841 results match your criteria stretches conserved

Mapping of sequences in the 5' region and 3' UTR of tomato ringspot virus RNA2 that facilitate cap-independent translation of reporter transcripts in vitro.

PLoS One 2021 9;16(4):e0249928. Epub 2021 Apr 9.

Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada.

Tomato ringspot virus (ToRSV, genus Nepovirus, family Secoviridae, order Picornavirales) is a bipartite positive-strand RNA virus, with each RNA encoding one large polyprotein. ToRSV RNAs are linked to a 5'-viral genome-linked protein (VPg) and have a 3' polyA tail, suggesting a non-canonical cap-independent translation initiation mechanism. The 3' untranslated regions (UTRs) of RNA1 and RNA2 are unusually long (~1. Read More

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Distinct intramolecular interactions regulate autoinhibition of vinculin binding in αT-catenin and αE-catenin.

J Biol Chem 2021 Mar 23:100582. Epub 2021 Mar 23.

Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261. Electronic address:

α-Catenin binds directly to β-catenin and connects the cadherin-catenin complex to the actin cytoskeleton. Tension regulates α-catenin conformation. Actomyosin-generated force stretches the middle(M)-region to relieve autoinhibition and reveal a binding site for the actin-binding protein vinculin. Read More

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An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans.

PLoS Biol 2021 Mar 15;19(3):e3000957. Epub 2021 Mar 15.

David Geffen School of Medicine, University of California (UCLA), Los Angeles, California, United States of America.

A forward genetic screening approach identified orf19.2500 as a gene controlling Candida albicans biofilm dispersal and biofilm detachment. Three-dimensional (3D) protein modeling and bioinformatics revealed that orf19. Read More

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Diverse telomeres in trypanosomatids.

Parasitology 2021 Feb 22:1-17. Epub 2021 Feb 22.

Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00Ostrava, Czech Republic.

Telomeres are the ends of linear eukaryotic chromosomes facilitating the resolution of the ‘end replication and protection’ problems, associated with linearity. At the nucleotide level, telomeres typically represent stretches of tandemly arranged telomeric repeats, which vary in length and sequence among different groups of organisms. Recently, a composition of the telomere-associated protein complex has been scrutinized in Trypanosoma brucei. Read More

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February 2021

Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3' CITE.

J Virol 2021 04 12;95(9). Epub 2021 Apr 12.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA

(OPMV) is a recently discovered umbravirus in the family OPMV has a plus-sense genomic RNA (gRNA) of 4,241 nucleotides (nt) from which replication protein p35 and p35 extension product p98, the RNA-dependent RNA polymerase (RdRp), are expressed. Movement proteins p27 (long distance) and p28 (cell to cell) are expressed from a 1,440-nt subgenomic RNA (sgRNA2). A highly conserved structure was identified just upstream from the sgRNA2 transcription start site in all umbraviruses, which includes a carmovirus consensus sequence, denoting generation by an RdRp-mediated mechanism. Read More

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Prediction of putative regulatory elements in the subgenomic promoters of cucumber green mottle mosaic virus and their interactions with the RNA dependent RNA polymerase domain.

Virusdisease 2020 Dec 5;31(4):503-516. Epub 2020 Dec 5.

Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India.

Characterization of the subgenomic RNA (sgRNA) promoter of many plant viruses is important to understand the expression of downstream genes and also to configure their genome into a suitable virus gene-vector system. Cucumber green mottle mosaic virus (CGMMV, genus ) is one of the RNA viruses, which is extensively being exploited as the suitable gene silencing and protein expression vector. Even though, characters of the sgRNA promoters (SGPs) of CGMMV are yet to be addressed. Read More

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December 2020

Genome Organization of a New Double-Stranded RNA LA Helper Virus From Wine Killer Yeast as Compared With Its Counterparts.

Front Microbiol 2020 23;11:593846. Epub 2020 Nov 23.

Departamento de Ciencias Biomédicas (Área de Microbiología), Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain.

Wine killer yeasts such as killer strains of and contain helper large-size (4.6 kb) dsRNA viruses (V-LA) required for the stable maintenance and replication of killer medium-size dsRNA viruses (V-M) which bear the genes that encode for the killer toxin. The genome of the new V-LA dsRNA from the Kbarr1 killer yeast (TdV-LAbarr1) was characterized by high-throughput sequencing (HTS). Read More

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November 2020

A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference.

Mol Biol Evol 2021 04;38(4):1641-1652

Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.

Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. Read More

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Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2.

bioRxiv 2020 Dec 1. Epub 2020 Dec 1.

Severe acute respiratory syndrome (SARS) and novel coronavirus disease (COVID-19) are caused by two closely related beta-coronaviruses, SARS-CoV and SARS-CoV-2, respectively. The envelopes surrounding these viruses are decorated with spike proteins, whose receptor binding domains (RBDs) initiate invasion by binding to the human angiotensin-converting enzyme 2 (ACE2). Subtle changes at the interface with ACE2 seem to be responsible for the enhanced affinity for the receptor of the SARS-CoV-2 RBD compared to SARS-CoV RBD. Read More

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December 2020

The Cyclically Seasonal Inversion O Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes.

Front Genet 2020 9;11:565836. Epub 2020 Oct 9.

Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain.

Chromosome inversions are important contributors to standing genetic variation in . Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. Read More

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October 2020

Spatial constraints on chromosomes are instrumental to meiotic pairing.

J Cell Sci 2020 11 30;133(22). Epub 2020 Nov 30.

Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria

In most eukaryotes, the meiotic chromosomal bouquet (comprising clustered chromosome ends) provides an ordered chromosome arrangement that facilitates pairing and recombination between homologous chromosomes. In the protist , the meiotic prophase nucleus stretches enormously, and chromosomes assume a bouquet-like arrangement in which telomeres and centromeres are attached to opposite poles of the nucleus. We have identified and characterized three meiosis-specific genes [meiotic nuclear elongation 1-3 ()] that control nuclear elongation, and centromere and telomere clustering. Read More

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November 2020

Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps.

Genetics 2020 10 26;216(2):499-519. Epub 2020 Aug 26.

Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514

It is increasingly evident that natural selection plays a prominent role in shaping patterns of diversity across the genome. The most commonly studied modes of natural selection are positive selection and negative selection, which refer to directional selection for and against derived mutations, respectively. Positive selection can result in hitchhiking events, in which a beneficial allele rapidly replaces all others in the population, creating a valley of diversity around the selected site along with characteristic skews in allele frequencies and linkage disequilibrium among linked neutral polymorphisms. Read More

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October 2020

The First Genetic Map for a Psoraleoid Legume () Reveals Highly Conserved Synteny with Phaseoloid Legumes.

Plants (Basel) 2020 Jul 31;9(8). Epub 2020 Jul 31.

Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.

We present the first genetic map of tedera ( (L.) C.H. Read More

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Diversity and genome mapping assessment of disordered and functional domains in trypanosomatids.

J Proteomics 2020 09 25;227:103919. Epub 2020 Jul 25.

Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil; Programa de Pós-graduação em Ciências da Saúde, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil; Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil. Electronic address:

The proteins that have structural disorder exemplify a class of proteins which is part of a new frontier in structural biology that demands a new understanding of the paradigm of structure/function correlations. In order to address the location, relative distances and the functional/structural correlation between disordered and conserved domains, consensus disordered predictions were mapped together with CDD domains in Leishmania braziliensis M2904, Leishmania infantum JPCM5, Trypanosoma cruzi CL-Brener Esmeraldo-like, Trypanosoma cruzi Dm28c, Trypanosoma cruzi Sylvio X10, Blechomonas ayalai B08-376 and Paratrypanosoma confusum CUL13 predicted proteomes. Our results depicts the role of protein disorder in key aspects of parasites biology highlighting: a) statistical significant association between genome structural location of protein disordered consensus stretches and functional domains; b) that disordered protein stretches appear in greater percentage at upstream or downstream position of the predicted domain; c) a possible role of structural disorder in several gene expression, control points that includes but are not limited to: i) protein folding; ii) protein transport and degradation; and iii) protein modification. Read More

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September 2020

New insights into no-go, non-stop and nonsense-mediated mRNA decay complexes.

Curr Opin Struct Biol 2020 12 17;65:110-118. Epub 2020 Jul 17.

University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom. Electronic address:

Eukaryotes possess a variety of translational control mechanisms which function in the surveillance of mRNAs, discriminating between normal and aberrant translation elongation and termination, triggering mRNA decay. The three major evolutionarily conserved eukaryotic pathways are No-Go, Non-Stop and Nonsense-Mediated mRNA Decay. Recent findings suggest that stalling of the ribosome, due to mRNA secondary structure or translation into poly(A)-stretches, leads to ribosome collisions which are detected by No-Go/Non-Stop mRNA decay factors. Read More

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December 2020

Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens.

Infect Genet Evol 2020 Oct 27;84:104382. Epub 2020 May 27.

Viral Immunology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address:

The 2019 novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak has caused a large number of deaths, with thousands of confirmed cases worldwide. The present study followed computational approaches to identify B- and T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. We identified 24 peptide stretches on the SARS-CoV-2 S protein that are well conserved among the reported strains. Read More

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October 2020

Bacterial lyso-form lipoproteins are synthesized via an intramolecular acyl chain migration.

J Biol Chem 2020 07 29;295(30):10195-10211. Epub 2020 May 29.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA

All bacterial lipoproteins share a variably acylated N-terminal cysteine residue. Gram-negative bacterial lipoproteins are triacylated with a thioether-linked diacylglycerol moiety and an -acyl chain. The latter is transferred from a membrane phospholipid donor to the α-amino terminus by the enzyme lipoprotein -acyltransferase (Lnt), using an active-site cysteine thioester covalent intermediate. Read More

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Molecular evolution of the proopiomelanocortin system in Barn owl species.

PLoS One 2020 5;15(5):e0231163. Epub 2020 May 5.

Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.

Examination of genetic polymorphisms in outbred wild-living species provides insights into the evolution of complex systems. In higher vertebrates, the proopiomelanocortin (POMC) precursor gives rise to α-, β-, and γ-melanocyte-stimulating hormones (MSH), which are involved in numerous physiological aspects. Genetic defects in POMC are linked to metabolic disorders in humans and animals. Read More

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Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins.

Sci Rep 2020 04 8;10(1):6040. Epub 2020 Apr 8.

Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India.

Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of N-linked glycosylations or N-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. Read More

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Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs.

BMC Genomics 2020 Mar 30;21(1):268. Epub 2020 Mar 30.

State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Background: Polydactyly is one of the most common congenital limb dysplasia in many animal species. Although preaxial polydactyly (PPD) has been comprehensively studied in humans as a common abnormality, the genetic variations in other animal species have not been fully understood. Herein, we focused on the pig, as an even-toed ungulate mammal model with its unique advantages in medical and genetic researches, two PPD families consisting of four affected and 20 normal individuals were sequenced. Read More

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Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation.

J Mol Biol 2020 03 24;432(7):2271-2288. Epub 2020 Feb 24.

Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA. Electronic address:

R-loops are a prevalent class of non-B DNA structures that have been associated with both positive and negative cellular outcomes. DNA:RNA immunoprecipitation (DRIP) approaches based on the anti-DNA:RNA hybrid S9.6 antibody revealed that R-loops form dynamically over conserved genic hotspots. Read More

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A willow sex chromosome reveals convergent evolution of complex palindromic repeats.

Genome Biol 2020 02 14;21(1):38. Epub 2020 Feb 14.

Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.

Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Read More

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February 2020

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods.

J Vis Exp 2019 12 21(154). Epub 2019 Dec 21.

United States Naval Research Laboratory;

Alphaviral enzymes are synthesized in a single polypeptide. The nonstructural polyprotein (nsP) is processed by its nsP2 cysteine protease to produce active enzymes essential for viral replication. Viral proteases are highly specific and recognize conserved cleavage site motif sequences (~6-8 amino acids). Read More

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December 2019

An Engineered Biomimetic MPER Peptide Vaccine Induces Weakly HIV Neutralizing Antibodies in Mice.

Ann Biomed Eng 2020 Jul 12;48(7):1991-2001. Epub 2019 Dec 12.

Department of Biomedical Engineering, State University of New York at Buffalo, Buffalo, NY, 14260, USA.

A vaccine that induces broadly neutralizing antibodies (bnAbs) against the human immunodeficiency virus (HIV) would be instrumental in controlling the disease. The membrane proximal external region (MPER) peptide is an appealing antigen candidate since it is conserved and is the target of several human bnAbs, such as 2F5. We previously found that liposomes containing cobalt porphyrin-phospholipid (CoPoP) can bind to a his-tagged MPER peptide, resulting in biomimetic antigen presentation on a lipid bilayer. Read More

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Sensitivity of the polyDetect computational pipeline for phylogenetic analyses.

Anal Biochem 2020 03 30;593:113516. Epub 2019 Nov 30.

Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA. Electronic address:

Alu elements are powerful phylogenetic markers. The combination of a recently-developed computational pipeline, polyDetect, with high copy number Alu insertions has previously been utilized to help resolve the Papio baboon phylogeny with high statistical support. Here, the polyDetect method was applied to the highly contentious Cebidae phylogeny within New World monkeys (NWM). Read More

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Changing of the guard: How the Lyme disease spirochete subverts the host immune response.

J Biol Chem 2020 01 21;295(2):301-313. Epub 2019 Nov 21.

Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.

Lyme disease, also known as Lyme borreliosis, is the most common tick-transmitted disease in the Northern Hemisphere. The disease is caused by the bacterial spirochete and other related species. One of the many fascinating features of this unique pathogen is an elaborate system for antigenic variation, whereby the sequence of the surface-bound lipoprotein VlsE is continually modified through segmental gene conversion events. Read More

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January 2020

Protein three-dimensional structures at the origin of life.

Interface Focus 2019 Dec 18;9(6):20190057. Epub 2019 Oct 18.

Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G128QQ, UK.

Proteins are relatively easy to synthesize, compared to nucleic acids and it is likely that there existed a stage prior to the RNA world which can be called the protein world. Some of the three-dimensional (3D) peptide structures in these proteins have, we argue, been conserved since then and may constitute the oldest biological relics in existence. We focus on 3D peptide motifs consisting of up to eight or so amino acid residues. Read More

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December 2019

Discovery of a Novel MHC Class I Lineage in Teleost Fish which Shows Unprecedented Levels of Ectodomain Deterioration while Possessing an Impressive Cytoplasmic Tail Motif.

Cells 2019 09 9;8(9). Epub 2019 Sep 9.

Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.

A unique new nonclassical MHC class I lineage was found in Teleostei (teleosts, modern bony fish, e.g., zebrafish) and Holostei (a group of primitive bony fish, e. Read More

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September 2019

FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking.

Cell Rep 2019 08 14;28(9):2373-2385.e7. Epub 2019 Aug 14.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA. Electronic address:

HIV-1 uses the microtubule network to traffic the viral capsid core toward the nucleus. Viral nuclear trafficking and infectivity require the kinesin-1 adaptor protein FEZ1. Here, we demonstrate that FEZ1 directly interacts with the HIV-1 capsid and specifically binds capsid protein (CA) hexamers. Read More

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CRISPR repeat sequences and relative spacing specify DNA integration by Pyrococcus furiosus Cas1 and Cas2.

Nucleic Acids Res 2019 08;47(14):7518-7531

Department of Microbiology, University of Georgia, Athens, GA 30602, USA.

Acquiring foreign spacer DNA into the CRISPR locus is an essential primary step of the CRISPR-Cas pathway in prokaryotes for developing host immunity to mobile genetic elements. Here, we investigate spacer integration in vitro using proteins from Pyrococcus furiosus and demonstrate that Cas1 and Cas2 are sufficient to accurately integrate spacers into a minimal CRISPR locus. Using high-throughput sequencing, we identified high frequency spacer integration occurring at the same CRISPR repeat border sites utilized in vivo, as well as at several non-CRISPR plasmid sequences which share features with repeats. Read More

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