Prevalence of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans: implications for a North African Neanderthal connection
We examined this locus in the Moroccan population for the occurrence of the critical variant rs10774671 and its respective haplotype blocks. The frequency of single-nucleotide polymorphisms (SNPs) in the cluster ofOAS immunity genes in 157 unrelated individuals of Moroccan origin was determined using an in-house exome database.OAS1 exon 6 of 71 SARS-CoV-2-positive individuals with asymptomatic/mild disease and 74 with moderate/severe disease was sequenced by the Sanger method. The genotypic, allelic, and haplotype frequencies of three SNPs were compared between these two groups. Finally, males in our COVID-19 series were g...
Source: Archives of Virology - April 25, 2024 Category: Virology Source Type: research
Genes, Vol. 15, Pages 542: Comparative Analysis of Virulence and Molecular Diversity of Puccinia striiformis f. sp. tritici Isolates Collected in 2016 and 2023 in the Western Region of China
This study aimed to evaluate the virulence and molecular diversity of 84 old Pst isolates, in comparison to 59 newer ones. By using 19 Chinese wheat differentials, we identified 98 pathotypes, showing virulence complexity ranging from 0 to 16. Associations between 23 Yr gene pairs showed linkage disequilibrium and have the potential for gene pyramiding. The new Pst isolates had a higher number of polymorphic alleles (1.97), while the older isolates had a slightly higher number of effective alleles, Shannon’s information, and diversity. The Gansu Pst population had the highest diversity (uh = 0.35), while the ...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Tesfay Gebrekirstos Gebremariam Fengtao Wang Ruiming Lin Hongjie Li Tags: Article Source Type: research
Genes, Vol. 15, Pages 544: Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides
In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis ch...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Yuanxin Wang Xueying Zhao Qianhui Chen Jun Yang Jun Hu Dong Jia Ruiyan Ma Tags: Article Source Type: research
Genes, Vol. 15, Pages 545: Integrated Analysis of Transcriptome and Metabolome Reveals Differential Responses to Alternaria brassicicola Infection in Cabbage (Brassica & nbsp;oleracea var. capitata)
Genes, Vol. 15, Pages 545: Integrated Analysis of Transcriptome and Metabolome Reveals Differential Responses to Alternaria brassicicola Infection in Cabbage (Brassica oleracea var. capitata)
Genes doi: 10.3390/genes15050545
Authors:
Jinzhou Lei
Wei Zhang
Fangwei Yu
Meng Ni
Zhigang Liu
Cheng Wang
Jianbin Li
Jianghua Song
Shenyun Wang
Black spot, caused by Alternaria brassicicola (Ab), poses a serious threat to crucifer production, and knowledge of how plants respond to Ab infection is essential for black spot management. In the current study, combined transcriptomic and metabolic analysis w...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Jinzhou Lei Wei Zhang Fangwei Yu Meng Ni Zhigang Liu Cheng Wang Jianbin Li Jianghua Song Shenyun Wang Tags: Article Source Type: research
Genes, Vol. 15, Pages 548: Non-Specific Epileptic Activity, EEG, and Brain Imaging in Loss of Function Variants in SATB1: A New Case Report and Review of the Literature
ia Santorelli
SATB1 (MIM #602075) is a relatively new gene reported only in recent years in association with neurodevelopmental disorders characterized by variable facial dysmorphisms, global developmental delay, poor or absent speech, altered electroencephalogram (EEG), and brain abnormalities on imaging. To date about thirty variants in forty-four patients/children have been described, with a heterogeneous spectrum of clinical manifestations. In the present study, we describe a new patient affected by mild intellectual disability, speech disorder, and non-specific abnormalities on EEG and neuroimaging. Family studies...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Flavia Privitera Stefano Pagano Camilla Meossi Roberta Battini Emanuele Bartolini Domenico Montanaro Filippo Maria Santorelli Tags: Article Source Type: research
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
ConclusionsThe accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available athttps://insaflu.insa.pt/ (online tool) andhttps://github.com/INSaFLU (code). (Source: Genome Medicine)
Source: Genome Medicine - April 25, 2024 Category: Genetics & Stem Cells Source Type: research
Genes, Vol. 15, Pages 543: Downregulation of Histone H3.3 Induces p53-Dependent Cellular Senescence in Human Diploid Fibroblasts
etoshi Tahara
Cellular senescence is an irreversible growth arrest that acts as a barrier to cancer initiation and progression. Histone alteration is one of the major events during replicative senescence. However, little is known about the function of H3.3 in cellular senescence. Here we found that the downregulation of H3.3 induced growth suppression with senescence-like phenotypes such as senescence-associated heterochromatin foci (SAHF) and β-galactosidase (SA-β-gal) activity. Furthermore, H3.3 depletion induced senescence-like phenotypes with the p53/p21-depedent pathway. In addition, we i...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Yuki Yamamoto Ryou-u Takahashi Masaki Kinehara Kimiyoshi Yano Tatsuya Kuramoto Akira Shimamoto Hidetoshi Tahara Tags: Article Source Type: research
Genes, Vol. 15, Pages 541: The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element
In this study, we isolated and characterized a sat-DNA, here named PcH-sat, in the limpet Patella caerulea using the restriction enzyme method, particularly HaeIII. Monomeric units of PcH-sat are 179 bp long, AT-rich (58.7%), and with an identity among monomers ranging from 91.6 to 99.8%. Southern blot showed that PcH-sat is conserved in P. depressa and P. ulyssiponensis, while a smeared signal of hybridization was present in the other three investigated limpets (P. ferruginea, P. rustica and P. vulgata). Dot blot showed that PcH-sat represents about 10% of the genome of P. caerulea, 5% of that of P. depressa, and 0.3% of ...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Agnese Petraccioli Nicola Maio Rosa Carotenuto Gaetano Odierna Fabio Maria Guarino Tags: Article Source Type: research
Genes, Vol. 15, Pages 540: Characterization of the Apoptotic and Antimicrobial Activities of Two Initiator Caspases of Sea Cucumber Apostichopus japonicus
Li Sun
Caspase (CASP) is a protease family that plays a vital role in apoptosis, development, and immune response. Herein, we reported the identification and characterization of two CASPs, AjCASPX1 and AjCASPX2, from the sea cucumber Apostichopus japonicus, an important aquaculture species. AjCASPX1/2 share similar domain organizations with the vertebrate initiator caspases CASP2/9, including the CARD domain and the p20/p10 subunits with conserved functional motifs. However, compared with human CASP2/9, AjCASPX1/2 possess unique structural features in the linker region between p20 and p10. AjCASPX1, but not AjCASPX2, ...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Hanshuo Zhu Zihao Yuan Hang Xu Li Sun Tags: Article Source Type: research
Genes, Vol. 15, Pages 539: Oxidative Stress Biomarkers in Male Infertility: Established Methodologies and Future Perspectives
Lucia Rocco
Male fertility can be affected by oxidative stress (OS), which occurs when an imbalance between the production of reactive oxygen species (ROS) and the body’s ability to neutralize them arises. OS can damage cells and influence sperm production. High levels of lipid peroxidation have been linked to reduced sperm motility and decreased fertilization ability. This literature review discusses the most commonly used biomarkers to measure sperm damage caused by ROS, such as the high level of OS in seminal plasma as an indicator of imbalance in antioxidant activity. The investigated biomarkers inclu...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Filomena Mottola Ilaria Palmieri Maria Carannante Angela Barretta Shubhadeep Roychoudhury Lucia Rocco Tags: Review Source Type: research
miR-17-92a-1 cluster host gene: a key regulator in colorectal cancer development and progression
AbstractColorectal cancer (CRC), recognized among the five most prevalent malignancies and most deadly cancers, manifests multifactorial influences stemming from environmental exposures, dietary patterns, age, and genetic predisposition. Although substantial progress has been made in comprehending the etiology of CRC, the precise genetic components driving its pathogenesis remain incompletely elucidated. Within the expansive repertoire of non-coding RNAs, particular focus has centered on the miR-17-92a-1 cluster host gene (MIR17HG) and its associated miRNAs, which actively participate in diverse cellular processes and freq...
Source: Clinical and Experimental Medicine - April 25, 2024 Category: Research Source Type: research
Prevalence of FSH-R Asn680Ser and Ala307Thr receptor polymorphism and their correlation with ART outcomes among infertile Indian-Asian women-a prospective cohort study
AbstractThe present prospective cohort study evaluated the prevalence of FSH-R receptor Asn680Ser and Ala307Thr among infertile Indian women and the correlation of these polymorphisms with ART outcomes. Total 804 infertile and 209 fertile controls were enrolled for FSH-R analysis. Correlation of different genotypes with ovarian reserve markers, IVF parameters, and cumulative live birth rates (CLBR) was done among women undergoing IVF. In fertile controls, at 680 position GG (Ser/Ser) was the most common genotype; but among infertile women, all the genotypes were equally distributed. There was no significant difference in o...
Source: Journal of Human Genetics - April 25, 2024 Category: Genetics & Stem Cells Source Type: research
Genes, Vol. 15, Pages 547: Statistical Genetic Approaches to Investigate Genotype-by-Environment Interaction: Review and Novel Extension of Models
iams-Blangero
Statistical genetic models of genotype-by-environment (G×E) interaction can be divided into two general classes, one on G×E interaction in response to dichotomous environments (e.g., sex, disease-affection status, or presence/absence of an exposure) and the other in response to continuous environments (e.g., physical activity, nutritional measurements, or continuous socioeconomic measures). Here we develop a novel model to jointly account for dichotomous and continuous environments. We develop the model in terms of a joint genotype-by-sex (for the dichotomous environment) and g...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Vincent P. Diego Eron G. Manusov Marcio Almeida Sandra Laston David Ortiz John Blangero Sarah Williams-Blangero Tags: Article Source Type: research
Genes, Vol. 15, Pages 546: Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis
Zinian Wu
Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight...
Source: Genes - April 25, 2024 Category: Genetics & Stem Cells Authors: Peng Wei Youzheng Li Mei Ke Yurong Hou Abudureyimu Aikebaier Zinian Wu Tags: Article Source Type: research
Identifying latent genetic interactions in genome-wide association studies using multiple traits
AbstractThe"missing" heritability of complex traits may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. We propose a new kernel-based method called Latent Interaction Testing (LIT) to screen for genetic interactions that leverages pleiotropy from multiple related traits without requiring the interacting variable to be specified or observed. Using simulated data, we demonstrate that LIT increases power to detect latent genetic interactions compared to univariate methods. We then apply LIT to obesity-related traits in the UK Bi...
Source: Genome Medicine - April 25, 2024 Category: Genetics & Stem Cells Source Type: research
