He reasoned that the loss of beneficial mutations because of clonal interference inhibits the adaptivity of asexually reproducing species. (wikipedia.org)
Clonal interference does not only play a role in the fixation of mutations in chromosomal DNA, but it also influences the stability or persistence of extrachromosomal DNA in the form of plasmids. (wikipedia.org)
Instead, mutators experience indirect selection, mediated by persistent statistical associations with fitness-affecting mutations elsewhere in the genome. (elifesciences.org)
So are you going to tackle my posts regarding the distribution of mutations along the selection coefficient axis? (uncommondescent.com)
This phenomenon is called clonal interference and causes competition among the mutations. (mercinewyork.com)
By sequencing samples from populations grown for 1,000 generations in rich growth medium, the team saw signs of rampant genetic hitchhiking - a phenomenon whereby sets of mutations arise together and spread through the population as a group, or 'clonal cohort. (genomeweb.com)
Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes," they continued, "and the deterministic action of selection on individual mutations, which favors parallel evolutionary solutions in replicate populations. (genomeweb.com)
Almost half the time that mutations related to (U.S. Food and Drug Administration)-approved indications for PARP inhibitor eligibility were detected in cfDNA, they were derived from blood-cell clonal hematopoiesis, and not related to prostate cancer," he said. (medicom-publishers.com)
These interfering clonal hematopoiesis mutations were particularly common in older age groups. (medicom-publishers.com)
We found that by incorporating a paired whole-blood control sample into the test we were easily able to distinguish prostate-cancer mutations in plasma cfDNA from blood-cell clonal hematopoiesis. (medicom-publishers.com)
but most of the currently available commercial cfDNA assays test only plasma, and cannot readily distinguish cancer mutations from blood cell interference. (medicom-publishers.com)
Dr. Joshi J. Alumkal of the University of Michigan, in Ann Arbor, who co-wrote an accompanying editorial, told Reuters Health by email that the results "provide a cautionary note on using cell-free DNA sequencing to identify patients with mutations in homologous recombination DNA-repair genes - gene mutations that are routinely used for PARP inhibitor treatment selection. (medicom-publishers.com)
He added, "Understanding whether these mutations are due to tumor cells versus clonal hematopoiesis is critical to make the most well-informed decisions about patient management. (medicom-publishers.com)
In primary tumors, mutations in driver genes frequently provide a survival advantage and give rise to a dominant clonal population. (spandidos-publications.com)
Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. (biomedcentral.com)
Evolutionary4
Clonal interference is a phenomenon in evolutionary biology, related to the population genetics of organisms with significant linkage disequilibrium, especially asexually reproducing organisms. (wikipedia.org)
In this way, clonal interference influences the evolutionary dynamics of plasmid-host adaptation, resulting in faster stabilisation of plasmids in a population. (wikipedia.org)
5) Evolutionary consequences of mating systems (e.g. clonal vs. sexual reproduction, bottlenecks, colonizing potential, efficacy of natural selection). (ethz.ch)
Multiple clonal cohorts are often present simultaneously, competing with each other in the same population," senior author Michael Desai, an organismic and evolutionary biology researcher at Harvard University, and his co-authors wrote. (genomeweb.com)
CRISPR5
We developed a procedure for rapid screening of clonal cell lines for the deletion of a protein of interest following CRISPR/Cas9 targeting in the absence of selective pressure based on dot immunoblots. (biomedcentral.com)
Clonal screening for CRISPR/Cas9-mediated editing events using dot immunoblot is a straightforward and efficient approach that facilitates rapid generation of genomic mutants to study gene function. (biomedcentral.com)
From RNA interference (RNAi) to CRISPR, there are several methods that researchers can use to manipulate gene function, each with its own strengths and weaknesses. (technologynetworks.com)
Utilizing complementary methods, including RNAi and CRISPR-knockout, -interference and -activation, enables researchers to have confidence in their results. (technologynetworks.com)
RNA interference (RNAi) was the primary tool for disrupting gene expression (along with zinc finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs)) but newer CRISPR-based technologies, including CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are viable options. (technologynetworks.com)
Tumor cells1
However, rather than actively modifying the environment, multiple mechanisms guide the evolution of tumor cells through the selection of subclones with the most adaptive phenotype by environmental factors ( 1 ). (spandidos-publications.com)
Mutation5
As the name suggests, clonal interference occurs in an asexual lineage ("clone") with a beneficial mutation. (wikipedia.org)
Whenever a beneficial mutation arises in a population, for example mutation A, the carrier of the mutation obtains a higher fitness compared to members of the population without mutation A by means of natural selection. (wikipedia.org)
This has to do with the fact that clonal interference also influences another part of the reproductive strategy of a population, namely mutation rate. (wikipedia.org)
Biebricher CK (1999) Mutation, competition and selection as measured with small RNA molecules. (springer.com)
Depending on the desired mutation, several experimental options exist in the isolation of clonal lines, such as selection with introduced markers, or screening by PCR amplification of genomic DNA. (biomedcentral.com)
Reproductive2
While this expectation has been confirmed by a number of observations [ 2 ], it does not explain the advantages of a mixed reproductive strategy involving clonal reproduction in particular. (biomedcentral.com)
Clonal reproduction and self-pollination are conductive to reproductive assurance in populations with pollinator scarcity, while sexual reproduction and cross-pollination can improve seed quality and genetic diversity of offspring, which could benefit population survival in the potential climate flunctations. (plant-ecology.com)
Stochastic3
Here, we use stochastic, agent-based simulations to show that neither the strength nor the sign of selection on mutators depend on their initial frequency, and while the overall probability of hitchhiking increases predictably with frequency, the per-capita probability of fixation remains unchanged. (elifesciences.org)
Here, we use stochastic, agent-based computer simulations to demonstrate that on the contrary, indirect selection on mutators is independent of frequency. (elifesciences.org)
Clonally variant gene expression (CVGE) lies at the base of a bet-hedging adaptive strategy consisting of the stochastic generation of phenotypic diversity followed by natural selection upon environmental changes (for a recent discussion on bet-hedging, see [14] ). (plos.org)
Populations4
The heterogeneity found in cells of carcinogenic tumours implies competition between sub-populations of cells in the tumour, hence clonal interference. (wikipedia.org)
Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. (biomedcentral.com)
Signals of recent positive selection in a worldwide sample of human populations. (academicinfluence.com)
Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. (biomedcentral.com)
RNAi1
Resistance to such inhibitors has already been observed, guiding the prediction of their use in combination therapies with other targeted agents such as RNA interference (RNAi). (biomedcentral.com)
Gene3
Reuters Health - 11/11/2020 - In men with prostate cancer, cell-free DNA (cfDNA) testing may be confounded by clonal hematopoiesis (CHIP) gene variants, leading some patients to be treated inappropriately with poly(ADP) ribose polymerase (PARP) inhibitors. (medicom-publishers.com)
To assess the technique, we probed clonal isolates of 293-TREx cells that were targeted with three separate sgRNAs against the HuR gene. (biomedcentral.com)
2) The estimation of amounts of clonal reproduction critically depends on the assumptions about multilocus gene associations. (biomedcentral.com)
Phenomenon2
When Muller introduced the phenomenon of clonal interference, he used it to explain why sexual reproduction evolved. (wikipedia.org)
The phenomenon of clonal interference also occurs in cancer and pre-cancer cell lineages within a patient. (wikipedia.org)
Critically1
Critically, a frequency-dependent framing of indirect selection on mutators implies a change in the sign or the strength of indirect selection with frequency. (elifesciences.org)
Phenotypic1
This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. (stanford.edu)
Borrego B, Novella IS, Giralt E, Andreu D, Domingo E (1993) Distinct repertoire of antigenic variants of foot-and-mouth disease virus in the presence or absence of immune selection. (springer.com)
As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. (ox.ac.uk)
We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. (ox.ac.uk)
However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. (ox.ac.uk)
Deterministic1
Deterministic evolution and stringent selection during preneoplasia. (stanford.edu)
Assumptions1
Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. (ox.ac.uk)
Loci2
The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. (ox.ac.uk)
An Imperial College London-led group used genome sequencing to search for loci that have been subject to artificial selection in lab rats. (genomeweb.com)
Artificial selection1
The principles on which laboratory evolution experiments are based, date back to scientists such as Antonie van Leeuwenhoek, Louis Pasteur, Robert Koch and most notably Charles Darwin, with their discoveries of microorganisms, the general acceptance of the germ theory and the importance of natural and artificial selection for biological evolution and breeding. (biomedcentral.com)
Sexual reproduction1
The maintenance of sexual reproduction (specifically, of its dioecious form) by natural selection in a highly competitive world has long been one of the major mysteries of biology, since both other known mechanisms of reproduction - asexual reproduction and hermaphroditism - possess apparent advantages over it. (wikizero.com)
Natural1
In the group selection shelterwood systems, natural regeneration is achieved by irregular, groupwise lowering of stand density in old stands. (biomedcentral.com)
Therapies1
Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies. (ox.ac.uk)
Frequency1
Clear differences were found in the reproduction pattern between two stands representing the two forest management types: 1) Clonal propagation is observed in both management systems, but with a distinctly higher frequency in the CWS. (biomedcentral.com)
Evolution1
Also, mutant spectra are the target on which selection and random drift act to shape the long-term evolution of viruses. (springer.com)
Fact2
This fact is ignored by most geneticists because selection scenarios become hopelessly complex and unworkable unless such interactions are conveniently set aside. (uncommondescent.com)
In fact, P. avium can be observed primarily in two systems of forest management, in "group selection shelterwood systems" (= high forest system, HFS in the following) and in relics of former "coppice with standards" systems (= CWS in the following). (biomedcentral.com)
Immune1
Optimum M-sequence Search via Immune Clonal Selection Algorithm. (xidian.edu.cn)
Human1
Through the late 1950s, macfarland burnet proposed the clonal alefacept selection theory, which states for human prescription drug misuse/ atric syndrome. (stonecottagegardens.com)
Multiple1
Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. (ox.ac.uk)
Degree1
3) Haplotype diversities are higher in the CWS and found to be associated with a large degree of heterozygosity for the second largest clonal group. (biomedcentral.com)
Infection1
To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. (ox.ac.uk)
Small1
Transient perturbations involve chemical inhibition (and activation) with small molecules, overexpression from non-integrating vectors, or knockdown by RNA interference [ 1 ]. (biomedcentral.com)
Order1
2008,' Comparison of download the writers of many SNP classics in reminder technological value-based history', Data Mining and Analytics 2008: journals of the Seventh Australasian Data Mining Conference( AusDM 2008), Conferences in Research and Practice in IT( CRPIT), Vol. 87, Australian Data Mining Conference, Australian Computer Society, Adelaide, Australia, Coverage Data TB and expression order consider treated written to children in clonal images covering extensive licenses. (lightseed.com)