Genes, Vol. 15, Pages 378: Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement
Lin Guoli Song Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort’s fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these...
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Shang Liu Hailiang Cheng Youping Zhang Man He Dongyun Zuo Qiaolian Wang Limin Lv Zhongxv Lin Guoli Song Tags: Article Source Type: research

Genes, Vol. 15, Pages 374: Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation
We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation. (Source: Genes)
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Marcel-Joseph Yared Agathe Marcelot Pierre Barraud Tags: Review Source Type: research

Genes, Vol. 15, Pages 376: Expression, Polymorphism, and Potential Functional Sites of the BMPR1A Gene in the Sheep Horn
In conclusion, we demonstrated that the BMPR1A gene is associated with horn type and identified some important functional sites which can be used as molecular markers in the breeding of sheep horns. (Source: Genes)
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Guoqing Zhang Mingxing Chu Hao Yang Hao Li Jianxin Shi Pingjie Feng Shoufeng Wang Zhangyuan Pan Tags: Article Source Type: research

Genes, Vol. 15, Pages 375: Transferability of Human and Environmental Microbiome on Clothes as a Tool for Forensic Investigations
In conclusion, our study offers supplementary insights into the potential utility of time-transferred microbiome analysis on garments for forensic applications. (Source: Genes)
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Noemi Procopio Giulia Sguazzi Emma V. Eriksson Nengi Ogbanga Frazer C. McKell Eleanor P. Newton Paola A. Magni Andrea Bonicelli Sarah Gino Tags: Article Source Type: research

Genes, Vol. 15, Pages 377: Genome and Epigenome Disorders and Male Infertility: Feedback from 15 Years of Clinical and Research Experience
Moncef Benkhalifa Infertility affects around 20% of couples of reproductive age; however, in some societies, as many as one-third of couples are unable to conceive. Different factors contribute to the decline of male fertility, such us environmental and professional exposure to endocrine disruptors, oxidative stress, and life habits with the risk of de novo epigenetics dysregulation. Since the fantastic development of new “omes and omics” technologies, the contribution of inherited or de novo genomes and epigenome disorders to male infertility have been further elucidated. Many other techn...
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Debbie Montjean Marion Beaumont Abdelhafid Natiq Noureddine Louanjli Andre Hazout Pierre Miron Thomas Liehr Rosalie Cabry Ilham Ratbi Moncef Benkhalifa Tags: Article Source Type: research

Genes, Vol. 15, Pages 373: Long-Term Tissue Preservation at Ambient Temperature for Post-Mass Fatality Incident DNA-Based Victim Identification
This study also proposes a simple process for the rapid and low-cost preservation of tissue samples for long-term storage at ambient temperatures in support of post-incident victim identification efforts. (Source: Genes)
Source: Genes - March 19, 2024 Category: Genetics & Stem Cells Authors: Xavier Liang Shun Chan Shumei Michelle Lai Danial Asyraaf bin Hamdan Yee Bin Ng Onn Siong Yim Christopher Kiu Choong Syn Tags: Brief Report Source Type: research

Genes, Vol. 15, Pages 371: Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles
runelli Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of differen...
Source: Genes - March 18, 2024 Category: Genetics & Stem Cells Authors: Marcello Mezzasalma Rachele Macirella Gaetano Odierna Elvira Brunelli Tags: Review Source Type: research

Genes, Vol. 15, Pages 372: Extraction of Innate Immune Genes in Dairy Cattle and the Regulation of Their Expression in Early Embryos
In conclusion, the bovine innate immunity gene set was determined and the co-expression network of innate immunity genes in the early embryonic stage of dairy cattle was constructed by comparing and analyzing the whole genome of bovines and humans. The findings in this study provide the basis for exploring the involvement and regulation of innate immune genes in the early embryonic development of dairy cattle. (Source: Genes)
Source: Genes - March 18, 2024 Category: Genetics & Stem Cells Authors: Xue Wang Lili Guo Wenguang Zhang Tags: Review Source Type: research

Genes, Vol. 15, Pages 369: PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis
This study implements a candidate-gene and a network-based approach to identify genetic markers associated with apremilast response in forty-nine Greek Ps patients. Our data revealed an association of sixty-four SNPs within or near PDE4 and CYP3A4 genes, four SNPs in ncRNAs ANRIL, LINC00941 and miR4706, which influence the abundance or function of PDE4s, and thirty-three SNPs within fourteen genes whose protein products either interact directly with PDE4 proteins or constitute components of the cAMP signaling pathway which is modulated by PDE4s. Notably, fifty-six of the aforementioned SNPs constitute eQTLs for the respect...
Source: Genes - March 17, 2024 Category: Genetics & Stem Cells Authors: Kalliopi Liadaki Efterpi Zafiriou Themistoklis Giannoulis Sofia Alexouda Kleoniki Chaidaki Polyxeni Gidarokosta Angeliki-Viktoria Roussaki-Schulze Sotirios G. Tsiogkas Athina Daponte Zissis Mamuris Dimitrios P. Bogdanos Nicholas K. Moschonas Theologia Sar Tags: Article Source Type: research

Genes, Vol. 15, Pages 370: Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis
This study demonstrates the integration of facial analysis (GestaltMatcher) and Human Phenotype Ontology analysis (CADA) within VarFish, an open-source variant analysis framework. Challenges related to non-open-source components were addressed by providing an open-source version of GestaltMatcher, facilitating on-premise facial analysis to address data privacy concerns. Performance evaluation on 163 patients recruited from a German multi-center study of rare diseases showed PEDIA’s superior accuracy in variant prioritization compared to individual scores. This study highlights the importance of further benchm...
Source: Genes - March 17, 2024 Category: Genetics & Stem Cells Authors: Meghna Ahuja Bhasin Alexej Knaus Pietro Incardona Alexander Schmid Manuel Holtgrewe Miriam Elbracht Peter M. Krawitz Tzung-Chien Hsieh Tags: Technical Note Source Type: research

Genes, Vol. 15, Pages 367: Dynamics of Mitochondrial DNA Copy Number and Membrane Potential in Mouse Pre-Implantation Embryos: Responses to Diverse Types of Oxidative Stress
cca L. Robker Mitochondria undergo a myriad of changes during pre-implantation embryo development, including shifts in activity levels and mitochondrial DNA (mtDNA) replication. However, how these distinct aspects of mitochondrial function are linked and their responsiveness to diverse stressors is not well understood. Here, we show that mtDNA content increased between 8-cell embryos and the blastocyst stage, with similar copy numbers per cell in the inner cell mass (ICM) and trophectoderm (TE). In contrast, mitochondrial membrane potential (MMP) was higher in TE than ICM. Culture in ambient oxygen (20% O2) altered bot...
Source: Genes - March 16, 2024 Category: Genetics & Stem Cells Authors: Yasmyn E. Winstanley Jun Liu Deepak Adhikari Macarena B. Gonzalez Darryl L. Russell John Carroll Rebecca L. Robker Tags: Article Source Type: research

Genes, Vol. 15, Pages 368: Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype
r Dovč Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the LPAR6 gene has been found to cause a frame shift and a premature stop codon. In addition to the rexoid coat, Cornish Rex cats also have a characteristic head, ear shape and body type. Analysis of the selection signatures in the Cornish Rex genome revealed several regions that are under selective pressure. One of the...
Source: Genes - March 16, 2024 Category: Genetics & Stem Cells Authors: Minja Zorc Tajda Horvat Anja Tan šek Tamara Ferme Peter Dov č Tags: Article Source Type: research

Genes, Vol. 15, Pages 365: Characterization and Functional Analysis of Fads Reveals & Delta;5 Desaturation Activity during Long-Chain Polyunsaturated Fatty Acid Biosynthesis in Dwarf Surf Clam Mulinia lateralis
Genes, Vol. 15, Pages 365: Characterization and Functional Analysis of Fads Reveals Δ5 Desaturation Activity during Long-Chain Polyunsaturated Fatty Acid Biosynthesis in Dwarf Surf Clam Mulinia lateralis Genes doi: 10.3390/genes15030365 Authors: Tianhao Teng Zhenghua Zheng Wenqian Jiao Na Liu Ao Wang Mengjiao Liu Le Xie Zujing Yang Jingjie Hu Zhenmin Bao Fatty acid desaturases (Fads), as key enzymes in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), catalyze the desaturation between defined carbons of fatty acyl chains and control the degree of unsaturation of fatt...
Source: Genes - March 15, 2024 Category: Genetics & Stem Cells Authors: Tianhao Teng Zhenghua Zheng Wenqian Jiao Na Liu Ao Wang Mengjiao Liu Le Xie Zujing Yang Jingjie Hu Zhenmin Bao Tags: Article Source Type: research

Genes, Vol. 15, Pages 366: Overexpression of NtGPX8a Improved Cadmium Accumulation and Tolerance in Tobacco (Nicotiana tabacum L.)
Xu Zhu Liu Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) remained unclear. Our investigation employed genome-wide analysis to identify 14 NtGPX genes in tobacco, revealing their organization into seven subgroups characterized by analogous conserved domain patterns. Notably, qPCR analysis highlighted NtGPX8a as markedly responsive to...
Source: Genes - March 15, 2024 Category: Genetics & Stem Cells Authors: Peng Ma Song Ji Xiang Chen Zu Xu Zhu Liu Tags: Article Source Type: research

Genes, Vol. 15, Pages 364: Advancements in Viral Gene Therapy for Gaucher Disease
-Un Han Gaucher disease, an autosomal recessively inherited lysosomal storage disorder, results from biallelic mutations in the GBA1 gene resulting in deficient activity of the enzyme glucocerebrosidase. In Gaucher disease, the reduced levels and activity of glucocerebrosidase lead to a disparity in the rates of formation and breakdown of glucocerebroside and glucosylsphingosine, resulting in the accumulation of these lipid substrates in the lysosome. This gives rise to the development of Gaucher cells, engorged macrophages with a characteristic wrinkled tissue paper appearance. There are both non-neuronopathic (type 1...
Source: Genes - March 15, 2024 Category: Genetics & Stem Cells Authors: Akhil Kulkarni Tiffany Chen Ellen Sidransky Tae-Un Han Tags: Review Source Type: research