Genes, Vol. 11, Pages 1404: Hsa-miR-375/RASD1 Signaling May Predict Local Control in Early Breast Cancer
Conclusion: This two-phase study demonstrates that hsa-miR-375/RASD1 signaling is able to predict local control in early breast cancer patients, which—to our knowledge—is the first clinical report on a miR combined with one of its downstream target proteins predicting LC in breast cancer. (Source: Genes)
Source: Genes - November 26, 2020 Category: Genetics & Stem Cells Authors: Barbara Zellinger Ulrich Bodenhofer Immanuela A. Engl änder Cornelia Kronberger Peter Strasser Brane Grambozov Gerd Fastner Markus Stana Roland Reitsamer Karl Sotlar Felix Sedlmayer Franz Zehentmayr Tags: Article Source Type: research

Genes, Vol. 11, Pages 1405: Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation
nfeng Liu Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) ...
Source: Genes - November 26, 2020 Category: Genetics & Stem Cells Authors: Wen Feng Pengju Zhao Xianrui Zheng Zhengzheng Hu Jianfeng Liu Tags: Article Source Type: research

Genes, Vol. 11, Pages 1406: Comparative Genomics and Functional Studies of Wheat BED-NLR Loci
obal Uauy Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genom...
Source: Genes - November 26, 2020 Category: Genetics & Stem Cells Authors: Clemence Marchal 10+ Wheat Genome Project 10+ Wheat Genome Project Georg Haberer Manuel Spannagl Cristobal Uauy Tags: Article Source Type: research

Genes, Vol. 11, Pages 1407: A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants
We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap a...
Source: Genes - November 26, 2020 Category: Genetics & Stem Cells Authors: Larisa N. Efremova Svetlana R. Strelnikova Guzel R. Gazizova Elena A. Minkina Roman A. Komakhin Tags: Article Source Type: research

Genes, Vol. 11, Pages 1397: Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes
Victor Wei Zhang Juntao Liu The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome seq...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Qingwei Qi Yulin Jiang Xiya Zhou Hua Meng Na Hao Jiazhen Chang Junjie Bai Chunli Wang Mingming Wang Jiangshan Guo Yunshu Ouyang Zhonghui Xu Mengsu Xiao Victor Wei Zhang Juntao Liu Tags: Article Source Type: research

Genes, Vol. 11, Pages 1398: Evaluation of the Ion AmpliSeq ™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples
Genes, Vol. 11, Pages 1398: Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples Genes doi: 10.3390/genes11121398 Authors: Diepenbroek Bayer Schwender Schiller Lim Lagacé Anslinger As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable “eye-witness&...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Diepenbroek Bayer Schwender Schiller Lim Lagac é Anslinger Tags: Article Source Type: research

Genes, Vol. 11, Pages 1399: Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation
This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation. Until eight days post-anthesis (DPA), both the seeds of the two varieties were white. The black sesame seed turned to yellow between 9 and 11 DPA and then black between 12 and 14 DPA. The black and white sesame showed similar trend-expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEG...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Linhai Wang Senouwa Segla Koffi Dossou Xin Wei Yanxin Zhang Donghua Li Jingyin Yu Xiurong Zhang Tags: Article Source Type: research

Genes, Vol. 11, Pages 1401: Evolution of Homeologous Gene Expression in Polyploid Wheat
In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of t...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Zhao Dong Nadon Ding Wang Dong Liu Jackson Xu Tags: Article Source Type: research

Genes, Vol. 11, Pages 1402: Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)
This study will contribute to a better knowledge of genes that have been targeted during peanut domestication. (Source: Genes)
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Alyr Pallu Sambou Nguepjop Seye Tossim Djiboune Sane Rami Fonceka Tags: Article Source Type: research

Genes, Vol. 11, Pages 1403: Insecticide Resistance Profiling of Anopheles coluzzii and Anopheles gambiae Populations in the Southern Senegal: Role of Target Sites and Metabolic Resistance Mechanisms
ia Gaye Faye Niang Wondji The emergence and spread of insecticide resistance among the main malaria vectors is threatening the effectiveness of vector control interventions in Senegal. The main drivers of this resistance in the Anopheles gambiae complex (e.g., An. gambiae and Anopheles coluzzii) remains poorly characterized in Senegal. Here we characterized the main target site and metabolic resistances mechanisms among the An. gambiae and An. coluzzii populations from their sympatric and allopatric or predominance area in Senegal. Larvae and pupae of An. gambiae s.l. were collected, reared to adulthood, an...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Gueye Tchouakui Dia Faye Ahmed Wondji Nguiffo Mugenzi Tripet Konat é Diabate Dia Gaye Faye Niang Wondji Tags: Article Source Type: research

Genes, Vol. 11, Pages 1400: MicroRNA-214 Inhibits Chicken Myoblasts Proliferation, Promotes Their Differentiation, and Targets the TRMT61A Gene
This study revealed the function and regulatory mechanism of miR-214 in the proliferation and differentiation of CPMs. (Source: Genes)
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Yanjun Duan Yulin Wu Xuemei Yin Tingting Li Fuxiang Chen Pengfei Wu Shanshan Zhang Jinyu Wang Genxi Zhang Tags: Article Source Type: research

Genes, Vol. 11, Pages 1395: Genome-Wide Association Study of Root System Development at Seedling Stage in Rice
This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium ...
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Hongjia Zhang Mar Lar San Seong-Gyu Jang Ja-Hong Lee Na-Eun Kim Ah-Rim Lee So-Yeon Park Fang-Yuan Cao Joong-Hyoun Chin Soon-Wook Kwon Tags: Article Source Type: research

Genes, Vol. 11, Pages 1396: The Genetic Complexity of Prostate Cancer
in Olivier Cussenot Prostate cancer (PCa) is a major concern in public health, with many genetically distinct subsets. Genomic alterations in PCa are extraordinarily complex, and both germline and somatic mutations are of great importance in the development of this tumor. The aim of this review is to provide an overview of genetic changes that can occur in the development of PCa and their role in potential therapeutic approaches. Various pathways and mechanisms proposed to play major roles in PCa are described in detail to provide an overview of current knowledge. (Source: Genes)
Source: Genes - November 25, 2020 Category: Genetics & Stem Cells Authors: Eva Comp érat Gabriel Wasinger Andr é Oszwald Renate Kain Geraldine Cancel-Tassin Olivier Cussenot Tags: Review Source Type: research

Genes, Vol. 11, Pages 1391: Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases
In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine. (Source: Genes)
Source: Genes - November 24, 2020 Category: Genetics & Stem Cells Authors: Viktor Hlavac Beatrice Mohelnikova-Duchonova Martin Lovecek Jiri Ehrmann Veronika Brynychova Katerina Kolarova Pavel Soucek Tags: Article Source Type: research

Genes, Vol. 11, Pages 1392: Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus
zabeth L.J. Watkin Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed ...
Source: Genes - November 24, 2020 Category: Genetics & Stem Cells Authors: Himel Nahreen Khaleque Homayoun Fathollazadeh Carolina Gonz ález Raihan Shafique Anna H. Kaksonen David S. Holmes Elizabeth L.J. Watkin Tags: Article Source Type: research

Genes, Vol. 11, Pages 1393: Aquatic Exposure to Abscisic Acid Transstadially Enhances Anopheles stephensi Resistance to Malaria Parasite Infection
We examined nutrient levels and gene expression to demonstrate that ABA can transstadially alter resistance to a rodent malaria parasite with hallmarks of previously observed mechanisms of resistance following provision of ABA in blood to A. stephensi. (Source: Genes)
Source: Genes - November 24, 2020 Category: Genetics & Stem Cells Authors: Dean M. Taylor Reagan S. Haney Shirley Luckhart Tags: Article Source Type: research

Genes, Vol. 11, Pages 1394: Role of PB1 Midbody Remnant Creating Tethered Polar Bodies during Meiosis II
net Chenevert Polar body (PB) formation is an extreme form of unequal cell division that occurs in oocytes due to the eccentric position of the small meiotic spindle near the oocyte cortex. Prior to PB formation, a chromatin-centered process causes the cortex overlying the meiotic chromosomes to become polarized. This polarized cortical subdomain marks the site where a cortical protrusion or outpocket forms at the oocyte surface creating the future PBs. Using ascidians, we observed that PB1 becomes tethered to the fertilized egg via PB2, indicating that the site of PB1 cytokinesis directed the precise site for PB2 emis...
Source: Genes - November 24, 2020 Category: Genetics & Stem Cells Authors: Alex McDougall Celine Hebras Gerard Pruliere David Burgess Vlad Costache Remi Dumollard Janet Chenevert Tags: Article Source Type: research

Genes, Vol. 11, Pages 1390: Bracon brevicornis Genome Showcases the Potential of Linked-Read Sequencing in Identifying a Putative Complementary Sex Determiner Gene
an Eveline C. Verhulst Bracon brevicornis is an ectoparasitoid of a wide range of larval-stage Lepidopterans, including several pests of important crops, such as the corn borer, Ostrinia nubilalis. It is also one of the earliest documented cases of complementary sex determination in Hymenoptera. Here, we present the linked-read-based genome of B. brevicornis, complete with an ab initio-derived annotation and protein comparisons with fellow braconids, Fopius arisanus and Diachasma alloeum. We demonstrate the potential of linked-read assemblies in exploring regions of heterozygosity and search for structural and homolo...
Source: Genes - November 24, 2020 Category: Genetics & Stem Cells Authors: Kim B. Ferguson Bart A. Pannebakker Alejandra Centuri ón Joost van den Heuvel Ronald Nieuwenhuis Frank F. M. Becker Elio Schijlen Andra Thiel Bas J. Zwaan Eveline C. Verhulst Tags: Article Source Type: research

Genes, Vol. 11, Pages 1385: Network Protein Interaction in Parkinson ’s Disease and Periodontitis Interplay: A Preliminary Bioinformatic Analysis
In this study, we conducted a protein–protein network interaction analysis with recognized genes encoding proteins with variants strongly associated with PD and periodontitis. Genes of interest were collected via the Genome-Wide Association Studies (GWAS) database. Then, we conducted a protein interaction analysis, using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, with a highest confidence cutoff of 0.9 and sensitivity analysis with confidence cutoff of 0.7. Our protein network casts a comprehensive analysis of potential protein–protein interactions between...
Source: Genes - November 23, 2020 Category: Genetics & Stem Cells Authors: Jo ão Botelho Paulo Mascarenhas Jos é João Mendes Vanessa Machado Tags: Article Source Type: research

Genes, Vol. 11, Pages 1386: Transcriptome-Wide Identification of  WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb
Genes, Vol. 11, Pages 1386: Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb Genes doi: 10.3390/genes11111386 Authors: Sheng Yao Fan Wu Qingqing Hao Kongshu Ji Pinus massoniana Lamb, an economically important conifer tree, is widely distributed in China. WRKY transcription factors (TFs) play important roles in plant growth and development, biological and abiotic stress. Nevertheless, there is little information about the WRKY genes in P. massoniana. By searching for conse...
Source: Genes - November 23, 2020 Category: Genetics & Stem Cells Authors: Sheng Yao Fan Wu Qingqing Hao Kongshu Ji Tags: Article Source Type: research

Genes, Vol. 11, Pages 1387: GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces
This study reveals that the use of fruit RNA-Seq SNP diversity is effective not only for identification of genomic regions that underlie variation in fruit traits, but also of variation related to additional plant traits and adaptive responses to climate variation. These results allowed validation of our approach because different marker-trait associations mapped on chromosomal regions where other candidate genes for the same traits were previously reported. In addition, previously uncharacterized chromosomal regions were targeted as potentially involved in the expression of variable phenotypes, thus demonstrating that our...
Source: Genes - November 23, 2020 Category: Genetics & Stem Cells Authors: Monica Rodriguez Alessandro Scintu Chiara M. Posadinu Yimin Xu Cuong V. Nguyen Honghe Sun Elena Bitocchi Elisa Bellucci Roberto Papa Zhangjun Fei James J. Giovannoni Domenico Rau Giovanna Attene Tags: Article Source Type: research

Genes, Vol. 11, Pages 1388: Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo
This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level. Physiochemical properties, multiple sequence alignment, and phylogenetic analysis were performed for 64 HSP genes in the Bubalus bubalis genome. Four genes were identified as belonging to the HSP90 family, 10 to HSP70, 39 to HSP40, 8 to HSPB, one for each HSPD, HSPH1, and HSP10, respectively. The aliphatic index was higher for HSP90 and HSP70 as compared to the HSP40 family, indicating their greater thermostability. Grand Average of hydropathicity Index values indicated the hydrophilic nature ...
Source: Genes - November 23, 2020 Category: Genetics & Stem Cells Authors: Rehman Nadeem Javed Hassan Luo Khalid Liu Tags: Article Source Type: research

Genes, Vol. 11, Pages 1389: Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family Under Abiotic Stresses in Medicago truncatula
ng Wang The trihelix transcription factor (GT) family is widely involved in regulating plant growth and development, and most importantly, responding to various abiotic stresses. Our study first reported the genome-wide identification and analysis of GT family genes in Medicago truncatula. Overall, 38 trihelix genes were identified in the M. truncatula genome and were classified into five subfamilies (GT-1, GT-2, SH4, GTγ and SIP1). We systematically analyzed the phylogenetic relationship, chromosomal distribution, tandem and segmental duplication events, gene structures and conserved motifs of MtGTs. ...
Source: Genes - November 23, 2020 Category: Genetics & Stem Cells Authors: Liu Zhang Ma Wang Wang Tags: Article Source Type: research

Genes, Vol. 11, Pages 1383: Fucosidosis —Clinical Manifestation, Long-Term Outcomes, and Genetic Profile—Review and Case Series
Genes, Vol. 11, Pages 1383: Fucosidosis—Clinical Manifestation, Long-Term Outcomes, and Genetic Profile—Review and Case Series Genes doi: 10.3390/genes11111383 Authors: Karolina M. Stepien Elżbieta Ciara Aleksandra Jezela-Stanek Fucosidosis is a neurodegenerative disorder which progresses inexorably. Clinical features include coarse facial features, growth retardation, recurrent upper respiratory infections, dysostosis multiplex, and angiokeratoma corporis diffusum. Fucosidosis is caused by mutations in the FUCA1 gene resulting in α-L-fucosidase deficiency. Only 36 pathogenic variants...
Source: Genes - November 22, 2020 Category: Genetics & Stem Cells Authors: Karolina M. Stepien El żbieta Ciara Aleksandra Jezela-Stanek Tags: Review Source Type: research

Genes, Vol. 11, Pages 1384: Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer
This study provides an unbiased, overarching perspective on the relationship of aaRSs with cancers and identifies certain aaRS family members as promising therapeutic targets or potential leads for developing biological therapy for cancer. (Source: Genes)
Source: Genes - November 22, 2020 Category: Genetics & Stem Cells Authors: Justin Wang Ingrid Vallee Aditi Dutta Yu Wang Zhongying Mo Ze Liu Haissi Cui Andrew I. Su Xiang-Lei Yang Tags: Article Source Type: research

Genes, Vol. 11, Pages 1380: Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method
Emily B. Hollister Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and fu...
Source: Genes - November 21, 2020 Category: Genetics & Stem Cells Authors: Tasha M. Santiago-Rodriguez Aaron Garoutte Emmase Adams Waleed Nasser Matthew C. Ross Alex La Reau Zachariah Henseler Tonya Ward Dan Knights Joseph F. Petrosino Emily B. Hollister Tags: Article Source Type: research

Genes, Vol. 11, Pages 1381: Differential Gene Expression in Longissimus Dorsi Muscle of Hanwoo Steers —New Insight in Genes Involved in Marbling Development at Younger Ages
In this study, we took muscle samples from 12 Hanwoo steers at the age of 18 and 30 months. From the contrast between age and marbling score, we identified in total 1883 differentially expressed genes (FDR < 0.05 and logarithm fold change ≥ 1.5) with 782 genes up-regulated and 1101 down-regulated. Differences in gene expression were higher between the ages x marbling groups rather than between high and low marbling groups. At 18 months of age, the genes SLC38A4, ABCA10, APOL6, and two novel genes (ENSBTAG00000015330 and ENSBTAG00000046041) were up-regulated in the high marbling group. From the protein...
Source: Genes - November 21, 2020 Category: Genetics & Stem Cells Authors: Sara de las Heras-Saldana Ki Yong Chung Hyounju Kim Dajeong Lim Cedric Gondro Julius H. J. van der Werf Tags: Article Source Type: research

Genes, Vol. 11, Pages 1382: A Novel Germline c.1267T & gt;A MEN1 Mutation in MEN1 Family —from Phenotype to Gene and Back
This report describes clinical, biochemical, radiographic, and genetic findings, the latter obtained using next generation sequencing (NGS), in three consanguineous patients. Gene panels in NGS consisted of 5 or 70 genes, including MEN1 and RET. The first patient suffered from recurrent primary hyperparathyroidism. Primary hyperparathyroidism and pituitary microadenomas were afterwards diagnosed in two of her daughters. No clinical nor radiological features of gastroenteropancreatic neuroendocrine tumors were found. All three family members were heterozygous for MEN1 NM_130799: c.1267T>A transversion, which is p...
Source: Genes - November 21, 2020 Category: Genetics & Stem Cells Authors: Wojciech Gierlikowski Agata Skwarek-Szewczyk Micha ł Popow Tags: Case Report Source Type: research

Genes, Vol. 11, Pages 1371: At the X-Roads of Sex and Genetics in Pulmonary Arterial Hypertension
reg Elliott Group 1 pulmonary hypertension (pulmonary arterial hypertension; PAH) is a rare disease characterized by remodeling of the small pulmonary arteries leading to progressive elevation of pulmonary vascular resistance, ultimately leading to right ventricular failure and death. Deleterious mutations in the serine-threonine receptor bone morphogenetic protein receptor 2 (BMPR2; a central mediator of bone morphogenetic protein (BMP) signaling) and female sex are known risk factors for the development of PAH in humans. In this narrative review, we explore the complex interplay between the BMP and estrogen signaling...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Meghan M. Cirulis Mark W. Dodson Lynn M. Brown Samuel M. Brown Tim Lahm Greg Elliott Tags: Review Source Type: research

Genes, Vol. 11, Pages 1372: Stem Cells: Current Status and Therapeutic Implications
y Cancer stem cells (CSCs) are a class of pluripotent cells that have been observed in most types of cancers. Evolving evidence suggests that CSCs, has the ability to self-renew and initiate tumors, may be responsible for promoting therapeutic resistance, tumor recurrence and metastasis. Tumor heterogeneity is originating from CSCs and its progenitors are recognized as major difficulty in efficaciously treating cancer patients. Therefore, understanding the biological mechanisms by which CSCs survive chemo- and-radiation therapy has the potential to identify new therapeutic strategies in the future. In this review, we s...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Kaladhar B. Reddy Tags: Review Source Type: research

Genes, Vol. 11, Pages 1373: New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses
Mulatu Geleta The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci we...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Sewalem Tsehay Rodomiro Ortiz Eva Johansson Endashaw Bekele Kassahun Tesfaye Cecilia Hammenhag Mulatu Geleta Tags: Article Source Type: research

Genes, Vol. 11, Pages 1374: Classification of Changes in the Fecal Microbiota Associated with Colonic Adenomatous Polyps Using a Long-Read Sequencing Platform
In this study, we examined the relevance between targeted operational taxonomic units and colonic polyps using short- and long-read sequencing platforms. The gut microbiota was assessed in 132 clinical subjects, including 53 healthy participants, 36 patients with occult blood in the gut, and 43 cases with adenomatous polyps. An elevation in the relative abundance of Klebsiella pneumonia, Fusobacterium varium, and Fusobacterium mortiferum was identified in patients with adenomatous polyps compared with the other groups using long-read sequencing workflow. In contrast, the relatively high abundances of Blautia luti, Bacteroi...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Po-Li Wei Ching-Sheng Hung Yi-Wei Kao Ying-Chin Lin Cheng-Yang Lee Tzu-Hao Chang Ben-Chang Shia Jung-Chun Lin Tags: Article Source Type: research

Genes, Vol. 11, Pages 1375: Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)
In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siber...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Larisa S. Biltueva Dmitry Yu. Prokopov Svetlana A. Romanenko Elena A. Interesova Manfred Schartl Vladimir A. Trifonov Tags: Article Source Type: research

Genes, Vol. 11, Pages 1376: Experimental Models to Study Autism Spectrum Disorders: hiPSCs, Rodents and Zebrafish
Allegue Laura Sánchez Autism Spectrum Disorders (ASD) affect around 1.5% of the global population, which manifest alterations in communication and socialization, as well as repetitive behaviors or restricted interests. ASD is a complex disorder with known environmental and genetic contributors; however, ASD etiology is far from being clear. In the past decades, many efforts have been put into developing new models to study ASD, both in vitro and in vivo. These models have a lot of potential to help to validate some of the previously associated risk factors to the development of the disorder, and to test new po...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Alba Pensado-L ópez Sara Veiga-R úa Ángel Carracedo Catarina Allegue Laura S ánchez Tags: Review Source Type: research

Genes, Vol. 11, Pages 1377: Mutations in Collagen Genes in the Context of an Isolated Population
Momirovska Genetic studies of population isolates have great potential to provide a unique insight into genetic differentiation and phenotypic expressions. Galičnik village is a population isolate located in the northwest region of the Republic of North Macedonia, established around the 10th century. Alport syndrome-linked nephropathy with a complex inheritance pattern has been described historically among individuals in the village. In order to determine the genetic basis of the nephropathies and to characterize the genetic structure of the population, 23 samples were genotyped using a custom-made next generation...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Zupan Matja šič Grubelnik Tasi ć Momirovska Tags: Article Source Type: research

Genes, Vol. 11, Pages 1378: The Genetic Basis of Obesity and Related Metabolic Diseases in Humans and Companion Animals
fan Obesity is one of the most prevalent health conditions in humans and companion animals globally. It is associated with premature mortality, metabolic dysfunction, and multiple health conditions across species. Obesity is, therefore, of importance in the fields of medicine and veterinary medicine. The regulation of adiposity is a homeostatic process vulnerable to disruption by a multitude of genetic and environmental factors. It is well established that the heritability of obesity is high in humans and laboratory animals, with ample evidence that the same is true in companion animals. In this review, we provide an o...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Natalie Wallis Eleanor Raffan Tags: Review Source Type: research

Genes, Vol. 11, Pages 1379: Genome-Wide Identification and Characterization of the TCP Gene Family in Cucumber (Cucumis sativus L.) and Their Transcriptional Responses to Different Treatments
In this study, we performed a genome-wide identification of putative TCP genes and analyzed their chromosomal location, gene structure, conserved motif, and transcript expression. A total of 27 putative TCP genes were identified and characterized in cucumber. All 27 putative CsTCP genes were classified into class I and class II. Class I comprised 12 CsTCPs and Class II contained 15 CsTCPs. The 27 putative CsTCP genes were randomly distributed in five of seven chromosomes in cucumber. Four putative CsTCP genes were found to contain putative miR319 target sites. Quantitative RT-PCR revealed that 27 putative CsTCP genes exhib...
Source: Genes - November 20, 2020 Category: Genetics & Stem Cells Authors: Wen Chen Du Zhang Zhang He Pan Cai Wang Tags: Article Source Type: research

Genes, Vol. 11, Pages 1370: Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions
Morales-Vazquez Luis G. Brieba The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS D...
Source: Genes - November 19, 2020 Category: Genetics & Stem Cells Authors: Antol ín Peralta-Castro Paola L. Garc ía-Medel Noe Baruch-Torres Carlos H. Trasvi ña-Arenas V íctor Juarez-Quintero Carlos M. Morales-Vazquez Luis G. Brieba Tags: Review Source Type: research

Genes, Vol. 11, Pages 1367: Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic
ras Reyes Víctor Manuel Pérez-Sánchez Héctor Aquiles Maldonado-Martínez Maybelline Robles-Estrada Enrique Bargalló-Rocha Paula Cabrera-Galeana Maritza Ramos-Ramírez Yolanda Irasema Chirino Luis Alonso Herrera Luis Ignacio Terrazas Javier Oliver Cecilia Frecha Sandra Perdomo Felipe Vaca-Paniagua Triple-negative breast cancer (TNBC) presents a marked diversity at the molecular level, which promotes a clinical heterogeneity that further complicates treatment. We performed a detailed whole exome sequencing profile of 29 Mexican patients with long fo...
Source: Genes - November 19, 2020 Category: Genetics & Stem Cells Authors: Ernesto Rojas-Jim énez Javier C ésar Mejía-Gómez Clara D íaz-Velásquez Rosal ía Quezada-Urban H éctor Martínez Gregorio Fernando Vallejo-Lecuona Aldo de la Cruz-Montoya Fany Iris Porras Reyes V íctor Manuel Pérez-Sánchez H éctor Aquiles Maldo Tags: Article Source Type: research

Genes, Vol. 11, Pages 1368: SWI/SNF Alterations in Squamous Bladder Cancers
fan Garczyk Nadine T. Gaisa Dysfunction of the SWI/SNF complex has been observed in various cancers including urothelial carcinomas. However, the clinical impact of the SWI/SNF complex in squamous-differentiated bladder cancers (sq-BLCA) remains unclear. Therefore, we aimed to analyze potential expression loss and genetic alterations of (putative) key components of the SWI/SNF complex considering the co-occurrence of genetic driver mutations and PD-L1 expression as indicators for therapeutic implications. Assessment of ARID1A, SMARCA2, SMARCA4, SMARCB1/INI1, SMARCC1, SMARCC2 and PBRM1 mutations in a TCGA data set of ...
Source: Genes - November 19, 2020 Category: Genetics & Stem Cells Authors: Fabian Achenbach Michael Rose Nadina Ortiz-Br üchle Lancelot Seillier Ruth Kn üchel Veronika Weyerer Arndt Hartmann Ronja Morsch Angela Maurer Thorsten H. Ecke Stefan Garczyk Nadine T. Gaisa Tags: Article Source Type: research

Genes, Vol. 11, Pages 1369: Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus
Jacquie Rand Grant Morahan Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by p...
Source: Genes - November 19, 2020 Category: Genetics & Stem Cells Authors: Lois Balmer Caroline Ann O ’Leary Marilyn Menotti-Raymond Victor David Stephen O ’Brien Belinda Penglis Sher Hendrickson Mia Reeves-Johnson Susan Gottlieb Linda Fleeman Dianne Vankan Jacquie Rand Grant Morahan Tags: Article Source Type: research

Genes, Vol. 11, Pages 1364: Genetic Mutations and Variants in the Susceptibility of Familial Non-Medullary Thyroid Cancer
eruko Kimura Thyroid cancer is the most frequent endocrine malignancy with the majority of cases derived from thyroid follicular cells and caused by sporadic mutations. However, when at least two or more first degree relatives present thyroid cancer, it is classified as familial non-medullary thyroid cancer (FNMTC) that may comprise 3–9% of all thyroid cancer. In this context, 5% of FNMTC are related to hereditary syndromes such as Cowden and Werner Syndromes, displaying specific genetic predisposition factors. On the other hand, the other 95% of cases are classified as non-syndromic FNMTC. Over the last ...
Source: Genes - November 18, 2020 Category: Genetics & Stem Cells Authors: Fab íola Yukiko Miasaki Cesar Seigi Fuziwara Gisah Amaral de Carvalho Edna Teruko Kimura Tags: Review Source Type: research

Genes, Vol. 11, Pages 1365: CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries
Hubert P. Endtz Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a global health concern and its treatment is problematic due to the rise in antimicrobial resistance (AMR). Rapid detection of patients infected with AMR positive S. Typhi is, therefore, crucial to prevent further spreading. Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas), is an adaptive immune system that initially was used for typing purposes. Later, it was discovered to play a role in defense against phages and plasmids, including ones that carry AMR genes, and, at present, i...
Source: Genes - November 18, 2020 Category: Genetics & Stem Cells Authors: Arif Mohammad Tanmoy Chinmoy Saha Mohammad Saiful Islam Sajib Senjuti Saha Florence Komurian-Pradel Alex van Belkum Rogier Louwen Samir Kumar Saha Hubert P. Endtz Tags: Article Source Type: research

Genes, Vol. 11, Pages 1366: Highly Rearranged Karyotypes and Multiple Sex Chromosome Systems in Armored Catfishes from the Genus Harttia (Teleostei, Siluriformes)
In this study, Harttia intermontana and two still undescribed species, morphologically identified as Harttia sp. 1 and Harttia sp. 2, were cytogenetically analyzed. Harttia intermontana has 2n = 52 and 2n = 53 chromosomes, while Harttia sp. 1 has 2n = 56 and 2n = 57 chromosomes in females and males, respectively, thus highlighting the occurrence of an XX/XY1Y2 multiple sex chromosome system in both species. Harttia sp. 2 presents 2n = 62 chromosomes for both females and males, with fission events explaining its karyotype diversification. Chromosomal locations of the rDNA sites were also quite different among species, reinf...
Source: Genes - November 18, 2020 Category: Genetics & Stem Cells Authors: Geize Aparecida Deon Larissa Glugoski Marcelo Ricardo Vicari Viviane Nogaroto Francisco de Menezes Cavalcante Sassi Marcelo de Bello Cioffi Thomas Liehr Luiz Antonio Carlos Bertollo Orlando Moreira-Filho Tags: Article Source Type: research

Genes, Vol. 11, Pages 1363: Hes5.9 Coordinate FGF and Notch Signaling to Modulate Gastrulation via Regulating Cell Fate Specification and Cell Migration in Xenopus tropicalis
eichao Chen Gastrulation drives the establishment of three germ layers and embryonic axes during frog embryonic development. Mesodermal cell fate specification and morphogenetic movements are vital factors coordinating gastrulation, which are regulated by numerous signaling pathways, such as the Wnt (Wingless/Integrated), Notch, and FGF (Fibroblast growth factor) pathways. However, the coordination of the Notch and FGF signaling pathways during gastrulation remains unclear. We identified a novel helix–loop–helix DNA binding domain gene (Hes5.9), which was regulated by the FGF and Notch signa...
Source: Genes - November 18, 2020 Category: Genetics & Stem Cells Authors: Xiao Huang Liyue Zhang Shanshan Yang Yongpu Zhang Mingjiang Wu Peichao Chen Tags: Article Source Type: research

Genes, Vol. 11, Pages 1361: Segregation Analysis of Rare NRP1 and NRP2 Variants in Families with Lymphedema
This study focuses on identifying rare variants in the NRP1 and NRP2 genes that could be linked to the development of lymphatic malformations in patients diagnosed with lymphedema. Two hundred and thirty-five Italian lymphedema patients, who tested negative for variants in known lymphedema genes, were screened for variants in NRP1 and NRP2. Two probands carried variants in NRP1 and four in NRP2. The variants of both genes segregated with lymphedema in familial cases. Although further functional and biochemical studies are needed to clarify their involvement with lymphedema and to associate NRP1 and NRP2 with lymphedema, we...
Source: Genes - November 17, 2020 Category: Genetics & Stem Cells Authors: Sandro Michelini Bruno Amato Maurizio Ricci Sercan Kenanoglu Dominika Veselenyiova Danjela Kurti Mirko Baglivo Elena Manara Munis Dundar Juraj Krajcovic Syed Hussain Basha Sasi Priya Roberta Serrani Giacinto A. D. Miggiano Barbara Aquilanti Giuseppina Mat Tags: Article Source Type: research

Genes, Vol. 11, Pages 1359: Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle
Namshin Kim Horses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse skeletal muscles to identify differentially expressed genes (DEGs) between tissues that have similar functions and to characterize these differences. We identified DEGs between different muscles using pairwise differential expression (DE) analyses of tissue transcriptome expression data and classi...
Source: Genes - November 17, 2020 Category: Genetics & Stem Cells Authors: Ho-Yeon Lee Jae-Yoon Kim Kyoung Hyoun Kim Seongmun Jeong Youngbum Cho Namshin Kim Tags: Article Source Type: research

Genes, Vol. 11, Pages 1360: Effect of 20(S)-Hydroxycholesterol on Multilineage Differentiation of Mesenchymal Stem Cells Isolated from Compact Bones in Chicken
This study also showed that the induction of osteogenesis and adipogenesis inhibition in cBMSCs by 20S is mediated through the hedgehog signaling mechanism. The results indicated that 20(S) could play an important role in the differentiation of chicken-derived MSCs and provided the theory basis on developing an intervention strategy to regulate skeletal, myogenic, and adipogenic differentiation in chicken, which will contribute to improving chicken bone health and meat quality. The current results provide the rationale for the further study of regulatory mechanisms of bioactive molecules on the differentiation of MSCs in c...
Source: Genes - November 17, 2020 Category: Genetics & Stem Cells Authors: Roshan Adhikari Chongxiao Chen Woo Kyun Kim Tags: Article Source Type: research

Genes, Vol. 11, Pages 1362: Genomic and Transcriptomic Analysis for Identification of Genes and Interlinked Pathways Mediating Artemisinin Resistance in Leishmania donovani
Ruchi Singh Current therapy for visceral leishmaniasis (VL), compromised by drug resistance, toxicity, and high cost, demands for more effective, safer, and low-cost drugs. Artemisinin has been found to be an effectual drug alternative in experimental models of leishmaniasis. Comparative genome and transcriptome analysis of in vitro-adapted artesunate-resistant (K133AS-R) and -sensitive wild-type (K133WT) Leishmania donovani parasites was carried out using next-generation sequencing and single-color DNA microarray technology, respectively, to identify genes and interlinked pathways contributing to drug resistance. Wh...
Source: Genes - November 17, 2020 Category: Genetics & Stem Cells Authors: Sushmita Ghosh Aditya Verma Vinay Kumar Dibyabhaba Pradhan Angamuthu Selvapandiyan Poonam Salotra Ruchi Singh Tags: Article Source Type: research

Genes, Vol. 11, Pages 1357: Identification of Milk Fat Metabolism-Related Pathways of the Bovine Mammary Gland during Mid and Late Lactation and Functional Verification of the ACSL4 Gene
In conclusion, the results displayed that ACSL4 expression regulates triglyceride metabolism in ruminant mammary cells. (Source: Genes)
Source: Genes - November 16, 2020 Category: Genetics & Stem Cells Authors: Yongliang Fan Ziyin Han Xubin Lu Huimin Zhang Abdelaziz Adam Idriss Arbab Juan J. Loor Yi Yang Zhangping Yang Tags: Article Source Type: research