Genes, Vol. 12, Pages 327: Evolutionary Genetics of Microbial Symbioses
ren Symbiosis is the living together of dissimilar organisms [...] (Source: Genes)
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Laura Baldo John Werren Tags: Editorial Source Type: research

Genes, Vol. 12, Pages 328: A Workflow for Selection of Single Nucleotide Polymorphic Markers for Studying of Genetics of Ischemic Stroke Outcomes
a Limborska In this paper we propose a workflow for studying the genetic architecture of ischemic stroke outcomes. It develops further the candidate gene approach. The workflow is based on the animal model of brain ischemia, comparative genomics, human genomic variations, and algorithms of selection of tagging single nucleotide polymorphisms (tagSNPs) in genes which expression was changed after ischemic stroke. The workflow starts from a set of rat genes that changed their expression in response to brain ischemia and results in a set of tagSNPs, which represent other SNPs in the human genes analyzed and influenced on t...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Gennady Khvorykh Andrey Khrunin Ivan Filippenkov Vasily Stavchansky Lyudmila Dergunova Svetlana Limborska Tags: Article Source Type: research

Genes, Vol. 12, Pages 329: Quantifying Fetal Reprogramming for Biomarker Development in the Era of High-Throughput Sequencing
Wang Gestational hypertensive disorders continue to threaten the well-being of pregnant women and their offspring. The only current definitive treatment for gestational hypertensive disorders is delivery of the fetus. The optimal timing of delivery remains controversial. Currently, the available clinical tools do not allow for assessment of fetal stress in its early stages. Placental insufficiency and fetal growth restriction secondary to gestational hypertensive disorders have been shown to have long-term impacts on offspring health even into their adulthood, becoming one of the major focuses of research in the field...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Fu-Sheng Chou Krystel Newton Pei-Shan Wang Tags: Review Source Type: research

Genes, Vol. 12, Pages 331: Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults
a Vongsangnak The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Rum...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Nachon Raethong Massalin Nakphaichit Narissara Suratannon Witida Sathitkowitchai Wanlapa Weerapakorn Suttipun Keawsompong Wanwipa Vongsangnak Tags: Article Source Type: research

Genes, Vol. 12, Pages 330: Optic Atrophy and Inner Retinal Thinning in CACNA1F-related Congenital Stationary Night Blindness
This study aimed to investigate inner retinal changes in CACNA1F-retinopathy by analyzing macular ganglion cell layer-inner plexiform layer (GCL-IPL) thickness and optic disc pallor in 22 subjects with molecularly confirmed CACNA1F-retinopathy. Detailed ocular phenotypic data including distance and color vision, refraction and electroretinogram (ERG) were collected. Distance vision was universally reduced (mean: 0.42 LogMAR), six had abnormal color vision and myopia was common (n = 15; mean: −6.32 diopters). Mean GCL-IPL thickness was significantly lower in patients (55.00 µm) compared to age-matched controls (...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Leahy Wright Grudzinska Pechhacker Audo Tumber Tavares MacDonald Locke VandenHoven Zeitz Heon Buncic Vincent Tags: Article Source Type: research

Genes, Vol. 12, Pages 332: Application of Genomics to Understand Salt Tolerance in Lentil
an Kaur Soil salinity is a major abiotic stress, limiting lentil productivity worldwide. Understanding the genetic basis of salt tolerance is vital to develop tolerant varieties. A diversity panel consisting of 276 lentil accessions was screened in a previous study through traditional and image-based approaches to quantify growth under salt stress. Genotyping was performed using two contrasting methods, targeted (tGBS) and transcriptome (GBS-t) genotyping-by-sequencing, to evaluate the most appropriate methodology. tGBS revealed the highest number of single-base variants (SNPs) (c. 56,349), and markers were more evenly...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Ruwani Dissanayake Noel O.I. Cogan Kevin F. Smith Sukhjiwan Kaur Tags: Article Source Type: research

Genes, Vol. 12, Pages 333: Current Knowledge on Genomic Profiling of Upper Tract Urothelial Carcinoma
e Montanari Recent research in next-generation sequencing characterized the genomic landscape of urothelial cancer. However, the majority of the studies focused on bladder cancer (BC). Upper urinary tract urothelial carcinomas (UTUC) and BC share some histological characteristics, but, considering the differences in terms of embryologic precursors, epidemiology, genetics, medical and surgical management and response to therapy, UTUC and BC should be considered as two distinct diseases. Our objective is to analyze through a literature search the latest updates and the current knowledge about the genomics of UTUC. We als...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Elisa De De Lorenzis Giancarlo Albo Fabrizio Longo Carolina Bebi Luca Boeri Emanuele Montanari Tags: Review Source Type: research

Genes, Vol. 12, Pages 334: Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa
In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Xue Leng Hanzeng Wang Shuang Zhang Chunpu Qu Chuanping Yang Zhiru Xu Guanjun Liu Tags: Article Source Type: research

Genes, Vol. 12, Pages 335: Loss of ZmLIPOXYGENASE4 Decreases Fusarium verticillioides Resistance in Maize Seedlings
riano Marocco Fusarium verticillioides is one of the most relevant fungal species in maize responsible for ear, stalk and seedling rot, as well as the fumonisin contamination of kernels. Plant lipoxygenases (LOX) synthesize oxylipins that play a crucial role in the regulation of defense mechanisms against pathogens and influence the outcome of pathogenesis. To better uncover the role of these signaling molecules in maize resistance against F. verticillioides, the functional characterization of the 9-LOX gene, ZmLOX4, was carried out in this study by employing mutants carrying Mu insertions in this gene (named as UFMulo...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Alessandra Lanubile Virginia Maria Grazia Borrelli Mario Soccio Paola Giorni Lorenzo Stagnati Matteo Busconi Adriano Marocco Tags: Article Source Type: research

Genes, Vol. 12, Pages 336: Prevalent Pathogenic Variants of ATP7B in Chinese Patients with Wilson ’s Disease: Geographical Distribution and Founder Effect
This study aimed to show the geographical distribution and haplotype spectrum of three prevalent pathogenic variants (p.R778L, p.P992L, p.T935M) in mainland Chinese population and clarify whether the founder effect may account for their origins. We firstly summarized the frequency and geographical distribution of p.R778L, p.P992L and p.T935M in 715 WD patients. Then, to construct haplotypes associated with the three variants, Sanger sequencing and microsatellite typing at three dinucleotide-repeat markers (D13S314, D13S301, D13S316) flanking the ATP7B gene were performed in 102 WD families. An obvious regional-specific dis...
Source: Genes - February 25, 2021 Category: Genetics & Stem Cells Authors: Guo-Min Yang Rou-Min Wang Nan Xia Zi-Wei Zheng Yi Dong Zhi-Ying Wu Tags: Article Source Type: research

Genes, Vol. 12, Pages 322: Autochthonous Austrian Varieties of Prunus avium L. Represent a Regional Gene Pool, Assessed Using SSR and AFLP Markers
This study reports the genotyping of 63 sweet cherry accessions using a harmonized set of 11 simple sequence repeat (SSR) markers optimized in two multiplexed PCR reactions. Thirty-eight distinct allelic profiles were identified. The set of SSR markers chosen proved highly informative in these germplasm; an average of 6.3 alleles per locus, a PIC value of 0.59 and above-average expected and observed heterozygosity levels were detected. Additionally, 223 amplified fragment length polymorphism (AFLP) markers derived from eight selective primer combinations were employed to further differentiate 17 closely related accessions,...
Source: Genes - February 24, 2021 Category: Genetics & Stem Cells Authors: Elisabeth Sch üller Felicidad Fern ández Fernández Laima Antanaviciute Ulrike Anhalt-Br üderl Andreas Spornberger Astrid Forneck Tags: Article Source Type: research

Genes, Vol. 12, Pages 323: IPEX Syndrome: Genetics and Treatment Options
Conclusions: The genetic defects determine a diagnostic approach and prognosis, making the knowledge of the genetics of IPEX syndrome fundamental to introducing novel treatment methods. (Source: Genes)
Source: Genes - February 24, 2021 Category: Genetics & Stem Cells Authors: Iwona Ben-Skowronek Tags: Review Source Type: research

Genes, Vol. 12, Pages 324: Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs
ovatsos Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 ...
Source: Genes - February 24, 2021 Category: Genetics & Stem Cells Authors: Vasiliki Kousteni Sofia Mazzoleni Katerina Vasileiadou Michail Rovatsos Tags: Article Source Type: research

Genes, Vol. 12, Pages 325: Post-Translational Mechanisms of Plant Circadian Regulation
omers The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the...
Source: Genes - February 24, 2021 Category: Genetics & Stem Cells Authors: Jiapei Yan Yeon Jeong Kim David E. Somers Tags: Review Source Type: research

Genes, Vol. 12, Pages 326: Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress
In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignifica...
Source: Genes - February 24, 2021 Category: Genetics & Stem Cells Authors: Vivek Yadav Zhongyuan Wang Xiaozhen Yang Chunhua Wei Xuan Changqing Xian Zhang Tags: Article Source Type: research

Genes, Vol. 12, Pages 315: The Sex Determination Cascade in the Silkworm
ing Huang In insects, sex determination pathways involve three levels of master regulators: primary signals, which determine the sex; executors, which control sex-specific differentiation of tissues and organs; and transducers, which link the primary signals to the executors. The primary signals differ widely among insect species. In Diptera alone, several unrelated primary sex determiners have been identified. However, the doublesex (dsx) gene is highly conserved as the executor component across multiple insect orders. The transducer level shows an intermediate level of conservation. In many, but not all examined inse...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Xu Yang Kai Chen Yaohui Wang Dehong Yang Yongping Huang Tags: Review Source Type: research

Genes, Vol. 12, Pages 316: Genomic Regions Associated with Variation in Pigmentation Loss in Saddle Tan Beagles
sen Loss of pigmentation is a hallmark of domestication, and dogs offer a unique model for understanding the genetics of fur coloration. The aim of this study was to use dense genetic mapping to map loci underlying variations in color and whiteness in a population of laboratory beagles. A total of 190 beagles with well-defined pedigrees were phenotyped for the amount of white color in six different body parts, including the saddle. All individuals were genotyped on 85,172 informative and valid SNP-markers and the genome-wide associations for the amount of white in each body part were determined. There was a large varia...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Mia E. Nord Per Jensen Tags: Article Source Type: research

Genes, Vol. 12, Pages 317: Investigating the Adoption of Clinical Genomics in Australia. An Implementation Science Case Study
ie Taylor Despite the overwhelming interest in clinical genomics, uptake has been slow. Implementation science offers a systematic approach to reveal pathways to adoption and a theory informed approach to addressing barriers presented. Using case study methodology, we undertook 16 in-depth interviews with nongenetic medical specialists to identify barriers and enablers to the uptake of clinical genomics. Data collection and analysis was guided by two evidence-based behaviour change models: the Theoretical Domains Framework (TDF), and the Capability, Opportunity Motivation Behaviour model (COM-B). Our findings revealed ...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Stephanie Best Janet C. Long Clara Gaff Jeffrey Braithwaite Natalie Taylor Tags: Article Source Type: research

Genes, Vol. 12, Pages 318: Embryonic Kidney Development, Stem Cells and the Origin of Wilms tumor
Kuure The adult mammalian kidney is a poorly regenerating organ that lacks the stem cells that could replenish functional homeostasis similarly to, e.g., skin or the hematopoietic system. Unlike a mature kidney, the embryonic kidney hosts at least three types of lineage-specific stem cells that give rise to (a) a ureter and collecting duct system, (b) nephrons, and (c) mesangial cells together with connective tissue of the stroma. Extensive interest has been raised towards these embryonic progenitor cells, which are normally lost before birth in humans but remain part of the undifferentiated nephrogenic rests in the pe...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Hao Li Peter Hohenstein Satu Kuure Tags: Review Source Type: research

Genes, Vol. 12, Pages 319: Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks
n Henriksson The reasons for selecting a gene for further study might vary from historical momentum to funding availability, thus leading to unequal attention distribution among all genes. However, certain biological features tend to be overlooked in evaluating a gene’s popularity. Here we present a meta-analysis of the reasons why different genes have been studied and to what extent, with a focus on the gene-specific biological features. From unbiased datasets we can define biological properties of genes that reasonably may affect their perceived importance. We make use of both linear and nonlinear computational...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Ionut Sebastian Mihai Debojyoti Das Gabija Mar šalkaite Johan Henriksson Tags: Article Source Type: research

Genes, Vol. 12, Pages 320: Differential Expression of BARD1 Isoforms in Melanoma
Walker Ryś Eccles Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, &phi...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: McDougall Powell Ratajska Lynch-Sutherland Hossain Wiggins Harazin-Lechowska Cybulska-Stopa Motwani Macaulay Reid Walker Ry ś Eccles Tags: Brief Report Source Type: research

Genes, Vol. 12, Pages 321: BPA and BPS Affect Connexin 37 in Bovine Cumulus Cells
This article focuses on the impact of bisphenols during oocyte maturation. Connexins (Cx) are gap junctional proteins that may be affected by bisphenols, providing insight into their mechanism during development. Cxs 37 and 43 are crucial in facilitating cell communication between cumulus cells and oocytes. Cumulus-oocyte complexes (COCs), denuded oocytes, and cumulus cells were exposed to 0.05 mg/mL BPA or BPS for 24 hours. Both compounds had no effect on Cx43. Cumulus cells exhibited a significant increase in Cx37 expression following BPA (p = 0.001) and BPS (p = 0.017) exposure. COCs treated with BPA had increased Cx37 ...
Source: Genes - February 23, 2021 Category: Genetics & Stem Cells Authors: Reem Sabry Charlotte Apps Jaqueline A. Reiter-Saunders Angela C. Saleh Sumetha Balachandran Elizabeth J. St. St.John Laura A. Favetta Tags: Article Source Type: research

Genes, Vol. 12, Pages 309: The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles
rhards Renate Ranka Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental pla...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Alisa Kazarina Elina Petersone-Gordina Janis Kimsis Jevgenija Kuzmicka Pawel Zayakin Žans Griškjans Guntis Gerhards Renate Ranka Tags: Article Source Type: research

Genes, Vol. 12, Pages 310: Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of Both African American and European American Ancestry
In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA. Multiple novel rare recurrent variants were identified in exonic regions, functionally classified as stop-gains and frameshifts for known ADHD genes. Deletion in introns of the protocadherins families and the ncRNA HGB8P were identified in two independent EA ...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Yichuan Liu Xiao Chang Hui-Qi Qu Lifeng Tian Joseph Glessner Jingchun Qu Dong Li Haijun Qiu Patrick Sleiman Hakon Hakonarson Tags: Article Source Type: research

Genes, Vol. 12, Pages 311: Clustering Single-Cell RNA-seq Data with Regularized Gaussian Graphical Model
u Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clus...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Zhenqiu Liu Tags: Article Source Type: research

Genes, Vol. 12, Pages 313: A Novel ATM Pathogenic Variant in an Italian Woman with Gallbladder Cancer
ola Concolino Gallbladder carcinoma (GBC) is one of the most aggressive malignancies with poor prognosis and a high fatality rate. The disease presents in advanced stages where the treatment is ineffective. Regarding GBC pathogenesis, as with other neoplasia, this tumor is a multifactorial disorder involving different causative factors such as environmental, microbial, metabolic, and molecular. Genetic alterations can be germline or somatic that involving proto-oncogenes, tumor suppressor genes, cell cycle genes, and growth factors. The ataxia telangiectasia mutated (ATM) gene, coding a serine/threonine kinase involved...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Elisa De De Paolis Andrea Urbani Lisa Salvatore Laura Foca Giampaolo Tortora Angelo Minucci Paola Concolino Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 312: Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution
a Symonová Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% acro...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Veronika Bor ůvková W. Mike Howell Dominik Matoulek Radka Symonov á Tags: Article Source Type: research

Genes, Vol. 12, Pages 314: Expression Pattern of Nitric Oxide Synthase during Development of the Marine Gastropod Mollusc, Crepidula fornicata
uo;Aniello Nitric Oxide (NO) plays a key role in the induction of larval metamorphosis in several invertebrate phyla. The inhibition of the NO synthase in Crepidula fornicata, a molluscan model for evolutionary, developmental, and ecological research, has been demonstrated to block the initiation of metamorphosis highlighting that endogenous NO is crucial in the control of this developmental and morphological process. Nitric Oxide Synthase contributes to the development of shell gland, digestive gland and kidney, being expressed in cells that presumably correspond to FMRF-amide, serotoninergic and catecolaminergic neur...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Marta Truchado-Garcia Filomena Caccavale Cristina Grande Salvatore D ’Aniello Tags: Article Source Type: research

Genes, Vol. 12, Pages 308: The Scope of Astrocyte Elevated Gene-1/Metadherin (AEG-1/MTDH) in Cancer Clinicopathology: A Review
kar Since its initial cloning in 2002, a plethora of studies in a vast number of cancer indications, has strongly established AEG-1 as a bona fide oncogene. In all types of cancer cells, overexpression and knockdown studies have demonstrated that AEG-1 performs a seminal role in regulating proliferation, invasion, angiogenesis, metastasis and chemoresistance, the defining cancer hallmarks, by a variety of mechanisms, including protein-protein interactions activating diverse oncogenic pathways, RNA-binding promoting translation and regulation of inflammation, lipid metabolism and tumor microenvironment. These findings h...
Source: Genes - February 22, 2021 Category: Genetics & Stem Cells Authors: Maheen Khan Devanand Sarkar Tags: Review Source Type: research

Genes, Vol. 12, Pages 306: BAF57/SMARCE1 Interacting with Splicing Factor SRSF1 Regulates Mechanical Stress-Induced Alternative Splicing of Cyclin D1
Conclusions: The splicing factor SRSF1 and BAF57/SMARCE1 are possibly responsible for the mechanical stress-induced alternative splicing of cyclin D1. (Source: Genes)
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: Jianguo Feng Xichao Xu Xin Fan Qian Yi Liling Tang Tags: Article Source Type: research

Genes, Vol. 12, Pages 305: Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation
Taisen Iguchi Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determinat...
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: Kenji Toyota Hitoshi Miyakawa Chizue Hiruta Tomomi Sato Hidekazu Katayama Tsuyoshi Ohira Taisen Iguchi Tags: Review Source Type: research

Genes, Vol. 12, Pages 306: BAF57/ SMARCE1 Interacting with Splicing Factor SRSF1 Regulates Mechanical Stress-Induced Alternative Splicing of Cyclin D1
Conclusions: The splicing factor SRSF1 and BAF57/SMARCE1 are possibly responsible for the mechanical stress-induced alternative splicing of cyclin D1. (Source: Genes)
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: Jianguo Feng Xichao Xu Xin Fan Qian Yi Liling Tang Tags: Article Source Type: research

Genes, Vol. 12, Pages 307: Epigenetic Regulation of Processes Related to High Level of Fibroblast Growth Factor 21 in Obese Subjects
Malczewska-Malec We hypothesised that epigenetics may play an important role in mediating fibroblast growth factor 21 (FGF21) resistance in obesity. We aimed to evaluate DNA methylation changes and miRNA pattern in obese subjects associated with high serum FGF21 levels. The study included 136 participants with BMI 27–45 kg/m2. Fasting FGF21, glucose, insulin, GIP, lipids, adipokines, miokines and cytokines were measured and compared in high serum FGF21 (n = 68) group to low FGF21 (n = 68) group. Human DNA Methylation Microarrays were analysed in leukocytes from each group (n = 16). Expression of miRNAs was evalu...
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: Teresa P łatek Anna Polus Joanna G óralska Urszula Ra źny Agnieszka Dziewo ńska Agnieszka Micek Aldona Dembi ńska-Kieć Bogdan Solnica Ma łgorzata Malczewska-Malec Tags: Article Source Type: research

Genes, Vol. 12, Pages 303: Waves Out of the Korean Peninsula and Inter- and Intra-Species Replacements in Freshwater Fishes in Japan
In this study, we analyzed the phylogeography of four freshwater fish taxa, Hemibarbus longirostris, dark chub Nipponocypris temminckii, Tanakia ssp. and Carassius ssp., whose distributions include both the Korean Peninsula and Western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. The replacements of indigenous populations by succeeding migrants may have also influenced the phylogeography. (Source: Genes)
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: Shoji Taniguchi Johanna Bertl Andreas Futschik Hirohisa Kishino Toshio Okazaki Tags: Article Source Type: research

Genes, Vol. 12, Pages 304: A Deadly Cargo: Gene Repertoire of Cytotoxic Effector Proteins in the Camelidae
Petr Horin Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to perforin, granulysin, and granzymes were identified in genomes of camelids and related ungulate species, and annotation of the corresponding genes was performed. A phylogenetic tree was constructed to study evolutionary relationships between the species analyzed. Re-sequencing of all genes in a panel of 10 drome...
Source: Genes - February 21, 2021 Category: Genetics & Stem Cells Authors: J án Futas Jan Oppelt Pamela Anna Burger Petr Horin Tags: Article Source Type: research

Genes, Vol. 12, Pages 293: G2PMineR: A Genome to Phenome Literature Review Approach
Buerki There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Wojahn Galla Melton Buerki Tags: Article Source Type: research

Genes, Vol. 12, Pages 294: Pancytopenia, Recurrent Infection, Poor Wound Healing, Heterotopia of the Brain Probably Associated with a Candidate Novel de Novo CDC42 Gene Defect: Expanding the Molecular and Phenotypic Spectrum
In conclusion, we report a candidate disease-causing variant, which requires further confirmation for the etiology of CDC42 pathogenesis. This represents the first case from the Saudi population. The current study adds to the spectrum of mutations in the CDC42 gene that might help in genetic counseling and contributes to the CDC42-related genetic and functional characterization. However, further studies into the molecular mechanisms that are involved are needed in order to determine the role of the CDC42 gene associated with aberrant cell migration and immune response. (Source: Genes)
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Asiri Alwadaani Umair Alhamoudi Almuhanna Nasir Alrfaei Tuwaijri Barhoumi Alyafee Almuzzaini Aldrees Ballow Alayyar Abdulrahman Alhaidan Ghasham Al-Ajaji Alsalamah Suwairi Alfadhel Tags: Article Source Type: research

Genes, Vol. 12, Pages 296: 4mCPred-CNN —Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network
Genes, Vol. 12, Pages 296: 4mCPred-CNN—Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network Genes doi: 10.3390/genes12020296 Authors: Zeeshan Abbas Hilal Tayara Kil To Chong Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is required. Although we have several techniques for the prediction of 4mC sites in different genomes based on both machine learning (ML) and convolution...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Zeeshan Abbas Hilal Tayara Kil To Chong Tags: Article Source Type: research

Genes, Vol. 12, Pages 298: Insights into the Transcriptional Regulation of Branching Hormonal Signaling Pathways Genes under Drought Stress in Arabidopsis
k Yun A large number of hormonal biosynthetic or signaling pathways genes controlling shoot branching are widely known for their roles in regulating plant growth and development, operating in synergetic or antagonistic manner. However, their involvement in abiotic stress response mechanism remains unexplored. Initially, we performed an in silico analysis to identify potential transcription binding sites for the basic leucine zipper 62 transcription factor (bZIP62 TF) in the target branching related genes. The results revealed the presence of cis-regulatory elements specific to two bZIP TFs, AtbZIP18 and AtbZIP69, rathe...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Nkulu Kabange Rolly Bong-Gyu Mun Byung-Wook Yun Tags: Brief Report Source Type: research

Genes, Vol. 12, Pages 295: Clinical and Mutational Spectrum of Xeroderma Pigmentosum in Egypt: Identification of Six Novel Mutations and Implications for Ancestral Origins
In this study, we describe clinical and genetic findings of 36 XP patients from Egypt, a highly consanguineous population from North Africa. Thorough clinical evaluation followed by Sanger sequencing of XPA and XPC genes were done. Six novel and seven previously reported mutations were identified. Phenotype-genotype correlation was investigated. We report clinical and molecular findings consistent with previous reports of countries sharing common population structure, and geographical and historical backgrounds with implications on common ancestral origins and historical migration flows. Clinical and genetic profiling impr...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Eman Rabie Khalda Amr Suher Zada Heba El-Sayed Mohamad El Darouti Ghada El-Kamah Tags: Article Source Type: research

Genes, Vol. 12, Pages 299: Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields
Oliver Stachs In cells, intrinsic endogenous direct current (DC) electric fields (EFs) serve as morphogenetic cues and are necessary for several important cellular responses including activation of multiple signaling pathways, cell migration, tissue regeneration and wound healing. Endogenous DC EFs, generated spontaneously following injury in physiological conditions, directly correlate with wound healing rate, and different cell types respond to these EFs via directional orientation and migration. Application of external DC EFs results in electrode polarity and is known to activate intracellular signaling events in sp...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Bhavani S. Kowtharapu Jyoti Damaraju Nitesh Kumar Singh Josefin Ziebart Rainer Bader Dirk Koczan Oliver Stachs Tags: Communication Source Type: research

Genes, Vol. 12, Pages 300: The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases
audia Donnini The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offer...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Camilla Ceccatelli Berti Giulia di Punzio Cristina Dallabona Enrico Baruffini Paola Goffrini Tiziana Lodi Claudia Donnini Tags: Review Source Type: research

Genes, Vol. 12, Pages 301: Understanding Rice-Magnaporthe Oryzae Interaction in Resistant and Susceptible Cultivars of Rice under Panicle Blast Infection Using a Time-Course Transcriptome Analysis
Amolkumar U. Solanke Rice blast is a global threat to food security with up to 50% yield losses. Panicle blast is a more severe form of rice blast and the response of rice plant to leaf and panicle blast is distinct in different genotypes. To understand the specific response of rice in panicle blast, transcriptome analysis of blast resistant cultivar Tetep, and susceptible cultivar HP2216 was carried out using RNA-Seq approach after 48, 72 and 96 h of infection with Magnaporthe oryzae along with mock inoculation. Transcriptome data analysis of infected panicle tissues revealed that 3553 genes differentially expresse...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Vishesh Kumar Priyanka Jain Sureshkumar Venkadesan Suhas Gorakh Karkute Jyotika Bhati Malik Zainul Abdin Amitha Mithra Sevanthi Dwijesh Chandra Mishra Krishna Kumar Chaturvedi Anil Rai Tilak Raj Sharma Amolkumar U. Solanke Tags: Article Source Type: research

Genes, Vol. 12, Pages 302: Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation
Enrique Gonzalez Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine remain unknown. In...
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Oscar Arrey-Salas Jos é Carlos Caris-Maldonado Bairon Hern ández-Rojas Enrique Gonzalez Tags: Article Source Type: research

Genes, Vol. 12, Pages 297: Functions of Forkhead Box O on Glucose Metabolism in Abalone Haliotis discus hannai and Its Responses to High Levels of Dietary Lipid
In conclusion, abalone foxo can be regulated by dietary lipid and can regulate gluconeogenesis or glycolysis in response to changes of dietary lipid levels, in which glycogen metabolism plays an important role. (Source: Genes)
Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Liu Wang Yanlin Guo Mingzhu Pan Xinxin Li Dong Huang Yue Liu Chenglong Wu Wenbing Zhang Kangsen Mai Tags: Article Source Type: research

Genes, Vol. 12, Pages 289: Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients
This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management. (Source: Genes)
Source: Genes - February 19, 2021 Category: Genetics & Stem Cells Authors: Ur šula Prosenc Zmrzljak Rok Ko šir Zoran Krivokapi ć Dragica Radojkovi ć Aleksandra Nikoli ć Tags: Article Source Type: research

Genes, Vol. 12, Pages 290: Deciphering Biochemical and Molecular Signatures Associated with Obesity in Context of Metabolic Health
This study aims to identify the clinical and genetic markers related to the two uncommon nutritional statuses—metabolically unhealthy normal-weight (MUNW) and metabolically healthy overweight/obese (MHOW) individuals in the physically active individuals. Physically active male volunteers (n = 120) were recruited, and plasma samples were analyzed for the clinical parameters. Triglycerides, HDL-Cholesterol, LDL-cholesterol, total cholesterol, C-reactive protein, and insulin resistance were considered as markers of metabolic syndrome. The subjects were classified as ‘healthy’ (0 metabolic abnormalities) or &...
Source: Genes - February 19, 2021 Category: Genetics & Stem Cells Authors: Daisy Masih Jitendra Kumar Tripathi Gurseen Rakhra Annu Vats Saroj Kumar Verma Prabhash Kumar Jha Manish Sharma Mohammad Zahid Ashraf Som Nath Singh Tags: Article Source Type: research

Genes, Vol. 12, Pages 291: Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray
ce de León Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduc...
Source: Genes - February 19, 2021 Category: Genetics & Stem Cells Authors: Marcos Calderon Manuel J. More Gustavo A. Guti érrez F. Abel Ponce de Le ón Tags: Article Source Type: research

Genes, Vol. 12, Pages 292: Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serin...
Source: Genes - February 19, 2021 Category: Genetics & Stem Cells Authors: Francesco Zapelloni Jos é A. Jurado-Rivera Dami à Jaume Carlos Juan Joan Pons Tags: Article Source Type: research

Genes, Vol. 12, Pages 288: Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis
This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus. (Source: Genes)
Source: Genes - February 19, 2021 Category: Genetics & Stem Cells Authors: Zhihui Guo Meilan Xu Hironori Nagano Lindsay V. Clark Erik J. Sacks Toshihiko Yamada Tags: Article Source Type: research