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Статті в журналах з теми "Allele distribution models"
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Yu, Haibing, Shu Wang, Wei Hu, Lin Xu, Yuanlin Ding, Danli Kong, and Haiyan Pan. "Association between Single-nucleotide Polymorphisms of RXRG and Genetic Susceptibility to Type 2 Diabetes in South China." Current Molecular Medicine 20, no. 6 (June 22, 2020): 408–14. http://dx.doi.org/10.2174/1566524020666191206163951.
Повний текст джерелаАнотація:
Objective: To investigate the relationship between genetic polymorphisms of RXRG rs1467664, rs3753898 and the genetic susceptibility of type 2 diabetes in the Chinese Han population from South China. Methods: In our case-control study, single-nucleotide polymorphisms (SNPs) rs1467664 and rs3753898 were genotyped by SNPscanTM kit in 1092 patients with T2D as cases and 1092 normal persons as controls. The distributions of genotype and allele frequencies in two groups were analyzed by the SPSS 20.0 software. Results: The distribution of genotypes and alleles of RXRG rs3753898 was statistically significant between the two groups, but there was no significant difference in the distribution of genotypes and alleles of the rs1467664. Before and after the adjustment of age, sex and BMI, rs3753898 in the two groups had statistical significance under the additive, dominant and recessive models (P<0.05), but no statistical differences were found under the overdominance and co-dominant genetic models (P>0.05). There was no significant difference in the genetic models of rs1467664 between the two groups (P>0.05). The haplotype, which consists of rs1467664 allele T and rs3753898 allele A was a high-risk factor for T2D, OR=1.27, 95% CI (1.09-1.47), Padj=0.002. Conclusion: Our results showed that the single nucleotide polymorphism of RXRG rs3753898 may be related to genetic susceptibility of type 2 diabetes. The haplotype consisting of the allele T of rs1467664 and the allele A of rs3753898 is a risk factor for type 2 diabetes, suggesting that the genetic variation of RXRG gene may be the genetic cause of diabetes mellitus in the Chinese Han population.
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Wenne, Roman, Małgorzata Zbawicka, Lis Bach, Petr Strelkov, Mikhail Gantsevich, Piotr Kukliński, Tomasz Kijewski, et al. "Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors." Genes 11, no. 5 (May 10, 2020): 530. http://dx.doi.org/10.3390/genes11050530.
Повний текст джерелаАнотація:
Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r2 between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m−3 of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.
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Mani, G. S., L. M. Cook, and R. Marvdashti. "WHAT CAN BE LEARNT ABOUT SELECTION FROM GENE FREQUENCY DISTRIBUTION?" Genetics 114, no. 3 (November 1, 1986): 971–82. http://dx.doi.org/10.1093/genetics/114.3.971.
Повний текст джерелаАнотація:
ABSTRACT Polymorphism has been studied at the Esterase 6 locus in the Yellow Fever mosquito Aedes aegypti (L.) in laboratory stocks. At least 12 alleles are present, with up to four coexisting in a stock. The allele frequency distribution is quite sharply peaked at a mode of about 0.25. The experimental data are compared with the results of simulation based on two models, one in which the initial global distribution is taken to be the stationary distribution obtained from the neutral model assuming M = 4μ Ne = 1 and the other in which the initial global distribution is generated from the experimental populations studied. The results suggest that the patterns observed are not likely to arise through random fluctuation of frequencies in neutral alleles, but that some kind of selection maintains polymorphism, either in the wild or in the laboratory, or both.
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Gan, Han L., Adrian Röllin, and Nathan Ross. "Dirichlet approximation of equilibrium distributions in Cannings models with mutation." Advances in Applied Probability 49, no. 3 (September 2017): 927–59. http://dx.doi.org/10.1017/apr.2017.27.
Повний текст джерелаАнотація:
AbstractConsider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is an important quantity in population genetics but has no tractable description in general. We provide upper bounds on the distributional distance between the Dirichlet distribution and this finite-population stationary distribution for the Wright–Fisher genealogy with general mutation structure and the Cannings exchangeable genealogy with parent independent mutation structure. In the first case, the bound is small if the population is large and the mutations do not depend too much on parent type; 'too much' is naturally quantified by our bound. In the second case, the bound is small if the population is large and the chance of three-mergers in the Cannings genealogy is small relative to the chance of two-mergers; this is the same condition to ensure convergence of the genealogy to Kingman's coalescent. These results follow from a new development of Stein's method for the Dirichlet distribution based on Barbour's generator approach and a probabilistic description of the semigroup of the Wright–Fisher diffusion due to Griffiths and Li (1983) and Tavaré (1984).
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De Sá, Nathalia Beatriz Ramos, Karina dos S. Silva, Marcelo Ribeiro-Alves, Diogo Gama Caetano, Fernanda Heloise Côrtes, Suwellen S. D. de Azevedo, Brenda Hoagland, et al. "Killer immunoglobulin-like receptor (KIR) genes are associated with the risk of episodes of high-level and detectable viremia among HIV controllers." F1000Research 10 (July 7, 2021): 546. http://dx.doi.org/10.12688/f1000research.53683.1.
Повний текст джерелаАнотація:
Background: HIV controllers (HICs) constitute a heterogeneous group of HIV-1 individuals able to suppress plasma viremia to low or undetectable levels in the absence of antiretroviral therapy. Host genetic factors may be involved in the sustained control of viral replication observed. We investigated the distribution and the potential impact of human leukocyte antigens (HLA)-B and -C alleles, killer immunoglobulin-like receptor (KIR) genes, single nucleotide polymorphisms (SNPs) of the NLRP3, CARD8 and IL-1β inflammasome genes, and CCR5Δ32 mutation on the viral control among HICs. Methods: In total, 28 HICs were categorized as persistent elite controllers (PECs, n = 7), ebbing elite controllers (EECs, n = 7), and viremic controllers (VCs, n = 14) according to the level of natural suppression of viremia. HLA alleles were assigned by sequencing-based typing, KIR alleles by polymerase chain reaction (PCR) sequence-specific amplification, SNPs by real-time PCR, and the CCR5Δ32 mutation by PCR. Results: Significant differences were observed in the pairwise comparisons of protective HLA-B alleles, KIR Bx genotype, KIR2DL3 + C1 pair, KIR2DL5, and KIR2DS5 allelic carrier frequencies among the HIC groups. Multivariate models showed that HICs without the KIR2DL3 allele or without KIR2DL3 + C1/C2 pair, with the HLA-C*08 allele or with the NLRP3 rs10754558-G SNP had a higher mean hazard of a viral load above 2,000 copies/mL, while a lower mean hazard of this event was observed for HICs with KIR2DL5, KIR2DS1, KIR2DS5, and KIR3DS1 alleles. Moreover, HICs with the KIR2DS5 allele had less risk of undergoing viral load (VL) blips within the same normalized period than those participants without this allele, while HICs without the KIR2DL3 allele had a mean higher risk of experiencing VL blips. Conclusions: These results indicate that innate immune mechanisms may play an essential role in modulating the sustained control of viral replication in HICs.
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Whittaker, John C., Roger M. Harbord, Nicola Boxall, Ian Mackay, Gary Dawson, and Richard M. Sibly. "Likelihood-Based Estimation of Microsatellite Mutation Rates." Genetics 164, no. 2 (June 1, 2003): 781–87. http://dx.doi.org/10.1093/genetics/164.2.781.
Повний текст джерелаАнотація:
Abstract Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.
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Schierup, Mikkel H., Xavier Vekemans, and Freddy B. Christiansen. "Evolutionary Dynamics of Sporophytic Self-Incompatibility Alleles in Plants." Genetics 147, no. 2 (October 1, 1997): 835–46. http://dx.doi.org/10.1093/genetics/147.2.835.
Повний текст джерелаАнотація:
The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act codominantly in both pollen and style (SSIcod), in the second, alleles form a dominance hierarchy in pollen and style (SSIdom). In the third model, alleles interact codominantly in the style and form a dominance hierarchy in the pollen (SSIdomcod). The SSIcod model behaves similarly to the model of gametophytic self-incompatibility, but the selection intensity is stronger. With dominance, dominant alleles invade the population more easily than recessive alleles and have a lower frequency at equilibrium. In the SSIdom model, recessive alleles have both a higher allele frequency and higher expected life span. In the SSIdomcod model, however, loss due to drift occurs more easily for pollen-recessive than for pollen-dominant alleles, and therefore, dominant alleles have a higher expected life span than the more recessive alleles. The process of allelic turnover in the SSIdomcod and SSIdom models is closely approximated by a random walk on a dominance ladder. Implications of the results for experimental studies of sporophytic self-incompatibility in natural populations are discussed.
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Ramil, E., AJ Sánchez, P. González-Pérez, A. Rodríguez-Antigüedad, N. Gómez-Lozano, P. Ortiz, R. Arroyo, V. De las Heras, C. Vilches, and A. García-Merino. "The cannabinoid receptor 1 gene (CNR1) and multiple sclerosis: an association study in two case-control groups from Spain." Multiple Sclerosis Journal 16, no. 2 (December 9, 2009): 139–46. http://dx.doi.org/10.1177/1352458509355071.
Повний текст джерелаАнотація:
Different studies point to the implication of the endocannabinoid system in multiple sclerosis (MS) and animal models of MS. The purpose of this study was to evaluate a possible association of MS with polymorphic markers at the CNR1 gene, encoding the cannabinoid 1 (CB1) receptor. We have performed a genetic analysis of an AAT repeat microsatellite localized in the downstream region of the CNR1 gene, in two case—control groups of MS patients and healthy controls (HC) from Spain (Madrid and Bilbao). MS patients with primary progressive MS (PPMS) had more commonly long ((AAT) ≥13) alleles and genotypes with a significant difference for genotype 7/8 in Madrid (p = 0.043) and in the sum of both groups (p = 0.016); short alleles were less frequently found in PPMS with a significant difference for allele 5 in the analysis of both groups together (p = 0.039). In patients with relapsing MS, no consistent differences in allele and genotype distribution were found. Disease severity and progression was unrelated to AAT repeat variations. In conclusion, long (AAT) ≥13 CNR1 genotypes could behave as risk factors for PPMS.
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Donnelly, Peter, and Paul Joyce. "Consistent ordered sampling distributions: characterization and convergence." Advances in Applied Probability 23, no. 02 (June 1991): 229–58. http://dx.doi.org/10.1017/s0001867800023478.
Повний текст джерелаАнотація:
This paper is concerned with models for sampling from populations in which there exists a total order on the collection of types, but only the relative ordering of types which actually appear in the sample is known. The need for consistency between different sample sizes limits the possible models to what are here called ‘consistent ordered sampling distributions'. We give conditions under which weak convergence of population distributions implies convergence of sampling distributions and conversely those under which population convergence may be inferred from convergence of sampling distributions. A central result exhibits a collection of ‘ordered sampling functions', none of which is continuous, which separates measures in a certain class. More generally, we characterize all consistent ordered sampling distributions, proving an analogue of de Finetti's theorem in this context. These results are applied to an unsolved problem in genetics where it is shown that equilibrium age-ordered population allele frequencies for a wide class of exchangeable reproductive models converge weakly, as the population size becomes large, to the so-called GEM distribution. This provides an alternative characterization which is more informative and often more convenient than Kingman's (1977) characterization in terms of the Poisson–Dirichlet distribution.
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Donnelly, Peter, and Paul Joyce. "Consistent ordered sampling distributions: characterization and convergence." Advances in Applied Probability 23, no. 2 (June 1991): 229–58. http://dx.doi.org/10.2307/1427746.
Повний текст джерелаАнотація:
This paper is concerned with models for sampling from populations in which there exists a total order on the collection of types, but only the relative ordering of types which actually appear in the sample is known. The need for consistency between different sample sizes limits the possible models to what are here called ‘consistent ordered sampling distributions'. We give conditions under which weak convergence of population distributions implies convergence of sampling distributions and conversely those under which population convergence may be inferred from convergence of sampling distributions. A central result exhibits a collection of ‘ordered sampling functions', none of which is continuous, which separates measures in a certain class. More generally, we characterize all consistent ordered sampling distributions, proving an analogue of de Finetti's theorem in this context. These results are applied to an unsolved problem in genetics where it is shown that equilibrium age-ordered population allele frequencies for a wide class of exchangeable reproductive models converge weakly, as the population size becomes large, to the so-called GEM distribution. This provides an alternative characterization which is more informative and often more convenient than Kingman's (1977) characterization in terms of the Poisson–Dirichlet distribution.
Дисертації з теми "Allele distribution models"
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Poncet, Bénédicte N. "Modèles de distribution d’allèles pour la détection de la variabilité génétique adaptative chez une espèce non modèle, Arabis alpina." Grenoble, 2010. http://www.theses.fr/2010GRENV034.
Повний текст джерелаАнотація:
Comprendre les bases moléculaires de l'adaptation est un enjeu majeur en biologie évolutive. L'adaptation locale est le patron de distribution de génotypes résultant de l'action de la sélection qui tend à différencier certaines populations vivant dans des environnements différents. Au niveau génétique, l'adaptation locale se traduit par des fréquences alléliques variant le long des gradients de sélection. L'objectif de ce travail de doctorat est d'étudier l'apport des modèles de distributions d'allèles dans l'étude de l'adaptation locale à travers le cas de la plante alpine Arabis alpina (Brassicaceae) en milieu naturel. Premièrement, un criblage génomique de 825 marqueurs AFLPs sur 678 plantes provenant de 198 sites des Alpes françaises et suisses a été réalisé. Il a nécessité le développement d'une méthode de sélection des marqueurs semi-automatique. Les conséquences de cette sélection des marqueurs sur l'estimation des structure et variabilité génétiques ont été explorées. Deuxièmement, des loci d'intérêt écologique ont été identifiés comme potentiellement sous sélection. Leurs distributions alléliques sont significativement corrélées à des variables environnementales climatiques et topographiques. Les effets confondants (admixture et isolement par la distance) ont été évalués et écartés dans notre cas d'étude. Troisièmement, certains loci d'intérêt écologique ont été séquencés afin d'identifier des gènes candidats et régions génomiques potentiellement sélectionnées, en recourant à la synténie entre les génomes d'A. Alpina et de l'espèce modèle, Arabidopsis thaliana. Finalement, l'approche corrélative de détection de la sélection a été comparée avec les approches plus classiques de génomique des populations permettant de la valider. L'ensemble de ces travaux suggère que les modèles de distribution d'allèles sont une première étape pertinente avant des études d'écologie fonctionnelle visant à mieux comprendre l'adaptation à différentes conditions environnementalesUnderstanding the molecular basis of adaptation is a major task in evolutionary biology. Local adaptation is the pattern of genotype distributions driven by the natural selection that tends to differentiate populations living in different environments. Genetically, local adaptation results in allele frequencies varying along selection gradients. Our objective is to infer the contribution of allele distribution models in the study of local adaptation through the case of the alpine plant Arabis alpina (Brassicaceae) in the wild. First, a genome scan of 825 AFLP markers genotyped on 678 plants from 198 sites in French and Swiss Alps has been completed and has required the development of a semi-automatic method to select the markers. The effects of this selection on the estimation of genetic structure and variability have been explored. Second, ecologically relevant loci were identified as potentially submitted to selection. Their allele distributions are significantly correlated with environmental variables and topographical conditions. The confounding effects (admixture and isolation by distance) were assessed and discarded in our study case. Some ecologically relevant loci have been sequenced to identify candidate genes and genomic regions potentially selected using the synteny between the genomes of A. Alpina and the model species Arabidopsis thaliana. Finally, the correlative approach to detect selection was compared with more traditional approaches of population genomic. These results suggest that the allele distribution models are a first step before the relevant functional ecology studies to better understand the adaptation to different environmental conditions
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Jäkel, Christian [Verfasser], Hans-Josef [Gutachter] Allelein, and Ulrich [Gutachter] Krause. "Entwicklung, Validierung und sicherheitstechnische Anwendung eines numerischen Ausbreitungsmodells für Flüssigwasserstoff = Development, validation and safety-related application of a numerical distribution model for liquid hydrogen / Christian Jäkel ; Gutachter: Hans-Josef Allelein, Ulrich Krause." Aachen : Universitätsbibliothek RWTH Aachen, 2018. http://d-nb.info/1192392426/34.
Повний текст джерелаКниги з теми "Allele distribution models"
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Saint-Paul, Gilles. Equilibrium allele distribution in trading populations. Bonn, Germany: IZA, 2006.
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Walsh, Bruce, and Michael Lynch. The Infinitesimal Model and Its Extensions. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0024.
Повний текст джерелаАнотація:
One standard approximation in quantitative genetics is the infinitesimal model, which assumes a large number of loci, each of small effect. In such a setting, the distribution of breeding values in unselected descendants is roughly multivariate normal and most of the (short-term) change in the additive variance under selection is through Bulmer effects (the generation of linkage disequilibrium) rather than by allele-frequency change. A variety of different infinitesimal models are found in the literature, and this chapter examines these different versions and the connections between them. It also examines the theory for moving beyond the infinitesimal approximation. Finally, this chapter shows that the much-debated worry over “missing heritability” simply follows under the infinitesimal setting.
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Walsh, Bruce, and Michael Lynch. Neutral Evolution in One- and Two-Locus Systems. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0002.
Повний текст джерелаАнотація:
This chapter reviews the population-genetic theory of neutral alleles in finite populations, examining the probabilities and times to loss or fixation, summary statistics for molecular variation, coalescent theory (the distribution of times back to common ancestry for a sample of alleles), and both mutation-drift and mutation-drift-migration equilibrium models.
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Darrigol, Olivier. Consolidation (1887–1895). Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198816171.003.0007.
Повний текст джерелаАнотація:
This chapter covers a period in which Boltzmann returned to the collision-based approach and consolidated it in answer to criticism and suggestions by William Thomson, Hendrik Lorentz, George Bryan, Gustav Kirchhoff, and Max Planck. He corrected errors in alleged counterexamples of equipartition by William Burnside and William Thomson; and in 1887, when the Dutch theorist Hendrik Lorentz detected an error in his earlier derivation of the H theorem for polyatomic gases, he devised a highly ingenious alternative. In 1894, he offered a new, simplified derivation of the Maxwell–Boltzmann distribution based on an idea by the British mathematician George Bryan. Together with Bryan, he also provided a kinetic-molecular model for the equalization of the temperatures of two contiguous gases. He denounced what he believed to be an error in Gustav Kirchhoff’s derivation of Maxwell’s distribution, and he strengthened Max Planck’s alternative derivation based on time reversal.
Частини книг з теми "Allele distribution models"
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Joost, Stéphane, Michael Kalbermatten, Etienne Bezault, and Ole Seehausen. "Use of Qualitative Environmental and Phenotypic Variables in the Context of Allele Distribution Models: Detecting Signatures of Selection in the Genome of Lake Victoria Cichlids." In Data Production and Analysis in Population Genomics, 295–314. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-870-2_17.
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Dumancas, Gerard G. "Applications of Supercomputers in Population Genetics." In Biotechnology, 693–719. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-8903-7.ch028.
Повний текст джерелаАнотація:
Population genetics is the study of the frequency and interaction of alleles and genes in population and how this allele frequency distribution changes over time as a result of evolutionary processes such as natural selection, genetic drift, and mutation. This field has become essential in the foundation of modern evolutionary synthesis. Traditionally regarded as a highly mathematical discipline, its modern approach comprises more than the theoretical, lab, and fieldwork. Supercomputers play a critical role in the success of this field and are discussed in this chapter.
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Láruson, Áki J., and Floyd A. Reed. "Adaptation and Natural Selection." In Population Genetics with R, 125–54. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780198829539.003.0007.
Повний текст джерелаАнотація:
Here non-random shifts in allele frequencies over time are introduced, as well as how to incorporate varying levels of selection into a model of a single population through time. This chapter highlights the difference between weak and strong selection, the dynamics of single allele versus genotype-level selection, and how selection strength and population size affect allele frequency distributions over time. Finally the inference of the selection coefficient from allele frequency data is discussed, alongside the concepts of overdominance and underdominance.
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Cutter, Asher D. "Neutral theories of molecular evolution." In A Primer of Molecular Population Genetics, 67–84. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198838944.003.0004.
Повний текст джерелаАнотація:
Chapter 4, “Neutral theories of molecular evolution,” outlines the logic and predictions of the neutral theory of molecular evolution and its derivatives as a simple conceptual framework for understanding DNA sequence evolution. It introduces the standard neutral model as a null model of evolutionary change in DNA sequences to describe patterns of polymorphism within species and divergence between species. An overview is provided for the molecular clock concept and for predictions about the amount of polymorphism and allele frequency distributions within populations. This chapter covers how population size and selection intersect to define nearly neutral fitness effects and their implications, as well as misinterpretations and misapplications of Neutral Theory. This overview provides a foundation for how theoretical predictions offer null models for tests of molecular evolution developed in later chapters.
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Cutter, Asher D. "The origins of molecular diversity." In A Primer of Molecular Population Genetics, 11–33. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198838944.003.0002.
Повний текст джерелаАнотація:
At its simplest, evolution is change in the relative abundance of alternative alleles, from one generation to the next. But where do these different alleles come from? As the ultimate origin of all genetic novelty, the input of new mutations into a population forms the critical first step for incorporating biological detail into how we conceive of genome evolution. Chapter 2, “The origins of molecular diversity,” summarizes the many mechanisms of mutation, the distribution of fitness effects, and how to characterize mutational processes themselves in conceptual models. It covers point mutations, indels, microsatellites, transposable elements, and other mutation types in the context of the genetic code and gene duplication, as well as the role of mutation accumulation experiments in understanding mutation rates and fitness effects. The infinite alleles, infinite sites, and stepwise mutation models are summarized, along with the concept of homoplasy and complexities to the mutation process in nature. These important extra pieces of biological realism connect more closely the mechanisms of evolution to show the path toward a deeper analysis of genomes.
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Del Percio, Enrique. "Argentina: The Philosophical Resistance to the Conquest of the Soul1." In A Post-Neoliberal Era in Latin America?, 159–76. Policy Press, 2019. http://dx.doi.org/10.1332/policypress/9781529200997.003.0008.
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In 1976, a terrible dictatorship was established in Argentina, even before Foucault claimed with crystal clarity that the fundamental difference between classical liberalism and neoliberalism was the substitution of the homo economicus −related to the exchange− by the homo economicus as entrepreneur of himself (lecture delivered on 14 March 1979); and also before Margaret Thatcher (in Ronald Butt’s interview, Sunday Times, 3 May 1981) confirmed Foucault´s analysis stating that: “Economics are the method; the object is to change the heart and soul”. In the same year, Milton Friedman received the Nobel Prize in Economics. The explicit purpose of the Military Junta was to promote a profound cultural transformation, based on the premise that the causes of the alleged “underdevelopment” were not so much economical but cultural and political. Nevertheless, as García Delgado and Molina (2006) pointed out, the problem is not related to a sort of inevitable structural poverty, due to the culture of our people. It is a matter of a decline in society, produced by the policy orientation of the dictatorship. Until then, the income distribution was similar to that of the countries from the Southern Europe with an almost frictional unemployment. Until the coup d’état, Argentina had a poverty rate of 8% and the best distributive structure of income in Latin America. However, 1976 was a turning point; the surge of the neoliberal model promoted a process of over-indebtedness, wealth concentration, unrestricted opening of markets with an unfavourable exchange rate for national industry, labour flexibilization, with the insertion in a competitive globalization of “savage capitalism” that “strengthened the asymmetries and transfers of resources from the periphery to the centre. This concept differs from thinking about inequality as a problem related to culture, corruption and poor institutional quality” (García Delgado, 2006).Despite the overwhelming adverse evidence, it is still a commonplace to blame all the ills of our society on that culture, the maximum expression of which would be Peronism. In fact, the great majority of disappeared people during the dictatorship were Peronist political, trade union and social leaders. The motto of the Ministry of Economics during the dictatorship was “towards a change of mentality”. The current Argentine situation, in terms of advances of neoliberalism as well as resistances to it, cannot be understood without referring to the dictatorship. In Poratti words, “the coup d’état of 1976 does not only put an end to a government, a political system and project, but also to a 'world' in which Argentinians were living at least from the independence project of 1810. In those days, there was not an abrupt differentiation between generations and, in many aspects, people could identify themselves, diachronically, with a historical line beyond the particular generational characteristics” (Various Authors, 2009).These aspects go along with others that appeared in other areas, such as the implementation of new computer and communication technologies and, as a consequence, individual and social fragmentation. The impact of these technologies on daily life was decisive to the emergence of what some authors, like Sloterdijk (2002), called “mass individualism.” No doubt, this is a necessary aspect to explain the rise of the neoliberal subjectivity in developed countries. Yet, in Argentina, the existence of political, social, trade-union and ecclesiastical movements based on popular roots, with solidarity as a fundamental value, hampered the conquest of the “heart and soul” in 1976; and they are still now an obstacle to be overcome by sectors interested in imposing a neoliberal model. It is impossible to explain any isolated phenomenon of popular resistance to the hegemonic attempts from neoliberalism without analysing the common conceptions and understandings found in Argentina. Indeed, the popular culture substrate in Argentina is made up, mainly, by the confluence of different cultures: Andean, Guaraní Indians, Afro and Criollo (native). All of them are characterized by their relational and solidarity conceptions, intrinsically opposed to a subjectivity that conceives the individual as an entrepreneur of himself/herself.
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Sassatelli, Monica. "Visual Arts Festivals and Globalisation, The rise of biennials." In Focus on World Festivals. Goodfellow Publishers, 2016. http://dx.doi.org/10.23912/978-1-910158-55-5-2985.
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Biennials or biennales are periodic, independent and international art exhibitions surveying trends in contemporary art; since the 1990s they have proliferated across the globe. Biennials are much more than curated displays, they constitute ‘festival-exhibitions’ working as “a public model and a shifting backdrop against which the meanings of contemporary art are constructed, maintained and sometimes irrevocably altered” (Ferguson et al., 2005: 48). Whilst most contemporary post-traditional festivals (Giorgi and Sassatelli, 2011) have ancient roots, it is only in recent years that they have become an almost ubiquitous fixture of cultural calendars in cities around the world. This current proliferation is even more striking for art biennials. They arguably originate from the Venice Biennale, held for the first time in 1895, but have long exceeded their European, Western origin to establish a global format. Up to the 1980s they were only reproduced in a handful of examples; today biennials and derivates (triennials and others) have become key institutional nodes linking production, consumption and distribution of contemporary art. With now over 150 biennials around the world, we are increasingly likely to encounter contemporary art through their mediation, directly as visitors or more indirectly via the nebula of critical discourse and more generally the media coverage they generate. The phenomenon attracting attention has become not just the biennials but more specifically the biennalisation of the art world. The term biennalisation is used within the art world itself as shorthand to refer to the proliferation and standardisation of biennial exhibitions under a common (if rather loose) format. Sociologically, biennalisation can thematise the shifting set of cultural classifications, practices and values that differentiate the contemporary art world, affecting both its content (now sometimes referred to as biennial art) and the type of rationale and experience it crystallises. As phenomena that increasingly represent themself “on a global scale” (Vogel 2010), biennials offer a unique vantage point to access what is often termed ‘global culture’. However, they remain rarely empirically studied in clearly defined contexts, especially beyond affirmation or negations of their measurable impact (Buchholz and Wuggenig, 2005). Reprising within the art world unsolved dilemmas in the analysis of cultural globalisation, alleged optimists see in biennials the “embracing of a democratic redistribution of cultural power” (De Duve 2009: 45); whilst pessimists point rather to the “recognition of a new form of cultural hegemony and re-colonization” (2009: 45). This chapter traces the rise of the biennial, across time and space, providing contextualisation and interpretation for what are now often hyperbolic accounts of “hundreds of biennials” (Seijdel 2009: 4) across the globe.
Тези доповідей конференцій з теми "Allele distribution models"
1
Ramsay, Travis. "Uncertainty Quantification of Allen-Cahn Phase Field Parameters in Multiphysics Simulation of Oil Shale Radio Frequency Heating." In SPE Annual Technical Conference and Exhibition. SPE, 2021. http://dx.doi.org/10.2118/205866-ms.
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Abstract Radio frequency (RF) heating represents a dielectric heating technique for converting kerogen-rich oil shale into liquid oil through in-situ pyrolysis. This process can be modeled using a multiphysics finite element based coupled thermal, phase field, mechanical and electromagnetic (TPME) numerical framework. This work focuses on the combination of a two-dimensional (2D) TPME multiphysics simulation with uncertainty quantification (UQ) that incorporates the Allen-Cahn phase field parameters, specifically those which describe the associated reaction-diffusion process as electromagnetic energy being converted to thermal energy in the RF heating process. The breadth of UQ performed in this study includes not only the Allen-Cahn parameters but also selected thermal, statistical rock-type distribution in the geological model, as well as electromagnetic parameters of the applied quasi-static Maxwell equation. A Non-Intrusive Polynomial Chaos (NIPC) is used for: considering the affect of Allen-Cahn phase field parameters on the evaluation of plausible conversion timelines of TPME simulation and the evaluation of summary statistics to predict the order of Polynomial Chaos Expansion (PCE) that is representative of full kerogen-rich zonal conversion response in a geologically descriptive finite element model. A sparse representation of polynomial chaos coefficients is highlighted in the process of computing summary statistics for the complex stochastically-driven TPME simulation results. Additionally, Monte Carlo (MC) simulations were performed in order to validate the results of the sparse NIPC representation. This is done considering MC is a widely recognized stochastic simulation process. Additionally, NIPC was used to illustrate the potential performance improvement that are possible, with a sparse polynomial chaos expansion enhanced by the incorporation of Least Angle Regression (LAR), as compared to MC simulation. Although the parametic uncertainty of the reaction-diffusion parameters of the Allen-Cahn was comprehensive, they did not accelerate the conversion timelines associated with the full zonal conversion of the kerogen-rich rock type in the statistical simulation results. By executing the stochastic simulations for a greater length of time the extent of full zonal conversion is examined in the RF modeling.
2
Judge, Carolyn Q., John A. Judge, and Christine M. Ikeda. "Impact Pressures on the Bottom of a Prismatic Planing Hull During Water Impact." In SNAME 13th International Conference on Fast Sea Transportation. SNAME, 2015. http://dx.doi.org/10.5957/fast-2015-033.
Повний текст джерелаАнотація:
High-speed planing boats are subject to repeated slamming impacts, which can cause structural damage and discomfort or injury to passengers. The structural and seakeeping aspects of the design of high-speed craft are mainly determined through empirical estimates of mean and peak pressures. The primary structural guideline (Allen and Jones, 1978) relies heavily on semi-empirical criteria that are not always accurate and have limited application. The Allen and Jones guidelines provide conservative estimates leading to sufficient structural design, but do not provide enough guidance to allow strategic reduction in structural weight. Structural design depends on the hull bottom pressures while information about the magnitudes of peak pressures, time durations, and locations along the hull is generally not available. Model tests conducted at the US Naval Academy have measured bottom pressures on a prismatic planing hull geometry during operation in waves (both regular and irregular). Pressures were measured at point locations and using a two-dimensional pressure pad to examine how pressures change in both time and space during a water impact. Rosen (2005) presents a method for reconstructing the momentary pressure distribution during a hull-water impact. This method allows the measurements of a propagating pressure segment in one position of the hull at one instant in time to be associated with other positions at other instants in time (as determined from several different point pressure measurements). Morabito (2014) presents an empirical method for calculating the pressure distribution on the bottom of prismatic planing hulls. The method can be extended to the impact problem by use of an “equivalent” planing velocity. This paper compares the planing pressures predicted by Morabito's empirical method with the recreated pressure distribution determined from Rosen's method.
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Hasanova, Aytakin. "PREDICTIVE GENETIC SCREENING." In The First International Scientific-Practical Conference- “Modern Tendencies of Dialogue in Multidenominational Society: philosophical, religious, legal view”. IRETC MTÜ, 2020. http://dx.doi.org/10.36962/mtdms202029.
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Human, as a species, is very variable, and his variability is at the basis of his social organization. This variability is maintained, in part, by the chance effects of gene assortment and the variation in these genes is the result of mutations in the past. If our remote ancestors had not mutated we would not he here; further, since no species is likely to he able to reduce its mutation rate substantially by the sort of selection to which it is exposed, we may regard mutations of recent origin as part of the price of having evolved. We are here: all of us have some imperfections we would wish not to have, and many of us are seriously incommoded by poor sight, hearing or thinking. Others among us suffer from some malformation due to faulty development. A few are formed lacking some essential substance necessary to metabolize a normal diet, to clot the blood, or to darken the back of the eye. We will all die and our deaths will normally be related to some variation in our immu-nological defences, in our ability to maintain our arteries free from occlusion, or in some other physiological aptitude. This massive variation, which is the consequence both of chance in the distribution of alleles and variety in the alleles themselves, imposes severe disabilities and handicaps on a substantial proportion of our population. The prospects of reducing this burden by artificial selection from counsel¬ling or selective feticide will be considered and some numerical estimates made of its efficiency and efficacy. Screening is a procedure by which populations are separated into groups, and is widely used for administrative and other purposes. At birth all babies are sexed and divided into two groups. Later the educable majority is selected from the ineducable minority; later still screening continues for both administrative and medical purposes. Any procedure by which populations are sifted into distinct groups is a form of screening, the word being derived from the coarse filter used to separate earth and stones. In medicine its essential features are that the population to be screen¬ed is not knowingly in need of medical attention and the action is taken on behalf of this population for its essential good. A simple example is provided by cervical smear examination, the necessary rationale for which must be the haimless and reliable detection of precancerous changes which can be prevented from becoming irreversible. Any rational decision on the development of such a service must be based on a balance of good and harm and any question of priorities in relation to other services must be based on costing. The balance of good and harm is a value judgement of some complexity. In the example of cervical smears anxiety and the consequences of the occasional removal of a healthy uterus must be weighed against the benefits of the complete removal of a cancerous one, and such matters cannot be costed in monetary terms. In fact, even such an apparently simple procedure as cervical screening is full of unknowns and many of these unknowns can only be resolved by extensive and properly designed studies. In genetic screening the matter is even more complicated, since the screening is often vicarious; that is, one person is screened in order to make a prediction on what may happen to someone else, usually their children, who may be un¬conceived or unborn. Further, the action of such screening may not be designed to ameliorate disease, but to eliminate a fetus which has a high chance of an affliction, or to prevent a marriage in which there is a mutual predisposition to producing abnormal children. These considerations impose very considerable dif¬ferences, since the relative values placed on marriage, on having children within marriage, and on inducing abortion, vary widely between individuals and between societies.
Звіти організацій з теми "Allele distribution models"
1
Chamovitz, Daniel, and Albrecht Von Arnim. Translational regulation and light signal transduction in plants: the link between eIF3 and the COP9 signalosome. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7696515.bard.
Повний текст джерелаАнотація:
The COP9 signalosome (CSN) is an eight-subunit protein complex that is highly conserved among eukaryotes. Genetic analysis of the signalosome in the plant model species Arabidopsis thaliana has shown that the signalosome is a repressor of light dependent seedling development as mutant Arabidopsis seedlings that lack this complex develop in complete darkness as if exposed to light. These mutant plants die following the seedling stage, even when exposed to light, indicating that the COP9 signalosome also has a central role in the regulation of normal photomorphogenic development. The biochemical mode of action of the signalosome and its position in eukaryotic cell signaling pathways is a matter of controversy and ongoing investigation, and recent results place the CSN at the juncture of kinase signaling pathways and ubiquitin-mediated protein degradation. We have shown that one of the many CSN functions may relate to the regulation of translation through the interaction of the CSN with its related complex, eukaryotic initiation factor (eIF3). While we have established a physical connection between eIF3 subunits and CSN subunits, the physiological and developmental significance of this interaction is still unknown. In an effort to understand the biochemical activity of the signalosome, and its role in regulating translation, we originally proposed to dissect the contribution of "h" subunit of eIF3 (eIF3h) along the following specific aims: (i) Isolation and phenotypic characterization of an Arabidopsis loss-of-function allele for eIF3h from insertional mutagenesis libraries; (ii) Creation of designed gain and loss of function alleles for eIF3h on the basis of its nucleocytoplasmic distribution and its yeast-two-hybrid interactions with other eIF3 and signalosome partner proteins; (iii) Determining the contribution of eIF3h and its interaction with the signalosome by expressing specific mutants of eIF3h in the eIF3h- loss-of function background. During the course of the research, these goals were modified to include examining the genetic interaction between csn and eif3h mutations. More importantly, we extended our effort toward the genetic analysis of mutations in the eIF3e subunit, which also interacts with the CSN. Through the course of this research program we have made several critical scientific discoveries, all concerned with the apparent diametrically opposed roles of eIF3h and eIF3e. We showed that: 1) While eIF3e is essential for growth and development, eIF3h is not essential for growth or basal translation; 2) While eIF3e has a negative role in translational regulation, eIF3h is positively required for efficient translation of transcripts with complex 5' UTR sequences; 3) Over-accumulation of eIF3e and loss-of-function of eIF3h both lead to cop phenotypes in dark-grown seedlings. These results were published in one publication (Kim et al., Plant Cell 2004) and in a second manuscript currently in revision for Embo J. Are results have led to a paradigm shift in translation research – eIF3 is now viewed in all systems as a dynamic entity that contains regulatory subuits that affect translational efficiency. In the long-term agronomic outlook, the proposed research has implications that may be far reaching. Many important plant processes, including developmental and physiological responses to light, abiotic stress, photosynthate, and hormones operate in part by modulating protein translation [23, 24, 40, 75]. Translational regulation is slowly coming of age as a mechanism for regulating foreign gene expression in plants, beginning with translational enhancers [84, 85] and more recently, coordinating the expression of multiple transgenes using internal ribosome entry sites. Our contribution to understanding the molecular mode of action of a protein complex as fundamental as eIF3 is likely to lead to advances that will be applicable in the foreseeable future.