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Potential recurrence of COVID-19 in a healthcare professional: SARS-CoV-2 genome sequencing confirms contagiousness after re-positivity.

Int J Infect Dis 2021 Sep 18. Epub 2021 Sep 18.

Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.

Re-positivity of SARS-CoV-2 tests is widely reported, raising discussion about guidance for patient discharge and ending isolation. The unsuccessful recovery of replication-competent virus and/or absence of secondary cases has suggested that re-positive patients are not contagious. We report SARS-CoV-2 re-positivity in a healthcare professional 16 days after three negative tests, with viral genome sequencing supporting contagiousness leading to secondary cases. Read More

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September 2021

Asymmetric viability in reciprocal crosses of zebrafish Danio rerio and pearl danio D. albolineatus.

J Fish Biol 2021 Sep 21. Epub 2021 Sep 21.

School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, USA.

Interspecies hybrids have long been studied to further understanding of speciation. Reciprocal crosses sometimes have asymmetric viability - a phenomenon termed "Darwin's corollary to Haldane's rule". It has been proposed that this asymmetry is caused by Dobzhansky-Muller incompatibilities between nuclear genes and cytoplasmic factors (e. Read More

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September 2021

First report of bean common mosaic virus infecting heavenly bamboo (Nandina domestica) in China.

Plant Dis 2021 Sep 21. Epub 2021 Sep 21.

Zhejiang A and F University, 12627, College of Forestry and Biotechnology, Hangzhou, Zhejiang, China;

Heavenly bamboo (Nandina domestica) is an evergreen ornamental plant with worldwide distribution. In May 2018, seven out of twenty N. domestica plants showing virus-like symptoms, such as yellow mosaic and curling, were observed in Lin'an, Zhejiang province. Read More

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September 2021

Strawberry, a new natural host of Brassica yellows virus in China.

Plant Dis 2021 Sep 21. Epub 2021 Sep 21.

China Agricultural University College of Horticulture, 534806, Department of Fruit Science, Beijing, China;

Brassica yellows virus (BrYV; genus Polerovirus, family Solemoviridae) has an icosahedral spherical virion with a positive-sense single-stranded RNA genome and it is distinguished from turnip yellows virus (TuYV) based on differences in ORF0 and ORF5 (Xiang et al., 2011). To investigate the occurrence and distribution of viruses infecting strawberry (Fragaria ananassa) in the main production areas in China, a survey of nine greenhouses (667 m2 each) was conducted in the cities of Yantai and Beijing, China in August 2020. Read More

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September 2021

A prion accelerates proliferation at the expense of lifespan.

Elife 2021 Sep 15;10. Epub 2021 Sep 15.

Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States.

In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Read More

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September 2021

Biallelic variants in YRDC cause a developmental disorder with progeroid features.

Hum Genet 2021 Sep 20. Epub 2021 Sep 20.

Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.

The highly conserved YrdC domain-containing protein (YRDC) interacts with the well-described KEOPS complex, regulating specific tRNA modifications to ensure accurate protein synthesis. Previous studies have linked the KEOPS complex to a role in promoting telomere maintenance and controlling genome integrity. Here, we report on a newborn with a severe neonatal progeroid phenotype including generalized loss of subcutaneous fat, microcephaly, growth retardation, wrinkled skin, renal failure, and premature death at the age of 12 days. Read More

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September 2021

Presence of male mitochondria in somatic tissues and their functional importance at the whole animal level in the marine bivalve Arctica islandica.

Commun Biol 2021 Sep 20;4(1):1104. Epub 2021 Sep 20.

Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany.

Metazoans normally possess a single lineage of mitochondria inherited from the mother (♀-type mitochondria) while paternal mitochondria are absent or eliminated in fertilized eggs. In doubly uniparental inheritance (DUI), which is specific to the bivalve clade including the ocean quahog, Arctica islandica, ♂-type mitochondria are retained in male gonads and, in a few species, small proportions of ♂-type mitochondria co-exist with ♀-type in somatic tissues. To the best of our knowledge, we report, for the first time in metazoan, the natural occurrence of male and female individuals with exclusively ♂-type mitochondria in somatic tissues of the bivalve A. Read More

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September 2021

Diagnostic utility of whole-genome sequencing for nephronophthisis.

NPJ Genom Med 2020 Sep 21;5(1):38. Epub 2020 Sep 21.

Service de Toxicologie et Génopathies, CHU Lille, F-59000, Lille, France.

Next-generation sequencing has revolutionized the molecular diagnosis of individuals affected by genetic kidney diseases. Indeed, rapid genetic testing in individuals with suspected inherited nephropathy has not only important implications for diagnosis and prognosis but also for genetic counseling. Nephronophthisis (NPHP) and related syndromes, a leading cause of end-stage renal failure, are autosomal recessive disorders characterized by the variable presentation and considerable locus heterogeneity with more than 90 genes described as single-gene causes. Read More

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September 2020

A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant.

Hortic Res 2020 Sep 21;7(1):153. Epub 2020 Sep 21.

Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021, China.

Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. Read More

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September 2020

Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy.

Proc Natl Acad Sci U S A 2021 Sep;118(39)

MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, 100084 Beijing, China;

Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of the bat innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the viral tolerance in bats. Here we report the establishment of genome-wide RNA interference (RNAi) and CRISPR libraries for the screening of the model megabat, We used the complementary RNAi and CRISPR libraries to interrogate cells for infection with two different viruses: mumps virus and influenza A virus, respectively. Read More

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September 2021

Clinical application of fetal genome-wide sequencing during pregnancy: position statement of the Canadian College of Medical Geneticists.

J Med Genet 2021 Sep 20. Epub 2021 Sep 20.

Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

Purpose And Scope: The aim of this position statement is to provide recommendations for Canadian healthcare professionals regarding the use of genome-wide sequencing (GWS) in the context of diagnostic testing of the fetus during pregnancy. This statement was developed to facilitate clinical translation of GWS as a prenatal diagnostic test and the development of best practices in Canada, but the applicability of this document is broader and aims to help professionals in other healthcare systems.

Methods Of Statement Development: A multidisciplinary group was assembled to review existing literature on fetal GWS for genetic diagnosis in the context of suspected monogenic diseases and to make recommendations relevant to the Canadian context. Read More

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September 2021

Pivotal Roles for Ribonucleases in Streptococcus pneumoniae Pathogenesis.

mBio 2021 Sep 21:e0238521. Epub 2021 Sep 21.

Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.

RNases perform indispensable functions in regulating gene expression in many bacterial pathogens by processing and/or degrading RNAs. Despite the pivotal role of RNases in regulating bacterial virulence factors, the functions of RNases have not yet been studied in the major human respiratory pathogen Streptococcus pneumoniae (pneumococcus). Here, we sought to determine the impact of two conserved RNases, the endoribonuclease RNase Y and exoribonuclease polynucleotide phosphorylase (PNPase), on the physiology and virulence of S. Read More

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September 2021

CK2 Phosphorylation of Human Papillomavirus 16 E2 on Serine 23 Promotes Interaction with TopBP1 and Is Critical for E2 Interaction with Mitotic Chromatin and the Viral Life Cycle.

mBio 2021 Sep 21:e0116321. Epub 2021 Sep 21.

Virginia Commonwealth Universitygrid.224260.0 (VCU), Philips Institute for Oral Health Research, School of Dentistry, Richmond, Virginia, USA.

During the human papillomavirus 16 (HPV16) life cycle, the E2 protein interacts with host factors to regulate viral transcription, replication, and genome segregation/retention. Our understanding of host partner proteins and their roles in E2 functions remains incomplete. Here we demonstrate that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1 and and that E2 is phosphorylated on this residue during the HPV16 life cycle. Read More

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September 2021

Metagenome-assembled genome (MAG) of Oceancaulis alexandrii NP7 isolated from Mediterranean Sea polluted marine sediments and its bioremediation potential.

G3 (Bethesda) 2021 Sep;11(9)

Stazione Zoologica Anton Dohrn, Istituto Nationale di Biologia, Ecologia e Biotecnologie marine, 80121 Naples, Italy.

Oceanicaulis alexandrii strain NP7 is a marine bacterium which belongs to the Hyphomonadaceae family and was isolated from sediments highly contaminated with metals and polycyclic aromatic hydrocarbons released for decades by industrial activities in the Gulf of Naples (Mediterranean Sea). Here, we report the partial genome sequence and annotation of O. alexandrii strain NP7 that contains a chromosome of 2,954,327 bp and encodes for 2914 predicted coding sequences (CDSs) and 44 RNA-encoding genes. Read More

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September 2021

Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

Am J Trop Med Hyg 2021 Sep 20. Epub 2021 Sep 20.

Global Health Research Complex, Division of Research, Texas A&M University, College Station, Texas.

To better understand the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant lineage distribution in a college campus population, we carried out viral genome surveillance over a 7-week period from January to March 2021. Among the sequences were three novel viral variants: BV-1 with a B.1. Read More

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September 2021

Label-free and reagentless electrochemical genosensor based on graphene acid for meat adulteration detection.

Biosens Bioelectron 2021 Sep 12;195:113628. Epub 2021 Sep 12.

Catalan Institute of Nanoscience and Nanotechnology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain. Electronic address:

With the increased demand for beef in emerging markets, the development of quality-control diagnostics that are fast, cheap and easy to handle is essential. Especially where beef must be free from pork residues, due to religious, cultural or allergic reasons, the availability of such diagnostic tools is crucial. In this work, we report a label-free impedimetric genosensor for the sensitive detection of pork residues in meat, by leveraging the biosensing capabilities of graphene acid - a densely and selectively functionalized graphene derivative. Read More

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September 2021

Whole-genome sequencing reveals large ATP8B1 deletion / duplications as "second mutations" missed by exome-based sequencing.

J Mol Diagn 2021 Sep 17. Epub 2021 Sep 17.

The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China. Electronic address:

Progressive familial intrahepatic cholestasis type 1 (PFIC1) results from biallelic pathogenic variants in ATP8B1. This study sought second pathogenic variants in ATP8B1 by whole-genome sequencing (WGS) in 4 unrelated low-GGT cholestasis patients in whom clinical suspicion of PFIC1 was high and gene-panel or Sanger sequencing had identified only one pathogenic variant in ATP8B1. Sanger sequencing confirmed WGS findings and determined the origin of each variant. Read More

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September 2021

Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of pv. isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000.

Phytopathology 2021 Sep 20. Epub 2021 Sep 20.

Agriculture and Agri-Food Canada Central Experimental Farm, 98674, Ottawa, Ontario, Canada;

pv. is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Read More

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September 2021

On the weak binding and spectroscopic signature of SARS-CoV-2 nsp14 interaction with RNA.

Chembiochem 2021 Sep 20. Epub 2021 Sep 20.

University of São Paulo USP Institute of Chemistry of São Carlos IQSC, Department of Physical Chemistry DFQ, Av Trabalhador São-carlense 400, 13560-970, São carlos, BRAZIL.

The SARS-CoV-2 non-structural protein 14 (nsp14), known as exoribonuclease is encoded from the large polyprotein of viral genome and is a major constituent of the transcription replication complex (TRC) machinery of the viral RNA synthesis. This protein is highly conserved among the coronaviruses and is a potential target for the development of a therapeutic drug. Here, we report the SARS-CoV-2 nsp14 expression, show its structural characterization, and ss-RNA exonuclease activity through vibrational and electronic spectroscopies. Read More

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September 2021

Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.

Mol Biol Evol 2021 Sep 20. Epub 2021 Sep 20.

Department of Biology, Lund University, Ecology Building, Lund, SE-223 62, Sweden.

How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Myr ago formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Read More

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September 2021

Case Report and Genomic Analysis of Cefiderocol-Resistant Escherichia coli Clinical Isolates.

Am J Clin Pathol 2021 Sep 20. Epub 2021 Sep 20.

Department of Pathology and Laboratory Medicine, Los Angeles, CA, USA.

Objectives: Cefiderocol is a novel siderophore cephalosporin with in vitro activity against multidrug-resistant (MDR), gram-negative bacteria and intrinsic structural stability to all classes of carbapenemases. We sought to identify gene variants that could affect the mechanism of action (MOA) of cefiderocol.

Methods: We report a case of bacteremia in a liver transplant candidate with a strain of carbapenem-resistant Escherichia coli that was found to be resistant to cefiderocol despite no prior treatment with this antimicrobial agent. Read More

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September 2021

Activation of Type I and Type II Interferon signaling in SARS-CoV-2-positive thyroid tissue of patients dying from COVID-19.

Thyroid 2021 Sep 19. Epub 2021 Sep 19.

University of Pisa, Department of Surgical, Medical, Molecular Pathology and Critical Area, Pisa, Italy;

Background: Thyroid dysfunctions have been reported after SARS-CoV-2 infection. However, the biological mechanisms behind these conditions remain unexplored. Herein, we report on changes of the immune transcriptome in autoptic thyroid tissues of people who have died from COVID-19. Read More

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September 2021

Single- and Two-Stage, Closed-Tube, Point-of-Care, Molecular Detection of SARS-CoV-2.

Anal Chem 2021 Sep 20. Epub 2021 Sep 20.

Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.

Short of a vaccine, frequent and rapid testing, preferably at home, is the most effective strategy to contain the COVID-19 pandemic. Herein, we report on single-stage and two-stage molecular diagnostic tests that can be carried out with simple or no instrumentation. Our single-stage amplification is reverse transcription-loop mediated isothermal amplification (RT-LAMP) with custom-designed primers targeting the ORF1ab and the N gene regions of the virus genome. Read More

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September 2021

Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay.

NAR Genom Bioinform 2021 Sep 16;3(3):lqab082. Epub 2021 Sep 16.

Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany.

To date, most reference genomes represent a mosaic consensus sequence in which the homologous chromosomes are collapsed into one sequence. This approach produces sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report an allele-specific genome assembly of the diploid parasite and reveal allelic variants affecting gene expression. Read More

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September 2021

Genomic stability at the coding regions of the multidrug transporter gene : insights into the development of alternative drug resistance mechanisms in human leukemia cells.

Cancer Drug Resist 2020 3;3:959-979. Epub 2020 Nov 3.

Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.

Aim: Despite considerable efforts to reverse clinical multidrug resistance (MDR), targeting the predominant multidrug transporter ABCB1/P-glycoprotein (P-gp) using small molecule inhibitors has been unsuccessful, possibly due to the emergence of alternative drug resistance mechanisms. However, the non-specific P-gp inhibitor cyclosporine (CsA) showed significant clinical benefits in patients with acute myeloid leukemia (AML), which likely represents the only proof-of-principle clinical trial using several generations of MDR inhibitors. Nevertheless, the mutational mechanisms that may underlie unsuccessful MDR modulation by CsA are not elucidated because of the absence of CsA-relevant cellular models. Read More

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November 2020

Tandem duplicate expression patterns are conserved between maize haplotypes of the -zein gene family.

Plant Direct 2021 Sep 14;5(9):e346. Epub 2021 Sep 14.

Department of Agronomy and Horticulture, Center for Plant Science Innovation University of Nebraska Lincoln Nebraska USA.

Tandem duplication gives rise to copy number variation and subsequent functional novelty among genes as well as diversity between individuals in a species. Functional novelty can result from either divergence in coding sequence or divergence in patterns of gene transcriptional regulation. Here, we investigate conservation and divergence of both gene sequence and gene regulation between the copies of the -zein gene family in maize inbreds B73 and W22. Read More

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September 2021

Tuberous sclerosis complex-lymphangioleiomyomatosis involving several visceral organs: A case report.

World J Clin Cases 2021 Aug;9(24):7085-7091

Department of Echocardiography, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.

Background: Lymphangioleiomyomatosis (LAM) is a rare cystic lung disease characterized by the proliferation, metastasis, and infiltration of smooth muscle cells in the lung and other tissues, which can be associated with tuberous sclerosis complex (TSC). The disorder of TSC has a variable expression, and there is great phenotypic variability.

Case Summary: A 32-year-old Chinese woman with a history of multiple renal angioleiomyolipoma presented with a productive cough persisting for over 2 wk. Read More

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Genomic Characterization of a Nalidixic Acid-Resistant Enteritidis Strain Causing Persistent Infections in Broiler Chickens.

Front Vet Sci 2021 1;8:725737. Epub 2021 Sep 1.

Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.

Virulent strains of subsp. serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Read More

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September 2021

Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia.

Iran J Microbiol 2021 Apr;13(2):145-155

Department of Biocatalyst, Centre for Bioindustrial Technology, Agency for Assessment and Application of Technology (BPPT), Laboratorium of Bioindustrial Technology, LAPTIAB BPPT, Puspiptek-Serpong, Tangerang Selatan, Indonesia.

Background And Objectives: In first May 2020, Indonesia has been successfully submitted the first three full-length sequence of SARS-CoV-2 to GISAID database. Until September 10, 2020, Indonesia had submitted 54 WGS. In this study, we have analyzed and annotated SARS-CoV-2 mutations in spike protein and main proteases. Read More

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