Adaptive immune system, also known as the acquired immune system or, more rarely, as the specific immune system, is composed of highly specialized, systemic cells and processes that eliminate or prevent pathogen growth. One of the two main immunity strategies found in vertebrates (the other being innate immunity), acquired immunity creates immunological memory after an initial response to a specific pathogen, leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.
In acquired immunity, pathogen-specific receptors are “acquired” during the lifetime of the organism (whereas in innate immunity pathogen-specific receptors are already encoded in the germline)… The acquired response is said to be “adaptive” because it prepares the body’s immune system for future challenges (though it can actually also be maladaptive when it results in autoimmunity). The system is highly adaptable because of somatic hypermutation (a process of accelerated somatic mutations), and V(D)J recombination (an irreversible genetic recombination of antigen receptor gene segments).
This mechanism allows a small number of genes to generate a vast number of different antigen receptors, which are then uniquely expressed on each individual lymphocyte. Because the gene rearrangement leads to an irreversible change in the DNA of each cell, all of the progeny (offspring) of that cell will then inherit genes encoding the same receptor specificity, including the Memory B cells and Memory T cells that are the keys to long-lived specific immunity. A theoretical framework explaining the workings of the acquired immune system is provided by immune network theory. This theory, which builds on established concepts of clonal selection, is being applied in the search for an HIV vaccine.
Adaptive response is a form of direct DNA repair in E. coli that is initiated against alkylation, particularly methylation, of guanine or thymine nucleotides or phosphate groups on the sugar-phosphate backbone of DNA. Under sustained exposure to low-level treatment with alkylating mutagens, E. coli can adapt to the presence of the mutagen, rendering subsequent treatment with high doses of the same agent less effective.
Ag means Antigen.
AlkB protein is a protein induced during an adaptive response and is involved in the direct reversal of alkylation damage. AlkB specifically removes alkylation damage to single stranded (SS) DNA caused by SN2 type of chemical agents. It efficiently removes methyl groups from 1-methyl adenines, 3-methyl cytosines in SS DNA. AlkB belongs to the Fe (II)/2-oxoglutarate-dependent dioxygenase superfamily and oxidatively demethylates the DNA substrate. Demethylation by AlkB is accompanied with release of CO2, succinate and formaldehyde.
Alkylation is the transfer of an alkyl group from one molecule to another.
Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within, or excluded from, the final, processed messenger RNA (mRNA) produced from that gene. Consequently the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions (see Figure). Notably, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes. Alternative splicing is sometimes termed differential splicing, but it does not increase gene expression.
Angelman syndrome (/’e nd lm n/; abbreviated AS) is a neuro-genetic disorder characterized by severe intellectual and developmental disability, sleep disturbance, seizures, jerky movements (especially hand-flapping), frequent laughter r smiling, and usually a happy demeanor.
Antigen is the substance that binds specifically to the respective antibody. Each antibody from the diverse repertoire binds a specific antigenic structure by means of its variable region interaction (CDR loops), an analogy being the fit between a lock and a key. Paul Ehrlich coined the term antibody (in German Antikörper) in his side-chain theory at the end of 19th century. The term antigen originally came from ANTIbody GENerator (see section History).
Antigen-presenting cell (APC) or accessory cell is a cell that displays foreign antigens complexed with major histocompatibility complexes (MHC’s) on their surfaces. T-cells may recognize these complexes using their T-cell receptors (TCRs). These cells process antigens and present them to T-cells.
Argonaute proteins are the catalytic components of the RNA-induced silencing complex (RISC), the protein complex responsible for the gene silencing phenomenon known as RNA interference (RNAi). Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity, which ypically leads to silencing of the target. Some of the Argonaute proteins have endonuclease activity directed against messenger RNA (mRNA) strands that display extensive complementarity to their bound small RNA, and this is known as Slicer activity. These proteins are also partially responsible for selection of the guide strand and destruction of the passenger strand of the siRNA substrate.
Assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
Autologous or Autotransplantation is the transplantation of organs, tissues or even proteins from one part of the body to another in the same individual. Tissue transplanted by such “autologous” procedure is referred to as an autograft or autotransplant. It is contrasted with xenotransplantation (from other species) and allotransplantation (from other individual of same species). A common example is when a piece of bone (usually from the hip) is removed and ground into a paste when reconstructing another portion of bone.
Avidity refers to the accumulated strength of multiple affinities of individual non-covalent binding interactions, such as between a protein receptor and its ligand, and is commonly referred to as functional affinity. As such, avidity is distinct from affinity, which describes the strength of a single interaction.
BALB/c is an albino, laboratory-bred strain of the House Mouse from which a number of common substrains are derived. Now over 200 generations from New York in 1920, BALB/c mice are distributed globally, and are among the most widely used inbred strains used in animal experimentation.
B6 mouse strain: C57BL/6, often referred to as “C57 black 6”, “C57” or “black 6” (standard abbreviation: B6), is a common inbred strain of laboratory mouse. It is the most widely used “genetic background” for genetically modified mice for use as models of human disease. They are the most widely used and best-selling mouse strain, due to the availability of congenic strains, easy breeding, and robustness.
B7 is a type of peripheral membrane protein found on activated antigen presenting cells (APC) that, when paired with either a CD28 or CD152 (CTLA-4) surface protein on a T cell, can produce a costimulatory signal to enhance or decrease the activity of a MHC-TCR signal between the APC and the T cell, respectively. Besides being present on activated APCs, B7 is also found on T-cells themselves. Binding of the B7 on T-cells to CTLA-4 causes inhibition of the activity of T-cells. There are two major types of B7 proteins: B7-1 or CD80, and B7-2 or CD86. However, it is not known if they differ significantly from each other. CD28 and CTLA-4 each interact with both B7-1 and B7-2.
Bacteremia (also bacteraemia or bacteræmia) is the presence of bacteria in the blood. The blood is normally a sterile environment, so the detection of bacteria in the blood (most commonly accomplished by blood cultures) is always abnormal.
Beckwith–Wiedemann syndrome (/’b k w ‘vi d .m n/; abbreviated BWS) is an overgrowth disorder usually (but not always) present at birth characterized by an increased risk of childhood cancer and certain congenital features.
C-value refers to the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases (notably among diploid organisms), the terms C-value and genome size are used interchangeably, however in polyploids the C-value may represent two or more genomes contained within the same nucleus. Greilhuber et al. have suggested some new layers of terminology and associated abbreviations to clarify this issue, but these somewhat complex additions have yet to be used by other authors.
CBySmn.CB17-Prkdcscid/J is a strain name of BALB/c SCID mouse.
CC49 (Iodine (125I)) is an iodine-125 radiolabelled monoclonal antibody for the detection of tumours. It is used in radioimmunoassays such as CA 72-4. CC49 has also been tested for the treatment of solid tumours, but without success. Iodine (131I) CC49 and lutetium (177Lu) CC49, for example, were shown to induce human anti-mouse antibodies; no tumour response was observed in Phase I and II clinical trials.
CD3 immunology (cluster of differentiation 3) T-cell co-receptor is a protein complex and is composed of four distinct chains. In mammals, the complex contains a CD3 chain, a CD3 chain, and two CD3 chains. These chains associate with a molecule known as the T-cell receptor (TCR) and the -chain to generate an activation signal in T lymphocytes. The TCR, -chain, and CD3 molecules together comprise the TCR complex.
CD3e molecule, epsilon also known as CD3E is a polypeptide which in humans is encoded by the CD3E gene which resides on chromosome 11.The protein encoded by this gene is the CD3-epsilon polypeptide, which together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. The epsilon polypeptide plays an essential role in T-cell development.
CD95 (Fas) Antibody: The FAS receptor (FasR), also known as apoptosis antigen 1 (APO-1 or APT), cluster of differentiation 95 (CD95) or tumor necrosis factor receptor superfamily member 6 (TNFRSF6) is a protein that in humans is encoded by the TNFRSF6 gene. The Fas receptor is a death receptor on the surface of cells that leads to programmed cell death (apoptosis). It is one of two apoptosis pathways, the other being the mitochondrial pathway. FasR is located on chromosome 10 in humans and 19 in mice. Similar sequences related by evolution (orthologs) are found in most mammals.
CDRs or Complementarity determining regions are regions within antibodies (also known as immunoglobulins), B-cell receptors and T-cell receptors where these proteins complement an antigen’s shape. Thus, CDRs determine the protein’s avidity (roughly, bonding strength) and specificity for specific antigens. The CDRs are the most variable part of the molecule, and contribute to the diversity of these molecules, allowing the antibody and the T-cell receptor to recognize a vast repertoire of antigens.
Cellular senescence is the phenomenon by which normal diploid cells cease to divide, normally after about 50 cell divisions in vitro. This phenomenon is also known as “replicative senescence”, the “Hayflick phenomenon”, or the Hayflick limit in honour of Dr. Leonard Hayflick, co-author with Paul Moorhead, of the first paper describing it in 1961. Cells can also be induced to senesce by certain toxins, irradiation, or the activation of certain oncogenes. In response to DNA damage (including shortened telomeres), cells either age or self-destruct (apoptosis, programmed cell death) if the damage cannot be easily repaired. In this ‘cellular suicide’, the death of one cell, or more, may benefit the organism as a whole. For example, in plants the death of the water-conducting xylem cells (tracheids and vessel elements) allows the cells to function more efficiently and so deliver water to the upper parts of a plant. The ones that do not self-destruct remain until destroyed by outside forces. Though they no longer replicate, senescent cells remain metabolically active and generally adopt phenotypes including flattened cell morphology, altered gene expression and secretion profiles (known as the senescence-associated secretory phenotype), and positive senescence-associated ß-galactosidase staining. In a study conducted in 2011 on mice, senescent cells were deliberately eradicated, which led to greater resistance against aging-associated diseases. Cellular senescence is causally implicated in generating age-related phenotypes, and removal of senescent cells can prevent or delay tissue dysfunction and extend healthspan.
Chemokines (Greek -kinos, movement) are a family of small cytokines, or signaling proteins secreted by cells. Their name is derived from their ability to induce directed chemotaxis in nearby responsive cells; they are chemotactic cytokines. Proteins are classified as chemokines according to shared structural characteristics such as small size (they are all approximately 8-10 kilodaltons in size), and the presence of four cysteine residues in conserved locations that are key to forming their 3-dimensional shape.
Chemokine receptors are cytokine receptors found on the surface of certain cells that interact with a type of cytokine called a chemokine. There have been 19 distinct chemokine receptors described in mammals. Each has a 7-transmembrane (7TM) structure and couples to G-protein for signal transduction within a cell, making them members of a large protein family of G protein-coupled receptors.
Following interaction with their specific chemokine ligands, chemokine receptors trigger a flux in intracellular calcium (Ca2+) ions (calcium signaling). This causes cell responses, including the onset of a process known as chemotaxis that traffics the cell to a desired location within the organism. Chemokine receptors are divided into different families, CXC chemokine receptors, CC chemokine receptors, CX3C chemokine receptors and XC chemokine receptors that correspond to the 4 distinct subfamilies of chemokines they bind.
Chemotherapy (often abbreviated to chemo) is the treatment of cancer with one or more cytotoxic anti-neoplastic drugs (“chemotherapeutic agents”) as part of a standardized regimen. Chemotherapy may be given with a curative intent or it may aim to prolong life or to palliate symptoms. It is often used in conjunction with other cancer treatments, such as radiation therapy or surgery. Certain chemotherapeutic agents also have a role in the treatment of other conditions, including ankylosing spondylitis, multiple sclerosis, Crohn’s disease, psoriasis, psoriatic arthritis, systemic lupus erythematosus, rheumatoid arthritis, and scleroderma. Traditional chemotherapeutic agents act by killing cells that divide rapidly, one of the main properties of most cancer cells. This means that chemotherapy also harms cells that divide rapidly under normal circumstances: cells in the bone marrow, digestive tract, and hair follicles. This results in the most common side-effects of chemotherapy: myelosuppression (decreased production of blood cells, hence also immunosuppression), mucositis (inflammation of the lining of the digestive tract), and alopecia (hair loss).
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to strengthen the DNA to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells: prokaryotic cells have a very different organization of their DNA which is referred to as a genophore (a chromosome without chromatin).
Cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA (often a chromosome). This term is constructed from the Latin word cis, which means “on the same side as”. A cis-element may be located upstream of the coding sequence of the gene it controls (in the promoter region or even further upstream), in an intron, or downstream of the gene’s coding sequence, either in the translated or untranscribed region. (See promoter location for explanation of notation.)
Citrullination or deimination is the conversion of the amino acid arginine in a protein into the amino acid citrulline. Enzymes called peptidylarginine deiminases (PADs) replace the aldimine group (=NH) by a ketone group (=O).
Citrullination is important because it controls the expression of genes, particularly in the developing embryo, and because the immune system often attacks citrullinated proteins, leading to autoimmune diseases such as rheumatoid arthritis and multiple sclerosis.
Citrulline is not one of the 20 standard amino acids encoded by DNA in the genetic code. Instead, it is a post-translational modification.
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is a main task of exploratory data mining, and a common technique for statistical data analysis, used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics.
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (triplets) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. Different organisms often show particular preferences for one of the several codons that encode the same amino acid- that is, a greater frequency of one will be found than expected by chance. How such preferences arise is a much debated area of molecular evolution.
Concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequences linked in series. These polymeric molecules are usually copies of an entire genome linked end to end and separated by cos sites (a protein binding nucleotide sequence that occurs once in each copy of the genome). Concatemers are frequently the result of rolling circle replication, and may be seen in the late stage of bacterial infection by phages. As an example, if the genes in the phage DNA are arranged ABC, then in a concatemer the genes would be ABCABCABCABC and so on. They are further broken by ribozymes.
During active infection, some species of viruses have been shown to replicate their genetic material via the formation of concatemers. In the case of human herpesvirus-6, its entire genome is made over and over on a single strand. These long concatemers are subsequently cleaved between the pac-1 and pac-2 regions by ribozymes when the genome is packaged into individual virions.
Congenic: In genetics, two organisms that differ in only one locus are defined as congenic or coisogenic.
CpG sites or CG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. “CpG” is shorthand for “—C—phosphate—G—”, that is, cytosine and guanine separated by only one phosphate; phosphate links any two nucleosides together in DNA. The “CpG” notation is used to distinguish this linear sequence from the CG base-pairing of cytosine and guanine. The CpG notation can also be interpreted as the cytosine being 5 prime to the guanine base.
Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. In mammals, methylating the cytosine within a gene can turn the gene off, a mechanism that is part of a larger field of science studying gene regulation that is called epigenetics. Enzymes that add a methyl group are called DNA methyltransferases.
In mammals, 70% to 80% of CpG cytosines are methylated.
Crohn’s disease, also known as Crohn syndrome and regional enteritis, is a type of inflammatory bowel disease that may affect any part of the gastrointestinal tract from mouth to anus, causing a wide variety of symptoms. It primarily causes abdominal pain, diarrhea (which may be bloody if inflammation is severe), vomiting, or weight loss
CTLA-4 (Cytotoxic T-Lymphocyte Antigen 4) , also known as CD152 (Cluster of differentiation 152), is a protein receptor that downregulates the immune system. CTLA4 is found on the surface of T cells, which lead the cellular immune attack on antigens. The T cell attack can be turned on by stimulating the CD28 receptor on the T cell. The T cell attack can be turned off by stimulating the CTLA4 receptor, which acts as an “off” switch. In humans, the CTLA4 protein is encoded by the CTLA4 gene.
Cyclins are a family of proteins that control the progression of cells through the cell cycle by activating cyclin-dependent kinase (Cdk) enzymes.
Cyclins were originally named because their concentration varies in a cyclical fashion during the cell cycle. (Note that the cyclins are now classified according to their conserved cyclin box structure, and not all these cyclins alter in level through the cell cycle.) The oscillations of the cyclins, namely fluctuations in cyclin gene expression and destruction by the ubiquitin mediated proteasome pathway, induce oscillations in Cdk activity to drive the cell cycle. A cyclin forms a complex with Cdk, which begins to activate the Cdk, but the complete activation requires phosphorylation, as well. Complex formation results in activation of the Cdk active site. Cyclins themselves have no enzymatic activity but have binding sites for some substrates and target the Cdks to specific subcellular locations.
Cyclin-dependent kinases (CDKs) are a family of protein kinases first discovered for their role in regulating the cell cycle. They are also involved in regulating transcription, mRNA processing, and the differentiation of nerve cells. They are present in all known eukaryotes, and their regulatory function in the cell cycle has been evolutionarily conserved. In fact, yeast cells can proliferate normally when their CDK gene has been replaced with the homologous human gene. CDKs are relatively small proteins, with molecular weights ranging from 34 to 40 kDa, and contain little more than the kinase domain. By definition, a CDK binds a regulatory protein called a cyclin. Without cyclin, CDK has little kinase activity; only the cyclin-CDK complex is an active kinase. CDKs phosphorylate their substrates on serines and threonines, so they are serine-threonine kinases. The consensus sequence for the phosphorylation site in the amino acid sequence of a CDK substrate is [S/T*]PX[K/R], where S/T* is the phosphorylated serine or threonine, P is proline, X is any amino acid, K is lysine, and R is arginine
Cyclin-dependent kinase complex (CDKC, cyclin-CDK) is a protein complex formed by the association of an inactive catalytic subunit of a protein kinase, cyclin-dependent kinase (CDK), with a regulatory subunit, cyclin. Once cyclin-dependent kinases bind to cyclin, the formed complex is in an activated state. Substrate specificity of the activated complex is mainly established by the associated cyclin within the complex. Activity of CDKCs is controlled by phosphorylation of target proteins, as well as binding of inhibitory proteins.
Cyclin-dependent kinase inhibitor 1C (p57, Kip2), also known as CDKN1C, is protein which in humans is encoded by the CDKN1C imprinted gene.
Cyclin-dependent kinase inhibitor 1C is a tight-binding inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations of CDKN1C are implicated in sporadic cancers and Beckwith-Wiedemann syndrome suggesting that it is a tumor suppressor candidate.
CDKN1C is a tumor suppressor human gene on chromosome 11 (11p15) and belongs to the cip/kip gene family. It encodes a cell cycle inhibitor that binds to G1 cyclin-CDK complexes. Thus p57KIP2 causes arrest of the cell cycle in G1 phase.
Cytochrome P450 superfamily of monooxygenases (officially abbreviated as CYP) is a large and diverse group of enzymes that catalyze the oxidation of organic substances. The substrates of CYP enzymes include metabolic intermediates such as lipids and steroidal hormones, as well as xenobiotic substances such as drugs and other toxic chemicals. CYPs are the major enzymes involved in drug metabolism and bioactivation, accounting for about 75% of the total number of different metabolic reactions.
Cytokines (Greek cyto-, cell; and -kinos, movement) are a diverse group of soluble proteins, peptides, or glycoproteins which act as hormonal regulators or signaling molecules at nano- to- picomolar concentrations and help in cell signaling. The term “cytokine” encompasses a large and diverse family of regulators produced throughout the body by cells of diverse embryological origin.
Cytokine has been used to refer to the immunomodulating agents, such as interleukins and interferons. They are regulators of host responses to infection, immune responses, inflammation, and trauma. Some of them are proinflammatory; these are necessary to initiate an inflammatory response necessary to recruit granulocytes, and later on, lymphocytes, to fight disease. Excessive inflammation, however, is sometimes the pathogenicity of certain diseases. Other cytokines are anti-inflammatory and serve to reduce inflammation and promote healing once the injury/infection/foreign body has been destroyed.
Cytokine receptors are receptors that bind cytokines. In recent years, the cytokine receptors have come to demand the attention of more investigators than cytokines themselves, partly because of their remarkable characteristics, and partly because a deficiency of cytokine receptors has now been directly linked to certain debilitating immunodeficiency states. In this regard, and also because the redundancy and pleiotropy of cytokines are, in fact, a consequence of their homologous receptors, many authorities are now of the opinion that a classification of cytokine receptors would be more clinically and experimentally useful.
Cytotoxicity is the quality of being toxic to cells. Examples of toxic agents are an immune cell or some types of venom (e.g. from the puff adder or brown recluse spider).
Demethylating agents are compounds that can inhibit methylation, resulting in the expression of the previously hypermethylated silenced genes (see methylation: methylation and cancer for more detail).
Dendrogram (from Greek dendron “tree” and gramma “drawing”) is a tree diagram frequently used to illustrate the arrangement of the clusters produced by hierarchical clustering. Dendrograms are often used in computational biology to illustrate the clustering of genes or samples.
Dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids. It is a quaternary structure of a protein.
A homo-dimer would be formed by two identical molecules (a process called homodimerization). A hetero-dimer would be formed by two different macromolecules (called heterodimerization).
Most dimers in biochemistry are not connected by covalent bonds. An example of a non-covalent heterodimer would be the enzyme reverse transcriptase, which is composed of two different amino acid chains. An exception is dimers that are linked by disulfide bridges such as the homodimeric protein NEMO.
Some proteins contain specialized domains to ensure dimerization (dimerization domains).
Dioxins or Polychlorinated dibenzodioxins (PCDDs), are a group of organic polyhalogenated compounds that are significant environmental pollutants. They are commonly but inaccurately referred to as dioxins for simplicity, because every PCDD molecule contains a dioxin skeletal structure as the central ring. This gives the molecule a dibenzo-p-dioxin ring system. Members of the PCDD family bioaccumulate in humans and wildlife because of their lipophilic properties, and may cause developmental disturbances and cancer.
DNA methylation is a biochemical process involving the addition of a methyl group to the cytosine or adenine DNA nucleotides. DNA methylation stably alters the expression of genes in cells as cells divide and differentiate from embryonic stem cells into specific tissues. The resulting change is normally permanent and unidirectional, preventing one organism from reverting to a stem cell or converting into another type of tissue. DNA methylation is typically removed during zygote formation and re-established through successive cell divisions during development. However, the latest research shows that hydroxylation of methyl groups occurs rather than complete removal of methyl groups in zygote. Some methylation modifications that regulate gene expression are heritable and cause genomic imprinting.
In addition, DNA methylation suppresses the expression of endogenous retroviral genes and other harmful stretches of DNA that have been incorporated into the genome of the host over time. DNA methylation also forms the basis of chromatin structure, which enables a single cell to grow into multiple organs or perform multiple functions. DNA methylation also plays a crucial role in the development of nearly all types of cancer.
DNA methylation at the 5 position of cytosine has the specific effect of reducing gene expression and has been found in every vertebrate examined. In adult somatic cells (cells in the body, not used for reproduction), DNA methylation typically occurs in a CpG dinucleotide context; non-CpG methylation is prevalent in embryonic stem cells, and has also been indicated in neural development.
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Domain is in (molecular biology) A part of a molecule or structure with common physico-chemical features or properties, as in polar domain, atp-binding domain, helical domain, etc.
Double minutes are small fragments of extrachromosomal DNA, which have been observed in a large number of human tumors including breast, lung, ovary, colon, and most notably, neuroblastoma. They are a manifestation of gene amplification during the development of tumors, which give the cells selective advantages for growth and survival. They frequently harbor amplified oncogenes and genes involved in drug resistance. Double minutes, like actual chromosomes, are composed of chromatin and replicate in the nucleus of the cell during cell division. Unlike typical chromosomes, they are composed of circular fragments of DNA, up to only a few million base pairs in size and contain no centromere or telomere.
Downregulation is the process by which a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external variable.An example of downregulation is the cellular decrease in the number of receptors to a molecule, such as a hormone or neurotransmitter, which reduces the cell’s sensitivity to the molecule. This phenomenon is an example of a locally acting negative feedback mechanism.
Eicosanoids (preferred IUPAC name icosanoids) are signaling molecules made by oxidation of 20-carbon fatty acids. They exert complex control over many bodily systems, mainly in inflammation or immunity, and as messengers in the central nervous system. The networks of controls that depend upon eicosanoids are among the most complex in the human body.
Eicosanoids are derived from either omega-3 ( -3) or omega-6 ( -6) fatty acids. The -6 eicosanoids are generally pro-inflammatory; -3s are much less so. The amounts and balance of these fats in a person’s diet will affect the body’s eicosanoid-controlled functions, with effects on cardiovascular disease, triglycerides, blood pressure, and arthritis. Anti-inflammatory drugs such as aspirin and other NSAIDs act by downregulating eicosanoid synthesis.
Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell’s function, or a piece of coding DNA.
Electroporation is a dynamic phenomenon that depends on the local transmembrane voltage at each point on the cell membrane. It is generally accepted that for a given pulse duration and shape, a specific transmembrane voltage threshold exists for the manifestation of the electroporation phenomenon (from 0.5 V to 1 V). This leads to the definition of an electric field magnitude threshold for electroporation (Eth). That is, only the cells within areas where E Eth are electroporated. If a second threshold (Eir) is reached or surpassed, electroporation will compromise the viability of the cells, i.e., irreversible electroporation.
Empirical evidence (also empirical data, sense experience, empirical knowledge, or the a posteriori) is a source of knowledge acquired by means of observation or experimentation. Empirical evidence is information that justifies a belief in the truth or falsity of an empirical claim. In the empiricist view, one can only claim to have knowledge when one has a true belief based on empirical evidence.
Endogenous retroviruses are endogenous viral elements that are derived from retroviruses, and they are abundant in the genomes of jawed vertebrates.
The replication cycle of a retrovirus entails the insertion (“integration”) of a DNA copy of the viral genome into the nuclear genome of the host cell. Most retroviruses infect somatic cells, but occasional infection of germline cells (cells that produce eggs and sperm) can also occur. Rarely, retroviral integration may occur in a germline cell that goes on to develop into a viable organism. This organism will carry the inserted retroviral genome as an integral part of its own genome – an “endogenous” retrovirus (ERV) that may be inherited by its offspring as a novel allele. Many ERVs have persisted in the genome of their hosts for millions of years. However, most of these have acquired inactivating mutations during host DNA replication and are no longer capable of producing virus. ERVs can also be partially excised from the genome by a process known as recombinational deletion, in which recombination between the identical sequences that flank newly integrated retroviruses results in deletion of the internal, protein-coding regions of the viral genome.
Role in genome evolution
Endogenous retroviruses can play an active role in shaping genomes. Most studies in this area have focused on the genomes of humans and higher primates, but other vertebrates, such as mice and sheep, have also been studied in depth. The long terminal repeat (LTR) sequences that flank ERV genomes frequently act as alternate promoters and enhancers, often contributing to the transcriptome by producing tissue-specific variants. In addition, the retroviral proteins themselves have been co-opted to serve novel host functions, particularly in reproduction and development. Recombination between homologous retroviral sequences has also contributed to gene shuffling and the generation of genetic variation. Furthermore, in the instance of potentially antagonistic effects of retroviral sequences, repressor genes have co-evolved to combat them.
Endotoxin was coined by Richard Friedrich Johannes Pfeiffer, who distinguished between exotoxins, which he classified as a toxin that is released by bacteria into the environment, and endotoxins, which he considered to be a toxin kept “within” the bacterial cell and to be released only after destruction of the bacterial cell wall. Today, the term ‘endotoxin’ is used synonymously with the term lipopolysaccharide, which is a major constituent of the outer cell membrane of Gram-negative bacteria. Larger amounts of endotoxins can be mobilized if Gram-negative bacteria are killed or destroyed by detergents. The term “endotoxin” came from the discovery that portions of Gram-negative bacteria themselves can cause toxicity. Studies of endotoxin over the next 50 years revealed that the effects of “endotoxin” are, in fact, due to lipopolysaccharide.
The key effects of endotoxins on vertebrates are mediated by their interaction with specific receptors on immune cells such as monocytes, macrophages, dendritic cells, and others. Upon challenge with endotoxin, these cells form a broad spectrum of immune mediators such as cytokines, nitric oxide, and eicosanoids.
Enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome.
Epigenetics is the study of heritable changes in gene activity which are not caused by changes in the DNA sequence; it can also be used to describe the study of stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable. Unlike simple genetics based on changes to the DNA sequence (the genotype), the changes in gene expression or cellular phenotype of epigenetics have other causes. The name epi- (Greek: – over, outside of, around) –genetics.
The term also refers to the changes themselves: functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These epigenetic changes may last through cell divisions for the duration of the cell’s life, and may also last for multiple generations even though they do not involve changes in the underlying DNA sequence of the organism; instead, non-genetic factors cause the organism’s genes to behave (or “express themselves”) differently. (There are objections to the use of the term epigenetic to describe chemical modification of histone, since it remains unclear whether or not histone modifications are heritable.)
One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism, including neurons, muscle cells, epithelium, endothelium of blood vessels, etc., by activating some genes while inhibiting the expression of others.
In 2011, it was demonstrated that the methylation of mRNA plays a critical role in human energy homeostasis. The obesity-associated FTO gene is shown to be able to demethylate N6-methyladenosine in RNA. This discovery launched the subfield of RNA epigenetics.
Episomes are closed circular DNA molecules that are replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses. Other examples include aberrant chromosomal fragments, such as double minute chromosomes, that can arise during artificial gene amplifications or in pathologic processes (e.g., cancer cell transformation). Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that the DNA is stably maintained and replicated with the host cell.
Epitope , also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells.Although epitopes are usually non-self proteins, sequences derived from the host that can be recognized are also epitopes.The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their structure and interaction with the paratope. A conformational epitope is composed of discontinuous sections of the antigen’s amino acid sequence. These epitopes interact with the paratope based on the 3-D surface features and shape or tertiary structure of the antigen. The proportion of epitopes that are conformational is unknown.
Exon is any nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA.
In many genes, each of the exons contain part of the open reading frame (ORF) that codes for a specific portion of the complete protein. However, the term exon is often misused to refer only to coding sequences for the final protein. This is incorrect, since many noncoding exons are known in human genes (Zhang 1998).
To the right is a diagram of a heterogeneous nuclear RNA (hnRNA), which is an unedited mRNA transcript, or pre-mRNAs. Exons can include both sequences that code for amino acids (red) and untranslated sequences (grey). Stretches of unused sequence called introns (blue) are removed, and the exons are joined together to form the final functional mRNA. The notation 5′ and 3′ refer to the direction of the DNA template in the chromosome and is used to distinguish between the two untranslated regions (grey).
Some of the exons will be wholly or part of the 5′ untranslated region (5′ UTR) or the 3′ untranslated region (3′ UTR) of each transcript. The untranslated regions are important for efficient translation of the transcript and for controlling the rate of translation and half-life of the transcript. Furthermore, transcripts made from the same gene may not have the same exon structure, since parts of the mRNA could be removed by the process of alternative splicing. Some mRNA transcripts have exons with no ORFs and, thus, are sometimes referred to as non-coding RNA.
Exonization is the creation of a new exon, as result of mutations in intronic sequences. Polycistronic messages have multiple ORFs in one transcript and also have small regions of untranslated sequence between each ORF.
Exotoxin is a toxin secreted by bacteria. An exotoxin can cause damage to the host by destroying cells or disrupting normal cellular metabolism. They are highly potent and can cause major damage to the host. Exotoxins may be secreted, or, similar to endotoxins, may be released during lysis of the cell.
Most exotoxins can be destroyed by heating. They may exert their effect locally or produce systemic effects. Well-known exotoxins include the botulinum toxin produced by Clostridium botulinum and the Corynebacterium diphtheriae exotoxin, which is produced during life-threatening symptoms of diphtheria.
Exotoxins are susceptible to antibodies produced by the immune system, but many exotoxins are so toxic that they may be fatal to the host before the immune system has a chance to mount defenses against it.
Ext is called Extracellular
Fab fragment or fragment antigen-binding is a region on an antibody that binds to antigens. It is composed of one constant and one variable domain of each of the heavy and the light chain. These domains shape the paratope — the antigen-binding site — at the amino terminal end of the monomer. The two variable domains bind the epitope on their specific antigens.
Fas ligand (FasL or CD95L) is a type-II transmembrane protein that belongs to the tumor necrosis factor (TNF) family. Its binding with its receptor induces apoptosis. Fas ligand/receptor interactions play an important role in the regulation of the immune system and the progression of cancer.
FasR is The Fas receptor (FasR), or CD9 or CD1785, is the most intensely studied member of the death receptor family. The gene is situated on chromosome 10 in humans and 19 in mice.
Fertility factor (first named F by one of its discoverers Esther Lederberg) allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation. The F factor is carried on the F episome, the first episome to be discovered. Unlike other plasmids, F factor is constitutive for transfer proteins due to the gene traJ. The F plasmid belongs to a class of conjugative plasmids that control sexual functions of bacteria with a fertility inhibition (Fin) system.
The most common functional segments constituting F factors are:
• OriT (Origin of Transfer): The sequence which marks the starting point of conjugative transfer.
• OriC (Origin of Replication): The sequence starting with which the plasmid-DNA will be replicated in the recipient cell.
• tra-region (transfer genes): Genes coding the F-Pilus and DNA transfer process.
• IS (Insertion Elements) composed of one copy of IS2, two copies of IS3, and one copy of IS1000: so-called “selfish genes” (sequence fragments which can integrate copies of themselves at different locations).
Fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework (stroma) for animal tissues, and plays a critical role in wound healing. Fibroblasts are the most common cells of connective tissue in animals.
Fibroblast activation protein, alpha (FAP) also known as seprase or 170 kDa melanoma membrane-bound gelatinase is a protein that in humans is encoded by the FAP gene .The protein encoded by this gene is a homodimeric integral membrane gelatinase belonging to the serine protease family. It is selectively expressed in reactive stromal fibroblasts of epithelial cancers, granulation tissue of healing wounds, and malignant cells of bone and soft tissue sarcomas. This protein is thought to be involved in the control of fibroblast growth or epithelial-mesenchymal interactions during development, tissue repair, and epithelial carcinogenesis.
Filamentous bacteriophage is a type of bacteriophage, or virus of bacteria, defined by its filament-like or rod-like shape. Filamentous phages usually contain a genome of single-stranded DNA and infect Gram-negative bacteria.
F Pilli or Conjugative pili Conjugative pili allow the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called “sex pili”, in analogy to sexual reproduction, because they allow for the exchange of genes via the formation of “mating pairs”. Perhaps the most well-studied is the F pilus of Escherichia coli, encoded by the F plasmid or fertility factor.
A pilus is typically 6 to 7 nm in diameter. During conjugation, a pilus emerging from donor bacterium ensnares the recipient bacterium, draws it in close, and eventually triggers the formation of a mating bridge, which establishes direct contact and the formation of a controlled pore that allows transfer of DNA from the donor to the recipient. Typically, the DNA transferred consists of the genes required to make and transfer pili (often encoded on a plasmid), and so is a kind of selfish DNA; however, other pieces of DNA are often co-transferred and this can result in dissemination of genetic traits, such as antibiotic resistance, among a bacterial population. Not all bacteria can make conjugative pili, but conjugation can occur between bacteria of different species.
Frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein. A frameshift mutation is not the same as a single-nucleotide polymorphism in which a nucleotide is replaced, rather than inserted or deleted. A frameshift mutation will in general cause the reading of the codons after the mutation to code for different amino acids. The frameshift mutation will also alter the first stop codon (“UAA”, “UGA” or “UAG”) encountered in the sequence. The polypeptide being created could be abnormally short or abnormally long, and will most likely not be functional.
Frameshift mutations are apparent in severe genetic diseases such as Tay-Sachs disease and Cystic Fibrosis; they increase susceptibility to certain cancers and classes of familial hypercholesterolaemia; in 1997, a frameshift mutation was linked to resistance to infection by the HIV retrovirus.
Fat mass and obesity-associated protein also known as alpha-ketoglutarate-dependent dioxygenase FTO is an enzyme that in humans is encoded by the FTO gene located on chromosome 16. As one homolog in the AlkB family proteins, it is the first mRNA demethylase that has been identified. Certain variants of the FTO gene appear to be correlated with obesity in humans.
Fusion proteins or chimeric proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes which originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins. Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics. Chimeric mutant proteins occur naturally when a complex mutation, such as a chromosomal translocation, tandem duplication, or retrotransposition creates a novel coding sequence containing parts of the coding sequences from two different genes. Naturally occurring fusion proteins are commonly found in cancer cells, where they may function as oncoproteins. The bcr-abl fusion protein is a well-known example of an oncogenic fusion protein, and is considered to be the primary oncogenic driver of chronic myelogenous leukemia. .
Gelatinase is a proteolytic enzyme that allows a living organism to hydrolyse gelatin into its sub-compounds (polypeptides, peptides, and amino acids) that can cross the cell membrane and be used by the organism. It is not a pepsin. Forms of gelatinases are expressed in several bacteria including Pseudomonas aeruginosa and Serratia marcescens. In humans, the gelatinases are matrix metalloproteinases MMP2 and MMP9.
Gene duplication doesn’t necessarily constitute a lasting change in a species’ genome. In fact, such changes often don’t last past the initial host organism. From the perspective of molecular genetics, amplification is one of many ways in which a gene can be overexpressed. Genetic amplification can occur artificially, as with the use of the polymerase chain reaction technique to amplify short strands of DNA in vitro using enzymes, or it can occur naturally, as described above. If it’s a natural duplication, it can still take place in a somatic cell, rather than a germline cell (which would be necessary for a lasting evolutionary change).
Role in cancer
Duplications of oncogenes are a common cause of many types of cancer. In such cases the genetic duplication occurs in a somatic cell and affects only the genome of the cancer cells themselves, not the entire organism, much less any subsequent offspring.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA), transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. The process of gene expression is used by all known life – eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses – to generate the macromolecular machinery for life. Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene in a cell or in a multicellular organism.
Gene knockout (abbreviation: KO) is a genetic technique in which one of an organism’s genes are made inoperative (“knocked out” of the organism). Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function. Researchers draw inferences from the difference between the knockout organism and normal individuals.
The term also refers to the process of creating such an organism, as in “knocking out” a gene. The technique is essentially the opposite of a gene knockin. Knocking out two genes simultaneously in an organism is known as a double knockout (DKO). Similarly the terms triple knockout (TKO) and quadruple knockouts (QKO) are used to describe three or four knocked out genes, respectively.
Gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.
In its earliest days, “gene finding” was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem.
Determining that a sequence is functional should be distinguished from determining the function of the gene or its product. Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation through gene knockout and other assays, although frontiers of bioinformatics research are making it increasingly possible to predict the function of a gene based on its sequence alone.
Gene prediction is one of the key steps in Genome annotation, following the filtering of non-coding regions and repeat masking.
Genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.
Some of the genetic sequence of an organism has functions other than encoding proteins. All DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code. Coding DNA can occasionally serve a regulatory function as well, as transcription factor binding sites are sometimes found within coding regions.
Genome annotation is the process of attaching biological information to sequences. It consists of three main steps:
1. Identifying portions of the genome that do not code for proteins
2. Identifying elements on the genome, a process called gene prediction, and
3. Attaching biological information to these elements.
Automatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation (a.k.a. curation) which involves human expertise. Ideally, these approaches co-exist and complement each other in the same annotation pipeline.
The basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on that. However, nowadays more and more additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl) rely on both curated data sources as well as a range of different software tools in their automated genome annotation pipeline.
Structural annotation consists of the identification of genomic elements.
• ORFs and their localisation
• gene structure
• coding regions
• location of regulatory motifs
Functional annotation consists of attaching biologicjal information to genomic elements.
• biochemical function
• biological function
• involved regulation and interactions
These steps may involve both biological experiments and in silico analysis. Proteogenomics based approaches utilize information from expressed proteins, often derived from mass spectrometry, to improve genomics annotations.
Genomic imprinting is an epigenetic phenomenon by which certain genes can be expressed in a parent-of-origin-specific manner. It may also ensure transposable elements remain epigenetically silenced throughout gametogenic reprogramming to maintain genome integrity. It is an inheritance process independent of the classical Mendelian inheritance. In Homo sapiens, imprinted alleles are silenced such that the genes are either expressed only from the non-imprinted allele inherited from the mother (e.g. H19 or CDKN1C), or in other instances from the non-imprinted allele inherited from the father (e.g. IGF-2). However, in plants parental genomic imprinting can refer to gene expression both solely or primarily from either parent’s allele. Forms of genomic imprinting have been demonstrated in fungi, plants and animals.
Genomic imprinting is an epigenetic process that can involve DNA methylation and histone modulation in order to achieve monoallelic gene expression without altering the genetic sequence. These epigenetic marks are established in the germline and can be maintained through mitotic divisions.
Appropriate expression of imprinted genes is important for normal development, with numerous genetic diseases associated with imprinting defects including Beckwith–Wiedemann syndrome, Silver–Russell syndrome, Angelman syndrome and Prader–Willi syndrome.
Germline of a mature or developing individual is the line (sequence) of germ cells that have genetic material that may be passed to a child.
For example, gametes such as the sperm or the egg are part of the germline. So are the cells that divide to produce the gametes, called gametocytes, the cells that produce those, called gametogonia, and all the way back to the zygote, the cell from which the individual developed.
Cells that are not in the germline are called somatic cells. This refers to all of the cells of body apart from the gametes. If there is a mutation or other genetic change in the germline, it can potentially be passed to offspring, but a change in a somatic cell will not be.
Germline cells are immortal, in the sense that they have reproduced indefinitely since the beginning of life. This is largely due to the activity of the enzyme known as telomerase. This enzyme extends the telomeres of the chromosome, preventing chromosome fusions and other negative effects of shortened telomeres. Most somatic cells, by comparison, can only divide around 30-50 times according to the Hayflick limit. Certain somatic cells, known as stem cells, also express telomerase and are potentially immortal.
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. Secreted extracellular proteins are often glycosylated. In proteins that have segments extending extracellularly, the extracellular segments are also glycosylated. Glycoproteins are often important integral membrane proteins, where they play a role in cell–cell interactions. Glycoproteins are also formed in the cytosol, but their functions and the pathways producing these modifications in this compartment are less well understood.
Glycosylation (see also chemical glycosylation) is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules. This enzymatic process produces one of the fundamental biopolymers found in cells (along with DNA, RNA, and proteins).
G proteins, also known as guanosine nucleotide-binding proteins, are a family of proteins involved in transmitting signals from a variety of different stimuli outside a cell into the inside of the cell. G proteins function as molecular switches. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). When they bind GTP, they are ‘on’, and, when they bind GDP, they are ‘off’. G proteins belong to the larger group of enzymes called GTPases. There are two classes of G proteins.
The first function as monomeric small GTPases while the second form and function as heterotrimeric G protein complexes. The latter class of complexes are made up of alpha ( ), beta (ß) and gamma ( ) subunits. In addition, the beta and gamma subunits can form a stable dimeric complex referred to as the beta-gamma complex. G proteins located within the cell are activated by G protein-coupled receptors (GPCRs) that span the cell membrane. Signaling molecules bind to a domain of the GPCR located outside the cell. An intracellular GPCR domain in turn activates a G protein.
The G protein activates a cascade of further signaling events that finally results in a change in cell function. G protein-coupled receptor and G proteins working together transmit signals from many hormones, neurotransmitters, and other signaling factors. G proteins regulate metabolic enzymes, ion channels, transporter, and other parts of the cell machinery, controlling transcription, motility, contractility, and secretion, which in turn regulate diverse systemic functions such as embryonic development, learning and memory, and homeostasis.
Graft in (surgery) is a tissue or organ transplanted from a donor to a recipient; in some cases the patient can be both donor and recipient.
H19 is a gene for a long noncoding RNA, found in humans and elsewhere. This gene seems to have a role in some forms of cancer. The H19 gene is also known as ASM, ASM1 and BWS, among others.
Hairpin ribozyme is a small section of RNA that can act as an enzyme known as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. The hairpin ribozyme is similar to the hammerhead ribozyme in that it does not require a metal ion for the reaction.
Hammerhead ribozyme is a RNA module that catalyzes reversible cleavage and joining reactions at a specific site within an RNA molecule. It serves as a model system for research on the structure and properties of RNA, and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications. Named for the resemblance of early secondary structure diagrams to a hammerhead shark hammerhead ribozymes RNAs were originally discovered in two classes of plant virus-like RNAs: satellite RNAs and viroids. They have subsequently been found to be widely dispersed within many forms of life.
The self-cleavage reactions, first reported in 1986, are part of a rolling circle replication mechanism. The hammerhead sequence is sufficient for self-cleavage and acts by forming a conserved three-dimensional tertiary structure.
Hayflick limit (or Hayflick phenomenon) is the number of times a normal human cell population will divide until cell division stops. Empirical evidence shows that the telomeres associated with each cell’s DNA will get slightly shorter with each new cell division until they shorten to a critical length.
The concept of the Hayflick limit was advanced by Leonard Hayflick in 1961, at the Wistar Institute in Philadelphia. Hayflick demonstrated that a population of normal human fetal cells in a cell culture will divide between 40 and 60 times. The population will then enter a senescence phase, which refutes the contention by Nobel laureate Alexis Carrel that normal cells are immortal. Each mitosis slightly shortens each of the telomeres on the DNA of the cells. Telomere shortening in humans eventually makes cell division impossible, and this aging of the cell population appears to correlate with the overall physical aging of the human body. This mechanism also appears to prevent genomic instability. Telomere shortening may also prevent the development of cancer in human aged cells by limiting the number of cell divisions. However, shortened telomeres impair immune function that might also increase cancer susceptibility.
HeLa cell /’hi l /, also Hela or hela cell, is a cell type in an immortal cell line used in scientific research. It is the oldest and most commonly used human cell line. The line was derived from cervical cancer cells taken on February 8, 1951, from Henrietta Lacks, a patient who eventually died of her cancer on October 4, 1951. The cell line was found to be remarkably durable and prolific as illustrated by its contamination of many other cell lines used in research.
Hierarchical clustering is a method of cluster analysis which seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two types:
• Agglomerative: This is a “bottom up” approach: each observation starts in its own cluster, and pairs of clusters are merged as one moves up the hierarchy.
• Divisive: This is a “top down” approach: all observations start in one cluster, and splits are performed recursively as one moves down the hierarchy.
Histone 3′ UTR stem-loop is an RNA element involved in nucleocytoplasmic transport of the histone mRNAs, and in the regulation of stability and of translation efficiency in the cytoplasm. The mRNAs of metazoan histone genes lack polyadenylation and a poly-A tail, instead 3′ end processing occurs at a site between this highly conserved stem-loop and a purine rich region around 20 nucleotides downstream (the histone downstream element, or HDE). The stem-loop is bound by a 31 kDa stem-loop binding protein (SLBP – also termed the histone hairpin binding protein, or HBP). Together with U7 snRNA binding of the HDE, SLBP binding nucleates the formation of the processing complex.
Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins of chromosomes. Depending on the target site, methylation can modify histones so that different portions of chromatin are activated or inactivated. In most cases, methylation and demethylation of histones turns the genes in DNA “off” and “on”, respectively, either by loosening or encompassing their tails, thereby allowing or blocking transcription factors and other proteins to access the DNA. This process is critical for the regulation of gene expression that allows different cells to express different portions of the genome.
Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction. Also termed lateral gene transfer (LGT), it contrasts with vertical transfer, the transmission of genes from the parental generation to offspring via sexual or asexual reproduction. HGT has been shown to be an important factor in the evolution of many organisms.
Horizontal gene transfer is the primary reason for bacterial antibiotic resistance, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticidesand in the evolution, maintenance, and transmission of virulence. This horizontal gene transfer often involves temperate bacteriophages and plasmids. Genes that are responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms (e.g., via F-pilus), subsequently arming the antibiotic resistant genes’ recipient against antibiotics, which is becoming a medical challenge to deal with. This is the most critical reason that antibiotics must not be consumed and administered to patients without appropriate prescription from a medical physician.
Most thinking in genetics has focused upon vertical transfer, but there is a growing awareness that horizontal gene transfer is a highly significant phenomenon and among single-celled organisms perhaps the dominant form of genetic transfer.
Artificial horizontal gene transfer is a form of genetic engineering.
Humoral immunity (also called the antibody-mediated system) is the aspect of immunity that is mediated by macromolecules (as opposed to cell-mediated immunity) found in extracellular fluids such as secreted antibodies, complement proteins and certain antimicrobial peptides. Humoral immunity is so named because it involves substances found in the humours, or body fluids.
Hybridoma technology is a technology of forming hybrid cell lines (called hybridomas) by fusing a specific antibody-producing B cell with a myeloma (B cell cancer) cell that is selected for its ability to grow in tissue culture and for an absence of antibody chain synthesis. The antibodies produced by the hybridoma are all of a single specificity and are therefore monoclonal antibodies (in contrast to polyclonal antibodies). The production of monoclonal antibodies was invented by César Milstein and Georges J. F. Köhler in 1975. They shared the Nobel Prize of 1984 for Medicine and Physiology with Niels Kaj Jerne, who made other contributions to immunology. The term hybridoma was coined by Leonard Herzenberg during his sabbatical in César Milstein’s laboratory in 1976/1977. .
Immortalised cell line is a population of cells from a multicellular organism which would normally not proliferate indefinitely but, due to mutation, have evaded normal cellular senescence and instead can keep undergoing division. The cells can therefore be grown for prolonged periods in vitro. The mutations required for immortality can occur naturally or be intentionally induced for experimental purposes. Immortal cell lines are a very important tool for research into the biochemistry and cell biology of multicellular organisms. Immortalised cell lines have also found uses in biotechnology.
An immortalised cell line should not be confused with stem cells, which can also divide indefinitely, but form a normal part of the development of a multicellular organism.
Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine. The major types of IBD are Crohn’s disease and ulcerative colitis.
Insert is a piece of DNA that is inserted into a larger DNA vector by a recombinant DNA technique, such as ligation or recombination. This allows it to be multiplied, selected, further manipulated or expressed in a host organism.
In silico is an expression used to mean “performed on computer or via computer simulation.” The phrase was coined in 1989 as an analogy to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology (see also systems biology) and refer to experiments done in living organisms, outside of living organisms, and where they are found in nature, respectively.
Insulin-like growth factor 2 (IGF-2) is one of three protein hormones that share structural similarity to insulin. The MeSH definition reads: “A well-characterized neutral peptide believed to be secreted by the liver and to circulate in the blood. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on somatotropin. It is believed to be a major fetal growth factor in contrast to Insulin-like growth factor 1, which is a major growth factor in adults”.
Interleukins are a group of cytokines (secreted proteins and signaling molecules) that were first seen to be expressed by white blood cells (leukocytes). The function of the immune system depends in a large part on interleukins, and rare deficiencies of a number of them have been described, all featuring autoimmune diseases or immune deficiency. The majority of interleukins are synthesized by helper CD4 T lymphocytes, as well as through monocytes, macrophages, and endothelial cells. They promote the development and differentiation of T and B lymphocytes, and hematopoietic cells. Interleukin receptors on astrocytes in the hippocampus are also known to be involved in the development of spatial memories in mice.
Innate immune system, also known as non-specific immune system and first line of defense, comprises the cells and mechanisms that defend the host from infection by other organisms in a non-specific manner. This means that the cells of the innate system recognize and respond to pathogens in a generic way, but unlike the adaptive immune system (which is only found in vertebrates), it does not confer long-lasting or protective immunity to the host. Innate immune systems provide immediate defense against infection, and are found in all classes of plant and animal life.
Innate immune system is an evolutionarily older defense strategy, and is the dominant immune system found in plants, fungi, insects, and in primitive multicellular organisms.
The major functions of the vertebrate innate immune system include:
• Recruiting immune cells to sites of infection, through the production of chemical factors, including specialized chemical mediators, called cytokines.
• Activation of the complement cascade to identify bacteria, activate cells and to promote clearance of dead cells or antibody complexes.
• The identification and removal of foreign substances present in organs, tissues, the blood and lymph, by specialised white blood cells.
• Activation of the adaptive immune system through a process known as antigen presentation.
• Acting as a physical and chemical barrier to infectious agents.
Intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.
Irritable bowel syndrome (IBS, or spastic colon) is a symptom-based diagnosis characterized by chronic abdominal pain, discomfort, bloating, and alteration of bowel habits. As a functional gastrointestinal disorder (FGID), IBS has no known organic cause. Diarrhea or constipation may predominate, or they may alternate (classified as IBS-D, IBS-C or IBS-A, respectively).
Jurkat cells (pronounced yur’kat) are an immortalized line of human T lymphocyte cells that are used to study acute T cell leukemia, T cell signaling, and the expression of various chemokine receptors susceptible to viral entry, particularly HIV. Jurkat cells are also useful in science because of their ability to produce interleukin 2. Their primary use, however, is to determine the mechanism of differential susceptibility of cancers to drugs and radiation. The Jurkat cell line (originally called JM) was established in the late 1970s from the peripheral blood of a 14 year old boy with T cell leukemia. Different derivatives of the Jurkat cell line can now be obtained from cell culture banks that have been mutated to lack certain genes.
kinase is a type of enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates, a process referred to as phosphorylation. Kinases are part of the larger family of phosphotransferases. Kinases are not to be confused with phosphorylases, which carry out phosphorolysis, the breaking of a bond using an inorganic phosphate group; or with phosphatases, which remove phosphate groups.
Klenow fragment is a large protein fragment produced when DNA polymerase I from E. coli is enzymatically cleaved by the protease subtilisin. First reported in 1970, it retains the 5′-3′ polymerase activity and the 3’ › 5’ exonuclease activity for removal of precoding nucleotides and proofreading, but loses its 5′ › 3′ exonuclease activity.
The other smaller fragment formed when DNA polymerase I from E. coli is cleaved by subtilisin retains the 5′-3′ exonuclease activity but does not have the other two activities exhibited by the Klenow fragment (i.e. 5′-> 3′ polymerase activity, and 3′->5′ exonuclease activity).
Lac operon is an operon required for the transport and metabolism of lactose in Escherichia coli and some other enteric bacteria. It consists of three adjacent structural genes, lacZ, lacY, and lacA. The genes encode ß-galactosidase, lactose permease, and thiogalactoside transacetylase (or galactoside O-acetyltransferase), respectively.
In its natural environment, the lac operon allows for the effective digestion of lactose. The lactose permease, which sits in the cytoplasmic membrane, transports lactose into the cell. ß-galactosidase, a cytoplasmic enzyme, subsequently cleaves lactose into glucose and galactose. However, it would be wasteful to produce the enzymes when there is no lactose available or if there is a more preferable energy source available, such as glucose. Gene regulation of the lac operon was the first genetic regulatory mechanism to be understood clearly and is one of the foremost examples of prokaryotic gene regulation. The lac operon is one of the most basic methods for explanation of how a repressor enzyme works within a cell on DNA and for that reason is discussed in many introductory molecular and cellular biology classes at universities.
L6 antigen is mainly expressed in lung, breast, colon, ovarian carcinomas, and healthy epithelial tissue in humans, Tumor-associated antigen L6 and the invasion of human lung cancer cells, Thus, TAL6 appears to be involved in cancer invasion and metastasis, The tumor-associated antigen L6 (TAL6), a distant member of the TM4SF, is expressed on most epithelial cell carcinomas and is a target for antibody-mediated therapy.
Ligase is a specific type of enzyme, a ligase, (EC 22.214.171.124) that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template, with DNA ligase creating the final phosphodiester bond to fully repair the DNA.
DNA ligase has applications in both DNA repair and DNA replication (see Mammalian ligases). In addition, DNA ligase has extensive use in molecular biology laboratories for recombinant DNA experiments (see Applications in molecular biology research). Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA.
Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts longer than 200 nucleotides (Perkel 2013). This somewhat arbitrary limit distinguishes long ncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs (Ma 2013).
Long ncRNA functions
Large scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate that long noncoding RNAs number in the order of tens of thousands in mammals. However, despite accumulating evidence suggesting that the majority of these are likely to be functional (Mercer 2009; Dinger 2009), only a relatively small proportion has been demonstrated to be biologically relevant. As of December 2012, ~127 LncRNAs have been functionally annotated in LncRNAdb (a database of literature described LncRNAs) (Amral 2011).
Long ncRNAs in the regulation of gene transcription
Long ncRNAs in gene-specific transcription
In eukaryotes, RNA transcription is a tightly regulated process. NcRNAs can target different aspects of this process, targeting transcriptional activators or repressors, different components of the transcription reaction including RNA polymerase (RNAP) II and even the DNA duplex to regulate gene transcription and expression (Goodrich 2006). In combination these ncRNAs may comprise a regulatory network that, including transcription factors, finely control gene expression in complex eukaryotes.
NcRNAs modulate the function of transcription factors by several different mechanisms, including functioning themselves as co-regulators, modifying transcription factor activity, or regulating the association and activity of co-regulators.
Long terminal repeats (LTRs) are identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA. They are used by viruses to insert their genetic material into the host genomes.
The HIV-1 LTR is approximately 640 bp in length and, like other retroviral LTRs, is segmented into the U3, R, and U5 regions. U3 and U5 has been further subdivided according to transcription factor sites and their impact on LTR activity and viral gene expression. The multi-step process of reverse transcription results in the placement of two identical LTRs, each consisting of a U3, R, and U5 region, at either end of the proviral DNA. The ends of the LTRs subsequently participate in integration of the provirus into the host genome. Once the provirus has been integrated, the LTR on the 5′ end serves as the promoter for the entire retroviral genome, while the LTR at the 3′ end provides for nascent viral RNA polyadenylation and, in HIV-1, HIV-2, and SIV, encodes the accessory protein, Nef.
All of the required signals for gene expression are found in the LTRs: Enhancer, promoter (can have both transcriptional enhancers or regulatory elements), transcription initiation (such as capping), transcription terminator and polyadenylation signal.
In HIV-1, the U5 region has been characterized according to functional and structural differences into several sub-regions as follows:
• TAR or trans-acting responsive element, plays a critical role in transcriptional activation via its interaction with viral proteins. It forms a highly stable stem-loop structure consisting of 26 base pairs with a bulge secondary structure that interfaces with the viral transcription activator protein Tat.
• Poly A play roles both in dimerization and genome packaging since it is necessary for cleavage and polyadenilation. It has been reported that sequences upstream (U3 region) and downstream (U5 region) are needed in order to make the cleavage process efficient.
• PBS or primer binding site, of 18 nucleotides long, it has a specific sequence that bind to tRNALys and are requirements for initiation of reverse transcription.
• Psi ( ) or the packaging signal is a unique motif that is associated with this process, although is not sufficient to specify for packaging. It is composed of four stem-loop (SL) structures with a major splicing donor site embedded in the second SL.
• DIS or dimer initiation site that mediates RNA-RNA interactions. Is a highly conserved stem-loop sequence found in many retroviruses and is characterized by a conserved stem and palindromic loop, when homodimerized, forms a “kissing-loop” complex.
The transcript begins, by definition, at the beginning of R, is capped, and proceeds through U5 and the rest of the provirus, usually terminating by the addition of a poly A tract just after the R sequence in the 3′ LTR.
The finding that both HIV LTRs can function as transcriptional promoters is not surprising since both elements are apparently identical in nucleotide sequence. Instead, the 3′ LTR acts in transcription termination and polyadenylation. However, it has been suggested that the transcriptional activity of the 5’LTR is far greater than that of the 3′ LTR, a situation that is very similar to that of other retroviruses.
During transcription of the human immunodeficiency virus type 1 provirus, polyadenylation signals present in the 5′ long terminal repeat (LTR) are disregarded while the identical polyadenylation signals present in the 3’LTR are utilized efficiently. It has been suggested that transcribed sequences present within the HIV-1 LTR U3 region act in cis to enhance polyadenylation within the 3′ LTR.
The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (cDNA) and ultimately dsDNA (double-stranded DNA) with full LTRs. The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. The first LTR sequences were derived by A.P. Czernilofsky and J. Shine in 1977 and 1980.
Retroviruses such as Human Immunodeficiency Virus (HIV) use this basic mechanism.
Dating retroviral insertions using LTRs
As 5′ and 3′ LTRs are identical upon insertion, the difference between paired LTRs can be used to estimate the age of ancient retroviral insertions. This method of dating is used by paleovirologists, though it fails to take into account confounding factors such as gene-conversion and homologous recombination.
M13 is a filamentous bacteriophage composed of circular single stranded DNA (ssDNA) which is 6407 nucleotides long encapsulated in approximately 2700 copies of the major coat protein P8, and capped with 5 copies of two different minor coat proteins (P9, P6, P3) on the ends. The minor coat protein P3 attaches to the receptor at the tip of the F pilus of the host Escherichia coli.
Major histocompatibility complex (MHC) is a set of cell surface molecules encoded by a large gene family in all vertebrates. MHC molecules mediate interactions of leukocytes, also called white blood cells (WBCs), which are immune cells, with other leukocytes or body cells. MHC determines compatibility of donors for organ transplant as well as one’s susceptibility to an autoimmune disease via crossreacting immunization. In humans, MHC is also called human leukocyte antigen (HLA). Protein molecules—either of the host’s own phenotype or of other biologic entities—are continually synthesized and degraded in a cell. Occurring on the cell surface, each MHC molecule displays a molecular fraction, called epitope, of a protein. The presented antigen can be either self or nonself. On the cell membrane, the MHC population in its entirety is like a meter indicating the balance of proteins within the cell.
mAb means Monoclonal Antibody.
Mediastinum is an undelineated group of structures in the thorax, surrounded by loose connective tissue. It is the central compartment of the thoracic cavity. It contains the heart, the great vessels of the heart, the esophagus, the trachea, the phrenic nerve, the cardiac nerve, the thoracic duct, the thymus, and the lymph nodes of the central chest.
Methyltransferase also known as a methylase is a type of transferase enzyme that transfers a methyl group from a donor to an acceptor.
Methylation often occurs on nucleic bases in DNA or amino acids in protein structures. Methytransferases use a reactive methyl group bound to sulfur in S-adenosyl methionine (SAM) as the methyl donor.
METTL3: N6-adenosine-methyltransferase 70 kDa subunit is an enzyme that in humans is encoded by the METTL3 gene.
This gene encodes the 70 kDa subunit of MT-A which is part of N6-adenosine-methyltransferase. This enzyme is involved in the posttranscriptional methylation of internal adenosine residues in eukaryotic mRNAs, forming N6-methyladenosine.
microRNA (abbr. miRNA) is a small non-coding RNA molecule (ca. 22 nucleotides) found in plants and animals, which functions in transcriptional and post-transcriptional regulation of gene expression. Encoded by eukaryotic nuclear DNA, miRNAs function via base-pairing with complementary sequences within mRNA molecules, usually resulting in gene silencing via translational repression or target degradation. The human genome may encode over 1000 miRNAs, which may target about 60% of mammalian genes and are abundant in many human cell types.
Mitogen is a chemical substance that encourages a cell to commence cell division, triggering mitosis. A mitogen is usually some form of a protein.
Mitogenesis is the induction (triggering) of mitosis, typically via a mitogen.
Mitogens trigger signal transduction pathways in which mitogen-activated protein kinase (MAPK) is involved, leading to mitosis.
Mitogen-activated protein kinases also known as MAP kinases are serine/threonine-specific protein kinases belonging to the CMGC (CDK/MAPK/GSK3/CLK) kinase group. The closest relatives of MAPKs are the cyclin-dependent kinases (CDKs). MAPKs are involved in directing cellular responses to a diverse array of stimuli, such as mitogens, osmotic stress, heat shock and proinflammatory cytokines. They regulate proliferation, gene expression, differentiation, mitosis, cell survival, and apoptosis – among many others. MAP kinases are found in eukaryotes only, but they are fairly diverse and encountered in all animals, fungi and plants, and even in an array of unicellular eukaryotes.
Mobile genetic elements (MGE) are a type of DNA that can move around within the genome. They include:
• Transposons (also called transposable elements)
o DNA transposons
o Insertion sequences
• Bacteriophage elements, like Mu, which integrates randomly into the genome
• Group II introns
The total of all mobile genetic elements in a genome may be referred to as the mobilome. Barbara McClintock was awarded the 1983 Nobel Prize in Physiology or Medicine “for her discovery of mobile genetic elements”.
Mobile genetic elements play a critical role in the spread of virulence factors, such as exotoxins and exoenzymes, amongst bacteria. Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed.
Mu Phage or Bacteriophage Mu or phage Mu is a temperate bacteriophage, a type of virus that infects bacteria.
Mucins are a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most metazoans. Mucins’ key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers. They often take an inhibitory role. Some mucins are associated with controlling mineralization, including nacre formation in mollusks, calcification in echinoderms and bone formation in vertebrates. They bind to pathogens as part of the immune system. Overexpression of the mucin proteins, especially MUC1, is associated with many types of cancer.
Multiple organ dysfunction syndrome (MODS), previously known as multiple organ failure (MOF) or multisystem organ failure (MSOF), is altered organ function in an acutely ill patient requiring medical intervention to achieve homeostasis. The use of “multiple organ failure” or “multisystem organ failure” should be avoided since that phrase was based upon physiological parameters to determine whether or not a particular organ was failing.
N6-Methyladenosine (m6A ) is an abundant modification in mRNA and is found within some viruses, and most eukaryotes including mammals, insects, plants and yeast. It is also found in tRNA, rRNA, and small nuclear RNA (snRNA) as well as several long non-coding RNA, such as Xist.
Adenosine methylation is directed by a large m6A methyltransferase complex containing METTL3 as the SAM-binding sub-unit. In vitro, this methyltransferase complex preferentially methylates RNA oligonucleotides containing GGACU and a similar preference was identified in vivo in mapped m6A sites in Rous sarcoma virus genomic RNA and in bovine prolactin mRNA.
Neuroblastoma (NB) is the most common extracranial solid cancer in childhood and the most common cancer in infancy, with an incidence of about six hundred and fifty cases per year in the U.S., and a hundred cases per year in the UK. Nearly half of neuroblastoma cases occur in children younger than two years. It is a neuroendocrine tumor, arising from any neural crest element of the sympathetic nervous system (SNS). It most frequently originates in one of the adrenal glands, but can also develop in nerve tissues in the neck, chest, abdomen, or pelvis.
Nonsteroidal anti-inflammatory drugs, usually abbreviated to NSAIDs /’ ns d/ EN-sed—but also referred to as nonsteroidal anti-inflammatory agents/analgesics (NSAIAs) or nonsteroidal anti-inflammatory medicines (NSAIMs)—are a class of drugs that provides analgesic and antipyretic (fever-reducing) effects, and, in higher doses, anti-inflammatory effects.
Novel means Original and of a kind not seen before.
Oligomer (\ -‘li-g -m r\, , or oligos, is Greek for “a few”) is a molecular complex that consists of a few monomer units, in contrast to a polymer that, at least in principle, consists of a nearly unlimited number of monomers. Dimers, trimers, and tetramers are, for instance, oligomers respectively composed of two, three and four monomers.
Oncogene is a gene that has the potential to cause cancer. In tumor cells, they are often mutated or expressed at high levels. Most normal cells undergo a programmed form of death (apoptosis). Activated oncogenes can cause those cells designated for apoptosis to survive and proliferate instead. Most oncogenes require an additional step, such as mutations in another gene, or environmental factors, such as viral infection, to cause cancer. Since the 1970s, dozens of oncogenes have been identified in human cancer. Many cancer drugs target the proteins encoded by oncogenes. .
Open reading frame (ORF) is the part of a reading frame that contains a start codon at the beginning and stop codon at the end and no stop codons in between. The transcription termination pause site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation.
Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop codons.
One common use of open reading frames is as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with other evidence, to initially identify candidate protein coding regions in a DNA sequence. The presence of an ORF does not necessarily mean that the region is ever translated. For example in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons. A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism’s coding regions. By itself even a long open reading frame is not conclusive evidence for the presence of a gene.
If a portion of a genome has been sequenced (e.g. 5′-ATCTAAAATGGGTGCC-3′), ORFs can be located by examining each of the three possible reading frames on each strand. In this sequence two out of three possible reading frames are entirely open, meaning that they do not contain a stop codon:
1. …A TCT AAA ATG GGT GCC…
2. …AT CTA AAA TGG GTG CC…
3. …ATC TAA AAT GGG TGC C…
Possible stop codons in DNA are “TGA”, “TAA” and “TAG”. Thus, the last reading frame in this example contains a stop codon (TAA), unlike the first two.
Operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be both co-transcribed and co-regulated to define an operon.
Originally, operons were thought to exist solely in prokaryotes, but since the discovery of the first operons in eukaryotes in the early 1990s, more evidence has arisen to suggest they are more common than previously assumed. In general, expression of prokaryotic operons leads to the generation of polycistronic mRNAs, while eukaryotic operons lead to monocistronic mRNAs.
Operons have also been found in viruses such as bacteriophages. For example, T7 phages have two operons—the first one codes for various products including a special T7 RNA polymerase which can bind to and transcribe the second operon—which includes a lysis gene meant to cause the host cell to burst.
Ori is the DNA sequence that signals for the origin of replication, sometimes referred to simply as origin. In E. coli, ori is some 250 nucleotides in length for the chromosomal origin (oriC). The plasmid ori sequences are similar to oriC.
During conjugation, the rolling circle mode of replication starts at the oriT (‘T’ for transfer) sequence of the FAT plasmid.
Bacteria have a single origin for replication. Eukaryotes have multiple replicons, each with an ori. The replicons range from 40 kb (yeast and Drosophila) to 300 kb (plants) in length.
Mitochondrial DNA in many organisms has two ori sequences. In humans, they are called oriH and oriL for the heavy and light strand of the DNA, each is the origin of replication.
Origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
DNA replication may proceed from this point bidirectionally or unidirectionally.
The specific structure of the origin of replication varies somewhat from species to species, but all share some common characteristics such as high AT content. The origin of replication binds the pre-replication complex, a protein complex that recognizes, unwinds, and begins to copy DNA.
Orthology is Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation (is the evolutionary process by which new biological species arise) event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. The term “ortholog” was coined in 1970 by Walter Fitch.
Palindromic sequence is a nucleic acid sequence (DNA or RNA) that is the same whether read 5′ (five-prime) to 3′ (three prime) on one strand or 5′ to 3′ on the complementary strand with which it forms a double helix.
pBluescript (pBS) or pBluescript II is a commercially available phagemid containing several useful sequences for use in cloning with bacteriophage. The sequences include a multiple cloning site sequence (MCS), antibiotic resistance sequence to ampicillin and an E. coli and f1 helper phage origin of replication. The multiple cloning site sequence is located within a LacZ controlled gene designed to provide a blue coloration when expressed in bacteria. This is usually achieved via X-gal found in agarose growth media used to culture bacteria with pBS. If the gene is disrupted by successful insertion of a DNA sequence, the bacteria exhibit a white coloration in Blue white screening, distinguishing successful recombination from those phagemids which were not altered. These recombinant plasmids can then be used in a variety of molecular techniques. Determining expression and developing genomic libraries are some applications for which the pBS recombinants can be used.
Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure.
pET22b is a Bacterial Plasmid Vector with ampR selectable marker.
phagemid or phasmid is a plasmid that contains an f1 origin of replication from a f1 phage. It can be used as a type of cloning vector in combination with filamentous phage M13. A phagemid can be replicated as a plasmid, and also be packaged as single stranded DNA in viral particles. Phagemids contain an origin of replication (ori) for double stranded replication, as well as an f1 ori to enable single stranded replication and packaging into phage particles. Many commonly used plasmids contain an f1 ori and are thus phagemids. Similarly to a plasmid, a phagemid can be used to clone DNA fragments and be introduced into a bacterial host by a range of techniques, such as transformation and electroporation.
piwi domain of an argonaute protein with bound siRNA, components of the RNA-induced silencing complex that mediates gene silencing by RNA interference.Piwi (sometimes also PIWI; originally P-element induced wimpy testis in Drosophila) class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells. Piwi proteins are highly conserved across evolutionary lineages and are present in both plants and animals. One of the major human homologues, whose upregulation is implicated in the formation of tumours such as seminomas, is called hiwi; other variants on the theme include the miwi protein in mice.piRNAs and Piwi proteins are thought to form an endogenous system for silencing the expression of selfish genetic elements such as retrotransposons and thus preventing the gene products of such sequences from interfering with germ cell formation.
Phrenic nerve is a nerve that originates in the neck (C3-C5) and passes down between the lung and heart to reach the diaphragm. It is important for breathing, as it passes motor information to the diaphragm and receives sensory information from it. There are two phrenic nerves, a left and a right one.
The phrenic nerve originates mainly from the 4th cervical nerve, but also receives contributions from the 5th and 3rd cervical nerves (C3-C5) in humans. Thus, the phrenic nerve receives innervation from parts of both the cervical plexus and the brachial plexus of nerves.
Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, particularly those in spermatogenesis. They are distinct from microRNA (miRNA) in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity.
It remains unclear how piRNAs are generated, but potential methods have been suggested, and it is certain their biogenesis pathway is distinct from miRNA and siRNA, while rasiRNAs are a piRNA subspecies.
Pluripotency (from the Latin plurimus, meaning very many, and potens, meaning having power) refers to a stem cell that has the potential to differentiate into any of the three germ layers: endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), or ectoderm (epidermal tissues and nervous system).
Polyadenylation is the addition of a poly(A) tail to a primary transcript RNA. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation. It, therefore, forms part of the larger process of gene expression.
The process of polyadenylation begins as the transcription of a gene finishes, or terminates. The 3′-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the RNA’s 3′ end. In some genes, these proteins may add a poly(A) tail at any one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing.
The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. However, in a few cell types, mRNAs with short poly(A) tails are stored for later activation by re-polyadenylation in the cytosol. In contrast, when polyadenylation occurs in bacteria, it promotes RNA degradation. This is also sometimes the case for eukaryotic non-coding RNAs.
In nuclear polyadenylation, a poly(A) tail is added to an RNA at the end of transcription. On mRNAs, the poly(A) tail protects the mRNA molecule from enzymatic degradation in the cytoplasm and aids in transcription termination, export of the mRNA from the nucleus, and translation. Almost all eukaryotic mRNAs are polyadenylated, with the exception of animal replication-dependent histone mRNAs. These are the only mRNAs in eukaryotes that lack a poly(A) tail, ending instead in a stem-loop structure followed by a purine-rich sequence, termed histone downstream element, that directs where the RNA is cut so that the 3′ end of the histone mRNA is formed.
Many eukaryotic non-coding RNAs are always polyadenylated at the end of transcription. There are small RNAs where the poly(A) tail is seen only in intermediary forms and not in the mature RNA as the ends are removed during processing, the notable ones being microRNAs. But, for many long noncoding RNAs – a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which mediates X chromosome inactivation – a poly(A) tail is part of the mature RNA.
Posttranslational modification (PTM) is a step in protein biosynthesis. Proteins are created by ribosomes translating mRNA into polypeptide chains. These polypeptide chains undergo PTM, (such as folding, cutting and other processes), before becoming the mature protein product.
A protein (also called a polypeptide) is a chain of amino acids. During protein synthesis, 20 different amino acids can be incorporated to become a protein. After translation, the posttranslational modification of amino acids extends the range of functions of the protein by attaching it to other biochemical functional groups (such as acetate, phosphate, various lipids and carbohydrates), changing the chemical nature of an amino acid (e.g. citrullination), or making structural changes (e.g. formation of disulfide bridges).
Also, enzymes may remove amino acids from the amino end of the protein, or cut the peptide chain in the middle. For instance, the peptide hormone insulin is cut twice after disulfide bonds are formed, and a propeptide is removed from the middle of the chain; the resulting protein consists of two polypeptide chains connected by disulfide bonds. Also, most nascent polypeptides start with the amino acid methionine because the “start” codon on mRNA also codes for this amino acid. This amino acid is usually taken off during post-translational modification.
Other modifications, like phosphorylation, are part of common mechanisms for controlling the behavior of a protein, for instance activating or inactivating an enzyme.
Post-translational modification of proteins is detected by mass spectrometry or Eastern blotting.
Prader–Willi syndrome (/’pr d r ‘v li/; abbreviated P.W.S) is a rare, genetic disorder in which seven genes (or some subset thereof) on chromosome 15 (q 11–13) are deleted or unexpressed (chromosome 15q partial deletion) on the paternal chromosome. It was first described in 1956 by Andrea Prader (1919–2001), Heinrich Willi (1900–1971), Alexis Labhart (1916 – 1994)), Andrew Ziegler, and Guido Fanconi of Switzerland. Characteristic of PWS is “low muscle tone, short stature, incomplete sexual development, cognitive disabilities, problem behaviors, and a chronic feeling of hunger that can lead to excessive eating and life-threatening obesity.”
Precursor mRNA (pre-mRNA) is an immature single strand of messenger ribonucleic acid (mRNA). Pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA). The term hnRNA is often used as a synonym for pre-mRNA, although, in the strict sense, hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA.
Once pre-mRNA has been completely processed, it is termed “mature messenger RNA”, “mature mRNA”, or simply “mRNA”.
Eukaryotic pre-mRNA exists only briefly before it is fully processed into mRNA. Pre-mRNAs include two different types of segments, exons and introns. Exons are segments that are retained in the final mRNA, whereas introns are removed in a process called splicing, which is performed by the spliceosome (except for self-splicing introns).
Additional processing steps attach modifications to the 5′ and 3′ ends of Eukaryotic pre-mRNA. These include a 5′ cap of 7-methylguanosine and a poly-A tail. In addition, eukaryotic pre-mRNAs have their introns spliced out by spliceosomes made up of small nuclear ribonucleoproteins.
When a pre-mRNA strand has been properly processed to an mRNA sequence, it is exported out of the nucleus and eventually translated into a protein – a process accomplished in conjunction with ribosomes.
Proinflammatory cytokine is a cytokine which promotes systemic inflammation.
Examples include IL-1 and TNF alpha.
Due to their proinflammatory action, they tend to make a disease worse by producing fever, inflammation, tissue destruction, and, in some cases, even shock and death.
Reducing the biological activities of proinflammatory cytokines can reduce the brunt of attack of diseases mediated by proinflammatory cytokines.[ Blocking IL-1 or TNF has been highly successful in patients with rheumatoid arthritis, inflammatory bowel disease, or graft-vs-host disease. However, the strategy has not been successful in humans with sepsis.
Progenitor cell is a biological cell that, like a stem cell, has a tendency to differentiate into a specific type of cell, but is already more specific than a stem cell and is pushed to differentiate into its “target” cell. The most important difference between stem cells and progenitor cells is that stem cells can replicate indefinitely, whereas progenitor cells can divide only a limited number of times. Controversy about the exact definition remains and the concept is still evolving.
Promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA (towards the 3′ region of the anti-sense strand, also called template strand and non-coding strand). Promoters can be about 100–1000 base pairs long.
Protein domain is a conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. Domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be “swapped” by genetic engineering between one protein and another to make chimeric proteins.
Protein precursor, also called a pro-protein or pro-peptide, is an inactive protein (or peptide) that can be turned into an active form by posttranslational modification. The name of the precursor for a protein is often prefixed by pro. Examples include proinsulin and proopiomelanocortin.
Protein precursors are often used by an organism when the subsequent protein is potentially harmful, but needs to be available on short notice and/or in large quantities. Enzyme precursors are called zymogens or proenzymes. Examples are enzymes of the digestive tract in humans.
Pseudouridine (abbreviated by the Greek letter psi- ) is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. is found in all species and in many classes of RNA except mRNA. is formed by enzymes called synthases, which post-transcriptionally isomerize specific uridine residues in RNA in a process termed pseudouridylation.
P-TEFb or positive transcription elongation factor, plays an essential role in the regulation of transcription by RNA polymerase II (Pol II) in eukaryotes.
RAGs or Recombination activating genes encode enzymes that play an important role in the rearrangement and recombination of the genes of immunoglobulin and T cell receptor molecules during the process of VDJ recombination. There are two recombination activating gene products known as RAG-1 and RAG-2, whose cellular expression is restricted to lymphocytes during their developmental stages. RAG-1 and RAG-2 are essential to the generation of mature B and T lymphocytes, two cell types that are crucial components of the adaptive immune system.
Ras is the name given to a family of related proteins found inside cells, including human cells. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells (cellular signal transduction). Ras is the prototypical member of the Ras superfamily of proteins, which are all related in 3D structure and regulate diverse cell behaviours. The name ‘Ras’ is an abbreviation of ‘Rat sarcoma’, reflecting the way the first members of the protein family were discovered. The name ras is also used to refer to the family of genes encoding those proteins.
Ras gene is the name given to a family of related proteins found inside cells, including human cells. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells (cellular signal transduction). Ras is the prototypical member of the Ras superfamily of proteins, which are all related in 3D structure and regulate diverse cell behaviours. The name ‘Ras’ is an abbreviation of ‘Rat sarcoma’, reflecting the way the first members of the protein family were discovered. The name ras is also used to refer to the family of genes encoding those proteins.
Reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.
A single strand of a nucleic acid molecule has a phosphoryl end, (called the 5′-end) and a hydroxyl, or (3′-end). These then define the 5’›3′ direction. There are three reading frames that can be read in this 5’›3′ direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic acid, an additional three reading frames may be read from the other, complementary strand in the 5’›3′ direction along this strand. As the two strands of a double stranded nucleic acid molecule are antiparallel, the 5’›3′ direction on the second strand corresponds to the 3’›5′ direction along the first strand.
In general, at most one reading frame in a given section of a nucleic acid is biologically relevant. Viral transcripts can be translated using multiple reading frames.
Reciprocal Control is the control in opposite way to inhibit and control the metabolic pathway. For example high activity of the calcium-dependent pathway can negatively regulate the cGMP-dependent pathway. We have termed these opposing regulatory mechanisms reciprocal control.
Recombinant Genetic recombination is the process by which two DNA molecules exchange genetic information, resulting in the production of a new combination of alleles.
Repeat associated small interfering RNA (rasiRNA) is a class of small RNA that is involved in the RNA interference (RNAi) pathway. RasiRNA are in fact Piwi-interacting RNAs (piRNAs), which are small RNA molecules that interact with Piwi proteins. Piwi proteins are a clade of the Argonaute family of proteins. In the germline, RasiRNA is involved in establishing and maintaining heterochromatin structure, controlling transcripts that emerge from repeat sequences, and silencing transposons and retrotransposons.
Replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication.
Repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator. A DNA-binding repressor blocks the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes into messenger RNA. An RNA-binding repressor binds to the mRNA and prevents translation of the mRNA into protein. This blocking of expression is called repression.
Restriction enzyme (or restriction endonuclease) is an enzyme that cuts DNA at or near specific recognition nucleotide sequences known as restriction sites. Restriction enzymes are commonly classified into three types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.
These enzymes are found in bacteria and archaea and provide a defense mechanism against invading viruses. Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction; while host DNA is protected by a modification enzyme (a methylase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.
Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially. These enzymes are routinely used for DNA modification in laboratories, and are a vital tool in molecular cloning.
Examples of restriction enzymes include:
Enzyme Source Recognition Sequence Cut
3’CTTAAG 5′—G AATTC—3′
3’GGWCC 5′— CCWGG—3′
3’CCTAGG 5′—G GATCC—3′
3’TTCGAA 5′—A AGCTT—3′
3’AGCT 5′—T CGA—3′
3’CGCCGGCG 5′—GC GGCCGC—3′
3’CTNAGT 5′—G ANTC—3′
3’CTAG 5′— GATC—3′
3’GTCGAC 5′—CAG CTG—3′
3’GGGCCC 5′—CCC GGG—3′
3’CCGG 5′—GG CC—3′
3’CTGCG 5′—NN NN—3′
3’TCGA 5′—AG CT—3′
3’CTATAG 5′—GAT ATC—3′
3’GTCGTCN25NN 5′—CAGCAGN25 NN—3′
3’CCATGG 5′—GGTAC C—3′
3’GACGTC 5′—CTGCA G—3′
3’CTCGAG 5′—GAGCT C—3′
3’CAGCTG 5′—G TCGAC—3′
3’TCATGA 5′—AGT ACT—3′
3’TGATCA 5′—A CTAGT—3′
3’CGTACG 5′—GCATG C—3′
3’TCCGGA 5′—AGG CCT—3′
3’AGATCT 5′—T CTAGA—3′
* = blunt ends
N = C or G or T or A
W = A or T
Restriction modification system (RM system) is used by bacteria, and perhaps other prokaryotic organisms to protect themselves from foreign DNA, such as the one borne by bacteriophages. This phenomenon was first noticed in the 1950s. Certain bacteria strains were found to inhibit (restrict) the growth of viruses grown in previous strains. This effect was attributed to sequence-specific restriction enzymes.
Bacteria have restriction enzymes, also called restriction endonucleases, which cleave double stranded DNA at specific points into fragments, which are then degraded further by other endonucleases. This prevents infection by effectively destroying the foreign DNA introduced by an infectious agent (such as a bacteriophage). Approximately one quarter of known bacteria possess RM systems and of those about one half have more than one type of system.
Given that the sequences of the restriction enzymes recognize are very short, the bacterium itself will almost certainly have many of these sequences present in its own DNA. Therefore, in order to prevent destruction of its own DNA by the restriction enzymes, the bacterium marks its own DNA by adding methyl groups to it. This modification must not interfere with the DNA base-pairing, and therefore, usually only a few specific bases are modified on each strand.
Endonucleases cleave internal/non-terminal phosphodiester bonds. Restriction endonucleases cleave internal phosphodiester bonds only after recognising specific sequences in DNA which are usually 4-6 base pairs long, and often palindromic.
Restriction sites, or restriction recognition sites, are locations on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences (because restriction enzymes usually bind as homodimers), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby. For example, the common restriction enzyme EcoRI recognizes the palindromic sequence GAATTC and cuts between the G and the A on both the top and bottom strands, leaving an overhang (an end-portion of a DNA strand with no attached complement) known as a sticky end on each end, of AATT. This overhang can then be used to ligate in (see DNA ligase) a piece of DNA with a complementary overhang (another EcoRI-cut piece, for example). Some restriction enzymes cut DNA at a restriction site in a manner which leaves no overhang, a blunt end.
Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49-78% of the genome is made up of retrotransposons. In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements. In mammals, almost half the genome (45% to 48%) is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2-3%.
Retroviral vector: Gene transfer systems based on viruses that have RNA as their genetic material.
Ribozyme (ribonucleic acid enzyme) is an RNA molecule that is capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. The 1981 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. Also termed catalytic RNA, ribozymes function within the ribosome (as part of the large subunit ribosomal RNA) to link amino acids during protein synthesis, and in a variety of RNA processing reactions, including RNA splicing, viral replication, and transfer RNA biosynthesis. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme and the hairpin ribozyme.
Rolling circle replication describes a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. Some eukaryotic viruses also replicate their DNA via a rolling circle mechanism.
Circular DNA replication
Rolling circle DNA replication is initiated by an initiator protein encoded by the plasmid or bacteriophage DNA, which nicks one strand of the double-stranded, circular DNA molecule at a site called the double-strand origin, or DSO. The initiator protein remains bound to the 5′ phosphate end of the nicked strand, and the free 3′ hydroxyl end is released to serve as a primer for DNA synthesis by DNA polymerase III. Using the unnicked strand as a template, replication proceeds around the circular DNA molecule, displacing the nicked strand as single-stranded DNA. Displacement of the nicked strand is carried out by a host-encoded helicase called PcrA (the abbreviation standing for plasmid copy reduced) in the presence of the plasmid replication initiation protein.
Continued DNA synthesis can produce multiple single-stranded linear copies of the original DNA in a continuous head-to-tail series called a concatemer. These linear copies can be converted to double-stranded circular molecules through the following process:
First, the initiator protein makes another nick to terminate synthesis of the first (leading) strand. RNA polymerase and DNA polymerase III then replicate the single-stranded origin (SSO) DNA to make another double-stranded circle. DNA polymerase I removes the primer, replacing it with DNA, and DNA ligase joins the ends to make another molecule of double-stranded circular DNA.
Rolling circle replication has found wide uses in academic research and biotechnology, and has been successfully used for amplification of DNA from very small amounts of starting material.
S-Adenosyl methionine (SAM-e, SAMe, SAM, AdoMet, ademetionine) is a common cosubstrate involved in methyl group transfers. SAM was first discovered in Italy by G. L. Cantoni in 1952. It is made from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase (EC 126.96.36.199). Transmethylation, transsulfuration, and aminopropylation are the metabolic pathways that use SAM. Although these anabolic reactions occur throughout the body, most SAM is produced and consumed in the liver.
Sarcoma (from the Greek sarx meaning “flesh”) is a cancer that arises from transformed cells of mesenchymal origin. Thus, malignant tumors made of cancerous bone, cartilage, fat, muscle, vascular, or hematopoietic tissues are, by definition, considered sarcomas. This is in contrast to a malignant tumor originating from epithelial cells, which are termed carcinoma. Human sarcomas are quite rare. Common malignancies, such as breast, colon, and lung cancer, are almost always carcinoma.
Satellite is a subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper or master virus for its multiplication. When a satellite encodes the coat protein in which its nucleic acid is encapsidated it is referred to as a satellite virus.
Secondary structure of a nucleic acid molecule refers to the basepairing interactions within a single molecule or set of interacting molecules, and can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNA’s and RNA’s tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complicated base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.
In a non-biological context, secondary structure is a vital consideration in the rational design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules.
Selfish DNA is a term for sequences of DNA that sensu stricto have two distinct properties:
• The DNA sequence spreads by forming additional copies of itself within the genome; and
• It makes no specific contribution to the reproductive success of its host organism. (It might or might not have significant deleterious effects.
In his 1976 book The Selfish Gene Richard Dawkins suggested the idea of selfish DNA in reaction to the then fairly new revelation of the large proportion of noncoding DNA in eukaryotic genomes. In 1980, two articles in the journal Nature expanded and discussed the concept. According to one of these articles:
The theory of natural selection, in its more general formulation, deals with the competition between replicating entities. It shows that, in such a competition, the more efficient replicators increase in number at the expense of their less efficient competitors. After a sufficient time, only the most efficient replicators survive.
— L.E. Orgel & F.H.C. Crick, Selfish DNA: the ultimate parasite.
In the purest forms of the concepts, units of genetically functional DNA might be viewed as “replicating entities” that effect their replication by manipulating the physiological activities of the cell that they control; in contrast, units of selfish DNA effect their replication by exploiting existing DNA and DNA-manipulating mechanisms in the cell, notionally without significantly affecting the fitness of the organism in other respects.
Irrespective of the strict definition of selfish DNA, there is no sharp, definitive boundary between the concepts of selfish DNA and genetically functional DNA. Often it also is difficult to establish whether a unit of noncoding DNA is functionally important or not, and if important, in what way. What is more, it is not always easy to distinguish between some instances of selfish DNA and some types of viruses.
• Transposons copy themselves to different loci inside the genome. These elements constitute a large fraction of eukaryotic genome sizes (C-values): about 45% of the human genome is composed of transposons and their defunct remnants.
• Homing endonuclease genes cleave DNA at its own site on the homologous chromosome, triggering the DNA double-stranded break repair system, which “repairs” the break by copying the HEG onto the homologous chromosome. HEGs have been characterized in yeast, and can only survive by passing between multiple isolated populations or species.
• Supernumerary B chromosomes are essential chromosomes that are transmitted in higher-than-expected frequencies, which leads to their accumulation in progenies.
Sensu is a Latin word meaning “in the sense of”. It is used in a number of fields including biology, geology, linguistics, and law. Commonly it refers to how strictly or loosely an expression is used in describing any particular concept, but it also appears in expressions that indicate the convention or context of the usage.
Seminoma (also known as pure seminoma or classical seminoma) is a germ cell tumor of the testis or, more rarely, the mediastinum or other extra-gonadal locations. It is a malignant neoplasm and is one of the most treatable and curable cancers, with a survival rate above 95% if discovered in early stages.
Testicular seminoma originates in the germinal epithelium of the seminiferous tubules. About half of germ cell tumors of the testis are seminomas. Treatment usually requires removal of one testis, but this does not affect fertility or other sexual functioning.
Sepsis (/’s ps s/; Greek , putrefaction and decay) is a potentially fatal whole-body inflammation (a systemic inflammatory response syndrome or SIRS) caused by severe infection. Sepsis can continue even after the infection that caused it is gone. Severe sepsis is sepsis complicated by organ dysfunction. Septic shock is sepsis complicated by a high lactate level or by shock that does not improve after fluid resuscitation. Bacteremia is the presence of viable bacteria in the blood. The term septicemia, the presence of microorganisms or their toxins in the blood, is no longer used by the consensus committee.
Sepsis is caused by the immune system’s response to a serious infection, most commonly bacteria, but also fungi, viruses, and parasites in the blood, urinary tract, lungs, skin, or other tissues. Sepsis can be thought of as falling within a continuum from infection to multiple organ dysfunction syndrome.
Common symptoms of sepsis include those related to a specific infection, but usually accompanied by high fevers, hot, flushed skin, elevated heart rate, hyperventilation, altered mental status, swelling, and low blood pressure. In the very young and elderly, or in people with weakened immune systems, the pattern of symptoms may be atypical, with hypothermia and without an easily localizable infection. Sepsis causes millions of deaths globally each year.
Serine proteases (or serine endopeptidases) are enzymes that cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the (enzyme’s) active site. They are found ubiquitously in both eukaryotes and prokaryotes. Serine proteases fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like) or subtilisin-like. In humans, they are responsible for co-ordinating various physiological functions, including digestion, immune response, blood coagulation and reproduction.
Severe combined immunodeficiency (SCID), (also known as “Alymphocytosis,” “Glanzmann–Riniker syndrome,” “Severe mixed immunodeficiency syndrome,” and “Thymic alymphoplasia”) is a genetic disorder characterized by the absence of functional T-lymphocytes, which results in a defective antibody response due to either direct involvement with B lymphocytes or through improper B lymphocyte activation due to non-functional T-helper cells. Consequently, both “arms” (B cells and T cells) of the adaptive immune system are impaired due to a defect in one of several possible genes. SCID is the most severe form of primary immunodeficiencies, and there are now at least nine different known genes in which mutations lead to a form of SCID. It is also known as the bubble boy disease because its victims are extremely vulnerable to infectious diseases and some of them, such as David Vetter, become famous for living in a sterile environment. SCID is the result of an immune system so highly compromised that it is considered almost absent.
Side-chain theory (German, Seitenkettentheorie) is a theory proposed by Paul Ehrlich (1854–1915) to explain the immune response in living cells. Ehrlich theorized from very early in his career that chemical structure could be used to explain why the immune response occurred in reaction to infection. He believed that toxins and antitoxins were chemical substances at a time when very little was known about their nature.
Ehrlich supposed that living cells have side-chains in the same way dyes have side-chains which are related to their coloring properties. These side chains can link with a particular toxin, just as Emil Fischer said enzymes must bind to their receptors “like a key in a lock.”
Ehrlich theorized that a cell under threat grew additional side-chains to bind the toxin, and that these additional side chains broke off to become the antibodies that are circulated through the body. It was these antibodies that Ehrlich first described as “magic bullets” in search of toxins.
In an attempt to explain the origin of serum antibody, Ehrlich proposed that cells in the blood expressed a variety of receptors, which he called “side-chain receptors,” that could react with infectious agents and inactivate them. Borrowing a concept used by Emil Fischer in 1894 to explain the interaction between an enzyme and its substrate, Ehrlich proposed that binding of the receptor to an infectious agent was like the fit between a lock and key. Ehrlich suggested that interaction between an infectious agent and a cell-bound receptor would induce the cell to produce and release more receptors with the same specificity. According to Ehrlich’s theory, the specificity of the receptor was determined before its exposure to antigen, and the antigen selected the appropriate receptor. Ultimately all aspects of Ehrlich’s theory would be proven correct with the minor exception that the “receptor” exists as both a soluble antibody molecule and as a cell-bound receptor; it is the soluble form that is secreted rather than the bound form released. Reference (Kuby Immunology)
Silencer is a DNA sequence capable of binding transcription regulation factors, called repressors. DNA contains genes and provides the template to produce messenger RNA (mRNA). That mRNA is then translated into proteins that activate or inactivate gene expression in cells. When a repressor protein binds to the silencer region of DNA, RNA polymerase—the enzyme that transcribes DNA into RNA—is prevented from binding to the promoter region. With the transcription of DNA into RNA blocked, the translation of RNA into proteins is impossible. Thus, silencers prevent genes from being expressed as proteins.
Silver–Russell dwarfism, also called Silver–Russell syndrome (SRS) or Russell–Silver syndrome (RSS) is a growth disorder occurring in approximately 1/50,000 to 1/100,000 births. In the United States it is usually referred to as Russell–Silver syndrome, and Silver–Russell syndrome elsewhere. It is one of 200 types of dwarfism and one of five types of primordial dwarfism and is one of the few forms that is considered treatable in some cases.
There is no statistical significance of the syndrome occurring in males or females.
Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response. There are two stages in this process:
1. A signaling molecule activates a specific receptor protein on the cell membrane.
2. A second messenger transmits the signal into the cell, eliciting a physiological response.
In either step, the signal can be amplified. Thus, one signalling molecule can cause many responses. A signal transduction functions much like a switch.
Single-chain variable fragment (scFv) is not actually a fragment of an antibody, but instead is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of the linker. The image to the right shows how this modification usually leaves the specificity unaltered.
These molecules were created to facilitate phage display, where it is highly convenient to express the antigen-binding domain as a single peptide. As an alternative, scFv can be created directly from subcloned heavy and light chains derived from a hybridoma. ScFvs have many uses, e.g., flow cytometry, immunohistochemistry, and as antigen-binding domains of artificial T cell receptors.
Unlike monoclonal antibodies, which are often produced in mammalian cell cultures, scFvs are more often produced in bacteria cell cultures such as E. coli.
siRNA (interfering RNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length. siRNA plays many roles, but it is most notable in the RNA interference (RNAi) pathway, where it interferes with the expression of specific genes with complementary nucleotide sequence. siRNA also acts in RNAi-related pathways, e.g., as an antiviral mechanism or in shaping the chromatin structure of a genome. The complexity of these pathways is only now being elucidated.
siRNAs and their role in post-transcriptional gene silencing (PTGS) in plants were first discovered by David Baulcombe’s group at the Sainsbury Laboratory in Norwich, England and reported in Science in 1999. Thomas Tuschl and colleagues soon reported in Nature that synthetic siRNAs could induce RNAi in mammalian cells. This discovery led to a surge in interest in harnessing RNAi for biomedical research and drug development.
Small nuclear RNA 7SK is an abundant found in metazoans. It plays a role in regulating transcription by controlling the positive transcription elongation factor P-TEFb 7SK is found in a small nuclear ribonucleoprotein complex (snRNP) with a number of other proteins that regulate the stability and function of the complex.
Small nuclear ribonucleic acid (snRNA), also commonly referred to as U-RNA, is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III, and studies have shown that their primary function is in the processing of pre-mRNA (hnRNA) in the nucleus. They have also been shown to aid in the regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), and maintaining the telomeres.
snRNPs (pronounced “snurps”), or small nuclear ribonucleic particles, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs. The action of snRNPs is essential to the removal of introns from pre-mRNA, a critical aspect of post-transcriptional modification of RNA, occurring only in the nucleus of eukaryotic cells. Additionally, U7 snRNP is not involved in splicing at all, as U7 snRNP is responsible to process the 3′ stem-loop of histone pre-mRNA.
Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.
Splicing is a modification of the nascent pre-messenger RNA (pre-mRNA) transcript in which introns are removed and exons are joined. For nuclear encoded genes, splicing takes place within the nucleus after or concurrently with transcription. Splicing is needed for the typical eukaryotic messenger RNA (mRNA) before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins,
snRNPs (snurps”), or small nuclear ribonucleic particles, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs), but there are also self-splicing introns.
Spliceosome is a large and complex molecular machine found primarily within the nucleus of eukaryotes. Spliceosome is assembled from snRNPs and protein complexes. Spliceosome removes introns from a transcribed pre-mRNA, a kind of primary transcript. This process is generally referred to as splicing. Only eukaryotes have spliceosomes and metazoans have a second spliceosome, the minor spliceosome.
Each spliceosome is composed of five small nuclear RNAs (snRNA), and a range of associated protein factors. When these small RNA are combined with the protein factors, they make an RNA-protein complex called snRNP.
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length. siRNA plays many roles, but it is most notable in the RNA interference (RNAi) pathway, where it interferes with the expression of specific genes with complementary nucleotide sequence. siRNA also acts in RNAi-related pathways, e.g., as an antiviral mechanism or in shaping the chromatin structure of a genome. The complexity of these pathways is only now being elucidated.
siRNAs and their role in post-transcriptional gene silencing (PTGS) in plants were first discovered by David Baulcombe’s group at the Sainsbury Laboratory in Norwich, England and reported in Science in 1999. Thomas Tuschl and colleagues soon reported in Nature that synthetic siRNAs could induce RNAi in mammalian cells. This discovery led to a surge in interest in harnessing RNAi for biomedical research and drug development.
Stem cells are undifferentiated biological cells, that can differentiate into specialized cells and can divide (through mitosis) to produce more stem cells. They are found in multicellular organisms. In mammals, there are two broad types of stem cells: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing adult tissues. In a developing embryo, stem cells can differentiate into all the specialized cells—ectoderm, endoderm and mesoderm (see induced pluripotent stem cells)—but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues.
There are three accessible sources of autologous adult stem cells in humans:
1. Bone marrow, which requires extraction by harvesting, that is, drilling into bone (typically the femur or iliac crest)
2. Adipose tissue (lipid cells), which requires extraction by liposuction, and
3. Blood, which requires extraction through apheresis, wherein blood is drawn from the donor (similar to a blood donation), passed through a machine that extracts the stem cells and returns other portions of the blood to the donor.
Stem cells can also be taken from umbilical cord blood just after birth. Of all stem cell types, autologous harvesting involves the least risk. By definition, autologous cells are obtained from one’s own body, just as one may bank his or her own blood for elective surgical procedures.
Highly plastic adult stem cells are routinely used in medical therapies, for example in bone marrow transplantation. Stem cells can now be artificially grown and transformed (differentiated) into specialized cell types with characteristics consistent with cells of various tissues such as muscles or nerves through cell culture. Embryonic cell lines and autologous embryonic stem cells generated through therapeutic cloning have also been proposed as promising candidates for future therapies. Research into stem cells grew out of findings by Ernest A. McCulloch and James E. Till at the University of Toronto in the 1960s.
Stroma (from Greek µ , meaning “layer, bed, bed covering”) refers to the connective, supportive framework of a biological cell, tissue, or organ. The stroma in animal tissue is contrasted with the parenchyma.
Subtilisin is a non-specific protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis. Subtilisins belong to subtilases, a group of serine proteases that initiate the nucleophilic attack on the peptide (amide) bond through a serine residue at the active site. Subtilisins typically have molecular weights of about 20,000 to 45,000 dalton. They can be obtained from certain types of soil bacteria, for example, Bacillus amyloliquefaciens from which they are secreted in large amounts.
Systemic inflammatory response syndrome (SIRS) is an inflammatory state affecting the whole body, frequently a response of the immune system to infection, but not necessarily so. It is related to sepsis, a condition in which individuals meet criteria for SIRS and have a known infection.
It is the body’s response to an infectious or noninfectious insult. Although the definition of SIRS refers to it as an “inflammatory” response, it actually has pro- and anti-inflammatory components.
T cell receptor or TCR is a molecule found on the surface of T lymphocytes (or T cells) that is responsible for recognizing antigens bound to major histocompatibility complex (MHC) molecules. The binding between TCR and antigen is of relatively low affinity and is degenerate: that is, many TCR recognize the same antigen and many antigens are recognized by the same TCR.
The TCR is composed of two different protein chains (that is, it is a heterodimer). In 95% of T cells, this consists of an alpha ( ) and beta (ß) chain, whereas in 5% of T cells this consists of gamma and delta ( / ) chains. This ratio changes during ontogeny and in diseased states.
When the TCR engages with antigenic peptide and MHC (peptide/MHC), the T lymphocyte is activated through a series of biochemical events mediated by associated enzymes, co-receptors, specialized adaptor molecules, and activated or released transcription factors.
Trans-acting (trans-regulatory, trans-regulation), in general, means “acting from a different molecule” (i.e., intermolecular). It may be considered the opposite of cis-acting (cis-regulatory, cis-regulation), which, in general, means “acting from the same molecule” (i.e., intramolecular).
Transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized mRNA that trigger processes which release the mRNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
Transfection is the process of deliberately introducing nucleic acids into cells. The term is often used for non-viral methods in eukaryotic cells. It may also refer to other methods and cell types, although other terms are preferred: “transformation” is more often used to describe non-viral DNA transfer in bacteria, non-animal eukaryotic cells and plant cells. In animal cells, transfection is the preferred term as transformation is also used to refer to progression to a cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-mediated DNA transfer.
The word transfection is a blend of trans- and infection. Genetic material (such as supercoiled plasmid DNA or siRNA constructs), or even proteins such as antibodies, may be transfected.
Transfection of animal cells typically involves opening transient pores or “holes” in the cell membrane, to allow the uptake of material. Transfection can be carried out using calcium phosphate, by electroporation, or by mixing a cationic lipid with the material to produce liposomes, which fuse with the cell membrane and deposit their cargo inside.
Transfection can result in unexpected morphologies and abnormalities in target cells.
Transferase is the general name for the class of enzymes that enact the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor). They are involved in hundreds of different biochemical pathways throughout biology, and are integral to some of life’s most important processes.
Transmembrane protein (TP) is a type membrane protein that spans from one side of a cell membrane through to the other side of the membrane. Many TPs function as gateways or “loading docks” to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as in the case of waste byproducts. As a response to the shape of certain molecules these “freight handling” TPs may have special ways of folding up or bending that will move a substance through the biological membrane.All transmembrane proteins are integral membrane proteins, but not all IMPs are transmembrane proteins.
Transposable element (TE, transposon or retrotransposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell’s genome size. Transposition often results in duplication of the TE. Barbara McClintock’s discovery of these jumping genes earned her a Nobel prize in 1983.
TEs make up a large fraction of the C-value of eukaryotic cells. They are generally considered non-coding DNA, although it has been unambiguously shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.
Trans-splicing is a special form of RNA processing in eukaryotes where exons from two different primary RNA transcripts are joined end to end and ligated.
In contrast “normal” (cis-)splicing processes a single molecule. That is, trans-splicing results in an RNA transcript that came from multiple RNA polymerases on the genome. This phenomenon can be exploited for molecular therapy to address mutated gene products.
Trans-splicing can be the mechanism behind certain oncogenic fusion transcripts. Trans-splicing is used by certain microbial organisms, notably protozoa of the Kinetoplastae class to produce variable surface antigens and change from one life stage to another.
Trimeric autotransporter adhesins shortened to TAAs, are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. They are, essentially, virulence factors, factors that make the bacteria harmful and infective to the host organism.
Tumor associated anitgen (TAL6) The L6 antigen is mainly expressed in lung, breast, colon, ovarian carcinomas, and healthy epithelial tissue in humans, Tumor-associated antigen L6 and the invasion of human lung cancer cells, Thus, TAL6 appears to be involved in cancer invasion and metastasis, The tumor-associated antigen L6 (TAL6), a distant member of the TM4SF, is expressed on most epithelial cell carcinomas and is a target for antibody-mediated therapy.
Tumor-associated glycoprotein 72 (TAG-72) is a glycoprotein found on the surface of many cancer cells.
Targeted cancer therapies are expected to be more effective than current treatments and less harmful to normal cells. There are targeted therapies for breast cancer, multiple myeloma, lymphoma, prostate cancer, melanoma and other cancers. The definitive experiments that showed that targeted therapy would reverse the malignant phenotype of tumor cells involved treating Her2/neu transformed cells with monoclonal antibodies in vitro and in vivo by Mark Greene’s laboratory and reported from 1985. Some have challenged use of the term, stating that drugs usually associated with the term are insufficiently selective. The phrase occasionally appears in scare quotes: “targeted therapy”.
Tumor-associated glycoprotein 72 (TAG-72) is a glycoprotein found on the surface of many cancer cells, including ovary, breast, colon, and pancreatic cells. It is a mucin-like molecule with a molar mass of over 1000 kDa. TAG-72 is a tumor marker and can be measured with radioimmunoassays like CA 72-4, which uses indium (111In) satumomab pendetide (is a mouse monoclonal antibody which is used for cancer diagnosis.) and iodine (125I) CC49 monoclonal antibody. This assay has a good specificity for gastric cancer, with a correlation to the neoplasia’s extension. It is used to identify relapses of the disease and to follow up the treatment. TAG-72 is also the target of the anti-cancer drugs anatumomab mafenatox and minretumomab.
U7 small nuclear RNA (U7 snRNP) is an RNA molecule involved in the 3′ end formation of metazoan(animal) histone pre-mRNAs. The 5′ end of U7 RNA is thought to base-pair to a conserved spacer element downstream of the cleavage site in histone pre-mRNA.
Ulcerative colitis (Colitis ulcerosa, UC) is a form of inflammatory bowel disease (IBD). Ulcerative colitis is a form of colitis, a disease of the colon (large intestine), that includes characteristic ulcers, or open sores. The main symptom of active disease is usually constant diarrhea mixed with blood, of gradual onset. IBD is often confused with irritable bowel syndrome (IBS).
Upregulation is the process by which a cell increase amount of a cellular component . An example of upregulation is the increased number of cytochrome P450 enzymes in liver cells when xenobiotic molecules such as dioxin are administered (resulting in greater degradation of these molecules).
Upstream and downstream both refer to a relative position in DNA or RNA. Each strand of DNA or RNA has a 5′ end and a 3′ end, so named for the carbons on the deoxyribose (or ribose) ring. Relative to the position on the strand, downstream is the region towards the 3′ end of the strand. Since DNA strands run in opposite directions, downstream on one strand is upstream on the other strand.
Transcription and translation of DNA and mRNA, respectively, have their direction defined by the newly synthesized strand, that is, in downstream direction (5′ › 3′). However, it is in the upstream direction (3′ › 5′) for the copied template strand.
Varkud satellite (VS) ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.
V(D)J recombination, also known as somatic recombination, is a mechanism of genetic recombination in the early stages of immunoglobulin (Ig) and T cell receptors (TCR) production of the immune system. V(D)J recombination takes place in the primary lymphoid tissue (the bone marrow for B cells, and Thymus for T cells). V(D)J recombination nearly randomly combines Variable, Diverse, and Joining gene segments in vertebrate lymphocytes, and because of its randomness in choosing different genes, is able to diversely encode proteins to match antigens from bacteria, viruses, parasites, dysfunctional cells such as tumor cells, and pollens.
Viroids are plant pathogens that consist of a short stretch (a few hundred nucleobases) of highly complementary, circular, single-stranded RNA. In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2 kilobases in size. The human pathogen Hepatitis D Virus is similar to viroids. Viroid genomes are extremely small in size, ranging from 246 to 467 nucleotides (nt), and consisting of fewer than 10,000 atoms. Viroids are not usually considered a form of life.
Viroids were discovered and named by Theodor Otto Diener, a plant pathologist at the Agricultural Research Service in Maryland, in 1971.
Virulence factors are molecules expressed and secreted by pathogens (bacteria, viruses, fungi and protozoa) that enable them to achieve the following:
• Colonization of a niche in the host (this includes adhesion to cells) for example, Trimeric Autotransporter Adhesins (TAA)
• Immunoevasion, evasion of the host’s immune response
• Immunosuppression, inhibition of the host’s immune response
• Entry into and exit out of cells (if the pathogen is an intracellular one)
• Obtain nutrition from the host.
Xenobiotic is a foreign chemical substance found within an organism that is not normally naturally produced by or expected to be present within that organism. It can also cover substances which are present in much higher concentrations than are usual. Specifically, drugs such as antibiotics are xenobiotics in humans because the human body does not produce them itself, nor are they part of a normal diet.
Xenograft is Tissue from an animal of one species used as a temporary graft (as in cases of severe burns) on an individual of another species.
X-gal (also abbreviated BCIG for 5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside) is an organic compound consisting of galactose linked to a substituted indole. The compound was synthesized by Jerome Horwitz and collaborators in Detroit, MI, in 1964. The formal chemical name is often shortened to less accurate but also less cumbersome phrases such as bromochloroindoxyl galactoside. The X from indoxyl may well be the source of the X in the X-gal contraction. X-gal is much used in molecular biology to test for the presence of an enzyme, ß-galactosidase. It is also used to detect activity of this enzyme in histochemistry and bacteriology. X-gal is one of many indoxyl glycosides and esters that yield insoluble blue compounds similar to indigo as a result of enzyme-catalyzed hydrolysis.
X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in female mammals is inactivated. The inactive X chromosome is silenced by it being packaged in such a way that it has a transcriptionally inactive structure called heterochromatin. As female mammals have two X chromosomes, X-inactivation prevents them from having twice as many X chromosome gene products as males, which only possess a single copy of the X chromosome.
Xist (X-inactive specific transcript (on-protein coding)) is an RNA gene on the X chromosome of the placental mammals that acts as major effector of the X inactivation process.
The X-inactivation center (or simply XIC) on the X chromosome is necessary and sufficient to cause X-inactivation. Chromosomal translocations which place the XIC on an autosome lead to inactivation of the autosome, and X chromosomes lacking the XIC are not inactivated.