821,765 results match your criteria dna sequences


Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

Genetics 2019 Sep;213(1):143-160

Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706.

Xue et al. describe a phenomenon in maize and its nearest wild relative, teosinte, by which backcross progeny of a specific teosinte and maize exhibit a sickly whole-plant phenotype involving changes in morphology, vigor, and viability.. Read More

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September 2019

Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

Genetics 2019 Sep;213(1):143-160

Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706.

Xue et al. describe a phenomenon in maize and its nearest wild relative, teosinte, by which backcross progeny of a specific teosinte and maize exhibit a sickly whole-plant phenotype involving changes in morphology, vigor, and viability.. Read More

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September 2019

Modulating Mistranslation Potential of tRNASer in Saccharomyces cerevisiae.

Genetics 2019 Nov;213(3):849-863

Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.

Mistranslation, incorporating an amino acid not specified by the "standard" genetic code, has applications in research and synthetic biology. Since mistranslation is toxic, its level must be modulated. Using a serine tRNA with a proline anticodon, we identify. Read More

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November 2019

Modulating Mistranslation Potential of tRNASer in Saccharomyces cerevisiae.

Genetics 2019 Nov;213(3):849-863

Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.

Mistranslation, incorporating an amino acid not specified by the "standard" genetic code, has applications in research and synthetic biology. Since mistranslation is toxic, its level must be modulated. Using a serine tRNA with a proline anticodon, we identify. Read More

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November 2019

Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene.

Genetics 2020 Mar;214(3):623-634

Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376.

Polycomb-group (PcG) proteins utilize epigenetic mechanisms to maintain the transcriptional silence of target genes. Recruitment of Drosophila PcG proteins to target genes requires the presence of a Polycomb Response Element (PRE). Some PcG target genes, including. Read More

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Sex Chromosome Pairing Mediated by Euchromatic Homology in Drosophila Male Meiosis.

Genetics 2020 Mar;214(3):605-616

Department of Biology, University of North Carolina, Greensboro, North Carolina 27402.

Drosophila males have evolved a unique system of chromosome segregation in meiosis that lacks recombination. Chromosomes pair at selected sequences suggesting that early steps of meiosis may also differ in this organism.. Read More

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Small RNA-Mediated De Novo Silencing of Ac/Ds Transposons Is Initiated by Alternative Transposition in Maize.

Genetics 2020 Jun;215(2):393-406

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260.

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they pose to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species. Read More

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Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System of Escherichia coli.

Genetics 2020 Feb;214(2):333-354

Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616.

In the Cairns-Foster adaptive mutation system, lac mutant cells are plated on lactose medium where 50 revertant colonies accumulate over 5 days above a non-growing lawn. A new model attributes this behavior to selective.. Read More

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February 2020

-regulatory elements in conserved non-coding sequences of nuclear receptor genes indicate for crosstalk between endocrine systems.

Open Med (Wars) 2021 12;16(1):640-650. Epub 2021 Apr 12.

Sahlgrenska University Hospital, Gothia Forum for Clinical Research, Gothenburg, Sweden.

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate gene expression when bound to specific DNA sequences. Crosstalk between steroid NR systems has been studied for understanding the development of hormone-driven cancers but not to an extent at a genetic level. This study aimed to investigate crosstalk between steroid NRs in conserved intron and exon sequences, with a focus on steroid NRs involved in prostate cancer etiology. Read More

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Molecular Species Identification of Six Forensically Important Iranian Flesh Flies (Diptera).

J Arthropod Borne Dis 2020 Dec 31;14(4):416-424. Epub 2020 Dec 31.

Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.

Background: Flesh flies (Diptera: Sarcophagidae) are considered as myiasis agents and important evidences in forensic investigations. However, their use has been restricted because, at all larval stages and female adults, morphological species identification is difficult or very challenging. This study investigated to test utility of mitochondrial cytochrome oxidase subunit I (mt-COI) sequences for differentiation of six forensically important Iranian flesh flies namely, , , , , and . Read More

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December 2020

periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA.

F1000Res 2021 24;10:141. Epub 2021 Feb 24.

The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK.

Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. Read More

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February 2021

Single-molecule imaging reveals replication fork coupled formation of G-quadruplex structures hinders local replication stress signaling.

Nat Commun 2021 05 5;12(1):2525. Epub 2021 May 5.

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.

Guanine-rich DNA sequences occur throughout the human genome and can transiently form G-quadruplex (G4) structures that may obstruct DNA replication, leading to genomic instability. Here, we apply multi-color single-molecule localization microscopy (SMLM) coupled with robust data-mining algorithms to quantitatively visualize replication fork (RF)-coupled formation and spatial-association of endogenous G4s. Using this data, we investigate the effects of G4s on replisome dynamics and organization. Read More

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The first detection of Dicrocoelium chinensis sporocysts from the land snail Aegista vulgivaga in Gifu Prefecture, Japan.

J Vet Med Sci 2021 Apr 30. Epub 2021 Apr 30.

Faculty of Applied Biological Science, Gifu University.

Trematodes of the genus Dicrocoelium are one of the most common parasites in ruminant animals; however, their life cycles in Japan are unclear. To find the sporocysts of D. chinensis in the natural field, we sampled 269 land snails (14 species) at a location with high level infection of sika deer in Gifu Prefecture, Honshu Island, Japan in autumn between 2017 and 2019. Read More

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Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India.

Virol J 2021 May 5;18(1):96. Epub 2021 May 5.

Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India.

Background: Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Read More

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Probability, Populations, Phylogenetics, and Hominin Speciation.

Hum Biol 2019 Sep;90(2):129-155

Department of Anthropology, San Francisco State University, San Francisco, California, USA,

A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mitochondrial DNA (mtDNA) sequences from the fossils of a number of Neandertals and the Denisovans in an attempt to understand the evolution of Middle Pleistocene human ancestors. Read More

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September 2019

Integrative taxonomy uncovers a new Culicoides (Diptera: Ceratopogonidae) biting midge species from Thailand.

Acta Trop 2021 May 2:105941. Epub 2021 May 2.

Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham 44150, Thailand.

Fully understanding biodiversity often requires an integrated approach especially for small insects because species diagnostic morphological characters are limited. In this study, morphological characters and DNA barcodes were used to examine previously recognized genetically divergent lineages detected in the biting midge, Culicoides arakawae (Arakawa), from Thailand. Morphological examinations revealed that specimens belonging to one lineage are morphologically different from C. Read More

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Extending Approximate Bayesian Computation with Supervised Machine Learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest.

Mol Ecol Resour 2021 May 5. Epub 2021 May 5.

CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.

Simulation-based methods such as Approximate Bayesian Computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. Read More

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Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid.

Biochemistry 2021 May 5. Epub 2021 May 5.

Department of Genetics, University of Georgia, Athens, Georgia 30602, United States.

d-Glucosaminate-6-phosphate ammonia-lyase (DGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that produces 2-keto-3-deoxygluconate 6-phosphate (KDG-6-P) in the metabolism of d-glucosaminic acid by serovar typhimurium. We have determined the crystal structure of DGL by SAD phasing with selenomethionine to a resolution of 2.58 Å. Read More

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Young and early-onset dilated cardiomyopathy with malignant ventricular arrhythmia and sudden cardiac death induced by the heterozygous LDB3, MYH6, and SYNE1 missense mutations.

Ann Noninvasive Electrocardiol 2021 May 5:e12840. Epub 2021 May 5.

Department of Cardiology, The Cardiovascular Center, Interventional Medical Center, Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.

Background: The whole exome sequencing (WES) with targeted gene analysis is an effective diagnostic tool for cardiomyopathy. The early-onset sudden cardiac death (SCD) was commonly associated with dilated cardiomyopathy (DCM) induced by pathogenic genetic mutations.

Methods: In a Chinese Han family, the patient of 24 years old occurred with early-onset and DCM and died of SCD associated with ICD storms induced by repetitive ventricular tachycardia/fibrillation (VT/F). Read More

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Data on G-quadruplex topology, and binding ability of G-quadruplex forming sequences found in the promoter region of biomarker proteins and those relations to the presence of nuclear localization signal in the proteins.

Data Brief 2021 Jun 1;36:107028. Epub 2021 Apr 1.

Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.

Aptamer is a nucleic acid ligand which specifically binds to its target molecule. Previously, we have designed an identification method of aptamer called "G-quadruplex (G4) promoter-derived aptamer selection (G4PAS)" [1]. In G4PAS procedure, putative G4 forming sequences (PQS) were explored in a promoter region of a target protein in human gene through computational analysis, and evaluated binding ability towards the gene product encoded in the downstream of the promoter. Read More

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Mutational and Kinetic Analysis of APE1 Endoribonuclease Activity.

Mol Biol 2021 29;55(2):211-224. Epub 2021 Apr 29.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.

Human apurinic/apyrimidinic endonuclease 1 (APE1) participates in the DNA repair system. It is believed that the main biological function of APE1 is Mg-dependent hydrolysis of AP-sites in DNA. On the base of structural data, kinetic studies, and mutation analysis, the key stages of APE1 interaction with damaged DNA were established. Read More

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Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo.

Nat Commun 2021 05 4;12(1):2509. Epub 2021 May 4.

Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Differential transcription of identical DNA sequences leads to distinct tissue lineages and then multiple cell types within a lineage, an epigenetic process central to progenitor and stem cell biology. The associated genome-wide changes, especially in native tissues, remain insufficiently understood, and are hereby addressed in the mouse lung, where the same lineage transcription factor NKX2-1 promotes the diametrically opposed alveolar type 1 (AT1) and AT2 cell fates. Here, we report that the cell-type-specific function of NKX2-1 is attributed to its differential chromatin binding that is acquired or retained during development in coordination with partner transcriptional factors. Read More

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The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral / Transcripts.

mBio 2021 05 4;12(3). Epub 2021 May 4.

Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany

Interferon-stimulated gene products (ISGs) play a crucial role in early infection control. The ISG zinc finger CCCH-type antiviral protein 1 (ZAP/ZC3HAV1) antagonizes several RNA viruses by binding to CG-rich RNA sequences, whereas its effect on DNA viruses is less well understood. Here, we decipher the role of ZAP in the context of human cytomegalovirus (HCMV) infection, a β-herpesvirus that is associated with high morbidity in immunosuppressed individuals and newborns. Read More

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The Genetic Diversity and Structure of the European Turtle Dove .

Animals (Basel) 2021 Apr 29;11(5). Epub 2021 Apr 29.

Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, Lithuania.

The European Turtle Dove, , a long-distance migrant wintering in Africa, is a widespread Palearctic species. This species is classified as vulnerable and is undergoing a long-term demographic decline. The results of the previous study (based on mitochondrial (mtDNA) cytochrome-b () sequences of birds from Western and Southern Europe) indicated that the species was not genetically structured. Read More

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Temporal Trend of ST131 Clone among Urinary Isolates in the Community: A Taiwan National Surveillance from 2002 to 2016.

Microorganisms 2021 Apr 29;9(5). Epub 2021 Apr 29.

National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan 350, Taiwan.

Sequence type (ST) 131 is a multidrug-resistant pandemic lineage of responsible for extraintestinal infections. Few surveillance data of ST131 included all antimicrobial-susceptible and -resistant isolates or focused on community-acquired urinary tract infection (UTI). From a population-based surveillance pool of 2997 outpatient urine isolates, 542 were selected for detection of ST131 based on ciprofloxacin and/or cefotaxime resistance. Read More

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Exosomes in Liquid Biopsy: The Nanometric World in the Pursuit of Precision Oncology.

Cancers (Basel) 2021 Apr 29;13(9). Epub 2021 Apr 29.

Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain.

Among the different components that can be analyzed in liquid biopsy, the utility of exosomes is particularly promising because of their presence in all biological fluids and their potential for multicomponent analyses. Exosomes are extracellular vesicles with an average size of ~100 nm in diameter with an endosomal origin. All eukaryotic cells release exosomes as part of their active physiology. Read More

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Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time.

Int J Mol Sci 2021 Apr 29;22(9). Epub 2021 Apr 29.

Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal.

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Read More

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Identification of Novel Fusion Transcripts in High Grade Serous Ovarian Cancer.

Int J Mol Sci 2021 Apr 30;22(9). Epub 2021 Apr 30.

Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA.

Fusion genes are structural chromosomal rearrangements resulting in the exchange of DNA sequences between genes. This results in the formation of a new combined gene. They have been implicated in carcinogenesis in a number of different cancers, though they have been understudied in high grade serous ovarian cancer. Read More

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Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America.

Viruses 2021 04 30;13(5). Epub 2021 Apr 30.

The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA.

Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly and their ssDNA genomes can be either monopartite or bipartite. Read More

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Dynamics of Specific cfDNA Fragments in the Plasma of Full Marathon Participants.

Genes (Basel) 2021 Apr 30;12(5). Epub 2021 Apr 30.

Laboratory of Laboratory-Sports Medicine, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki, Japan.

Plasma cell-free DNA (cfDNA) is frequently analyzed using liquid biopsy to investigate cancer markers. We hypothesized that this concept might be applicable in exercise physiology. Here, we aimed to identify specific cfDNA (spcfDNA) sequences in the plasma of healthy humans using next-generation sequencing (NGS) and clearly define the dynamics regarding spcfDNA-fragment levels upon extreme exercises, such as running a full marathon. Read More

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