug assessment, clinical toxicology, and nutrition.
Metabolomics For Plant Improvement : Status And ProspectsSandeep Gunalan
This document discusses metabolomics, which is the study of metabolites in organisms. It describes key terms like metabolome and different omics approaches. Metabolomics deals with identifying and quantifying small molecules like peptides, amino acids, and organic acids. It is important for understanding genetic improvement and crop performance under stress. Different extraction and analytical techniques are used like LC-MS and NMR. Case studies show how metabolomics identified compounds related to thrips resistance in chili and changes in flavonoids, polyamines and alkaloids during pollen development in tomatoes under heat stress. Limitations and prospects of metabolomics in discovering biomarkers and beneficial compounds are also covered.
This document discusses secondary metabolites produced by plants. It notes that nearly 70-80% of the world's population relies on herbal medicines. Secondary metabolites are phytochemicals not directly involved in plant metabolism and include pharmaceuticals, flavors, fragrances and more. Producing these compounds through plant cell cultures allows control over production conditions and quality. Key advantages of this method include production according to market demands, independence from environmental factors, consistent quality, ease of product recovery, and ability to produce novel compounds. The document outlines various strategies for optimizing secondary metabolite production in plant cell cultures, including selection of high-yielding cell lines, culture conditions, addition of precursors, use of elicitors, biotransformation, and downstream
Metabolomics is the systematic study of small molecule metabolites in a biological system. It involves identifying and quantifying metabolites on a large scale to investigate the biochemical processes and phenotype of cells, tissues or organisms. Some key points are:
- Metabolomics studies the metabolome, which is the complete set of small molecule metabolites present under certain conditions.
- It provides insights into cellular processes by capturing the biochemical activity and state through metabolic profiling or fingerprinting.
- Metabolomics has applications in fields like biomarker discovery, personalized medicine, agriculture and food/environmental testing.
Transcriptome analysis is the study of the set of all RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNAs produced in a population of cells. The transcriptome can vary between different cell types, body parts, and environmental conditions. Transcriptomics aims to catalogue all transcript species and quantify changing expression levels during development and in different conditions. The two main techniques are DNA microarrays and RNA sequencing. Microarrays involve fluorescent labeling and hybridization of samples to probe arrays, while RNA sequencing replaces hybridization with sequencing of individual cDNAs produced from target RNA.
Somaclonal variation refers to genetic variations that can arise during plant tissue culture and regeneration. When plant cells or tissues are cultured in vitro, genetic and epigenetic changes can occur, resulting in phenotypically different regenerated plants (somaclones) compared to the original plant. Somaclonal variation is caused by factors like culture conditions, genotype, explant source, and selection method used. It can generate variations in chromosome structure, number, and gene mutations. Somaclonal variation has been used to develop novel variants with improved traits like disease resistance, abiotic stress tolerance, and altered plant morphology. However, extensive field testing is required to evaluate variants due to possible genetic instability and undesirable effects.
Anther culture:- the in vitro culturing of anthers containing microspores or immature pollen grains on a nutrient medium for the purpose of generating haploid plantlets.
Culturing anthers for the purpose of obtaining Double Haploid is not easy with many field crop species, particularly with the cereals, cotton, and grain legumes.
Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
Metabolome refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites)
Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the ‘-omics’ family of systems biology technologies.
A presentation covering the process of protoplast culture including protoplast isolation, protoplast fusion, culture of protoplast, its application, factors affecting protoplast culture and the future of protoplasts.
Plant tissue culture is used to produce valuable secondary metabolites. There are three main methods: cell suspension cultures, hairy root cultures, and immobilized cell cultures. Cell suspension cultures are the most common. They involve transferring plant cells or callus to liquid medium to grow as a suspension. Medium components, regulators, precursors, elicitors, and environmental factors can be manipulated to enhance metabolite production. Hairy root cultures use plant cells transformed by bacteria to produce root-like structures that also synthesize metabolites. Immobilized cell cultures entrap or affix cells to allow contact while protecting from shear stress. Each method aims to produce metabolites through optimized bioprocessing conditions at large scales.
This document discusses callus and suspension cultures. Callus culture involves culturing explants on agar medium to form an unorganized cell mass called callus. Suspension cultures involve culturing tissues or cells in liquid medium, producing single cells and clumps. There are three types of suspension cultures: batch, continuous, and immobilized. Batch cultures use a limited nutrient supply until growth declines. Continuous cultures drain out used medium and add fresh medium to maintain a steady state. Immobilized cultures encapsulate plant cells in gels like agarose.
Arabidopsis thaliana was the very first plant whose genome was sequenced by the Arabidopsis Initiative (AGI) in the year 1966-2000. mouse ear cress has been the plant model ever since 1985.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
Its about how fruit ripening occurs and how we can manipulate ripening process by using biotechnology to delay ripening and to reduce postharvest losses
The document provides an overview of the history and techniques of transcriptome analysis. It discusses how RNA was separated from DNA with the formulation of the central dogma in 1958. Key developments include the discoveries of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. The document outlines techniques such as serial analysis of gene expression (SAGE) and RNA sequencing (RNA-seq) that allow comprehensive analysis of gene expression patterns. It provides details on the basic steps and advantages of SAGE and describes how next generation sequencing revolutionized transcriptome analysis through massive parallel sequencing.
secondary metabolites of plant by K. K. SAHU SirKAUSHAL SAHU
METABOLITES : Introduction . . .
The chemical compounds produced by plants are collectively called as phytochemicals.
Primary metabolites – participating in nutrition and metabolic processes inside the plant.
Secondary metabolites – those chemical compounds that do not participate in metabolism of plants but influencing the
ecological interactions between the plant and its environment.
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
Organogenesis, in plant tissue cultureKAUSHAL SAHU
Introduction
Definition
Types of organogenesis
Organogenesis through callus formation (indirect organogenesis)
Growth regulators for indirect organogenesis
Organogenesis through adventitious organ (direct organogenesis)
Growth regulators for direct organogenesis
Factor affecting the soot bud differentiation
Organogenic differentiation
Application of organogenesis
Conclusion
References
Molecular mechanism of male sterility in plant systemShilpa Malaghan
This document summarizes a seminar on molecular approaches for genetic engineering of male sterility. It begins by defining male sterility as the inability of flowering plants to produce functional pollen. It then describes different types of male sterility including genic, cytoplasmic, and chemically-induced sterility. The document discusses the molecular basis of male sterility and anther development, using the T cytoplasm in maize as a model system. It also outlines several genetic engineering approaches that have been used to induce male sterility in crops like tobacco, including the use of ribonuclease genes, a deacetylase system, a two-component barnase system, and engineering chloroplast-induced sterility.
Gene expression and transcript profiling involves determining the pattern of genes expressed at the transcriptional level under specific circumstances by measuring the expression of thousands of genes simultaneously. This allows one to understand cellular function. Common techniques for profiling include DNA microarrays, RNA sequencing, and EST tags. DNA microarrays involve hybridizing cDNA or cRNA samples to probes on a chip to determine relative abundance of sequences. RNA sequencing uses next-generation sequencing to reveal presence and quantity of RNA in a sample.
The document provides an overview of metabolomics and its applications in biomedical research. It begins with definitions of metabolomics and discusses how it compares to other "omics" approaches like genomics and proteomics. Key points made include that metabolomics offers a unique way to study the relationship between genotype, phenotype and environment, and that metabolites represent the ultimate downstream effects of various biological factors. The document then covers sample collection and processing, analytical techniques like NMR and mass spectrometry, and data analysis using multivariate statistics. In conclusion, metabolomics provides an unbiased way to study metabolic changes in health and disease.
Somaclonal variation refers to genetic variations that can arise during plant tissue culture and regeneration. When plant cells or tissues are cultured in vitro, genetic and epigenetic changes can occur, resulting in phenotypically different regenerated plants (somaclones) compared to the original plant. Somaclonal variation is caused by factors like culture conditions, genotype, explant source, and selection method used. It can generate variations in chromosome structure, number, and gene mutations. Somaclonal variation has been used to develop novel variants with improved traits like disease resistance, abiotic stress tolerance, and altered plant morphology. However, extensive field testing is required to evaluate variants due to possible genetic instability and undesirable effects.
Anther culture:- the in vitro culturing of anthers containing microspores or immature pollen grains on a nutrient medium for the purpose of generating haploid plantlets.
Culturing anthers for the purpose of obtaining Double Haploid is not easy with many field crop species, particularly with the cereals, cotton, and grain legumes.
Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
Metabolome refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites)
Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the ‘-omics’ family of systems biology technologies.
A presentation covering the process of protoplast culture including protoplast isolation, protoplast fusion, culture of protoplast, its application, factors affecting protoplast culture and the future of protoplasts.
Plant tissue culture is used to produce valuable secondary metabolites. There are three main methods: cell suspension cultures, hairy root cultures, and immobilized cell cultures. Cell suspension cultures are the most common. They involve transferring plant cells or callus to liquid medium to grow as a suspension. Medium components, regulators, precursors, elicitors, and environmental factors can be manipulated to enhance metabolite production. Hairy root cultures use plant cells transformed by bacteria to produce root-like structures that also synthesize metabolites. Immobilized cell cultures entrap or affix cells to allow contact while protecting from shear stress. Each method aims to produce metabolites through optimized bioprocessing conditions at large scales.
This document discusses callus and suspension cultures. Callus culture involves culturing explants on agar medium to form an unorganized cell mass called callus. Suspension cultures involve culturing tissues or cells in liquid medium, producing single cells and clumps. There are three types of suspension cultures: batch, continuous, and immobilized. Batch cultures use a limited nutrient supply until growth declines. Continuous cultures drain out used medium and add fresh medium to maintain a steady state. Immobilized cultures encapsulate plant cells in gels like agarose.
Arabidopsis thaliana was the very first plant whose genome was sequenced by the Arabidopsis Initiative (AGI) in the year 1966-2000. mouse ear cress has been the plant model ever since 1985.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
Its about how fruit ripening occurs and how we can manipulate ripening process by using biotechnology to delay ripening and to reduce postharvest losses
The document provides an overview of the history and techniques of transcriptome analysis. It discusses how RNA was separated from DNA with the formulation of the central dogma in 1958. Key developments include the discoveries of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. The document outlines techniques such as serial analysis of gene expression (SAGE) and RNA sequencing (RNA-seq) that allow comprehensive analysis of gene expression patterns. It provides details on the basic steps and advantages of SAGE and describes how next generation sequencing revolutionized transcriptome analysis through massive parallel sequencing.
secondary metabolites of plant by K. K. SAHU SirKAUSHAL SAHU
METABOLITES : Introduction . . .
The chemical compounds produced by plants are collectively called as phytochemicals.
Primary metabolites – participating in nutrition and metabolic processes inside the plant.
Secondary metabolites – those chemical compounds that do not participate in metabolism of plants but influencing the
ecological interactions between the plant and its environment.
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
Organogenesis, in plant tissue cultureKAUSHAL SAHU
Introduction
Definition
Types of organogenesis
Organogenesis through callus formation (indirect organogenesis)
Growth regulators for indirect organogenesis
Organogenesis through adventitious organ (direct organogenesis)
Growth regulators for direct organogenesis
Factor affecting the soot bud differentiation
Organogenic differentiation
Application of organogenesis
Conclusion
References
Molecular mechanism of male sterility in plant systemShilpa Malaghan
This document summarizes a seminar on molecular approaches for genetic engineering of male sterility. It begins by defining male sterility as the inability of flowering plants to produce functional pollen. It then describes different types of male sterility including genic, cytoplasmic, and chemically-induced sterility. The document discusses the molecular basis of male sterility and anther development, using the T cytoplasm in maize as a model system. It also outlines several genetic engineering approaches that have been used to induce male sterility in crops like tobacco, including the use of ribonuclease genes, a deacetylase system, a two-component barnase system, and engineering chloroplast-induced sterility.
Gene expression and transcript profiling involves determining the pattern of genes expressed at the transcriptional level under specific circumstances by measuring the expression of thousands of genes simultaneously. This allows one to understand cellular function. Common techniques for profiling include DNA microarrays, RNA sequencing, and EST tags. DNA microarrays involve hybridizing cDNA or cRNA samples to probes on a chip to determine relative abundance of sequences. RNA sequencing uses next-generation sequencing to reveal presence and quantity of RNA in a sample.
The document provides an overview of metabolomics and its applications in biomedical research. It begins with definitions of metabolomics and discusses how it compares to other "omics" approaches like genomics and proteomics. Key points made include that metabolomics offers a unique way to study the relationship between genotype, phenotype and environment, and that metabolites represent the ultimate downstream effects of various biological factors. The document then covers sample collection and processing, analytical techniques like NMR and mass spectrometry, and data analysis using multivariate statistics. In conclusion, metabolomics provides an unbiased way to study metabolic changes in health and disease.
This ppt explains the basics of mass spectrometry and in application in pharmacognosy. Hope this helps you guys. Like, comment and save. If you hav problem downloading, send your email address; i'll post it for you by mail :)
Enjoy the presentation.
High-performance liquid chromatography (HPLC) involves forcing a pressurized liquid solvent through a column containing a stationary solid phase to separate and analyze compounds. It was developed in the 1960s and commercialized in the late 1960s and early 1970s. Key developments included the use of higher pressures up to 20,000 psi and particles sizes of 2 microns or less, allowing for faster separations. HPLC uses differences in how compounds partition between the liquid mobile phase and solid stationary phase to achieve separation. Common applications include pharmaceutical analysis, environmental testing, and forensic and clinical analysis.
HPLC is a separation technique used in pharmaceutical analysis to separate, identify, and quantify components in mixtures. It works by pumping a mobile phase through a column containing adsorbent packing material. Samples are injected into the mobile phase and the components elute from the column at different rates depending on their interactions with the stationary and mobile phases. Detectors then convert the separated components into electrical signals to allow for qualitative and quantitative analysis. Common applications of HPLC include analysis of drugs and metabolites in biological samples.
High Performance Liquid Chromatography(HPLC).pptxOMJHA20
This document provides an overview of high performance liquid chromatography (HPLC). It begins by defining chromatography and describing the basic components and principles of HPLC. These include a stationary phase, mobile phase, pump to apply high pressure to the mobile phase, and detector. HPLC uses small particle sizes in the stationary phase and high pressure to achieve high resolution separation of mixtures. The document then discusses various applications of HPLC in fields like pharmaceuticals, forensics, food, and clinical analysis. It compares HPLC to other techniques like thin layer chromatography and capillary electrophoresis. In summary, HPLC is a powerful analytical technique that uses high pressure to separate mixtures using small stationary phase particles, detectors, and varying mobile phase compositions.
The document provides an overview of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). It discusses the principles, instrumentation, and applications of both techniques. For GC-MS, it describes how the carrier gas transports compounds through the column where they are separated and then ionized before being detected by the mass spectrometer. For LC-MS, it explains how compounds are separated by the liquid mobile phase and HPLC column before being ionized, typically by electrospray ionization, and detected based on their mass-to-charge ratio. Common applications of these techniques include analysis of metabolites, toxins, pesticides, and other compounds.
The document discusses liquid chromatography mass spectrometry (LC-MS), which combines liquid chromatography separation with mass spectrometry detection. LC separates compounds by their physical and chemical properties, while MS separates them by mass. The mass spectrometer acts as both a detector for LC and provides identification of compounds through their unique mass spectra. Common ionization methods used include electrospray ionization and atmospheric pressure chemical ionization. Common mass analyzers are quadrupole, time-of-flight, magnetic sector, and ion trap analyzers.
Mass Spectrometry in chemistry and basic sciences.pptxJohamSarfrazAli1
Inductively coupled plasma mass spectrometry (ICP-MS) allows for analysis of elements at very low concentrations. It works by ionizing analyte atoms from liquid samples using plasma and then detecting the resulting ions using a mass spectrometer. ICP-MS provides high sensitivity, accuracy, and a wide linear dynamic range. It has numerous applications including environmental analysis, clinical analysis, and analysis of geological and metallurgical samples. The key components are the inductively coupled plasma ion source, interface between the plasma and mass spectrometer, quadrupole or time-of-flight mass analyzer, and detector.
MALDI-TOF mass spectrometry is a soft ionization technique used to analyze biomolecules like proteins, peptides, and polymers. It works by mixing the sample with an organic matrix and applying it to a metal plate. A pulsed laser is used to desorb the sample-matrix mixture, ionizing the analyte via proton transfer. The ions are then analyzed by a time-of-flight mass spectrometer, which measures the time it takes ions to reach the detector based on their mass-to-charge ratio. MALDI-TOF MS has applications in fields like proteomics, microbiology, and pharmaceutical analysis by providing identification and quantification of proteins, metabolites, and microorganisms.
High performance liquid chromatography (HPLC) is a technique that forces a solvent through a column under high pressure to separate samples into their constituent parts. HPLC uses a pump to force a mobile phase through a column containing a stationary phase, and a detector measures the analytes as they elute from the column. There are several types of HPLC that separate samples based on polarity (normal phase), hydrophobic interactions (reverse phase), molecular size (size-exclusion), or ionic charge (ion-exchange). HPLC has many applications in fields like pharmaceuticals, environmental analysis, forensics, food and flavors, and clinical testing.
High- performance Liquid Chromatography”/
(High- pressure Liquid Chromatography) is a powerful tool in analysis, it yields High Performance and high speed compared to traditional columns chromatography
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.
Advanced techniques in analysis of organic compoundUpasana Mohapatra
Upasana Mohapatra submitted a research paper on advanced techniques for analysis of organic compounds. The paper described several techniques including chromatography-spectrometry combinations like HPLC-NMR that allow identification of organic molecules. Elemental analysis, electrochemistry, chromatography, and molecular spectrometry each provide different information for organic compound analysis. HPLC-NMR in particular allows complex mixtures to be separated and identified using NMR. The techniques discussed provide powerful tools for identification of organic compounds in various applications like metabolite analysis.
Molecular weight determination and Characterization of Enzymes Ayushisomvanshi1
This presentation shows about how the determination of molecular weight is done and what are the different ways or method to determine the molecular weight. This presentation also tells about the enzymes and its characterization.
mass spectrometry, also called mass spectroscopy, analytic technique by which chemical substances are identified by the sorting of gaseous ions in electric and magnetic fields according to their mass-to-charge ratios.
This document provides an overview of gas chromatography-mass spectrometry (GC-MS). It describes how GC separates components using a carrier gas and column, while MS identifies components by mass. It discusses how the two techniques are combined via an interface, allowing both separation and identification in a single run. Key components of a GC-MS system like the gas chromatograph, interface, and mass spectrometer are also outlined.
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.
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
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.
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.
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
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.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
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.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
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/
2. What is Plant Metabolomics..?
• Quantitative and Qualitative analysis, elucidation of all metabolites in Plants under
specific conditions
• Metabolome-Entire complement of small molecules in plant, Ultimate phenotype of cells,
Information of gene expression and modulation of protein function, environmental cues
• Metabolome-Stephen Oliver
3. IMPORTANCE
• Ability to detect vast array of metabolites from single extract, allowing speedy and
precise analysis of metabolites
• Comprehensive view of plant metabolites like small organic compounds, which
participate in different cellular events, representing absolute physiological state of cell
• Valuable tool for advancing our understanding of primary and secondary metabolism
in plants and is revolutionizing field of plant biology
4. LIMITATIONS…
• Enormous complexity and diversity of plant metabolomes and incomplete knowledge of plant
metabolic pathways
• Require wide spectrum of chemistries and instrumentation with wide dynamic range
• Impossible to extract and analyze all metabolites in a plant cell in single analysis metabolome
• Identification and structural elucidation of molecules from analytical detector signals
• Lack of universal metabolite-specific libraries and known reference compounds- major limitation
to definitive identification of metabolites
6. SAMPLING: FROM WHOLE PLANT TO SINGLE CELL
• Harvesting and quenching
• Plant material harvest- as fast as possible by immediate freezing plant tissue in liquid
nitrogen (i.e. shock freezing) and storing at −80°C
• Quick inactivation of enzymatic reactions and metabolic processes- avoid fluctuations in
the levels of fast turnover metabolites (e.g. glycolytic intermediates)
• Finely homogenized fresh-frozen plant tissues, a process often performed using a pre-
cooled pestle and mortar filled with liquid nitrogen
• Aliquots of fine powdered plant tissue must be rapidly weighed in pre-cooled
polypropylene microfuge tubes to ensure that plant material does not thaw
(Jorge. T et al, 2016)
7. Extraction Of Metabolites
• Chemical stability of metabolites is not affected
• Analytical recoveries of metabolites throughout extraction are complete
• Variability in metabolite concentrations during the extraction is minimized
• Amount of tissue -differ between extraction methods
• Polar organic solvents -both hydrophilic and hydrophobic compounds
• Solvent systems- Combination of polar and Non-polar organic solvents- used to separate
polar phase (hydrophilic metabolites) from a non-polar phase (hydrophobic metabolites-
lipids)
(Jorge. T et al, 2016)
8. Pre-analytical Requirements
• Concentrate metabolite(s) of interest
• Prevent sample carryover in chromatographic systems
• Eliminate interfering components from the plant matrix
• LC and CE allow direct analysis of non-volatile metabolites
• In LC-MS- Plant extract is usually re-dissolved in a solvent with same composition of
initial conditions of LC mobile phase
• CE-MS- Includes very low organic solvent consumption without need for extensive
sample pretreatment
(Jorge. T et al, 2016)
9. ANALYTICAL TECHNOLOGIES
• Separation methods
• Gas chromatography- For analyzing compounds that can be vaporized without
decomposition
• High performance liquid chromatography – Form of column chromatography that
pumps a sample of mixture or analyte in a solvent(mobile phase) at high pressure through
a column with chromatographic packing material(stationary phase)
• Much wider range of analytes can potentially be measured
• Capillary electrophoresis- separates ions based on their electrophoretic mobility with
the use of an applied voltage
10. Detection Methods
• Nuclear Magnetic Resonance Spectroscopy- Only detection technique- does not rely
on separation of analytes, and sample can be recovered for further analysis
• All kinds of small molecule metabolites can be measured simultaneously
• Mass spectrometry- Ionizes chemical species and sorts ions based on their mass to charge
ratio
16. • Extract – in Room temp. at least 30 min before NMR measurement to avoid bad shimming
• Load NMR tube into the spectrometer, Set sample temp. to 298 K and leave for thermal
equilibration
• H-NMR - metabolomic data of a sample within a relatively short time (5–10 min for 64–
128 scans)
• Tune and match NMR tube and Lock spectrometer frequency to the deuterium resonance
arising from NMR solvents
NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
17. • Shim the sample by manual or automated method
• Standard 1H NMR spectroscopy is done
• Convert NMR spectra to a suitable form for further multivariate analysis and
carry out PCA
• Identify as many of metabolites as possible, by comparison with NMR signals
to reference compounds or by 2D NMR spectra
19. • Unbiased, rapid, non-destructive technique- requires little sample preparation and lessens
chance of sample loss
• In this, No analyte separation process involved- provide selectivity without separation,
and does not require sample derivatisation prior to analysis
• NMR spectrum of a multicomponent extract is result of superposition of collective
spectra of all NMR-visible individual compounds present in sample under study
• NMR analysis- global view of all metabolites (primary and secondary) in a sample
Advantages
20. ELECTRO-SPRAY IONIZATION
• ESI- soft ionization technique extensively used for production
• of gas phase ions (without fragmentation) of thermally labile large supramolecules
21. GAS CHROMATOGRAPHY- MASS SPECTROMETRY
• Separation of analytes -depends on analyte interactions with stationary face and boiling
point
• Only Volatile compounds- separated on GC column, non-volatile metabolites must be
derivatize polar compounds containing functional groups such as –OH, –SH or –NH
• Portion of sample is introduced into inlet of GC instrument
• Inlet temperature is higher than 250°C, at which many metabolites are evaporated
22. • Whole sample is introduced onto high resolution capillary column(10- 60 m)
• Metabolites eluting from GC- ionized by Electron-impact (EI), Here vaporized
metabolites impacted by a beam of electrons with sufficient energy to fragment
and ionize molecule
• EI results in molecular ion fragmentation, which is of great importance for
structural interpretation of the metabolites
• To identify compounds, databases of ion fragmentation patterns of molecules, as
NIST are used
23. Advantages
• Capable of analyzing volatile compounds and requires extensive chemical derivatization
procedures to increase volatility and thermo-stability
• To profile a wide range of metabolites with different physico-chemical properties in a
single plant extract, while providing structural information of detected metabolites
• GC-MS- highly reproducible technique than LC-MS, due to electron ionization (EI)
method, in which gas-phase molecules interact with kinetically activated electrons at
accepted average standard energy of 70 eV
26. LIQUID CHROMATOGRAPHY- MASS SPECTROMETRY
• LC-MS- To profile a small set of known metabolites or compound classes of the plant
metabolome, an approach referred to as target metabolite analysis
• Ionization method- Electrospray ionization (ESI)- introduces little internal energy and
gives little information on structure because few fragments are generated
• Provides additional structural information- aid in identification of new or unusual
metabolites or in characterization of known metabolites in cases where ambiguity exists
27.
28. FOURIER-TRANSFORM ION CYCLOTRON-RESONANCE
MASS SPECTROMETRY
• For determining mass to charge ratio based on cyclotron frequency of ions in a fixed
magnetic field, provides mass accuracy
• Water(W) and Chloroform(C) fractions- reconstituted in methanol/ water (1:1)
• Methanol(M) and Acetonitrile(A) fractions suspended in respective pure solvent. For
metabolites analysis, all fractions diluted 1000-fold in appropriate solvent
• M and A fractions diluted in same solvent for positive and negative-ion mode analysis
• W and C fractions diluted in methanol in methanol/water (1:1) for ESI
(Maia. M et al, 2016 )
29. Standard leucine encephalin added to all samples at concentration of 0.5 mg/ml, and was
used as standard for control and quality assessment of particular analytical precision
Extracted metabolites were analyzed by direct infusion in FTICR-MS with preset flow
rate
31. DIRECT ANALYSIS IN REAL TIME- MASS SPECTROMETRY
• It enables rapid analyzing of solids, liquids, and gases at atmospheric pressure without sample
preparation
• Helium is conducted via an axial tube and supports a corona discharge- engenders ions, electrons,
and excited atoms
• Helium passes through other two chambers, where electrons are removed, passing into atmospheric
reaction zone- include only electronically excited substances
• Released atoms in tube cause environmental gas to undergo gas-phase reaction ionization cascade
•
32. • These ions- chemical ionizing reagents near surface of analyzed sample, resulting
in analyte ions finally getting transferred to mass analyzer
• Penning ionization is most important step in DART-MS
• Flow rate of carrier gas and temperature are two major factors that affect DART
ionization performance
• Prominent features of DART- high throughput, minor cross-contamination, and
simplicity
• Typically used to analyze small molecular compounds with m/z of 50–1200
33.
34.
35. • Advantages
• Samples can be analyzed directly without the extraction process
• Low sample consumption
• Sample analysis cycle was sharply shortened
• Disadvantages
• Polar compounds are difficult to ionize
• Ion suppression
36. REFERENCES
• J. WILLIAM ALLWOOD, RIC C. H. DE VOS, ANNICK MOING, CATHERINE DEBORDE,
ALEXANDER ERBAN, JOACHIM KOPKA, ROYSTON GOODACRE, AND ROBERT D.
HALL, 2011, Plant Metabolomics and Its Potential for Systems Biology Research:
Background Concepts, Technology, and Methodology, Methods in Enzymology, 500: 299-
336.
• Gullberg, J. 2005, Metabolomics: A Tool for Studying Plant Biology, Swedish University of
Agricultural Sciences, 1-61.
• TIAGO F. JORGE, ANA T. MATA, AND CARLA ANTÓNIO, 2016, Mass spectrometry as a
quantitative tool in plant metabolomics, Philos. Trans. Math. Phys. Eng. Sci, 374(2079): 1-34.
• ROBERT VERPOORTE, 2010, NMR-based metabolomic analysis of plants, Nat. Protocol,
237, 1-34.
• JUN-LING REN, AI-HUA ZHANG, LING KONG AND XI-JUN WANG, 2018, Advances in mass
spectrometry-based metabolomics for investigation of metabolites, 40, 1-31.