In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor, examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Sequence homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either an event or a duplication event. Homology among proteins or DNA is inferred from their sequence similarity, significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions, the word homology, coined in about 1656, derives from the Greek ὁμόλογος homologos from ὁμός homos same and λόγος logos relation.
Homology is the relationship between biological structures or sequences that are derived from a common ancestor, for example, many insects possess two pairs of flying wings. In beetles, the first pair of wings has evolved into a pair of hard wing covers, the same major forearm bones are found in fossils of lobe-finned fish such as Eusthenopteron. The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not present in their last common ancestor but rather evolved separately. For example, the wings of insects and birds evolved independently in widely separated groups, the wings of a sycamore maple seed and the wings of a bird are analogous but not homologous, as they develop from quite different structures. A structure can be homologous at one level, but only analogous at another, for example, in the pterosaurs, the wing involves both the forelimb and the hindlimb. Analogy is called homoplasy in cladistics, and convergent or parallel evolution in evolutionary biology, specialised terms are used in taxonomic research.
Primary homology is that initially conjectured by a researcher based on similar structure or anatomical connections, secondary homology is implied by parsimony analysis, where a character that only occurs once on a tree is taken to be homologous. As implied in this definition, many cladists consider homology to be synonymous with synapomorphy, homologies provide the fundamental basis for all biological classification, although some may be highly counter-intuitive. The homologies between these have been discovered by comparing genes in evolutionary developmental biology, among insects, the stinger of the female honey bee is a modified ovipositor, homologous with ovipositors in other insects such as the Orthoptera and those Hymenoptera without stingers. The three small bones in the ear of mammals including humans, the malleus, incus. The malleus and incus develop in the embryo from structures that form jaw bones in lizards, both lines of evidence show that these bones are homologous, sharing a common ancestor.
Among the many homologies in mammal reproductive systems and testicles are homologous, in many plants, defensive or storage structures are made by modifications of the development of primary leaves and roots
The Online Computer Library Center is a US-based nonprofit cooperative organization dedicated to the public purposes of furthering access to the worlds information and reducing information costs. It was founded in 1967 as the Ohio College Library Center, OCLC and its member libraries cooperatively produce and maintain WorldCat, the largest online public access catalog in the world. OCLC is funded mainly by the fees that libraries have to pay for its services, the group first met on July 5,1967 on the campus of the Ohio State University to sign the articles of incorporation for the nonprofit organization. The group hired Frederick G. Kilgour, a former Yale University medical school librarian, Kilgour wished to merge the latest information storage and retrieval system of the time, the computer, with the oldest, the library. The goal of network and database was to bring libraries together to cooperatively keep track of the worlds information in order to best serve researchers and scholars. The first library to do online cataloging through OCLC was the Alden Library at Ohio University on August 26,1971 and this was the first occurrence of online cataloging by any library worldwide.
Membership in OCLC is based on use of services and contribution of data, between 1967 and 1977, OCLC membership was limited to institutions in Ohio, but in 1978, a new governance structure was established that allowed institutions from other states to join. In 2002, the structure was again modified to accommodate participation from outside the United States. As OCLC expanded services in the United States outside of Ohio, it relied on establishing strategic partnerships with networks, organizations that provided training, support, by 2008, there were 15 independent United States regional service providers. OCLC networks played a key role in OCLC governance, with networks electing delegates to serve on OCLC Members Council, in early 2009, OCLC negotiated new contracts with the former networks and opened a centralized support center. OCLC provides bibliographic and full-text information to anyone, OCLC and its member libraries cooperatively produce and maintain WorldCat—the OCLC Online Union Catalog, the largest online public access catalog in the world.
WorldCat has holding records from public and private libraries worldwide. org, in October 2005, the OCLC technical staff began a wiki project, WikiD, allowing readers to add commentary and structured-field information associated with any WorldCat record. The Online Computer Library Center acquired the trademark and copyrights associated with the Dewey Decimal Classification System when it bought Forest Press in 1988, a browser for books with their Dewey Decimal Classifications was available until July 2013, it was replaced by the Classify Service. S. The reference management service QuestionPoint provides libraries with tools to communicate with users and this around-the-clock reference service is provided by a cooperative of participating global libraries. OCLC has produced cards for members since 1971 with its shared online catalog. OCLC commercially sells software, e. g. CONTENTdm for managing digital collections, OCLC has been conducting research for the library community for more than 30 years.
In accordance with its mission, OCLC makes its research outcomes known through various publications and these publications, including journal articles, reports and presentations, are available through the organizations website. The most recent publications are displayed first, and all archived resources, membership Reports – A number of significant reports on topics ranging from virtual reference in libraries to perceptions about library funding
A lipase is any enzyme that catalyzes the hydrolysis of fats. Lipases are a subclass of the esterases, lipases perform essential roles in the digestion and processing of dietary lipids in most, if not all, living organisms. Genes encoding lipases are present in certain viruses. Most lipases act at a position on the glycerol backbone of a lipid substrate. Several other types of lipase activities exist in nature, such as phospholipases and sphingomyelinases, some lipases are expressed and secreted by pathogenic organisms during an infection. Lipases are involved in biological processes which range from routine metabolism of dietary triglycerides to cell signaling. Thus, some activities are confined to specific compartments within cells while others work in extracellular spaces. In the example of lysosomal lipase, the enzyme is confined within an organelle called the lysosome and bacteria may secrete lipases to facilitate nutrient absorption from the external medium. Certain wasp and bee venoms contain phospholipases that enhance the effects of injury, as biological membranes are integral to living cells and are largely composed of phospholipids, lipases play important roles in cell biology.
Malassezia globosa, a fungus that is thought to be the cause of dandruff, uses lipase to break down sebum into oleic acid and increase skin cell production. The main lipases of the digestive system are pancreatic lipase and pancreatic lipase related protein 2. Humans have several other related enzymes, including hepatic lipase, endothelial lipase, not all of these lipases function in the gut. Other lipases include LIPH, LIPI, LIPJ, LIPK, LIPM, LIPN, MGLL, DAGLA, DAGLB, there are a diverse array of phospholipases, but these are not always classified with the other lipases. Lipases serve important roles in human practices as ancient as yogurt, lipases are being exploited as cheap and versatile catalysts to degrade lipids in more modern applications. Industrial application of lipases requires process intensification for continuous processing using tools like continuous flow microreactors at small scale, lipases are generally animal sourced, but can be sourced microbially. Blood tests for lipase may be used to investigate and diagnose acute pancreatitis.
Measured serum lipase values may vary depending on the method of analysis, lipase can assist in the breakdown of fats into lipids in those undergoing pancreatic enzyme replacement therapy. It is a key component in Sollpura, alpha toxin Lysosomal acid lipase deficiency Peripheral membrane proteins Phospholipase A Phospholipase C Triglyceride lipase 25
A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA.
The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns.
By convention, the top strand is written from the 5 end to the 3 end and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
A diglyceride, or diacylglycerol, is a glyceride consisting of two fatty acid chains covalently bonded to a glycerol molecule through ester linkages. Two possible forms exist,1, 2-diacylglycerols and 1, 3-diacylglycerols, dAGs can acts as surfactants and are commonly used as emulsifiers in processed foods. Diglycerides are a component of many seed oils and are normally present at ~1-6%. Industrial production is achieved by a glycerolysis reaction between triglycerides and glycerol, the raw materials this may be either vegetable or animal fats. Diglycerides, generally in a mix with monoglycerides, are common food additives used as emulsifiers. The values given in the labels for total fat, saturated fat. They often are included in products, ice cream, peanut butter, chewing gum, whipped toppings, confections. Although inositol trisphosphate diffuses into the cytosol, diacylglycerol remains within the plasma membrane, iP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, whereas DAG is a physiological activator of protein kinase C.
The production of DAG in the membrane translocation of PKC from the cytosol to the plasma membrane. Munc13 Activation, Diacylglycerol has been shown to some of its excitatory actions on vesicle release through interactions with the presynaptic priming protein family Munc13. Binding of DAG to the C1 domain of Munc13 increases the fusion competence of synaptic vesicles resulting in potentiated release, Diacylglycerol can be mimicked by the tumor-promoting compounds phorbol esters. Synthesis of diacylglycerol begins with glycerol-3-phosphate, which is derived primarily from dihydroxyacetone phosphate, glycerol-3-phosphate is first acylated with acyl-coenzyme A to form lysophosphatidic acid, which is acylated with another molecule of acyl-CoA to yield phosphatidic acid. Phosphatidic acid is de-phosphorylated to form diacylglycerol, dietary fat is mainly composed of triglycerides. Because triglycerides cannot be absorbed by the system, triglycerides must first be enzymatically digested into monoacylglycerol, diacylglycerol.
Diacylglycerol is a precursor to triacylglycerol, which is formed in the addition of a fatty acid to the diacylglycerol under the catalysis of diglyceride acyltransferase. Since diacylglycerol is synthesized via phosphatidic acid, it will contain a saturated fatty acid at the C-1 position on the glycerol moiety. Diacylglycerol can be phosphorylated to phosphatidic acid by diacylglycerol kinase, Activation of PKC-θ by diacylglycerol may cause insulin resistance in muscle by decreasing IRS1-associated PI3K activity. Similarly, activation of PKCε by diacyglycerol may cause resistance in the liver
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, 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
A lipoprotein is a biochemical assembly whose purpose is to transport hydrophobic lipid molecules in water, as in blood or ECF. Apolipoproteins are embedded in the membrane, both stabilising the complex and giving it functional identity determining its fate, thus the complex serves to emulsify the fats. Many enzymes, structural proteins, adhesins, the lipids are often an essential part of the complex, even if they seem to have no catalytic activity by themselves. To isolate transmembrane lipoproteins from their associated biological membranes, detergents are often needed, because fats are insoluble in water, these cannot be transported in blood on its own. Instead, they are attached to proteins that function as transport vehicles. The role of lipoprotein particles is to transport triacylglycerols and cholesterol in the blood all the tissues of the body. The most common being the liver and the adipocytes of adipose tissue, particles are synthesized in the small intestine and the liver, but interestingly not in the adipocytes.
The lipoprotein particles have hydrophilic groups of phospholipids, such characteristics make them soluble in the salt water-based blood pool. Triglyceride-fats and cholesteryl esters are carried internally, shielded from the water by the phospholipid monolayer, the interaction of the proteins forming the surface of the particles determines whether triglycerides and cholesterol will be added to or removed from the lipoprotein transport particles. Regarding atheroma development and progression as opposed to regression, the key issue has always been cholesterol transport patterns, the handling of lipoprotein particles in the body is referred to as lipoprotein particle metabolism. The hepatocytes are the platform for the handling of triacylglycerols and cholesterol. While adipocytes are the storage cells for triacylglycerols, they do not produce any lipoproteins. Bile emulsifies fats contained in the chyme, pancreatic lipase cleaves triacylglycerol molecules into two fatty acids and one 2-monoacylglycerol, enterocytes readily absorb these small molecules from the chymus.
Inside of the enterocytes, fatty acids and monoacylglycerides are transformed again into triacylglycerides, these lipids are assembled with apolipoprotein B-48 into nascent chylomicrons. These particles are secreted into the lacteals in a process that depends heavily on apolipoprotein B-48. As they circulate through the vessels, nascent chylomicrons bypass the liver circulation and are drained via the thoracic duct into the bloodstream. In the blood stream, nascent chylomicron particles interact with HDL particles resulting in HDL donation of apolipoprotein C-II, the chylomicron at this stage is considered mature. Via apolipoprotein C-II, mature chylomicrons activate lipoprotein lipase, an enzyme on endothelial cells lining the blood vessels, LPL catalyzes the hydrolysis of triacylglycerol that ultimately releases glycerol and fatty acids from the chylomicrons
Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid.
In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households.
In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a source of data which can be used by Wikimedia projects such as Wikipedia. This is similar to the way Wikimedia Commons provides storage for files and access to those files for all Wikimedia projects. Wikidata is powered by the software Wikibase, Wikidata is a document-oriented database, focused on items. Each item represents a topic and is identified by a number, prefixed with the letter Q—for example. This enables the basic information required to identify the topic the item covers to be translated without favouring any language, information is added to items by creating statements. Statements take the form of pairs, with each statement consisting of a property. The creation of the project was funded by donations from the Allen Institute for Artificial Intelligence, the Gordon and Betty Moore Foundation, at this time, only the first phase was available. Historically, a Wikipedia article would include a list of links, being links to articles on the same topic in other editions of Wikipedia.
Initially, Wikidata was a repository of interlanguage links. No Wikipedia language editions were able to access Wikidata, so they needed to continue to maintain their own lists of interlanguage links, on 14 January 2013, the Hungarian Wikipedia became the first to enable the provision of interlanguage links via Wikidata. This functionality was extended to the Hebrew and Italian Wikipedias on 30 January, to the English Wikipedia on 13 February, on 23 September 2013, phase 1 went live on Wikimedia Commons. The first aspects of the second phase were deployed on 4 February 2013, the values were initially limited to two data types, with more data types to follow later. The first new type, was deployed on 6 March, the ability of the various language editions of Wikipedia to access data added to Wikidata as part of phase two was rolled out progressively between 27 March and 25 April 2013. On 16 September 2015, Wikidata began allowing so-called arbitrary access, for example, in the past the article about Berlin you could not access data about Germany, but with arbitrary access it could.
On 27 April 2016 arbitrary access was activated on Wikimedia Commons, phase 3 will involve database querying and the creation of lists based on data stored on Wikidata. As of October 2016 two tools for querying Wikidata were available, AutoList and PetScan, additionally to a public SPARQL endpoint, there is concern that the project is being influenced by lobbying companies, PR professionals and search engine optimizers. As of December 2015, according to Wikimedia statistics, half of the information in Wikidata is unsourced, another 30% is labeled as having come from Wikipedia, but with no indication as to which article
Ensembl genome database project
Ensembl is one of several well known genome browsers for the retrieval of genomic information. Similar databases and browsers are found at NCBI and the University of California, the human genome consists of three billion base pairs, which code for approximately 20, 000–25,000 genes. However the genome alone is of use, unless the locations. One option is manual annotation, whereby a team of scientists tries to locate genes using experimental data from scientific journals, however this is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers to do the complex pattern-matching of protein to DNA. In the Ensembl project, sequence data are fed into the gene annotation system which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis, Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, in addition, the Ensembl website provides computer-generated visual displays of much of the data.
Over time the project has expanded to additional species as well as a wider range of genomic data, including genetic variations. Central to the Ensembl concept is the ability to automatically generate graphical views of the alignment of genes and these are shown as data tracks, and individual tracks can be turned on and off, allowing the user to customise the display to suit their research interests. The interface enables the user to zoom in to a region or move along the genome in either direction, the graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA. Externally produced data can be added to the display, either via a DAS server on the internet, or by uploading a file in one of the supported formats, such as BAM, BED. Graphics are generated using a suite of custom Perl modules based on GD, in addition to its website, Ensembl provides a Perl API that models biological objects such as genes and proteins, allowing simple scripts to be written to retrieve data of interest.
The same API is used internally by the web interface to display the data and it is divided in sections like the core API, the compara API, the variation API, and the functional genomics API. The Ensembl website provides information on how to install and use the API. This software can be used to access the public MySQL database, the users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema. Large datasets can be retrieved using the BioMart data-mining tool and it provides a web interface for downloading datasets using complex queries. Last, there is an FTP server which can be used to download entire MySQL databases as some selected data sets in other formats. The annotated genomes include most fully sequenced vertebrates and selected model organisms, all of them are eukaryotes, there are no prokaryotes