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Microbial Metabolomics Analysis

2021-01-24T16:49:08.532Z

Microbial metabolomics is a study of the complete set of metabolites within a microorganism. Microorganism is a bunch of small creatures which can not be easily identified by naked eyes, and exist in multiple forms, including bacteria, fungi, and some algea, and have the most diverse metabolic characteristics. Each microorganism generally has relatively small genome and proteomes, and the genome and proteome data information are far less than that of the eukaryotes. However, the metabolome of each microorganism is very distinctive, and reflects the cellular activity in a more direct way.

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Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates and products of metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles.The metabolome represents the complete set of metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.

Clinical Metabolomics

Metabolomic disturbances have been associated with many human diseases, including cancer, diabetes, and cardiovascular disease. Metabolomics provides a link between metabolic pathways and the upstream genome that governs them. With the advances in analytical technologies, metabolomics is becoming a powerful tool for identifying diagnostic biomarkers of diseases, elucidating the pathological mechanisms, discovering novel drug targets, predicting drug responses, interpreting the mechanisms of drug action, as well as enabling precision treatment of patients.

Metabolites

Metabolites are the substrates, intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1.5 kDa in size.] However, there are exceptions to this depending on the sample and detection method. For example, macromolecules such as lipoproteins and albumin are reliably detected in NMR-based metabolomics studies of blood plasma. In plant-based metabolomics, it is common to refer to "primary" and "secondary" metabolites. A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function.

Metabonomics

Metabonomics is defined as "the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification". The word origin is from the Greek μεταβολή meaning change and nomos meaning a rule set or set of laws.

Exometabolomics

Exometabolomics, or "metabolic footprinting", is the study of extracellular metabolites. It uses many techniques from other subfields of metabolomics, and has applications in biofuel development, bioprocessing, determining drugs' mechanism of action, and studying intercellular interactions.

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Plant Metabolomics in a Changing World in Plant Genetics and breeding

2020-12-16T15:19:47.890Z

Metabolites are indispensable component of plant metabolism owing to their influence on plant biomass and architecture. In recent years, metabolomics has established itself as one of the major breakthroughs in science, paving the way for accurate metabolite profiling in microbes, plants and animals.

Metabolomics has the ability to detect a vast array of metabolites from a single extract, thus allowing speedy and precise analysis of metabolites. In other words, metabolomics offers a comprehensive view of cellular metabolites like small organic compounds, which participate in different cellular events, thus representing the absolute physiological state of a cell.

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Metabolites are the substrates, intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1.5 kDa in size. However, there are exceptions to this depending on the sample and detection method. For example, macromolecules such as lipoproteins and albumin are reliably detected in NMR-based metabolomics studies of blood plasma.In plant-based metabolomics, it is common to refer to "primary" and "secondary" metabolites. A primary metabolite is directly involved in the normal growth, development, and reproduction

Clinical Metabolomics

Metabolites

Metabonomics

Metabolomics is also the study of small molecules which resides in cells, biofluids, and tissues. The studies are extensively conducted with an aim to analyze biochemical activities of these small molecules and their interactions with biological systems. Metabolomics has wide variety of applications in disease diagnosis, drug discovery, enzyme discovery, and others.

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Metagenomics and Metatranscriptomics Bioinformatics Analysis

2020-12-10T15:08:30.737Z

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

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While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.

Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before. Recent studies use either "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities.

Shotgun metagenomics

Advances in bioinformatics, refinements of DNA amplification, and the proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples, allowing the adaptation of shotgun sequencing to metagenomic samples (known also as whole metagenome shotgun or WMGS sequencing). The approach, used to sequence many cultured microorganisms and the human genome, randomly shears DNA, sequences many short sequences, and reconstructs them into a consensus sequence. Shotgun sequencing reveals genes present in environmental samples.

High-throughput sequencing

An advantage to high throughput sequencing is that this technique does not require cloning the DNA before sequencing, removing one of the main biases and bottlenecks in environmental sampling. The first metagenomic studies conducted using high-throughput sequencing used massively parallel 454 pyrosequencing. Three other technologies commonly applied to environmental sampling are the Ion Torrent Personal Genome Machine, the Illumina MiSeq or HiSeq and the Applied Biosystems SOLiD system.

The data generated by metagenomics experiments are both enormous and inherently noisy, containing fragmented data representing as many as 10,000 species. The sequencing of the cow rumen metagenome generated 279 gigabases, or 279 billion base pairs of nucleotide sequence data, while the human gut microbiome gene catalog identified 3.3 million genes assembled from 567.7 gigabases of sequence data.Collecting, curating, and extracting useful biological information from datasets of this size represent significant computational challenges for researchers.

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Metagenomic Next Generation Sequencing in clinical Microbiology

2020-09-02T14:15:19.770Z

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

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Next generation sequencing is any of several high-throughput sequencing methods whereby billions of nucleic acid fragments can be simultaneously and independently sequenced. Contrast this technique to classical methods such as Sanger sequencing (also known as dideoxynucleotide chain termination sequencing), which processes one nucleotide sequence per reaction.

Metagenomic NGS (mNGS) is simply running all nucleic acids in a sample, which may contain mixed populations of microorganisms, and assigning these to their reference genomes to understand which microbes are present and in what proportions. The ability to sequence and identify nucleic acids from multiple different taxa for metagenomic analysis makes this a powerful new platform that can simultaneously identify genetic material from entirely different kingdoms of organisms.

Metagenomics sequencing workflow

There are several steps involved in a sequencing based metagenomics project. These include DNA extraction, library preparation, sequencing, assembly, annotation and statistical analysis.

Sample extraction

A reproducible method to extract DNA from microbial communities is essential for surveying and whole genome metagenomic analysis. Isolation and extraction must yield high quality nucleic acid for subsequent library preparation and sequencing. Sampling variation can have an effect on comparisons, and abundance measurements. This introduces several challenges as some samples must be delivered anaerobically. Exposure to oxygen or freezing can change the dynamic composition of a given microbial community. For example, freezing, thawing and subsequent bead-beating can affect the cell wall of Gram-positive bacteria, and introduce artifacts compared to extraction performed on fresh samples.

Library preparation

One of the biggest considerations for library preparation of environmental samples for shotgun metagenomic sequencing has to do with amplification. Certain types of samples (water, swabs) yield small amounts of DNA, necessitating amplification during library preparation. Amplification by PCR can over amplify certain fragments over others confounding abundance and microbial diversity measurements. Often the user does not have a choice when faced with low inputs of DNA.

Annotation

Once assembled, genes can be predicted and functionally annotated. Genes are typically predicated in one of three ways: 1) de novo gene prediction, 2) protein family classification, 3) fragment recruitment (binning). Functional annotation is performed by classifying predicted metagenomics proteins into protein families using sequence or hidden Markov models (HMM) databases.

Metagenomics, is a field where genomic analysis of microbial DNA from environmental communities is studied. Metagenomic sequencing enables scientists to analyze genes in the given sample. The method enables researchers to assess bacterial diversity and identify the presence of microbes in various environments. Steps involved in metagenomics sequencing include DNA extraction, library preparation, sequencing, assembly, annotation and statistical analysis.

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Metabolomics Bioinformatics Analysis

2020-08-14T13:27:47.358Z

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mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism.[3] One of the challenges of systems biology and functional genomics is to integrate genomics, transcriptomic, proteomic, and metabolomic information to provide a better understanding of cellular biology.

Clinical Metabolomics

Metabolites

Metabonomics

Exometabolomics

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How Bioinformatics Changing the Biotechnology in World?

2020-06-15T06:07:45.573Z

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.Biochemical processes give rise to the complexity of life.

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Biochemistry analyzers are new-generation analyzers that are used by hospitals, diagnostic centers, pharmaceutical and biopharmaceutical companies, and contract research organizations to perform various tasks such as routine biochemistry tests, electrolytic tests, hormonal assays, drug-enzyme investigations among others. These analyzers are gaining significant popularity in the market as it is capable of performing multi-functional applications with reliable results. These analyzers are available in the market with various levels of automation.

Biochemistry is the study of the structure and function of biological molecules such as proteins, nucleic acids, carbohydrates and lipids. Biochemistry is also used to describe techniques suited to understanding the interactions and functions of biological molecules, including traditional techniques such as Western blotting, co-immunoprecipitation, and chromatography methods.

Carbohydrates

Two of the main functions of carbohydrates are energy storage and providing structure. One of the common sugars known as glucose is carbohydrate, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.

Biochemistry is closely related to molecular biology, the study of the molecular mechanisms of biological phenomena.

Lipids

Lipids comprise a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear, open-chain aliphatic molecules, while others have ring structures. Some are aromatic (with a cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid.

Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).

Proteins

Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids. An amino acid consists of an alpha carbon atom attached to an amino group, –NH2, a carboxylic acid group, –COOH (although these exist as –NH3+ and –COO− under physiologic conditions), a simple hydrogen atom, and a side chain commonly denoted as "–R". The side chain "R" is different for each amino acid of which there are 20 standard ones. It is this "R" group that made each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein.

Nucleic acids

Nucleic acids, so-called because of their prevalence in cellular nuclei, is the generic name of the family of biopolymers. They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group.

The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The phosphate group and the sugar of each nucleotide bond with each other to form the backbone of the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine, cytosine, guanine, thymine, and uracil. The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid (similar to a zipper). Adenine binds with thymine and uracil, thymine binds only with adenine, and cytosine and guanine can bind only with one another.

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Biochemistry and Molecular Biology the Science icon in Biotechnology

2020-06-11T18:32:20.615Z

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.Biochemical processes give rise to the complexity of life.

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Carbohydrates

Biochemistry is closely related to molecular biology, the study of the molecular mechanisms of biological phenomena.

Lipids

Proteins

Nucleic acids

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