1.
BRENDA
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BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is a resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction, kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a user interface that allows a convenient and sophisticated access to the data. BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology in Braunschweig and was published as a series of books. Its name was originally an acronym for the Braunschweig Enzyme Database, from 1996 to 2007, BRENDA was located at the University of Cologne. There, BRENDA developed into a publicly accessible enzyme information system, in 2007, BRENDA returned to Braunschweig. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics, a major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the interface are also incorporated into the BRENDA database. The latest update was performed in January 2015, Database, The database contains more than 40 data fields with enzyme-specific information on more than 7000 EC numbers that are classified according to the IUBMB. Currently, BRENDA contains manually annotated data from over 140,000 different scientific articles, each enzyme entry is clearly linked to at least one literature reference, to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 110,000 enzyme ligands, the term ligand is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors, the origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides. Furthermore, cross-references to external resources such as sequence and 3D-structure databases. Extensions, Since 2006, the data in BRENDA is supplemented with information extracted from the literature by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA, AMENDA, DRENDA and KENDA were introduced and these text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed. Data access, There are several tools to access to the data in BRENDA
2.
MetaCyc
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The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc is also used in engineering and metabolomics research. MetaCyc contains extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, MetaCyc data on reactions includes predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds. It also provides enzyme mini-reviews and literature references, MetaCyc data on metabolites includes chemical structures, predicted Gibbs free energies of formation, and links to external databases
3.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
4.
PubMed
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
5.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research
6.
Entrez
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The name Entrez was chosen to reflect the spirit of welcoming the public to search the content available from the NLM. Entrez Global Query is a search and retrieval system that provides access to all databases simultaneously with a single query string. Entrez can efficiently retrieve related sequences, structures, and references, the Entrez system can provide views of gene and protein sequences and chromosome maps. Some textbooks are available online through the Entrez system. The Entrez front page provides, by default, access to the global query, all databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to limit parts of the search statement to particular fields. This returns a unified results page, that shows the number of hits for the search in each of the databases, Entrez also provides a similar interface for searching each particular database and for refining search results. The Limits feature allows the user to narrow a search a web forms interface, the History feature gives a numbered list of recently performed queries. Results of previous queries can be referred to by number and combined via boolean operators, search results can be saved temporarily in a Clipboard. Users with a MyNCBI account can save queries indefinitely and also choose to have updates with new search results e-mailed for saved queries of most databases and it is widely used in the field of biotechnology as a reference tool for students and professionals alike. Entrez searches the following databases, PubMed, biomedical literature citations and abstracts, including Medline - articles from journals, in addition to using the search engine forms to query the data in Entrez, NCBI provides the Entrez Programming Utilities for more direct access to query results. The eUtils are accessed by posting specially formed URLs to the NCBI server, there was also an eUtils SOAP interface which was terminated on July 2015. In 1991, entrez was introduced in CD form, in 1993, a client-server version of the software provided connectivity with the internet. In 1994, NCBI established a website, and Entrez was a part of initial release. In 2001, Entrez bookshelf was released and in 2003, the Entrez Gene database was developed, Entrez search engine form Entrez Help
7.
UniProt
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UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains an amount of information about the biological function of proteins derived from the research literature. The UniProt consortium comprises the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy servers that are a resource for proteomics tools. In 2002, EBI, SIB, and PIR joined forces as the UniProt consortium, each consortium member is heavily involved in protein database maintenance and annotation. Until recently, EBI and SIB together produced the Swiss-Prot and TrEMBL databases and these databases coexisted with differing protein sequence coverage and annotation priorities. Swiss-Prot aimed to provide reliable protein sequences associated with a level of annotation. Recognizing that sequence data were being generated at a pace exceeding Swiss-Prots ability to keep up, meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass, a database of protein sequences and curated families. The consortium members pooled their resources and expertise, and launched UniProt in December 2003. UniProt provides four core databases, UniProtKB, UniParc, UniRef, UniProt Knowledgebase is a protein database partially curated by experts, consisting of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. As of 19 March 2014, release 2014_03 of UniProtKB/Swiss-Prot contains 542,782 sequence entries, UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from literature and biocurator-evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to all known relevant information about a particular protein. Annotation is regularly reviewed to keep up with current scientific findings, the manual annotation of an entry involves detailed analysis of the protein sequence and of the scientific literature. Sequences from the gene and the same species are merged into the same database entry. Differences between sequences are identified, and their cause documented, a range of sequence analysis tools is used in the annotation of UniProtKB/Swiss-Prot entries. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry and these predictions include post-translational modifications, transmembrane domains and topology, signal peptides, domain identification, and protein family classification. Relevant publications are identified by searching databases such as PubMed, the full text of each paper is read, and information is extracted and added to the entry
8.
Locus (genetics)
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A locus in genetics is the position on a chromosome. Each chromosome carries many genes, humans estimated haploid protein coding genes are 19, 000-20,000, a variant of the similar DNA sequence located at a given locus is called an allele. The ordered list of known for a particular genome is called a gene map. Gene mapping is the process of determining the locus for a biological trait. The chromosomal locus of a gene might be written 3p22.1, here 3 means chromosome 3, p means p-arm. And 22 refers to region 2, band 2 and this is read as two two, not as twenty-two. So the entire locus is read as three P two two point one, the cytogenetic bands are counting from the centromere out toward the telomeres. A range of loci is specified in a similar way. For example, the locus of gene OCA1 may be written 11q1. 4-q2.1, meaning it is on the arm of chromosome 11. The ends of a chromosome are labeled pter and qter, a centisome is defined as 1% of a chromosome length. Chromosomal translocation Cytogenetic notation Karyotype Null allele Michael, R. Cummings, belmont, California, Brooks/Cole Overview at ornl. gov Chromosome Banding and Nomenclature from NCBI
9.
Chromosome 1 (human)
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Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide pairs, which are the basic units of information for DNA. It represents about 9% of the total DNA in human cells, identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies, in January 2017, two estimates differed by 12%, with one estimate giving 5,078 genes, and the other estimate giving 4,474 genes. It was the last completed chromosome, sequenced two decades after the beginning of the Human Genome Project, some of these diseases are hearing loss, Alzheimer disease, glaucoma and breast cancer. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases, patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. The following diseases are some of those related to genes on chromosome 1, reuters Wed May 17,2006 Final genome chapter published BBC NEWS
10.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
11.
Glycosidic bond
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In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide and the group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside, glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one also considers S-glycosidic bonds, where the oxygen of the bond is replaced with a sulfur atom. In the same way, N-glycosidic bonds, have the glycosidic oxygen replaced with nitrogen. Substances containing N-glycosidic bonds are known as glycosylamines. C-glycosyl bonds have the oxygen replaced by a carbon, the term C-glycoside is considered a misnomer by IUPAC and is discouraged. All of these modified glycosidic bonds have different susceptibility to hydrolysis, one distinguishes between α- and β-glycosidic bonds based on the relative stereochemistry of the anomeric position and the stereocenter furthest from C1 in the saccharide. An α-glycosidic bond is formed when both carbons have the same stereochemistry, whereas a β-glycosidic bond occurs when the two carbons have different stereochemistry. One complicating issue is that the alpha and beta conformations were originally defined based on the orientation of the major constituents in a Haworth projection. In this case, for D-sugars, a beta conformation would see the major constituent at each carbon drawn above the plane of the ring, for L-sugars, the definitions would then, necessarily, reverse. This is worth noting as these older definitions still permeate the literature, pharmacologists often join substances to glucuronic acid via glycosidic bonds in order to increase their water solubility, this is known as glucuronidation. Many other glycosides have important physiological functions, Nüchter et al. have shown a new approach to Fischer Glycosylation. Employing a microwave oven equipped with refluxing apparatus in a reactor with pressure bombs, Nüchter et al. were able to achieve 100% yield of α-. This method can be performed on a multi-kilogram scale, ondruschka, and W. Lautenschläger, Synthetic Communications 31,1277. Vishal Y Joshis method Joshi et al, d-glucose is first protected by forming the peracetate by addition of acetic anhydride in acetic acid, and then addition of hydrogen bromide which brominates at the 5-position. On addition of the alcohol ROH and lithium carbonate, the OR replaces the bromine and it was suggested by Joshi et al. that lithium acts as the nucleophile that attacks the carbon at the 5-position and through a transition state the alcohol is substituted for the bromine group. Glycoside hydrolases, are enzymes that break glycosidic bonds, glycoside hydrolases typically can act either on α- or on β-glycosidic bonds, but not on both
12.
Chitin
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Chitin n is a long-chain polymer of an N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. The structure of chitin is comparable to the cellulose, forming crystalline nanofibrils or whiskers. In terms of function, it may be compared to the protein keratin, chitin has proved versatile for several medicinal, industrial and biotechnological purposes. The English word chitin comes from the French word chitine, which first appeared in 1821 and derived from the Greek word χιτών, a similar word, chiton, refers to a marine animal with a protective shell. The structure of chitin was solved by Albert Hofmann in 1929, chitin is a modified polysaccharide that contains nitrogen, it is synthesized from units of N-acetyl-D-glucosamine. Therefore, chitin may be described as cellulose with one group on each monomer replaced with an acetyl amine group. This allows for increased hydrogen bonding between adjacent polymers, giving the chitin-polymer matrix increased strength, in its pure, unmodified form, chitin is translucent, pliable, resilient, and quite tough. Combined with calcium carbonate, as in the shells of crustaceans and molluscs and this composite material is much harder and stiffer than pure chitin, and is tougher and less brittle than pure calcium carbonate. Another difference between pure and composite forms can be seen by comparing the body wall of a caterpillar to the stiff. The elaborate chitin gyroid construction in butterfly wings creates a model of optical devices having potential for innovations in biomimicry, scarab beetles in the genus Cyphochilus also utilize chitin to form extremely thin scales that diffusely reflect white light. These scales are networks of randomly ordered filaments of chitin with diameters on the scale of hundreds of nanometres, the multiple scattering of light is thought to play a role in the unusual whiteness of the scales. In addition, some wasps, such as Protopolybia chartergoides, orally secrete material containing predominantly chitin to reinforce the outer nest envelopes. Chitosan is produced commercially by deacetylation of chitin, chitosan is soluble in water, chitin producing organisms like protozoa, fungi, arthropods, and nematodes are often pathogens in other species. Keratinocytes in skin can also react to chitin or chitin fragments, according to in vitro studies, chitin is sensed by receptors, such as FIBCD1, KLRB1, REG3G, Toll-like receptor 2, CLEC7A, and mannose receptors. Plants also have receptors that can cause a response to chitin, namely chitin elicitor receptor kinase 1, the first chitin receptor was cloned in 2006. When the receptors are activated by chitin, genes related to plant defense are expressed, and jasmonate hormones are activated, commensal fungi that have ways to interact with the host immune response that as of 2016 were not well understood. Some pathogens produce chitin-binding proteins that mask the chitin they shed from these receptors, zymoseptoria tritici is an example of a fungal pathogen that has such blocking proteins, it is a major pest in wheat crops. Chitin was probably present in the exoskeletons of Cambrian arthropods such as trilobites, the oldest preserved chitin dates to the Oligocene, about 25 million years ago, consisting of a scorpion encased in amber
13.
Cell wall
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A cell wall is a structural layer surrounding some types of cells, situated outside the cell membrane. It can be tough, flexible, and sometimes rigid and it provides the cell with both structural support and protection, and also acts as a filtering mechanism. Cell walls are present in most prokaryotes, in algae, plants and fungi, a major function is to act as pressure vessels, preventing over-expansion of the cell when water enters. The composition of cell walls varies between species and may depend on type and developmental stage. The primary cell wall of plants is composed of the polysaccharides cellulose, hemicellulose. Often, other such as lignin, suberin or cutin are anchored to or embedded in plant cell walls. Algae possess walls made of glycoproteins and polysaccharides such as carrageenan, in bacteria, the cell wall is composed of peptidoglycan. The cell walls of archaea have various compositions, and may be formed of glycoprotein S-layers, pseudopeptidoglycan, Fungi possess cell walls made of the glucosamine polymer chitin. Unusually, diatoms have a wall composed of biogenic silica. A plant cell wall was first observed and named by Robert Hooke in 1665, in 1804, Karl Rudolphi and J. H. F. Link proved that cells had independent cell walls, before, it had been thought that cells shared walls and that fluid passed between them this way. The mode of formation of the wall was controversial in the 19th century. Hugo von Mohl advocated the idea that the wall grows by apposition. Carl Nägeli believed that the growth of the wall in thickness, each theory was improved in the following decades, the apposition theory by Eduard Strasburger, and the intussusception theory by Julius Wiesner. In 1930, Ernst Münch coined the term apoplast in order to separate the living symplast from the dead plant region, Cell walls serve similar purposes in those organisms that possess them. They may give cells rigidity and strength, offering protection against mechanical stress, in multicellular organisms, they permit the organism to build and hold a definite shape. Cell walls also limit the entry of large molecules that may be toxic to the cell and they further permit the creation of stable osmotic environments by preventing osmotic lysis and helping to retain water. Their composition, properties, and form may change during the cell cycle, in most cells, the cell wall is flexible, meaning that it will bend rather than holding a fixed shape, but has considerable tensile strength
14.
Fungus
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A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants, a characteristic that places fungi in a different kingdom from plants, bacteria and some protists, is chitin in their cell walls. Similar to animals, fungi are heterotrophs, they acquire their food by absorbing dissolved molecules, growth is their means of mobility, except for spores, which may travel through the air or water. Fungi are the principal decomposers in ecological systems and this fungal group is distinct from the structurally similar myxomycetes and oomycetes. The discipline of biology devoted to the study of fungi is known as mycology, in the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the size of their structures. Fungi include symbionts of plants, animals, or other fungi and they may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform a role in the decomposition of organic matter and have fundamental roles in nutrient cycling. Since the 1940s, fungi have been used for the production of antibiotics, Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, the fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans, losses of crops due to fungal diseases or food spoilage can have a large impact on human food supplies and local economies. The fungus kingdom encompasses a diversity of taxa with varied ecologies, life cycle strategies. However, little is known of the biodiversity of Kingdom Fungi. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla. The English word fungus is directly adopted from the Latin fungus, used in the writings of Horace, a group of all the fungi present in a particular area or geographic region is known as mycobiota, e. g. the mycobiota of Ireland. Like plants, fungi grow in soil and, in the case of mushrooms, form conspicuous fruit bodies. The fungi are now considered a kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes and they have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols, disaccharides, and polysaccharides
15.
Exoskeleton
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An exoskeleton is the external skeleton that supports and protects an animals body, in contrast to the internal skeleton of, for example, a human. In usage, some of the kinds of exoskeletons are known as shells. Examples of animals with exoskeletons include insects such as grasshoppers and cockroaches, the shells of certain sponges and the various groups of shelled molluscs, including those of snails, clams, tusk shells, chitons and nautilus, are also exoskeletons. Some animals, such as the tortoise, have both an endoskeleton and an exoskeleton, exoskeletons have a role in defense from pests and predators, support, and in providing an attachment framework for musculature. Exoskeletons contain chitin, the addition of calcium carbonate makes them harder and stronger, ingrowths of the arthropod exoskeleton known as apodemes serve as attachment sites for muscles. These structures are composed of chitin, and are six times as strong. Similar to tendons, apodemes can stretch to store energy for jumping. Many different species produce exoskeletons, which are composed of a range of materials, bone, cartilage, or dentine is used in the Ostracoderm fish and turtles. Chitin forms the exoskeleton in arthropods including insects, arachnids such as spiders, crustaceans such as crabs and lobsters, calcium carbonates constitute the shells of molluscs, brachiopods, and some tube-building polychaete worms. Silica forms the exoskeleton in the microscopic diatoms and radiolaria, one species of mollusc, the scaly-foot gastropod, even makes use of the iron sulfides greigite and pyrite. Some organisms, such as some foraminifera, agglutinate exoskeletons by sticking grains of sand, contrary to a common misconception, echinoderms do not possess an exoskeleton, as their test is always contained within a layer of living tissue. Exoskeletons have evolved many times,18 lineages evolved calcified exoskeletons alone. Further, other lineages have produced tough outer coatings analogous to an exoskeleton and this coating is constructed from bone in the armadillo, and hair in the pangolin. The armor of reptiles like turtles and Ankylosaurs is constructed of bone, crocodiles have bony scutes, since exoskeletons are rigid, they present some limits to growth. Organisms with open shells can grow by adding new material to the aperture of their shell, as is the case in snails, bivalves, a true exoskeleton, like that found in arthropods, must be shed when it is outgrown. A new exoskeleton is produced beneath the old one, as the old one is shed, the new skeleton is soft and pliable. The animal will pump itself up to expand the new shell to maximal size, when the shell has set, the empty space inside the new skeleton can be filled up as the animal eats. Failure to shed the exoskeleton once outgrown can result in the animal being suffocated within its own shell and this is the mechanism behind some insect pesticides, such as Azadirachtin
16.
Bacillus
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Bacillus is a genus of gram-positive, rod-shaped bacteria and a member of the phylum Firmicutes. Bacillus species can be obligate aerobes, or facultative anaerobes and they will test positive for the enzyme catalase when there has been oxygen used or present. Ubiquitous in nature, Bacillus includes both free-living and parasitic pathogenic species and these characteristics originally defined the genus, but not all such species are closely related, and many have been moved to other genera of the Firmicutes. Many species of Bacillus can produce copious amounts of enzymes which are use of in different industries. B. subtilis has proved a model for research. Other species of Bacillus are important pathogens, causing anthrax and food poisoning, many Bacillus species are able to secrete large quantities of enzymes. A portion of the Bacillus thuringiensis genome was incorporated into corn crops, the resulting GMOs are therefore resistant to some insect pests. Bacillus subtilis is one of the best understood prokaryotes, in terms of molecular and cellular biology and its superb genetic amenability and relatively large size have provided the powerful tools required to investigate a bacterium from all possible aspects. Recent improvements in fluorescent microscopy techniques have provided insight into the dynamic structure of a single cell organism. Bacillus species are almost ubiquitous in nature, e. g. in soil, B. thuringiensis produces a toxin that can kill insects and thus has been used as insecticide. Two Bacillus species are considered significant, B. anthracis, which causes anthrax, and B. cereus. A third species, B. thuringiensis, is an important insect pathogen, the type species is B. subtilis, an important model organism. It is also a notable food spoiler, causing ropiness in bread, some environmental and commercial strains of B. coagulans may play a role in food spoilage of highly acidic, tomato-based products. An easy way to isolate Bacillus species is by placing nonsterile soil in a test tube with water, shaking, placing in melted mannitol salt agar, colonies are usually large, spreading, and irregularly shaped. Under the microscope, the Bacillus cells appear as rods, the cell wall is composed of teichoic and teichuronic acids. The role of the cytoskeleton in shape generation and maintenance is important The genus Bacillus was named in 1835 by Christian Gottfried Ehrenberg and he had seven years earlier named the genus Bacterium. Bacillus was later amended by Ferdinand Cohn to further describe them as spore-forming, Gram-positive, like other genera associated with the early history of microbiology, such as Pseudomonas and Vibrio, the 266 species of Bacillus are ubiquitous. The genus has a very large ribosomal 16S diversity and is environmentally diverse, several studies have tried to reconstruct the phylogeny of the genus
17.
Vibrio
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Vibrio is a genus of Gram-negative bacteria, possessing a curved-rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in water, Vibrio species are facultative anaerobes that test positive for oxidase. All members of the genus are motile and have polar flagella with sheaths, Vibrio species typically possess two chromosomes, which is unusual for bacteria. Each chromosome has a distinct and independent origin of replication, and are conserved together over time in the genus, recent phylogenies have been constructed based on a suite of genes. O. F. Müller described eight species of the genus Vibrio, some of the other species are today assigned to eukaryote taxa, e. g. to the euglenoid Peranema or to the diatom Bacillaria. However, Vibrio Müller,1773 became regarded as the name of a genus. Filippo Pacini isolated micro-organisms he called vibrions from cholera patients in 1854, several species of Vibrio are pathogens. Most disease-causing strains are associated with gastroenteritis, but can also infect open wounds and they can be carried by numerous marine animals, such as crabs or prawns, and have been known to cause fatal infections in humans during exposure. Pathogenic Vibrio species include V. cholerae, V. parahaemolyticus, V. cholerae is generally transmitted by contaminated water. Pathogenic Vibrio species can cause illness, usually associated with eating undercooked seafood. The pathogenic features can be linked to quorum sensing where bacteria are able to express their virulence factor via their signalling molecules, V. vulnificus outbreaks commonly occur in warm climates and small, generally lethal, outbreaks occur regularly. An outbreak occurred in New Orleans after Hurricane Katrina, and several cases occur most years in Florida. As of 2013 in the United States, Vibrio infections as a whole were up 43% when compared with the rates observed in 2006-2008, V. vulnificus, the most severe strain, has not increased. Foodborne Vibrio infections are most often associated with eating raw shellfish, many Vibrio species are also zoonotic. They cause disease in fish and shellfish, and are causes of mortality among domestic marine life. Medical care depends on the presentation and the presence of underlying medical conditions. Because Vibrio gastroenteritis is self-limited in most patients, no medical therapy is required. Patients who cannot tolerate oral fluid replacement may require intravenous fluid therapy, although most Vibrio species are sensitive to antibiotics such as doxycycline or quinolones, antibiotic therapy does not shorten the course of the illness or the duration of pathogen excretion
18.
Arthropod
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An arthropod is an invertebrate animal having an exoskeleton, a segmented body, and jointed appendages. Arthropods form the phylum Arthropoda, which includes the insects, arachnids, myriapods, arthropods are characterized by their jointed limbs and cuticle made of chitin, often mineralised with calcium carbonate. The arthropod body plan consists of segments, each with a pair of appendages, the rigid cuticle inhibits growth, so arthropods replace it periodically by moulting. Their versatility has enabled them to become the most species-rich members of all guilds in most environments. They have over a million described species, making up more than 80% of all described living species, some of which. Arthropods range in size from the microscopic crustacean Stygotantulus up to the Japanese spider crab, arthropods primary internal cavity is a hemocoel, which accommodates their internal organs, and through which their haemolymph – analogue of blood – circulates, they have open circulatory systems. Like their exteriors, the organs of arthropods are generally built of repeated segments. Their nervous system is ladder-like, with paired ventral nerve cords running through all segments and their heads are formed by fusion of varying numbers of segments, and their brains are formed by fusion of the ganglia of these segments and encircle the esophagus. The respiratory and excretory systems of arthropods vary, depending as much on their environment as on the subphylum to which they belong, arthropods also have a wide range of chemical and mechanical sensors, mostly based on modifications of the many setae that project through their cuticles. Aquatic species use internal or external fertilization. Almost all arthropods lay eggs, but scorpions give birth to live young after the eggs have hatched inside the mother, arthropod hatchlings vary from miniature adults to grubs and caterpillars that lack jointed limbs and eventually undergo a total metamorphosis to produce the adult form. The level of care for hatchlings varies from nonexistent to the prolonged care provided by scorpions. The evolutionary ancestry of arthropods dates back to the Cambrian period, the group is generally regarded as monophyletic, and many analyses support the placement of arthropods with cycloneuralians in a superphylum Ecdysozoa. Overall however, the relationships of Metazoa are not yet well resolved. Likewise, the relationships between various groups are still actively debated. Arthropods contribute to the food supply both directly as food, and more importantly indirectly as pollinators of crops. Some species are known to spread disease to humans, livestock. The word arthropod comes from the Greek ἄρθρον árthron, joint, and πούς pous, i. e. foot or leg, arthropods are invertebrates with segmented bodies and jointed limbs
19.
Zooplankton
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Plankton are organisms drifting in oceans, seas, and bodies of fresh water. The word zooplankton is derived from the Greek zoon, meaning animal, individual zooplankton are usually microscopic, but some are larger and visible with the naked eye. Zooplankton is a categorization spanning a range of organism sizes including small protozoans, although zooplankton are primarily transported by ambient water currents, many have locomotion, used to avoid predators or to increase prey encounter rate. Ecologically important protozoan zooplankton groups include the foraminiferans, radiolarians and dinoflagellates and this wide phylogenetic range includes a similarly wide range in feeding behavior, filter feeding, predation and symbiosis with autotrophic phytoplankton as seen in corals. Zooplankton feed on bacterioplankton, phytoplankton, other zooplankton, detritus, as a result, zooplankton are primarily found in surface waters where food resources are abundant. Just as any species can be limited within a geographical region, however, species of zooplankton are not dispersed uniformly or randomly within a region of the ocean. As with phytoplankton, ‘patches’ of zooplankton species exist throughout the ocean, zooplankton patchiness can also be influenced by biological factors, as well as other physical factors. Biological factors include breeding, predation, concentration of phytoplankton, the physical factor that influences zooplankton distribution the most is mixing of the water column that affects nutrient availability and, in turn, phytoplankton production. Since they are small, zooplankton can respond rapidly to increases in phytoplankton abundance, for instance. Zooplankton can also act as a disease reservoir, crustacean zooplankton have been found to house the bacterium Vibrio cholerae, which causes cholera, by allowing the cholera vibrios to attach to their chitinous exoskeletons. This symbiotic relationship enhances the ability to survive in an aquatic environment, as the exoskeleton provides the bacterium with carbon. A global coverage database of zooplankton biomass and abundance data
20.
Coccidioides
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Coccidioides is a genus of dimorphic ascomycetes in the family Onygenaceae. The host acquires the disease by respiratory inhalation of spores disseminated in their natural habitat, the causative agents of coccidioidomycosis are Coccidioides immitis and Coccidioides posadasii. Both C. immitas and C. posadasii are indistinguishable during laboratory testing, coccidioidomycosis is amazingly diverse in terms of its scope of clinical presentation, as well as clinical severity. About 60% of Coccidioides infections as determined by serologic conversion are asymptomatic, the most common clinical syndrome in the other 40% of infected patients is an acute respiratory illness characterized by fever, cough, and pleuritic pain. Skin manifestations, such as erythema nodosum, are common with Coccidioides infection. Coccidioides infection can cause a severe and difficult-to-treat meningitis in AIDS and other immunocompromised patients, infection can sometimes cause acute respiratory distress syndrome and fatal multilobar pneumonia. The risk of infection increases with age. Both C. immitis and C. posadasii were viewed as desert saprophytes, the soil fungus Coccidioides was discovered in 1892 by Alejandro Posadas, a medical student, in an Argentinian soldier with widespread disease. Biopsy specimens revealed organisms that resembled the protozoan Coccidia, in 1896, Gilchrist and Rixford named the organism Coccidioides immitis. Ophüls and Moffitt proved that C. immitis was a rather than a protozoan in 1900. In 2002, C. immitis was divided into a species, C. posadasii. This article cites public domain text from the CDC, as shown, Coccidioides in Index Fungorum Coccidioides sp. National Center for Biotechnology Information, Coccidioides
21.
CHI3L1
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Chitinase-3-like protein 1, also known as YKL-40, is a secreted glycoprotein that is approximately 40kDa in size that in humans is encoded by the CHI3L1 gene. The name YKL-40 is derived from the three N-terminal amino acids present on the form and its molecular mass. YKL-40 is expressed and secreted by various cell-types including macrophages, chondrocytes, fibroblast-like synovial cells, vascular smooth muscle cells, the biological function of YKL-40 is unclear. It is not known to have a specific receptor and its pattern of expression is associated with pathogenic processes related to inflammation, extracellular tissue remodeling, fibrosis and solid carcinomas and asthma. Chitinases catalyze the hydrolysis of chitin, which is an abundant glycopolymer found in insect exoskeletons, the glycoside hydrolase 18 family of chitinases includes eight human family members. This gene encodes a member of the glycosyl hydrolase 18 family. The protein lacks chitinase activity and is secreted by activated macrophages, chondrocytes, neutrophils, the protein is thought to play a role in the process of inflammation and tissue remodeling. YKL-40 lacks chitinase activity due to mutations within the active site, YKL-40 has been linked to activation of the AKT pro-survival signaling pathway. YKL-40 promotes angiogenesis through VEGF-dependent and independent pathways, YKL-40 is a migration factor for primary astrocytes and its expression is controlled by NFI-X3, STAT3 and AP-1. CHI3l1 is induced by a variety of cancers and in the presence of semaphorin 7A can inhibit multiple anti-tumor immune system responses, activating an antiviral immune pathway known as the RIG-like helicase has the ability to counter CHI3l1 induction. Cancer cells can offset RLH by stimulating NLRX1, poly, an RNA-like molecule, can stimulate RLH activation. RLH activation can inhibit the expression of receptor IL-13Rα2pand lmonary metastasisre. It stores NK cell accumulation and activation and it augments the expression of IFN-α/β, chemerin and its receptor ChemR23, p-cofilin, LIMK2 and PTEN and inhibiting BRAF and NLRX1 in a MAVS-dependent manner. It is assumed that YKL-40 plays a role in cell proliferation, survival, invasiveness. It is suggested that YKL-40 is a associated with a poorer clinical outcome in genetically defined subgroups of different tumors. YKL-40 was recently introduced into clinical practice, a few techniques are available for its detection. YKL-40 is a Th2 promoting cytokine that is present at levels in the tumor microenvironment. Elevated levels of YKL-40 correlate strongly with stage and outcome of various types of cancer, targeting YKL-40 with neutralizing antibodies is effective as a treatment in animal models of glioblastoma multiforme
22.
Monosaccharide
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Monosaccharides, also called simple sugars, are the most basic units of carbohydrates. They are fundamental units of carbohydrates and cannot be hydrolyzed to simpler compounds. The general formula is CnH 2nOn and they are the simplest form of sugar and are usually colorless, water-soluble, and crystalline solids. Some monosaccharides have a sweet taste, examples of monosaccharides include glucose, fructose and galactose. Monosaccharides are the blocks of disaccharides and polysaccharides. Further, each carbon atom that supports a group is chiral, giving rise to a number of isomeric forms. For instance, galactose and glucose are both aldohexoses, but have different physical structures and chemical properties, with few exceptions, monosaccharides have this chemical formula, Cxy, where conventionally x ≥3. Monosaccharides can be classified by the x of carbon atoms they contain, triose tetrose, pentose, hexose, heptose. The most important monosaccharide, glucose, is a hexose, examples of heptoses include the ketoses mannoheptulose and sedoheptulose. Monosaccharides with eight or more carbons are rarely observed as they are quite unstable, in aqueous solutions monosaccharides exist as rings. Simple monosaccharides have a linear and unbranched carbon skeleton with one carbonyl functional group, therefore, the molecular structure of a simple monosaccharide can be written as HnmH, where n +1 + m = x, so that its elemental formula is CxH2xOx. By convention, the atoms are numbered from 1 to x along the backbone. If the carbonyl is at position 1, the molecule begins with a formyl group H− and is technically an aldehyde, in that case, the compound is termed an aldose. Otherwise, the molecule has a group, a carbonyl −− between two carbons, then it is formally a ketone, and is termed a ketose. Ketoses of biological interest usually have the carbonyl at position 2, the various classifications above can be combined, resulting in names such as aldohexose and ketotriose. A more general nomenclature for open-chain monosaccharides combines a Greek prefix to indicate the number of carbons with the suffixes -ose for aldoses, in the latter case, if the carbonyl is not at position 2, its position is then indicated by a numeric infix. So, for example, H4H is pentose, H3H is pentulose, two monosaccharides with equivalent molecular graphs may still be distinct stereoisomers, whose molecules differ in the three-dimensional arrangement of the bonds of certain atoms. This happens only if the molecule contains a center, specifically a carbon atom that is chiral
23.
N-Acetylglucosamine
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N-Acetylglucosamine is a monosaccharide and a derivative of glucose. It is an amide between glucosamine and acetic acid and it has a molecular formula of C8H15NO6, a molar mass of 221.21 g/mol, and it is significant in several biological systems. It is part of a biopolymer in the cell wall, built from alternating units of GlcNAc and N-acetylmuramic acid. This layered structure is called peptidoglycan, GlcNAc is the monomeric unit of the polymer chitin, which forms the outer coverings of insects and crustaceans. It is the component of the radulas of mollusks, the beaks of cephalopods. Polymerized with glucuronic acid, it forms hyaluronan, GlcNAc has been reported to be an inhibitor of elastase release from human polymorphonuclear leukocytes, however this is much weaker than the inhibition seen with N-acetylgalactosamine. It has been proposed as a treatment for diseases. Keratan sulfate Chitin N-Acetyllactosamine synthase N-Acetylgalactosamine Wheat germ agglutinin, a plant lectin that binds to this substrate Re Multiple Sclerosis
24.
Glycoside hydrolase family 18
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In molecular biology, Glycoside hydrolase family 18 is a family of glycoside hydrolases. Glycoside hydrolases EC3.2.1. are a group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, some members of this family, CAZY GH_18, belong to the chitinase class II group which includes chitinase, chitodextrinase and the killer toxin of Kluyveromyces lactis. Another chitinase II member is the novel gene Chitinase domain-containing protein 1, the family also includes various glycoproteins from mammals, cartilage glycoprotein and the oviduct-specific glycoproteins are two examples. This article incorporates text from the public domain Pfam and InterPro IPR001223
25.
Glycoside hydrolase family 19
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In molecular biology, Glycoside hydrolase family 19 is a family of glycoside hydrolases. Glycoside hydrolases EC3.2.1. are a group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, Glycoside hydrolase family 19 CAZY GH_19 comprises enzymes with only one known activity, chitinase. Chitinases are enzymes that catalyze the hydrolysis of the beta-1, 4-N-acetyl-D-glucosamine linkages in chitin polymers, chitinases belong to glycoside hydrolase families 18 or 19. Chitinases of family 19 are enzymes from plants that function in the defence against fungal, class IA/I and IB/II enzymes differ in the presence or absence of a N-terminal chitin-binding domain. The catalytic domain of these enzymes consist of about 220 to 230 amino acid residues and this article incorporates text from the public domain Pfam and InterPro IPR000726
26.
Glycoside hydrolase family 20
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In molecular biology, glycoside hydrolase family 20 is a family of glycoside hydrolases. Glycoside hydrolases EC3.2.1. are a group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, glycoside hydrolase family 20 CAZY GH_20 comprises enzymes with several known activities, beta-hexosaminidase, lacto-N-biosidase. Carbonyl oxygen of the C-2 acetamido group of the acts as the catalytic nucleophile/base in this family of enzymes. The two beta chains are derived from the cleavage of a precursor, mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside. This article incorporates text from the public domain Pfam and InterPro IPR015883
27.
Hexosaminidase
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Hexosaminidase is an enzyme involved in the hydrolysis of terminal N-acetyl-D-hexosamine residues in N-acetyl-β-D-hexosaminides. Functional lysosomal β-hexosaminidase enzymes are dimeric in structure, three isozymes are produced through the combination of α and β subunits to form any one of three active dimers, The α and β subunits are encoded by separate genes, HEXA and HEXB respectively. Beta-hexosaminidase and the cofactor GM2 activator protein catalyze the degradation of the GM2 gangliosides, gene mutations in HEXB often result in Sandhoff disease, whereas, mutations in HEXA decrease the hydrolysis of GM2 gangliosides, which is the main cause of Tay-Sachs disease. A Michaelis complex consisting of a residue, a GalNAc residue on the GM2 ganglioside. A glutamate residue works as an acid by donating its hydrogen to the oxygen atom on the GalNAc residue. An aspartate residue positions the C2-acetamindo group so that it can be attacked by the nucleophile, the aspartate residue stabilizes the positive charge on the nitrogen atom in the oxazolinium ion intermediate. Following the formation of the oxazolinium ion intermediate, water attacks the electrophillic acetal carbon, glutamate acts as a base by deprotonating the water leading to the formation of the product complex and the GM3ganglioside. There are numerous mutations that lead to hexosaminidase deficiency including gene deletions, nonsense mutations, Tay-Sachs disease occurs when hexosaminidase A loses its ability to function. Over 100 different mutations have been discovered just in infantile cases of Tay-Sachs disease alone, the most common mutation, which occurs in over 80 percent of Tay-Sachs patients, results from a four base pair addition in exon 11 of the Hex A gene. This insertion leads to a stop codon, which causes the Hex A deficiency. Children born with Tay-Sachs usually die between two and four years of age from aspiration and pneumonia, Tay-Sachs causes cerebral degeneration and blindness. Patients also experience flaccid extremities and seizures, at this point in time, there has been no cure or effective treatment of Tay-Sachs disease. NAG-thiazoline, NGT, acts as mechanism based inhibitor of hexosaminidase A, in patients with Tay-Sachs disease, NGT acts as a molecular chaperone by binding in the active site of hexosaminidase A which helps create a properly folded hexosaminidase A. The stable dimer conformation of hexosaminidase A has the ability to leave the endoplasmic reticulum and is directed to the lysosome where it can perform the degradation of GM2 gangliosides. The two subunits of hexosaminidase A are shown below, The bifunctional protein NCOAT that is encoded by the MGEA5 gene possesses both hexosaminidase and histone acetyltransferase activities, NCOAT is also known as hexosaminidase C and has distinct substrate specificities compared to lysosomal hexosaminidase A. A single-nucleotide polymorphism in the human O-GlcNAcase gene is linked to diabetes mellitus type 2, a fourth mammalian hexosaminidase polypeptide which has been designated hexosaminidase D has recently been identified. GeneReviews/NCBI/NIH/UW entry on hexosaminidase A deficiency, Tay-Sachs disease hexosaminidase A at the US National Library of Medicine Medical Subject Headings EC3.2.1.52
28.
Isoelectric point
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The isoelectric point, is the pH at which a particular molecule carries no net electrical charge in the statistical mean. The standard nomenclature to represent the point is pH, although pI is also commonly seen. The net charge on the molecule is affected by pH of its environment and can become more positively or negatively charged due to the gain or loss, respectively. Surfaces naturally charge to form a double layer, in the common case when the surface charge-determining ions are H+/OH−, the net surface charge is affected by the pH of the liquid in which the solid is submerged. The pI value can affect the solubility of a molecule at a given pH, such molecules have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution. Biological amphoteric molecules such as proteins contain both acidic and basic functional groups, amino acids that make up proteins may be positive, negative, neutral, or polar in nature, and together give a protein its overall charge. At a pH below their pI, proteins carry a net positive charge, isoelectric focusing is also the first step in 2-D gel polyacrylamide gel electrophoresis. For an amino acid with one amine and one carboxyl group. P I = p K a 1 + p K a 22 The pH of a gel is determined by the buffer used for that gel. If the pH of the buffer is above the pI of the protein being run, if the pH of the buffer is below the pI of the protein being run, the protein will migrate to the negative pole of the gel. If the protein is run with a buffer pH that is equal to the pI and this is also true for individual amino acids. In the two examples the isoelectric point is shown by the vertical line. In glycine the pK values are separated by nearly 7 units so the concentration of the neutral species, glycine may exist as a zwitterion at the isoelectric point, but the equilibrium constant for the isomerization reaction in solution H2NCH2CO2H ⇌ H3N+CH2CO2− is not known. The other example, adenosine monophosphate is shown to illustrate the fact that a species may, in principle. In fact the concentration of H32+ is negligible at the point in this case. If the pI is greater than the pH, the molecule will have a positive charge, a number of algorithms for estimating isoelectric points of peptides and proteins have been developed. Most of them use Henderson–Hasselbalch equation with different pK values, for instance, within the model proposed by Bjellqvist and co-workers the pKs were determined between closely related immobilines, by focusing the same sample in overlapping pH gradients. Some improvements in the methodology have also proposed
29.
Vacuole
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A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are formed by the fusion of multiple membrane vesicles and are effectively just larger forms of these, the organelle has no basic shape or size, its structure varies according to the needs of the cell. In seeds, stored proteins needed for germination are kept in protein bodies, vacuoles also play a major role in autophagy, maintaining a balance between biogenesis and degradation, of many substances and cell structures in certain organisms. They also aid in the lysis and recycling of misfolded proteins that have begun to build up within the cell, thomas Boller and others proposed that the vacuole participates in the destruction of invading bacteria and Robert B Mellor proposed organ-specific forms have a role in housing symbiotic bacteria. In protists, vacuoles have the function of storing food which has been absorbed by the organism and assisting in the digestive. The vacuole probably evolved several times independently, even within the Viridiplantae, contractile vacuoles were first observed by Spallanzani in protozoa, although mistaken for respiratory organs. Dujardin named these stars as vacuoles, in 1842, Schleiden applied the term for plant cells, to distinguish the structure with cell sap from the rest of the protoplasm. In 1885, de Vries named the vacuoule membrane as tonoplast, large vacuoles are found in three genera of filamentous sulfur bacteria, the Thioploca, Beggiatoa and Thiomargarita. The cytosol is extremely reduced in these genera and the vacuole can occupy between 40–98% of the cell, the vacuole contains high concentrations of nitrate ions and is therefore thought to be a storage organelle. Gas vacuoles, which are freely permeable to gas, are present in species of Cyanobacteria. They allow the bacteria to control their buoyancy, most mature plant cells have one large vacuole that typically occupies more than 30% of the cells volume, and that can occupy as much as 80% of the volume for certain cell types and conditions. Strands of cytoplasm often run through the vacuole, a vacuole is surrounded by a membrane called the tonoplast and filled with cell sap. Also called the membrane, the tonoplast is the cytoplasmic membrane surrounding a vacuole. As a membrane, it is involved in regulating the movements of ions around the cell. The low pH of the vacuole also allows degradative enzymes to act, although single large vacuoles are most common, the size and number of vacuoles may vary in different tissues and stages of development. For example, developing cells in the meristems contain small provacuoles and cells of the vascular cambium have many small vacuoles in the winter, aside from storage, the main role of the central vacuole is to maintain turgor pressure against the cell wall. Proteins found in the tonoplast control the flow of water into and out of the vacuole through active transport, pumping potassium ions into, due to osmosis, water will diffuse into the vacuole, placing pressure on the cell wall. If water loss leads to a significant decline in turgor pressure, turgor pressure exerted by the vacuole is also essential in supporting plants in an upright position
30.
Blood
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Blood is a body fluid in humans and other animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away from those same cells. In vertebrates, it is composed of blood cells suspended in blood plasma, plasma, which constitutes 55% of blood fluid, is mostly water, and contains dissipated proteins, glucose, mineral ions, hormones, carbon dioxide, and blood cells themselves. Albumin is the protein in plasma, and it functions to regulate the colloidal osmotic pressure of blood. The blood cells are red blood cells, white blood cells. The most abundant cells in blood are red blood cells. These contain hemoglobin, a protein, which facilitates oxygen transport by reversibly binding to this respiratory gas. In contrast, carbon dioxide is mostly transported extracellularly as bicarbonate ion transported in plasma, vertebrate blood is bright red when its hemoglobin is oxygenated and dark red when it is deoxygenated. Some animals, such as crustaceans and mollusks, use hemocyanin to carry oxygen, insects and some mollusks use a fluid called hemolymph instead of blood, the difference being that hemolymph is not contained in a closed circulatory system. In most insects, this blood does not contain oxygen-carrying molecules such as hemoglobin because their bodies are small enough for their system to suffice for supplying oxygen. Jawed vertebrates have an immune system, based largely on white blood cells. White blood cells help to resist infections and parasites, platelets are important in the clotting of blood. Arthropods, using hemolymph, have hemocytes as part of their immune system, Blood is circulated around the body through blood vessels by the pumping action of the heart. Medical terms related to blood often begin with hemo- or hemato- from the Greek word αἷμα for blood. In terms of anatomy and histology, blood is considered a form of connective tissue, given its origin in the bones. The average adult has a volume of roughly 5 litres. These blood cells consist of erythrocytes, leukocytes, and thrombocytes, by volume, the red blood cells constitute about 45% of whole blood, the plasma about 54. 3%, and white cells about 0. 7%. Whole blood exhibits non-Newtonian fluid dynamics, if all human hemoglobin were free in the plasma rather than being contained in RBCs, the circulatory fluid would be too viscous for the cardiovascular system to function effectively. One microliter of blood contains,4.7 to 6.1 million,4.2 to 5.4 million erythrocytes, Red blood cells contain the bloods hemoglobin, mature red blood cells lack a nucleus and organelles in mammals
31.
Cartilage
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It is not as hard and rigid as bone, but it is stiffer and less flexible than muscle. Because of its rigidity, cartilage often serves the purpose of holding tubes open in the body, cartilage is classified in three types, elastic cartilage, hyaline cartilage and fibrocartilage, which differ in relative amounts of collagen and proteoglycan. Cartilage does not contain blood vessels or nerves, nutrition is supplied to the chondrocytes by diffusion. The compression of the cartilage or flexion of the elastic cartilage generates fluid flow. Compared to other tissues, cartilage has a very slow turnover of its extracellular matrix. In embryogenesis, the system is derived from the mesoderm germ layer. Following the initial chondrification that occurs during embryogenesis, cartilage growth consists mostly of the maturing of immature cartilage to a mature state. The division of cells within cartilage occurs very slowly, and thus growth in cartilage is not based on an increase in size or mass of the cartilage itself. The articular cartilage function is dependent on the composition of the extracellular matrix. The ECM consists mainly of proteoglycan and collagens, the main proteoglycan in cartilage is aggrecan, which, as its name suggests, forms large aggregates with hyaluronan. These aggregates are negatively charged and hold water in the tissue, the collagen, mostly collagen type II, constrains the proteoglycans. The ECM responds to tensile and compressive forces that are experienced by the cartilage, cartilage growth thus refers to the matrix deposition, but can also refer to both the growth and remodeling of the extracellular matrix. Due to the stress on the patellofemoral joint during resisted knee flexion. The mechanical properties of articular cartilage in load bearing joints such as knee and hip have been studied extensively at macro, micro and these mechanical properties include the response of cartilage in frictional, compressive, shear and tensile loading. Cartilage is resilient and displays viscoelastic properties, lubricin, a glycoprotein abundant in cartilage and synovial fluid, plays a major role in bio-lubrication and wear protection of cartilage. Cartilage has limited capabilities, Because chondrocytes are bound in lacunae. Therefore, cartilage damage is difficult to heal, also, because hyaline cartilage does not have a blood supply, the deposition of new matrix is slow. Damaged hyaline cartilage is replaced by fibrocartilage scar tissue
. PMID 16332766.
