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  • Brassinosteroid Priming Improves Peanut Drought Tolerance via Eliminating Inhibition on Genes in Photosynthesis and Hormone Signaling
    Genes (IF 3.759) Pub Date : 2020-08-11
    Luping Huang; Lei Zhang; Ruier Zeng; Xinyue Wang; Huajian Zhang; Leidi Wang; Shiyuan Liu; Xuewen Wang; Tingting Chen

    Drought negatively affects the growth and yield of terrestrial crops. Seed priming, pre-exposing seed to a compound, could induce improved tolerance and adaptation to stress in germinated plants. To understand the effects and regulatory mechanism of seed priming with brassinosteroid (BR) on peanut plants, we treated seeds with five BR concentrations and examined dozens of physiological and biochemical

    更新日期:2020-08-11
  • Omics Application in Animal Science—A Special Emphasis on Stress Response and Damaging Behaviour in Pigs
    Genes (IF 3.759) Pub Date : 2020-08-11
    Claudia Kasper; David Ribeiro; André M. de Almeida; Catherine Larzul; Laurence Liaubet; Eduard Murani

    Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to

    更新日期:2020-08-11
  • CRISPR/Cas9 in Cancer Immunotherapy: Animal Models and Human Clinical Trials
    Genes (IF 3.759) Pub Date : 2020-08-11
    Khalil Khalaf; Krzysztof Janowicz; Marta Dyszkiewicz-Konwińska; Greg Hutchings; Claudia Dompe; Lisa Moncrieff; Maurycy Jankowski; Marta Machnik; Urszula Oleksiewicz; Ievgeniia Kocherova; Jim Petitte; Paul Mozdziak; Jamil A. Shibli; Dariusz Iżycki; Małgorzata Józkowiak; Hanna Piotrowska-Kempisty; Mariusz T. Skowroński; Paweł Antosik; Bartosz Kempisty

    Even though chemotherapy and immunotherapy emerged to limit continual and unregulated proliferation of cancer cells, currently available therapeutic agents are associated with high toxicity levels and low success rates. Additionally, ongoing multi-targeted therapies are limited only for few carcinogenesis pathways, due to continually emerging and evolving mutations of proto-oncogenes and tumor-suppressive

    更新日期:2020-08-11
  • Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains
    Genes (IF 3.759) Pub Date : 2020-08-09
    Joana Abrantes; Ana M. Lopes; Evelyne Lemaitre; Harri Ahola; Fereshteh Banihashem; Clément Droillard; Stéphane Marchandeau; Pedro J. Esteves; Aleksija Neimanis; Ghislaine Le Gall-Reculé

    Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains

    更新日期:2020-08-10
  • Centromeric Transcription: A Conserved Swiss-Army Knife
    Genes (IF 3.759) Pub Date : 2020-08-09
    Ganesan Arunkumar; Daniël P. Melters

    In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions

    更新日期:2020-08-10
  • Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function
    Genes (IF 3.759) Pub Date : 2020-08-10
    Elisa Balzano; Simona Giunta

    Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized

    更新日期:2020-08-10
  • Quantitative Proteomics Comparison of Total Expressed Proteomes of Anisakis simplex Sensu Stricto, A. pegreffii, and Their Hybrid Genotype
    Genes (IF 3.759) Pub Date : 2020-08-10
    Susana C. Arcos; Lee Robertson; Sergio Ciordia; Isabel Sánchez-Alonso; Mercedes Careche; Noelia Carballeda-Sanguiao; Miguel Gonzalez-Muñoz; Alfonso Navas

    The total proteomes of Anisakis simplex s.s., A. pegreffii and their hybrid genotype have been compared by quantitative proteomics (iTRAQ approach), which considers the level of expressed proteins. Comparison was made by means of two independent experiments considering four biological replicates of A. simplex and two each for A. pegreffii and hybrid between both species. A total of 1811 and 1976 proteins

    更新日期:2020-08-10
  • The Evolution of Gene Therapy in the Treatment of Metabolic Liver Diseases
    Genes (IF 3.759) Pub Date : 2020-08-10
    Carlos G. Moscoso; Clifford J. Steer

    Monogenic metabolic disorders of hepatic origin number in the hundreds, and for many, liver transplantation remains the only cure. Liver-targeted gene therapy is an attractive treatment modality for many of these conditions, and there have been significant advances at both the preclinical and clinical stages. Viral vectors, including retroviruses, lentiviruses, adenovirus-based vectors, adeno-associated

    更新日期:2020-08-10
  • EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives
    Genes (IF 3.759) Pub Date : 2020-08-10
    Roberto Mariotti; Angjelina Belaj; Raul De La Rosa; Lorenzo Leòn; Federico Brizioli; Luciana Baldoni; Soraya Mousavi

    Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work

    更新日期:2020-08-10
  • Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis
    Genes (IF 3.759) Pub Date : 2020-08-10
    Reyhaneh Naderi; Homa Saadati Mollaei; Arne Elofsson; Saman Hosseini Ashtiani

    (1) Background: Psoriasis is a multifactorial chronic inflammatory disorder of the skin, with significant morbidity, characterized by hyperproliferation of the epidermis. Even though psoriasis’ etiology is not fully understood, it is believed to be multifactorial, with numerous key components. (2) Methods: In order to cast light on the complex molecular interactions in psoriasis vulgaris at both protein–protein

    更新日期:2020-08-10
  • The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)
    Genes (IF 3.759) Pub Date : 2020-08-10
    Urban Kunej; Aida Dervishi; Valérie Laucou; Jernej Jakše; Nataša Štajner

    The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative

    更新日期:2020-08-10
  • The Characterization of chIFITMs in Avian Coronavirus Infection In Vivo, Ex Vivo and In Vitro
    Genes (IF 3.759) Pub Date : 2020-08-10
    Angela Steyn; Sarah Keep; Erica Bickerton; Mark Fife

    The coronaviruses are a large family of enveloped RNA viruses that commonly cause gastrointestinal or respiratory illnesses in the infected host. Avian coronavirus infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of chickens that can affect the kidneys and reproductive systems resulting in bird mortality and decreased reproductivity. The interferon-inducible transmembrane

    更新日期:2020-08-10
  • A Four-Methylated lncRNAs-Based Prognostic Signature for Hepatocellular Carcinoma
    Genes (IF 3.759) Pub Date : 2020-08-08
    Le-En Liao; Dan-Dan Hu; Yun Zheng

    Currently, an increasing number of studies suggest that long non-coding RNAs (lncRNAs) and methylation-regulated lncRNAs play a critical role in the pathogenesis of various cancers including hepatocellular carcinoma (HCC). Therefore, methylated differentially expressed lncRNAs (MDELs) may be critical biomarkers of HCC. In this study, 63 MDELs were identified by screening The Cancer Genome Atlas (TCGA)

    更新日期:2020-08-09
  • Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells
    Genes (IF 3.759) Pub Date : 2020-08-08
    Eva Bianconi; Raffaella Casadei; Flavia Frabetti; Carlo Ventura; Federica Facchin; Silvia Canaider

    In humans, sexual dimorphism can manifest in many ways and it is widely studied in several knowledge fields. It is increasing the evidence that also cells differ according to sex, a correlation still little studied and poorly considered when cells are used in scientific research. Specifically, our interest is on the sex-related dimorphism on the human mesenchymal stem cells (hMSCs) transcriptome. A

    更新日期:2020-08-09
  • Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato
    Genes (IF 3.759) Pub Date : 2020-08-07
    Isidore Diouf; Elise Albert; Renaud Duboscq; Sylvain Santoni; Frédérique Bitton; Justine Gricourt; Mathilde Causse

    Water deficit (WD) leads to significant phenotypic changes in crops resulting from complex stress regulation mechanisms involving responses at the physiological, biochemical and molecular levels. Tomato growth and fruit quality have been shown to be significantly affected by WD stress. Understanding the molecular mechanism underlying response to WD is crucial to develop tomato cultivars with relatively

    更新日期:2020-08-08
  • The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets
    Genes (IF 3.759) Pub Date : 2020-08-07
    Martin Bodner; Walther Parson

    STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further

    更新日期:2020-08-08
  • Anaphase Bridges: Not All Natural Fibers Are Healthy
    Genes (IF 3.759) Pub Date : 2020-08-07
    Alice Finardi; Lucia F. Massari; Rosella Visintin

    At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which

    更新日期:2020-08-08
  • A Synonymous Exonic Splice Silencer Variant in IRF6 as a Novel and Cryptic Cause of Non-Syndromic Cleft Lip and Palate
    Genes (IF 3.759) Pub Date : 2020-08-07
    Beau Sylvester; Frederick Brindopke; Akiko Suzuki; Melissa Giron; Allyn Auslander; Richard L. Maas; Becky Tsai; Hanlin Gao; William Magee; Timothy C. Cox; Pedro A. Sanchez-Lara

    Missense, nonsense, splice site and regulatory region variants in interferon regulatory factor 6 (IRF6) have been shown to contribute to both syndromic and non-syndromic forms of cleft lip and/or palate (CL/P). We report the diagnostic evaluation of a complex multigeneration family of Honduran ancestry with a pedigree structure consistent with autosomal-dominant inheritance with both incomplete penetrance

    更新日期:2020-08-08
  • The Gut Microbiota Profile in Children with Prader–Willi Syndrome
    Genes (IF 3.759) Pub Date : 2020-08-07
    Ye Peng; Qiming Tan; Shima Afhami; Edward C. Deehan; Suisha Liang; Marie Gantz; Lucila Triador; Karen L. Madsen; Jens Walter; Hein M. Tun; Andrea M. Haqq

    Although gut microbiota has been suggested to play a role in disease phenotypes of Prader–Willi syndrome (PWS), little is known about its composition in affected children and how it relates to hyperphagia. This cross-sectional study aimed to characterize the gut bacterial and fungal communities of children with PWS, and to determine associations with hyperphagia. Fecal samples were collected from 25

    更新日期:2020-08-08
  • The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures
    Genes (IF 3.759) Pub Date : 2020-08-07
    Elliott C. R. Hall; Christopher Murgatroyd; Georgina K. Stebbings; Brian Cunniffe; Lee Harle; Matthew Salter; Aroul Ramadass; Jurjen W. Westra; Ewan Hunter; Alexandre Akoulitchev; Alun G. Williams

    The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions

    更新日期:2020-08-08
  • Extracurricular Functions of tRNA Modifications in Microorganisms
    Genes (IF 3.759) Pub Date : 2020-08-07
    Ashley M. Edwards; Maame A. Addo; Patricia C. Dos Santos

    Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of

    更新日期:2020-08-08
  • Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry
    Genes (IF 3.759) Pub Date : 2020-08-07
    Massimo Iorizzo; Julien Curaba; Marti Pottorff; Mario G. Ferruzzi; Philipp Simon; Pablo F. Cavagnaro

    Purple or black carrots (Daucus carota ssp. sativus var. atrorubens Alef) are characterized by their dark purple- to black-colored roots, owing their appearance to high anthocyanin concentrations. In recent years, there has been increasing interest in the use of black carrot anthocyanins as natural food dyes. Black carrot roots contain large quantities of mono-acylated anthocyanins, which impart a

    更新日期:2020-08-08
  • New Perspectives on SNARE Function in the Yeast Minimal Endomembrane System
    Genes (IF 3.759) Pub Date : 2020-08-06
    James H. Grissom; Verónica A. Segarra; Richard J. Chi

    Saccharomyces cerevisiae is one of the best model organisms for the study of endocytic membrane trafficking. While studies in mammalian cells have characterized the temporal and morphological features of the endocytic pathway, studies in budding yeast have led the way in the analysis of the endosomal trafficking machinery components and their functions. Eukaryotic endomembrane systems were thought

    更新日期:2020-08-06
  • Increased Accumulation of Medium-Chain Fatty Acids by Dynamic Degradation of Long-Chain Fatty Acids in Mucor circinelloides
    Genes (IF 3.759) Pub Date : 2020-08-05
    Syed Ammar Hussain; Alexis Garcia; Md. Ahsanul Kabir Khan; Shaista Nosheen; Yao Zhang; Mattheos A. G. Koffas; Victoriano Garre; Soo Chan Lee; Yuanda Song

    Concerns about global warming, fossil-fuel depletion, food security, and human health have promoted metabolic engineers to develop tools/strategies to overproduce microbial functional oils directly from renewable resources. Medium-chain fatty acids (MCFAs, C8–C12) have been shown to be important sources due to their diverse biotechnological importance, providing benefits ranging from functional lipids

    更新日期:2020-08-05
  • Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations
    Genes (IF 3.759) Pub Date : 2020-08-05
    Faisal Ramzan; Mehmet Gültas; Hendrik Bertram; David Cavero; Armin Otto Schmitt

    Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype–phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic

    更新日期:2020-08-05
  • Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1
    Genes (IF 3.759) Pub Date : 2020-08-05
    Franco Röckel; Carina Moock; Ulrike Braun; Florian Schwander; Peter Cousins; Erika Maul; Reinhard Töpfer; Ludger Hausmann

    Grapevine (Vitis vinifera) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. The unique and heritable mutation has been known for a long time but the underlying genetic mechanism still is not yet understood

    更新日期:2020-08-05
  • High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover
    Genes (IF 3.759) Pub Date : 2020-08-05
    Mustafa M. H. Abd El-Wahab; Maha Aljabri; Mohamed S. Sarhan; Gamal Osman; Shichen Wang; Mahmoud Mabrouk; Hattem M. El-Shabrawi; Ahmed M. M. Gabr; Ahmed M. Abd El-Haliem; Donal M. O'Sullivan; Mohamed El-Soda

    Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA

    更新日期:2020-08-05
  • Lights and Shadows of TORCH Infection Proteomics
    Genes (IF 3.759) Pub Date : 2020-08-05
    Janaina Macedo-da-Silva; Claudio Romero Farias Marinho; Giuseppe Palmisano; Livia Rosa-Fernandes

    Congenital abnormalities cause serious fetal consequences. The term TORCH is used to designate the most common perinatal infections, where: (T) refers to toxoplasmosis, (O) means "others" and includes syphilis, varicella-zoster, parvovirus B19, zika virus (ZIKV), and malaria among others, (R) refers to rubella, (C) relates to cytomegalovirus infection, and (H) to herpes simplex virus infections. Among

    更新日期:2020-08-05
  • Pathological Consequences of Hepatic mTORC1 Dysregulation
    Genes (IF 3.759) Pub Date : 2020-08-05
    Chun-Seok Cho; Allison Ho Kowalsky; Jun Hee Lee

    The mammalian target of rapamycin complex 1 (mTORC1) is a central regulator of metabolism that integrates environmental inputs, including nutrients, growth factors, and stress signals. mTORC1 activation upregulates anabolism of diverse macromolecules, such as proteins, lipids, and nucleic acids, while downregulating autolysosomal catabolism. mTORC1 dysregulation is often found in various diseases,

    更新日期:2020-08-05
  • The Impact of Coilin Nonsynonymous SNP Variants E121K and V145I on Cell Growth and Cajal Body Formation: The First Characterization
    Genes (IF 3.759) Pub Date : 2020-08-05
    Yue Yao; Heng Wee Tan; Zhan-Ling Liang; Gao-Qi Wu; Yan-Ming Xu; Andy T. Y. Lau

    Coilin is the main component of Cajal body (CB), a membraneless organelle that is involved in the biogenesis of ribonucleoproteins and telomerase, cell cycle, and cell growth. The disruption of CBs is linked to neurodegenerative diseases and potentially cancers. The coilin gene (COIL) contains two nonsynonymous SNPs: rs116022828 (E121K) and rs61731978 (V145I). Here, we investigated for the first time

    更新日期:2020-08-05
  • Vitamin D Pathway Genetic Variation and Type 1 Diabetes: A Case–Control Association Study
    Genes (IF 3.759) Pub Date : 2020-08-05
    Joana T. Almeida; Dircea Rodrigues; Joana Guimarães; Manuel C. Lemos

    Vitamin D has immunomodulatory effects, and its deficiency has been implicated in the autoimmune process of type 1 diabetes. Serum vitamin D levels are influenced by variants in genes involved in the synthesis, transport, hydroxylation and degradation of vitamin D. The aim of this study was to assess if single nucleotide polymorphisms (SNPs) at the DHCR7 (rs12785878), GC (rs2282679), CYP2R1 (rs2060793)

    更新日期:2020-08-05
  • DNA6mA-MINT: DNA-6mA Modification Identification Neural Tool
    Genes (IF 3.759) Pub Date : 2020-08-05
    Mobeen Ur Rehman; Kil To Chong

    DNA N6-methyladenine (6mA) is part of numerous biological processes including DNA repair, DNA replication, and DNA transcription. The 6mA modification sites hold a great impact when their biological function is under consideration. Research in biochemical experiments for this purpose is carried out and they have demonstrated good results. However, they proved not to be a practical solution when accessed

    更新日期:2020-08-05
  • Exploring the lncRNAs Related to Skeletal Muscle Fiber Types and Meat Quality Traits in Pigs
    Genes (IF 3.759) Pub Date : 2020-08-04
    Rongyang Li; Bojiang Li; Aiwen Jiang; Yan Cao; Liming Hou; Zengkai Zhang; Xiying Zhang; Honglin Liu; Kee-Hong Kim; Wangjun Wu

    The alteration in skeletal muscle fiber is a critical factor affecting livestock meat quality traits and human metabolic diseases. Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs with a length of more than 200 nucleotides. However, the mechanisms underlying the regulation of lncRNAs in skeletal muscle fibers remain elusive. To understand the genetic basis of lncRNA-regulated skeletal

    更新日期:2020-08-04
  • Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis
    Genes (IF 3.759) Pub Date : 2020-08-04
    Dominique J. Wiener; Kátia R. Groch; Magdalena A.T. Brunner; Tosso Leeb; Vidhya Jagannathan; Monika M. Welle

    The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were

    更新日期:2020-08-04
  • Structural Insights into TOR Signaling
    Genes (IF 3.759) Pub Date : 2020-08-04
    Lucas Tafur; Jennifer Kefauver; Robbie Loewith

    The Target of Rapamycin (TOR) is a highly conserved serine/threonine protein kinase that performs essential roles in the control of cellular growth and metabolism. TOR acts in two distinct multiprotein complexes, TORC1 and TORC2 (mTORC1 and mTORC2 in humans), which maintain different aspects of cellular homeostasis and orchestrate the cellular responses to diverse environmental challenges. Interest

    更新日期:2020-08-04
  • Nuclear Regulation of Wnt/β-Catenin Signaling: It’s a Complex Situation
    Genes (IF 3.759) Pub Date : 2020-08-04
    Christin C. Anthony; David J. Robbins; Yashi Ahmed; Ethan Lee

    Wnt signaling is an evolutionarily conserved metazoan cell communication pathway required for proper animal development. Of the myriad of signaling events that have been ascribed to cellular activation by Wnt ligands, the canonical Wnt/β-catenin pathway has been the most studied and best understood. Misregulation of Wnt/β-catenin signaling has been implicated in developmental defects in the embryo

    更新日期:2020-08-04
  • Genetic Analysis Using a Multi-Parent Wheat Population Identifies Novel Sources of Septoria Tritici Blotch Resistance
    Genes (IF 3.759) Pub Date : 2020-08-04
    Adnan Riaz; Petra KockAppelgren; James Gerard Hehir; Jie Kang; Fergus Meade; James Cockram; Dan Milbourne; John Spink; Ewen Mullins; Stephen Byrne

    Zymoseptoria tritici is the causative fungal pathogen of septoria tritici blotch (STB) disease of wheat (Triticum aestivum L.) that continuously threatens wheat crops in Ireland and throughout Europe. Under favorable conditions, STB can cause up to 50% yield losses if left untreated. STB is commonly controlled with fungicides; however, a combination of Z. tritici populations developing fungicide resistance

    更新日期:2020-08-04
  • Classifying Breast Cancer Subtypes Using Deep Neural Networks Based on Multi-Omics Data
    Genes (IF 3.759) Pub Date : 2020-08-04
    Yuqi Lin; Wen Zhang; Huanshen Cao; Gaoyang Li; Wei Du

    With the high prevalence of breast cancer, it is urgent to find out the intrinsic difference between various subtypes, so as to infer the underlying mechanisms. Given the available multi-omics data, their proper integration can improve the accuracy of breast cancer subtype recognition. In this study, DeepMO, a model using deep neural networks based on multi-omics data, was employed for classifying

    更新日期:2020-08-04
  • ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa Running Title: crpP-Bearing ICEs in Pseudomonas aeruginosa
    Genes (IF 3.759) Pub Date : 2020-08-04
    João Botelho; Filipa Grosso; Luísa Peixe

    The ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas

    更新日期:2020-08-04
  • The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
    Genes (IF 3.759) Pub Date : 2020-08-03
    Maria A. Sierra; Qianhao Li; Smruti Pushalkar; Bidisha Paul; Tito A Sandoval; Angela R. Kamer; Patricia Corby; Yuqi Guo; Ryan Richard Ruff; Alexander V. Alekseyenko; Xin Li; Deepak Saxena

    There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by

    更新日期:2020-08-03
  • Splicing Factor Transcript Abundance in Saliva as a Diagnostic Tool for Breast Cancer
    Genes (IF 3.759) Pub Date : 2020-08-03
    Mercedes Bentata; Guy Morgenstern; Yuval Nevo; Gillian Kay; Avital Granit Mizrahi; Mark Temper; Ofra Maimon; Liza Monas; Reham Basheer; Asa Ben-Hur; Tamar Peretz; Maayan Salton

    Breast cancer is the second leading cause of death in women above 60 years in the US. Screening mammography is recommended for women above 50 years; however, 22% of breast cancer cases are diagnosed in women below this age. We set out to develop a test based on the detection of cell-free RNA from saliva. To this end, we sequenced RNA from a pool of ten women. The 1254 transcripts identified were enriched

    更新日期:2020-08-03
  • Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.
    Genes (IF 3.759) Pub Date : 2020-08-03
    Erli Niu; Chengying Jiang; Wei Wang; Yu Zhang; Shenlong Zhu

    Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea

    更新日期:2020-08-03
  • Transcriptomic Analysis Revealed the Common and Divergent Responses of Maize Seedling Leaves to Cold and Heat Stresses
    Genes (IF 3.759) Pub Date : 2020-08-03
    Yongsheng Li; Xingrong Wang; Yue Li; Yanjun Zhang; Zuowang Gou; Xusheng Qi; Jinlin Zhang

    Temperature stresses (TS), including cold and heat stress, adversely affect the growth, development, and yield of maize (Zea mays L.). To clarify the molecular mechanisms of the tolerance of maize seedling leaves to TS, we applied transcriptomic sequencing of an inbred maize line, B73, with seedlings exposed to various temperature conditions, including normal temperature (NT, 25 °C), cold (4, 10, and

    更新日期:2020-08-03
  • Mutation Spectrum and De Novo Mutation Analysis in Stickler Syndrome Patients with High Myopia or Retinal Detachment
    Genes (IF 3.759) Pub Date : 2020-08-03
    Li Huang; Chonglin Chen; Zhirong Wang; Limei Sun; Songshan Li; Ting Zhang; Xiaoling Luo; Xiaoyan Ding

    Stickler syndrome is a connective tissue disorder that affects multiple systems, including the visual system. Seven genes were reported to cause Stickler syndrome in patients with different phenotypes. In this study, we aimed to evaluate the mutation features of the phenotypes of high myopia and retinal detachment. Forty-two probands diagnosed with Stickler syndrome were included. Comprehensive ocular

    更新日期:2020-08-03
  • Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population
    Genes (IF 3.759) Pub Date : 2020-08-01
    Fatma A Aljasmi; Ranjit Vijayan; Naganeeswaran Sudalaimuthuasari; Abdul-Kader Souid; Noushad Karuvantevida; Raja Almaskari; Hidaya Mohammed Abdul Kader; Biduth Kundu; Khaled Michel Hazzouri; Khaled M. A. Amiri

    In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity

    更新日期:2020-08-01
  • Bats Out of Africa: Disentangling the Systematic Position and Biogeography of Bats in Cabo Verde
    Genes (IF 3.759) Pub Date : 2020-08-01
    Ianna Borloti; Herculano Dinis; Raquel Vasconcelos

    Cabo Verde Archipelago presents one of the largest knowledge gaps in the distribution and taxonomy of bats in the world. Old works indicated that there are five species classified as European taxa. We have conducted an integrative taxonomy to revise the systematic position and distribution of Cabo Verdean bats with molecular, morphological, and ecological data, to test their native or exotic origin

    更新日期:2020-08-01
  • Characterizing Gene Copy Number of Heat Shock Protein Gene Families in the Emerald Rockcod, Trematomus bernacchii
    Genes (IF 3.759) Pub Date : 2020-07-31
    Anthony D. Tercero; Sean P. Place

    The suborder Notothenioidae is comprised of Antarctic fishes, several of which have lost their ability to rapidly upregulate heat shock proteins in response to thermal stress, instead adopting a pattern of expression resembling constitutive genes. Given the cold-denaturing effect that sub-zero waters have on proteins, evolution in the Southern Ocean has likely selected for increased expression of molecular

    更新日期:2020-07-31
  • Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia
    Genes (IF 3.759) Pub Date : 2020-07-31
    Yaqi Cheng; Yaru Su; Shoubi Wang; Yurun Liu; Lin Jin; Qi Wan; Ying Liu; Chaoyang Li; Xuan Sang; Liu Yang; Chang Liu; Zhichong Wang

    Background: Acute myeloid leukemia (AML) is one of the most common malignant and aggressive hematologic tumors, and its pathogenesis is associated with abnormal post-transcriptional regulation. Unbalanced competitive endogenous RNA (ceRNA) promotes tumorigenesis and progression, and greatly contributes to tumor risk classification and prognosis. However, the comprehensive analysis of the circular RNA

    更新日期:2020-07-31
  • Effect of Mutations on mRNA and Globin Stability: The Cases of Hb Bernalda/Groene Hart and Hb Southern Italy
    Genes (IF 3.759) Pub Date : 2020-07-31
    Giovanna Cardiero; Gennaro Musollino; Maria Grazia Friscia; Rosario Testa; Lucrezia Virruso; Caterina Di Girgenti; Mercedes Caldora; Rosario Colella Bisogno; Carlo Gaudiano; Giuseppe Manco; Giuseppina Lacerra

    We identified two unstable variants in the third exon of α-globin genes: Hb Bernalda/Groene Hart (HBA1:c.358C>T), and Hb Caserta (HBA2:c.79G>A) in cis to Hb Sun Prairie (HBA2:c.391G>C), also named Hb Southern Italy. These mutations occurred in the H helix of the α-globin that is involved in heme contacting, specific recognition of α-hemoglobin-stabilizing protein (AHSP), and α1β1 interactions. The

    更新日期:2020-07-31
  • Preimplantation Genetic Testing for Monogenic Disorders
    Genes (IF 3.759) Pub Date : 2020-07-31
    Martine De Rycke; Veerle Berckmoes

    Preimplantation genetic testing (PGT) has evolved into a well-established alternative to invasive prenatal diagnosis, even though genetic testing of single or few cells is quite challenging. PGT-M is in theory available for any monogenic disorder for which the disease-causing locus has been unequivocally identified. In practice, the list of indications for which PGT is allowed may vary substantially

    更新日期:2020-07-31
  • Expression of Stress-Mediating Genes is Increased in Term Placentas of Women with Chronic Self-Perceived Anxiety and Depression
    Genes (IF 3.759) Pub Date : 2020-07-31
    Cristina A. Martinez; Ina Marteinsdottir; Ann Josefsson; Gunilla Sydsjö; Elvar Theodorsson; Heriberto Rodriguez-Martinez

    Anxiety, chronical stress, and depression during pregnancy are considered to affect the offspring, presumably through placental dysregulation. We have studied the term placentae of pregnancies clinically monitored with the Beck’s Anxiety Inventory (BAI) and Edinburgh Postnatal Depression Scale (EPDS). A cutoff threshold for BAI/EPDS of 10 classed patients into an Index group (>10, n = 23) and a Control

    更新日期:2020-07-31
  • RNA Editing and Modifications in Mood Disorders
    Genes (IF 3.759) Pub Date : 2020-07-31
    Alessandro Barbon; Chiara Magri

    Major depressive disorder (MDD) is a major health problem with significant limitations in functioning and well-being. The World Health Organization (WHO) evaluates MDD as one of the most disabling disorders in the world and with very high social cost. Great attention has been given to the study of the molecular mechanism underpinning MDD at the genetic, epigenetic and proteomic level. However, the

    更新日期:2020-07-31
  • Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods
    Genes (IF 3.759) Pub Date : 2020-07-31
    Małgorzata Marta Rogala; Jan Gawor; Robert Gromadka; Magdalena Kowalczyk; Jakub Grzesiak

    Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar

    更新日期:2020-07-31
  • Contactin 1: An Important and Emerging Oncogenic Protein Promoting Cancer Progression and Metastasis
    Genes (IF 3.759) Pub Date : 2020-07-31
    Yan Gu; Taosha Li; Anil Kapoor; Pierre Major; Damu Tang

    Even with recent progress, cancer remains the second leading cause of death, outlining a need to widen the current understanding on oncogenic factors. Accumulating evidence from recent years suggest Contactin 1 (CNTN1)’s possession of multiple oncogenic activities in a variety of cancer types. CNTN1 is a cell adhesion molecule that is dysregulated in many human carcinomas and plays important roles

    更新日期:2020-07-31
  • Exercise and High-Fat Diet in Obesity: Functional Genomics Perspectives of Two Energy Homeostasis Pillars
    Genes (IF 3.759) Pub Date : 2020-07-31
    Abdelaziz Ghanemi; Aicha Melouane; Mayumi Yoshioka; Jonny St-Amand

    The heavy impact of obesity on both the population general health and the economy makes clarifying the underlying mechanisms, identifying pharmacological targets, and developing efficient therapies for obesity of high importance. The main struggle facing obesity research is that the underlying mechanistic pathways are yet to be fully revealed. This limits both our understanding of pathogenesis and

    更新日期:2020-07-31
  • Drought-Induced Regulatory Cascades and Their Effects on the Nutritional Quality of Developing Potato Tubers
    Genes (IF 3.759) Pub Date : 2020-07-30
    Letitia Da Ros; Raed Elferjani; Raju Soolanayakanahally; Sateesh Kagale; Shankar Pahari; Manoj Kulkarni; Jazeem Wahab; Benoit Bizimungu

    Competition for scarce water resources and the continued effects of global warming exacerbate current constraints on potato crop production. While plants’ response to drought in above-ground tissues has been well documented, the regulatory cascades and subsequent nutritive changes in developing tubers have been largely unexplored. Using the commercial Canadian cultivar “Vigor”, plants were subjected

    更新日期:2020-07-30
  • Dramatic Increase in Content of Diverse Flavonoids Accompanied with Down-Regulation of F-Box Genes in a Chrysanthemum (Chrysanthemum × morifolium (Ramat.) Hemsl.) Mutant Cultivar Producing Dark-Purple Ray Florets
    Genes (IF 3.759) Pub Date : 2020-07-30
    Yeong Deuk Jo; Jaihyunk Ryu; Ye-Sol Kim; Kyung-Yun Kang; Min Jeong Hong; Hong-Il Choi; Gah-Hyun Lim; Jin-Baek Kim; Sang Hoon Kim

    Anthocyanins (a subclass of flavonoids) and flavonoids are crucial determinants of flower color and substances of pharmacological efficacy, respectively, in chrysanthemum. However, metabolic and transcriptomic profiling regarding flavonoid accumulation has not been performed simultaneously, thus the understanding of mechanisms gained has been limited. We performed HPLC-DAD-ESI-MS (high-performance

    更新日期:2020-07-30
  • Displacement of Slow-Turnover DNA Glycosylases by Molecular Traffic on DNA
    Genes (IF 3.759) Pub Date : 2020-07-30
    Anna V. Yudkina; Anton V. Endutkin; Eugenia A. Diatlova; Nina A. Moor; Ivan P. Vokhtantsev; Inga R. Grin; Dmitry O. Zharkov

    In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed

    更新日期:2020-07-30
  • miR-101b Regulates Lipid Deposition and Metabolism of Primary Hepatocytes in Teleost Yellow Catfish Pelteobagrus fulvidraco
    Genes (IF 3.759) Pub Date : 2020-07-29
    Guang-Hui Chen; Tao Zhao; Xiao-Lei Wei; Dian-Guang Zhang; Mei-Qin Zhuo; Zhi Luo

    Excessive fat deposition in the hepatocytes, associated with excess dietary fat intake, was related to the occurrence of fatty livers in fish. miR-101b plays the important roles in controlling lipid metabolism, but the underlying mechanism at the post-transcriptional level remains unclear. The purpose of this study is to explore the roles and mechanism of miR-101b-mediating lipid deposition and metabolism

    更新日期:2020-07-29
  • Association between Platelet-Specific Collagen Receptor Glycoprotein 6 Gene Variants, Selected Biomarkers, and Recurrent Pregnancy Loss in Korean Women
    Genes (IF 3.759) Pub Date : 2020-07-29
    Hui Jeong An; Eun Hee Ahn; Jung Oh Kim; Chang Soo Ryu; Han Sung Park; Sung Hwan Cho; Ji Hyang Kim; Woo Sik Lee; Jung Ryeol Lee; Young Ran Kim; Nam Keun Kim

    This paper investigates whether glycoprotein 6 (GP6) gene polymorphisms are a risk factor for recurrent pregnancy loss (RPL) in Korean women. Genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism and real-time polymerase chain reaction amplification. We identified five polymorphisms in the GP6 gene: rs1654410 T>C, rs1671153 T>G, rs1654419 G>A, rs12610286 A>G

    更新日期:2020-07-29
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