PCR chimeras also occur in DNA sequencing. In this case, the most common mechanism of chimera formation is that incomplete extension during the PCR results in partial sequence strands that can act as primers in subsequent PCR cycles on similar but non identical sequences. Extension of such hybrid priming events causes the formation of chimeric sequences. [ 1 ]


Some computational methods have been devised to detect and remove chimeras, like:


A read is a sequence of nucleic acids determined through high-throughput DNA or RNA sequencing, corresponding to a DNA or RNA fragment. A chimeric read or split read means that multiple subsections of that read  align  to different positions in a  reference genome . [ 15 ]  They are not always a sign of the presence of a PCR chimera and often used to detect  structural variations . [ 3 ]


In  developmental biology ,  choriogenesis  is the formation of the  chorion , an outer membrane of the placenta that eventually forms  chorionic villi  that allow the transfer of blood and nutrients from mother to fetus. [ 1 ]


Identical twins have identical  genomes  in the immediate aftermath of twinning.  About two-thirds of  monozygotic twins  share the same placenta, arising by cleavage before the fourth day of development; the other third have separate placentas because cleavage has taken place after the fourth day after choriogenesis has begun. [ 2 ]


Placentas vary with respect to the transport of nutrients and hormones, a variance that may influence  epigenesis .  For example, the pattern of  X chromosome inactivation  is affected by placental status. There is a weak link between variance in IQ test findings and chorion type. A study in 1978 shows that white monochorionic identical twins display less IQ variance one from another than do white dichorionic identical twins, although similar results could not be repeated with black twins. [ 3 ]   There is weak evidence that monozygotic twins sharing a placenta have a higher concordance rate for  schizophrenia  than monozygotic twins with separate placentas.  Sharing a placenta increases the risk for infection, and infection in pregnancy has been shown to be a risk factor for schizophrenia.  Equally striking is evidence for increasing difference in genomic expression between identical twins as they are once again implicating environmental intercession.


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


Chromosome jumping  is a tool of molecular biology that is used in the physical  mapping  of  genomes .  It is related to several other tools used for the same purpose, including  chromosome walking .


Chromosome jumping is used to bypass regions difficult to  clone , such as those containing  repetitive DNA , that cannot be easily mapped by chromosome walking, and is useful in moving along a chromosome rapidly in search of a particular  gene . Unlike chromosome walking, chromosome jumping is able to start on one point of the chromosome in order to traverse potential distant point of the same chromosome without cloning the intervening sequences. [ 1 ]  The ends of a large DNA fragment is the target cloning section of the chromosome jumping while the middle section gets removed by sequences of chemical manipulations prior to the cloning step.  [ 2 ]


Chromosome jumping enables two ends of a DNA sequence to be cloned without the middle section. Genomic DNA may be partially digested using restriction endonuclease and with the aid of DNA ligase, the fragments are circularized at low concentration. [ 2 ] [ 3 ]  From a known  sequence , a  primer  is designed to  sequence  across the circularized junction. This primer is used to jump 100  kb -300 kb intervals: a sequence 100 kb away would have come near the known sequence on circularization, it permits jumping and sequencing in an alternative manner. Thus, sequences not reachable by chromosome walking can be sequenced. [ 2 ]  Chromosome walking can also be used from the new jump position (in either direction) to look for  gene -like sequences, or additional jumps can be used to progress further along the chromosome. Combining chromosome jumping to chromosome walking through the chromosome allows bypassing repetitive DNA for the search of the target gene.


Chromosome  jumping library  is different from chromosome walking due to the manipulations executed before the  cloning  step. In order to construct the library of chromosome jumping, individual clones originate from random points in the genome (general jumping libraries first basic protocol) or from the termini of specific restriction fragments (specific jumping libraries alternate protocol) should be identified.  [ 1 ] [ 4 ]


One example to build a library is a classified as a rare-cutting  restriction endonuclease  such as NotI.  [ 5 ] [ 6 ]  In order to construct and characterize a library based from NotI-digested human DNA, random clones were analyzed by  restriction mapping . [ 3 ]  Due to the wide distribution of fragment sizes made by the complete digestion with NotI, the library was constructed into two fractions, low and high plasmid concentration. [ 3 ]  Clones that possessed unique end fragments were then analyzed by hybridization to  Pulse Field Gradient  (PFG)  Southern blots . [ 3 ]  Examining the results gathered for single and double digests of human DNA with enzymes NotI, BssHII, and NruI, a restriction map with 850 kb was region containing the linking and jumping clones were created. [ 3 ]  Furthermore, NotI fragments of 250 and 350 kb jumps were evident in the two end clones derived corresponding to  genetic distances of 0.25 and 0.35 cM. [ 3 ]


The advantages of chromosome jumping are:


However, despite these advantages, chromosome jumping is still restricted by the capacity of the  cloning vector  which is the distance of the ends of the two fragments which can be approximately hundreds of kilobases. [ 2 ]  Additionally, because the jump does not clone the intervening DNA, chromosome walking would have to be done to identify all the genes present in the DNA.  [ 7 ]  Regardless, it is still deemed to be beneficial due to the possibility to jump over hundred kilobases in comparison to chromosome walking.


Chromosome jumping libraries help address the complication of  standard cloning techniques  with large molecular distances. This process allowed the possibility to use the chromosome jumping library for other genetic disorders that requires 100 kilobases jumps. [ 4 ]  Particularly for genetic disorders such as  cystic fibrosis , its gene is located in  human chromosome 7 , was able to utilize the chromosome jumping library to search for a jumping clone, met oncogene.  [ 4 ]  Identification of the cystic fibrosis was complicated due to it existing in eukaryotic genes that is composed with  coding (exons)  and  non-coding (introns)  segments, where introns are small in size making them difficult for detection. [ 7 ]  Another struggle in recognizing cystic fibrosis gene is because mammalian cells contains variety of repetitive DNA that can lead to incorrect cloning and blockage of  DNA Replication  and can cause instability. [ 8 ]  Both these complications, traditional cloning techniques are unable to process because large yield of exons would have to be visible to produce a signal for the cystic fibrosis gene to be identified and DNA would have to be free of any repetitive elements.  [ 7 ]


Chromosomal landing  is a genetic technique used to identify and isolate clones in a genetic library. Chromosomal landing reduces the problem of analyzing large, and/or highly repetitive genomes by minimizing the need for chromosome walking. [ 1 ]  It is based on the principle that the expected average between- marker   distances  can be smaller than the average insert length of a clone library containing the gene of interest.


From the abstract of  PMID   7716809 :


The  ciliate, dasycladacean and  Hexamita  nuclear code  (translation table  6 ) is a  genetic code  used by certain  ciliate ,  dasycladacean  and  Hexamita  species.


The ciliate macronuclear code has not been determined completely. The codon UAA is known to code for Gln only in the Oxytrichidae.


Cis-acting replication elements (cre)  bring together the 5′ and 3′ ends during replication of positive-sense single-stranded RNA viruses (for example Picornavirus, Flavivirus, Coronavirus, Togaviruses, Hepatitis C virus) and double-stranded RNA viruses (for example rotavirus and reovirus). [ 2 ]


Cre  are regions of the viral RNA that act as regulatory signals for essential steps in the virus life cycle [ 3 ] .  These regions typically fold into loop-like structures and are located in the protein-making part of the genome called the translated region or flanking these regions in parts of the genome called the untranslated region. [ 3 ] [ 4 ]


These folded RNA structures interact with proteins from the virus or host to manage processes like making new viral proteins and replicating the virus’ genetic material. [ 5 ]  The exact shape and role of these structures vary between different types of viruses. [ 5 ]


The replication process of some positive-sense RNA viruses (ie. enteroviruses) proceeds via protein-primed replication. [ 6 ]  This refers to replication that requires the binding of a protein to the RNA to begin. [ 6 ]  Viral protein genome-linked (VPg) plays the essential role of the protein primer that initiates the replication process in these viruses. [ 6 ] [ 7 ]  However, VPg only becomes an active primer when two uridine nucleotides are added to a tyrosine molecule located on the protein  [ 7 ] .The addition of two uridines to a tyrosine molecule is a process called uridylylation. [ 7 ]  The uridylylation of the tyrosine molecule on VPg is guided by  cre s. [ 7 ]  Once the two necessary uridines have been added, VPg is able to prime the initiation of viral replication. [ 7 ]


Cre s also affect viral replication through RNA-RNA interactions, specifically interactions between the  cre  and other regions of the viral genome. [ 8 ]  These complex and dynamic interactions are necessary for the efficient synthesis of viral DNA and ensure proper internal ribosome entry site (IRES) function. [ 8 ]  The IRES allows for the recruitment of host ribosomes and the translation of the viral genome in a cap-independent manner. [ 9 ]  This is an essential step in viral replication as a lot of positive-sense RNA viruses do not possess the chemical cap on the 5' end of their genome necessary for host ribosomes to translate their RNA into protein. [ 10 ]  Cap-independent translation bypasses this problem, allowing the virus to generate the proteins it needs for replication.


Additionally,  cre s have been shown to interact with several different host proteins. [ 11 ]  In Enterovirus A71,  cre s were shown to bind to the cellular factor insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) with a cooperative relationship.  Cre -IGF2BP2 interaction resulted in the increase of both viral replication and IGF2BP2 expression. [ 12 ]


Coronavirus is another example of a positive sense RNA virus that uses  cre s for many functions including RNA synthesis, transcription and virus particle formation. [ 13 ] [ 14 ]  Its single stranded genome contains 3  cre  structures located at the 3’ end of the genome that does not produce protein and 5 at the 5’ end. [ 13 ]  Studies investigating the possible RNA-RNA interactions in coronavirus have found that replication of the viral genome is initiated once the 5’  cre  binds to the 3' end of the coronavirus genome. [ 15 ] [ 16 ]  This interaction enables the recruitment of RNA dependent RNA polymerase which is a protein used to make new RNA strands. Once RNA synthesis is complete  cre s are also used to package the viral genome into newly formed virus particles. [ 17 ]


Cre  have been identified as attractive antiviral targets for the treatment of diseases caused by viral infections such as hepatitis. [ 18 ] [ 19 ]  In the context of Hepatitis B Virus, scientists have proposed the development of small molecules that could disrupt the binding of  cre s to the viral polymerase causing early replication inhibition. [ 19 ]


In simple words, the  cistrome  refers a collection of  regulatory elements  of a set of genes, including transcription factor binding sites and histone modifications. More specifically, "the set of  cis-acting  targets of a  trans-acting  factor on a genome-wide scale, also known as the  in vivo  genome-wide location of  transcription factor   binding sites  or  histone  modifications". [ 1 ]  The term cistrome is a  portmanteau  of  cistr  (from  cistron ) +  ome  (from  genome ). The term cistrome was coined by investigators at the  Dana–Farber Cancer Institute  and  Harvard Medical School . [ 2 ]


Technologies such as  chromatin immunoprecipitation  combined with microarray analysis " ChIP-on-chip " or with massively parallel DNA sequencing " ChIP-Seq " have greatly facilitated the definition of the cistrome of  transcription factors  and other  chromatin  associated proteins.


Codon reassignment  is the  biological process  via which the  genetic code  of a cell is changed as a response to the environment. It may be caused by alternative  tRNA   aminoacylation , in which the cell modifies the target  aminoacid  of some particular type of transfer-RNA. [ 1 ]   This process has been identified in  bacteria ,  yeast  and human  cancer cells . [ 1 ]


In human cancer cells, codon reassignment can be triggered by  tryptophan  depletion, resulting in proteins where the tryptophan aminoacid is substituted by  phenylalanine . [ 1 ]


A  coenogamete  is a multi-nucleate  gamete  (a gamete with more than one  nucleus ). [ 1 ]  Fusion of coengametes creates  coenocytes .


They exist amongst members of the phylum  Porifera  (sponges) under kingdom  Animalia  and division  Zygomycota  of kingdom  Fungi .


This  poriferan - (or sponge-) related article is a  stub . You can help Wikipedia by  expanding it .


Cohorts for Heart and Aging Research in Genomic Epidemiology , abbreviated  CHARGE , is a  consortium  formed to facilitate meta-analyses of  genome-wide association studies  of  aging  and  cardiovascular  traits, and the replication of  genotype – phenotype  associations identified in such studies. CHARGE was initially launched in 2008 as a voluntary collaboration between five  prospective cohort studies : the Age, Gene/Environment Susceptibility-Reykjavik Study (AGES) in  Iceland , the  Atherosclerosis Risk in Communities  Study, the Cardiovascular Health Study, and the  Framingham Heart Study  in the  United States , and the  Rotterdam Study  in  the Netherlands . Other cohort studies have joined the consortium since its founding, including the  Multi-Ethnic Study of Atherosclerosis  and the  Coronary Artery Risk Development in Young Adults Study . [ 1 ] [ 2 ]  The organization of the consortium consists of a Research Steering Committee, an Analysis Committee, a Genotyping Committee, and roughly 35 phenotype-specific  working groups . [ 3 ]


A8TX70 H0Y935


NM_001278298 NM_153264


NP_001265227 NP_694996


Collagen alpha-5(VI) chain  also known as  von Willebrand factor A domain-containing protein 4  is a  protein  that in humans is encoded by the COL6A5  gene .


COL6A5 is a part of the  Collagen VI  gene family which produce collagen components for the  Extracellular matrix  of most connective tissues. [ 5 ]  In the human genome, part of the collagen VI family is located on  chromosome 3q  in order of COL6A4, COL6A5, COL6A6. [ 5 ]   Transcription  of COL6A5 only occurs in skin, lung, testis, colon, and small intestine cells. [ 5 ]


COL20A1  is a  collagen  gene.


NM_030820 NM_001318751 NM_001318752 NM_001318753 NM_001318754


NP_001305680 NP_001305681 NP_001305682 NP_001305683 NP_110447


Collagen alpha-1(XXI) chain  is a  protein  that in humans is encoded by the  COL21A1   gene . [ 3 ]  The protein is an  extracellular matrix  component of blood vessel walls, secreted by  smooth-muscle  cells. The protein may contribute to the extracellular matrix assembly of the vascular network during  blood vessel formation . [ 4 ]


COL22A1  is a human gene encoding for  collagen . The associated protein is thought to contribute to the stabilization of  myotendinous junctions  and strengthen  skeletal muscle attachments  during  muscle contraction .  [ 4 ]


Collagen, type XXVIII, alpha 1  also known as  COL28A1  is a  protein  that in humans is encoded by the  COL28A1   gene . [ 5 ]  This protein belongs to a class of collagens that contain  von Willebrand factor type A domains . [ 6 ]  The protein is encoded by the  COL28A1   gene  which contains 45  exons  and is found of the p arm of chromosome 7. [ 6 ]


A  concatemer  is a long continuous  DNA  molecule that contains multiple copies of the same DNA sequence linked in series. These  polymeric  molecules are usually copies of an entire  genome  linked end to end and separated by  cos  sites (a  protein  binding  nucleotide sequence  that occurs once in each copy of the genome). Concatemers are frequently the result of  rolling circle replication , and may be seen in the late stage of infection of bacteria by  phages . As an example, if the genes in the phage DNA are arranged ABC, then in a concatemer the genes would be ABCABCABCABC and so on (assuming synthesis was initiated between genes C and A). They are further broken by  ribozymes . [ 1 ]


During active infection, some species of viruses have been shown to replicate their genetic material via the formation of concatemers. [ 2 ]  In the case of  human herpesvirus-6 , its entire genome is made over and over on a single strand. These long concatemers are subsequently cleaved between the pac-1 and pac-2 regions by  ribozymes  when the genome is packaged into individual virions.


Bacteriophage T4  replicating DNA was labeled with tritiated  thymidine  and examined by  autoradiography . [ 3 ]   The observed  DNA replication  intermediates included circular and branched circular concatemeric structures that likely arose by  rolling circle replication .


When assembling concatemers from synthetic oligonucleotides, increasing salt concentration to 200 mM was found to be a major optimizing factor due to its ability to enhance ionic strength, which hastened the formation of concatemers. [ 4 ]


In  genetics , two  organisms  that differ in only one  locus  and a linked segment of chromosome are defined as  congenic . [ 1 ]  Similarly, organisms that are  coisogenic  differ in one locus only and not in the surrounding chromosome. Unlike congenic organisms, coisogenic organisms cannot be bred and only occur through spontaneous or targeted mutation at the locus.


Congenic  strains  are generated in the laboratory by mating two inbred strains (usually rats or mice), and back-crossing the descendants 5–10 generations with one of the original strains, known as the  recipient  strain. Typically selection for either phenotype or genotype is performed prior to each back-cross generation. In this manner either an interesting phenotype, or a defined chromosomal region assayed by genotype, is passed from the  donor  strain onto an otherwise uniform  recipient  background.  Congenic mice or rats can then be compared to the pure recipient strain to determine whether they are phenotypically different if selection was for a genotypic region, or to identify the critical genetic locus, if selection was for a phenotype.


Speed congenics can be produced in as little as five back-cross generations, [ 2 ]  through the selection at each generation of offspring that not only retain the desired chromosomal fragment, but also 'lose' the maximum amount of background genetic information from the donor strain. This is also known as  marker-assisted  congenics, due to the use of genetic markers, typically  microsatellite  markers, but now, more commonly,  single nucleotide polymorphism  markers (SNPs). The process can be further aided by the  superovulation  of females, to produce many more eggs.


Congenic strains are discussed in detail in Lee Silver's online book  Mouse Genetics: Concepts and Applications :


Constitutive ablation  refers to  gene expression  which results in  cell death . [ 1 ]  Constitutive cell ablation can be induced by  diphtheria toxin  (DT) in zebrafish. [ 2 ]


CHLC  (or Cooperative Human Linkage Center) was a  National Institutes of Health  project to map a large number of human genome  markers , prior to the completion of the  Human Genome Project . The project was stopped in 1999.


The  Core binding factor  (CBF) is a group of  heterodimeric   transcription factors .


Core binding factors are composed of:


C 0 t filtration , or  CF , is a technique that uses the principles of DNA renaturation kinetics ( i . e .  Cot analysis ) to separate the  repetitive DNA   sequences  that dominate many  eukaryotic   genomes  from "gene-rich" single/low-copy sequences. [ 1 ] [ 2 ]  This allows DNA sequencing to concentrate on the parts of the genome that are most informative and interesting.


Briefly, when sheared genomic DNA in solution is heated to near  boiling temperature , the  molecular  forces holding complementary  base pairs  together are disrupted, and the two strands of each  double-helix   dissociate  or ‘denature.’  If the  denatured  DNA is then slowly returned to a cooler  temperature , sequences will begin to ‘reassociate’ (renature) with complementary strands.


The temperature at which renaturation occurs can be regulated so that little or no sequence mismatch is tolerated.  The rate at which a sequence finds a complementary strand with which to  hybridize  is directly related to how common that sequence is in the genome.  In other words, those sequences that are extremely abundant (on average) find complementary strands with which to pair relatively quickly while single-copy sequences take much longer to find complements.


In CF, genomic DNA is heat-denatured and allowed to renature to a  Cot value  (Cot = DNA  concentration  x time x a factor based on the  cation  concentration of the buffer) at which the majority of repetitive elements have reassociated but single and low-copy elements remain single stranded.   Double-stranded , repetitive DNA is separated from single-stranded, low-copy DNA by  hydroxyapatite   chromatography  or other means.


CF allows the single/low copy sequences and the repetitive sequences of a genome to be studied independently of each other.  It can also be used to fractionate highly repetitive DNA from moderately repetitive sequences or to further fractionate isolated kinetic components.  CF is most accurately performed if  fractionation  is based upon the results of a Cot analysis.


The capsule biosynthesis, or  CPS operon , is a  section  of the  genome  present in some  Escherichia coli , of which regulates the production of  polysaccharides  making up the  bacterial capsule . [ 1 ]  These polysaccharides help protect the  bacteria  from harsh environments, toxic chemicals, and  bacteriophages .


The CPS operon contains genes which code for the following proteins:


The CPS operon is likely  transcriptionally  regulated by the Rcs (regulation of capsule synthesis) proteins. [ 1 ]  Reduced levels of membrane-derived  oligosaccharides  result in autophosphorylation of RcsC. This results in a phosphate group being transferred from RcsC to RcsB. RcsB then binds to RcsA, forming a complex which acts on the CPS promoter and activates transcription of the CPS genes.


The same operon is present in  Klebsiella  species, possibly as a result of  horizontal gene transfer . [ 1 ]


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


In  genetics , the  crossover value  is the linked frequency of  chromosomal crossover  between two  gene  loci ( markers ). For a fixed set of genetic and environmental conditions,  recombination  in a particular region of a linkage structure ( chromosome )  tends to be constant and the same is then true for the crossover value which is used in the production of  genetic maps . [ 1 ] [ 2 ]


Crossover implies the exchange of chromosomal segments between non-sister  chromatids , in  meiosis  during the production of  gametes . The effect is to assort the  alleles  on parental chromosomes, so that the gametes carry  recombinations  of  genes  different from either parent. This has the overall effect of increasing the variety of  phenotypes  present in a population.


The process of non-sister  chromatid exchanges, including the crossover value, can be observed directly in stained  cells , and indirectly by the presence or absence of  genetic markers  on the chromosomes. The visible  crossovers  are called  chiasmata .


The large-scale effect of crossover is to spread  genetic variations  within a population, as well  as genetic basis for the selection of the most adaptable  phenotypes . The crossover value depends on the mutual distance of the genetic  loci  observed. The crossover value is equal to the recombination value or fraction when the distance between the markers in question is short.


In  population genetics ,  cryptic relatedness  occurs when individuals in a  genetic association  study are more closely related to another population than assumed by the investigators. This can act as a  confounding factor  in both  case-control  and  genome-wide  association studies, [ 1 ] [ 2 ]  as well as in studies of  genetic diversity . Along with  population stratification , it is one of the most prominent confounding factors that can lead to inflated  false positive  rates in gene-association studies. [ 3 ] [ 4 ]  It is often corrected for by including a  polygenic  component in the  statistical model  being used to detect genetic associations. [ 5 ]  Other approaches that have been developed to attempt to control for cryptic relatedness are the  genomic control  method and the use of extended  likelihood ratio tests . [ 6 ]


Cytochrome P450, family 6 , also known as  CYP6 , is a  cytochrome P450   family  found in  Insect   genome . CYP6 and  CYP9 , another insect CYP family, belong to the same clan as mammalian  CYP3  and  CYP5  families. [ 1 ]


The first two CYP6 subfamilies represented by  CYP6A1  and  CYP6B1  shared only 32.7% identity, [ 2 ]  less than the typical CYP subfamilies, which share at least 40% amino acid identity. [ 3 ]


Many of the  enzymes  in this family like  CYP6G1  ( DDT -R) in  Drosophila melanogaster [ 4 ]  and  CYP6B  in  Helicoverpa armigera [ 5 ]  are related to  insecticide resistance .


Cytochrome P450, family 9 , also known as  CYP9 , is a  cytochrome P450   family  found in  Insect   genome , [ 1 ] [ 2 ]  CYP9 and insect  CYP6 family  belong to the same clan as mammalian  CYP3  and  CYP5  families. [ 3 ]  The first gene identified in this family is the  CYP9A1  from the  Heliothis virescens  ( tobacco budworm ), which is involved in  thiodicarb   insecticide resistance . [ 4 ]  Subfamily  CYP9A  in  Lepidopteran  play important roles in insecticide resistance, can metabolize  esfenvalerate  efficiently. [ 5 ]


Cytochrome P450, family 10 , also known as  CYP10 , is a  cytochrome P450   family  found in  Lophotrochozoa  belongs to  Mitochondrial clan  CYP s , which is located in the  inner membrane  of  mitochondria (IMM). The first gene identified in this family is the  CYP10A1  from the  Lymnaea stagnalis  ( pond snail ), which is highly expressed in the female  gonadotropic hormone  producing  dorsal bodies . [ 1 ]


Cytochrome P450, family 11 , also known as  CYP11 , is a  chordate   cytochrome P450   monooxygenase   family . This family contains many  enzymes involved in steroidogenesis , such as  Cholesterol side-chain cleavage enzyme  (CYP11A1),  Steroid 11β-hydroxylase  (CYP11B1) and  Aldosterone synthase  (CYP11B2). [ 3 ]  CYP11 can be divided into A to E five subfamilies, [ 4 ]  and CYP11A are the  ohonologues  to CYP11C, which  duplicated  during  2R event , and the  tetrapod 's CYP11B evolved from CYP11C of its  fish  ancestors, [ 2 ]  CYP11D and F found in  amphioxus . [ 4 ]  These are not the typical CYP subfamilies, which share at least 40% amino acid identity, [ 5 ]  members between CYP11A and B subfamily are only 37.5-38.8% identical, [ 6 ]  and the CYP11D and E genes seen in modern  lancelet  ( Branchiostoma floridae , an ancient branch of chordate animals) is 39% identical to  catfish  CYP11A1. [ 2 ] [ 4 ]


The  Cyp11a2  is a  fish   gene  encoding a  CYP450   monooxygenase , [ 1 ]  which was originally identified in  Zebrafish  ( Danio rerio ), [ 2 ]  is the  isozyme  and  paralogous  of fish  CYP11A1 , catalyzes conversion of  cholesterol  to  pregnenolone . [ 3 ]


Cytochrome P450, family 12 , also known as  CYP12 , is a  cytochrome P450   family  found in  insect   genome  belongs to  Mitochondrial clan  CYP s , which is located in the  inner membrane  of  mitochondria (IMM). [ 1 ] [ 2 ]  The first gene identified in this family is the  CYP12A1  from the  Musca domestica  ( house fly ), which is involved in  insecticide resistance . [ 3 ]  CYP12A1 protein localization in  mitochondria  by  immunohistochemistry  and absolute dependence on mitochondrial  electron donors   adrenodoxin reductase  and  adrenodoxin . [ 3 ]


Rabbit   gene   CYP8B1  was named CYP12 at the beginning of its discovery, because it hydroxylated its  sterol   substrate  on the 12 position. [ 4 ]  However, CYP12 is a family of insect P450s found in mitochondria, so this gene was renamed to CYP8B1. [ 5 ]


Cytochrome P450, family 13 , also known as  CYP13 , is a  nematoda   cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP13A1  from the  Caenorhabditis elegans .


CYP13 can be divided into subfamily  CYP13A  and  CYP13B , [ 1 ]  and the CYP13B was named  CYP16 family  at the beginning of its discovery, which have been discontinued and been changed to the current name, because its genetic relationship with the subfamily CYP13A. [ 2 ]


Cytochrome P450, family 14 , also known as  CYP14 , is a  nematoda   cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP14A1  from the  Caenorhabditis elegans . [ 2 ]  The function of most genes in this family is unknown. [ 3 ]


Cytochrome P450, family 15 , also known as  CYP15 , is an  animal   cytochrome P450   family  found in  insect   genome , [ 1 ]  involved in  juvenile hormone   biosynthesis . [ 2 ]  The first gene identified in this family is the DpCYP15A1 from the  Diploptera punctata  ( Pacific beetle cockroach ), encodes an  epoxidase  of  methyl farnesoate , a  precursor  of  juvenile hormone , alone with its ortholog TcCYP15A1 in  Tribolium castaneum  ( red flour beetle ). [ 3 ]


Cytochrome P450, family 16 , also known as  CYP16 , is an  animal   cytochrome P450   monooxygenase   family . This family was the last  vertebrate  CYP family recognized, [ 1 ]  and is absent from the  mammal  and  zebrafish  genome, but found in other  fish  and many  invertebrates  including some very old branches, such as  Trichoplax  and  Oscarella carmela .  Synteny  mapping of CYP16 family members showing linkages to  CYP26  family members, means the  tetrapod 's CYP26 may evolved from CYP16 of fish. [ 2 ]


In the past, CYP16 family refers to some  nematoda  ( roundworms )  genes , which have been discontinued and changed to the Cytochrome P450, family 13, subfamily B ( CYP13B ), because its genetic relationship with the subfamily  CYP13A . [ 3 ]


Cytochrome P450, family 18 , also known as  CYP18 , is an animal  cytochrome P450   family  found in  insect   genomes . [ 1 ]  It is involved in  insecticide resistance . [ 2 ]  The first member gene identified was CYP18A1, from a  Drosophila melanogaster  fly, acting as a  dimethylnitrosamine   demethylase . [ 3 ]


Cytochrome P450, family 23 , also known as  CYP23 , is a  nematoda   cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP23A1  from the  Caenorhabditis elegans , [ 2 ] [ 3 ]  is a  homolog  of the human gene  CYP7B1 . [ 4 ]


Cytochrome P450, family 25 , also known as  CYP25 , is a  nematoda   cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP25A1  from the  Caenorhabditis elegans . [ 2 ]


Cytochrome P450, family 26 , also known as  CYP26 , is an  mammal   cytochrome P450   monooxygenase   family  found in  human genome . [ 1 ]  There are three members in the human genome,  CYP26A1 ,  CYP26B1  and  CYP26C1 . [ 2 ] [ 3 ]   Synteny  mapping of CYP26 family members showing linkages to  CYP16  family members of many  invertebrates , means the  tetrapod 's CYP26 may evolved from CYP16 of fish. [ 4 ]


Cytochrome P450, family 27 , also known as  CYP27 , is a  Deuterostome   cytochrome P450   monooxygenase   family  found in  human genome . [ 1 ] [ 2 ]  This family belongs to  Mitochondrial clan  CYP s , which is located in the  inner membrane  of  mitochondria (IMM). There are three members in the human genome,  CYP27A1 ,  CYP27B1  and  CYP27C1 , [ 3 ]  and an ortholog CYP27F1 in  sea urchins ,  Strongylocentrotus purpuratus . [ 4 ]


Cytochrome P450, family 52 , also known as  CYP52 , is a  cytochrome P450   family  in fungi participate in the  assimilation  of  alkanes  and  fatty acids , which the most ancient function was the  oxidation  of C4-C11 alkanes. [ 1 ]  The first gene identified in this family is the alkane-inducible cytochrome P450 (P450alk) gene from the  yeast   Candida tropicalis , with CYP Symbol  CYP52A1 . [ 2 ]


Cytochrome P450, family 53 , also known as  CYP53 , is a  cytochrome P450   monooxygenase   family  in  fungi  related to  hydrocarbon   assimilation . [ 1 ]  They are distributed in both  Ascomycota  and  Basidiomycota , could be used as  anti-fungal drug  target. [ 2 ]  The first gene identified in this family is the  CYP53A1  from  Aspergillus niger  encoding the  Benzoate 4-monooxygenase  (bphA). [ 3 ]


Cytochrome P450, family 55 , also known as  CYP55 , is a  cytochrome P450   family  in  fungi  supposed to derived from  horizontal gene transfer  of  Actinomycetes   CYP105 family  member in the ancestor of all  Dikarya  ( Ascomycota  and  Basidiomycota ). [ 1 ] [ 2 ]  The first gene identified in this family is the  CYP55A1  from  Fusarium oxysporum  encoding the  NADPH  dependent  reductase  of  nitrous oxide  ( P450nor cytochrome P450nor ). [ 3 ] [ 4 ]


Cytochrome P450, family 74 , also known as  CYP74 , is a  cytochrome P450   family  in land  plant  supposed to derived from  horizontal gene transfer  of marine  animal  CYPs. [ 1 ] [ 2 ]


Cytochrome P450, family 76 , also known as  CYP76 , is a  cytochrome P450   family  in land  plants , [ 1 ] [ 2 ]  related to the  biosynthesis  of many plant  monoterpenes  and  diterpenes  such as  8-hydroxygeraniol , [ 3 ] [ 2 ]   tanshinone  and  alkannin . [ 4 ] [ 5 ]  The first gene identified in this family is the  CYP76A1  and  CYP76A2  from the  eggplant . [ 1 ]


Cytochrome P450, family 105 , also known as  CYP105 , is a  cytochrome P450   monooxygenase   family  in  bacteria , predominantly found in the  phylum   Actinomycetota  and the  order   Actinomycetales . [ 2 ] [ 3 ]  The first three genes and subfamilies identified in this family is the  herbicide -inducible  P-450SU1  ( CYP105A1 , subfamily  A )  and P-450SU2 ( CYP105B1 , subfamily  B ) from  Streptomyces griseolus [ 4 ] [ 5 ]  and choP ( CYP105C1 , subfamily  C ) from  Streptomyces sp ' s  cholesterol oxidase   promoter region . [ 6 ] [ 1 ]


CYP105 enzymes is widely used in industry, such as the production of  pravastatin . [ 3 ]


Cytochrome P450, family 107 , also known as  CYP107 , is a  cytochrome P450   monooxygenase   family  in  bacteria , [ 2 ] [ 1 ]  found to be conserved and highly populated in  Streptomyces  and  Bacillus  species. [ 3 ]  The first gene identified in this family is  Cytochrome P450 eryF  (CYP107A1) from  Saccharopolyspora erythraea . [ 4 ]  Many enzymes of this family are involved in the synthesis of  macrolide   antibiotics . [ 2 ] [ 5 ]  The members of this family are widely distributed in  Alphaproteobacteria ,  cyanobacterial ,  Mycobacterium ,  Bacillota , and  Streptomyces  species, which may be due to  horizontal gene transfer  driven by  selection pressure . [ 6 ]


Cytochrome P450, family 109 , also known as  CYP109 , is a  cytochrome P450   monooxygenase   family , [ 1 ]  many members are associated with fatty acid hydroxylation. [ 2 ]  The first gene identified in this family is the  CYP109A1  and  CYP109B1  from  Bacillus subtilis . [ 3 ]  CYP109 is one of the only three P450 families shared in  bacteria  and  archaea , the other two are  CYP147  and  CYP197 . [ 1 ]  Genes in this family are co-present on archaeal  plasmids  and chromosomes, implying the plasmid-mediated  horizontal gene transfer  of these genes from bacteria to archaea. [ 1 ]


Cytochrome P450, family 123 , also known as  CYP123 , is a  cytochrome P450   monooxygenase   family  in  bacteria . The first gene in this family to identify function is  CYP123A9  from  Rhodococcus  sp, which catalysis  estrone  to  16-hydroxyestrone  in the  estradiol  degradation pathway of  bacteria . [ 1 ]


Cytochrome P450, family 139 , also known as  CYP139 , is a  cytochrome P450   monooxygenase   family  in  bacteria . The first gene identified in this family is  CYP139A1  from  Mycobacterium tuberculosis . Most member of this family belonged to the subfamily A, and involved in the synthesis of secondary  metabolites  in many  mycobacterial  species. [ 1 ]


Cytochrome P450, family 147 , also known as  CYP147 , is a  cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP147B1  from  Streptomyces avermitilis . CYP147 is one of the only three P450 families shared in  bacteria  and  archaea , the other two are  CYP197  and  CYP109 . [ 1 ]


Cytochrome P450, family 197 , also known as  CYP197 , is a  cytochrome P450   monooxygenase   family . [ 1 ]  The first gene identified in this family is the  CYP197A1  from  Bacillus halodurans . [ 2 ]  CYP197 is one of the only three P450 families shared in  bacteria  and  archaea , the other two are  CYP147  and  CYP109 . [ 1 ]  Genes in this family are co-present on archaeal  plasmids  and chromosomes, implying the plasmid-mediated  horizontal gene transfer  of these genes from bacteria to archaea. [ 1 ]


Cytochrome P450, family 305 , also known as  CYP305 , is an  animal   cytochrome P450   family  found in  insect   genome . [ 1 ] [ 2 ]  The first gene identified in this family is the CYP305A1 from the  Drosophila melanogaster  ( Fruit fly ). [ 3 ] [ 4 ]


Cytochrome P450, family 710 , also known as  CYP710 , is a  plant   cytochrome P450   monooxygenase   family , the proteins encoded by its family members are mainly  sterol  22-desaturase, which was widely distributed in plants, [ 1 ]  and take participate in  Phytosteroidogenesis . [ 2 ]  CYP710 family is considered to be the plant  orthologous  of fungi  CYP61  family, which is lost in  animal . [ 3 ]  The CYP61/CYP710 ancestor gene diverged from a  gene duplication  of ancestor  CYP51  in early  eukaryotes [ 4 ]


The following table summarizes symbols and abbreviations used in  cytogenetics : [ 1 ] [ 2 ]


Cytonuclear discordance  describes the discrepancy in  phylogenetic  relationships using  mitochondrial DNA  (mtDNA) versus nuclear genes (or  nuclear DNA , nDNA). In other words, mitochondrial and nuclear gene sequences may lead to different, if not contradictory, phylogenetic trees that show the relationships among  species . In theory, nuclear DNA and mtDNA sequences should lead to similar phylogenetic tree topologies among species but this is often not the case.


Other terms for the concept are  Nuclear-mitochondrial discordance  or  mito-nuclear discordance .


An example are Australian  rock-wallabies  ( Petrogale ) in which several species form a monophyletic group with nDNA genes, but not with mtDNA. This cytonuclear discordance involves at least four  operational taxonomic units  (OTUs) across four species. [ 1 ]


Another example is the relationship among grasshoppers ( Orthoptera ). Phylogenies based on complete mitogenomes recovered some species as para- or polyphyletic. By contrast, a phylogeny based on nuclear genes derived from  transcriptomic  data retrieved all species as monophyletic clusters. [ 2 ]


Many other taxonomic groups display cytonuclear discordance, e.g.  Burmese pythons [ 3 ]  or vipers of the genus  Cerastes . [ 4 ]


The  D arm  is a feature in the  tertiary structure  of  transfer RNA  (tRNA). It is composed of the two D stems and the D loop. The D loop contains the base  dihydrouridine , for which the arm is named. [ 1 ]  The D loop's main function is that of recognition. It is widely believed that it acts as a recognition site for  aminoacyl-tRNA synthetase , an  enzyme  involved in the  aminoacylation  of the tRNA molecule. [ 1 ] [ 2 ]  The D stem is also believed to have a recognition role although this has yet to be verified.


It is a highly variable region and is notable for its unusual conformation due to the over-crowding on one of the  guanosine  residues. It appears to play a large role in the stabilization of the tRNA's tertiary structure.


A  de Finetti diagram  is a  ternary plot  used in  population genetics . It is named after the  Italian   statistician   Bruno de Finetti  (1906–1985) and is used to graph the  genotype frequencies  of  populations , where there are two  alleles  and the population is  diploid . It is based on an  equilateral triangle , and  Viviani's theorem : the sum of the perpendicular distances from  any  interior point to the sides of said triangle is a constant equal to the length of the triangle's  altitude .


The de Finetti diagram is used extensively in  A.W.F. Edwards ' book " Foundations of Mathematical Genetics" .  The sum of the lengths, representing allele frequencies, is set to be 1.  In its simplest form the diagram can be used to show the range of genotype frequencies for which  Hardy–Weinberg equilibrium  is satisfied (the curve within the diagram).  A. W. F. Edwards and  Chris Cannings  extended its use to demonstrate the changes that occur in allele frequencies under  natural selection .


This  applied mathematics –related article is a  stub . You can help Wikipedia by  expanding it .


A  de novo mutation  (DNM) is any mutation or alteration in the genome of an individual organism (human, animal, plant, microbe, etc.) that was not inherited from its parents. This type of mutation spontaneously occurs during the process of  DNA replication  during  cell division . De novo mutations, by definition, are present in the affected individual but absent from both biological parents' genomes. These mutations can occur in any cell of the offspring, but those in the germ line (eggs or sperm) can be passed on to the next generation. [ 1 ]


In most cases, such a mutation has little or no effect on the affected organism due to the redundancy and robustness of the genetic code. However, in rare cases, it can have notable and serious effects on overall health, physical appearance, and other traits. Disorders that most commonly involve  de novo mutations  include  cri-du-chat syndrome ,  1p36 deletion syndrome , genetic  cancer syndromes , and certain forms of  autism , among others. [ 2 ]


The rate at which de novo mutations occur is not static and can vary among different organisms and even among individuals. In humans, the average number of spontaneous mutations (not present in the parents) an infant has in its genome is approximately 43.86. [ 3 ]


Various factors can influence this rate. For instance, a study in September 2019 by the  University of Utah Health  revealed that certain families have a higher spontaneous mutation rate than average. This finding indicates that the rate of de novo mutation can have a hereditary component, suggesting that it may "run in the family". [ 4 ]


Additionally, the age of parents, particularly the paternal age, can significantly impact the rate of de novo mutations. Older parents, especially fathers, tend to have a higher risk of having children with de novo mutations due to the higher number of cell divisions in the male germ line as men age. [ 5 ]


In genetic counselling, parents are often told that after having a first child with a condition caused by a de novo mutation the risk of a having a second child with the same mutation is 1 – 2%. However, this does not reflect the variation in risk among different families due to  genetic mosaicism . A personalised risk assessment can now quantify people's risk, and found that the risk for most people is less than 1 in 1000. [ 6 ] [ 7 ]


De novo mutations play a crucial role in evolution by providing new genetic variation upon which natural selection can act. They serve as a primary source of genetic diversity, enabling species to adapt to changing environments over time. [ 8 ]


This comes from two Latin words:


Chromosome 17p13.1 deletion syndrome  is a  phenotype  in humans that is designed DEL17P13.1. [ 1 ] [ 2 ]


In  genetics  and especially  genetic engineering ,  deletion mapping  is a technique used to find out the  mutation  sites within a  gene .


The principle of deletion mapping involves crossing a strain which has a  point mutation  in a gene, with multiple strains who each carry a  deletion  in a different region of the same gene. Wherever  recombination  occurs between the two strains to produce a  wild-type  (+) gene (regardless of frequency), the point mutation cannot lie within the region of the deletion. If recombination cannot produce any wild-type genes, then it is reasonable to conclude that the point mutation and deletion are found within the same stretch of  DNA .


This example should demonstrate how the principle works:


Suppose you have a  gene X , which in wild-type (+) form can be shown linearly like so:


5'-------------------------------------------------------------------------------------------------------------------3'  gene X, +


Suppose a strain of organisms has a point mutation in the gene (now called  gene X, –  to denote that it is no longer wild-type):


5'----------------------------------------------------X--------------------------------------------------------------3'  gene X, –


Now suppose you have two strains of organisms, each with deletions in gene X at different sites, called  del-1  and  del-2 , respectively (the dotted line indicates the site of deletion):


5'-------------------(..............................................)------------------------------------------------3'  del-1


5'------------------------------------------------------------(............................................)---------3'  del-2


Because the point mutation lies within the deletion of del-1, there will be no wild-type (+) recombinants between the point mutant and the del-1 mutant. However, in a cross between the point mutant and the del-2 mutant, there could be a successful wild-type (+) recombinant produced.


In genetic recombination, if a mutant allele in the donor is within the sequence corresponding to the region deleted in the recipient, then no (+) recombinants will be obtained (as in the cross with del-1). To repair a deletion by recombination, the donor must have wild-type DNA sequence in the region corresponding to the DNA deleted in the recipient (as in the cross against del-2). In other words, there is a feasible recombination possibility between the point mutant and del-2 in which a length of DNA could be made that contained neither the point mutation, nor the deletion, indicating that the mutations in these two strains cannot be in the same region.


Note that not all crossovers between the point mutant and del-2 will yield (+) recombinants; in this case only those crossover events that occur between the point mutant and the 5' end of the deletion would inherit the wild-type sequence.


" Desoxyribonucleic acid " and "desoxyribonucleate" are archaic terms for  DNA ,  deoxyribonucleic acid , and its salts, respectively.  The terms are used in this sense in various classic papers in  genetics , such as Avery, MacLeod, and McCarty (1944). [ 1 ]


Direct repeats  are a type of genetic sequence that consists of two or more repeats of a specific sequence. [ 1 ]  In other words, the direct repeats are  nucleotide  sequences present in multiple copies in the  genome . Generally, a direct repeat occurs when a sequence is repeated with the same pattern downstream. [ 1 ]   There is  no inversion [ clarification needed ]  and no  reverse complement  associated with a direct repeat. It may or may not have intervening nucleotides. The nucleotide sequence written in bold characters signifies the repeated sequence.


Linguistically, a typical direct repeat is comparable to saying "bye-bye". [ 1 ]


There are several types of repeated sequences:


A tract of  repetitive DNA  in which a motif of a few base pairs is tandemly repeated numerous times (e.g. 5 to 50 times) is referred to as  microsatellite  DNA.  Thus direct repeat tandem sequences are a form of microsattelite DNA.  The process of  DNA mismatch repair  plays a prominent role in the formation of direct trinucleotide repeat expansions. [ 2 ]   Such repeat expansions underlie several neurological and developmental disorders in humans. [ 2 ]


In directly repeated sequences of the  tobacco  plant  genome ,  DNA double-strand breaks  can be efficiently repaired by  homologous recombination  between the repeated sequences. [ 3 ]


A  DNA analyzer  is a device used to determine characteristics of a person's  DNA . For example,  genetic fingerprinting  can be conducted with a portable DNA analyzer. [ 1 ]


National DNA Day  is a United States holiday  celebrated  on April 25. It commemorates the day in 1953 when  James Watson ,  Francis Crick ,  Maurice Wilkins ,  Rosalind Franklin  and colleagues published papers in the journal  Nature  on the structure of  DNA . [ 1 ] [ 2 ] [ 3 ]  Furthermore, in early April 2003 it was declared that the  Human Genome Project  was very close to complete, and "the remaining tiny gaps were considered too costly to fill." [ 4 ] [ 5 ]


In the  United States , DNA Day was first celebrated on April 25, 2003, by proclamation of both the  Senate [ 6 ]  and the  House of Representatives . [ 7 ]  However, they only declared a one-time celebration, not an annual holiday. Every year from 2003 onward, annual DNA Day celebrations have been organized by the  National Human Genome Research Institute  (NHGRI), starting as early as April 23 in 2010, April 15 in 2011 [ 8 ]  and April 20 in 2012. [ 9 ]  April 25 has since been declared "International DNA Day" [ 10 ] [ 11 ] [ 12 ]  and "World DNA Day" [ 13 ] [ 14 ]  by several groups.


Genealogical DNA testing  companies and  genetic genealogy  publishers run annual sales around DNA Day, seeking interest from the public and promoting their services. [ 15 ]


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


DNA ligase (NAD + )  ( EC   6.5.1.2 ,  polydeoxyribonucleotide synthase (NAD + ) ,  polynucleotide ligase (NAD + ) ,  DNA repair enzyme ,  DNA joinase ,  polynucleotide synthetase (nicotinamide adenine dinucleotide) ,  deoxyribonucleic-joining enzyme ,  deoxyribonucleic ligase ,  deoxyribonucleic repair enzyme ,  deoxyribonucleic joinase ,  DNA ligase ,  deoxyribonucleate ligase ,  polynucleotide ligase ,  deoxyribonucleic acid ligase ,  polynucleotide synthetase ,  deoxyribonucleic acid joinase ,  DNA-joining enzyme ,  polynucleotide ligase (nicotinamide adenine dinucleotide) ) is an  enzyme  with  systematic name   poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming) . [ 1 ]  This enzyme  catalyses  the following  chemical reaction


Catalyses the formation of a  phosphodiester  at the site of a single-strand break in duplex DNA.


DNA Repair and Mutagenesis  is a college-level textbook about  DNA repair  and  mutagenesis  written by  Errol Friedberg , Graham Walker, Wolfram Siede,  Richard D. Wood , and Roger Schultz. [ 1 ]  In its second edition as of 2009,  DNA Repair and Mutagenesis  contains over 1,000 pages, 10,000 references and 700 illustrations and has been described as "the most comprehensive book available in [the] field." [ 2 ] [ 3 ]


DNA‐templated organic synthesis  (DTS) is a way to control the  reactivity  of synthetic molecules by using nature's  molarity ‐based approach. Historically, DTS was used as a model of  prebiotic   nucleic acid  replication. Now however, it is capable of translating  DNA sequences  into complex small‐molecule and  polymer  products of multistep  organic synthesis . [ 1 ]


The  DNA base editors , developed at  Harvard University  under  David Liu , allow altering the genomic structure of  DNA . The base editors include BE3, BE4 and ABE7.


BE3 and its later version, BE4 allow to change the  nucleobase  C to T and nucleobase G to A. ABE7 allows to change A-T base pairs into G-C base pairs. The system works by rearranging the  atoms  in the target base pair and then tricking cells into fixing the other DNA strand to make the change permanent. [ 2 ] [ 3 ] [ 4 ] [ 5 ]


In  genetics ,  dyad symmetry  refers to two areas of a  DNA  strand whose base pair sequences are  inverted repeats  of each other. They are often described as  palindromes .


For example, the following shows dyad symmetry between sequences GAATAC and GTATTC which are reverse complements of each other.


Since the two reverse complementary sequences will fold and base-pair with each other, the sequence of bases between them form a  hairpin loop . This structure is thought to destabilize the binding of  RNA polymerase  enzyme to DNA (hence terminating  transcription ). Dyad symmetry is known to have a role in the  rho independent method of transcription termination  in  E. coli .  [ citation needed ]  Regions of dyad symmetry in the DNA sequence stall the RNA polymerase  enzyme  as it transcribes them.


Temperate  bacteriophages  integrate into the host  genome  at specific interrupted dyad symmetry sequences using the phage encoded enzyme integrase (see  prophage integration ). [ 1 ]


The  E-site  is the third and final  binding site  for  t-RNA  in the  ribosome  during  translation , a part of  protein synthesis . [ 1 ]   The "E" stands for exit, and is accompanied by the  P-site  (for peptidyl) which is the second binding site, and the  A-site  (aminoacyl), which is the first binding site. It is involved in  cellular processes . [ 2 ]


The  echinoderm and flatworm mitochondrial code  (translation table  9 ) is a  genetic code  used by the  mitochondria  of certain  echinoderm  and  flatworm  species. [ 1 ]


This article incorporates text from the  United States National Library of Medicine , which is in the  public domain .
 [ 1 ]


Ecological Genetics  is a 1964 book by the British biologist  E. B. Ford  on  ecological genetics . Ford founded the field and it is considered his  magnum opus . The fourth and final  edition  was published in 1975.


Ford's work was celebrated in 1971 by  Ecological Genetics and Evolution , a series of essays edited by Robert Creed, publ. Blackwell, Oxford. This included contributions from  Cyril Darlington ,  Miriam Rothschild ,  Theodosius Dobzhansky ,  Bryan Clarke ,  A.J. Cain , Sir  Cyril Clarke  and others.


Ford and  Ronald Fisher  represented one side of a dispute with the American  Sewall Wright  over the relative roles of  selection  and  drift  in  evolution . [ 1 ]


Ecological Genetics  had also Polish [ 2 ]  and French [ 3 ] [ 4 ]  editions.


This article about a book on  ecology  is a  stub . You can help Wikipedia by  expanding it .


In  population genetics ,  ecotypic variation  is the type of genetic variation found in large, continuous geographic populations. Variation of this kind is  homogeneous , due to factors such as  gene flow . In 1954  Ernst Mayr  wrote a landmark paper attacking the idea that subspecies in ecotypic populations would lead to the formation of incipient species. [ 1 ]  According to Mayr, species formation occurs in populations which are small and isolated, that is, populations which exemplified  typostrophic variation .


Effective number of codons  (abbreviated as  ENC  or  Nc ) is a measure to study the state of  codon usage biases  in genes and genomes. [ 1 ]  The way that ENC is computed has obvious similarities to the computation of  effective population size  in  population genetics . [ 2 ]  Although it is easy to compute ENC values, it has been shown that this measure is one of the best measures to show codon usage bias. [ 3 ]


Since the original suggestion of the ENC, several investigators have tried to improve the method, [ 4 ] [ 5 ]  but it seems that there is much room to improve this measure. [ 6 ] [ 7 ] [ 8 ] [ 9 ] [ 10 ] [ 11 ]


EHA101  was one of the first and most widely used  Agrobacterium   helper plasmid  for plant gene transfer. Created in 1985 in the laboratory of  Mary-Dell Chilton  at  Washington University in St. Louis , it was named after the  graduate student  who constructed it.  The EH stands for "Elizabeth Hood" and A for " Agrobacterium ". The EHA101 helper strain is a derivative of A281, the hypervirulent  A. tumefaciens  strain that causes large, fast-growing tumors on  solanaceous  plants. [ 1 ] [ 2 ]  This strain is used for moving genes of interest into many hundreds of species of plants all over the world.


For  recalcitrant  crops such as  maize ,  wheat , and  rice , the EHA helper strains are often employed for gene transfer. [ 3 ] [ 4 ] [ 5 ]  These strains are efficient at promoting T-DNA transfer because of the hypervirulence of the  vir genes [ 2 ]  suggesting that a higher success rate can be achieved on these "hard to transform" crops or  cultivars .


The chromosomal background of EHA101 is C58C1, a cured  nopaline  strain. [ 1 ]  The helper strains were derived from A281, which is A136(pTiBo542). A281 was genetically engineered through a double crossover, site-directed deletion to yield EHA101, a T-DNA deleted strain useful for target gene transfer into plants. [ 2 ]  EHA101 is resistant to  kanamycin  by way of an npt I gene in place of T-DNA. The parent strain, A281, does not show  antibiotic resistances  at higher levels than normal  A. tumefaciens  strains. Moreover, other transconjugant strains in the C58C1 background, do not show these increased resistances to antibiotics. Therefore, these characteristics are not simply a manifestation of the chromosomal background, but most likely an interaction of this Ti plasmid and the C58 chromosomal background.


The npt I gene in place of the T-DNA in EHA101 requires that binary plasmids that are put into the strain encode a drug resistance other than kanamycin. Strains EHA105 was generated from EHA101 through  site-directed deletion  of the kanamycin resistance gene from the Ti plasmid, otherwise the strains are identical. [ 6 ]  This latter strain has been useful to plant biotechnologists who use kanamycin as a selectable marker on their binary plasmids.


Electroelution  is a method used to extract a  nucleic acid  or a  protein  sample from an  electrophoresis   gel  by applying a negative  current  in the plane of the smallest dimension of the gel, drawing the  macromolecule  to the surface for extraction and subsequent analysis. [ 2 ]
For example,  electroblotting  and  preparative native PAGE  are based upon the same  principle . [ 3 ] [ 4 ]


Using this method,  DNA  fragments can be recovered from a particular region of  agarose  or  polyacrylamide  gels. The gel piece containing the fragment is excised (cut out from the whole gel) and placed in a  dialysis  bag with  buffer . Electrophoresis causes the DNA to migrate out of the gel into the dialysis bag buffer. The DNA fragments are recovered from this buffer and purified, using  phenol–chloroform extraction  followed by  ethanol precipitation . This method is simple, rapid and yields high recovery (75%) of DNA fragments from gel pieces. [ 3 ]


Proteins are continuously  eluted  from a gel column and separated in different fractions according their  isoelectric point . [ 1 ]  Preparative native PAGE yields more than 95% recovery of  metalloproteins . [ 4 ]


The  Electronic Medical Records and Genomics Network  (abbreviated the  eMERGE Network ) is a consortium of American medical institutions dedicated to advancing the use of  electronic medical records  for  genomics  research. It was established in 2007 and is funded by the  National Human Genome Research Institute  (NHGRI). [ 1 ]  eMERGE's Administrative Coordinating Center is located at  Vanderbilt University Medical Center . [ 2 ]


eMERGE's first phase, known as eMERGE-I, began after the NHGRI awarded grants to five institutions:  Group Health Cooperative ,  Marshfield Clinic ,  Mayo Clinic ,  Northwestern University , and  Vanderbilt University . The second phase, eMERGE-II, began in August 2011, involving the same five sites as phase I plus two new ones: the  Geisinger Clinic  and  Mount Sinai School of Medicine . [ 3 ]


The Emx gene family has two members:  EMX1  and  EMX2 . The Emx genes are responsible for encoding these two  transcription factors ; the homeodomain is responsible for binding to target DNA sequences to regulate  transcription . [ 1 ]


The  Enterosoma genetic code  (tentative code number 34) translates AGG to methionine, as determined by the codon assignment software Codetta; [ 1 ]  it was further shown that this recoding is associated with a special tRNA with the appropriate anticodon and tRNA identity elements. The code is found in a small clade of species within the Enterosoma genus, according to the GTDB taxonomy system  [ 2 ]  release 220. Codetta called the Enterosoma code for the following genome assemblies: GCA_002431755.1, GCA_002439645.1, GCA_002436825.1, GCA_002451385.1, GCA_002297105.1, GCA_002297045.1, GCA_002404995.1, and GCA_900549915.1.


The Estonian Biocentre  (EBC;  Estonian :  Eesti Biokeskus ) is a  genetics  and  genomics   research institute  located in  Tartu ,  Estonia . It's a joint venture between the  University of Tartu  and the  National Institute of Chemical Physics and Biophysics . The goal of the EBC is to promote research and technological development (RTD) in gene and cell technologies in  Estonia . The EBC is regulated by a nine-member Scientific Council, comprising researchers from the EBC and external members, and is advised by an international Advisory Board, currently consisting of five members from different countries.


The EBC was established in 1986, and the current director is Prof.  Richard Villems . [ 1 ]


This Estonian university, college or other education institution article is a  stub . You can help Wikipedia by  expanding it .


European Society of Gene & Cell Therapy (ESGCT)  formerly  European Society of Gene Therapy (ESGT)  is a legally registered professional body which emerged from a small  working group  in 1992 that focused on human  gene therapy .


The objectives of the ESGT include the following:


The official journal of the ESGT is  The Journal of Gene Medicine .


The ESGT works with other entities in the scientific communities in the event that an  adverse effect  to a specific gene therapy is discovered. Investigations the ESGT has been involved with include the adverse effects discovered during the French  X-SCID  gene therapy trial. The ESGT hosted a forum of 500 researchers from various facilities around the world, including representatives from the  Stanford University  and the  Sloan Kettering Cancer Research Center .


The  European Society of Human Genetics  ( ESHG ) is a non-profit organization that promotes research, facilitates communication and encourages best practice in applications of human and medical genetics, particularly in Europe. [ 1 ]
The society organizes the annual European Human Genetics Conference and publishes the  European Journal of Human Genetics . [ 2 ]


Exploding the Gene Myth: How Genetic Information is Produced and Manipulated by Scientists, Physicians, Employers, Insurance Companies, Educators, and Law Enforcers  is a 1993 book by biologist  Ruth Hubbard  and her son  Elijah Wald , published by  Beacon Press .
The book is critical of many potential and actual uses of  human genetic  information, such as attempts to develop personalized medical treatments for  diseases  based on an individual's  genome . [ 1 ]  A second edition was published in 1999, adding discussions of  cloning  and  pharming , among other subjects. [ 2 ]


In his review of the book's first edition,  Alan H. Goodman  praised it as a "worthwhile read" and "an antidote to the rise of  geneticization ", while also admitting that he did not consider it to be "categorically the best book it could have been". [ 3 ]  In another mixed review, William J. McIntyre criticized the authors' biased presentation of the role played by  DNA  in human traits, while also describing the book as "good and valuable reading". [ 4 ]  Behavior geneticist  David Rowe  praised the book's discussion of socially controversial aspects of human genetics, but claimed that it failed to provide "either an evenhanded or accurate treatment of  molecular  and  behavioral genetics ." [ 5 ]


Expressome  may refer to:


External transcribed spacer  ( ETS ) refers to a piece of non-functional  RNA , closely related to the  internal transcribed spacer , which is situated outside structural ribosomal RNAs (rRNA) on a common precursor transcript. [ 1 ]  ETS sequences characteristic to an organism can be used to trace its  phylogeny . [ 2 ]


An  extrachromosomal array  is a method for  mosaic analysis  in  genetics . It is a  cosmid , and contains two functioning ( wild-type ) closely linked  genes : a  gene of interest  and a  mosaic marker . Such an array is injected into  germ line  cells, which already contain mutant (specifically,  loss of function )  alleles  of all three genes in their  chromosomal DNA . The cosmid, which is not packed correctly during  mitosis , is occasionally present in only one daughter cell following cell division. The daughter cell containing the array expresses the gene of interest; the cell lacking the array does not.


The  mosaic marker  is a gene which exhibits a visible  phenotype  change between the functioning and non-functioning alleles. For example,  ncl-1 , located in chromosomal DNA, exhibits a larger  nucleolus  than the wild-type allele, which is in the array. Thus, cells which exhibit larger nucleoli have usually not retained the extrachromosomal array.


The  gene of interest  is the target of the mosaic analysis. Cells lacking the extrachromosomal array also lack the functional gene of interest. Cells which develop normally without the array do not require the gene of interest for normal function. Cells which do not develop normally are said to require the gene. In this way, those cell lineages which require a specific gene can be identified.


Extrachromosomal arrays replace an earlier technique involving a duplicated piece of chromosome called a  free duplication . The latter technique required that the gene of interest and the mosaic marker be closely linked on the duplication; the former allows free choice of mosaic marker and target gene.


Miller LM, Waring DA, Kim SK (1996). Mosaic analysis using a  ncl-1  (+) extrachromosomal array reveals that  lin-31  acts in the Pn.p cells during  Caenorhabditis elegans  vulval development.  Genetics 143  (3): 1181-1191.


In  genetic epidemiology ,  family studies  are studies of whether a disease or trait "runs in a family". In other words, they are studies aimed at detecting the presence or absence of  familial aggregation  for the disease or trait, in which having a  family history  is associated with greater risk. The family research design can also be used to estimate  penetrance  for a given  genotype , to conduct  genetic association  studies, and to study potential modifiers of an individual's genetic risk. [ 1 ] [ 2 ]  If a family study shows that a trait is familial, this is a necessary, but not sufficient, criterion for it to be established as genetically influenced. [ 3 ]


There are three main types of family studies in genetics:


Fay and Wu's H  is a  statistical test  created by and named after two researchers  Justin Fay  and  Chung-I Wu . [ 1 ]  The purpose of the test is to distinguish between a  DNA sequence  evolving randomly ("neutrally") and one evolving under  positive selection . This test is an advancement over  Tajima's D , [ 2 ]  which is used to differentiate neutrally evolving sequences from those evolving non-randomly (through  directional selection  or  balancing selection , demographic expansion or contraction or  genetic hitchhiking ). Fay and Wu's H is frequently used to identify sequences which have experienced  selective sweeps  in their evolutionary history.


Imagine a DNA sequence which has very few polymorphisms in its alleles across different populations. This could arise due to at least three causes:


Now, when you calculate Tajima's D using all the alleles across all populations, because there is an excess of rare  polymorphisms , Tajima's D will show up negative and will tell you that the particular sequence was evolving non-randomly. However, you don't know whether this is because of some  selection  acting or whether there was some  selective sweep  recently or due to population expansion/contraction. To know that, you calculate Fay and Wu's H. [ 3 ]


Fay and Wu's H not only uses population polymorphism data but also data from an outgroup species. Due to the outgroup species, you can now tell what the ancestral state of the allele was before the two lineages split. If, for example, the ancestral allele was different, you can now say that there was a selective sweep in that region (could be due to linkage too). The magnitude of the selective sweep will be decided by the strength of H. If the allele was the same, it means the sequence is experiencing negative selection and the ancestral state is maintained. On the other hand, an H close to 0 means that there is no evidence of deviation from  neutrality .


A significantly positive Fay and Wu's H indicates a deficit of moderate- and high-frequency derived single nucleotide polymorphisms (SNPs) relative to equilibrium expectations, whereas a significant negative Fay and Wu's H indicates an excess of high-frequency derived SNPs. [ 4 ]


Computational tools:


In  statistical genetics ,  Felsenstein's tree-pruning algorithm  (or  Felsenstein's tree-peeling algorithm ), attributed to  Joseph Felsenstein , is an  algorithm  for efficiently computing the  likelihood  of an  evolutionary tree  from  nucleic acid  sequence data.  [ 1 ] [ 2 ]


The algorithm is often used as a subroutine in a search for a  maximum likelihood  estimate for an evolutionary tree. Further, it can be used in a hypothesis test for whether evolutionary rates are constant (by using  likelihood ratio tests ).  It can also be used to provide error estimates for the parameters describing an evolutionary tree.


The  likelihood  of a tree

 T

 {\displaystyle T}

  is, by definition, the probability of observing certain data

 D

 {\displaystyle D}

  (

 D

 {\displaystyle D}

  being a nucleotide sequence alignment for example  i.e.  a succession of

 n

 {\displaystyle n}

  DNA site

 s

 {\displaystyle s}

 ) given the tree. It is often written :

 P
 (
 D

 |

 T
 )

 {\displaystyle P(D|T)}

 .


Here is an example of an evolutionary tree on arbitrary sequence data

 D

 {\displaystyle D}

 :


This is a key value and is often quite complicated to compute. To ease the computations, Felsenstein and his colleagues used several assumptions that are still widely used today. The  main assumption  is that  mutations between DNA sites are independent  of each other. This permits to compute the likelihood as a simple product of probabilities. Now you can divide the data

 D

 {\displaystyle D}

  between several

 D

 s

 {\displaystyle D_{s}}

  for each nucleotide site

 s

 {\displaystyle s}

  inside of

 D

 {\displaystyle D}

 . The global likelihood of the tree will be the product of the likelihoods of each site:


P
 (
 D

 |

 T
 )
 =

 ∏

 s
 =
 1

 n

 P
 (

 D

 s

 |

 T
 )

 {\displaystyle P(D|T)=\prod _{s=1}^{n}{P(D_{s}|T)}}


If I reuse the example above,

 D

 1

 {\displaystyle D_{1}}

  tree would be:


The  second assumption  concerns the  models of DNA sequence evolution . The computation of the likelihood needs the nucleotide frequencies as well as the transition probabilities (when a mutation occurs, probability of going from a nucleotide to another). The simplest model is the  Jukes-Cantor model , assuming equal nucleotide frequencies

 (

 π

 A

 =

 π

 G

 =

 π

 C

 =

 π

 T

 =

 1
 4

 )

 {\displaystyle \left(\pi _{A}=\pi _{G}=\pi _{C}=\pi _{T}={1 \over 4}\right)}

  and equal transition probabilities from

 X

 {\displaystyle X}

  to

 Y

 {\displaystyle Y}

  (

 p

 A
 →
 T

 =

 p

 A
 →
 C

 =

 p

 A
 →
 G

 =

 1
 4

 (
 1
 −

 e

 −
 μ
 l

 )

 {\displaystyle p_{A\rightarrow T}=p_{A\rightarrow C}=p_{A\rightarrow G}={\frac {1}{4}}(1-e^{-\mu l})}

  and

 p

 A
 →
 A

 =

 e

 −
 μ
 l

 +

 1
 4

 (
 1
 −

 e

 −
 μ
 l

 )

 {\displaystyle p_{A\rightarrow A}=e^{-\mu l}+{\frac {1}{4}}(1-e^{-\mu l})}

 ) and idem for the other bases. Here

 μ

 {\displaystyle \mu }

  is the global  mutation rate  of the model.


Felsenstein proposed to decomposed computations even more by using "partial likelihoods" in the computation of

 P
 (

 D

 s

 |

 T
 )

 {\displaystyle P(D_{s}|T)}

 . Here is how it works.


Assume we are on a node

 k

 {\displaystyle k}

  on the tree

 T

 {\displaystyle T}

 .

 k

 {\displaystyle k}

  has two daughter nodes

 i

 {\displaystyle i}

  and

 j

 {\displaystyle j}

  and, for each DNA base

 X
 =
 {
 A
 ,
 T
 ,
 C
 ,
 G
 }

 {\displaystyle X=\{A,T,C,G\}}

  present on

 k

 {\displaystyle k}

 , we can define a partial likelihood

 w

 k

 (
 X
 )

 {\displaystyle w_{k}(X)}

  such as:


w

 k

 (
 X
 )
 =
 (

 ∑

 Y

 p

 X
 →
 Y

 ⋅

 w

 i

 (
 Y
 )
 )
 ⋅
 (

 ∑

 Z

 p

 X
 →
 Z

 ⋅

 w

 j

 (
 Z
 )
 )

 {\displaystyle w_{k}(X)=(\sum _{Y}p_{X\rightarrow Y}\centerdot w_{i}(Y))\centerdot (\sum _{Z}p_{X\rightarrow Z}\centerdot w_{j}(Z))}


where

 Y

 {\displaystyle Y}

  and

 Z

 {\displaystyle Z}

  are also DNA bases.

 p

 X
 →
 Y

 {\displaystyle p_{X\rightarrow Y}}

  is the transition probability from nucleotide

 X

 {\displaystyle X}

  to nucleotide

 Y

 {\displaystyle Y}

  (idem for

 p

 X
 →
 Z

 {\displaystyle p_{X\rightarrow Z}}

 ).

 w

 i

 (
 Y
 )

 {\displaystyle w_{i}(Y)}

  is the partial likelihood of the daughter node

 i

 {\displaystyle i}

 , evaluated on nucleotide

 Y

 {\displaystyle Y}

  (idem for

 w

 j

 (
 Z
 )

 {\displaystyle w_{j}(Z)}

 ).


Using this formula, one has to start from the tips of the tree

 T

 {\displaystyle T}

 , then move towards the root and compute the partial likelihoods of each necessary node on the way (4 partial likelihoods per node). Having finished at the root of the tree, the likelihood of the tree (for this particular site) is then the sum of the partial likelihoods of the root times the appropriated nucleotide frequency.


P
 (

 D

 s

 |

 T
 )
 =

 ∑

 X

 p

 X

 ⋅

 w

 r

 (
 X
 )

 {\displaystyle P(D_{s}|T)=\sum _{X}p_{X}\centerdot w_{r}(X)}


After doing so for every site

 s

 {\displaystyle s}

 , one can finally obtain the likelihood of the global evolutionary tree by multiplying each "sublikelihood".


FREP  is a database of  mouse   repeat sequences  derived from  cDNAs [ 1 ]


Gag/pol translational readthrough site  (or  Retroviral readthrough element ) is a  cis-regulatory element  found in retroviruses. [ 1 ]  The readthrough site facilitates the mechanism of  translation  readthrough of the stop codon at the gag-pol junction producing the gag and pol fusion  protein  in certain  retroviruses .
Retroviruses whose gag and pol genes are in the same reading frame often depend upon approximately 5% read-through of the gag UAG termination codon to form the gag-pol polyprotein. This readthrough is usually dependent on a  pseudoknot  located eight nucleotides downstream of the  stop codon  (UAG). Sequence conservation is found in the second pseudoknot loop.


Gendicine  is a  gene therapy  medication used to treat patients with  head and neck squamous cell carcinoma  linked to  mutations  in the  TP53  gene . It consists of recombinant  adenovirus  engineered to code for  p53 protein  (rAd-p53) and is manufactured by  Shenzhen SiBiono GeneTech .


Gendicine was the first gene therapy product to obtain regulatory approval for clinical use in humans [ 1 ]  after Chinese  State Food and Drug Administration  approved it in 2003. [ 2 ]  As of 2024, Gendicine has not been approved for use in the  United States  and the  European Union .


Gendicine enters the tumour cells by way of  receptor-mediated endocytosis  and begins to over-express genes coding for the p53 protein needed to fight the tumour. [ 3 ]  Ad-p53 seems to act by stimulating the apoptotic pathway in tumour cells, which increases the expression of tumour suppressor genes and immune response factors (such as the ability of  natural killer (NK) cells  to exert "bystander" effects). It also decreases the expression of  multi-drug resistance ,  vascular endothelial growth factor  and matrix metalloproteinase-2 genes and blocking transcriptional survival signals.


p53 mutation status of the tumour cells and response to Ad-p53 treatment are not closely correlated. [ 4 ]  Ad-p53 appears to act synergistically with conventional treatments such as  chemo-  and  radiotherapy . This synergy still exists in patients with chemotherapy and radiotherapy-resistant tumors. Gendicine produces fewer side effects than conventional therapy.


Contusugene ladenovec (Advexin), a similar gene therapy developed by  Introgene  that also uses adenovirus to deliver the p53 gene, was turned down by the FDA in 2008 [ 5 ]  and withdrawn by the maker from the EMA approval shortly after. [ 6 ]


Gene order  is the permutation of  genome  arrangement. A fair amount of research has been done trying to determine whether  gene  orders evolve according to a molecular clock ( molecular clock hypothesis ) or in jumps ( punctuated equilibrium ). By comparing gene orders in dissimilar organisms, scientists are able to develop a  molecular phylogeny  tree. [ 1 ]  When organisms have similar gene orders, meaning they have likely diverged recently, it is called  synteny .


Some research on gene orders in animals' mitochondrial genomes reveal that the mutation rate of gene orders is not a constant in some degrees. [ 2 ]


Methods for  genome mapping , determining the gene order, include: [ 3 ] [ 4 ]


All of these methods can lead to a gene sequence or a DNA sequence by which genes can be identified and compared.


Gene pyramiding  is the simultaneous selection for and/or introduction of multiple genes during  plant breeding . [ 1 ]  Objectives of gene pyramiding includes 1) enhancing trait performance by combining two or more complementary genes, 2) remedying deficits by introgressing genes from other sources, 3) increasing the durability. [ 2 ]  For example, pyramiding has been successfully demonstrated in  Oryza sativa  for  rice blast , producing durable multi-race  resistance  simultaneously. [ 3 ]  Pyramiding and Marker Assisted Selection can be combined as  Marker-Assisted Pyramiding . [ 4 ]   Gene stacking  can be achieved a few different ways, and pyramiding is one of those methods. [ 5 ]


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


Gene stacking  is the combination of more than one gene for  plant disease resistance , or  crop   productivity , or other  horticultural  traits. [ T 1 ]  In  plant breeding  traditionally that means  breeding  those genes in, but increasingly also can mean  genetic engineering . [ T 1 ]  This can be achieved a few different ways, and  gene pyramiding  is one of those methods. [ T 2 ]  Stacking of  transgenes  is yet more difficult than stacking natural genes, but especially in the case of  pest   resistance  genes which require a significant financial investment to insert, is advantageous over other methods. [ 1 ]   Pathosystems  with rapid evolution in the pathogen have long been considered good targets of stacking, to broaden and prolong resistance. [ 2 ] [ 3 ]


Assaying  for successful insertion of  R genes  is much more difficult than for one at a time. [ 4 ]  A simple challenge assay will only tell between complete failure/some unknown degree of success. [ 4 ]  Building a new technique specifically for the multiple genes you are attempting to insert may be necessary. [ 4 ]


Gene therapy for blood diseases  is a novel field of  research  investigating ways in which components of  blood  can be  genetically modified  to treat  hematologic diseases . [ 1 ]


Source: [ 2 ]


CAR T-cell therapy is a type of personalized  cancer immunotherapy  designed to strengthen the patient’s own  immune system  to better fight cancer. The process begins by extracting  T-cells , a type of immune cell, from an individual patient’s blood. The surface of cancer cells contains unique markers called  antigens . The patient’s T-cells are genetically modified in laboratories to include chimeric antigen receptors (CARs). The CARs are designed to recognize the specific cancer antigens and bind to them, allowing T-cells to target and attack the cancer cells. The genetically modified T-cells are administered back to the patients as a treatment.


Leukemia is a group of blood cancers commonly found in children younger than 15 and elders older than 55. [ 3 ]  In 2017,  tisagenlecleucel (Kymriah™) , [ 2 ]  the first CAR-T cell therapy approved by the  FDA , became available to anyone up to the age of 25 with  acute lymphoblastic leukemia  (ALL). Until 2022, a total of six CAR-T therapies have been approved by the FDA, all of which target blood cancers. [ 4 ]  These CAR-T therapies have been shown to have high efficacy in eradicating leukemia cancer, including in patients with advanced-stage, treatment-resistant ( refractory ) or returned ( relapsed ) leukemia. [ 5 ]  They also have a high  remission  rate in comparison to other traditional  cancer treatments . [ 2 ]


Patients in the U.S. suffering from sickle cell disease can now receive targeted  gene therapies  using  hematopoietic stem cells . [ 6 ]  Hematopoietic stem cells are stem cells which differentiate and give rise to  red blood cells ,  white blood cells  and  platelets . [ 7 ]  These therapies involve removing hematopoietic stem cells from the patient and making specific edits to the genome of the hematopoietic stem cells. These edits in the genome of the hematopoietic stem cells are to reverse the effects of sickle cell disease. The cells are then re-administered into the patient. The hematopoietic stem cells are then able to produce red blood cells with the factors which promote proper red blood cell shape reducing the effects of sickle cell disease.


Beta thalassemia is a heritable disorder, characterized by the inability to make  beta globin protein , and in turn reduced functioning of  hemoglobin  (which beta globin is a part of). [ 8 ]  In December 2023, the  European Medicines Agency  recommended approval for a cell based gene therapy that works through the  CRISPR/Cas9  system. The therapy known as Casgevy [ 9 ]  works through editing a dysfunctional protein that interferes with creation of  adult hemoglobin . This gene is known as the  BCL11A , and when people have Beta thalassemia, their bodies do not make enough adult hemoglobin. Casgevy uses precise gene editing of stem cells, and reduces the activity of  BCL11A . With the subsequent reduction of adult hemoglobin,  fetal hemoglobin  (HbF) genes are turned back on, allowing the cells to produce enough hemoglobin. Typically, the body stops making fetal hemoglobin around 6 months of age, and starts making adult hemoglobin. [ 10 ]  These serve similar functions, however fetal hemoglobin has a higher binding affinity for  oxygen  than adult hemoglobin, but both are functional at transporting oxygen in the body. [ 10 ]  Stem cells edited by Casgevy are then  transfused  back into the body where they can create more HbF and therefore make more functional red blood cells that have this edit. With this therapy, patients who would regularly need  blood transfusions  can now produce enough hemoglobin for themselves. [ 11 ]


Human immunodeficiency virus  (HIV) is a disease that, once contacted, attacks cells that are necessary to fight off  infections . It can be transmitted in many different ways, including through sexual contact, blood contamination, the sharing of needles, or from mother to infant. [ 12 ]  If left untreated, HIV can result in  acquired immunodeficiency syndrome  (AIDS). [ 13 ]  HIV weakens an individual’s  immune system , leading to increased risk of fatal infections and cancers. [ 14 ]  In 2023, around 40 million people globally were living with HIV. [ 15 ]  Despite options available for the treatment and management of HIV (e.g.,  highly active antiretroviral therapy ; HAART), they come with limitations including the need for indefinite daily treatment. [ 16 ]  Attempts to generate a long-term HIV-resistant immune system have been promising with results from a case report of a patient who developed  acute myeloid leukemia  after HIV infection. [ 17 ]  Previously, researchers had found a version of a  gene  (an  allele ) that was resistant to HIV. These researchers therefore found a donor who had two copies of this allele ( homozygous ) and extracted their stem cells in an attempt to produce HIV resistance in the patient with acute myeloid leukemia. After stem cell transplantation from this donor, the patient tested and remained HIV-negative at 20 months post-transplantation and was able to discontinue use of antiviral therapies. [ 17 ]


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


GeneReviews  is an online database containing standardized  peer-reviewed  articles that describe specific  heritable diseases . It was established in 1997 as  GeneClinics  by Roberta A Pagon ( University of Washington ) with funding from the  National Institutes of Health . [ 1 ]  Its focus is primarily on single-gene disorders, providing current disorder-specific information on diagnosis, management, and genetic counseling. Links to disease-specific and/or general consumer resources are included in each article when available. The database is published on the  National Center for Biotechnology Information  Bookshelf site. Articles are updated every four to five years or as needed, and revised whenever significant changes in clinically relevant information occur. Articles are searchable by author, title, gene, and name of disease or protein, and are available free of charge. [ 2 ]


This article related to  health informatics  is a  stub . You can help Wikipedia by  expanding it .


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


GeneSweep  or  Gene Sweepstake  was a  sweepstake  and  scientific wager  for scientists to bet on the total number of  genes  in the  human genome . [ 3 ] [ 4 ] [ 5 ] [ 6 ] [ 7 ] [ 8 ]  The sweepstake was started at a  Cold Spring Harbor Laboratory  conference in 2000. [ 2 ] [ 9 ] [ 10 ] [ 11 ] [ 12 ]  Initially, bets could be placed for $1, which was raised to $5 in 2001 and to $20 in 2002. [ 2 ]  The cost of placing a bet increased significantly because later participants were expected to have much more accurate information available to inform their guesses. [ 13 ]  By May 23, 2000, 228 bets had been placed, with the average number of predicted genes among them being 62,598. [ 14 ]


On May 30, 2003,  Ewan Birney  of the  European Bioinformatics Institute , who had organized the pool, [ 2 ]  announced the winner: Lee Rowen of the  Institute for Systems Biology . [ 15 ]  Rowen had guessed that the human genome would contain 25,947 genes, which was the closest to the estimated number of 24,847 given by the  Ensembl genome database project . In addition to being the winning guess, this was also the lowest of the more than 460 bets that were placed. [ 1 ]  Rowen split the $1,200 prize pool with Paul Dear of the  Medical Research Council  (MRC) and Olivier Jaillon of  Genoscope . Rowen credited  Jean Weissenbach  of Genoscope with convincing her that the true number of human genes would be relatively low. All three winners shared the prize because they were the only betters who guessed under 30,000, and Birney was certain that the total number of genes was less than that. [ 16 ]  The  sweepstakes  had always been planned to end in 2003, because Birney had expected that Ensembl would have completed counting the number of human genes by then. Once it became clear that they would need more time to arrive at an exact number, Birney initially planned on extending the sweepstakes for five more years. However, David Stewart convinced Birney to choose a winner by pointing out that the rules specified that a winner had to be chosen in 2003, with no exceptions. Birney noted that, though the exact number was still unknown, there was no doubt that the number of human genes was much less than 26,000, and he announced that 21,000 was the best estimate in a 2003 talk. [ 17 ]


As of 2018 [update]  there is continuing debate amongst scientists about the total number of genes in the human genome, with most estimates ranging from 19,000 and 22,000. [ 18 ] [ 19 ]


The Genetic Basis of Evolutionary Change  is a book by  Richard Lewontin  about  evolutionary genetics . Originally published by  Columbia University Press  in 1974, the book originated in a series of lectures, known as the "Jesup lectures", that Lewontin gave at  Columbia University  in 1969. [ 1 ]  In a blurb promoting the book, Columbia University Press claimed that it "will surely become one of the landmarks in twentieth-century science", [ 2 ]  for which they were criticized by some of the book's reviewers.  James F. Crow , for example, argued that the Columbia employees who chose to describe the book in this way "should have their wrists slapped", adding, "...this is not  the Origin of Species . It is just a thoughtful, readable, and very stimulating book." [ 3 ]


In his review of  The Genetic Basis of Evolutionary Change , Donald J. Nash described it as "...a fine addition to the series of volumes on  evolutionary biology  published by Columbia University Press." [ 1 ]   Joseph Felsenstein  also reviewed the book favorably, describing it as "...the book we always knew Dick Lewontin could write" and "...a brilliant comprehensive introductory review of the controversy over the  evolutionary significance of  protein   polymorphisms ." [ 4 ]  In his review of the book, James F. Crow described it as "a fine book", praising Lewontin for his "gift for seeing problems clearly, for marshalling the relevant evidence, and for presenting all this in an interesting way." Crow concluded that "[i]n the areas in which there has been the greatest controversy, Lewontin has presented the scientific issues fairly and objectively." However, Crow also criticized Lewontin for inserting "irrelevant social and political statements" into several parts of the book. [ 3 ]  In his review of the book for  Science ,  Bryan Clarke  described it as "...a remarkable book", adding that "[i]t will, no doubt, be necessary fare for future generations of undergraduates, and it will certainly benefit their intellectual nutrition. [ 5 ]


The Genetic Basis of Evolutionary Change  has been retrospectively  described as a "landmark book". [ 6 ]  In 1999, philosopher  Michael Ruse  wrote that Lewontin, by publishing the book, had "thereby establish[ed] himself (if there had been hitherto doubt) as the dominant figure in the genetics of evolution". [ 7 ]


In biology,  genetic demixing [ 1 ]  refers to a phenomenon in which an initial mixture of individuals with
two or more distinct  genotypes  rearranges in the course of time,
giving birth to a spatial organization where some or all genotypes are concentrated in distinct patches.


The  Genetic Information Research Institute  ( GIRI ) is a non-profit institution that was founded in 1994 by  Jerzy Jurka . The mission of the institute "is to understand biological processes which alter the genetic makeup of different organisms, as a basis for potential gene therapy and genome engineering techniques." [ 1 ]  The institute specializes in applying computer tools to analysis of  DNA  and  protein  sequence information. GIRI develops and maintains Repbase Update, a  database  of prototypic  sequences  representing  repetitive DNA  from different  eukaryotic  species, and Repbase Reports, an electronic journal established in 2001. [ 2 ]  Repetitive DNA is primarily derived from  transposable elements  (TEs), which include  DNA transposons  belonging to around 20 superfamilies and  retrotransposons  that can also be sub-classified into subfamilies . The majority of known superfamilies of DNA transposons were discovered or co-discovered at GIRI, including  Helitron ,  Academ, Dada, Ginger, Kolobok, Novosib, Sola, Transib, Zator, PIF/Harbinger  and  Polinton/Maverick . An ancient element from the  Transib  superfamily was identified as the evolutionary precursor of the  Recombination activating gene . GIRI has hosted three international conferences devoted to the genomic impact of eukaryotic transposable elements. [ 3 ]


37°25′09″N   122°05′17″W  /  37.4193°N 122.0880°W  /  37.4193; -122.0880


Genetic structure  refers to any pattern in the  genetic  makeup of individuals within a population. [ 1 ]


Genetic structure allows for information about an individual to be inferred from other members of the same population. In trivial terms, all populations have genetic structure, because all populations can be characterized by their  genotype  or  allele  frequencies: if only 1% of a large sample of  moths  drawn from a single population have spotted wings, then it is safe to assume that any unknown individual is unlikely to have spotted wings.


A more complicated example arises in dense  thickets  of plants, where plants tend to be  pollinated  by near neighbours, and  seeds  tend to fall and  germinate  near the maternal plant. In such a scenario, plants tend to be more closely related to nearby plants than they are to distant plants; and yet they are more likely to breed with nearby plants than they are with distant plants. Thus an inbreeding cycle is created that perpetuates the pattern of plants being closely related to near neighbors. This is a form of genetic structure because one can infer much about the genetic makeup of any individual plant simply by studying plants in their immediate neighborhoods.


Geneticization  is a term that has been widely used by critics of  genetic medicine  since the early 1990s. [ 1 ]  Originally coined by  Abby Lippman  in a series of three papers published in the 1990s (specifically in 1991, 1992, and 1994), [ 1 ]  geneticization refers to the increasing tendency to define differences between individuals as largely or entirely due to  genetics . [ 2 ]  This includes the growing framing and understanding of human diseases and behaviors in genetic terms. [ 3 ]   Henk A. M. J. ten Have  has defined geneticization as "...a  heuristic  tool that can help to re-focus the moral debate on the implications of new genetic knowledge towards interpersonal relations, the power of medicine, the cultural context and social constraints, rather than emphasizing issues as personal autonomy and individual rights." [ 4 ]


It is common for social scientists and bioethicists to argue that geneticization leads to a growing belief in  genetic determinism  and  essentialism  in the general public, and that this, in turn, increases  discrimination ,  stigma , and  inequality . [ 5 ] [ 3 ]  When Lippman originally coined the term "geneticization", for example, she was concerned about the potential for geneticization to increase public belief in biological essentialism, thereby reinforcing racism and discrimination against people with  disabilities . [ 6 ]  Some proponents of the heuristic of geneticization also argue that the media's coverage of genetics contributes to geneticization. [ 7 ]  However, the empirical evidence on the link between geneticization and genetic determinism, and between genetic determinism, discrimination and inequality, is ambiguous, suggesting that the phenomenon of geneticization may not always follow the simple pattern that proponents of the concept ascribe to it. [ 5 ]


Genome in a Bottle  is a consortium hosted by  NIST  and dedicated to characterization of benchmark human genomes. [ 1 ] [ 2 ]  The  NCBI  is serving as the repository for the detailed information on samples, genotypes, raw sequencing reads and mapped reads, via a dedicated FTP site. [ 3 ]


Genome India Project  (GIP) is a research initiative led by the  Bangalore -based  Indian Institute of Science 's Centre for Brain Research and involves over 20 universities across the country in an effort to gather samples, compile data, conduct research, and create an ‘Indian reference genome' grid. [ 1 ]


The initiative is funded by  Department of Biotechnology  (DBT) to sequence at least 10,000 Indian genomes in phase 1. The goal of the research is to develop predictive diagnostic indicators for several high-priority diseases and other uncommon and genetic disorders. In phase 2, the project would collect genetic samples from patients with three broad categories -  cardiovascular diseases ,  mental illness , and  cancer . [ 2 ]


The list includes: [ 3 ]


In  genome-wide association studies ,  genome-wide significance  (abbreviated  GWS ) is a specific threshold for determining the  statistical significance  of a reported  association  between a given  single-nucleotide polymorphism  (SNP) and a  given  trait . The most commonly accepted threshold is  p  < 5 × 10 −8 , which is based on performing a  Bonferroni correction  for all the independent common SNPs across the  human genome . [ 1 ]  If a  p -value is found to be lower than this threshold in a genome-wide association study, the  null hypothesis  of no true SNP-association will typically be rejected. [ 2 ]  However, there has been some criticism of this threshold, with a 2012 study suggesting that a significant number of associations with  p -values just above this threshold are genuine, replicable associations. The authors of this study concluded that their finding "...suggests a possible relaxation in the current GWS threshold." [ 3 ]  More recently, it has been suggested that the conventional threshold should be modified to take into account the increasing prevalence of low- frequency  genetic variants in genome-wide association studies. [ 4 ]