miR-616 overexpression has been observed in  androgen -independent  prostate cancer  cells, specifically in  malignant  tissue compared with  benign  forms. It is notably resistant to  castration  in  LNCaP  cells, due to an enhanced ability to  proliferate   in vivo . [ 1 ]  It has been found to interact with the tissue factor pathway inhibitor TFPI-2, and to directly target its mRNA at the three  3'UTR . Further, inhibition of TFPI-2 by miR-616 means inversely correlated expression of the two.


mir-618 microRNA  is a short  non-coding RNA  molecule belonging both to the family of  microRNAs  and to that of  small interfering RNAs  (siRNAs). MicroRNAs function to regulate the  expression  levels of other genes by several mechanisms, whilst siRNAs are involved primarily with the  RNA interference  (RNAi) pathway.


Decreased levels of miR-618 have been observed in  estradiol(E2) -stimulated  MCF-7   breast cancer  cells following hormone deprivation. Intracellular miR-618 levels can be regulated by E2 via the  ER2 receptor . This points towards a possible of this miRNA, amongst others, in modulating the final gene responses to the  oestrogen  family of hormones in breast cancer cells. [ 1 ]


Altered expression of miR-618 has been seen in the human  lymphoblastoid  TK6 cell line, with downregulation following stress-related stimulated  microgravity  in TK6 cells. This further influences several genes involved in regulation of the NF-κB-related pathway network. [ 2 ]


mir-624 microRNA  is a short  non-coding RNA  molecule belonging both to the family of  microRNAs  and to that of  small interfering RNAs  (siRNAs). MicroRNAs function to regulate the  expression  levels of other genes by several mechanisms, whilst siRNAs are involved primarily with the  RNA interference  (RNAi) pathway. siRNAs have been linked through some members to the regulation of  cancer  cell growth, specifically in  prostate   adenocarcinoma .


miR-624 has been found to be upregulated in the WI-38 cell line of human  fibroblasts  in growth arrest states; there was a 1.9 fold increase observed in both cell  quiescence  and  senescence , and a further increased 2.1 fold increase with  H 2 O 2 -premature senescence. [ 1 ]  It has additionally been found to target the (CASP3) gene responsible for encoding the protein  caspase 3 .


In  molecular biology   mir-625 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms. Many microRNAs play important roles in cancer development and progression.


mir-625 has been shown to be  down regulated  in  gastric cancers . This is important, as mir-625 is responsible for the regulation of  metastasis  in gastric tumour cells, and therefore downregulation of mir-625 results in increased metastasis. [ 1 ]  mir-625 is thought to act by inhibiting the  ILK  protein. [ 1 ]


In molecular biology  mir-632 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-632 has been identified as one of three key miRNAs associated with the anti-ageing  myelodysplastic syndromes  (MDS). In particular, its levels show high discrimination between MDS and normal controls, and expression is decreased in MDS. [ 1 ]  In this way it can be used as a potential diagnostic marker for MDS.


miR-632 targets the coding region of the  DNAJB6 protein , a member of the  Heat Shock Protein 40  (HSP40) family which shows constitutive expression. DNAJB6 is known to be a negative regulator of tumour progression in breast cancer and its levels are compromised in advanced tumour progression. miR-632 has been linked to be  downregulation  of DNAJB6 and is capable of silencing both spliced variants of this protein. [ 2 ]  It is currently unknown whether miR-632 may be just one of many negative regulators controlling DNAJB6 levels.


In  molecular biology   mir-633 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-633 has been linked to  acute lymphoblastic leukaemia  (ALL) and as having a potential role in the development of leukaemia, due to abnormal expression in ALL subjects. [ 1 ]  It may be of use for prediction of relapse potential and in development of personalised leukaemia treatments.


miR-633 expression in  endometrial  carcinoma cells upon treatment with  progesterone  saw a 50% decrease in expression levels. These point towards a possible critical role of miR-633, alongside other miRNAs, in the regulation of posttranscriptional gene expression on progesterone treatment. [ 2 ]


In  molecular biology   mir-636 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-636 has been identified as one of three key miRNAs associated with the anti-ageing  myelodysplastic syndromes  (MDS). Its levels correspond to high discrimination between MDS and normal controls, and expression is decreased in MDS. [ 1 ]  In this way it can be used as a potential diagnostic marker for MDS.


Resistance to  glucocorticoids  (GC) used in the treatment of blood-related  malignancies  greatly impairs their clinical utility. The active glucocorticoid receptor GR-α is required for an effective response to GCs, but this is significantly downregulated in GC-resistant cell lines MM.1Re and MM.1RL. miR-636 has been found to be differentially expressed between GC-sensitive and GC-resistant MM.1 cell lines. It has therefore been identified as a possible candidate responsible for postranscriptional silencing of GR-α in GC-resistant cells. [ 2 ]


In  molecular biology   mir-638 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-638 has been implicated in the pathogenesis of  lupus nephritis  (LN), with intra-renal expression levels differing between normal and lupus nephritis patients. [ 1 ]  The degree of difference in expression levels further correlates with the degree of disease severity in each LN patient.


miR-638 levels are significantly downregulated in gastric cancer cell lines, along with deregulation of 23 other miRNAs. [ 2 ]  Thus miR-628 is likely to be involved in the development and progression of gastric cancer.


miR-638 has additionally been found to be upregulated in the K562 leukaemic cell line. [ 3 ]


In  molecular biology   mir-650 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-650 is one of a group of six miRNAs with altered expression levels in diabetic and non-diabetic heart failure. This altered expression corresponds to various enriched cardiac dysfunctions. [ 1 ]


miR-650 has further been reported to target a homologous DNA region in the promoter region of the  NDRG2  gene. [ 2 ]   There is direct regulation of this gene at a transcriptional level, leading to repressed  NDRG2  expression.


In  molecular biology   mir-652 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms, with expression levels of miRNAs and respective target mRNAs negatively correlated.


miR-652 expression is specific to cells of the  myeloid  lineage, in this instance to monocytes and granulocytes. [ 1 ]


miR-652 serum levels are significantly altered in alcoholic- or  hepatitis-C -induced liver cirrhosis patients. They have been found to be down-regulated in the circulating monocytes of such patients, thus supporting the idea of an miR-652 role in the mediation of fibrogenic and inflammatory processes in the  pathogenesis  of liver cirrhosis. [ 2 ]


Circulating levels of miR-652 show gradual elevation with progression of liver cancer, as is also the case with miRNAs let-7a, let-7f, miR-34a, miR-98, miR-331 and miR-338. [ 3 ]


In molecular biology  mir-657 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-661 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-671 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-671 expression levels have been found to be vary significantly between the alcoholic and non-alcoholic forms of  fatty liver disease . [ 1 ]


miR-671 has been seen to negatively regulate the  CDR1  (Cerebellar Degeneration-Related protein 1) gene, through the targeting and cleavage of a circular  antisense  transcript of the  CDR1  locus. There is a partnered decrease in CDR1 mRNA levels with this downregulation. [ 2 ]


miR-671 is able to bind to and repress  fibronection type 1 (FN1)  mRNA at its  3'untranslated region  binding site. [ 3 ]


In molecular biology  mir-672 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-672 is underexpressed in  neuroblastoma  cells and has been associated with cancer pathways. [ 1 ]  It has further been identified as one of six miRNAs significantly downregulated in  dorsal root ganglia  following  sciatic nerve  entrapment. [ 2 ]  Additionally, miR-672 has been found to be  X-linked  and to show preferential expression in testes and ovaries. [ 3 ]


In  molecular biology   mir-675 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-675 overexpression brings about reduced  proliferation  in a range of embryonic and extraembryonic  stem cell lines . It has been found to be embedded in the first exon of the  large intergenic non-coding RNA  H19, which is responsible for limiting placental growth prior to birth. There is upregulation of the targets of miR-675 in placentas lacking H19; these include the  insulin-like growth factor 1 receptor  (IGF1R). Thus placentas lacking miR-675 continue to grow. It is possible that controlled miR-675 release from H19 may enable a rapid inhibition of cell proliferation in response to cellular stress or  oncogenic  signals. [ 1 ]


miR-675 has been found to be upregulated in  osteoarthritic  cartilage, alongside H19. [ 2 ]  Indeed, there is co-regulation of these two RNAs. The  COL2A1  gene associated with osteoarthritis through altered expression levels compared with in normal tissue is upregulated by miR-675 overexpression. It has been proposed that miR-675 may modulate  collagen type II  levels via an unknown target molecule, and there is potential for a diagnostic metabolic balance indicator in osteoarthritis through this microRNA.


In  molecular biology   mir-711 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-711 is able to distinguish between malignant  cutaneous T-cell lymphomas  and benign skin disorders with high accuracy. [ 1 ]


miR-711 has been found to target and suppress  Heat Shock Protein  70.3  in vitro  at a post-transcriptional level via its  3' untranslated region . [ 2 ]   Ischaemic preconditioning  brings about reduced miR-711 levels, with downregulated cardiac myocyte levels further dependent upon  NF-kappa B .


In molecular biology,  mir-720 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-720 expression has been found to vary in the serum levels of women carrying fetuses with and without  neural tube defects . [ 1 ]  miR-720 is significantly downregulated following child delivery, thus suggesting a role in pregnancy as well as a possible placental derivation.


miR-720 is upregulated in  myelodysplastic syndromes , [ 2 ]  in molar tooth germ in newborn mice following anti-miR-214 injection [ 3 ]  and in  mesangial cells  (specialised smooth muscle cells in the kidneys) treated with microRNA inhibitor. [ 4 ]


miR-720 was shown to target the pluripotency factor Nanog and to upregulate DNMTs. [ 5 ]  miR-720 controlled stem cell phenotype, proliferation, and differentiation of human dental pulp cells. Dental pulp includes mesenchymal (stem) cells, blood vessels, blood and peripheral nerves. Repression of the pluripotency factor Nanog and upregulation of DNMTs in dental pulp cells by miR-720 initiated odontoblastic differentiation. Therefore, it was suggested that odontoblastic differentiation of dental pulp stem cells required miR-720 that repressed Nanog and induced Dnmt3a and Dnmt3b.


In molecular biology  mir-744 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-744 plays a role in tumour development and growth in mouse cell lines. Its expression induces  cyclin B1  expression, whilst knockdown sees a resultant decreased level of mouse cyclin B through the  Ccnb1  gene. [ 1 ]  Short-term overexpression of miR-744 in mouse cell lines has been seen to enhance cell proliferation, whilst chromosomal instability and  in vivo  suppression are concurrent with a prolonged expression.


Multiple miR-744 binding sites have been identified in the proximal  3' untranslated region  of  transforming growth factor beta 1 (TGF-β1) . Direct targeting of TGF-β1 by miR-744 has been identified, and transfection is seen to inhibit  endogenous  TGF-β1 synthesis by directing post-transcriptional regulation. [ 2 ]


miR-744 directly targets translation elongation factor and known protooncogene  EEF1A2 . [ 3 ]  mIR-744 also upregulates during  resveratrol  treatment of MCF7 breast cancer cells. [ 4 ]


In molecular biology  mir-764 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


Expression of the mature miR-764-5p sequence is upregulated during  osteoblast  differentiation in both skull-specific  calvarial  and osteoblast  progenitor cells . The channel-forming integral protein, CHIP, is regulated by miR-764-5p at its  3'UTR , and there is negative correlation between expression of the two. Increased CHIP levels are observed with inhibition of miR-764-5p, whilst enhanced miR-764-3p expression sees decreased CHIP levels. [ 1 ]  The differentiation fate of osteoblast progenitor cells is altered by impaired miR-764-3p levels due to CHIP. Osteoblast differentiation from progenitor cells has been shown to be positively regulated by repressed CHIP translation.


In molecular biology  mir-765 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-765 has been identified as a diagnostic marker for  traumatic brain injury  (TBI), due to significantly elevated levels in the plasma of TBI patients. Furthermore, combination with either miR-16 or miR-92a allows extremely accurate distinction between TBI patients and healthy controls. [ 1 ]


Increased miR-765 expression is observed in  Von Hippel-Lindau disease  compared with the sporadic benign forms of  pheochromocytomas . [ 2 ]  It has been linked to neuronal plasticity through the  neurotrophic tyrosine kinase receptor type 3  (NTRK3) gene. A NTRK3  3'UTR  variant, ss102661458, is located in a functional target site of miR-765 and is able to significantly affect miRNA-mediated NTRK3 regulation. Through this there is restoration of the altered gene expression by miR-765. NTRK3 is underexpressed with high or overexpressed levels of miR-765, thus pointing towards a possible involvement of this relationship in pheochromocytoma pathogenesis. [ 3 ]


In molecular biology  mir-767 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In  molecular biology ,  mir-786 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-786 is involved in control of the defecation motor programme, together with miR-240. [ 1 ]  These two miRNAs are necessary for normal defecation programme rhythmicity, and average cycle time has been found to be increased in miR-24/786  C. elegans . [ 2 ]  Decreased cycle times have conversely been observed with miR-52 knockout in  C. elegans .


In molecular biology  mir-802 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-802 expression in the kidney is stimulated by a high potassium intake, along with  caveolin-1  expression, one of the many miR-802 protein targets. Surface expression of  Renal Outer Medullary Potassium  (ROMK) channels has been found to be enhanced in the plasma membrane of the distal  nephron  of the kidney by miR-802 expression. Caveolin-1 conversely inhibits ROMK channel activity, and expression of the two shows a clear inverse relationship. Co-expression of miR-802 with caveolin-1 blocks miR-802's upregulatory effects on ROMK channels. [ 1 ]  miR-802 thus functions to mediate the stimulatory effect of a high potassium diet on ROMK activity through suppression of caveolin-1 expression, this leading to an increased surface expression of ROMK channels.


Human chromosome 21  (Hsa21) has been found to harbour over 400 different genes, with miR-802 among these. Along with miRNAs-99a, -125b-2, -155 and let-7c, miR-802 is overexpressed in brain and heart specimens of  Down syndrome  individuals, resulting in suppression of specific target proteins. This suppression in turn contributes towards the common phenotypic alterations observed in Down syndrome patients. [ 2 ]


In molecular biology  mir-824 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-828 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-854 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-872 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-872 has been found to be expressed in  sertoli cells  and to post-transcriptionally target the  Sod-1  gene, which encodes the copper/zinc-binding  superoxide dismutase 1 (SOD-1)  enzyme. [ 1 ]  Overproduction of SOD-1 increases oxidative damage and through this results in enhanced  apoptosis  and cell death.


Insulin infusion in rats has seen increased levels of  heme-oxygenase 1  expression, blocked by inhibited activation of  PI3K  or  protein kinase C . miR-872 levels are reduced with inhibition of adipocytes of the  3T3-L1  cell line, along with those of miRNAs-155 and -183. Insulin is therefore able to increase expression of HO-1 through miR-872 downregulation, as well as via pathways dependent upon PI3K and protein kinase C. [ 2 ]


In molecular biology  mir-873 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


Significant miR-873 reductions have been observed in the brains of dysmasculinised second generation males following the introduction of prenatal stress factors.  Sexual dimorphisms  in the brain are altered and there is female-like expression of key  neurodevelopment  genes. The common target gene for miR-873, β-glycan, has increased expression. [ 1 ]  It is thought that miR-873, along with other miRNAs, may play a role in organisation of the sexually dimorphic brain due to a marked response to organisational testosterone.


miR-873 is associated with  translational  regulation of factors involved in  chromatin  remodelling, and is downregulated by the  human T-cell leukaemia virus type 1  (HTLV-1) transactivating protein, Tax. [ 2 ]  Specifically, it has been found to directly target the chromatin remodelling factors  p300  and p/CAF.


In molecular biology  mir-874 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-885 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


The miR-885-5p form of this microRNA acts as a tumour suppressor in  neuroblastoma , through interference with cell cycle progression and cell survival. It is found at 3p25.3, a chromosome region frequently deleted in primary neuroblastoma, [ 1 ]  and expression results in  p53 protein  accumulation and pathway activation. Altered expression of multiple genes is observed with miR-885-5p, including the  CDK2  and  MCM5  genes encoding  cyclin-dependent kinase 2  and mini-chromosome maintenance protein  MCM5 , and also with several p53 target genes. [ 1 ]


Circulating miRNAs (microRNAs) are emerging as promising  biomarkers  for several pathological conditions. similarly, miR-885-5p found as a potential marker for  liver  disease condition. It is significantly elevated in the patients sera with liver pathologies, and researcher suggested that serum miRNAs could serve as novel complementary biomarkers for the detection and assessment of liver pathologies. [ 2 ]  These unique miRNAs may be clinically applicable to predict prognosis and distant metastasis in colorectal cancer (CRC). The direct comparison of expression patterns of metastasis-specific microRNAs (miRNAs) in primary CRCs (pCRCs) and matched liver metastases (LMs) provides a feasibility of their clinical application as metastasis-specific biomarkers. [ 3 ]  In a clinical study it has been found that miR-885-5p is increased in plasma from pre-eclampsia compared with healthy pregnant women, and it is released into circulation mainly inside exosomes. [ 4 ]


In search of an effective therapeutic strategy for improving colon cancer treatment, a novel role of miR-885-3p  has been observed in tumor  angiogenesis   by targeting BMPR1A, which regulates a proangiogenic factor, and provide new evidence that targeting miRNAs might be an effective therapeutic strategy. [ 5 ]


In molecular biology  mir-938 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-938 has been found to directly target the  SMAD3  gene, which encodes the main downstream  TGF-β  polypeptide  SMAD3 . This microRNA is overexpressed in non-functioning pituitary adenomas (NFPAs) compared with normal pituitary tissue. [ 1 ]  Downregulation of TGF-β signalling is likely to play a role in the regulation of signalling pathways in NFPA tumorigenesis, thus also implicating SMAD3 and miR-938.


In molecular biology  mir-939 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


miR-939 directly regulates and  translationally  blocks the gene expression of human inducible  nitric oxide synthase  (hiNOS) by binding to its  3'UTR . There is dual regulation of hiNOS gene expression, with  cytokines  inducing hiNOS  transcription  whilst also increasing miR-939 levels. [ 1 ]  Two functional binding sites within the hiNOS 3'UTR are essential for miR-939-mediated translational blockade and miR-939 has been shown to decrease cytokine-induced hiNOS expression, despite hiNOS mRNA levels and stability remaining unaffected. It has further been found that endogenous miR-939 expression in the liver may be induced by cytokines.


In  molecular biology   mir-3180 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms. [ 1 ]  The  mir-10 microRNA precursor  is a short  non-coding RNA  gene that is part of an RNA gene family which contains mir-3180-1, mir-3180-2, mir-3180-3, mir-3180-4 and mir-3180-5.  They have now been predicted or experimentally confirmed in a wide range of cancers in humans. [ 2 ] [ 3 ]  ( MIPF0000894 ,  mir-3180 ) mir-3180 has currently only been identified in human  Homo sapiens .


The presence of mir-3180 has been detected in a range of  catarrhine  monkeys. It has been identified in primates including  human  ( Homo sapiens ),  Sumatran orangutan  ( Pongo abelii ),  western lowland gorilla  ( Gorilla gorilla gorilla ),  Northern white-cheeked gibbon  ( Nomascus leucogenys ),  Chlorocebus sabaeus  ( Chlorocebus sabaeus ),  Olive baboon  ( Papio anubis ) and  Rhesus monkey  ( Macaca mulatta ). [ 4 ] [ 5 ]  In some of these species the presence of mir-3180 has been shown experimentally, in others the genes encoding mir-3180 might have been predicted computationally.


The  mir-3180   genes  are found within the  Chromosome 16 . In  humans  there are five mir-3180 clusters, these contain five genes encoding miRNAs ( mir-3180-1 ,  mir-3180-2 ,  mir-3180-3 ,  mir-3180-4  and  mir-3180-5 ). The  mir-3180  genes have the following locations:


hsa-mir-3180-1	chr16
Start: 14911220
End: 14911313
Strand: +


hsa-mir-3180-2	chr16
Start: 16309879
End: 16309966
Strand: +


hsa-mir-3180-3	chr16
Start: 18402178
End: 18402271
Strand: -


hsa-mir-3180-4	chr16
Start: 15154850
End: 15155002
Strand: -


hsa-mir-3180-5	chr16
Start: 2135977
End: 2136129
Strand: -


Recently there has been much interest in abnormal levels of expression of microRNAs in  cancers . Upregulation of mir-3180 has been found in cancers. Increased levels of mir-3180 have been found in  colon cancer . [ 6 ]


In  molecular biology   mir-iab-4 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In molecular biology  mir-M7 microRNA  is a short  RNA  molecule.  MicroRNAs  function to regulate the expression levels of other genes by several mechanisms.


In  genealogy , a  mirror tree  is a  family tree  reconstructed through estimates of  consanguinity . [ 1 ] [ 2 ]


5CUZ ,  5CV0


NM_133839 NM_001348198 NM_001348199 NM_001348200


NP_598600 NP_001335127 NP_001335128 NP_001335129


Methylmalonic aciduria and homocystinuria type D protein, mitochondrial  also known as  MMADHC  is a  protein  that in humans is encoded by the  MMADHC   gene . [ 5 ]


This gene encodes a  protein localized in cytosol and mitochondria that is involved in an early step of  vitamin B 12  metabolism. Vitamin B 12  (cobalamin) is essential for normal development and survival in humans. [ 6 ]


Mutations in this gene cause  methylmalonic aciduria  and homocystinuria type cblD (MMADHC), a disorder of cobalamin metabolism that is characterized by decreased levels of the coenzymes  adenosylcobalamin  and  methylcobalamin . [ 5 ]


Matrix metalloproteinase 15  also known as  MMP15  is an  enzyme  that in humans is encoded by the  MMP15   gene . [ 5 ] [ 6 ]


Proteins of the  matrix metalloproteinase  (MMP) family are involved in the breakdown of  extracellular matrix  in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proenzymes which are activated when cleaved by extracellular  proteinases . However, the protein encoded by this gene is a member of the membrane-type MMP (MT-MMP) subfamily; members of this subfamily can be anchored to the extracellular membrane by either a transmembrane domain or  glycophosphatidylinositol  linkage, suggesting that these proteins are expressed at the cell surface rather than secreted in a soluble form. [ 7 ]


In  genetics , a  morbid map  is a chart or diagram of  diseases  and the  chromosomal  location of  genes  the diseases are associated with. A morbid map exists as an appendix of the  Online Mendelian Inheritance in Man  (OMIM) knowledgebase, listing chromosomes and the genes mapped to specific sites on those chromosomes, and this format most clearly reveals the relationship between gene and phenotype. [ 1 ]


An  organism  which has been treated with a  morpholino  antisense  oligo  to temporarily knock down expression of a targeted  gene  is called a  morphant .


This term was coined by Prof. Steve Ekker [ 1 ]  to describe the  zebrafish  with which he was experimenting; by knocking down  embryonic  gene expression using Morpholinos, Prof. Ekker "phenocopied" known zebrafish mutations, that is, he raised embryos that had the same  morphological   phenotype  as embryonic zebrafish with specific gene  mutations .  Prof. Ekker's papers [ 2 ]  and presentations describing morphant phenocopies of mutant phenotypes, in combination with Prof. Janet Heasman's earlier work [ 3 ]  with Morpholinos in  Xenopus  embryos, led to rapid adoption of Morpholino technology by the  developmental biology  community.


The  mSin3 interaction domain  (SID) is an interaction domain which is present on several transcriptional repressor proteins including TGFβ ( transforming growth factor  β) and Mad. It interacts with the paired  amphipathic   alpha-helix  2 (PAH2) domain of  mSin3 , a  transcriptional  repressor domain that is attached to transcription repressor proteins such as the  mSin3A  corepressor.


Action of  histone deacetylase  1 and 2 (HDAC1/2) is induced by the interaction of mSin3A with a multi-protein complex containing HDAC1/2. Transcription is also repressed by histone deacetylase-independent means.


Mitochondrially encoded 16S RNA  (often abbreviated as  16S ) is the  mitochondrial   large subunit ribosomal RNA [ 1 ] [ 2 ]  that in humans is encoded by the  MT-RNR2   gene . The MT-RNR2 gene also encodes the  Humanin  polypeptide that has been the target of  Alzheimer's disease  research. [ 3 ]


The 16S rRNA is the mitochondrial homologue of the  prokaryotic 23S  and  eukaryotic nuclear 28S  ribosomal RNAs. [ 4 ]


Mitochondrially encoded tRNA alanine  also known as  MT-TA  is a  transfer RNA , which in humans is encoded by the  mitochondrial   MT-TA   gene . [ 3 ]


MT-TA is a small 69 nucleotide  RNA  (human mitochondrial map position 5587-5655) that transfers the amino acid  alanine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


It has been reported that the 5650G-A mutation on  MT-TA  may cause muscular dystrophy. [ 4 ]


Mitochondrially encoded tRNA cysteine  also known as  MT-TC  is a  transfer RNA  which in humans is encoded by the  mitochondrial   MT-TC   gene . [ 3 ]


MT-TC is a small 82 nucleotide  RNA  (human mitochondrial map position 5761–5826) that transfers the amino acid  cysteine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


Mitochondrially encoded tRNA methionine  also known as  MT-TM  is a  transfer RNA  which in humans is encoded by the  mitochondrial   MT-TM   gene . [ 1 ]


MT-TM is a small 68 nucleotide  RNA  (human mitochondrial map position 4402-4469) that transfers the amino acid  methionine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


Mitochondrially encoded tRNA glutamine  also known as  MT-TQ  is a  transfer RNA  which in humans is encoded by the  mitochondrial   MT-TQ   gene . [ 1 ]


MT-TQ is a small 72 nucleotide  RNA  (human mitochondrial map position 4329-4400) that transfers the amino acid  glutamine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


Mitochondrially encoded tRNA serine 1 (UCN)  also known as  MT-TS1  is a  transfer RNA  which in humans is encoded by the  mitochondrial   MT-TS1   gene . [ 1 ]


MT-TS1 is a small 69 nucleotide  RNA  (human mitochondrial map position 7446-7514) that transfers the amino acid  serine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


Mitochondrially encoded tRNA serine 2 (AGU/C)  also known as  MT-TS2  is a  transfer RNA  which in humans is encoded by the  mitochondrial   MT-TS2   gene . [ 1 ]


MT-TS2 is a small 59 nucleotide  RNA  (human mitochondrial map position 12207-12265) that transfers the amino acid  serine  to a growing  polypeptide  chain at the  ribosome  site of  protein  synthesis during  translation .


Mu hemoglobin  is a  predicted  protein encoded in the  HBM   gene . The mRNA is expressed at moderate levels, but the protein has not been detected by mass spectrometry. [ 1 ] [ 2 ] [ 3 ]  The order of genes is: 5' -  zeta  - pseudozeta -  mu  - pseudoalpha-1 -  alpha-2  -  alpha-1  -  theta1  - 3'.


Multicistronic message  is an archaic term for  Polycistronic .  Monocistronic, bicistronic and tricistronic are also used to describe mRNA with single, double and triple coding areas (exons).


Note that the base word  cistron  is no longer used in genetics, and has been replaced by  intron  and  exon  in eukaryotic mRNA.  However, the mRNA found in bacteria is mainly polycistronic.  This means that a single bacterial mRNA strand can be translated into several different proteins.  This will occur if spacers separate the different proteins, and each spacer has to have a  Shine-Dalgarno  sequence located upstream of the start  codon .


Multiple abstract variance analysis (MAVA) , is a statistical technique used to estimate the proportion of variance in a  phenotypic trait  due to  genetic  and  environmental  factors. It was developed by psychologist  Raymond B. Cattell  in order to enable the analysis of data from multiple independent sources to estimate the causes of trait variation. Cattell originally described the technique in a 1960 paper. [ 1 ] [ 2 ]  MAVA aims to estimate the relative genetic and environmental contributions to trait variation by comparing variances between families to those within families on the trait under study. As such, it is considered a "more systematic and comprehensive approach" than the classical  correlation  method of  heritability  estimation. [ 3 ]  MAVA later formed the basis of Cattell's  16PF Questionnaire . [ 4 ]


MAVA has been criticized for inconsistencies between some of the mathematical  equations  used in the method, [ 5 ]  and for introducing "...numerous new theoretical constructs
without any clear empirical basis". [ 6 ]  Critics of the method have also noted that it requires the introduction of additional parameters whenever a new type of genetic relationship is considered, which precludes a complete analysis of the causes of trait variation. [ 7 ]


In  natural selection ,  negative selection [ 1 ]   or  purifying selection  is the selective removal of  alleles  that are  deleterious . This can result in  stabilising selection  through the purging of deleterious  genetic polymorphisms  that arise through random mutations. [ 2 ] [ 3 ]


Purging of deleterious alleles can be achieved on the  population genetics  level, with as little as a single  point mutation  being the unit of selection. In such a case, carriers of the harmful point mutation have fewer offspring each generation, reducing the frequency of the mutation in the gene pool.


In the case of strong negative selection on a locus, the purging of deleterious variants will result in the occasional removal of  linked  variation, producing a decrease in the level of variation surrounding the locus under selection. The incidental purging of non-deleterious alleles due to such spatial proximity to deleterious alleles is called  background selection . [ 4 ]  This effect increases with  lower mutation rate but decreases with higher recombination rate. [ 5 ]


Purifying selection can be split into purging by non-random mating ( assortative mating ) and purging by  genetic drift . Purging by genetic drift can remove primarily deeply recessive alleles, whereas natural selection can remove any type of deleterious alleles. [ 6 ]


The idea that those  genes  of an organism that are expressed in the  haploid  stage are under more efficient  natural selection  than those genes expressed exclusively in the diploid stage is referred to as the “masking theory”. [ 7 ]   This theory implies that purifying selection is more efficient in the haploid stage of the life cycle where fitness effects are more fully expressed than in the diploid stage of the life cycle.  Evidence supporting the masking theory has been reported in the single-celled yeast  Saccharomyces cerevisiae . [ 8 ]  Further evidence of strong purifying selection in haploid tissue-specific genes, in support of the masking theory, has been reported for the plant,  Scots Pine . [ 7 ]


NmsR A  and  NmsR B  (Neisseria metabolic switch regulator), RcoF1  and  RcoF2  ( RNA regulating colonization factor ) as well as  NgncR_162  and  NgncR_163   ( Neisseria gonorrhoeae non-coding RNA ) are all names of neisserial sibling  small regulatory RNAs  described and independently named in three publications. [ 1 ] [ 2 ] [ 3 ]  NmsR B /RcoF1/NgncR_163 was shown to be the predominant sibling.  The sRNAs are tandemly arranged, structurally nearly identical and share 70% sequence identity. They translationally down-regulate genes involved in basic metabolic processes including tricarboxylic acid cycle enzymes and amino acid uptake and degradation. The target genes include:  fumC ,  sdhC ,  gltA ,  sucC ,  prpB  and  prpC . [ 2 ] [ 3 ]  The expression of the sRNAs is presumably under the control of RelA, as shown for  N. meningitidis . [ 1 ]  Furthermore, the sRNAs interact with Hfq protein and target repression of putative colonization factor of the human nasopharynx PrpB mRNA, hence one of the proposed names is  RNA regulating colonization factor. [ 2 ]


A  neochromosome  is a  chromosome  that is not normally found in nature.   Cancer -associated neochromosomes are found in some cancer cells. [ 1 ] [ 2 ]


Neochromosomes have also been created using  genetic engineering  techniques. [ 3 ] [ 4 ]


Cancer-associated neochromosomes are giant supernumerary chromosomes. They harbor the mutations that drive certain cancers (highly amplified copies of key  oncogenes , such as  MDM2 ,  CDK4 ,  HMGA2 ). They may be circular or linear chromosomes. They have functional  centromeres , and  telomeres  when linear. They are rare overall, being found in about 3% of cancers, but are common in certain rare cancers. For example, they are found in 90% of parosteal  osteosarcomas . [ 2 ]


Neochromosomes from well- and de-differentiated  liposarcoma  have been studied at high resolution by isolation (using flow sorting) and sequencing, as well as microscopy. They consist of hundreds of fragments of DNA, often derived from multiple normal chromosomes, stitched together randomly, and contain high levels of DNA amplification (~30-60 copies of some genes). [ 2 ]


Using  statistical inference  and  mathematical modelling , the process of how neochromosomes initially form and evolve has been made clearer. Fragments of DNA produced following  chromothriptic  shattering of  chromosome 12  undergo  DNA repair  to form of a circular or  ring chromosome . This undergoes hundreds of circular  breakage-fusion-bridge cycles , causing random amplification and deletion of DNA with selection for the amplification of key oncogenes. DNA from additional chromosomes is somehow added during this process. Erosion of  centromeres  can lead to the formation of  neocentromeres  or the capture of new native centromeres from other chromosomes. The process ends when the neochromosome forms a linear chromosome following the capture of telomeric caps, which can be chromothriptically derived.


NgAgo  is a  single-stranded DNA  (ssDNA)-guided  Argonaute   endonuclease , an acronym for  N atronobacterium   g regoryi   A r go naute. NgAgo binds 5′  phosphorylated  ssDNA of ~24  nucleotides  (gDNA) to guide it to its target site and will make DNA  double-strand breaks  at the gDNA site. Like the  CRISPR/Cas  system, NgAgo was reported by Chunyu Han et al. to be suitable for  genome editing , [ 1 ]  but this has not been replicated. In contrast to  Cas9 , the NgAgo–gDNA system does not require a  protospacer adjacent motif  (PAM).


NgAgo was proposed to be useful for genome editing in May 2016 because of the system’s high accuracy and efficiency, which was said to minimize off-target effects. The specificity of the gDNA is essential, as cleavage efficiency is impaired by a single nucleotide mismatch between the guide and target molecules. Using 5’ phosphorylated ssDNAs as guide molecules reduces the possibility of cellular oligonucleotides misleading NgAgo. A guide molecule can only be attached to NgAgo during the expression of the protein. Once the guide is loaded, NgAgo cannot swap free floating ssDNA for its gDNA. Designing, synthesizing, and adjusting the concentration of ssDNAs is easier compared to systems using sgRNA. The required dosage of ssDNA is less than that of a sgRNA expression plasmid. [ 1 ]


Doubts about the technique were raised on gene editing forums as early as June and have persisted. [ 2 ]  There have been several allegations that this procedure is impossible to  reproduce .  Nature Biotechnology , which originally published the research, is investigating. [ 3 ] [ 4 ]  In November 2016, a letter was published in  Protein & Cell  questioning the research and the lead author's claim that replication requires "superb experimental skill". [ 5 ]  The same month,  Nature Biotechnology  published a critical correspondence article by three groups [ 6 ]  and an accompanying expression of concern by the editors on the original article. [ 7 ]  The authors retracted the study in a statement published in Nature Biotechnology on 3 August 2017, citing the continued inability of the research community to replicate their results. [ 8 ]  In 2018, an investigation led by Han's university concluded that while Han's findings were flawed, he and his team did not intend to deceive the scientific community. [ 9 ]  In April 2019, a  preprint  article found that NgAgo does have the ability to edit genes and implied that previous results might have been difficult to reproduce due to difficulties related to purification of the active protein. [ 10 ] [ 11 ]


Nla III  is a type II  restriction enzyme  isolated from  Neisseria lactamica . [ 1 ]  As part of the  restriction modification system ,  Nla III is able to prevent foreign DNA from integrating into the host genome by cutting double stranded DNA into fragments at specific sequences. [ 2 ]  This results in further degradation of the fragmented foreign DNA and prevents it from infecting the host genome. [ 3 ]


Nla III recognizes the  palindromic  and complementary DNA sequence of CATG/GTAC and cuts outside of the G-C base pairs. This cutting pattern results in  sticky ends  with GTAC overhangs at the  3' end . [ 4 ]


Nla III from N. lactamica contains two key components: a methylase and an endonuclease. [ 5 ]  The methylase is critical to recognition, while the endonuclease is used for cutting. [ 5 ]  The gene ( Nla IIIR) is 693 bp long and creates the specific 5’-CATG-3’ endonuclease. [ 6 ]  A homolog of  Nla IIIR is  iceA1  from  Helicobacter pylori . [ 6 ]  In  H. pylori , there exists a similar methylase gene called  hpyIM  which is downstream of  iceA1 . [ 7 ]   ICEA1  is an endonuclease that also recognizes the 5’-CATG-3’ sequence. [ 6 ]   IceA1  in  H. pylori  is similar to that of  NlaIII  in  N. lactamica .


Nla III contains an  ICEA  protein that encompasses the 4 to 225 amino acid region. [ 6 ] [ 8 ]   H. pylori  also contains the same protein. [ 9 ]   H. pylori  infection often leads to gastrointestinal issues such as peptic ulcers, gastric adenocarcinoma and lymphoma. [ 10 ]  Researchers speculate that  ICEA  proteins serve as potential markers for gastric cancer  [ 7 ]


Nla III  isoschizomers  recognize and cut the same recognition sequence 5’-CATG-3’. [ 11 ]  Endonucleases that cut at this sequence include:


NlaIII  can be used in many different experimental procedures [ 12 ]  such as:


Non-allelic homologous recombination  ( NAHR ) is a form of  homologous recombination  that occurs between two lengths of  DNA  that have high sequence similarity, but are not  alleles . [ 1 ] [ 2 ] [ 3 ]


It usually occurs between sequences of DNA that have been previously  duplicated  through evolution, and therefore have  low copy repeats  (LCRs). These repeat elements typically range from 10–300 kb in length and share 95-97% sequence identity. [ 4 ]  During  meiosis , LCRs can misalign and subsequent  crossing-over  can result in genetic rearrangement. [ 4 ]  When non-allelic homologous recombination occurs between different LCRs,  deletions  or further  duplications  of the DNA can occur. This can give rise to rare  genetic disorders ,  caused by the loss or increased copy number of genes within the deleted or duplicated region. It can also contribute to the  copy number variation  seen in some gene clusters. [ 5 ]


As LCRs are often found in "hotspots" in the human genome, some  chromosomal  regions are particularly prone to NAHR. [ 1 ]  Recurrent rearrangements are nucleotide sequence variations found in multiple individuals, sharing a common size and location of break points. [ 4 ]  Therefore, multiple patients may manifest with similar deletions or duplications, resulting in the description of genetic  syndromes . Examples of these include  NF1 microdeletion syndrome ,  17q21.3 recurrent microdeletion syndrome  or  3q29 microdeletion syndrome . [ 6 ] [ 7 ] [ 8 ]


A  nonsense suppressor  is a factor which can inhibit the effect of the  nonsense mutation . Nonsense suppressors can be generally divided into two classes: a) a mutated  tRNA  which can bind with a termination codon on  mRNA ; b) a mutation on  ribosomes  decreasing the effect of a termination codon. It is believed that nonsense suppressors keep a low concentration in the cell and do not disrupt normal  translation  most of the time. In addition, many genes do not have only one termination codon, and cells commonly use  ochre codons  as the termination signal, whose nonsense suppressors are usually inefficient. [ 1 ] [ 2 ] [ 3 ]


Nonsense suppressors are a useful genetic tool, but can also result in problematic side effects, since all identical stop codons in the genome will also be suppressed to the same degree. Genes with different or multiple stop codons will be unaffected.


SUP35 , a nonsense suppressor identified by  Wickner  in 1994, is a  prion protein .


In synthetic biology, artificial suppressor elongator tRNAs are used to incorporate  unnatural amino acids  at nonsense codons placed in the coding sequence of a gene. [ 4 ]  Start codons can also be suppressed with suppressor initiator tRNAs, such as the amber stop codon suppressor tRNA fMet2 (CUA). [ 5 ]  The amber initiator tRNA is charged with methionine [ 6 ]  and glutamine. [ 7 ]


In recent research, a novel gene therapy approach is provided by Jiaming Wang and Yue Zhang. [ 8 ]  They use an adeno-associated virus (AAV) vector to deliver a new suppressor tRNA (sup-tRNA tyr ) into a mouse model carrying a nonsense mutation( Idua-W401X ,TCG→TAG). This model recapitulates a human LSD, mucopolysaccharidosis disease type I (or Hurler Syndrome), caused by absence of the enzyme α-l-iduronidase (IDUA) leading to accumulation of  glycosaminoglycans  (GAG) and resulting pathogenesis. [ 9 ]  This method rescues the pathogenic defects and is essentially stable for 6 months.


Escherichia coli  strains carrying nonsense suppressor genes had a central role in the early work on  bacteriophage  genetics. [ 10 ]  In particular,  E. coli  strains carrying amber suppressors (suppressors of the UAG  nonsense codon ) enabled the isolation and propagation of  bacteriophage T4  mutants defective in phage assembly,  morphogenesis ,  DNA replication ,  DNA repair  and  genetic recombination  and thus facilitated the early study of these processes at a fundamental level. [ 11 ] [ 12 ]


Nonsense suppression by altered tRNA was demonstrated in the archaeon  Haloferax  volcana  for the chain terminating stop codons UAG (amber), UAA (ochre) and UGA (opal). [ 13 ]


Normalized chromosome value  (NCV) is a mathematical calculation for comparing each  chromosome  under tested in  cell free DNA  (cfDNA) for detecting genetic disorder of the fetus. NCV calculation removes variation within and between  sequencing  runs to optimize test precision. [ 1 ] [ 2 ]


NrrF  is a  non-coding RNA  which is regulated by the  Ferric uptake regulator  (Fur) protein in bacteria. This non-coding RNA was identified in  Neisseria meningitidis  and is involved in iron regulation of the  succinate dehydrogenase  genes sdhA and sdhC. [ 1 ] [ 2 ]  NrrF acts as an  antisense RNA  and is complementary to the junction between the second and third genes of the sdh operon (sdhD and sdhA).  Secondary structure  predictions have indicated that this interaction occurs in a single stranded loop region of the NrrF RNA. Under low iron concentration NrrF is present at a high concentration and forms a duplex with the transcript in  Hfq  dependent manner. The RNA  chaperone  Hfq acts to enhance binding of NrrF or stabilizes the NrrF/sdh transcript duplex. Binding of NrrF results in down regulation of the sdhCDAB mRNA transcript results in a Fur-dependent positive regulation of succinate dehydrogenase.  Another NrrF RNA target is mRNA  petABC , coding for  cytochrome  bc1  ( an essential components of the  N. meningitidis  respiratory chain). Interaction between NrrF and the 5′ untranslated region of the  petABC  mRNA results in its repression. [ 3 ]


NrrF appears to be restricted to the Neisseria species and no homologues have yet been identified in other species.


Nuclear sexing  is a technique for genetic  sex determination  in those species where XX chromosome pair is present. Nuclear sexing can be done by identifying  Barr body , a drumstick like appendage located in the rim of the nucleus in somatic cells. Barr body is the inactive  X chromosome  which lies condensed in the nucleus of somatic cells. A typical human (or other XY-based organism) female has only one Barr body per somatic cell, while a typical human male has none. Though a Barr body can be sought in any human nucleated cell, circulating  mononuclear cells  are commonly used for this purpose. These cells are cultured, and treated with chemicals such as  colcemid  to arrest  mitosis  in  metaphase . [ 1 ]
A minimum of 30 percent of sex chromatin indicates genetic female sex.


Nucleotide diversity  is a concept in  molecular genetics  which is used to measure the degree of  polymorphism  within a population.
 [ 1 ]


One commonly used measure of nucleotide diversity was first introduced by  Nei  and  Li  in 1979. This measure is defined as the average number of  nucleotide  differences per site between two  DNA  sequences in all possible pairs in the sample population, and is denoted by

 π

 {\displaystyle \pi }

 .


An estimator for

 π

 {\displaystyle \pi }

  is given by:


where

 x

 i

 {\displaystyle x_{i}}

  and

 x

 j

 {\displaystyle x_{j}}

  are the respective frequencies of the

 i

 {\displaystyle i}

  th and

 j

 {\displaystyle j}

  th sequences,

 π

 i
 j

 {\displaystyle \pi _{ij}}

  is the number of nucleotide differences per nucleotide site between the

 i

 {\displaystyle i}

  th and

 j

 {\displaystyle j}

  th sequences,  and

 n

 {\displaystyle n}

  is the number of sequences in the sample. The term in front of the sums guarantees an unbiased estimator, which does not depend on how many sequences you sample. [ 2 ]


Nucleotide diversity is a measure of  genetic variation .  It is usually associated with other statistical measures of population diversity, and is similar to  expected heterozygosity .  This statistic may be used to monitor diversity within or between ecological populations, to examine the genetic variation in crops and related species, [ 3 ]  or to determine evolutionary relationships. [ 4 ]


Nucleotide diversity can be calculated by examining the DNA sequences directly, or may be estimated from molecular marker data, such as Random Amplified Polymorphic DNA ( RAPD ) data  [ 5 ]  and Amplified Fragment Length Polymorphism ( AFLP ) data. [ 6 ]


Oligotyping  is a  diagnostic  or  molecular biological  method for classification of  organisms  by short intervals of primary  DNA sequence .


Oligotyping 'systems' are sets of recognized target sequences which identify the members of the categories within the classification.  The classification may be for the purpose of primary biological  taxonomy , or for a functional classification.


Oligotyping has been used for classifying  bacteria , [ 1 ]  identifying bacterial antibiotic resistance genes, [ 2 ]  identifying genetic factors in human infectious disease, [ 3 ]  and performing histocompatibility tests for human blood or bone marrow donors/recipients .


Organellar DNA (oDNA)  is  DNA  contained in  organelles  (such as mitochondria and chloroplasts), outside the  nucleus  of  eukaryotic cells . [ 1 ]


The traits encoded by this type of DNA, in animals, generally pass from mother to offspring rather than from the father in a process called  cytoplasmic inheritance . This is due to the  ovum  provided from the mother being larger than the male  sperm cell , and therefore has more organelles, where the organellar DNA is found. [ 2 ]


Although  maternal inheritance  is most common, there are also paternal and biparental patterns of inheritance that take place. [ 3 ]  The latter two patterns of inheritance are found most often in plants. [ 1 ]


Recombination of organelle DNA is very limited, meaning that any traits that are encoded by the oDNA are likely to remain the same as they are passed from generation to generation. [ 4 ]


Unlike  nuclear DNA , which is present as linear  molecules  inside the  chromosomes , the entire  genomes  of chloroplasts and mitochondria are present on a single molecule of double-stranded circular DNA molecule; this is very similar structure to a bacterial chromosome. [ 1 ]


Although the functionality and genetic structure vary significantly between different organelles and their host species, genetic characteristic patterns allow the differentiation between nucleolar and organellar DNA. A recently published machine-learning approach using only the genome sequences and multiple genome annotation tools can classify them. [ 5 ]


A  parahaplogroup  is a term used in  genetics  to identify a  paraphyletic   haplogroup .


They are normally described with the name of their parent haplogroup plus an  asterisk  (for instance: F*, U2*), meaning that it includes all derivates from the parent haplogroup (F or U2 in the examples) except those mentioned elsewhere. [ 1 ]


Sometimes it is specified which other  subclades  are excluded and then the parent name is followed by the sign "x" and the list of those excluded haplogroups, separated by commas. This is often stated between brackets. For example: NxR means all derivates from  haplogroup N  except  haplogroup R , or K(xP,NO) means all derivates from  haplogroup K  except those belonging to  P  and  NO .


Parasitic chromosomes  are "selfish"  chromosomes  that propagate throughout cell divisions, even if they confer no benefit to the overall organism's survival. Parasitic chromosomes can persist even if slightly detrimental to survival, as is characteristic of some selfish genetic elements. Parasitic chromosomes are often  B chromosomes , such that they are not necessarily present in the majority of the species population and are not needed for basic life functions, in contrast to  A chromosomes . Parasitic chromosomes are classified as  selfish genetic elements . [ 1 ]


Parasitic chromosomes, if detrimental to an organism's survival, often are selected against by  natural selection  over time, but if the chromosome is able to act like a selfish DNA element, it can spread throughout a population. An example of a parasitic chromosome is the b24 chromosome in  grasshoppers . [ 1 ] [ 2 ]


In  genetics , the  partial dominance hypothesis  states that  inbreeding depression  is the result of the frequency increase of  homozygous   deleterious   recessive  or partially recessive  alleles . The hypothesis can be explained by looking at a population that is divided into a large number of separately inbred lines. Deleterious alleles will eventually be eliminated from some lines and become fixed in other lines, while some lines disappear because of fixation of deleterious alleles. This will cause an overall decline in population and trait value, but then increase to a trait value that is equal to or greater than the trait value in the original population. Crossing inbred lines restores fitness in the overdominance hypothesis and a fitness increase in the partial dominance hypothesis. [ 1 ]


A  paucimorphism  is a  genetic   sequence variant  with a  allele  frequency of 0.0005<q<0.05. [ 1 ]


pComb3H , a derivative of  pComb3  optimized for expression of human fragments, is a  phagemid  used to express proteins such as  zinc finger proteins  and antibody fragments on phage pili for the purpose of  phage display  selection. [ 1 ]


For the purpose of phage production, it contains the bacterial ampicillin resistance gene (for B-lactamase), allowing the growth of only transformed bacteria. [ citation needed ]


The  pelB leader sequence  is a sequence of  amino acids  which, when attached to a  protein , directs the protein to the bacterial  periplasm , where the sequence is removed by a  signal peptidase . [ 1 ]  Specifically, pelB refers to pectate lyase B of  Erwinia carotovora  CE. The leader sequence consists of the 22 N-terminal  amino acid  residues. This leader sequence can be attached to any other protein (on the DNA level) resulting in a transfer of such a fused protein to the periplasmic space of  Gram-negative bacteria , such as  Escherichia coli , often used in  genetic engineering .
Protein secretion can increase the stability of cloned gene products. For instance it was shown that the half-life of the recombinant proinsulin is increased 10-fold when the protein is secreted to the periplasmic space. (vijji. Narne, R.S.Ramya)


One of pelB's possible applications is to direct coat protein-antigen fusions to the cell surface for the construction of engineered  bacteriophages  for the purpose of  phage display .


The  Pectobacterium carotovorum  pelB leader sequence commonly used in molecular biology has the sequence  MKYLLPTAAAGLLLLAAQPAMA  ( UniProt  Q04085).


The Penn Genome Frontiers Institute , previously known as the Penn Genomics Institute, was established in January 2001 to provide a focus for all aspects of and participants in the genomics community at  University of Pennsylvania ,  Children's Hospital of Philadelphia  (CHOP) and the  Wistar Institute .


The  pGLO  plasmid is an engineered  plasmid  used in  biotechnology  as a vector for creating  genetically modified organisms .  The plasmid contains several  reporter genes , most notably the  green fluorescent protein  (GFP) and the ampicillin resistance gene.  GFP was isolated from the jelly fish  Aequorea victoria . Because it shares a bidirectional  promoter  with a gene for metabolizing  arabinose , the GFP gene is expressed in the presence of arabinose, which makes the transgenic organism express its fluorescence under  UV light .  GFP can be induced in bacteria containing the pGLO plasmid by growing them on +arabinose plates. pGLO is made by  Bio-Rad Laboratories .


pGLO is made up of three genes that are joined together using recombinant DNA technology. They are as follows:


Like most other circular plasmids, the pGLO plasmid contains an  origin of replication  (ori), which is a region of the plasmid where replication will originate.
The pGLO plasmid was made famous by researchers in  France  who used it to produce a green fluorescent  rabbit  named  Alba .


Other features on pGLO, like most other plasmids, include a selectable marker and an MCS ( multiple cloning site ) located at the end of the GFP gene. The plasmid is 5371  base pairs  long. In  supercoiled  form, it runs on an  agarose gel  in the 4200–4500 range. [ 1 ] [ 2 ] [ 3 ]


The GFP gene was first observed by Osamu Shimomura [ 4 ]  and his team in 1962 while studying the jellyfish  Aequorea victoria  that have a ring of blue light under their umbrella .  Shimomura and his team isolated the protein  aequorin  from thousands of jellyfish until they gathered enough for a full analysis of the protein. It was through the study of aequorin that Shimomura discovered small amounts of GFP which glows green when aequorin emits blue light. After successfully discovering how GFP works with aequorin in the jellyfish, he set it aside to study bioluminescence in other organisms.


In 1994 Marty Chalfie [ 4 ]  and his team were able to successfully create bacteria and round worms that expressed the GFP protein. Soon after, Roger Tsien [ 5 ]  and his team were able to create mutant GFP that can emit a range of colors, not just green.


The three scientists hold the Nobel Prize in Chemistry for 2008 [ 6 ]  for the discovery and development of the green fluorescent protein, GFP.


Phenotype modification  is the process of experimentally altering an organism's  phenotype  to investigate the impact of phenotype on the fitness. [ 1 ]


Phenotype modification has been used to assess the impact of  parasite  mechanical presence on fish host behaviour. [ 2 ]


Phage immunoprecipitation sequencing  (PhIP-Seq) is method that combines barcoded DNA  high-throughput sequencing  and  proteomics  to determine the levels of binding of  antibodies  to  epitopes . It has been used to study the autoantibody repertoire of autoimmune diseases like  multiple sclerosis ,  type 2 diabetes  and  rheumatoid arthritis . [ 1 ] [ 2 ]


Phylostratum  is a set of  genes  from an organism that coalesce to founder genes having common  phylogenetic  origin. [ 1 ] [ 2 ] [ 3 ]  This term was coined by  Domazet and Tautz to describe the gene origination. [ 3 ]


A  plant geneticist  is a  scientist  involved with the study of  genetics  in  botany . Typical work is done with  genes  in order to isolate and then develop certain plant  traits . Once a certain trait, such as plant height, fruit sweetness, or tolerance to cold, is found, a plant geneticist works to improve breeding methods to ensure that future plant generations possess the desired traits.


Plant genetics played a key role in the modern-day theories of  heredity , beginning with  Gregor Mendel 's study of pea plants in the 19th century. The occupation has since grown to encompass advancements in  biotechnology  that have led to greater understanding of  plant breeding  and  hybridization . Commercially, plant geneticists are sometimes employed to develop methods of making produce more nutritious, or altering plant pigments to make the food more enticing to consumers.


This  botany  article is a  stub . You can help Wikipedia by  expanding it .


The  Plant Genome Mapping Laboratory  ( PGML ) [ 1 ]  is a department of the  University of Georgia , directed by Dr.  Andrew H. Paterson . Research focuses on the study of major crop species such as  sorghum  and  cotton , as well as other species such as  Bermuda Grass ,  Brassica  and  Peanut . Research topics include whole genome genetic mapping and physical mapping;  polyploidy ; ancient whole genome duplications;  comparative genomics ; gene cloning; drought tolerance; seed shattering and cotton fiber qualities. PGML has led in the sequencing of the sorghum genome and the cotton genome.


This article about a university or other tertiary education institution in the U.S. state of Georgia is a  stub . You can help Wikipedia by  expanding it .


This article about a  botany  organization is a  stub . You can help Wikipedia by  expanding it .


Polymerase (RNA) III (DNA directed) polypeptide G (32kD)-like  also known as  POLR3GL  is a  protein  which in humans is encoded by the  POLR3GL  gene. [ 1 ] [ 2 ]


The  Pribnow box  (also known as the  Pribnow-Schaller box ) is a sequence of  TATAAT  of six  nucleotides  ( thymine ,  adenine ,  thymine , etc.) that is an essential part of a  promoter  site on  DNA  for  transcription  to occur in  bacteria . [ 1 ] [ 2 ]  It is an idealized or  consensus sequence —that is, it shows the most frequently occurring base at each position in many promoters analyzed; individual promoters often vary from the consensus at one or more positions. It is also commonly called the  -10 sequence  or  element , because it is centered roughly ten base pairs upstream from the site of initiation of transcription.


The Pribnow box has a function similar to the  TATA box  that occurs in promoters in  eukaryotes  and  archaea : it is recognized and bound by a subunit of  RNA polymerase  during initiation of transcription. [ 3 ]  This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand. The AT-richness is important to allow this separation, since  adenine  and  thymine  are easier to break apart (not only due to fewer  hydrogen bonds , but also due to weaker  base stacking  effects). [ 4 ]


It is named after  David Pribnow  and  Heinz Schaller . [ citation needed ] [ 1 ] [ 2 ]


The term "Pribnow box" is used in episode 13 of  Neon Genesis Evangelion , in reference to the chamber holding simulation  Evangelions  for testing purposes.


The  Principle of genetics  is a genetics textbook authored by  D. Peter Snustad & Michael J. Simmons , an emeritus professor of biology, published by John Wiley & Sons, Inc..
The 6th edition of the book was published on 2012. [ 1 ] [ 2 ]


The book is sectioned into four parts. The first part, Genetics and the Scientific Method briefly review the  History of genetics  and the various methods used in genetic study. The second part focus on  Mendelian inheritance , the third part deals with  Molecular genetics  and the last section deals with  Quantitative genetics  and  Evolutionary Genetics . [ 3 ] [ 4 ]


The book had been reviewed and rated high by several editors and geneticists. [ 5 ] [ 6 ]


Probabilistic genotyping  is the use of statistical methods and mathematical algorithms in  DNA Profiling . It may be used instead of manual methods in difficult situations, such as when a DNA sample is very small or includes a mixture of multiple individuals' DNA. [ 1 ]  Probabilistic genotyping, unlike  traditional methods , avoids the need for subjective judgment. [ 1 ]  The reliability of the method has been questioned by some defense lawyers because the source code of some probabilistic genotyping programs is  proprietary . [ 2 ]


In  medical genetics  and other medical fields, a  proband ,  propositus  (male proband), or  proposita  (female proband) [ 1 ]  is a particular subject (human or other animal) being studied or reported on. [ 2 ]  On  pedigrees , the proband is noted with a square (male) or circle (female) shaded accordingly. Denoting the proband is important, so the relationship to other individuals can be seen and patterns established.


In most cases, the proband is the first affected family member who seeks medical attention for a  genetic disorder . [ 2 ]  Among the  ancestors  of the proband, other subjects may manifest the disease, but the proband typically refers to the member seeking medical attention or being studied, even if affected ancestors are known.  Often, affected ancestors are unknown due to the lack of information regarding those individuals or about the disease at the time they lived. Other ancestors might be undiagnosed due to the incomplete  penetrance  or variable  expressivity .


The diagnosis of a proband raises the  index of suspicion  for the proband's relatives and some of them may be diagnosed with the same disease. Conventionally, when drawing a pedigree chart, instead of the first diagnosed person, the proband may be chosen from among the affected  ancestors  (parents, grandparents) from the first generation where the disease is found.


The term "proband" is also used in  genealogy , where it denotes the root node of an  ahnentafel , also referred to as the  progenitor .


"Proband" was also the term for the individual being tested in a  trial by ordeal [ 3 ]


Progeny Testing  is a test of the value for  selective breeding  of an individual's  genotype  by looking at the  progeny  produced by different matings. [ 1 ]


It is used in the  breeding  of both  plants  and  animals , but is most commercially important in  animal breeding  to determine the true breeding value of an animal (especially males) which are used extensively for propagation of best germplasm. The extensive use of artificial insemination in domestic animals has helped in increasing the selection intensity on male animals. This selection tool is usually used for characters that are sex-limited, expressed after death (meat characteristics) and usually with low heritability, for example, milk or egg production in females. A bull, for example, cannot be assessed for milk production, however, the performance of its female offspring can be used to determine the use of the animal for future crosses.


A progeny test is performed by mating the male with a number of females to produce many progenies in a different environment and over a long time period involving different seasons to nullify the impact of season, management and environment in breeding value estimation. The average performance of the offspring is then found, giving a measure of the male's respective value to the breeder.


In animals, the progeny testing could be conducted in a large herd or involving associated herds or in the field in farmers place. The field-based progeny testing is highly required when the selected bulls are to be distributed in a large area to many farmers in different environments. Conducting a field-based progeny testing, especially in  smallholder  production systems of Asia and Africa, require huge resources both financial and infrastructural - a large AI network, robust and dynamic data collection and analysis system. Usually, the breeding companies conduct progeny testing of their bulls so that they can be commercially promoted. But when the breeding organisations are Government controlled (e.g. India), the onus of conducting the testing also lies with them if required genetic improvement is to be achieved. [ 2 ]


pSC101  is a  DNA   plasmid  that is used as a  cloning   vector  in genetic cloning experiments. pSC101 was the first cloning vector, used in 1973 by  Herbert Boyer  and  Stanley Norman Cohen . Using this plasmid they have demonstrated that a  gene  from a frog could be transferred into bacterial cells and then expressed by the bacterial cells.  The plasmid is a natural plasmid from  Salmonella panama . [ 1 ]


In the early 1970s, [ 2 ]   Herbert Boyer  and  Stanley Norman Cohen  produced pSC101, the first plasmid vector for cloning purposes. Soon after successfully cloning two pSC101 plasmids together to create one large plasmid, they published the results describing the experiment, in 1973. [ 2 ]  The cloning of genes into plasmids occurred soon after.
In 1980, [ 2 ]  pSC101 became the first patented commercial DNA cloning vector when patents were awarded to Boyer and Cohen. The "SC" stands for Stanley Cohen. Although the original pSC101 only contained tetracycline resistance and a restriction site for EcoRI, the commercially available pSC101 gained restriction sites for several enzymes, including HindIII, in addition to the EcoRI site.


Pseudodiploid   or  pseudoploid  refers to one of the essential components in  viral  reproduction. It means having two  RNA   genomes  per  virion  but giving rise to only one  DNA  copy in infected cells.


The term is also used to refer to cells that are  diploid , but have  chromosomal translocations . [ 1 ]


Retrovirions  for example are considered pseudoploid – they have two genomes within each  capsid , but in general only one  provirus  is seen after infection with a single virion.


Retrovirus particles contain two copies of the RNA genome held together by multiple regions of base pairing (strongest pairing at 5’ ends) which is also called 70S complex ( dimer  of 35S genomes). This gives viruses evolutionary advantages such as the ability to survive extensive damage to their  genomes , as at least parts of both genomes are used during the  reverse transcription  process. It also explains the high rates of  genetic recombination  in retroviruses. The retroviral genome is coated by a viral  nucleocapsid  protein that may function like a single stranded binding protein and therefore enhances processivity and facilitates template exchanges. The nucleocapsid first organizes RNA genomes within the virion and then facilitates reverse transcription within the infected cell.


The  pterobranchia mitochondrial code  (translation table  24 ) is a  genetic code  used by the  mitochondrial  genome of  Rhabdopleura compacta  ( Pterobranchia ). The Pterobranchia are one of the two groups in the  Hemichordata  which together with the  Echinodermata  and  Chordata  form the three major lineages of  deuterostomes .  AUA translates to  isoleucine  in  Rhabdopleura  as it does in the Echinodermata and  Enteropneusta  while AUA encodes  methionine  in the Chordata. The assignment of AGG to  lysine  is not found elsewhere in deuterostome mitochondria but it occurs in some taxa of  Arthropoda . [ 1 ]  This code shares with many other mitochondrial codes the reassignment of the UGA STOP to  tryptophan , and AGG and AGA to an amino acid other than  arginine .  The initiation  codons  in  Rhabdopleura compacta  are ATG and GTG. [ 1 ]


Code 24 is very similar to the  mitochondrial code 33  for the Pterobranchia. [ 2 ]


A  putative gene  is an alignment segment of  DNA  that is believed to be a  gene . Putative genes can share sequence similarities to already characterized genes and thus can be inferred to share a similar function, yet the exact function of putative genes remains unknown. [ 1 ]  Newly identified sequences are considered putative gene candidates when  homologs  of those sequences are found to be associated with the phenotype of interest. [ 2 ]


Examples of studies involving putative genes include the discovery of 30 putative receptor genes found in rat vomeronasal organ (VNO) [ 3 ]  and the identification of 79 putative TATA boxes found in many plant genomes. [ 4 ]


In order to define and characterize a biosynthetic gene cluster, all the putative genes within said cluster must first be identified and their functions must be characterized. This can be performed by complementation and knock out experiments. In the process of characterizing putative genes, the genome under study becomes increasingly well understood as more interactions can be identified. [ 5 ]  Identification of putative genes is necessary to study genomic evolution, as significant proportion of genomes make up larger families of related genes. Genomic evolution occurs by processes such as duplication of individual genes, genome segments, or entire genomes. These processes can result in  loss of function , altered function, or  gain of function , and have drastic affects on the phenotype. [ 6 ] [ 7 ]


DNA mutations outside of a putative gene can act by positional effect, in which they alter the gene expression. These alterations leave the transcription unit and promoter of the gene intact, but may involve distal promoters, enhancer/silencer elements, or the local chromatin environment. These mutations can be associated with diseases or disorders associated with the gene.


Putative genes can be identified by clustering large groups of sequences by patterns and arranging by mutual similarity [ 8 ]  or can be inferred by potential  TATA boxes . [ 9 ]


Putative genes can also be identified by recognizing differences between well-known gene clusters and gene clusters with a unique profiling. [ 10 ]


Software tools have been developed in order to automatically identify putative genes. This is done by searching for gene families and testing the validity of uncharacterized genes by comparison to already identified genes. [ 11 ]


Protein products can be identified and used to characterize the putative gene that codes for it. [ 12 ]


In biology, the  PYLIS downstream sequence  (PYLIS:  py rro l ysine  i nsertion  s equence ) is a  stem-loop  structure that appears on some  mRNA  sequences. This  structural motif  was previously thought to cause the UAG (amber)  stop codon  to be translated to the  amino acid   pyrrolysine  instead of ending the protein translation. [ 1 ] [ 2 ] [ 3 ]  However, it has been shown that PYLIS has no effect upon the efficiency of the UAG suppression, [ 4 ]  hence even its name is, in fact, incorrect.


R-banding  is a  cytogenetics  technique that produces the reverse of the  G-band  stain on  chromosomes . R-banding is obtained by incubating the slides in hot phosphate buffer, then a subsequent treatment of  giemsa dye . Resulting chromosome patterns shows darkly stained R bands, the complement to G-bands. Darkly colored R bands are  guanine-cytosine  rich, and  adenine - thymine  rich regions are more readily denatured by heat. The technique is useful for analyzing  genetic deletions  or  chromosomal translocations  that involve the telomeres of  chromosomes . [ 1 ]


Random man not excluded  ( RMNE ) is a type of measure in  population genetics  to estimate the probability that an individual  randomly  picked out of the general population would not be excluded from matching a given piece of genetic data.


RMNE is frequently employed in cases where other types of tests such as  random match possibility  are not possible because the sample in question is degraded or contaminated with multiple sources of DNA. [ 1 ]


A  rare variant  is a  genetic variant  which occurs at low  frequency  in a population. [ 1 ]   Rare variants play a significant role in both complex and  Mendelian  disease and are responsible for a portion of the missing  heritability  of complex diseases. The theoretical case for a significant role of rare variants is that  alleles  that strongly predispose an individual to disease will be kept at low frequencies in populations by  purifying selection . [ 2 ]  Rare variants are increasingly being studied, as a consequence of  whole exome  and  whole genome sequencing  efforts. While these variants are individually infrequent in populations, there are many in human populations, and they can be unique to specific populations.  They are more likely to be  deleterious  than common variants, as a result of rapid population growth and weak purifying selection. [ 3 ]   They have been suspected of acting independently or along with  common variants  to cause disease states. [ 4 ]


Some methods, such as genetic burden tests, have been specifically developed to study genetic association of rare variants. [ 5 ]  These methods aggregate rare variants over genetic regions, such as genes or whole pathways, and evaluate cumulative effects of multiple genetic variants. These methods may increase
power when multiple variants in the region are associated with a disease or a trait. In addition, compared to a  genome-wide association study , a region or gene based test performs much fewer tests resulting in a less stringent multiple-hypothesis correction than the  genome-wide significance . [ 6 ]  Some examples of these methods are SKAT, [ 7 ]  SKAT-O, [ 5 ]  ARIEL test, [ 8 ]  aSUM [ 9 ]  and STAAR. [ 10 ]   SNP annotations  help to prioritize rare functional variants, and incorporating these annotations can effectively boost the power of genetic association of rare variants analysis of  whole exome  and  whole genome sequencing  studies. [ 11 ]   [ 12 ]


A  recognition sequence  is a  DNA sequence  to which a  structural motif  of a  DNA-binding domain  exhibits  binding specificity . Recognition sequences are  palindromes . [ 1 ]


The  transcription factor   Sp1  for example, binds the sequences 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3', where (G/T) indicates that the domain will bind a  guanine  or  thymine  at this position.


The  restriction endonuclease   PstI  recognizes, binds, and cleaves the sequence 5'-CTGCAG-3'.


A  recognition sequence  is different from a  recognition site . A given recognition sequence can occur one or more times, or not at all, on a specific DNA fragment. A  recognition site  is specified by the position of the site. For example, there are two PstI recognition sites in the following DNA sequence fragment, starting at base 9 and 31 respectively. A recognition sequence is a specific sequence, usually very short (less than 10 bases). Depending on the degree of specificity of the protein, a DNA-binding protein can bind to more than one specific sequence. For PstI, which has a single sequence specificity, it is 5'-CTGCAG-3'. It is always the same whether at the first recognition site or the second in the following example sequence. For Sp1, which has multiple (16) sequence specificity as shown above, the two recognition sites in the following example sequence fragment are at 18 and 32, and their respective recognition sequences are 5'-GGGGCGGAGC-3' and 5'-TGGGCGGAAC-3'.


5'-AACGTTAG CTGCAG TC GGGGCGGAGC TAGG CTGCAG GAAT TGGGCGGAAC CT-3'


Recombinases  are  genetic recombination   enzymes .


DNA recombinases are widely used in multicellular organisms to manipulate the structure of  genomes , and to control  gene expression . These enzymes, derived from  bacteria  ( bacteriophages ) and  fungi , catalyze directionally sensitive DNA exchange reactions between short (30–40  nucleotides ) target  site sequences that are specific to each recombinase . These reactions enable four basic functional modules: excision/insertion, inversion, translocation and  cassette  exchange, which have been used individually or combined in a wide range of configurations to control gene expression. [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ]


Recombinases have a central role in  homologous recombination  in a wide range of organisms.  Such recombinases have been described in  archaea ,  bacteria ,  eukaryotes  and  viruses .


The archaeon  Sulfolobus solfataricus  RadA recombinase catalyzes  DNA  pairing and strand exchange, central steps in recombinational repair. [ 6 ]   The RadA recombinase has greater similarity to the eukaryotic  Rad51  recombinase than to the bacterial RecA recombinase. [ 6 ]


RecA  recombinase appears to be universally present in bacteria.  RecA has multiple functions, all related to  DNA repair .  RecA has a central role in the repair of replication forks stalled by  DNA damage  and in the bacterial sexual process of natural  genetic transformation . [ 7 ] [ 8 ]


Eukaryotic  Rad51  and its related family members are homologous to the archaeal RadA and bacterial RecA recombinases.  Rad51 is highly conserved from yeast to humans.  It has a key function in the recombinational repair of DNA damages, particularly double-strand damages such as double-strand breaks.  In humans, over- or under- expression  of Rad51 occurs in a wide variety of  cancers .


During  meiosis  Rad51 interacts with another recombinase,  Dmc1 , to form a presynaptic filament that is an intermediate in  homologous recombination . [ 9 ]   Dmc1 function appears to be limited to meiotic recombination.  Like Rad51, Dmc1 is homologous to bacterial RecA.


Some DNA viruses encode a recombinase that facilitates homologous recombination.  A well-studied example is the UvsX recombinase encoded by  bacteriophage T4 . [ 10 ]   UvsX is homologous to bacterial RecA.  UvsX, like RecA, can facilitate the assimilation of linear single-stranded DNA into an homologous DNA duplex to produce a  D-loop .


The  Recombination detection program  (RDP) is a computer program used to analyse nucleotide sequence data and identify evidence of genetic recombination.  Besides applying a large number of different recombination detection methods it also implements various   phylogenetic tree  construction methods and recombination hotspot tests. The latest version is RDP4. [ 1 ]


Redlove  apples are a series of  cultivars  bred by Markus Kobelt in Switzerland. They are  hybrids  from cross-pollination of red-fleshed and scab-resistant plants. Cultivars include 'Redlove Calypso', 'Redlove Circe', 'Redlove Era', and 'Redlove Odysso'. [ 1 ]  Some have a high  antioxidant  content with 30–40% more than an average apple. The fruit are red on the outside and inside, with a white line in the middle. The apples are sold as a protected, trade-marked variety. Licences for commercial production are sold worldwide and can be acquired from Lubera AG.


The  relaxosome  is the  complex of proteins  that facilitates  plasmid  transfer during  bacterial conjugation .  The proteins are encoded by the  tra operon  on a fertility plasmid in the region near the origin of transfer,  oriT .  The most important of these proteins is  relaxase , which is responsible for beginning the conjugation process by cutting at the  nic  site via  transesterification .  This nicking results in a  DNA - Protein  complex with the relaxosome bound to a single strand of the plasmid DNA and an exposed 3' hydroxyl group.  Relaxase also unwinds the plasmid being conjugated with its  helicase  properties.  The relaxosome interacts with integration host factors within the oriT.


Other genes that code for relaxosome components include  TraH , which stabilizes the relaxosome's structural formation,  TraI , which encodes for the relaxase protein,  TraJ , which recruits the complex to the oriT site,  TraK , which increases the 'nicked' state of the target plasmid, and  TraY , which imparts single-stranded DNA character on the oriT site.   TraM  plays a particularly important role in relaxase interaction by stimulating 'relaxed' DNA formation.


This  bacteria -related article is a  stub . You can help Wikipedia by  expanding it .


The  repeatome  can be defined as the complement of repeated sequences in a genome. The eukaryotic repeatomes typically comprise variable amounts of multiple components including  transposable elements  (TEs) and  endogenous viruses ,  simple sequence repeats , segmental duplications, ribosomal DNA and other ribozymes, multi-copy gene families, pseudogenes, as well as highly conserved and repeated protein domains.
Because of their relative high duplication rate as compared to other genomic components, TEs are typically predominant contributors to eukaryotic repeatomes and the product of their decay is thought to be a major source of genomic dark matter. [ 1 ] [ 2 ] [ 3 ]


A  replicon  is a region of an organism's genome that is independently replicated from a single  origin of replication [ citation needed ] . A bacterial chromosome contains a single origin, and therefore the whole bacterial chromosome is a replicon. The chromosomes of  archaea  and  eukaryotes  can have multiple origins of replication, and so their chromosomes may consist of several replicons [ citation needed ] . The concept of the replicon was formulated in 1963 by  François Jacob ,  Sydney Brenner , and Jacques Cuzin as a part of their replicon model for replication initiation. According to the replicon model, two components control replication initiation: the replicator and the initiator. The replicator is the entire DNA sequence (including, but not limited to the origin of replication) required to direct the initiation of DNA replication. The initiator is the protein that recognizes the replicator and activates replication initiation. [ 1 ]


Sometimes in  bacteriology , the term "replicon" is only used to refer to chromosomes containing a single origin of replication and therefore excludes the genomes of  archaea  and  eukaryotes  which can have several origins. [ 2 ]


For most  prokaryotic   chromosomes , the replicon is the entire chromosome. One notable exception comes from  archaea , where two  Sulfolobus  species have been shown to contain three replicons. Examples of bacterial species that have been found to possess multiple replicons include  Rhodobacter sphaeroides  (two),  Vibrio cholerae , [ 3 ]  and  Burkholderia multivorans  (three). These "secondary" (or tertiary) chromosomes are often described as molecules that are intermediate between a true  chromosome  and a  plasmid  and are sometimes called " chromids ". Various  Azospirillum  species possess seven replicons;  A. lipoferum , for instance, has one bacterial chromosome, five chromids, and one plasmid. [ 4 ]
 Plasmids  and  bacteriophages  are usually replicated as single replicons, but large plasmids in  Gram-negative bacteria  have been shown to carry several replicons. [ 5 ]


For  eukaryotic  chromosomes, there are multiple replicons per chromosome.  Known examples range in size from 10 to 330  kilobases . A cluster of replicons replicates simultaneously. But different clusters start replicating at different times during  S phase , depending on their location along the chromosomes. In general, clusters nearer the  centromere  replicate earlier. Fine structure analysis of chromosomal origins of replication is limited to a single  model  eukaryote,  Saccharomyces cerevisiae . Therefore, no general picture of a replicon as replicator and initiator in eukaryotes has been achieved.


In the case of  mitochondria , the definition of replicons is somewhat confused, as they use unidirectional replication with two separate origins.


Non-cellular entities  such as  viruses ,  plasmids ,  transposons ,  retrotransposons ,  viroids ,  virusoids  and  RNA satellites  are also replicons.  Patrick Forterre  of the  Pasteur Institute  has coined the term "orphan replicon" to refer to those that are not viruses; i.e., that lack a  capsid . [ 6 ]


A  restriction fragment  is a  DNA  fragment resulting from the cutting of a DNA strand by a  restriction enzyme  (restriction endonucleases), a process called restriction. [ 1 ]  Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site. Most restriction sites are  palindromic , (the sequence of nucleotides is the same on both strands when read in the 5' to 3' direction of each strand), and are four to eight  nucleotides  long. Many cuts are made by one restriction enzyme because of the chance repetition of these sequences in a long DNA molecule, yielding a set of restriction fragments. A particular DNA molecule will always yield the same set of restriction fragments when exposed to the same restriction enzyme.  Restriction fragments can be analyzed using techniques such as  gel electrophoresis  or used in  recombinant DNA  technology. [ 2 ]


In recombinant DNA technology, specific restriction endonucleases are used that will isolate a particular gene and cleave the sugar phosphate backbones at different points (retaining symmetry), so that the double-stranded restriction fragments have single-stranded ends. These short extensions, called  sticky ends , can form  hydrogen bonded  base pairs with complementary sticky ends on any other DNA cut with the same enzyme (such as a bacterial plasmid).


In  agarose gel electrophoresis , the restriction fragments yield a band pattern characteristic of the original DNA molecule and restriction enzyme used, for example the relatively small DNA molecules of viruses and plasmids can be identified simply by their restriction fragment patterns. If the nucleotide differences of two different  alleles  occur within the restriction site of a particular restriction enzyme, digestion of segments of DNA from individuals with different alleles for that particular gene with that enzyme would produce different fragments and that will each yield different band patterns in gel electrophoresis.


Rho utilisation site , also known by the acronym  rut , is a sequence of RNA in  bacteria  upstream of the terminator region which serves as a binding site for the protein known as  rho factor . This sequence is necessary in rho-dependent termination of  DNA transcription  in bacteria. The common feature of the rut site is an abundance of  cytosine  and paucity of  guanine  residues, although these sequences vary widely in different  genes  with little homology. [ 1 ]


A few algorithms have been developed to predict such sites. [ 2 ] [ 3 ]


RivX sRNA  is a  non-coding RNA  molecule involved in the interface between two key regulators of virulence in the human pathogen  Streptococcus pyogenes  ( Group A  Streptoccus , also known as GAS): the  CovR/S system [ 1 ]  and  Mga  regulator. [ 2 ]  This RNA, along with its downstream  protein-coding gene   RivR , are the first discovered links between these two important regulation networks. [ 2 ]  An extra protein linking the two pathways, TrxR, was described a year later. [ 3 ]  The adjoining of these two pathways could allow a consistently high  virulence  of  S. pyogenes  despite a variety of environmental conditions. [ 2 ]


RivX is thought to be co-transcribed with RivR  mRNA  before post-transcriptional processing releases the sRNA. It was found to be a non-coding transcript through  site-directed mutagenesis  experimentation. [ 2 ]


In total, the GAS genome is now predicted to encode 75 total sRNAs, a number approximately equal to the number of transcription factors encoded by the genome, which shows the importance of RNA regulation in GAS. [ 4 ]


RNase PH  is a  tRNA nucleotidyltransferase , present in  archaea  and  bacteria , that is involved in  tRNA  processing. Contrary to hydrolytic enzymes, it is a  phosphorolytic  enzyme, meaning that it uses  inorganic  phosphate as a reactant to cleave nucleotide-nucleotide bonds, releasing diphosphate  nucleotides . The active structure of the proteins is a homohexameric complex, consisting of three  ribonuclease  (RNase) PH dimers. [ 1 ]  RNase PH has  homologues  in many other organisms, which are referred to as RNase PH-like proteins. The part of another larger protein with a  domain  that is very similar to RNase PH is called an  RNase PH domain  (RPD).


Two highly related exoribonuclease complexes:


In  genetics ,  rs6311  is a gene variation—a  single nucleotide polymorphism  (SNP)—in the human  HTR2A   gene  that codes for the  5-HT 2A   receptor . 5-HT 2A  is a  neuroreceptor , and several scientific studies have investigated the effect of the genetic variation on personality, e.g., personality traits measured with the  Temperament and Character Inventory [ 1 ] [ 2 ] [ 3 ] [ 4 ]
or with a psychological task measuring impulsive behavior. [ 5 ]
The SNP has also been investigated in  rheumatology  studies. [ 6 ] [ 7 ]


Some research studies may refer to this gene variation as a C/T SNP, [ 2 ]  while others refer to it as a G/A polymorphism in the promoter region, thus writing it as, e.g., −1438 G/A or 1438G>A. [ 8 ] [ 9 ] [ 10 ]


As of 2008 [update] ,  meta-analysis  of research studies indicates that people with the A- allele  may have slightly elevated risk of  schizophrenia . [ 11 ]


rs6313 ,  rs6314 , and  rs7997012  are other investigated SNPs in the HTR2A gene.


In  genetics ,  rs6313  also called  T102C  or  C102T  is a gene variation—a  single nucleotide polymorphism  (SNP)—in the human  HTR2A   gene  that codes for the  5-HT 2A   receptor .
The SNP is a  synonymous substitution  located in exon 1 of the gene where it is involved in coding the 34th  amino acid  as  serine . [ 1 ]


As 5-HT 2A  is a  neuroreceptor  the SNP has been investigated in connection with  brain functions  and  neuropsychiatric disorders , and it is perhaps the most investigated SNP for its gene.
Two other SNPs in HTR2A have also received much attention:  rs6311  and  His452Tyr  (rs6314).
The T102C polymorphism has been shown to be in complete  linkage disequilibrium  with the rs6311 (A-1438G).
 [ 2 ]
A less well investigated SNP of this gene is  rs7997012 .


Meta-analyses  seem to indicate that the SNP is directly associated with  schizophrenia , [ 3 ]
with  Alzheimer's disease , [ 4 ]
and two initial studies seem to indicate that it is not associated with  Parkinson's disease . [ 5 ]


There have been multiple studies of the effect of this SNP on  clozapine  treatment response in  schizophrenia . [ 6 ]
A meta-analysis published in 1998 found an association. [ 7 ]


Many individual studies have been done to investigate possible effects of the rs6313 polymorphism on  phenotypes  such as  personality traits  or disorders and their  endophenotypes .


The C- allele  has been associated with higher  extraversion  personality scores among  borderline personality disorder
 [ 8 ]  patients and the presence of visual and auditory  hallucinations  in patients with  late-onset Alzheimer's disease .
 [ 9 ]
Multiple studies have found that individuals with schizophrenia who are homozygous for the C-allele tend to do worse on working memory tasks than do individuals with a T-allele.
 [ 10 ]
 [ 11 ]
 [ 12 ]
Rs6313 has also been shown to be associated with  novelty seeking  among Italian  mood disorder  patients
 [ 13 ]  and  reward dependence  in a German population.
 [ 14 ]  The SNP may also be associated with  rheumatoid arthritis .
 [ 15 ]
One study found no association between the SNP and suicidal behavior in a Chinese population,
 [ 16 ]  and another found no association with fibromyalgia syndrome.
 [ 17 ]


In  genetics ,  rs6314 , also called  His452Tyr  or  H452Y , is a gene variation, a  single nucleotide polymorphism  (SNP), in the  HTR2A  gene that codes for the  5-HT 2A  receptor .
The SNP is located in exon 3 of the gene and the change between C and T results in a change between  histidine  (His) and  tyrosine  (Tyr) at the 452nd  amino acid , i.e., it is a  missense substitution . [ 1 ]


As 5-HT 2A  is a  neuroreceptor  the SNP has been investigated in connection with  neuropsychiatric disorders [ 2 ]
and other brain-related variables.
A 2003 study looked at memory performance and found that His/His subjects performed better. [ 3 ]
Another study reported that the SNP had an effect on the  memory  performance in young adults. [ 4 ]
This has been replicated by another group. [ 5 ]


The His452Tyr variant may influence  cell signaling . [ 6 ]


rs6311 ,  rs6313  and  rs7997012  are other investigated SNPs in the  HTR2A  gene.


In  genetics ,  rs7997012  is a gene variation—a  single nucleotide polymorphism  (SNP)—in  intron  2 of the human  HTR2A   gene  that codes for the  5-HT 2A  receptor .
The SNP varies between  adenine  (A) and  guanine  (G) DNA bases with the G-allele being most frequent. [ 1 ]
A research study found it to be related to  antidepressant  treatment. [ 2 ]
The research group reported that a polymorphism ( rs1954787 ) on another gene, the  GRIK4 , has also shown a treatment-response-association in this kind of treatment. [ 3 ]
In a Japanese study rs7997012 was not associated with either  major depressive disorder  or  bipolar disorder . [ 4 ]


Rs6311 ,  rs6313  and  His452Tyr  (rs6314) are other SNPs in the HTR2A gene.
There are many more, even in intron 2 alone. [ 5 ]