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An IL-1β homologue induced inflammation and antibacterial immune defense in Siberian sturgeon (Acipenser baeri).

Fish Shellfish Immunol 2021 Sep 16. Epub 2021 Sep 16.

Beijing Fisheries Research Institute & Beijing Key Laboratory of Fishery Biotechnology, Beijing, 100068, People's Republic of China; National Freshwater Fisheries Engineering Technology Research Center, Beijing, 100068, People's Republic of China. Electronic address:

Interleukin-1β is a key pro-inflammatory cytokine functioning in initiation of inflammatory responses against bacterial- and viral-infections. In the present study, a putative IL-1β counterpart was identified from Siberian sturgeon (Acipenser baeri) and designated as AbIL-1β. The Abil-1β cDNA sequence consists of 1130 bp with an open reading frame (ORF) of 585 bp, which encodes a 194 amino acid (aa) protein. Read More

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September 2021

Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses.

Front Genet 2021 30;12:714152. Epub 2021 Aug 30.

Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France.

There is growing evidence that peptides encoded by small open-reading frames (sORF or smORF) can fulfill various cellular functions and define a novel class regulatory molecules. To which extend transcripts encoding only smORF peptides compare with canonical protein-coding genes, yet remain poorly understood. In particular, little is known on whether and how smORF-encoding RNAs might need tightly regulated expression within a given tissue, at a given time during development. Read More

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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA strain 9-11.

Arch Virol 2021 Sep 15. Epub 2021 Sep 15.

State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.

The complete genome sequence of a double-stranded RNA (dsRNA) virus, Rhizoctonia solani dsRNA virus 11 (RsRV11), isolated from Rhizoctonia solani AG-1 IA strain 9-11 was determined. The RsRV11 genome is 9,555 bp in length and contains three conserved domains: structural maintenance of chromosomes (SMC) superfamily, phosphoribulokinase (PRK), and RNA-dependent RNA polymerase (RdRp). The RsRV11 genome has two non-overlapping open reading frames (ORFs). Read More

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September 2021

Novel anti-repression mechanism of H-NS proteins by a phage protein.

Nucleic Acids Res 2021 Sep 14. Epub 2021 Sep 14.

Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Read More

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September 2021

Cognitive maps of social features enable flexible inference in social networks.

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

Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, RI 02912;

In order to navigate a complex web of relationships, an individual must learn and represent the connections between people in a social network. However, the sheer size and complexity of the social world makes it impossible to acquire firsthand knowledge of all relations within a network, suggesting that people must make inferences about unobserved relationships to fill in the gaps. Across three studies ( = 328), we show that people can encode information about social features (e. Read More

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September 2021

Association of CD2AP neuronal deposits with Braak neurofibrillary stage in Alzheimer's disease.

Brain Pathol 2021 Sep 12:e13016. Epub 2021 Sep 12.

Neurovascular Research Laboratory, Vall d'Hebron Research Institute, Universitat Autonoma de Barcelona, Barcelona, Spain.

Genome-wide association studies have described several genes as genetic susceptibility loci for Alzheimer's disease (AD). Among them, CD2AP encodes CD2-associated protein, a scaffold protein implicated in dynamic actin remodeling and membrane trafficking during endocytosis and cytokinesis. Although a clear link between CD2AP defects and glomerular pathology has been described, little is known about the function of CD2AP in the brain. Read More

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September 2021

Characterization of a G protein α subunit encoded gene from the dimorphic fungus-Tremella fuciformis.

Antonie Van Leeuwenhoek 2021 Sep 12. Epub 2021 Sep 12.

College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.

Tremella fuciformis is a dimorphic fungus which can undertake the reversible transition between yeast and pseudohypha forms. G protein α subunit (Gα) carries different signals to regulate a variety of biological processes in eukaryotes, including fungal dimorphism. In this study, a novel Gα subunit encoded gene, TrGpa1, was firstly cloned from T. Read More

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September 2021

A variant ECE1 allele contributes to reduced pathogenicity of Candida albicans during vulvovaginal candidiasis.

PLoS Pathog 2021 Sep 10;17(9):e1009884. Epub 2021 Sep 10.

Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America.

Vulvovaginal candidiasis (VVC), caused primarily by the human fungal pathogen Candida albicans, results in significant quality-of-life issues for women worldwide. Candidalysin, a toxin derived from a polypeptide (Ece1p) encoded by the ECE1 gene, plays a crucial role in driving immunopathology at the vaginal mucosa. This study aimed to determine if expression and/or processing of Ece1p differs across C. Read More

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September 2021

Virulent Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria.

Front Microbiol 2021 24;12:706700. Epub 2021 Aug 24.

Department of Biochemistry, Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou, China.

Phage-host interactions are likely to have the most critical aspect of phage biology. Phages are the most abundant and ubiquitous infectious acellular entities in the biosphere, where their presence remains elusive. Here, the novel lytic bacteriophage, named MSK, was isolated from the lysed culture of C (phix174 host). Read More

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Myocilin-associated Glaucoma: A Historical Perspective and Recent Research Progress.

Mol Vis 2021 20;27:480-493. Epub 2021 Aug 20.

School of Biotechnology, Jawaharlal Nehru University (JNU), Delhi, India.

Glaucoma a debilitating disease, is globally the second most common kind of permanent blindness. Primary open-angle glaucoma (POAG) is its most prevalent form and is often linked with alterations in the myocilin gene (). encodes the myocilin protein, which is expressed throughout the body, but primarily in trabecular meshwork (TM) tissue in the eyes. Read More

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Complete genome sequence of a novel mitovirus from the phytopathogenic fungus Fusarium oxysporum.

Arch Virol 2021 Sep 8. Epub 2021 Sep 8.

Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China.

Fusarium oxysporum is a cosmopolitan plant pathogen that causes fusarium wilt and fusarium root rot in many economically important crops. There is still limited information about mycoviruses that infect F. oxysporum. Read More

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September 2021

Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers.

Front Cell Dev Biol 2021 12;9:703374. Epub 2021 Aug 12.

School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

Detection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Read More

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Complete genome sequence of camellia virus A, a tentative new member of the genus Waikavirus.

Arch Virol 2021 Sep 4. Epub 2021 Sep 4.

National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.

A new positive-strand RNA virus genome was discovered in Camellia japonica plants. The complete genome of the virus is 12,570 nt in size, excluding the poly(A) tail, and contains one large open reading frame (ORF1) and two small open reading frames (ORF2, ORF3). ORF1 and ORF2 are homologous to sequences of waikaviruses, while ORF3 has no relatives in the databases. Read More

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September 2021

Molecular Cloning, Functional and Biophysical Characterization of an Antimicrobial Peptide from Rhizosphere Soil.

Protein Pept Lett 2021 Sep 3. Epub 2021 Sep 3.

Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India.

Aim: This study was designed to screen and identify an antimicrobial peptide from rhizosphere soil. The study was further focused towards overexpression, purification and characterization of this antimicrobial peptide, and to functionally validate its efficiency and efficacy as an antimicrobial agent. Yet the study was further aimed at corroborating structural and functional studies using biophysical tools. Read More

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September 2021

[In silico cloning, expression and bioinformatics analysis of NtODB from common tobacco].

Sheng Wu Gong Cheng Xue Bao 2021 Aug;37(8):2836-2844

Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530001, Guangxi, China.

It has been reported that ODB genes play an important role in homologous recombination-directed DNA repair, suggesting their potential applications in plant breeding. To analyze the expression characteristics of tobacco NtODB gene, the cDNA sequence of NtODB was obtained using in silico cloning technique. The physicochemical properties, signal peptide, and advanced structures of the predicted protein were analyzed using bioinformatics tools. Read More

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Drug repurposing in COVID-19: A review with past, present and future.

Metabol Open 2021 Aug 26:100121. Epub 2021 Aug 26.

Dr. B R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, 110007, India.

The coronavirus SARS-CoV-2 which causes the COVID-19 disease is a global public health emergency. Coronavirus are single-stranded positive-sense RNA viruses and their genome size is approximately 30 kb, which encodes some important structural proteins. The interaction between viral Spike protein and ACE2 on the host cell surface is of significant interest since it initiates the infection process. Read More

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circ-EIF6 encodes EIF6-224aa to promote TNBC progression via stabilizing MYH9 and activating the Wnt/beta-catenin pathway.

Mol Ther 2021 Aug 25. Epub 2021 Aug 25.

Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China; Pathology Tissue Bank, Qilu Hospital of Shandong University, Ji'nan, Shandong, China; Research Institute of Breast Cancer, Shandong University, Ji'nan, Shandong, China. Electronic address:

The protein-coding ability of circular RNAs (circRNAs) has recently been a hot topic, but the expression and roles of protein-coding circRNAs in triple-negative breast cancer (TNBC) remain uncertain. By intersecting circRNA sequencing data from clinical samples and cell lines, we identified a circRNA, termed circ-EIF6, which predicted a poorer prognosis and correlated with clinicopathological characteristics in a cohort of TNBC patients. Functionally, we showed that circ-EIF6 promoted the proliferation and metastasis of TNBC cells in vitro and in vivo. Read More

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A ras-related nuclear protein Ran participates in the 20E signaling pathway and is essential for the growth and development of Locusta migratoria.

Pestic Biochem Physiol 2021 Oct 4;178:104945. Epub 2021 Aug 4.

Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China. Electronic address:

The small GTPase Ran is a member of the Ras superfamily of small GTP-binding proteins, which plays a key role in the translocation of RNA and proteins through the nuclear pore complex. In this study, the full-length cDNA sequence of LmRan gene was obtained, which consists of 648-nucleotides open reading frame (ORF) and encodes 215 amino acids. RT-qPCR results revealed that LmRan was expressed in all developmental days and tissues investigated. Read More

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October 2021

Integrated Phenotypic-Genotypic Analysis of   from Different Niches.

Foods 2021 Jul 25;10(8). Epub 2021 Jul 25.

State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.

Increasing attention has been paid to the potential probiotic effects of . To explore the genetic diversity of , 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of   were 1. Read More

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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia.

PLoS Negl Trop Dis 2021 Aug 26;15(8):e0009665. Epub 2021 Aug 26.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Read More

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Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from SCSIO 5802.

Mar Drugs 2021 Jul 31;19(8). Epub 2021 Jul 31.

CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.

We have previously shown deep-sea-derived SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10--HSAF () and a new compound, koyanamide A (), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Read More

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DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A in human vulnerable atherosclerotic plaque.

Clin Epigenetics 2021 Aug 21;13(1):161. Epub 2021 Aug 21.

Department of Cardiology, China-Japan Friendship Hospital, Beijing, China.

Background: Atherosclerotic plaque vulnerability is a key feature of atheroprogression and precipitating acute cardiovascular events. Although the pivotal role of epigenetic regulation in atherosclerotic plaque destabilization is being recognized, the DNA methylation profile and its potential role in driving the progression and destabilization of atherosclerotic cardiovascular disease remains largely unknown. We conducted a genome-wide analysis to identify differentially methylated genes in vulnerable and non-vulnerable atherosclerotic lesions to understand more about pathogenesis. Read More

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The oldest co-opted gag gene of a human endogenous retrovirus shows placenta-specific expression and is upregulated in diffuse large B-cell lymphomas.

Mol Biol Evol 2021 Aug 19. Epub 2021 Aug 19.

Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.

Vertebrate genomes contain endogenous retroviruses (ERVs) that represent remnants of past germline infections by ancient retroviruses. Despite comprising 8% of the human genome, the human ERVs (HERVs) do not encode a replication competent retrovirus. However, some HERV genes have been co-opted to serve host functions, most notably the viral envelope-derived syncytins involved in placentation. Read More

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Integrated Surveillance for Antimicrobial Resistance in From Clinical and Retail Meat Sources Reveals Genetically Related Isolates Harboring Quinolone- and Ceftriaxone-Resistant Determinants.

Open Forum Infect Dis 2021 Aug 26;8(8):ofab213. Epub 2021 Apr 26.

Pennsylvania Veterinary Laboratory, Harrisburg, Pennsylvania, USA.

Background: Antimicrobial resistance in foodborne pathogens, including nontyphoidal (NTS), is a public health concern. Pennsylvania conducts integrated surveillance for antimicrobial resistance in NTS from human and animal sources.

Methods: During 2015-2017, clinical laboratories submitted 4478 NTS isolates from humans and 96 isolates were found in 2520 retail meat samples. Read More

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Autophagy impairment by African swine fever virus.

J Gen Virol 2021 08;102(8)

The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.

African swine fever is a devastating disease of domestic swine and wild boar caused by a large double-stranded DNA virus that encodes for more than 150 open reading frames. There is no licensed vaccine for the disease and the most promising current candidates are modified live viruses that have been attenuated by deletion of virulence factors. Like many viruses African swine fever virus significantly alters the host cell machinery to benefit its replication and viral genes that modify host pathways represent promising targets for development of gene deleted vaccines. Read More

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Hepatitis E Virus RNA-Dependent RNA Polymerase is Involved in RNA Replication and Infectious Particle Production.

Hepatology 2021 Aug 13. Epub 2021 Aug 13.

Division of Gastroenterology and Hepatology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

Background And Aims: Hepatitis E virus (HEV) is one of the most common causes of acute hepatitis worldwide. Its positive-strand RNA genome encodes three open reading frames (ORF). ORF1 is translated into a large protein composed of multiple domains and known as the viral replicase. Read More

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Characterization of a novel Tombusviridae species isolated from Paris polyphylla var. yunnanensis.

Arch Virol 2021 Aug 13. Epub 2021 Aug 13.

Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.

A novel virus, Paris virus 2 (ParV2), was isolated from diseased Paris polyphylla var. yunnanensis, and its complete genome sequence was determined and analyzed. ParV2 is a positive-sense single-stranded RNA (+ssRNA) virus with a genome size of 4,118 nucleotides. Read More

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Transcriptional regulation of 9 by cohesin-mediated chromosome tethering in human granulosa cells.

Biochem Biophys Rep 2021 Sep 24;27:101086. Epub 2021 Jul 24.

Fujita Health University School of Medicine, Toyoake, Aichi, 470-1192, Japan.

Human spans a region of chromosome 15 of approximately 130 kb and encodes aromatase, an enzyme required for estrogen synthesis. In the human granulosa cell-line KGN, there are seven open chromatin regions within the locus. In this study, we demonstrate that two of these regions ~40 kb upstream and ~15 kb downstream of the promoter are cohesin-loading sites, physically interacting with the promoter to negatively and positively regulate transcription, respectively. Read More

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September 2021

A ubiquitin-like protein encoded by the "noncoding" RNA TINCR promotes keratinocyte proliferation and wound healing.

PLoS Genet 2021 Aug 5;17(8):e1009686. Epub 2021 Aug 5.

Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

Although long noncoding RNAs (lncRNAs) are transcripts that do not encode proteins by definition, some lncRNAs actually contain small open reading frames that are translated. TINCR (terminal differentiation-induced ncRNA) has been recognized as a lncRNA that contributes to keratinocyte differentiation. However, we here show that TINCR encodes a ubiquitin-like protein that is well conserved among species and whose expression was confirmed by the generation of mice harboring a FLAG epitope tag sequence in the endogenous open reading frame as well as by targeted proteomics. Read More

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Shifts in Estimated Preferred Directions During Simulated BMI Experiments With No Adaptation.

Front Syst Neurosci 2021 19;15:677688. Epub 2021 Jul 19.

Brain-Computer Interfaces for Rehabilitation Laboratory, Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.

Experiments with brain-machine interfaces (BMIs) reveal that the estimated preferred direction (EPD) of cortical motor units may shift following the transition to brain control. However, the cause of those shifts, and in particular, whether they imply neural adaptation, is an open issue. Here we address this question in simulations and theoretical analysis. Read More

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