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Section: Components of the binary vector system > Vir helper plasmid. The vir helper plasmid contains the vir genes that originated from the Ti plasmid of Agrobacterium. These genes code for a series of proteins that cut the binary vector at the left and right border sequences, and facilitate transfer and integration o... | Wikipedia - Transfer DNA binary system - Components of the binary vector system > Vir helper plasmid | 339 | 1,348 | null |
Section: Components of the binary vector system > Advantages of using two plasmids. Modularity: multiple vectors carrying different genes of interest can be introduced into a single vir strain without altering the helper plasmid. It allows researchers to independently design and manipulate the T-DNA region without affe... | Wikipedia - Transfer DNA binary system - Components of the binary vector system > Advantages of using two plasmids | 328 | 1,545 | null |
Section: Development of T-DNA binary vectors. The pBIN19 vector was developed in the 1980s and is one of the first and most widely used binary vectors. The pGreen vector, which was developed in 2000, is a newer version of the binary vector that allows for a choice of promoters, selectable markers and reporter genes. An... | Wikipedia - Transfer DNA binary system - Development of T-DNA binary vectors | 337 | 1,537 | null |
Section: Applications of the Binary Vector System in Genetic Engineering > Insect resistant maize. A binary system has been used to insert Bacillus thuringiensis (Bt) toxin genes into crops, conferring resistance to pests. But toxins, such as Cry1Ac or Cry2Ab, are highly specific to certain insect pests and do not harm... | Wikipedia - Transfer DNA binary system - Applications of the Binary Vector System in Genetic Engineering > Insect resistant maize | 157 | 742 | null |
Section: Applications of the Binary Vector System in Genetic Engineering > Golden Rice. T-DNA binary system was used to introduce multiple genes to engineer provitamin A biosynthesis in rice endosperm, addressing vitamin A deficiency in developing countries. Vitamins A deficiency is a major cause of preventable blindne... | Wikipedia - Transfer DNA binary system - Applications of the Binary Vector System in Genetic Engineering > Golden Rice | 269 | 1,400 | null |
Article: Transformation efficiency. Transformation efficiency refers to the ability of a cell to take up and incorporate exogenous DNA, such as plasmids, during a process called transformation. The efficiency of transformation is typically measured as the number of transformants (cells that have taken up the exogenous ... | Wikipedia - Transformation efficiency - Summary | 218 | 1,148 | null |
Section: Measurement. By measuring the transformation efficiency, we can utilize the information from our experiment to evaluate how effectively our transformation went. This is a quantification of how many cells were altered by 1 μg of plasmid DNA. In essence, it is a sign that the transformation experiment was succes... | Wikipedia - Transformation efficiency - Measurement | 334 | 1,678 | null |
This can be calculated by multiplying the number of colonies by the volume of the culture plated and dividing by the amount of DNA used. Quantitative PCR (qPCR) - This method utilizes the fact that the plasmid DNA will have a specific gene or sequence that is not present in the host cell genome, and therefore can be us... | Wikipedia - Transformation efficiency - Measurement | 320 | 1,567 | null |
10–100 pg of DNA may be used for transformation, more DNA may be necessary for low-efficiency transformation (generally saturation level is reached at over 10 ng). After transformation, 1% and 10% of the cells are plated separately, the cells may be diluted in media as necessary for ease of plating. Further dilution ma... | Wikipedia - Transformation efficiency - Measurement | 199 | 802 | null |
Section: Factors affecting transformation efficiency. Individual cells are capable of taking up many DNA molecules, but the presence of multiple plasmids does not significantly affect the occurrence of successful transformation events. A number of factors may affect the transformation efficiency: Plasmid size – A study... | Wikipedia - Transformation efficiency - Factors affecting transformation efficiency | 338 | 1,756 | null |
coli cells are more susceptible to be made competent when it is growing rapidly, cells are therefore normally harvested in the early log phase of cell growth when preparing competent cells. The optimal optical density for harvesting cells normally lies around 0.4, although it may vary with different cell strains. A hig... | Wikipedia - Transformation efficiency - Factors affecting transformation efficiency | 345 | 1,705 | null |
Transformation conditions – The method of preparation of competent cells, the length of time of heat shock, temperature of heat shock, incubation time after heat shock, growth medium used, pH and various additives, all can affect the transformation efficiency of the cells. The presence of contaminants as well as ligase... | Wikipedia - Transformation efficiency - Factors affecting transformation efficiency | 333 | 1,611 | null |
Section: Efficiency of transformation methods > Electroporation. Electroporation tends to be more efficient than chemical methods and can be applied to a wide range of species and to strains that were previously resistant and recalcitrant to transformation techniques. Electroporation has been found to have an average y... | Wikipedia - Transformation efficiency - Efficiency of transformation methods > Electroporation | 237 | 1,098 | null |
Section: Efficiency of transformation methods > Chemical transformation. Chemical transformation or heat shock can be performed in a simple laboratory setup, typically yielding transformation efficiencies that are adequate for cloning and subcloning applications, approximately 106 CFU/μg. One of the early methods used ... | Wikipedia - Transformation efficiency - Efficiency of transformation methods > Chemical transformation | 159 | 708 | null |
Section: Restriction barriers to an efficient transformation. Some bacterial cells have restriction-modification systems that can degrade exogenous plasmids that are foreign to the host cell. This can greatly reduce the efficiency of transformation. This is due to restriction systems in the recipient cells that target ... | Wikipedia - Transformation efficiency - Restriction barriers to an efficient transformation | 152 | 821 | null |
Article: Transgressive segregation. In genetics, transgressive segregation is the formation of extreme phenotypes, or transgressive phenotypes, observed in segregated hybrid populations compared to phenotypes observed in the parental lines. The appearance of these transgressive (extreme) phenotypes can be either positi... | Wikipedia - Transgressive segregation - Summary | 182 | 885 | null |
Section: Causes. Genetic There are many causes for transgressive segregation in hybrids. One cause can be due to recombination of additive alleles. Recombination results in new pairs of alleles at two or more loci. These different pairs of alleles can give rise to new phenotypes if gene expression has been changed at t... | Wikipedia - Transgressive segregation - Causes | 341 | 1,593 | null |
All of these causes lead to the appearance of these extreme phenotypes and creates a hybrid species that will deviate away from the parent species niche and eventually create an individual "hybrid" species. Environmental Other than the genetic factors solely causing transgressive segregation, environmental factors can ... | Wikipedia - Transgressive segregation - Causes | 252 | 1,398 | null |
Section: Examples of transgressive segregation. In Kenya, there is a fungus called septoria tritici blotch (STB) that diminishes yield in wheat crop. The parent species of wheat had little resistance toward STB, but the hybrid species due to transgressive segregation showed a higher resistance toward STB and therefore ... | Wikipedia - Transgressive segregation - Examples of transgressive segregation | 322 | 1,555 | null |
Section: Testing for transgressive segregation. There are many ways to test if transgressive segregation occurred within a population. One common way to test for transgressive segregation is to use a Dunnett's test. This test looks at whether the hybrid species' performance was different from the control group by looki... | Wikipedia - Transgressive segregation - Testing for transgressive segregation | 191 | 894 | null |
Section: The case of trios: one affected child per family > Description of the test. We first describe the TDT in the case where families consist of trios (two parents and one affected child). Our description follows the notations used in Spielman, McGinnis & Ewens (1993). The TDT measures the over-transmission of an a... | Wikipedia - Transmission disequilibrium test - The case of trios: one affected child per family > Description of the test | 196 | 785 | null |
The TDT tests whether the proportions b/b + c and c/b + c are compatible with probabilities (0.5, 0.5). This hypothesis can be tested using a binomial (asymptotically chi-square) test with one degree of freedom: χ 2 = [ b − ( b + c ) / 2 ] 2 ( b + c ) / 2 + [ c − ( b + c ) / 2 ] 2 ( b + c ) / 2 = ( b − c ) 2 b + c ... | Wikipedia - Transmission disequilibrium test - The case of trios: one affected child per family > Description of the test | 210 | 440 | null |
Section: The case of trios: one affected child per family > Outline of the test derivation. A derivation of the test consists of using a population genetics model to obtain the expected proportions for the quantities a, b, c, d in the table above. In particular, one can show that under nearly all disease models the exp... | Wikipedia - Transmission disequilibrium test - The case of trios: one affected child per family > Outline of the test derivation | 306 | 1,089 | null |
Section: Extension to two affected child per family > Extension of the test. The TDT can be readily extended beyond the case of trios. We keep following the notations of Spielman, McGinnis & Ewens (1993). Consider a total of h heterozygous parents. We use the fact that the transmission to different children are indepen... | Wikipedia - Transmission disequilibrium test - Extension to two affected child per family > Extension of the test | 297 | 919 | null |
Section: Extension to two affected child per family > Relation with another linkage statistic. The comparison with the more traditional (at least at the time when the TDT was proposed) linkage test proposed by Blackwelder and Elston 1985 is informative. The Blackwelder and Elston approach uses the total number of haplo... | Wikipedia - Transmission disequilibrium test - Extension to two affected child per family > Relation with another linkage statistic | 299 | 999 | null |
One can derive a simple chi-square statistic with 2 degrees of freedom: χ t o t a l 2 = ( i − h / 4 ) 2 h / 4 + ( h − i − j − h / 2 ) 2 h / 2 + ( j − h / 4 ) 2 h / 4 = χ t d t 2 + χ h s 2 . {\displaystyle \chi _{total}^{2}={\frac {(i-h/4)^{2}}{h/4}}+{\frac {(h-i-j-h/2)^{2}}{h/2}}+{\frac {(j-h/4)^{2}}{h/4}}=\chi _{tdt}^... | Wikipedia - Transmission disequilibrium test - Extension to two affected child per family > Relation with another linkage statistic | 230 | 530 | null |
Section: Modified version. More recently, Wittkowski KM, Liu X. (2002/2004) proposed a modification to the TDT that can be more powerful under some alternatives, although the asymptotic properties under the null hypothesis are equivalent. The motivating idea for this modification is the fact that, while the transmissio... | Wikipedia - Transmission disequilibrium test - Modified version | 213 | 1,053 | null |
In this modified TDT test the children are stratified by parental type and the modified test statistic becomes: χ 2 = ( [ n P Q − n Q Q ] P Q ∼ Q Q + 2 × [ n P P − n Q Q ] P Q ∼ P Q + [ n P P − n P Q ] P P ∼ P Q ) 2 [ n P Q + n Q Q ] P Q ∼ Q Q + 4 × [ n P P + n Q Q ] P Q ∼ P Q + [ n P Q + n P P ] P P ∼ P Q {\displaysty... | Wikipedia - Transmission disequilibrium test - Modified version | 347 | 617 | null |
Article: Triangle of U. The triangle of U ( OO) is a theory about the evolution and relationships among the six most commonly known members of the plant genus Brassica. The theory states that the genomes of three ancestral diploid species of Brassica combined to create three common tetraploid vegetables and oilseed cro... | Wikipedia - Triangle of U - Summary | 195 | 888 | null |
Section: Woo's theory. The six species are The code in the "Chr.count" column specifies the total number of chromosomes in each somatic cell, and how it relates to the number n of chromosomes in each full genome set (which is also the number found in the pollen or ovule), and the number x of chromosomes in each compone... | Wikipedia - Triangle of U - Woo's theory | 306 | 1,241 | null |
Section: Further relationships. The framework proposed by Woo, although backed by modern studies, leaves open questions about the time and place of hybridization and which species is the maternal or paternal parent. B. napus (AACC) is dated to have originated about 8,000 or 38,000–51,000 years ago. The homologous part ... | Wikipedia - Triangle of U - Further relationships | 218 | 885 | null |
Section: Further relationships > Allohexaploid species. In 2011 and 2018, novel allohexaploids (AABBCC) located at the "center" of the triangle of U were created by different means, for example by crossing B. rapa (AA) with B. carinata (BBCC), or B. nigra (BB) with B. napus (AACC), or B. oleracea (CC) with B. juncea (A... | Wikipedia - Triangle of U - Further relationships > Allohexaploid species | 183 | 629 | null |
Article: Trinucleotide repeat expansion. A trinucleotide repeat expansion, also known as a triplet repeat expansion, is the DNA mutation responsible for causing any type of disorder categorized as a trinucleotide repeat disorder. These are labelled in dynamical genetics as dynamic mutations. Triplet expansion is caused... | Wikipedia - Trinucleotide repeat expansion - Summary | 343 | 1,774 | null |
Section: History. The first documentation of anticipation in genetic disorders was in the 1800s. However, from the eyes of geneticists, this relationship was disregarded and attributed to ascertainment bias; because of this, it took almost 200 years for a link between onset of disease and trinucleotide repeats (TNR) to... | Wikipedia - Trinucleotide repeat expansion - History | 342 | 1,468 | null |
Repeat composition and location are used to determine the mechanism of a given expansion. Onwards from 1995, it was also possible to observe the formation of hairpins in triplet repeats, which consisted of repeating CG pairs and a mismatch. During the decade after evidence that linked TNR to onset of disease was found,... | Wikipedia - Trinucleotide repeat expansion - History | 348 | 1,824 | null |
Section: Overall structure > Location. In terms of location, these triplet repeats can be found in both coding and non-coding regions. CAG and GCN repeats, which lead to polyglutamine and polyalanine tracts respectively, are normally found in the coding regions. At the 5' untranslated region, CGG and CAG repeats are fo... | Wikipedia - Trinucleotide repeat expansion - Overall structure > Location | 212 | 945 | null |
Section: Overall structure > Intermediates. Depending on the sequence of the repeat, at least three intermediates with different secondary structures are known to form. A CGG repeat will form a G-quadruplex due to Hoogsteen base pairing, while a GAA repeat forms a triplex due to negative supercoiling. CAG, CTG, and CGG... | Wikipedia - Trinucleotide repeat expansion - Overall structure > Intermediates | 204 | 869 | null |
Section: Instability > Threshold. In trinucleotide repeat expansion there is a certain threshold or maximum amount of repeats that can occur before a sequence becomes unstable. Once this threshold is reached the repeats will start to rapidly expand causing longer and longer expansions in future generations. Once it hit... | Wikipedia - Trinucleotide repeat expansion - Instability > Threshold | 230 | 1,295 | null |
Section: Instability > Parental influence. Research suggests that there is a direct, important correlation between the sex of the parent that transmits the mutation and the degree and phenotype of disorder in the child., The degree of repeat expansion and whether or not an expansion will occur has been directly linked ... | Wikipedia - Trinucleotide repeat expansion - Instability > Parental influence | 248 | 1,382 | null |
Section: Mechanisms > Unequal homologous exchange. One proposed but highly unlikely mechanism that plays a role in trinucleotide expansion transmission occurs during meiotic or mitotic recombination. It is suggested that during these processes it is possible for a homologous repeat misalignment, commonly known for caus... | Wikipedia - Trinucleotide repeat expansion - Mechanisms > Unequal homologous exchange | 268 | 1,308 | null |
Section: Mechanisms > DNA replication > Small scale expansions. These expansions can occur through either strand slippage or flap ligation. Okazaki fragments are a key element of the proposed error in DNA replication. It is suggested that the small size of Okazaki fragments, typically between 150 and 200 nucleotides lo... | Wikipedia - Trinucleotide repeat expansion - Mechanisms > DNA replication > Small scale expansions | 336 | 1,649 | null |
Expansions occur when the fork reverses and restarts, which forms a chicken-foot structure. This structure results in the unstable intermediate forming on the nascent leading strand, leading to further TRE. Furthermore, this intermediate can avoid mismatch repair due to its affinity for the MSH-2-MSH3 complex, which st... | Wikipedia - Trinucleotide repeat expansion - Mechanisms > DNA replication > Small scale expansions | 178 | 814 | null |
Section: Mechanisms > DNA replication > Large scale expansions. Two mechanisms have been proposed for large scale repeats: template switching and break-induced replication. Template switching, a mechanism for large scale GAA repeats that can double the number of triplet repeats, has been proposed. GAA repeats expand wh... | Wikipedia - Trinucleotide repeat expansion - Mechanisms > DNA replication > Large scale expansions | 291 | 1,413 | null |
Section: Disorders > Fragile X syndrome > Background. Fragile X syndrome is the second most common form of intellectual disability affecting 1 in 2,000-4,000 women and 1 in 4,000-8,000 men, women being twice as likely to inherit this disability due to their XX chromosomes. This disability arises from a mutation at the ... | Wikipedia - Trinucleotide repeat expansion - Disorders > Fragile X syndrome > Background | 183 | 903 | null |
Section: Disorders > Fragile X syndrome > Genetic causation. Fragile X syndrome is caused by expansion of CGG repeats in the FMR1 gene. In males without fragile X syndrome, the CGG repeat number ranges from 53 to 200 while those affected have greater than 200 repeats of this trinucleotide sequence located at the end of... | Wikipedia - Trinucleotide repeat expansion - Disorders > Fragile X syndrome > Genetic causation | 329 | 1,546 | null |
Section: Disorders > Huntington's disease > Causation. This autosomal dominant disorder results from the expansions of a trinucleotide repeat which involves CAG in exon 1 of the IT15 gene. The majority of all juvenile HD cases stem from the transmission of a high CAG trinucleotide repeat number that is a result of pate... | Wikipedia - Trinucleotide repeat expansion - Disorders > Huntington's disease > Causation | 230 | 1,113 | null |
Section: Disorders > Myotonic dystrophy > Background. Myotonic dystrophy is a rare muscular disorder in which numerous bodily systems are affected. There are four forms of Myotonic Dystrophy: mild phenotype and late-onset, onset in adolescence/young adulthood, early childhood featuring only learning disabilities, and a... | Wikipedia - Trinucleotide repeat expansion - Disorders > Myotonic dystrophy > Background | 243 | 1,229 | null |
Section: Disorders > Myotonic dystrophy > Causation. Myotonic dystrophy results from a (CTG)n trinucleotide repeat expansion that resides in a 3' untranslated region of a serine/threonine kinase coding transcript. This (CTG)n trinucleotide repeat is located within leukocytes; the length of the repeat and the age of the... | Wikipedia - Trinucleotide repeat expansion - Disorders > Myotonic dystrophy > Causation | 167 | 708 | null |
Section: Point of occurrence > Fragile X syndrome. The precise timing of TNR occurrence varies by disease. Although the exact timing for FXS is not certain, research has suggested that the earliest CGG expansions for this disorder are seen in primary oocytes. It has been proposed that the repeat expansion happens in th... | Wikipedia - Trinucleotide repeat expansion - Point of occurrence > Fragile X syndrome | 200 | 992 | null |
Section: Point of occurrence > Myotonic dystrophy type 1. Many similarities can be drawn between DM1 and FXS involving aspects of mutation. Full maternal inheritance is present within DM1, repeat expansion length is linked to maternal age and the earliest instance of expansions is seen in the two-cell stage of preimpla... | Wikipedia - Trinucleotide repeat expansion - Point of occurrence > Myotonic dystrophy type 1 | 239 | 1,087 | null |
Section: Point of occurrence > Huntington's disease. In Huntington's disease (HD), the exact timing has not been determined; however there are a number of proposed points during germ cell development at which expansion is thought to occur. In four HD samples examined, CAG repeat expansion lengths were more variable in ... | Wikipedia - Trinucleotide repeat expansion - Point of occurrence > Huntington's disease | 156 | 815 | null |
Section: Therapeutics > RNA interference (RNAi). RNA interference is a mechanism that can be used to silence the expression of genes, RNAi is a naturally occurring process that is leveraged using synthetic small interfering RNAs (siRNAs) that are used to change the action and duration of the natural RNAi process. Anoth... | Wikipedia - Trinucleotide repeat expansion - Therapeutics > RNA interference (RNAi) | 315 | 1,419 | null |
Section: Therapeutics > Antisense oligonucleotides. Antisense oligonucleotides (ASOs) are small strand single stranded oligodeoxynucleotides approximately 15-20 nucleic acids in length that can alter the expression of a protein. The goal of using these antisense oligonucleotides are the decrease in protein expression o... | Wikipedia - Trinucleotide repeat expansion - Therapeutics > Antisense oligonucleotides | 349 | 1,694 | null |
The synthetic oligonucleotides are negatively charged molecules that are chemically modified in order for the molecule to regulate the gene expression within the cell. Some issues that come about this process is the toxicity and variability that can come about with chemical modification. The goal of the ASO is to modul... | Wikipedia - Trinucleotide repeat expansion - Therapeutics > Antisense oligonucleotides | 198 | 933 | null |
Article: Tumor mutational burden. Tumour mutational burden (abbreviated as TMB) is a genetic characteristic of tumorous tissue that can be informative to cancer research and treatment. It is defined as the number of non-inherited mutations per million bases (Mb) of investigated genomic sequence, and its measurement has... | Wikipedia - Tumor mutational burden - Summary | 323 | 1,708 | null |
Scientists postulate that high TMB is associated with an increased amount of neoantigens, which are tumour specific markers displayed by cells. An increase in these antigens may then lead to increased detection of cancer cells by the immune system and more robust activation of cytotoxic T-lymphocytes. Activation of T-c... | Wikipedia - Tumor mutational burden - Summary | 174 | 821 | null |
Section: Importance > TMB as a Biomarker. One survival mechanism in tumors is to increase the expression of immune checkpoint molecules that can bind to tumor-specific T-cells and inactivate them, so that the tumor cells cannot be detected and killed. ICIs have been shown to improve patients' response and the survival ... | Wikipedia - Tumor mutational burden - Importance > TMB as a Biomarker | 340 | 1,559 | null |
Section: Importance > Treatment Response. TMB has been found to correlate with patient response to therapies such as immune checkpoint inhibitors (ICIs). An analysis of a large cohort of patients receiving ICI therapy revealed that higher TMB levels (≥ 20 mutations/Mb) corresponded to a 58% response rate to ICIs while ... | Wikipedia - Tumor mutational burden - Importance > Treatment Response | 163 | 736 | null |
Section: Importance > Patient Prognosis. Associations have been reported between TMB and patient outcome in a variety of cancers. In one study, scientists observed differences in survival rates, with high TMB individuals having a median progression-free survival of 12.8 months and a median overall survival not reached ... | Wikipedia - Tumor mutational burden - Importance > Patient Prognosis | 287 | 1,429 | null |
Section: TMB in different cancers. There is a large variation in TMB values across different cancer types as the number of somatic mutations can span from 0.01 to 400 mutations per megabase of genome. It has been shown that melanoma, NSCLC and other squamous carcinomas have the highest levels of TMB in this order, whil... | Wikipedia - Tumor mutational burden - TMB in different cancers | 334 | 1,480 | null |
Section: TMB calculation. There are disparities between how TMB is calculated in clinical and research settings. Broadly, whole genome sequencing, whole exome sequencing, and panel based approaches can be used to help to calculate TMB. Studies of TMB from research perspectives typically incorporate whole exome sequenci... | Wikipedia - Tumor mutational burden - TMB calculation | 257 | 1,403 | null |
Section: TMB calculation > Factors that Influence TMB Calculation > Tissue Preprocessing. Typically, tumor tissues are fixated in formalin to preserve tissue and cellular morphology in the formalin-fixed paraffin-embedded (FFPE) protocols. While FFPE offers a cost-effective method to store tissues for long durations of... | Wikipedia - Tumor mutational burden - TMB calculation > Factors that Influence TMB Calculation > Tissue Preprocessing | 180 | 846 | null |
Section: TMB calculation > Factors that Influence TMB Calculation > Sequencing Strategy. Different sequencing strategies enable different number of genes to be included in the calculation of TMB (with WGS and WES approaches allowing a greater quantity of genes to be analyzed). While panel based approaches analyze compa... | Wikipedia - Tumor mutational burden - TMB calculation > Factors that Influence TMB Calculation > Sequencing Strategy | 161 | 881 | null |
Section: TMB calculation > Factors that Influence TMB Calculation > Bioinformatics Pipeline. In most calculations of TMB, synonymous variants and germline variants are filtered out as they are unlikely to be directly involved in creating neoantigens. However, some pipelines maintain synonymous variants. To account for ... | Wikipedia - Tumor mutational burden - TMB calculation > Factors that Influence TMB Calculation > Bioinformatics Pipeline | 177 | 931 | null |
Section: Issues and future directions. One approved biomarker of ICI therapy is PD-L1 expression, but the predictive power of this biomarker is affected by factors such as assay interpretation and lack of standard methods. TMB is also affected by these factors in addition to accessibility issues. Biological factors lik... | Wikipedia - Tumor mutational burden - Issues and future directions | 348 | 1,745 | null |
Article: Uniparental inheritance. Uniparental inheritance is a non-Mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father. This phenomenon is most commonly observed in ... | Wikipedia - Uniparental inheritance - Summary | 225 | 1,093 | null |
Section: Examples > Organelles. Although most of the eukaryotic sub-cellular parts do not have their own DNA nor are capable of replication independent of the nucleus, there are some exceptions such as mitochondria and chloroplasts. Not only are these organelles capable of independent DNA replication, translation, and ... | Wikipedia - Uniparental inheritance - Examples > Organelles | 193 | 904 | null |
Section: History. Like all other genetic concepts, the discovery of uniparental inheritance stems from the days of an Augustinian priest known as Gregor Johann Mendel. The soon-to-be "father of modern genetics" spent his days conducting hybridization experiments on pea plants(Pisum sativum) in his monastery's garden. D... | Wikipedia - Uniparental inheritance - History | 340 | 1,562 | null |
Section: History > Poky mutants of Neurospora. A well studied example of uniparental inheritance involves the poky mutants of Neurospora crassa. The original poky mutant was isolated by Mitchell and Mitchell in 1952 as a spontaneously occurring slow growing variant. In genetic crosses, the poky phenotype was found to b... | Wikipedia - Uniparental inheritance - History > Poky mutants of Neurospora | 205 | 898 | null |
Article: Upstream activating sequence. An upstream activating sequence or upstream activation sequence (UAS) is a cis-acting regulatory sequence found in yeast like Saccharomyces cerevisiae. It is distinct from the promoter and increases the expression of a neighbouring gene. Due to its essential role in activating tra... | Wikipedia - Upstream activating sequence - Summary | 272 | 1,440 | null |
Section: Examples > GAL1-GAL10 intergenic region (UASG). The property of the GAL1-GAL10 to bind the GAL4 protein is utilised in the GAL4/UAS technique for controlled gene mis-expression in Drosophila. This is the most popular form of binary expression in Drosophila melanogaster, a system which has been adapted for many... | Wikipedia - Upstream activating sequence - Examples > GAL1-GAL10 intergenic region (UASG) | 325 | 1,427 | null |
The role of specific regions of UASG was analyzed by inserting oligonucleotides with different binding properties, leading to the successful identification of a region responsible for the creation of an ordered array. The sequence identified overlapped a binding site for GAL4 protein, which is a positive regulator for ... | Wikipedia - Upstream activating sequence - Examples > GAL1-GAL10 intergenic region (UASG) | 219 | 1,081 | null |
Section: Examples > Inositol-sensitive upstream activation sequence (UASINO). The inositol-sensitive upstream activation sequence (UASINO) has a consensus sequence 5'-CATGTGAAAT-3' and is present in the promoter regions of genes that encode enzymes of phospholipid biosynthesis. These enzymes are regulated by inositol a... | Wikipedia - Upstream activating sequence - Examples > Inositol-sensitive upstream activation sequence (UASINO) | 316 | 1,356 | null |
Section: Viruses > SARS-CoV-2. It was said in 2013 that "there is no universally accepted definition for the terms 'strain', 'variant', and 'isolate' in the virology community, and most virologists simply copy the usage of terms from others". The lack of precise definition continued in 2020; in the context of the Varia... | Wikipedia - Variant (biology) - Viruses > SARS-CoV-2 | 152 | 625 | null |
Section: Background. A karyotype (Fig 1) is the characteristic chromosome complement of a eukaryote species. A karyotype is typically presented as an image of the chromosomes from a single cell arranged from largest (chromosome 1) to smallest (chromosome 22), with the sex chromosomes (X and Y) shown last. Historically,... | Wikipedia - Virtual karyotype - Background | 152 | 726 | null |
Section: Method. Recently, platforms for generating high-resolution karyotypes in silico from disrupted DNA have emerged, such as array comparative genomic hybridization (arrayCGH) and SNP arrays. Conceptually, the arrays are composed of hundreds to millions of probes which are complementary to a region of interest in ... | Wikipedia - Virtual karyotype - Method | 345 | 1,564 | null |
Section: Method > Different platforms for virtual karyotyping. Array-based karyotyping can be done with several different platforms, both laboratory-developed and commercial. The arrays themselves can be genome-wide (probes distributed over the entire genome) or targeted (probes for genomic regions known to be involved... | Wikipedia - Virtual karyotype - Method > Different platforms for virtual karyotyping | 343 | 1,320 | null |
Section: Applications > Detecting copy-number changes. Copy number changes can be seen in both germline and tumor samples. Copy number changes can be detected by arrays with non-polymorphic probes, such as arrayCGH, and by SNP-based arrays. Human beings are diploid, so a normal copy number is always two for the non-sex... | Wikipedia - Virtual karyotype - Applications > Detecting copy-number changes | 349 | 1,475 | null |
Section: Applications > Loss of heterozygosity (LOH), autozygous segments, and uniparental disomy. Autozygous segments and uniparental disomy (UPD) are diploid/'copy neutral' genetic findings and therefore are only detectable by SNP-based arrays. Both autozygous segments and UPD will show loss of heterozygosity (LOH) w... | Wikipedia - Virtual karyotype - Applications > Loss of heterozygosity (LOH), autozygous segments, and uniparental disomy | 343 | 1,285 | null |
Also in contrast to autozygosity, UPD can develop in tumor cells, and this is referred to as acquired UPD or copy neutral LOH in the literature (Fig 6). Acquired UPD is quite common in both hematologic and solid tumors, and is reported to constitute 20 to 80% of the LOH seen in human tumors. Acquired UPD can serve as t... | Wikipedia - Virtual karyotype - Applications > Loss of heterozygosity (LOH), autozygous segments, and uniparental disomy | 190 | 756 | null |
Section: Examples of clinical cancer applications > Neuroblastoma. Based on a series of 493 neuroblastoma samples, it has been reported that overall genomic pattern, as tested by array-based karyotyping, is a predictor of outcome in neuroblastoma: Tumors presenting exclusively with whole chromosome copy number changes ... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Neuroblastoma | 276 | 1,155 | null |
Section: Examples of clinical cancer applications > Renal-cell carcinoma. Renal epithelial neoplasms have characteristic cytogenetic aberrations that can aid in classification. See also Atlas of Genetics and Cytogenetics in Oncology and Haematology. Clear cell carcinoma: loss of 3p Papillary carcinoma: trisomy 7 and 17... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Renal-cell carcinoma | 232 | 950 | null |
Section: Examples of clinical cancer applications > Chronic lymphocytic leukemia. Array-based karyotyping is a cost-effective alternative to FISH for detecting chromosomal abnormalities in chronic lymphocytic leukemia (CLL). Several clinical validation studies have shown >95% concordance with the standard CLL FISH pane... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Chronic lymphocytic leukemia | 327 | 1,383 | null |
Section: Examples of clinical cancer applications > Multiple myeloma. Avet-Loiseau, et al. in Journal of Clinical Oncology, used SNP array karyotyping of 192 multiple myeloma (MM) samples to identify genetic lesions associated with prognosis, which were then validated in a separate cohort (n = 273). In MM, lack of a pr... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Multiple myeloma | 267 | 1,091 | null |
Section: Examples of clinical cancer applications > Oligodendroglioma. The 1p/19q co-deletion is considered a "genetic signature" of oligodendroglioma. Allelic losses on 1p and 19q, either separately or combined, are more common in classic oligodendrogliomas than in either astrocytomas or oligoastrocytomas. In one stud... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Oligodendroglioma | 316 | 1,132 | null |
This allows assessment of other key loci in glial tumors, such as EGFR and TP53 copy number status. Whereas the prognostic relevance of 1p and 19q deletions is well established for anaplastic oligodendrogliomas and mixed oligoastrocytomas, the prognostic relevance of the deletions for low-grade gliomas is more controve... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Oligodendroglioma | 235 | 912 | null |
Section: Examples of clinical cancer applications > Glioblastoma. Yin et al. studied 55 glioblastoma and 6 GBM cell lines using SNP array karyotyping. Acquired UPD was identified at 17p in 13/61 cases. A significantly shortened survival time was found in patients with 13q14 (RB) deletion or 17p13.1 (p53) deletion/acqui... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Glioblastoma | 276 | 1,102 | null |
Section: Examples of clinical cancer applications > Acute lymphoblastic leukemia. Cytogenetics, the study of characteristic large changes in the chromosomes of cancer cells, has been increasingly recognized as an important predictor of outcome in acute lymphoblastic leukemia (ALL).NB: Balanced translocations cannot be ... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Acute lymphoblastic leukemia | 343 | 1,442 | null |
Section: Examples of clinical cancer applications > Myelodysplastic syndrome. Myelodysplastic syndrome (MDS) has remarkable clinical, morphological, and genetic heterogeneity. Cytogenetics play a decisive role in the World Health Organization's classification-based International Prognostic Scoring System (IPSS) for MDS... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Myelodysplastic syndrome | 257 | 990 | null |
Section: Examples of clinical cancer applications > Myeloproliferative neoplasms/myeloproliferative disorders. Philadelphia chromosome–negative myeloproliferative neoplasms (MPNs) including polycythemia vera, essential thrombocythemia, and primary myelofibrosis show an inherent tendency for transformation into leukemia... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Myeloproliferative neoplasms/myeloproliferative disorders | 341 | 1,459 | null |
Section: Examples of clinical cancer applications > Colorectal cancer. Identification of biomarkers in colorectal cancer is particularly important for patients with stage II disease, where less than 20% have tumor recurrence. 18q LOH is an established biomarker associated with high risk of tumor recurrence in stage II ... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Colorectal cancer | 205 | 856 | null |
Section: Examples of clinical cancer applications > Malignant rhabdoid tumors. Malignant rhabdoid tumors are rare, highly aggressive neoplasms found most commonly in infants and young children. Due to their heterogenous histologic features, diagnosis can often be difficult and misclassifications can occur. In these tum... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Malignant rhabdoid tumors | 350 | 1,350 | null |
Section: Examples of clinical cancer applications > Uveal melanoma. The most important genetic alteration associated with poor prognosis in uveal melanoma is loss of an entire copy of Chromosome 3 (Monosomy 3), which is strongly correlated with metastatic spread. Gains on chromosomes 6 and 8 are often used to refine th... | Wikipedia - Virtual karyotype - Examples of clinical cancer applications > Uveal melanoma | 175 | 748 | null |
Section: Limitations. Unlike karyotypes obtained from conventional cytogenetics, virtual karyotypes are reconstructed by computer programs using signals obtained from disrupted DNA. In essence, the computer program will correct translocations when it lines up the signals in chromosomal order. Therefore, virtual karyoty... | Wikipedia - Virtual karyotype - Limitations | 341 | 1,584 | null |
Article: Weismann barrier. The Weismann barrier, proposed by August Weismann, is the strict distinction between the "immortal" germ cell lineages producing gametes and "disposable" somatic cells in animals (but not plants), in contrast to Charles Darwin's proposed pangenesis mechanism for inheritance. In more precise t... | Wikipedia - Weismann barrier - Summary | 345 | 1,635 | null |
Section: Immortality of the germline. The Russian biologist and historian Zhores A. Medvedev, reviewing Weismann's theory a century later, considered that the accuracy of genome replicative and other synthetic systems alone could not explain the "immortal" germ cell lineages proposed by Weismann. Rather Medvedev though... | Wikipedia - Weismann barrier - Immortality of the germline | 172 | 888 | null |
Article: X hyperactivation. X hyperactivation refers to the process in Drosophila by which genes on the X chromosome in male flies become twice as active as genes on the X chromosome in female flies. In Drosophila, there is a stark difference between the X and Y chromosome as most genetic material has been lost on the ... | Wikipedia - X hyperactivation - Summary | 342 | 1,614 | null |
This remaining portion contains an early stop codon resulting in no sex-lethal protein being made. In females, the sex-lethal protein inhibits the male-specific lethal (msl) gene complex that would normally activate X-linked genes, increasing the male transcription rate. The msl gene complex was named due to the loss-o... | Wikipedia - X hyperactivation - Summary | 330 | 1,536 | null |
Article: X-inactivation. X-inactivation (also called Lyonization, after English geneticist Mary Lyon) is a process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packaged into a transcriptionally inactive structure called heterochr... | Wikipedia - X-inactivation - Summary | 273 | 1,342 | null |
Section: Mechanism > Cycle of X-chromosome activation in rodents. The paragraphs below have to do only with rodents and do not reflect XI in the majority of mammals. X-inactivation is part of the activation cycle of the X chromosome throughout the female life. The egg and the fertilized zygote initially use maternal tr... | Wikipedia - X-inactivation - Mechanism > Cycle of X-chromosome activation in rodents | 290 | 1,318 | null |
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