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  • A New Perspective on the Origin of DNA Double-Strand Breaks and Its Implications for Ageing
    Genes (IF 3.759) Pub Date : 2021-01-26
    Bhabesh Kumar Tripathy; Kavita Pal; Snehal Shabrish; Indraneel Mittra

    It is estimated that 10–50 DNA double-strand breaks (DSBs) occur in a nucleated human cell per cell cycle. We reviewed the present state of knowledge and hypothesized that the currently accepted mechanisms cannot explain such high frequency of DSBs occurring daily under normal physiological conditions. We propose an alternative model that implicates illegitimate genomic integration into healthy cells

    更新日期:2021-01-26
  • Evaluating the Role of Circulating Dendritic Cells in Methimazole-Treated Pediatric Graves’ Disease Patients
    Genes (IF 3.759) Pub Date : 2021-01-26
    Aleksandra Starosz; Karolina Stożek; Marcin Moniuszko; Kamil Grubczak; Artur Bossowski

    Graves’ disease (GD) is hyperthyroidism associated with organ-specific autoimmune inflammation. GD occurs more frequently in adults than in children; however, pediatric patients are a therapeutic challenge due to cycles of remissions and relapses requiring constant monitoring at every stage of treatment administered. Dendritic cells (DCs) are considered to be a link between innate and adaptive immunity

    更新日期:2021-01-26
  • Chromosomal Polymorphism and Speciation: The Case of the Genus Mazama (Cetartiodactyla; Cervidae)
    Genes (IF 3.759) Pub Date : 2021-01-26
    David Javier Galindo; Gabriela Siqueira Martins; Miluse Vozdova; Halina Cernohorska; Svatava Kubickova; Agda Maria Bernegossi; Dita Kadlcikova; Jiri Rubes; José Maurício Barbanti Duarte

    Chromosomal polymorphism plays a major role in speciation processes in mammals with high rates of karyotypic evolution, as observed in the family Cervidae. One remarkable example is the genus Mazama that comprises wide inter- and intra-specific chromosomal variability. To evaluate the impact of chromosomal polymorphisms as reproductive barriers within the genus Mazama, inter-specific hybrids between

    更新日期:2021-01-26
  • Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes
    Genes (IF 3.759) Pub Date : 2021-01-26
    Jahangheer S. Shaik; Deborah E. Dobson; David L. Sacks; Stephen M. Beverley

    A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study the products of controlled, laboratory-based experiments where known strains or species are

    更新日期:2021-01-26
  • Expression of BARD1 β Isoform in Selected Pediatric Tumors
    Genes (IF 3.759) Pub Date : 2021-01-26
    Anna Jasiak; Natalia Krawczyńska; Mariola Iliszko; Katarzyna Czarnota; Kamil Buczkowski; Joanna Stefanowicz; Elżbieta Adamkiewicz-Drożyńska; Grzegorz Cichosz; Ewa Iżycka-Świeszewska

    Currently, many new possible biomarkers and mechanisms are being searched and tested to analyse pathobiology of pediatric tumours for the development of new treatments. One such candidate molecular factor is BARD1 (BRCA1 Associated RING Domain 1)—a tumour-suppressing gene involved in cell cycle control and genome stability, engaged in several types of adult-type tumours. The data on BARD1 significance

    更新日期:2021-01-26
  • Effects of mitoTALENs-Directed Double-Strand Breaks on Plant Mitochondrial Genomes
    Genes (IF 3.759) Pub Date : 2021-01-25
    Shin-ichi Arimura

    Mitochondrial genomes in flowering plants differ from those in animals and yeasts in several ways, including having large and variable sizes, circular, linear and branched structures, long repeat sequences that participate in homologous recombinations, and variable genes orders, even within a species. Understanding these differences has been hampered by a lack of genetic methods for transforming plant

    更新日期:2021-01-25
  • Epigenetic Evolution of ACE2 and IL-6 Genes: Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates
    Genes (IF 3.759) Pub Date : 2021-01-25
    Eric R. Sang; Yun Tian; Laura C. Miller; Yongming Sang

    The current novel coronavirus disease (COVID-19) has spread globally within a matter of months. The virus establishes a success in balancing its deadliness and contagiousness, and causes substantial differences in susceptibility and disease progression in people of different ages, genders and pre-existing comorbidities. These host factors are subjected to epigenetic regulation; therefore, relevant

    更新日期:2021-01-25
  • Cytogenetic Analysis of the Asian Box Turtles of the Genus Cuora (Testudines, Geoemydidae)
    Genes (IF 3.759) Pub Date : 2021-01-25
    Lorenzo Clemente; Sofia Mazzoleni; Eleonora Pensabene; Tomáš Protiva; Philipp Wagner; Uwe Fritz; Lukáš Kratochvíl; Michail Rovatsos

    The Asian box turtle genus Cuora currently comprises 13 species with a wide distribution in Southeast Asia, including China and the islands of Indonesia and Philippines. The populations of these species are rapidly declining due to human pressure, including pollution, habitat loss, and harvesting for food consumption. Notably, the IUCN Red List identifies almost all species of the genus Cuora as Endangered

    更新日期:2021-01-25
  • Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms
    Genes (IF 3.759) Pub Date : 2021-01-25
    Kefena Effa; Sonia Rosenbom; Jianlin Han; Tadelle Dessie; Albano Beja-Pereira

    Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that

    更新日期:2021-01-25
  • Genome Analysis of Sable Fur Color Links a Lightened Pigmentation Phenotype to a Frameshift Variant in the Tyrosinase-Related Protein 1 Gene
    Genes (IF 3.759) Pub Date : 2021-01-25
    Andrey D. Manakhov; Maria Y. Mintseva; Tatiana V. Andreeva; Pavel A. Filimonov; Alexey A. Onokhov; Irina Е. Chernova; Sergey N. Kashtanov; Evgeny I. Rogaev

    Sable (Martes zibellina) is one of the most valuable species of fur animals. Wild-type sable fur color varies from sandy-yellow to black. Farm breeding and 90 years of directional selection have resulted in a generation of several sable breeds with a completely black coat color. In 2005, an unusually chocolate (pastel) puppy was born in the Puschkinsky State Fur Farm (Russia). We established that the

    更新日期:2021-01-25
  • Special Issue “Forensic Genetics and Genomics”
    Genes (IF 3.759) Pub Date : 2021-01-25
    Emiliano Giardina; Michele Ragazzo

    Note: In lieu of an abstract, this is an excerpt from the first page. The technological and scientific progress that we have experienced in recent years has contributed to characterization of the complex processes underlying human biology and evolution[...]

    更新日期:2021-01-25
  • Deregulated Immune Pathway Associated with Palbociclib Resistance in Preclinical Breast Cancer Models: Integrative Genomics and Transcriptomics
    Genes (IF 3.759) Pub Date : 2021-01-25
    Kamal Pandey; Eunbyeol Lee; Nahee Park; Jin Hur; Young Bin Cho; Nar Bahadur Katuwal; Seung Ki Kim; Seung Ah Lee; Isaac Kim; Hee Jung An; Sohyun Hwang; Yong Wha Moon

    Recently, cyclin-dependent kinase (CDK) 4/6 inhibitors have been widely used to treat advanced hormone receptor-positive breast cancer. Despite promising clinical outcomes, almost all patients eventually acquire resistance to CDK4/6 inhibitors. Here, we screened genes associated with palbociclib resistance through genomics and transcriptomics in preclinical breast cancer models. Palbociclib-resistant

    更新日期:2021-01-25
  • Acknowledgment to Reviewers of Genes in 2020
    Genes (IF 3.759) Pub Date : 2021-01-25
    Genes Editorial Office

    Note: In lieu of an abstract, this is an excerpt from the first page. Peer review is the driving force of journal development, and reviewers are gatekeepers who ensure that Genes maintains its standards for the high quality of its published papers [...]

    更新日期:2021-01-25
  • Transcriptional Differences between Canine Cutaneous Epitheliotropic Lymphoma and Immune-Mediated Dermatoses
    Genes (IF 3.759) Pub Date : 2021-01-25
    Nadja Gerber; Magdalena A. T. Brunner; Vidhya Jagannathan; Tosso Leeb; Nora M. Gerhards; Monika M. Welle; Martina Dettwiler

    Canine cutaneous epitheliotropic T-cell lymphoma (CETL) and immune-mediated T-cell predominant dermatoses (IMD) share several clinical and histopathological features, but differ substantially in prognosis. The discrimination of ambiguous cases may be challenging, as diagnostic tests are limited and may prove equivocal. This study aimed to investigate transcriptional differences between CETL and IMD

    更新日期:2021-01-25
  • Functional Haplotype of LIPC Induces Triglyceride-Mediated Suppression of HDL-C Levels According to Genome-Wide Association Studies
    Genes (IF 3.759) Pub Date : 2021-01-22
    Yu-Huang Liao; Leay-Kiaw Er; Semon Wu; Yu-Lin Ko; Ming-Sheng Teng

    Hepatic lipase (encoded by LIPC) is a glycoprotein in the triacylglycerol lipase family and mainly synthesized in and secreted from the liver. Previous studies demonstrated that hepatic lipase is crucial for reverse cholesterol transport and modulating metabolism and the plasma levels of several lipoproteins. This study was conducted to investigate the suppression effect of high-density lipoprotein

    更新日期:2021-01-24
  • The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea
    Genes (IF 3.759) Pub Date : 2021-01-23
    Mike Dyall-Smith; Friedhelm Pfeiffer; Pei-Wen Chiang; Sen-Lin Tang

    The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in

    更新日期:2021-01-24
  • BARD1 Pathogenic Variants Are Associated with Triple-Negative Breast Cancer in a Spanish Hereditary Breast and Ovarian Cancer Cohort
    Genes (IF 3.759) Pub Date : 2021-01-23
    Paula Rofes; Jesús del Valle; Sara Torres-Esquius; Lídia Feliubadaló; Agostina Stradella; José Marcos Moreno-Cabrera; Adriana López-Doriga; Elisabet Munté; Rafael de Cid; Olga Campos; Raquel Cuesta; Àlex Teulé; Èlia Grau; Judit Sanz; Gabriel Capellá; Orland Díez; Joan Brunet; Judith Balmaña; Conxi Lázaro

    Only a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance breast cancer 1 and 2 genes (BRCA1 and BRCA2). BRCA1-associated ring domain 1 (BARD1), nuclear partner of BRCA1, has been suggested as a potential HBOC risk gene, although its prevalence and penetrance are variable according to populations and type of tumor. We aimed

    更新日期:2021-01-24
  • Peripheral Anomalies in USH2A Cause Central Auditory Anomalies in a Mouse Model of Usher Syndrome and CAPD
    Genes (IF 3.759) Pub Date : 2021-01-24
    Peter A. Perrino; Dianne F. Newbury; R. Holly Fitch

    Central auditory processing disorder (CAPD) is associated with difficulties hearing and processing acoustic information, as well as subsequent impacts on the development of higher-order cognitive processes (i.e., attention and language). Yet CAPD also lacks clear and consistent diagnostic criteria, with widespread clinical disagreement on this matter. As such, identification of biological markers for

    更新日期:2021-01-24
  • Pharmacogenetic Testing of Cytochrome P450 Drug Metabolizing Enzymes in a Case Series of Patients with Prader-Willi Syndrome
    Genes (IF 3.759) Pub Date : 2021-01-24
    Janice Forster; Jessica Duis; Merlin G. Butler

    Prader-Willi syndrome (PWS) is associated with co-morbid psychiatric symptoms (disruptive behavior, anxiety, mood disorders, and psychosis) often requiring psychotropic medications. In this clinical case series of 35 patients with PWS, pharmacogenetic testing was obtained to determine allele frequencies predicting variations in activity of cytochrome (CYP) P450 drug metabolizing enzymes 2D6, 2B6, 2C19

    更新日期:2021-01-24
  • Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)
    Genes (IF 3.759) Pub Date : 2021-01-21
    Corey Kirkland; Marta Farré

    The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is

    更新日期:2021-01-22
  • Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution
    Genes (IF 3.759) Pub Date : 2021-01-22
    Martine Roovers; Louis Droogmans; Henri Grosjean

    The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical

    更新日期:2021-01-22
  • Role of Sigma-1 Receptor in Calcium Modulation: Possible Involvement in Cancer
    Genes (IF 3.759) Pub Date : 2021-01-22
    Ilaria Pontisso; Laurent Combettes

    Ca2+ signaling plays a pivotal role in the control of cellular homeostasis and aberrant regulation of Ca2+ fluxes have a strong impact on cellular functioning. As a consequence of this ubiquitous role, Ca2+ signaling dysregulation is involved in the pathophysiology of multiple diseases including cancer. Indeed, multiple studies have highlighted the role of Ca2+ fluxes in all the steps of cancer progression

    更新日期:2021-01-22
  • Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses
    Genes (IF 3.759) Pub Date : 2021-01-22
    Yan-Ran Sheng; Shun-Yu Hou; Wen-Ting Hu; Chun-Yan Wei; Yu-Kai Liu; Yu-Yin Liu; Lu Jiang; Jing-Jing Xiang; Xiao-Xi Sun; Cai-Xia Lei; Hui-Ling Wang; Xiao-Yong Zhu

    It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscopic

    更新日期:2021-01-22
  • Identification of Variants (rs11571707, rs144848, and rs11571769) in the BRCA2 Gene Associated with Hereditary Breast Cancer in Indigenous Populations of the Brazilian Amazon
    Genes (IF 3.759) Pub Date : 2021-01-22
    Elizabeth Ayres Fragoso Dobbin; Jéssyca Amanda Gomes Medeiros; Marta Solange Camarinha Ramos Costa; Juliana Carla Gomes Rodrigues; João Farias Guerreiro; José Eduardo Kroll; Sandro José de Souza; Paulo Pimentel de Assumpção; Ândrea Ribeiro-dos-Santos; Sidney Emanuel Batista dos Santos; Rommel Mario Rodríguez Burbano; Marianne Rodrigues Fernandes; Ney Pereira Carneiro dos Santos

    Estimates show that 5–10% of breast cancer cases are hereditary, caused by genetic variants in autosomal dominant genes; of these, 16% are due to germline mutations in the BRCA1 and BRCA2 genes. The comprehension of the mutation profile of these genes in the Brazilian population, particularly in Amazonian Amerindian groups, is scarce. We investigated fifteen polymorphisms in the BRCA1 and BRCA2 genes

    更新日期:2021-01-22
  • Senescence: The Compromised Time of Death That Plants May Call on Themselves
    Genes (IF 3.759) Pub Date : 2021-01-22
    Matin Miryeganeh

    Plants synchronize their life history events with proper seasonal conditions, and as the fitness consequences of each life stage depend on previous and/or subsequent one, changes in environmental cues create cascading effects throughout their whole life cycle. For monocarpic plants, proper senescence timing is very important as the final production of plants depends on it. Citing available literatures

    更新日期:2021-01-22
  • Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe
    Genes (IF 3.759) Pub Date : 2021-01-22
    Ulrike H Taron; Johanna L A Paijmans; Axel Barlow; Michaela Preick; Arati Iyengar; Virgil Drăgușin; Ștefan Vasile; Adrian Marciszak; Martina Roblíčková; Michael Hofreiter

    The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils

    更新日期:2021-01-22
  • The FLA4-FEI Pathway: A Unique and Mysterious Signaling Module Related to Cell Wall Structure and Stress Signaling
    Genes (IF 3.759) Pub Date : 2021-01-22
    Georg J. Seifert

    Cell wall integrity control in plants involves multiple signaling modules that are mostly defined by genetic interactions. The putative co-receptors FEI1 and FEI2 and the extracellular glycoprotein FLA4 present the core components of a signaling pathway that acts in response to environmental conditions and insults to cell wall structure to modulate the balance of various growth regulators and, ultimately

    更新日期:2021-01-22
  • Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age
    Genes (IF 3.759) Pub Date : 2021-01-22
    Catarina Xavier; Mayra Eduardoff; Barbara Bertoglio; Christina Amory; Cordula Berger; Andrea Casas-Vargas; Johannes Pallua; Walther Parson

    The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols

    更新日期:2021-01-22
  • From Transcriptomics to Treatment in Inherited Optic Neuropathies
    Genes (IF 3.759) Pub Date : 2021-01-22
    Michael James Gilhooley; Nicholas Owen; Mariya Moosajee; Patrick Yu Wai Man

    Inherited optic neuropathies, including Leber Hereditary Optic Neuropathy (LHON) and Dominant Optic Atrophy (DOA), are monogenetic diseases with a final common pathway of mitochondrial dysfunction leading to retinal ganglion cell (RGC) death and ultimately loss of vision. They are, therefore, excellent models with which to investigate this ubiquitous disease process—implicated in both common polygenetic

    更新日期:2021-01-22
  • Clinical Spectrum and Genetic Diagnosis of 54 Consecutive Patients Aged 0–25 with Bilateral Cataracts
    Genes (IF 3.759) Pub Date : 2021-01-21
    Suzannah Bell; Samantha Malka; Ian Christopher Lloyd; Mariya Moosajee

    Childhood cataract affects 2.5–3.5 per 10,000 children in the UK, with a genetic mutation identified in 50–90% of bilateral cases. However, cataracts can also manifest in adolescence and early adulthood in isolation, as part of a complex ocular phenotype or with systemic features making accurate diagnosis more challenging. We investigate our real-world experience through a retrospective review of consecutive

    更新日期:2021-01-21
  • Novel KCNH1 Mutations Associated with Epilepsy: Broadening the Phenotypic Spectrum of KCNH1-Associated Diseases
    Genes (IF 3.759) Pub Date : 2021-01-21
    Randi Von Wrede; Monika Jeub; Idil Ariöz; Christian E. Elger; Hubertus von Voss; Hanns-Georg Klein; Albert J. Becker; Susanne Schoch; Rainer Surges; Wolfram S. Kunz

    Here, we describe four patients suffering from a rather broad spectrum of epilepsy-related disorders, ranging from developmental and epileptic encephalopathy with intellectual disability (DEE) to genetic generalized epilepsy (GGE), which all harbor novel KCNH1 mutations. In one family, we found a weak association of a novel nonsense mutation with epilepsy, suggesting reduced penetrance, and which shows

    更新日期:2021-01-21
  • Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement
    Genes (IF 3.759) Pub Date : 2021-01-21
    Maria Elena Onore; Annalaura Torella; Francesco Musacchia; Paola D’Ambrosio; Mariateresa Zanobio; Francesca Del Vecchio Blanco; Giulio Piluso; Vincenzo Nigro

    Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome

    更新日期:2021-01-21
  • A SINE Insertion in F8 Gene Leads to Severe Form of Hemophilia A in a Family of Rhodesian Ridgebacks
    Genes (IF 3.759) Pub Date : 2021-01-21
    Alexandra Kehl; Anita Haug Haaland; Ines Langbein-Detsch; Elisabeth Mueller

    Hemophilia A is the most common coagulation factor disorder in humans and dogs. The disease is characterized by the lack or diminished activity of Factor VIII (FVIII), caused by variants in the F8 gene and inherited as an X chromosomal trait. Two related male Rhodesian Ridgebacks were diagnosed with Hemophilia A due to reduced FVIII activity. The purpose of the study was to determine the genetic cause

    更新日期:2021-01-21
  • Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome
    Genes (IF 3.759) Pub Date : 2021-01-21
    Eugene V. Korotkov; Yulia M. Suvorova; Dmitrii O. Kostenko; Maria A. Korotkova

    In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee

    更新日期:2021-01-21
  • Ensemble-AMPPred: Robust AMP Prediction and Recognition Using the Ensemble Learning Method with a New Hybrid Feature for Differentiating AMPs
    Genes (IF 3.759) Pub Date : 2021-01-21
    Supatcha Lertampaiporn; Tayvich Vorapreeda; Apiradee Hongsthong; Chinae Thammarongtham

    Antimicrobial peptides (AMPs) are natural peptides possessing antimicrobial activities. These peptides are important components of the innate immune system. They are found in various organisms. AMP screening and identification by experimental techniques are laborious and time-consuming tasks. Alternatively, computational methods based on machine learning have been developed to screen potential AMP

    更新日期:2021-01-21
  • Characterization of New ATM Deletion Associated with Hereditary Breast Cancer
    Genes (IF 3.759) Pub Date : 2021-01-21
    Sandra Parenti; Claudio Rabacchi; Marco Marino; Elena Tenedini; Lucia Artuso; Sara Castellano; Chiara Carretta; Selene Mallia; Laura Cortesi; Angela Toss; Elena Barbieri; Rossella Manfredini; Mario Luppi; Tommaso Trenti; Enrico Tagliafico

    Next-generation sequencing (NGS)-based cancer risk screening with multigene panels has become the most successful method for programming cancer prevention strategies. ATM germ-line heterozygosity has been described to increase tumor susceptibility. In particular, families carrying heterozygous germ-line variants of ATM gene have a 5- to 9-fold risk of developing breast cancer. Recent studies identified

    更新日期:2021-01-21
  • Special Issue: Genetic Perspectives in Thyroid Cancer
    Genes (IF 3.759) Pub Date : 2021-01-20
    Susana Nunes Silva

    Note: In lieu of an abstract, this is an excerpt from the first page. Thyroid cancer is not just a common type of cancer, it is the most frequently diagnosed endocrine malignancy worldwide [...]

    更新日期:2021-01-20
  • Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host
    Genes (IF 3.759) Pub Date : 2021-01-20
    Jarrett F. Lebov; Brendan J. M. Bohannan

    Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis

    更新日期:2021-01-20
  • A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures
    Genes (IF 3.759) Pub Date : 2021-01-20
    Utpal Smart; Jennifer Churchill Cihlar; Sammed N. Mandape; Melissa Muenzler; Jonathan L. King; Bruce Budowle; August E. Woerner

    Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment

    更新日期:2021-01-20
  • Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis
    Genes (IF 3.759) Pub Date : 2021-01-20
    DeAnna Baker Frost; Willian da Silveira; E. Starr Hazard; Ilia Atanelishvili; Robert C. Wilson; Jonathan Flume; Kayleigh L. Day; James C. Oates; Galina S. Bogatkevich; Carol Feghali-Bostwick; Gary Hardiman; Paula S. Ramos

    The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing

    更新日期:2021-01-20
  • Splicing Genomics Events in Cervical Cancer: Insights for Phenotypic Stratification and Biomarker Potency
    Genes (IF 3.759) Pub Date : 2021-01-20
    Flavia Zita Francies; Sheynaz Bassa; Aristotelis Chatziioannou; Andreas Martin Kaufmann; Zodwa Dlamini

    Gynaecological cancers are attributed to the second most diagnosed cancers in women after breast cancer. On a global scale, cervical cancer is the fourth most common cancer and the most common cancer in developing countries with rapidly increasing mortality rates. Human papillomavirus (HPV) infection is a major contributor to the disease. HPV infections cause prominent cellular changes including alternative

    更新日期:2021-01-20
  • Morphological Abnormalities and Gene Expression Changes Caused by High Incubation Temperatures in Zebrafish Xenografts with Human Cancer Cells
    Genes (IF 3.759) Pub Date : 2021-01-19
    Pablo Cabezas-Sainz; Carlos Coppel; Alba Pensado-López; Pedro Fernandez; Laura Muinelo-Romay; Rafael López-López; Juan A. Rubiolo; Laura Sánchez

    Published studies show that most of the human cancer xenograft studies in zebrafish embryos have used incubation temperatures in the range of 32–34 °C for 3–6 days post-injection, trying to find a compromise temperature between the zebrafish embryos (28 °C) and the human injected cells (37 °C). While this experimental setup is widely used, a question remains: is possible to overcome the drawbacks caused

    更新日期:2021-01-19
  • Merging Genomics and Transcriptomics for Predicting Fusarium Head Blight Resistance in Wheat
    Genes (IF 3.759) Pub Date : 2021-01-19
    Sebastian Michel; Christian Wagner; Tetyana Nosenko; Barbara Steiner; Mina Samad-Zamini; Maria Buerstmayr; Klaus Mayer; Hermann Buerstmayr

    Genomic selection with genome-wide distributed molecular markers has evolved into a well-implemented tool in many breeding programs during the last decade. The resistance against Fusarium head blight (FHB) in wheat is probably one of the most thoroughly studied systems within this framework. Aside from the genome, other biological strata like the transcriptome have likewise shown some potential in

    更新日期:2021-01-19
  • Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny
    Genes (IF 3.759) Pub Date : 2021-01-19
    Lidia Ruiz-Roldán; María de Toro; Yolanda Sáenz

    Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these isolates. Thus, the aim of this study was to analyze the resistome, virulome, and phylogenetic relationship

    更新日期:2021-01-19
  • Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus)
    Genes (IF 3.759) Pub Date : 2021-01-19
    Shannon E. Keating; Madison Blumer; L. Lee Grismer; Aung Lin; Stuart V. Nielsen; Myint Kyaw Thura; Perry L. Wood; Evan S. H. Quah; Tony Gamble

    Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed

    更新日期:2021-01-19
  • HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas
    Genes (IF 3.759) Pub Date : 2021-01-19
    Yiyun Sun; Dandan Xu; Chundong Zhang; Yitao Wang; Lian Zhang; Deqian Qiao; Youquan Bu; Ying Zhang

    We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter. This gene pair synergistically promoted the development of non-small cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remains obscure. In the present

    更新日期:2021-01-19
  • Embryo Genetics
    Genes (IF 3.759) Pub Date : 2021-01-19
    Carmen Rubio; Carlos Simón

    Advances in embryo and reproductive genetics have influenced clinical approaches to overcome infertility. Since the 1990s, many attempts have been made to decipher the genetic causes of infertility and to understand the role of chromosome aneuploidies in embryo potential. At the embryo stage, preimplantation genetic testing for chromosomal abnormalities and genetic disorders has offered many couples

    更新日期:2021-01-19
  • Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population
    Genes (IF 3.759) Pub Date : 2021-01-19
    Donglin Ruan; Zhanwei Zhuang; Rongrong Ding; Yibin Qiu; Shenping Zhou; Jie Wu; Cineng Xu; Linjun Hong; Sixiu Huang; Enqin Zheng; Gengyuan Cai; Zhenfang Wu; Jie Yang

    Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF)

    更新日期:2021-01-19
  • A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity
    Genes (IF 3.759) Pub Date : 2021-01-19
    Mingji Lu; Rolf Daniel

    Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified

    更新日期:2021-01-19
  • The Desmin (DES) Mutation p.A337P Is Associated with Left-Ventricular Non-Compaction Cardiomyopathy
    Genes (IF 3.759) Pub Date : 2021-01-19
    Olga Kulikova; Andreas Brodehl; Anna Kiseleva; Roman Myasnikov; Alexey Meshkov; Caroline Stanasiuk; Anna Gärtner; Mikhail Divashuk; Evgeniia Sotnikova; Sergey Koretskiy; Maria Kharlap; Viktoria Kozlova; Elena Mershina; Polina Pilus; Valentin Sinitsyn; Hendrik Milting; Sergey Boytsov; Oxana Drapkina

    Here, we present a small Russian family, where the index patient received a diagnosis of left-ventricular non-compaction cardiomyopathy (LVNC) in combination with a skeletal myopathy. Clinical follow-up analysis revealed a LVNC phenotype also in her son. Therefore, we applied a broad next-generation sequencing gene panel approach for the identification of the underlying mutation. Interestingly, DES-p

    更新日期:2021-01-19
  • Overexpression of Activated AMPK in the Anopheles stephensi Midgut Impacts Mosquito Metabolism, Reproduction and Plasmodium Resistance
    Genes (IF 3.759) Pub Date : 2021-01-19
    Chioma Oringanje; Lillian R. Delacruz; Yunan Han; Shirley Luckhart; Michael A. Riehle

    Mitochondrial integrity and homeostasis in the midgut are key factors controlling mosquito fitness and anti-pathogen resistance. Targeting genes that regulate mitochondrial dynamics represents a potential strategy for limiting mosquito-borne diseases. AMP-activated protein kinase (AMPK) is a key cellular energy sensor found in nearly all eukaryotic cells. When activated, AMPK inhibits anabolic pathways

    更新日期:2021-01-19
  • Satellite DNA in Neotropical Deer Species
    Genes (IF 3.759) Pub Date : 2021-01-19
    Miluse Vozdova; Svatava Kubickova; Natália Martínková; David Javier Galindo; Agda Maria Bernegossi; Halina Cernohorska; Dita Kadlcikova; Petra Musilová; Jose Mauricio Duarte; Jiri Rubes

    The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV

    更新日期:2021-01-19
  • Identification of Potential Risk Genes and the Immune Landscape of Idiopathic Pulmonary Arterial Hypertension via Microarray Gene Expression Dataset Reanalysis
    Genes (IF 3.759) Pub Date : 2021-01-19
    Jing Xu; Yicheng Yang; Yuejin Yang; Changming Xiong

    Gene dysfunction and immune cell infiltration play an essential role in the pathogenesis of idiopathic pulmonary arterial hypertension (IPAH). We aimed to investigate the immune landscape and novel differentially expressed genes (DEGs) of IPAH. In addition, potential druggable molecular targets for IPAH were also explored. In this study, the GSE117261 dataset was reanalyzed to explore the immune landscape

    更新日期:2021-01-19
  • Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)
    Genes (IF 3.759) Pub Date : 2021-01-19
    Alessio Iannucci; Alexey I. Makunin; Artem P. Lisachov; Claudio Ciofi; Roscoe Stanyon; Marta Svartman; Vladimir A. Trifonov

    The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic

    更新日期:2021-01-19
  • Suprabasin—A Review
    Genes (IF 3.759) Pub Date : 2021-01-18
    Miroslav Pribyl; Zdenek Hodny; Iva Kubikova

    Among the ~22,000 human genes, very few remain that have unknown functions. One such example is suprabasin (SBSN). Originally described as a component of the cornified envelope, the function of stratified epithelia-expressed SBSN is unknown. Both the lack of knowledge about the gene role under physiological conditions and the emerging link of SBSN to various human diseases, including cancer, attract

    更新日期:2021-01-18
  • Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir
    Genes (IF 3.759) Pub Date : 2021-01-18
    Amanda R. De La Torre; Benjamin Wilhite; Daniela Puiu; John Bradley St. Clair; Marc W. Crepeau; Steven L. Salzberg; Charles H. Langley; Brian Allen; David B. Neale

    Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of

    更新日期:2021-01-18
  • Defining the Rhizobium leguminosarum Species Complex
    Genes (IF 3.759) Pub Date : 2021-01-18
    J. Peter W. Young; Sara Moeskjær; Alexey Afonin; Praveen Rahi; Marta Maluk; Euan K. James; Maria Izabel A. Cavassim; M. Harun-or Rashid; Aregu Amsalu Aserse; Benjamin J. Perry; En Tao Wang; Encarna Velázquez; Evgeny E. Andronov; Anastasia Tampakaki; José David Flores Félix; Raúl Rivas González; Sameh H. Youseif; Marc Lepetit; Stéphane Boivin; Beatriz Jorrin; Gregory J. Kenicer; Álvaro Peix; Michael

    Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based

    更新日期:2021-01-18
  • Litter Size of Sheep (Ovis aries): Inbreeding Depression and Homozygous Regions
    Genes (IF 3.759) Pub Date : 2021-01-18
    Lin Tao; Xiaoyun He; Xiangyu Wang; Ran Di; Mingxing Chu

    Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns

    更新日期:2021-01-18
  • Hereditary Optic Neuropathies: Induced Pluripotent Stem Cell-Based 2D/3D Approaches
    Genes (IF 3.759) Pub Date : 2021-01-18
    Marta García-López; Joaquín Arenas; M. Esther Gallardo

    Inherited optic neuropathies share visual impairment due to the degeneration of retinal ganglion cells (RGCs) as the hallmark of the disease. This group of genetic disorders are caused by mutations in nuclear genes or in the mitochondrial DNA (mtDNA). An impaired mitochondrial function is the underlying mechanism of these diseases. Currently, optic neuropathies lack an effective treatment, and the

    更新日期:2021-01-18