Genes, Vol. 12, Pages 1635: ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective
onia Gazzarrini Jian Wu Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential...
Source: Genes - October 18, 2021 Category: Genetics & Stem Cells Authors: Wenqiang Pan Jiahui Liang Juanjuan Sui Jingru Li Chang Liu Yin Xin Yanmin Zhang Shaokun Wang Yajie Zhao Jie Zhang Mingfang Yi Sonia Gazzarrini Jian Wu Tags: Review Source Type: research

Genes, Vol. 12, Pages 1636: The Origin of Plasma-Derived Bacterial Extracellular Vesicles in Healthy Individuals and Patients with Inflammatory Bowel Disease: A Pilot Study
Noble Simon R. Carding The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in gut permeability (“leaky gut”), enabling luminal antigens and bacterial products such as nanosized bacterial extracellular vesicles (BEVs) to access the circulatory system. Blood-derived BEVs contain various cargoes and may be useful biomarkers for diagnosis and monitoring of disease status and relapse in conditions such as inflammatory bowel disease (IBD). To progress this concept, we developed a rapid, cost-effective protocol to isolate BEV-associated D...
Source: Genes - October 18, 2021 Category: Genetics & Stem Cells Authors: Emily Jones R égis Stentz Andrea Telatin George M. Savva Catherine Booth David Baker Steven Rudder Stella C. Knight Alistair Noble Simon R. Carding Tags: Article Source Type: research

Genes, Vol. 12, Pages 1637: Generalizability of GWA-Identified Genetic Risk Variants for Metabolic Traits to Populations from the Arabian Peninsula
se Thanaraj The Arabian Peninsula, located at the nexus of Africa, Europe, and Asia, was implicated in early human migration. The Arab population is characterized by consanguinity and endogamy leading to inbreeding. Global genome-wide association (GWA) studies on metabolic traits under-represent the Arab population. Replicability of GWA-identified association signals in the Arab population has not been satisfactorily explored. It is important to assess how well GWA-identified findings generalize if their clinical interpretations are to benefit the target population. Our recent study from Kuwait, which performed genome-...
Source: Genes - October 18, 2021 Category: Genetics & Stem Cells Authors: Prashantha Hebbar Mohamed Abu-Farha Jehad Abubaker Arshad Mohamed Channanath Fahd Al-Mulla Thangavel Alphonse Thanaraj Tags: Review Source Type: research

Genes, Vol. 12, Pages 1638: Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage
Liu Huan Wang Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 7...
Source: Genes - October 18, 2021 Category: Genetics & Stem Cells Authors: Joram Kiriga Waititu Quan Cai Ying Sun Yinglu Sun Congcong Li Chunyi Zhang Jun Liu Huan Wang Tags: Article Source Type: research

Genes, Vol. 12, Pages 1630: Marek ’s Disease Virus Telomeric Integration Profiles of Neoplastic Host Tissues Reveal Unbiased Chromosomal Selection and Loss of Cellular Diversity during Tumorigenesis
Genes, Vol. 12, Pages 1630: Marek’s Disease Virus Telomeric Integration Profiles of Neoplastic Host Tissues Reveal Unbiased Chromosomal Selection and Loss of Cellular Diversity during Tumorigenesis Genes doi: 10.3390/genes12101630 Authors: Marla C. Glass Justin M. Smith Hans H. Cheng Mary E. Delany The avian α-herpesvirus known as Marek’s disease virus (MDV) linearly integrates its genomic DNA into host telomeres during infection. The resulting disease, Marek’s disease (MD), is characterized by virally-induced lymphomas with high mortality. The temporal dynamics of MDV-positive (MDV+) ...
Source: Genes - October 17, 2021 Category: Genetics & Stem Cells Authors: Marla C. Glass Justin M. Smith Hans H. Cheng Mary E. Delany Tags: Article Source Type: research

Genes, Vol. 12, Pages 1632: Telomerase (hTERT) Overexpression Reveals a Promising Prognostic Biomarker and Therapeutical Target in Different Clinical Subtypes of Pediatric Acute Lymphoblastic Leukaemia
Filho Maria Elisabete Amaral de Moraes Raquel Carvalho Montenegro André Salim Khayat Caroline Aquino Moreira-Nunes Acute Lymphoblastic Leukemia (ALL) is a neoplasm of the hematopoietic system defined as a clonal expansion of an abnormal lymphoid precursor cell. It mostly affects children under five years of age and is the most common tumor to afflict pediatric patients. The expression of the human telomerase gene (hTERT) in patients with ALL has been studied as a biomarker and could become a new therapeutic target. We evaluate the role of hTERT gene expression in ALL pediatric patients, through quantita...
Source: Genes - October 17, 2021 Category: Genetics & Stem Cells Authors: Beatriz Maria Dias Nogueira Laudre ísa da Costa Pantoja Emerson Lucena da Silva Fernando Augusto Rodrigues Mello J únior Eliel Barbosa Teixeira Alayde Vieira Wanderley Jersey Heitor da Silva Mau és Manoel Odorico de Moraes Filho Maria Elisabete Amaral Tags: Article Source Type: research

Genes, Vol. 12, Pages 1631: Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line
na-Dzerve Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stab...
Source: Genes - October 17, 2021 Category: Genetics & Stem Cells Authors: Nityanand Jain Ingrida Mitre Dina Nitisa Valdis Pirsko Inese Cakstina-Dzerve Tags: Article Source Type: research

Genes, Vol. 12, Pages 1633: Mechanisms of Genome Instability in the Fragile X-Related Disorders
din The Fragile X-related disorders (FXDs), which include the intellectual disability fragile X syndrome (FXS), are disorders caused by expansion of a CGG-repeat tract in the 5′ UTR of the X-linked FMR1 gene. These disorders are named for FRAXA, the folate-sensitive fragile site that localizes with the CGG-repeat in individuals with FXS. Two pathological FMR1 allele size classes are distinguished. Premutation (PM) alleles have 54–200 repeats and confer the risk of fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI). PM alleles are prone to both ...
Source: Genes - October 17, 2021 Category: Genetics & Stem Cells Authors: Bruce E. Hayward Karen Usdin Tags: Review Source Type: research

Genes, Vol. 12, Pages 1634: Maternal One-carbon Metabolism during the Periconceptional Period and Human Foetal Brain Growth: A Systematic Review
M. Steegers-Theunissen Melek Rousian The maternal environment during the periconceptional period influences foetal growth and development, in part, via epigenetic mechanisms moderated by one-carbon metabolic pathways. During embryonic development, one-carbon metabolism is involved in brain development and neural programming. Derangements in one-carbon metabolism increase (i) the short-term risk of embryonic neural tube-related defects and (ii) long-term childhood behaviour, cognition, and autism spectrum disorders. Here we investigate the association between maternal one-carbon metabolism and foetal and neonatal brai...
Source: Genes - October 17, 2021 Category: Genetics & Stem Cells Authors: Eleonora Rubini Inge M. M. Baijens Alex Hor ánszky Sam Schoenmakers Kevin D. Sinclair Melinda Zana Andr ás Dinnyés R égine P. M. Steegers-Theunissen Melek Rousian Tags: Review Source Type: research

Genes, Vol. 12, Pages 1628: Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development
In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-sp...
Source: Genes - October 16, 2021 Category: Genetics & Stem Cells Authors: Saara K. Luna Fr édéric J. J. Chain Tags: Article Source Type: research

Genes, Vol. 12, Pages 1629: High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy
. Wilmott Recent advances in single-cell transcriptomics have greatly improved knowledge of complex transcriptional programs, rapidly expanding our knowledge of cellular phenotypes and functions within the tumour microenvironment and immune system. Several new single-cell technologies have been developed over recent years that have enabled expanded understanding of the mechanistic cells and biological pathways targeted by immunotherapies such as immune checkpoint inhibitors, which are now routinely used in patient management with high-risk early-stage or advanced melanoma. These technologies have method-specific streng...
Source: Genes - October 16, 2021 Category: Genetics & Stem Cells Authors: Camelia Quek Xinyu Bai Georgina V. Long Richard A. Scolyer James S. Wilmott Tags: Review Source Type: research

Genes, Vol. 12, Pages 1626: Prenatal Diagnosis of Combined Maternal 4q Interstitial Deletion and Paternal 15q Microduplication
This report can provide a reference for prenatal diagnosis and genetic counseling in patients who have similar cytogenetic abnormalities, and underlines the importance of reporting unusual variant chromosomes for diagnostic genetic purposes. (Source: Genes)
Source: Genes - October 16, 2021 Category: Genetics & Stem Cells Authors: Francesco Libotte Marco Fabiani Katia Margiotti Antonella Viola Alvaro Mesoraca Claudio Giorlandino Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 1627: Intermittent Hypoxia Alters the Circadian Expression of Clock Genes in Mouse Brain and Liver
David F. Smith At least one-third of adults in the United States experience intermittent hypoxia (IH) due to health or living conditions. The majority of these adults suffer with sleep breathing conditions and associated circadian rhythm disorders. The impact of IH on the circadian clock is not well characterized. In the current study, we used an IH mouse model to understand the impact of IH on the circadian gene expression of the canonical clock genes in the central (the brain) and peripheral (the liver) tissues. Gene expression was measured using a Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-...
Source: Genes - October 16, 2021 Category: Genetics & Stem Cells Authors: Bala S. C. Koritala Yin Yeng Lee Shweta S. Bhadri Laetitia S. Gaspar Corinne Stanforth Gang Wu Marc D. Ruben Lauren J. Francey David F. Smith Tags: Article Source Type: research

Genes, Vol. 12, Pages 1623: Prevalence and Clinical Characteristics of Hearing Loss Caused by MYH14 Variants
In this study, genetic screening for MYH14 variants was carried out using a large series of Japanese hearing-loss patients to reveal more detailed information. Massively parallel DNA sequencing of 68 target candidate genes was applied in 8074 unrelated Japanese hearing-loss patients (including 1336 with ADNSHL) to identify genomic variations responsible for hearing loss. We identified 11 families with 10 variants. The prevalence was found to be 0.14% (11/8074) among all hearing-loss patients and 0.82% (11/1336) among ADNSHL patients. Nine of the eleven variants identified were novel. The patients typically showed late-onse...
Source: Genes - October 15, 2021 Category: Genetics & Stem Cells Authors: Ken Hiramatsu Shin-ya Nishio Shin-ichiro Kitajiri Tomohiro Kitano Hideaki Moteki Shin-ichi Usami Tags: Article Source Type: research

Genes, Vol. 12, Pages 1625: Structural Protein Analysis of Driver Gene Mutations in Conjunctival Melanoma
l L. Karp In recent years, there has been tremendous enthusiasm with respect to detailing the genetic basis of many neoplasms, including conjunctival melanoma (CM). We aim to analyze five proteins associated with CM, namely BRAF, NRAS, c-KIT, NF1, and PTEN. We evaluated each protein for its intrinsically disordered protein regions (IDPRs) and its protein-protein interactions (PPI) with the Predictor of Natural Disordered Protein Regions (PONDR®) and the Search Tool for the Retrieval of Interacting Genes (STRING®). Our PONDR® analysis found high levels of IDPRs in all five proteins with mutations linked to C...
Source: Genes - October 15, 2021 Category: Genetics & Stem Cells Authors: Mak B. Djulbegovic Vladimir N. Uversky J. William Harbour Anat Galor Carol L. Karp Tags: Article Source Type: research

Genes, Vol. 12, Pages 1624: WDR36-Associated Neurodegeneration: A Case Report Highlights Possible Mechanisms of Normal Tension Glaucoma
Ross WDR36 is one of a number of genes implicated in the pathogenesis of adult-onset primary open angle glaucoma (POAG). Here we describe in detail the phenotype of a patient with pathogenic variation in WDR36 who presented with a protracted history of central vision loss. On exam visual acuities were at 20/100 level, had a tritan color defect and showed central arcuate visual field defects on visual field testing. Enlarged cup-to-disk ratios with normal intraocular pressures were associated with severe thinning of the ganglion cell layer (GCL) and retinal nerve fiber layer consistent with a clinical diagnosis of norm...
Source: Genes - October 15, 2021 Category: Genetics & Stem Cells Authors: Elana Meer Tomas S. Aleman Ahmara G. Ross Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 1617: Isolation of RNA from Acute Ischemic Stroke Clots Retrieved by Mechanical Thrombectomy
Adnan H. Siddiqui Mechanical thrombectomy (MT) for large vessel acute ischemic stroke (AIS) has enabled biologic analyses of resected clots. While clot histology has been well-studied, little is known about gene expression within the tissue, which could shed light on stroke pathophysiology. In this methodological study, we develop a pipeline for obtaining useful RNA from AIS clots. A total of 73 clot samples retrieved by MT were collected and stored in RNALater and in 10% phosphate-buffered formalin. RNA was extracted from all samples using a modified Chemagen magnetic bead extraction protocol on the PerkinElmer Chem...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Vincent M. Tutino Sarah Fricano Kirsten Frauens Tatsat R. Patel Andre Monteiro Hamid H. Rai Muhammad Waqas Lee Chaves Kerry E. Poppenberg Adnan H. Siddiqui Tags: Article Source Type: research

Genes, Vol. 12, Pages 1616: Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis)
C. Neal Stewart The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely an...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Yongil Yang Cory Gardner Pallavi Gupta Yanhui Peng Cristiano Piasecki Reginald J. Millwood Tae-Hyuk Ahn C. Neal Stewart Tags: Article Source Type: research

Genes, Vol. 12, Pages 1618: A Two-Year Clinical Description of a Patient with a Rare Type of Low-GGT Cholestasis Caused by a Novel Variant of USP53
na Ryzhkova Here, we report a novel truncating mutation in the ubiquitin-specific peptidase gene (USP53) causing low-γ-GT (GGT) cholestasis. Genetic testing was carried out, including clinical exome sequencing for the proband and Sanger sequencing for the proband and his parents. The proband harbored a novel c.1017_1057del (p.(Cys339TrpfsTer7)) mutation in the ubiquitin carboxyl-terminal hydrolase (UCH) domain of USP53; we describe the clinical and laboratory features of the patient with a rare type of low-GGT cholestasis caused by this variant. The clinical presentation was found to be similar to that of phenoty...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Olga Shatokhina Natalia Semenova Nina Demina Elena Dadali Alexander Polyakov Oxana Ryzhkova Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 1619: More Than a Moggy; A Population Genetics Analysis of the United Kingdom ’s Non-Pedigree Cats
Genes, Vol. 12, Pages 1619: More Than a Moggy; A Population Genetics Analysis of the United Kingdom’s Non-Pedigree Cats Genes doi: 10.3390/genes12101619 Authors: Jennifer Irving McGrath Wengang Zhang Regina Hollar Alison Collings Roger Powell Rob D. Foale Nicola Thurley Jeffrey A. Brockman Richard J. Mellanby Danièlle A. Gunn-Moore Jeffrey J. Schoenebeck The domestic cat is one of the most popular pets in the world. It is estimated that 89–92% of domestic cats in the UK are non-pedigree Domestic shorthair (DSH), Domestic longhair (DLH), or Domestic semi-longhair cats (DSLH). D...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Jennifer Irving McGrath Wengang Zhang Regina Hollar Alison Collings Roger Powell Rob D. Foale Nicola Thurley Jeffrey A. Brockman Richard J. Mellanby Dani èlle A. Gunn-Moore Jeffrey J. Schoenebeck Tags: Article Source Type: research

Genes, Vol. 12, Pages 1620: Roles of Glutathione in Mediating Abscisic Acid Signaling and Its Regulation of Seed Dormancy and Drought Tolerance
Ayele Plant growth and development and interactions with the environment are regulated by phytohormones and other signaling molecules. During their evolution, plants have developed strategies for efficient signal perception and for the activation of signal transduction cascades to maintain proper growth and development, in particular under adverse environmental conditions. Abscisic acid (ABA) is one of the phytohormones known to regulate plant developmental events and tolerance to environmental stresses. The role of ABA is mediated by both its accumulated level, which is regulated by its biosynthesis and catabolism, an...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Murali Krishna Koramutla Manisha Negi Belay T. Ayele Tags: Review Source Type: research

Genes, Vol. 12, Pages 1621: Detection of Spinal Muscular Atrophy Patients Using Dried Saliva Spots
In conclusion, these results suggest that our system with DSS is applicable to SMA patient detection in the real world. (Source: Genes)
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Yogik Onky Silvana Wijaya Hisahide Nishio Emma Tabe Eko Niba Kentaro Okamoto Haruo Shintaku Yasuhiro Takeshima Toshio Saito Masakazu Shinohara Hiroyuki Awano Tags: Article Source Type: research

Genes, Vol. 12, Pages 1622: Association of CYP26C1 Promoter Hypomethylation with Small Vessel Occlusion in Korean Subjects
In this study, we measured the level of DNA methylation in the CYP26C1 promoter and the 5′ untranslated region of 115 normal subjects and 56 patients with SVO in Korea. The DNA methylation level of each subject was measured by bisulfite amplicon sequencing, and statistical analysis was performed using the general linear model or Pearson’s correlation. The average level of DNA methylation was markedly lower in patients with SVO than in normal subjects (20.4% vs. 17.5%). We found that the methylation of CYP26C1 has a significant positive correlation with blood parameters including white blood cells, hematocrit, l...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Eun-Ji Lee Myung-Sunny Kim Nam-Hui Yim Min Ho Cha Tags: Article Source Type: research

Genes, Vol. 12, Pages 1612: Genetics and Genomics of Reproductive Medicine
o The rapidity of innovations has meant that reproductive medicine today represents clear example of how complex but essential an adaptation of clinical practice and laboratory techniques to new knowledge is in the context of the dynamic evolution of medicine [...] (Source: Genes)
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Rossella Tomaiuolo Tags: Editorial Source Type: research

Genes, Vol. 12, Pages 1613: Genetic Loci Underlying Awn Morphology in Barley
Hong Barley awns are highly active in photosynthesis and account for 30–50% of grain weight in barley. They are diverse in length, ranging from long to awnless, and in shape from straight to hooded or crooked. Their diversity and importance have intrigued geneticists for several decades. A large collection of awnness mutants are available—over a dozen of them have been mapped on chromosomes and a few recently cloned. Different awnness genes interact with each other to produce diverse awn phenotypes. With the availability of the sequenced barley genome and application of new mapping and gene cloning strateg...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Biguang Huang Weiren Wu Zonglie Hong Tags: Review Source Type: research

Genes, Vol. 12, Pages 1615: Disruptive NADSYN1 Variants Implicated in Congenital Vertebral Malformations
ang Zhihong Wu Nan Wu Genetic perturbations in nicotinamide adenine dinucleotide de novo (NAD) synthesis pathway predispose individuals to congenital birth defects. The NADSYN1 encodes the final enzyme in the de novo NAD synthesis pathway and, therefore, plays an important role in NAD metabolism and organ embryogenesis. Biallelic mutations in the NADSYN1 gene have been reported to be causative of congenital organ defects known as VCRL syndrome (Vertebral-Cardiac-Renal-Limb syndrome). Here, we analyzed the genetic variants in NADSYN1 in an exome-sequenced cohort consisting of patients with congenital vertebral malfo...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Jiachen Lin Lina Zhao Sen Zhao Shengjie Li Zhengye Zhao Zefu Chen Zhifa Zheng Jiashen Shao Yuchen Niu Xiaoxin Li Jianguo Terry Zhang Zhihong Wu Nan Wu Tags: Article Source Type: research

Genes, Vol. 12, Pages 1614: Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder
Cadet Methamphetamine (METH)-use disorder (MUD) is a very serious, potentially lethal, biopsychosocial disease. Exposure to METH causes long-term changes to brain regions involved in reward processing and motivation, leading vulnerable individuals to engage in pathological drug-seeking and drug-taking behavior that can remain a lifelong struggle. It is crucial to elucidate underlying mechanisms by which exposure to METH leads to molecular neuroadaptive changes at transcriptional and translational levels. Changes in gene expression are controlled by post-translational modifications via chromatin remodeling. This review ...
Source: Genes - October 14, 2021 Category: Genetics & Stem Cells Authors: Subramaniam Jayanthi Michael T. McCoy Jean Lud Cadet Tags: Review Source Type: research

Genes, Vol. 12, Pages 1609: Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern
Tringe Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans genera that appears to be a distinct genus and species. The genome is derived from sediments of a hypersaline (97–148 ppt chloride) unrestored industrial saltern that has been observed to be a significant methane ...
Source: Genes - October 13, 2021 Category: Genetics & Stem Cells Authors: Clifton P. Bueno de Mesquita Jinglie Zhou Susanna M. Theroux Susannah G. Tringe Tags: Article Source Type: research

Genes, Vol. 12, Pages 1610: Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress
This study focused on the molecular response process and gene expression profiles of S. japonica to low (9 °C)-temperature stress in comparison with normal temperature (25 °C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. The results were 81 GO subgroups and 18 EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) keywords. Differentially expressed...
Source: Genes - October 13, 2021 Category: Genetics & Stem Cells Authors: Mohammad Vatanparast Youngjin Park Tags: Article Source Type: research

Genes, Vol. 12, Pages 1611: FLT4 Mutations Are Associated with Segmental Lymphatic Dysfunction and Initial Lymphatic Aplasia in Patients with Milroy Disease
This study explored mutations in the Fms-related tyrosine kinase 4/vascular endothelial growth factor receptor 3 gene (FLT4) and lymphatic defects in patients with Milroy disease (MD). Twenty-nine patients with lower limb lymphedema were enrolled. Sixteen patients had a familial history of MD, while 13 patients exhibited sporadic MD. Clinical signs, FLT4 mutations, indocyanine green (ICG) lymphography findings, and skin tissue immunohistochemical staining results were evaluated. Twenty-eight variants in FLT4 were identified. Twelve of these have previously been reported, while 16 are novel. Of the 28 variants, 26 are misse...
Source: Genes - October 13, 2021 Category: Genetics & Stem Cells Authors: Ningfei Liu Minzhe Gao Tags: Article Source Type: research

Genes, Vol. 12, Pages 1607: An Investigation of the Role of Common and Rare Variants in a Large Italian Multiplex Family of Multiple Sclerosis Patients
Miriam Zuccalà Domizia Vecchio Maria Liguori Cristoforo Comi Giancarlo Comi Vittorio Martinelli Massimo Filippi Maurizio Leone Filippo Martinelli-Boneschi Domenico Caputo Manuela Sironi Franca Rosa Guerini Sandra D’Alfonso Known multiple sclerosis (MS) susceptibility variants can only explain half of the disease’s estimated heritability, whereas low-frequency and rare variants may partly account for the missing heritability. Thus, here we sought to determine the occurrence of rare functional variants in a large Italian MS multiplex family with five affected members. For thi...
Source: Genes - October 13, 2021 Category: Genetics & Stem Cells Authors: Nadia Barizzone Rachele Cagliani Chiara Basagni Ferdinando Clarelli Laura Mendozzi Cristina Agliardi Diego Forni Martina Tosi Elisabetta Mascia Francesco Favero Davide Cor à Lucia Corrado Melissa Sorosina Federica Esposito Miriam Zuccal à Domizia Vecchi Tags: Article Source Type: research

Genes, Vol. 12, Pages 1608: Association and Genetic Expression between Genes Involved in HPA Axis and Suicide Behavior: A Systematic Review
Conclusions: Our findings suggest that key stress pathway genes are significantly associated with SB and show potential as biomarkers for SB. (Source: Genes)
Source: Genes - October 13, 2021 Category: Genetics & Stem Cells Authors: Yazm ín Hernández-Díaz Alma Delia Genis-Mendoza Thelma Beatriz Gonz ález-Castro Carlos Alfonso Tovilla-Z árate Isela Esther Ju árez-Rojop Mar ía Lilia López-Narváez Humberto Nicolini Tags: Review Source Type: research

Genes, Vol. 12, Pages 1599: Multiplex Protein Biomarker Profiling in Patients with Familial Hypercholesterolemia
ladimir Blaha Familial hypercholesterolemia (FH), is an autosomal dominant disorder caused by mutations in the LDLR, APOB, PCSK9, and APOE genes and is characterized by high plasma levels of total and low-density lipoprotein (LDL) cholesterol. Our study aimed to analyze the influences of two different therapies on a wide spectrum of plasma protein biomarkers of cardiovascular diseases. Plasma from FH patients under hypolipidemic therapy (N = 18; men = 8, age 55.4 ± 13.1 years) and patients under combined long-term LDL apheresis/hypolipidemic therapy (N = 14; men = 7; age 58.0 ± 13.6 years) were analyzed i...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Dana Dlouha Milan Blaha Eva Rohlova Jaroslav A. Hubacek Vera Lanska Jakub Visek Vladimir Blaha Tags: Article Source Type: research

Genes, Vol. 12, Pages 1600: Erratum: Ali et al. In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes. Genes 2021, 12, 1264
Ponsuksili The authors wish to make the following correction to their paper published in Genes [...] (Source: Genes)
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Asghar Ali Eduard Murani Frieder Hadlich Xuan Liu Klaus Wimmers Siriluck Ponsuksili Tags: Erratum Source Type: research

Genes, Vol. 12, Pages 1601: Impact of ABCG2 Gene Polymorphism on the Predisposition to Psoriasis
In this study, we aimed to evaluate the role of ABCG2 gene polymorphisms on the susceptibility to psoriasis. The genotype distribution of two ABCG2 single nucleotide polymorphisms (SNPs), rs2231142 and rs2231137, was examined in 410 psoriasis patients and 1,089 gender-matched non-psoriasis controls. We found that heterozygotes (GT) for rs2231142 was associated with a decreased risk of psoriasis (p = 0.001; adjusted OR = 0.532; 95% CI, 0.370–0.765) after adjusting for age, as compared with homozygotes for the major allele (GG). Subjects who carried at least one polymorphic allele (homozygote or heterozygote for the mi...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Yu-Huei Huang Lai-Chu See Ya-Ching Chang Wen-Hung Chung Lun-Ching Chang Shun-Fa Yang Shih-Chi Su Tags: Article Source Type: research

Genes, Vol. 12, Pages 1602: Metabolomics for Crop Breeding: General Considerations
ashuk The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breedi...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Dmitry Y. Litvinov Gennady I. Karlov Mikhail G. Divashuk Tags: Review Source Type: research

Genes, Vol. 12, Pages 1603: Genetic and Epigenetic Changes in Plants in Response to Abiotic Stress
g The current global climate crisis has led to drought, high salinity, and abnormal temperatures (heat and cold), and is a serious threat to crop productivity [...] (Source: Genes)
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Jong-Joo Cheong Tags: Editorial Source Type: research

Genes, Vol. 12, Pages 1604: Interrogating Mitochondrial Biology and Disease Using CRISPR/Cas9 Gene Editing
aacute;hová Mitochondrial disease originates from genetic changes that impact human bodily functions by disrupting the mitochondrial oxidative phosphorylation system. MitoCarta is a curated and published inventory that sheds light on the mitochondrial proteome, but the function of some mitochondrially-localised proteins remains poorly characterised. Consequently, various gene editing systems have been employed to uncover the involvement of these proteins in mitochondrial biology and disease. CRISPR/Cas9 is an efficient, versatile, and highly accurate genome editing tool that was first introduced over a decade ag...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Jia Xin Tang Angela Pyle Robert W. Taylor Monika Ol áhová Tags: Review Source Type: research

Genes, Vol. 12, Pages 1605: Autism Spectrum Disorders: Analysis of Mobile Elements at 7q11.23 Williams –Beuren Region by Comparative Genomics
Genes, Vol. 12, Pages 1605: Autism Spectrum Disorders: Analysis of Mobile Elements at 7q11.23 Williams–Beuren Region by Comparative Genomics Genes doi: 10.3390/genes12101605 Authors: Francesca Anna Cupaioli Chiara Fallerini Maria Antonietta Mencarelli Valentina Perticaroli Virginia Filippini Francesca Mari Alessandra Renieri Alessandra Mezzelani Autism spectrum disorders (ASD) are a group of complex neurodevelopmental disorders, characterized by a deficit in social interaction and communication. Many genetic variants are associated with ASD, including duplication of 7q11.23 encompassing 26&ndash...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Francesca Anna Cupaioli Chiara Fallerini Maria Antonietta Mencarelli Valentina Perticaroli Virginia Filippini Francesca Mari Alessandra Renieri Alessandra Mezzelani Tags: Article Source Type: research

Genes, Vol. 12, Pages 1606: Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes
Lin Sun Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory gene...
Source: Genes - October 12, 2021 Category: Genetics & Stem Cells Authors: Shuai Zhang Ruixue Wang Cheng Huang Ludan Zhang Lin Sun Tags: Article Source Type: research

Genes, Vol. 12, Pages 1598: Genes Associated with Disturbed Cerebral Neurogenesis in the Embryonic Brain of Mouse Models of Down Syndrome
a Down syndrome (DS), also known as trisomy 21, is the most frequent genetic cause of intellectual disability. Although the mechanism remains unknown, delayed brain development is assumed to be involved in DS intellectual disability. Analyses with human with DS and mouse models have shown that defects in embryonic cortical neurogenesis may lead to delayed brain development. Cre-loxP-mediated chromosomal engineering has allowed the generation of a variety of mouse models carrying various partial Mmu16 segments. These mouse models are useful for determining genotype–phenotype correlations and identifying dosage-sen...
Source: Genes - October 11, 2021 Category: Genetics & Stem Cells Authors: Keiichi Ishihara Tags: Review Source Type: research

Genes, Vol. 12, Pages 1597: Genotype Phenotype Correlation in Dent Disease 2 and Review of the Literature: OCRL Gene Pleiotropism or Extreme Phenotypic Variability of Lowe Syndrome?
Franca Anglani Dent disease is a rare X-linked renal tubulopathy due to CLCN5 and OCRL (DD2) mutations. OCRL mutations also cause Lowe syndrome (LS) involving the eyes, brain and kidney. DD2 is frequently described as a mild form of LS because some patients may present with extra-renal symptoms (ESs). Since DD2 is a rare disease and there are a low number of reported cases, it is still unclear whether it has a clinical picture distinct from LS. We retrospectively analyzed the phenotype and genotype of our cohort of 35 DD2 males and reviewed all published DD2 cases. We analyzed the distribution of mutations along the O...
Source: Genes - October 11, 2021 Category: Genetics & Stem Cells Authors: Lisa Gianesello Jennifer Arroyo Dorella Del Prete Giovanna Priante Monica Ceol Peter C. Harris John C. Lieske Franca Anglani Tags: Article Source Type: research

Genes, Vol. 12, Pages 1596: The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape
i The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particu...
Source: Genes - October 10, 2021 Category: Genetics & Stem Cells Authors: Vincenzo Cavalieri Tags: Review Source Type: research

Genes, Vol. 12, Pages 1595: Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology
Annelies de Klein Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated w...
Source: Genes - October 10, 2021 Category: Genetics & Stem Cells Authors: Erwin Brosens Rutger W. W. Brouwer Hannie Douben Yolande van Bever Alice S. Brooks Rene M. H. Wijnen Wilfred F. J. van IJcken Dick Tibboel Robbert J. Rottier Annelies de Klein Tags: Review Source Type: research

Genes, Vol. 12, Pages 1593: Development of New Cancer Treatment by Identifying and Focusing the Genetic Mutations or Altered Expression in Gynecologic Cancers
y Lai With the advent of next-generation sequencing (NGS), The Cancer Genome Atlas (TCGA) research network has given gynecologic cancers molecular classifications, which impacts clinical practice more and more. New cancer treatments that identify and target pathogenic abnormalities of genes have been in rapid development. The most prominent progress in gynecologic cancers is the clinical efficacy of poly(ADP-ribose) polymerase (PARP) inhibitors, which have shown breakthrough benefits in reducing hazard ratios (HRs) (HRs between 0.2 and 0.4) of progression or death from BRCA1/2 mutated ovarian cancer. Immune checkpoint ...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: Yun-Hsin Tang Chiao-Yun Lin Chyong-Huey Lai Tags: Review Source Type: research

Genes, Vol. 12, Pages 1594: Identification and Comprehensive Structural and Functional Analyses of the EXO70 Gene Family in Cotton
Ren Ya-Di Xing The EXO70 gene is a vital component of the exocytosis complex and participates in biological processes ranging from plant cell division to polar growth. There are many EXO70 genes in plants and their functions are extensive, but little is known about the EXO70 gene family in cotton. Here, we analyzed four cotton sequence databases, identified 165 EXO70 genes, and divided them into eight subgroups (EXO70A–EXO70H) based on their phylogenetic relationships. EXO70A had the most exons (≥11), whereas the other seven each had only one or two exons. Hence, EXO70A may have many important functions. Th...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: Ya-Qian Zhu Lu Qiu Lu-Lu Liu Lei Luo Xin-Pei Han Yao-Hua Zhai Wen-Jing Wang Mao-Zhi Ren Ya-Di Xing Tags: Article Source Type: research

Genes, Vol. 12, Pages 1589: A Cold-Shock Protein from the South Pole-Dwelling Soil Bacterium Arthrobacter sp. Confers Cold Tolerance to Rice
Gang-Seob Lee Low temperature is a critical environmental factor restricting the physiology of organisms across kingdoms. In prokaryotes, cold shock induces the expression of various genes and proteins involved in cellular processes. Here, a cold-shock protein (ArCspA) from the South Pole-dwelling soil bacterium Arthrobacter sp. A2-5 was introduced into rice, a monocot model plant species. Four-week-old 35S:ArCspA transgenic rice plants grown in a cold chamber at 4 °C survived for 6 days. Cold stress significantly decreased the chlorophyll content in WT plants after 4 days compared with that in 35S:ArCspA transge...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: So Young Kim Joung Sug Kim Woosuk Cho Kyong Mi Jun Xiaoxuan Du Kyung Do Kim Yeon-Ki Kim Gang-Seob Lee Tags: Article Source Type: research

Genes, Vol. 12, Pages 1586: DNA Methylation of Pig FUT3 Promoter Alters mRNA Expression to Regulate E. coli F18 Susceptibility
henglong Wu Post-weaning diarrhea (PWD) is frequently associated with E. coli F18 infections in piglets. However, the underlying molecular mechanism concerning the resistance of E. coli F18 in local weaned piglets in China is not clearly understood. In the present study, by a comparative analysis of the transcriptome, a-1,3-fucosyltransferase (FUT3) was evaluated as a key candidate correlated with resistance to E. coli F18 in Sutai and Meishan piglets. Functional analysis demonstrated that FUT3 acts as a key positive regulator of E. coli F18 susceptibility in newly food accustomed piglets. However, the core promoter of...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: Zhengchang Wu Dongfeng Shi Jian Jin Hairui Fan Wenbin Bao Shenglong Wu Tags: Article Source Type: research

Genes, Vol. 12, Pages 1584: Opportunities and Challenges to Improve a Public Research Program in Plant Breeding and Enhance Underutilized Plant Genetic Resources in the Tropics
Carolina González The American tropics are hotspots of wild and domesticated plant biodiversity, which is still underutilized by breeding programs despite being conserved at regional gene banks. The improvement of those programs depends on long-term public funds and the maintenance of specialized staff. Unfortunately, financial ups and downs complicate staff connectivity and their research impact. Between 2000 and 2010, Agrosavia (Corporación Colombiana de Investigación Agropecuaria) dramatically decreased its public financial support. In 2017, we surveyed all 52 researchers from Agrosavia involved...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: Ivania Cer ón-Souza Carlos H. Galeano Katherine Tehelen Hugo R. Jim énez Carolina Gonz ález Tags: Article Source Type: research

Genes, Vol. 12, Pages 1587: Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.) against Thai Xoc Strains
In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functiona...
Source: Genes - October 9, 2021 Category: Genetics & Stem Cells Authors: Tripop Thianthavon Wanchana Aesomnuk Mutiara K. Pitaloka Wannapa Sattayachiti Yupin Sonsom Phakchana Nubankoh Srihunsa Malichan Kanamon Riangwong Vinitchan Ruanjaichon Theerayut Toojinda Samart Wanchana Siwaret Arikit Tags: Article Source Type: research