gene frequencies
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2022 ◽  
Vol 12 ◽  
Mark Chernyshev ◽  
Mateusz Kaduk ◽  
Martin Corcoran ◽  
Gunilla B. Karlsson Hedestam

Macaques are frequently used to evaluate candidate vaccines and to study infection-induced antibody responses, requiring an improved understanding of their naïve immunoglobulin (IG) repertoires. Baseline gene usage frequencies contextualize studies of antigen-specific immune responses, providing information about how easily one may stimulate a response with a particular VDJ recombination. Studies of human IgM repertoires have shown that IG VDJ gene frequencies vary several orders of magnitude between the most and least utilized genes in a manner that is consistent across many individuals but to date similar analyses are lacking for macaque IgM repertoires. Here, we quantified VDJ gene usage levels in unmutated IgM repertoires of 45 macaques, belonging to two species and four commonly used subgroups: Indian and Chinese origin rhesus macaques and Indonesian and Mauritian origin cynomolgus macaques. We show that VDJ gene frequencies differed greatly between the most and least used genes, with similar overall patterns observed in macaque subgroups and individuals. However, there were also clear differences affecting the use of specific V, D and J genes. Furthermore, in contrast to humans, macaques of both species utilized IGHV4 family genes to a much higher extent and showed evidence of evolutionary expansion of genes of this family. Finally, we used the results to inform the analysis of a broadly neutralizing HIV-1 antibody elicited in SHIV-infected rhesus macaques, RHA1.V2.01, which binds the apex of the Env trimer in a manner that mimics the binding mode of PGT145. We discuss the likelihood that similar antibodies could be elicited in different macaque subgroups.

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3589
Wayne Tsang ◽  
Annika Linde ◽  
Janina A. Krumbeck ◽  
Guangxi Wu ◽  
Young J. Kim ◽  

Feline chronic gingivostomatitis (FCGS) is a severe immune-mediated inflammatory disease with concurrent oral dysbiosis (bacterial and fungal). Broad-spectrum antibiotics are used empirically in FCGS. Still, neither the occurrence of antimicrobial-resistant (AMR) bacteria nor potential patterns of co-occurrence between AMR genes and fungi have been documented in FCGS. This study explored the differential occurrence of AMR genes and the co-occurrence of AMR genes with oral fungal species. Briefly, 14 clinically healthy (CH) cats and 14 cats with FCGS were included. Using a sterile swab, oral tissue surfaces were sampled and submitted for 16S rRNA and ITS-2 next-generation DNA sequencing. Microbial DNA was analyzed using a proprietary curated database targeting AMR genes found in bacterial pathogens. The co-occurrence of AMR genes and fungi was tested using point biserial correlation. A total of 21 and 23 different AMR genes were detected in CH and FCGS cats, respectively. A comparison of AMR-gene frequencies between groups revealed statistically significant differences in the occurrence of genes conferring resistance to aminoglycosides (ant4Ib), beta-lactam (mecA), and macrolides (mphD and mphC). Two AMR genes (mecA and mphD) showed statistically significant co-occurrence with Malassezia restricta. In conclusion, resistance to clinically relevant antibiotics, such as beta-lactams and macrolides, is a significant cause for concern in the context of both feline and human medicine.

2021 ◽  
Nathalie Feiner ◽  
Reinder Radersma ◽  
Louella Vasquez ◽  
Markus Ringnér ◽  
Björn Nystedt ◽  

AbstractEnvironmental stress can result in epigenetic modifications that are passed down several generations. Such epigenetic inheritance can have significant impact on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. Here, we used whole-genome bisulfite sequencing on individual water fleas (Daphnia magna) to assess whether environmentally-induced DNA methylation can persist for up to four generations. Genetically identical females were exposed to a control treatment, one of three natural stressors (high temperature, zinc, microcystin), or the methylation-inhibitor 5-azacytidine. After exposure, lines were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) between controls and F1 individuals whose mothers (and therefore they themselves as germ cells) were exposed to one of the three natural stressors. Between 46% and 58% of these environmentally-induced DMPs persisted until generation F4 without attenuation in their magnitude of differential methylation. DMPs were enriched in exons and largely stressor-specific, suggesting a possible role in environment-dependent gene regulation. In contrast, treatment with the compound 5-azacytidine demonstrated that pervasive hypo-methylation upon exposure is reset almost completely after a single generation. These results suggest that environmentally-induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of fresh-water communities.Author summaryWater fleas are important keystone species mediating eco-evolutionary dynamics in lakes and ponds. It is currently an open question in how far epigenetic inheritance contributes to the ability of Daphnia populations to adapt to environmental stress. Using a range of naturally occurring stressors and a multi-generational design, we show that environmentally-induced DNA methylation variants are stably inherited for at least four generations in Daphnia magna. The induced variation in DNA methylation are stressor-specific and almost exclusively found in exons, bearing the signatures of functional adaptations. Our findings imply that ecological adaptations of Daphnia to seasonal fluctuations can be underpinned by epigenetic inheritance of DNA methylation without changes in gene frequencies.

2021 ◽  
Jose Marcelo Soriano Viana

The current theoretical knowledge concerning the influence of epistasis on heterosis is based on simplified multiplicative model. The objective of this study was to assess the impact of epistasis in the heterosis and combining ability analyses, assuming additive model, hundreds of genes, linkage disequilibrium (LD), dominance, and seven types of digenic epistasis. We developed the quantitative genetics theory for supporting the simulation of the individual genotypic values in nine populations, the selfed populations, the 36 interpopulation crosses, 180 doubled haploids (DHs) and their 16,110 crosses, assuming 400 genes in 10 chromosomes of 200 cM. Epistasis only affects population heterosis if there is LD. Only additive x additive and dominance x dominance epistasis can affect the components of the heterosis and combining ability analyses of populations. Both analyses can lead to completely wrong inferences regarding the identification of the superior populations, the populations with greater differences of gene frequencies, and the populations with maximum variability, when the number of interacting genes and the magnitude of the epistatic effects are high. There was a decrease in the average heterosis by increasing the number of epistatic genes and the magnitude of their epistatic effects. The same results are generally true for the combining ability analysis of DHs. Surprisingly, the combining ability analyses of subsets of 20 DHs showed no significant average impact of epistasis on the identification of the most divergent ones, even assuming a high number of epistatic genes and great magnitude of their effects. However, a significant negative effect can occur.

S. Nihar ◽  
S. Naveen Kumar ◽  
Wilfred Ruban ◽  
H.M. Yathish ◽  
R. Nagaraja ◽  

Background: Recent developments in molecular genetics lead to addressing certain poultry diseases via breeding for disease resistance. The present study was carried to identify and compare the genetic polymorphism in Chicken Mx1 and TVB genes among the indigenous and Giriraja chicken using PCR-RFLP technique. Methods: Blood samples were collected from 50 indigenous and 50 Giriraja birds and DNA isolation was done by Phenol: Chloroform: Isoamyl alcohol method. PCR amplification of Chicken Mx1 (exon 14) and Chicken TVB (exon 3) genes was carried out followed by RFLP analysis. Result: PCR product sizes of 301 bp and 303 bp of Mx1 and TVB genes, respectively were successfully amplified. RFLP analysis of Mx1 gene with Hyp8I restriction enzyme revealed three genotypes AA, AB and BB. In indigenous birds genotypic frequencies of AA, AB and BB were 0.314, 0.493 and 0.194, respectively and gene frequencies were 0.56 and 0.44 for alleles A and B, respectively. In Giriraja birds, genotypic frequencies for AA, AB and BB were 0.27, 0.499 and 0.23, respectively and gene frequencies were 0.52 and 0.48 for alleles A and B, respectively. RFLP analysis of TVB gene with NlaIII restriction enzyme revealed two genotypes viz., AA and AB. In indigenous birds genotypic frequencies of AA and AB were 0.81 and 0.18, respectively and gene frequencies were 0.9 and 0.1 for alleles A and B, respectively. In Giriraja birds genotypic frequencies for AA and AB were 0.774 and 0.211, respectively and gene frequencies were 0.88 and 0.12 for alleles A and B, respectively.

2021 ◽  
pp. 1-17
Guido Barbujani

In 1978, Paolo Menozzi, Alberto Piazza, and Luca Cavalli-Sforza paved the ground for a new multidisciplinary approach to the study of human prehistory, interpreting genetic evidence in the light of archaeological information. By producing synthetic maps of allele frequencies and summarizing them by principal component analysis (PCA), they identified an association between patterns in genetic diversity across Europe and in the Neolithic archaeological record showing the earliest documented dates of farming societies. Based on this observation, they proposed a model of demic diffusion from the Near East. They argued that the observed patterns were the result of population growth due to increased food availability in early farming communities, westward dispersal of early farmers, and relative isolation between dispersing farmers and local hunter-gatherers. These results played a major role in our understanding of the Neolithic transition, but were also criticized on methodological grounds. For instance, it has become increasingly clear that the interpretation of PCA plots is less straightforward than originally thought, and correlations should be corroborated by explicit comparison of alternative demographic models. Despite these valid criticisms, genetic and genomic studies, including those involving ancient DNA, have largely confirmed the crucial role of the Neolithic transition as a process of demographic change in European prehistory, with some qualifications. Today, there is still much to be learned about the details of that complex history, but many researchers regard the European population structure as largely reflecting the genetic consequences of three major migrations: from Africa in Upper Paleolithic times, from the Near East at the beginning of the Neolithic, and from the eastern steppes in the Bronze Age. This deep structure has not been erased, despite many additional processes involving historical migrations, isolation (i.e., drift) and local gene flow, and has been recognized thanks to the pioneering work of Menozzi, Piazza and Cavalli-Sforza. Based on “Menozzi P, Piazza A, Cavalli-Sforza LL Synthetic maps of human gene frequencies in Europeans. Science 1978;201:786-792.”

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Nilupaer Shafeng ◽  
Deng-feng Han ◽  
Yun-fang Ma ◽  
Rena Abudusalamu ◽  
Binuer Ayitimuhan

Abstract Background The relationship between the HLA-B*1502 gene and maculopapular exanthema (MPE) induced by antiepileptic drugs (AEDs) has not yet been elucidated. In this study, we investigated the association between AED-induced MPE (AED-MPE) and the HLA-B*1502 gene in patients in Northwest China. Methods We enrolled 165 subjects including nine patients with AED-MPE and 156 AED-tolerant patients as controls. HLA-B*1502 gene polymorphism was detected using digital fluorescence molecular hybridization (DFMH). The results of HLA genotyping were expressed as positive or negative for the HLA-B*1502 allele. An analysis of AED-MPE risk factors was performed using binary logistic regression, and differences in genotype frequencies between groups were assessed with the continuity correction chi-square test. Results We found that the HLA-B*1502 gene was a risk factor for AED-MPE (P = 0.028). The incidence of MPE induced by the two types of AEDs was different, and the incidence of aromatic AEDs use was higher that of non-aromatic AEDs use (P = 0.025). The comparison of the gene frequencies of the HLA-B*1502 allele between the two groups taking aromatic AEDs was also statistically significant (P = 0.045). However, there were no significant differences in terms of age, gender, ethnicity, or region in patients with MPE induced by AEDs. In addition, no association between the HLA-B1502 allele and CBZ- or OXC-induced MPE was found. Conclusions In northwestern China, the HLA-B*1502 allele was associated with aromatic AED-MPE. Since MPE can develop into Stevens–Johnson syndrome (SJS) or toxic epidermal necrolysis (TEN), the HLA-B*1502 gene should be evaluated before administering AEDs.

2021 ◽  
Vol 3 (1) ◽  
pp. 101-107
N. N. Salti ◽  
M. Shaya

Except for two reports on Lebanese immigrants, there have been no studies on the major histocompatibility [MHC] antigens in the Lebanese population. We describe the frequency and distribution of MHC class I antigens present in the A, B and C loci based on data obtained from 200 healthy unrelated individuals from different parts of Lebanon. The highest gene frequencies were as follows:A2 [24.8%], B35 [17.9%] and Cw4 [18.6%], making this haplotype the commonest. Comparison of genetic distances revealed a pattern closer to the Caucasoid population than to the Mongoloid, Oriental or Black populations

2021 ◽  
Vol 4 (3) ◽  
pp. 3355-3367
Jorge Arturo Tello Cetina ◽  
Mariel Sinai Garrido Balam ◽  
Flavia Jovita Cruz Pérez ◽  
Nidia Isabel Jiménez Suaste ◽  
Luis Joaquín Alberto Mota Pino ◽  

It was determined the population genetic structure of the red octopus Octopus maya in the states of Campeche and Yucatan in Yucatan Peninsula, Mexico, through the expression of isozymes in polyacrylamide gels. Mantle samples from 25 octopuses, captured in nine sites of the Yucatan Peninsula, were used to characterize the genotypic expression revealed by the expression of 26 loci in thirty enzyme systems. Program TFPGA version 1.3 (Tools for Population Genetic Analyses), was used to process data of allozyme gene frequencies of the studied populations. The parameters determined were: descriptive statistics, F statistics, genetic distances, Hardy - Weinberg, UPGMA and the number of migrants as an indicator of gene flow. The average number of alleles per locus, percentage of polymorphic loci, average and direct and direct heterozygosity were: 1.08 ± 0.05 to 1.15 ± 0.04. P95 26.9231% to 34.6154, Have 0.1142 to 0.1390 and Hdir = 0.0354 to 0.0938 respectively. Heterozygosity values in a range of 0.3506 to 0.4793 and G6PDH for ARGK with an average heterozygosity value of 0.1824, Fisher average value of 0.5313 and 0.0140 Fst indicates a heterozygous deficiency but it is within the ranges reported for marine invertebrate species. The number of migrants derived from the Slatkin equation is 1824 per generation, globally indicates some degree of variability between sites and is consistent with the low values of Nei genetic distance found, particularly the node showing the separation of the population of Lagartos River and Dzilam Bravo from the other locations with an obtained value of 0.0004. From the results of this study, it is concluded that locations of Octopus maya have a certain level of interpopulation genetic variability that does not reflect its fragility.

2021 ◽  
pp. JCO.21.00531
Nicholas J. Boddicker ◽  
Chunling Hu ◽  
Jeffrey N. Weitzel ◽  
Peter Kraft ◽  
Katherine L. Nathanson ◽  

PURPOSE The prevalence of germline pathogenic variants (PVs) in established breast cancer predisposition genes in women in the general population over age 65 years is not well-defined. However, testing guidelines suggest that women diagnosed with breast cancer over age 65 years might have < 2.5% likelihood of a PV in a high-penetrance gene. This study aimed to establish the frequency of PVs and remaining risks of breast cancer for each gene in women over age 65 years. METHODS A total of 26,707 women over age 65 years from population-based studies (51.5% with breast cancer and 48.5% unaffected) were tested for PVs in germline predisposition gene. Frequencies of PVs and associations between PVs in each gene and breast cancer were assessed, and remaining lifetime breast cancer risks were estimated for non-Hispanic White women with PVs. RESULTS The frequency of PVs in predisposition genes was 3.18% for women with breast cancer and 1.48% for unaffected women over age 65 years. PVs in BRCA1, BRCA2, and PALB2 were found in 3.42% of women diagnosed with estrogen receptor (ER)–negative, 1.0% with ER-positive, and 3.01% with triple-negative breast cancer. Frequencies of PVs were lower among women with no first-degree relatives with breast cancer. PVs in CHEK2, PALB2, BRCA2, and BRCA1 were associated with increased risks (odds ratio = 2.9-4.0) of breast cancer. Remaining lifetime risks of breast cancer were ≥ 15% for those with PVs in BRCA1, BRCA2, and PALB2. CONCLUSION This study suggests that all women diagnosed with triple-negative breast cancer or ER-negative breast cancer should receive genetic testing and that women over age 65 years with BRCA1 and BRCA2 PVs and perhaps with PALB2 and CHEK2 PVs should be considered for magnetic resonance imaging screening.

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