Genetic Information Research Institute
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Genetic Information Research Institute
The Genetic Information Research Institute (GIRI) is a non-profit institution that was founded in 1994 by Jerzy Jurka. The mission of the institute "is to understand biological processes which alter the genetic makeup of different organisms, as a basis for potential gene therapy and genome engineering techniques." The institute specializes in applying computer tools to analysis of DNA and protein sequence information. GIRI develops and maintains Repbase Update, a database of prototypic sequences representing repetitive DNA from different eukaryotic species, and Repbase Reports, an electronic journal established in 2001. Repetitive DNA is primarily derived from transposable elements (TEs), which include DNA transposons belonging to around 20 superfamilies and retrotransposons Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations ( transposon ...
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Genetic Information Research Institute (logo)
The Genetic Information Research Institute (GIRI) is a non-profit institution that was founded in 1994 by Jerzy Jurka. The mission of the institute "is to understand biological processes which alter the genetic makeup of different organisms, as a basis for potential gene therapy and genome engineering techniques." The institute specializes in applying computer tools to analysis of DNA and protein sequence information. GIRI develops and maintains Repbase Update, a database of prototypic sequences representing repetitive DNA from different eukaryotic species, and Repbase Reports, an electronic journal established in 2001. Repetitive DNA is primarily derived from transposable elements (TEs), which include DNA transposons belonging to around 20 superfamilies and retrotransposons that can also be sub-classified into subfamilies . The majority of known superfamilies of DNA transposons were discovered or co-discovered at GIRI, including Helitron, ''Academ, Dada, Ginger, Kolobok, Novosib, S ...
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Jerzy Jurka
Jerzy Władysław Jurka (June 4, 1950 – July 19, 2014) was a Polish-American computational and molecular biologist. He served as the assistant director of research at the Linus Pauling Institute prior to founding the Genetic Information Research Institute. He collaborated with several notable scientists including Linus Pauling, George Irving Bell, Roy Britten, Temple Smith, and Emile Zuckerkandl. His Erdős number is 3, using the path through Temple Smith and Stanislaw Ulam. Research Dr. Jurka is best known for his work on eukaryotic transposable elements (TEs), including the discovery of the major families of Alu elements. He also proposed the mechanism of Alu proliferation and discovered their paternal transmission. The majority of known types of class II TEs, or DNA transposons, were discovered or co-discovered by his team at the Genetic Information Research Institute, based on DNA sequence analysis. The first one, reported in 2001 with Vladimir Kapitonov, became known as ' ...
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Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ...
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Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ...
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Sequences
In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is called the ''length'' of the sequence. Unlike a set, the same elements can appear multiple times at different positions in a sequence, and unlike a set, the order does matter. Formally, a sequence can be defined as a function from natural numbers (the positions of elements in the sequence) to the elements at each position. The notion of a sequence can be generalized to an indexed family, defined as a function from an ''arbitrary'' index set. For example, (M, A, R, Y) is a sequence of letters with the letter 'M' first and 'Y' last. This sequence differs from (A, R, M, Y). Also, the sequence (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence. Sequences can be ''finite'', as in these examples, or ''infinit ...
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Repetitive DNA
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. In many organisms, a significant fraction of the genomic DNA is repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. Some of these repeated sequences are necessary for maintaining important genome structures such as telomeres or centromeres. Repeated sequences are categorized into different classes depending on features such as structure, length, location, origin, and mode of multiplication. The disposition of repetitive elements throughout the genome can consist either in directly-adjacent arrays called tandem repeats or in repeats dispersed throughout the genome called interspersed repeats. Tandem repeats and interspersed repeats are further categorized into subclasses based on the length of the repeated sequence and/or the mode of multiplication. ...
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Eukaryotic
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacteria and Archaea (both prokaryotes) make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the Asgard archaea. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among archaea. Eukaryotes represent a small minority of the number of organisms, but, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs. Their name comes from the Greek εὖ (''eu'', "well" or "good") and κάρυον (''karyon'', "nut" or "kernel"). Euka ...
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Transposable Elements
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance in personalized medicine is becoming increasingly relevant, as well as gaining more attention in data analytics given the difficulty of analysis in very high dimensional spaces. Transposable elements make up a large fraction of the genome and are responsible for much of the C-value, mass of DNA in a eukaryotic cell. Although TEs are selfish genetic elements, many are important in genome function and evolution. Transposons are also very useful to researchers as a means to alter DNA inside a living organism. There are at least two classes of TEs: Class I TEs or retrotransposons generally ...
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DNA Transposon
DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons, that move through an RNA intermediate. DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence. After replicating and propagating in a host, all transposon copies become inactivated and are lost unless the transposon passes to a genome by starting a new life cycle with horizontal transfer. It is important to note that DNA transposons do not randomly insert themselves into the geno ...
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Retrotransposons
Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate. Through reverse transcription, retrotransposons amplify themselves quickly to become abundant in eukaryote , eukaryotic genomes such as maize (49–78%) and humans (42%). They are only present in eukaryotes but share features with retroviruses such as HIV, for example, discontinuous reverse transcriptase-mediated extrachromosomal recombination. These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI [P-element induced wimpy testis]-interacting RNAs (piRNAs). piRNA is a recently discovered class of ncRNAs, which are in the length range of ~24-32 nucleotides. Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) be ...
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Helitron (biology)
Helitrons are one of the three groups of eukaryotic class 2 transposable elements (TEs) so far described. They are the eukaryotic rolling-circle transposable elements which are hypothesized to transpose by a rolling circle replication mechanism via a single-stranded DNA intermediate. They were first discovered in plants ('' Arabidopsis thaliana'' and ''Oryza sativa'') and in the nematode '' Caenorhabditis elegans'', and now they have been identified in a diverse range of species, from protists to mammals. Helitrons make up a substantial fraction of many genomes where non-autonomous elements frequently outnumber the putative autonomous partner. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for Helitron transposition. History Helitrons were the first group of TEs to be discovered by computational analysis of whole genome sequences. The first Helitron ...
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Recombination Activating Gene
The recombination-activating genes (RAGs) encode parts of a protein complex that plays important roles in the rearrangement and recombination of the genes encoding immunoglobulin and T cell receptor molecules. There are two recombination-activating genes RAG1 and RAG2, whose cellular expression is restricted to lymphocytes during their developmental stages. The enzymes encoded by these genes, RAG-1 and RAG-2, are essential to the generation of mature B cells and T cells, two types of lymphocyte that are crucial components of the adaptive immune system. Function In the vertebrate immune system, each antibody is customized to attack one particular antigen (foreign proteins and carbohydrates) without attacking the body itself. The human genome has at most 30,000 genes, and yet it generates millions of different antibodies, which allows it to be able to respond to invasion from millions of different antigens. The immune system generates this diversity of antibodies by shuffling, ...
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