42,374 results match your criteria consensus sequences


The efficiency of susceptibility-weighted MRI in the differentiation of endometriomas from haemorrhagic ovarian cysts.

Abdom Radiol (NY) 2021 Jul 27. Epub 2021 Jul 27.

Department of İnternal Medicine, Fatih State Hospital, Trabzon, Turkey.

Objectives: The aim of the study was to investigate the efficiency of susceptibility-weighted magnetic resonance (MR) imaging (SWIs) in differentiating endometriomas from haemorrhagic ovarian cysts.

Materials And Methods: Between July 2017 and January 2019, 89 ovarian cystic lesions (57 endometriomas and 32 haemorrhagic cysts) that were identified as complicated cystic lesions on ultrasonography (US) and underwent lower abdominal MRI with susceptibility weighting were retrospectively evaluated. Final diagnoses were obtained with surgical pathological correlation and radiological-clinical follow-up. 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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Mol Pharmacol 2021 Jul 26. Epub 2021 Jul 26.

Pharmacology, University of Texas Southwestern Medical Center, United States

The WNK (with-no lysine (K)) kinases and their downstream effector kinases, OSR1 (oxidative stress responsive 1) and SPAK (SPS/STE20-related proline-alanine rich kinase), have well-established functions in the maintenance of cell volume and ion homeostasis. Mutations in these kinases have been linked to an inherited form of hypertension, neurological defects, and other pathologies. A rapidly expanding body of evidence points to the involvement of WNKs in regulating multiple diverse cellular processes as well as the progression of some forms of cancer. Read More

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Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria.

mBio 2021 Jul 27:e0107421. Epub 2021 Jul 27.

Department of Earth Sciences, University of Delawaregrid.33489.35, Newark, Delaware, USA.

Iron (Fe) oxidation is one of Earth's major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Read More

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Prevalence of gp160 polymorphisms known to be related to decreased susceptibility to temsavir in different subtypes of HIV-1 in the Los Alamos National Laboratory HIV Sequence Database.

J Antimicrob Chemother 2021 Jul 23. Epub 2021 Jul 23.

ViiV Healthcare, 36 East Industrial Road, Branford, CT 06405, USA.

Background: Fostemsavir, a prodrug of the gp120-directed attachment inhibitor temsavir, is indicated for use in heavily treatment-experienced individuals with MDR HIV-1. Reduced susceptibility to temsavir in the clinic maps to discrete changes at amino acid positions in gp160: S375, M426, M434 and M475.

Objectives: To query the Los Alamos National Laboratory (LANL) HIV Sequence Database for the prevalence of polymorphisms at gp160 positions of interest. 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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Analyses of lamprey meis genes reveals that conserved inputs from hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube.

Dev Biol 2021 Jul 23. Epub 2021 Jul 23.

Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA. Electronic address:

Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the Sea Lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Read More

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Empirical evaluation of methods for genome assembly.

PeerJ Comput Sci 2021 9;7:e636. Epub 2021 Jul 9.

Department of Multimedia Engineering, Dongguk University, Seoul, South Korea.

Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and assembly is a key initiative that has facilitated gene discovery and other studies. Read More

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Recommendations of the Mexican College of Rheumatology for the management of psoriatic arthritis.

Reumatol Clin (Engl Ed) 2021 Jul 22. Epub 2021 Jul 22.

Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico. Electronic address:

Psoriatic arthritis is a chronic systemic inflammatory disease that affects the skin, musculoskeletal structures and other organs and systems compromising functionality, quality of life and reducing the life expectancy of patients. It is a complex disease that requires specialist and timely care and management. The alternatives for treating the manifestations of psoriatic arthritis have increased and the effect of the different agents on specific manifestations has been clarified in recent studies. Read More

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A molecular sensor for cholesterol in the human serotonin receptor.

Sci Adv 2021 Jul 23;7(30). Epub 2021 Jul 23.

CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.

The function of several G protein-coupled receptors (GPCRs) exhibits cholesterol sensitivity. Cholesterol sensitivity of GPCRs could be attributed to specific sequence and structural features, such as the cholesterol recognition/interaction amino acid consensus (CRAC) motif, that facilitate their cholesterol-receptor interaction. In this work, we explored the molecular basis of cholesterol sensitivity exhibited by the serotonin receptor, the most studied GPCR in the context of cholesterol sensitivity, by generating mutants of key residues in CRAC motifs in transmembrane helix 2 (TM2) and TM5 of the receptor. Read More

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QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Flowering Time.

Int J Mol Sci 2021 Jul 15;22(14). Epub 2021 Jul 15.

National Key Laboratory of Crop Genetic Improvement, Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

Timely flowering is important for seed formation and maximization of rapeseed () yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. Read More

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Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest.

Evol Appl 2021 Jul 15;14(7):1844-1866. Epub 2021 May 15.

Université Côte d'Azur INRAE CNRS ISA Sophia Antipolis France.

Despite reproducing without sexual recombination, is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. Read More

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Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family.

BMC Genomics 2021 Jul 23;22(1):567. Epub 2021 Jul 23.

Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.

Background: Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The available transcriptomes of limber pine (Pinus flexilis) allow us to characterize NLR genes and related resistance gene analogs (RGAs) in host resistance against Cronartium ribicola, the causal fungal pathogen of white pine blister rust (WPBR) on five-needle pines throughout the world. We previously mapped a limber pine major gene locus (Cr4) that confers complete resistance to C. Read More

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Glutamate Chemical Exchange Saturation Transfer Imaging and Functional Alterations of Hippocampus in Rat Depression Model: A Pilot Study.

J Magn Reson Imaging 2021 Jul 22. Epub 2021 Jul 22.

School of Medical Imaging, Binzhou Medical University, Yantai, China.

Background: Adjusting abnormal glutamate neurotransmission is a crucial mechanism in the treatment of depression. However, few non-invasive techniques could effectively detect changes in glutamate neurotransmitters, and no consensus exists on whether glutamate could affect resting-state function changes in depression.

Purpose: To study the changes in glutamate chemical exchange saturation transfer (GluCEST) value in the hippocampus of rat model exposed to chronic unpredictable mild stress (CUMS), and to explore the effect of this change on the activity of hippocampal glutamatergic neurons. Read More

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Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.

Nucleic Acids Res 2021 Jul 21. Epub 2021 Jul 21.

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.

The most common form of DNA methylation involves the addition of a methyl group to a cytosine base in the context of a cytosine-phosphate-guanine (CpG) dinucleotide. Genomes from more primitive organisms are more abundant in CpG sites that, through the process of methylation, deamination and subsequent mutation to thymine-phosphate-guanine (TpG) sites, can produce new transcription factor binding sites. Here, we examined the evolutionary history of the over 36 000 glucocorticoid receptor (GR) consensus binding motifs in the human genome and identified a subset of them in regulatory regions that arose via a deamination and subsequent mutation event. Read More

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Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species.

Mol Ecol Resour 2021 Jul 20. Epub 2021 Jul 20.

Department of Systems and Computing Engineering, Universidad de los Andes, Bogotá, Colombia.

Genotyping-by-Sequencing (GBS) is a widely used and cost-effective technique for obtaining large numbers of genetic markers from populations by sequencing regions adjacent to restriction cut sites. Although a standard reference-based pipeline can be followed to analyze GBS reads, a reference genome is still not available for a large number of species. Hence, reference-free approaches are required to generate the genetic variability information that can be obtained from a GBS experiment. Read More

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Identification and Characterization of Cancer Stem-Like Cells in ALK-Positive Anaplastic Large Cell Lymphoma Using the SORE6 Reporter.

Curr Issues Mol Biol 2021 Jul 2;43(2):543-557. Epub 2021 Jul 2.

Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada.

Transcription factors Sox2 and Oct4 are essential in maintaining the pluripotency of embryonic stem cells and conferring stemness in cancer stem-like (CSL) cells. SORE6, an in-vitro reporter system, was designed to quantify the transcription activity of Sox2/Oct4 and identify CSL cells in non-hematologic cancers. Using SORE6, we identified and enriched CSL cells in ALK-positive anaplastic large cell lymphoma (ALK + ALCL). Read More

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Structural Insight into the Interaction of Sendai Virus C Protein with Alix To Stimulate Viral Budding.

J Virol 2021 Jul 21:JVI0081521. Epub 2021 Jul 21.

Department of Virology, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan.

The Sendai virus (SeV), belonging to the genus of the family , harbors an accessory protein, named C protein, which facilitates the viral pathogenicity in mice. In addition, the C protein is known to stimulate the budding of virus-like particles through the binding to the host ALG-2 interacting protein X (Alix), a component of the endosomal sorting complexes required for transport (ESCRT) machinery. However, siRNA-mediated gene knockdown studies suggested that neither Alix nor C protein are related to the SeV budding. Read More

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Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.

mSphere 2021 Jul 21:e0021921. Epub 2021 Jul 21.

Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. Read More

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Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.

mSystems 2021 Jul 20:e0064221. Epub 2021 Jul 20.

Department of Biology, University of Waterloogrid.46078.3d, Waterloo, Ontario, Canada.

Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the and phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin "archaeomes" dominated by putative ammonia oxidizers of the class ( phylum, formerly ). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17. Read More

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Search for Highly Divergent Tandem Repeats in Amino Acid Sequences.

Int J Mol Sci 2021 Jul 1;22(13). Epub 2021 Jul 1.

Center of Bioengineering Research Center of Biotechnology RAS, 119071 Moscow, Russia.

We report a Method to Search for Highly Divergent Tandem Repeats (MSHDTR) in protein sequences which considers pairwise correlations between adjacent residues. MSHDTR was compared with some previously developed methods for searching for tandem repeats (TRs) in amino acid sequences, such as T-REKS and XSTREAM, which focus on the identification of TRs with significant sequence similarity, whereas MSHDTR detects repeats that significantly diverged during evolution, accumulating deletions, insertions, and substitutions. The application of MSHDTR to a search of the Swiss-Prot databank revealed over 15 thousand TR-containing amino acid sequences that were difficult to find using the other methods. Read More

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Grass carp (Ctenopharyngodon idella) interferon regulatory factor 8 down-regulates interferon1 expression via interaction with interferon regulatory factor 2 in vitro.

Mol Immunol 2021 Jul 16;137:202-211. Epub 2021 Jul 16.

School of Life Science, Nanchang University, Nanchang, 330031, China. Electronic address:

Interferon regulatory factor 8 (IRF8), also known as interferon consensus sequence-binding protein (ICSBP), is a negative regulatory factor of interferon (IFN) and plays an important role in cell differentiation and innate immunity in mammals. In recent years, some irf8 homologous genes have been cloned and confirmed to take part in innate immune response in fish, but the mechanism still remains unclear. In this paper, a grass carp (Ctenopharyngodon idella) irf8 gene (Ciirf8) was cloned and characterized. Read More

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First Report of Downy Mildew on Sweet Basil Caused By Peronospora belbahrii in India.

Plant Dis 2021 Jul 19. Epub 2021 Jul 19.

CSIR-CIMAP, 30083, Plant Pathology, Lucknow, Uttar Pradesh, India;

Sweet basil (Ocimum basilicum L.; Family Lamiaceae) is an annual aromatic and medicinal plant grown in tropical and subtropical regions of the world. In India, it is cultivated as a commercial crop on ~8,000 ha. Read More

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NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells.

iScience 2021 Jul 24;24(7):102762. Epub 2021 Jun 24.

Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.

Spermatogonial stem cells (SSCs) sustain spermatogenesis and fertility throughout adult male life. The conserved RNA-binding protein NANOS2 is essential for the maintenance of SSCs, but its targets and mechanisms of function are not fully understood. Here, we generated a fully functional epitope-tagged mouse allele and applied the highly stringent cross-linking and analysis of cDNAs to define NANOS2 RNA occupancy in SSC lines. Read More

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HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences.

BMC Bioinformatics 2021 Jul 17;22(1):373. Epub 2021 Jul 17.

Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.

Background: SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1. Read More

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Ultra Rapid Lispro Demonstrates Similar Time in Target Range to Lispro With a Hybrid Closed-Loop System.

Diabetes Technol Ther 2021 Jul 16. Epub 2021 Jul 16.

Eli Lilly and Company, Medical, Lilly Corporate Center, Indianapolis, Indiana, United States, 46285;

Background: Automated insulin delivery systems are associated with improved glycemic outcomes for patients with diabetes. Ultra rapid lispro (URLi), which has an accelerated pharmacokinetic profile and shows superior postprandial glucose control compared to lispro (Humalog®), is a potential candidate for use in these systems.

Methods: In this double-blind, crossover trial over two 4-week treatment periods, we evaluated URLi in a hybrid closed-loop system using the Medtronic MiniMedTM 670G system (670G). Read More

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Hospital transmission of borderline oxacillin-resistant evaluated by whole-genome sequencing.

J Med Microbiol 2021 Jul;70(7)

Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands.

is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant (MRSA) infections is high but attention towards borderline oxacillin-resistant (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations. BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking. Read More

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The Complete Mitochondrial DNA of : Maxicircles and Minicircles.

Front Cell Infect Microbiol 2021 29;11:672448. Epub 2021 Jun 29.

Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain.

The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA or kDNA or mtDNA, consists of a few maxicircles and thousands of minicircles concatenated together into a huge complex network. These structures present species-specific sizes, from 20 to 40 Kb in maxicircles and from 0.5 to 10 Kb in minicircles. Read More

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Meta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2.

Front Microbiol 2021 29;12:676314. Epub 2021 Jun 29.

Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China, and is the causative agent for the worldwide COVID-19 pandemic. SARS-CoV-2 is a positive-sense single-stranded RNA virus belonging to the betacoronavirus genus. Due to the error-prone nature of the viral RNA-dependent polymerase complex, coronaviruses are known to acquire new mutations at each cycle of genome replication. Read More

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Viral populations of SARS-CoV-2 in upper respiratory tract, placenta, amniotic fluid and umbilical cord blood support viral replication in placenta.

Clin Microbiol Infect 2021 Jul 11. Epub 2021 Jul 11.

Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Universitari, Vall D'Hebron Barcelona Hospital Campus, Barcelona, Spain.

A woman at the first stage of labour infected with SARS-CoV-2 was admitted to our hospital with symptomatology compatible with mild respiratory disease. Respiratory and non-respiratory samples from the mother were all positive for the virus, but not from the baby. Laboratory tests rejected vertical transmission. Read More

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