153,011 results match your criteria sequences revealed


Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ().

RNA Biol 2021 Jul 27:1-12. Epub 2021 Jul 27.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. Read More

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Genome Analysis of Programmed DNA Elimination in Parasitic Nematodes.

Authors:
Jianbin Wang

Methods Mol Biol 2021 ;2369:251-261

Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.

Two distinct groups of parasitic nematodes use programmed DNA elimination to silence germline-expressed genes in the somatic cells (ascarids) or for sex determination (Strongyloides spp.). In the ascarids, DNA is lost only in pre-somatic cells during early embryogenesis, leading to a reduced somatic genome compared to the intact germ cell genome. Read More

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January 2021

Genome-Scale Analysis of Acetobacterium woodii Identifies Translational Regulation of Acetogenesis.

mSystems 2021 Jul 27:e0069621. Epub 2021 Jul 27.

Department of Biological Sciences, Korea Advanced Institute of Science and Technologygrid.37172.30, Daejeon, Republic of Korea.

Acetogens synthesize acetyl-CoA via the CO-fixing Wood-Ljungdahl pathway. Despite their ecological and biotechnological importance, their translational regulation of carbon and energy metabolisms remains unclear. Here, we report how carbon and energy metabolisms in the model acetogen Acetobacterium woodii are translationally controlled under different growth conditions. Read More

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Phase-contrast acceleration mapping with synchronized encoding.

Magn Reson Med 2021 Jul 27. Epub 2021 Jul 27.

Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Purpose: To develop a phase-contrast (PC) -based method for direct and unbiased quantification of the acceleration vector field by synchronization of the spatial and acceleration encoding time points. The proposed method explicitly aims at in-vitro applications, requiring high measurement accuracy, as well as the validation of clinically relevant acceleration-encoded sequences.

Methods: A velocity-encoded sequence with synchronized encoding (SYNC SPI) was modified to allow direct acceleration mapping by replacing the bipolar encoding gradients with tripolar gradient waveforms. Read More

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Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses.

Elife 2021 Jul 27;10. Epub 2021 Jul 27.

Department of Health Sciences, Institute for Animal and Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark.

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Read More

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Natural Products with tandem Anti-inflammatory, Immunomodulatory and Anti-SARS-CoV/2 effects: A Drug Discovery Perspective against SARS-CoV-2.

Curr Med Chem 2021 Jul 25. Epub 2021 Jul 25.

Programa de Pós-Graduação em Química, CFM, Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis, Brazil.

Background: COVID-19 is still causing victims with long-term health consequences, mass deaths, and collapsing healthcare systems around the world. The disease has no efficient drugs. However, previous studies revealed that SARS-CoV-2 and SARS-CoV have 96% and 86. Read More

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Genetic variability of bovine herpesvirus type 4 (BoHV-4) field strains from Turkish cattle herds.

Vet Ital 2021 May 11;57(1):49-59. Epub 2021 May 11.

Virology Department, Ankara University, Veterinary Medicine, Ankara, Turkey.

Bovine herpesvirus type 4 (BoHV‑4) is a common virus in the world that is detected in clinically ill or in apparently healthy cattle. This study provides a molecular characterization of BoHV‑4 strains from 24 cattle some showing respiratory and/or reproductive problems and some without any apparent clinical sign. This study also reported the growth properties of five BoHV‑4 field isolates. Read More

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Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.

FEBS Lett 2021 Jul 27. Epub 2021 Jul 27.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

The endoplasmic reticulum transmembrane protein vesicle-associated membrane protein-associated protein (VAP) plays a central role in the formation and function of membrane contact sites (MCS) through its interactions with proteins. The major sperm protein (MSP) domain of VAP binds to a variety of sequences which are referred to as FFAT-like motifs. In this study, we investigated the interactions of eight peptides containing FFAT-like motifs with the VAP-A MSP domain (VAP-A ) by solution NMR. Read More

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Combining repetition suppression and pattern analysis provides new insights into the role of M1 and parietal areas in skilled sequential actions.

J Neurosci 2021 Jul 26. Epub 2021 Jul 26.

The Brain and Mind Institute, University of Western Ontario, London, ON N6A 5B7, Canada

How does the brain change during learning? In functional magnetic resonance imaging studies, both multivariate pattern analysis and repetition suppression (RS) have been used to detect changes in neuronal representations. In the context of motor sequence learning, the two techniques have provided discrepant findings: pattern analysis showed that only premotor and parietal regions, but not primary motor cortex (M1), develop a representation of trained sequences. In contrast, RS suggested trained sequence representations in all these regions. Read More

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Discovery of genomic variation across a generation.

Hum Mol Genet 2021 Jul 22. Epub 2021 Jul 22.

The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.

Over the past thirty years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared to the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA-approximately 30 megabase pairs (Mb)-being 'structurally variable', mostly in the form of indels and copy number changes. Read More

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Comparative assessment of NOIR-SS and ddPCR for ctDNA detection of EGFR L858R mutations in advanced L858R-positive lung adenocarcinomas.

Sci Rep 2021 Jul 22;11(1):14999. Epub 2021 Jul 22.

Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.

Genotyping epidermal growth factor receptor (EGFR) is an essential process to indicate lung adenocarcinoma patients for the most appropriate treatment. Liquid biopsy using circulating tumor DNA (ctDNA) potentially complements the use of tumor tissue biopsy for identifying genotype-specific mutations in cancer cells. We assessed the performance of a high-fidelity sequencing method that uses molecular barcodes called the nonoverlapping integrated read sequencing system (NOIR-SS) for detecting EGFR L858R-mutated alleles in 33 advanced or recurrent patients with L858R mutation-positive lung adenocarcinoma revealed by matched tissue biopsy. Read More

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Lineage analysis of human papillomavirus type 39 in cervical samples of Iranian women.

Virol J 2021 Jul 22;18(1):152. Epub 2021 Jul 22.

Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, 14155, Iran.

Background: The data with regards to the regional variants of distinct HPV types is of great value. Accordance with this, this study aimed to investigate the sequence variations of E6 gene and long control region of HPV 39 among normal, premalignant and malignant cervical samples in order to characterize the frequent HPV 39 variants circulating in Tehran, Iran.

Methods: In total, 70 cervical samples (45 normal, 16 premalignant, and 9 malignant samples) infected with HPV 39 were analyzed by nested-PCR and sequencing. Read More

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Mitotic recombination in yeast: what we know and what we don't know.

Curr Opin Genet Dev 2021 Jul 23;71:78-85. Epub 2021 Jul 23.

Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States. Electronic address:

Saccharomyces cerevisiae is at the forefront of defining the major recombination mechanisms/models that repair targeted double-strand breaks during mitosis. Each of these models predicts specific molecular intermediates as well as genetic outcomes. Recent use of single-nucleotide polymorphisms to track the exchange of sequences in recombination products has provided an unprecedented level of detail about the corresponding intermediates and the extents to which different mechanisms are utilized. Read More

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Structural evolution of SLA promoter in mosquito-borne flaviviruses: A sequence-structure based phylogenetic framework.

Virology 2021 Jul 21;562:110-120. Epub 2021 Jul 21.

Department of Microbiology and FST, GITAM Institute of Science, GITAM (Deemed to be University), Rushikonda, Visakhapatnam, 530045, Andhra Pradesh, India. Electronic address:

All the flaviviruses have a Y-shaped stem-loop secondary structure known as the SLA element, and the structural features of this element are crucial to initiating the infection cycle. The present study particularly investigated how flaviviruses retained the common core SLA element secondary structure during the species evolution by selecting mosquito-borne flaviviruses (MBFVs) as a case study. The detailed search of nucleotide substitutions in species-wise consensus SLA secondary structure models suggested that the compensatory and hemi-compensatory base changes in the helices are crucial to preserving the common core secondary structure. Read More

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Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil.

Syst Appl Microbiol 2021 Jul 17;44(5):126233. Epub 2021 Jul 17.

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan.

Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875, Red259, and Red421 were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Read More

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Epidemiological and genetic characterization of Measles Virus circulating strains at Marseille, France during 2017-2019 measles outbreak.

J Infect 2021 Jul 23. Epub 2021 Jul 23.

IHU Méditerranée Infection, Marseille, France; MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Universite, Marseille, France; Assistance Publique - Hôpitaux de Marseille (AP-HM), Marseille, France. Electronic address:

Objectives: We attempted to establish a molecular investigation by Next Generation sequencing of the measles virus (MeV) strains circulating in Marseille-France during the last outbreak that occurred between 2017-2019.

Methods: The circulating MeV were isolated from clinical samples using cell culture method and whole genomes were sequenced by Illumina Miseq Next Generation. Genotyping and comparative analyses were assessed by phylogenetic reconstructions. Read More

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Designing specific bacterial 16S primers to sequence and quantitate plant endo-bacteriome.

Sci China Life Sci 2021 Jul 22. Epub 2021 Jul 22.

State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Plant endophytic bacteria colonize the internal tissues of plants and interact with plants closely. The past two decades have witnessed the increasing application of next-generation 16S rRNA gene sequencing in the investigation of bacterial communities. However, deciphering plant endo-bacterial communities by this method is difficult because of the co-amplification of massive plant organellar DNAs with bacterial 16S. Read More

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A newly developed PCR-based method revealed distinct Fusobacterium nucleatum subspecies infection patterns in colorectal cancer.

Microb Biotechnol 2021 Jul 26. Epub 2021 Jul 26.

Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.

Fusobacterium nucleatum, which has four subspecies (nucleatum, animalis, vincentii and polymorphum), plays an important role in promoting colorectal cancer (CRC). However, as there is no efficient method of differentiating these subspecies in the context of a rich gut microbiota, the compositions in CRC remain largely unknown. In this study, a PCR-based differentiation method enabling profiling of F. Read More

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miRNA-34 and miRNA-210 target hexamerin genes enhancing their differential expression during early brain development of honeybee (Apis mellifera) castes.

Insect Mol Biol 2021 Jul 26. Epub 2021 Jul 26.

Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil.

During the honeybee larval stage, queens develop larger brains than workers, with morphological differentiation appearing at the fourth larval phase (L4), just after a boost in nutritional difference both prospective females experience. The molecular promoters of this caste-specific brain development are already ongoing in previous larval phases. Transcriptomic analyses revealed a set of differentially expressed genes in the L3 brains of queens and workers, which represents the early molecular response to differential feeding females receive during larval development. Read More

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High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes.

Biol Open 2021 Jul 19;10(7). Epub 2021 Jul 19.

Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

Vector-borne pathogens cause many human infectious diseases and are responsible for high mortality and morbidity throughout the world. They can also cause livestock epidemics with dramatic social and economic consequences. Due to its high costs, vector-borne disease surveillance is often limited to current threats, and the investigation of emerging pathogens typically occurs after the reports of clinical cases. Read More

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Binding Studies of Aloe-Active Compounds with G-Quadruplex Sequences.

ACS Omega 2021 Jul 9;6(28):18344-18351. Epub 2021 Jul 9.

Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.

G-quadruplex, a unique DNA quartet motif with a pivotal role in regulation of the gene expression, has been established as a potent therapeutic target for the treatment of cancer. Small-molecule-mediated stabilization of the G-quadruplex and thus inhibition of the expression from the oncogene promoter and telomere region may be a promising anticancer strategy. -derived natural compounds like aloe emodin, aloe emodin-8-glucoside, and aloin have significant anticancer activity. Read More

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Malectin/Malectin-like domain-containing proteins: A repertoire of cell surface molecules with broad functional potential.

Cell Surf 2021 Dec 24;7:100056. Epub 2021 Jun 24.

Department of Biochemistry and Molecular Biology, University of Massachusetts, USA.

Cell walls are at the front line of interactions between walled-organisms and their environment. They support cell expansion, ensure cell integrity and, for multicellular organisms such as plants, they provide cell adherence, support cell shape morphogenesis and mediate cell-cell communication. Wall-sensing, detecting perturbations in the wall and signaling the cell to respond accordingly, is crucial for growth and survival. Read More

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December 2021

Molecular characterization and phylogenetic analysis of VIIl sub-genotype of avian orthoavulavirus 1 isolated from Eurasian magpie ().

Iran J Vet Res 2021 ;22(2):155-160

BSc Student in Veterinary Laboratory Sciences, Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special of Modern Technologies, Amol, Iran.

Background: Newcastle disease (ND) has been categorized as a highly contagious viral disease, remaining as a constant threat to both wild birds and commercial chickens.

Aims: In this study, we recovered and characterized the avian orthoavulavirus 1 (AOaV-1) strain, nominated as EM1, from the Eurasian magpie ().

Methods: The nucleotide and amino acid sequence of the fusion protein (F protein) of EM1 were determined and its phylogenetic relationship was investigated with well-characterized AOaV-1 genotypes, which originated from wild bird species and chickens around the world. Read More

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January 2021

Case Report: Diagnosis of Human Alveolar Echinococcosis via Next-Generation Sequencing Analysis.

Front Genet 2021 9;12:666225. Epub 2021 Jul 9.

Department of Neurology, The First Medical Center, Chinese PLA General Hospital, Beijing, China.

Alveolar echinococcosis (AE) is a rare parasitic disease caused by the infection of . AE may mimic malignancy both in clinical presentation and radiological imaging, which is often misdiagnosed as metastatic tumor. Recently, next-generation sequencing (NGS) technologies are increasingly being used to address a diverse range of biological questions. Read More

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Root Endophytes and Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs.

Front Plant Sci 2021 9;12:704985. Epub 2021 Jul 9.

School of Minerals Processing and Bioengineering, Central South University, Changsha, China.

is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes' role in , and whether genetic exchange happens between and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. Read More

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Phylogenomics With Hyb-Seq Unravels Korean Evolution.

Front Plant Sci 2021 8;12:645735. Epub 2021 Jul 8.

National Institute of Biological Resources, Incheon, South Korea.

The genus (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the species delimitation along with their indistinguishable morphology. Read More

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Identification and Characterization of s Mutations Associated With Early Blooming in Sweet Cherry, and Validation of DNA-Based Markers for Selection.

Front Plant Sci 2021 8;12:621491. Epub 2021 Jul 8.

Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain.

Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Read More

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Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of to Extreme Acid Mine Drainage Environments.

Front Microbiol 2021 8;12:705839. Epub 2021 Jul 8.

Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.

Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Read More

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An Overview of 24 Years of Molecular Phylogenetic Studies in () With Notes on Systematics, Geographic Distribution, Lifestyle, and Edibility.

Front Microbiol 2021 9;12:689374. Epub 2021 Jul 9.

Centro de Biociências, Departamento de Micologia, Programa de Pós-Graduação em Biologia de Fungos, Universidade Federal de Pernambuco (UFPE), Recife, Brazil.

The order () is represented by gasteroid fungi with expanded and sequestrate basidiomata, known as stinkhorns and false truffles. In phalloids, the first DNA sequence was published in 1997, and after that, some studies aimed to resolve phylogenetic conflicts and propose new species based on DNA markers; however, the number of families and genera in the order still generates controversies among researchers. Thus, this work aims to provide an overview of diversity represented by selected DNA markers available in public databases. Read More

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Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction.

Front Microbiol 2021 8;12:666936. Epub 2021 Jul 8.

HydroSciences Montpellier, University of Montpellier, CNRS, IRD, Montpellier, France.

Soil microbiota are vital for successful revegetation, as they play a critical role in nutrient cycles, soil functions, and plant growth and health. A rehabilitation scenario of the abandoned Kettara mine (Morocco) includes covering acidic tailings with alkaline phosphate mine wastes to limit water infiltration and hence acid mine drainage. Revegetation of phosphate wastes is the final step to this rehabilitation plan. Read More

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