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Multilocus Sequence Typing
Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. The first MLST scheme to be developed was for '' Neisseria meningitidis'', the causative agent of meningococcal meningitis and septicaemia. Since its introduction for the research of evolutionary history, MLST has been used not only for human pathogens but also for plant pathogens. Principle MLST directly measures the DNA sequence variations in a set of housekeeping genes and characterizes strains by their unique allelic profiles. The principle of MLST is simple: the technique involves PCR amplification followed by DNA sequencing. Nucleotide differences between strains can be checked at a variable number of genes depending on the degree of discrimination desired. The workflow of MLST involves: 1) data collection, 2) data analysis and 3) multilocus sequence a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Biology
Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactions. Though cells and other microscopic structures had been observed in living organisms as early as the 18th century, a detailed understanding of the mechanisms and interactions governing their behavior did not emerge until the 20th century, when technologies used in physics and chemistry had advanced sufficiently to permit their application in the biological sciences. The term 'molecular biology' was first used in 1945 by the English physicist William Astbury, who described it as an approach focused on discerning the underpinnings of biological phenomena—i.e. uncovering the physical and chemical structures and properties of biological molecules, as well as their interactions with other molecules and how these interactions explain observ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Acetyl Coenzyme A Acetyltransferase
Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are enzymes which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate pathway. Thiolases are ubiquitous enzymes that have key roles in many vital biochemical pathways, including the beta oxidation pathway of fatty acid degradation and various biosynthetic pathways. Members of the thiolase family can be divided into two broad categories: degradative thiolases (EC 2.3.1.16) and biosynthetic thiolases (EC 2.3.1.9). These two different types of thiolase are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase (EC:2.3.1.9) and 3-ketoacyl-CoA thiolase (EC:2.3.1.16). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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PFGE
Pulsed-field gel electrophoresis (PFGE) is a technique used for the separation of large DNA molecules by applying an electric field that periodically changes direction to a gel matrix. Unlike standard agarose gel electrophoresis, which can separate DNA fragments of up to 50 kb, PFGE resolves fragments up to 10 Mb. This allows for the direct analysis of genomic DNA. History In 1984, David C. Schwartz and Charles Cantor published the first successful application of alternating electric fields for the separation of large DNA molecules. This technique, which they named PFGE, resulted in the development of several variations, including Orthogonal Field Alternation Gel Electrophoresis (OFAGE), Transverse Alternating Field Electrophoresis (TAFE), Field-Inversion Gel Electrophoresis (FIGE), and Clamped Homogeneous Electric Fields (CHEF), among others. Procedure The procedure for PFGE is similar to that of standard agarose gel electrophoresis, with the main exception being the applica ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Minimum Spanning Tree
A minimum spanning tree (MST) or minimum weight spanning tree is a subset of the edges of a connected, edge-weighted undirected graph that connects all the vertices together, without any cycles and with the minimum possible total edge weight. That is, it is a spanning tree whose sum of edge weights is as small as possible. More generally, any edge-weighted undirected graph (not necessarily connected) has a minimum spanning forest, which is a union of the minimum spanning trees for its connected components. There are many use cases for minimum spanning trees. One example is a telecommunications company trying to lay cable in a new neighborhood. If it is constrained to bury the cable only along certain paths (e.g. roads), then there would be a graph containing the points (e.g. houses) connected by those paths. Some of the paths might be more expensive, because they are longer, or require the cable to be buried deeper; these paths would be represented by edges with larger weight ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Dendrogram
A dendrogram is a diagram representing a Tree (graph theory), tree graph. This diagrammatic representation is frequently used in different contexts: * in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. * in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heat map, heatmaps. * in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree. The name ''dendrogram'' derives from the two ancient greek words (), meaning "tree", and (), meaning "drawing, mathematical figure". Clustering example For a clustering example, suppose that five taxa (a to e) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes repre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Isolation (microbiology)
In microbiology, the term isolation refers to the separation of a strain from a natural, mixed population of living microbes, as present in the environment, for example in water or soil, or from living beings with skin flora, oral flora or gut flora, in order to identify the microbe(s) of interest. Historically, the laboratory techniques of isolation first developed in the field of bacteriology and parasitology (during the 19th century), before those in virology during the 20th century. History The laboratory techniques of isolating microbes first developed during the 19th century in the field of bacteriology and parasitology using light microscopy. 1860 marked the successful introduction of liquid medium by Louis Pasteur. The liquid culture pasteur developed allowed for the visulization of promoting or inhibiting growth of specific bacteria. This same technique is utilized today through various mediums like Mannitol salt agar, a solid medium. Solid cultures were developed in 1 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Tryptophanase
The enzyme tryptophanase () catalyzes the chemical reaction :L-tryptophan + H2O \rightleftharpoons indole + pyruvate + NH3 This enzyme belongs to the family of lyases, specifically in the "catch-all" class of carbon-carbon lyases. The systematic name of this enzyme class is L-tryptophan indole-lyase (deaminating; pyruvate-forming). Other names in common use include L-tryptophanase, and L-tryptophan indole-lyase (deaminating). This enzyme participates in tryptophan metabolism and nitrogen metabolism. It has 2 cofactors: pyridoxal phosphate, and potassium Potassium is a chemical element; it has Symbol (chemistry), symbol K (from Neo-Latin ) and atomic number19. It is a silvery white metal that is soft enough to easily cut with a knife. Potassium metal reacts rapidly with atmospheric oxygen to .... Structural studies As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1AX4, 2C44, and 2OQX. Retrieved from Protein Dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Dihydroorotase
Dihydroorotase (, ''carbamoylaspartic dehydrase'', ''dihydroorotate hydrolase'') is an enzyme which converts carbamoyl aspartic acid into 4,5-dihydroorotic acid in the biosynthesis of pyrimidines. It forms a multifunctional enzyme with carbamoyl phosphate synthetase and aspartate transcarbamoylase. Dihydroorotase is a zinc metalloenzyme Metalloprotein is a generic term for a protein that contains a metal ion cofactor. A large proportion of all proteins are part of this category. For instance, at least 1000 human proteins (out of ~20,000) contain zinc-binding protein domains al .... See also * Pyrimidine biosynthesis References External links * * EC 3.5.2 {{transferase-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Diaminopimelate Decarboxylase
The enzyme diaminopimelate decarboxylase () catalyzes the cleavage of carbon-carbon bonds in ''meso''- 2,6-diaminoheptanedioate (diaminopimelate) to produce CO2 and L-lysine, the essential amino acid. It employs the cofactor pyridoxal phosphate, also known as PLP, which participates in numerous enzymatic transamination, decarboxylation and deamination reactions. This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is ''meso''-2,6-diaminoheptanedioate carboxy-lyase (L-lysine-forming).DAP-decarboxylase catalyzes the final step in the meso-diaminopimelate/lysine biosynthetic pathway. Lysine is used for protein synthesis and used in the peptidoglycan layer of Gram-positive bacteria cell walls. This enzyme is not found in humans, but the ortholog is ornithine decarboxylase. Structure DAPDC is a PLP-dependent enzyme belonging to the alanine racemase family. This enzyme is gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Threonine Dehydrogenase
In enzymology, a L-threonine 3-dehydrogenase () is an enzyme that catalyzes the chemical reaction :L-threonine + NAD+ \rightleftharpoons L-2-amino-3-oxobutanoate + NADH + H+ Thus, the two substrates of this enzyme are L-threonine and NAD+, whereas its 3 products are L-2-amino-3-oxobutanoate, NADH, and H+. This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is L-threonine:NAD+ oxidoreductase. Other names in common use include L-threonine dehydrogenase, threonine 3-dehydrogenase, and threonine dehydrogenase. This enzyme participates in glycine, serine and threonine metabolism. Structural studies As of late 2007, 3 structures A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phosphoribosylaminoimidazole Synthetase
Phosphoribosylglycinamide formyltransferase (), also known as glycinamide ribonucleotide transformylase (GAR Tfase), is an enzyme with systematic name ''10-formyltetrahydrofolate:5'-phosphoribosylglycinamide N-formyltransferase''. This enzyme catalyses the following chemical reaction : 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide \rightleftharpoons tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide This tetrahydrofolate (THF)–dependent enzyme catalyzes a nucleophilic acyl substitution of the formyl group from 10-formyltetrahydrofolate (fTHF) to N1-(5-phospho-D-ribosyl)glycinamide (GAR) to form N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide (fGAR) as shown above. This reaction plays an important role in the formation of purine through the ''de novo'' purine biosynthesis pathway. This pathway creates inosine monophosphate (IMP), a precursor to adenosine monophosphate (AMP) and guanosine monophosphate (GMP). AMP is a building block for important ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |