507,392 results match your criteria data sequences

Heterocapsa busanensis sp. nov. (Peridiniales, Dinophyceae): A new marine thecate dinoflagellate from Korean coastal waters.

Eur J Protistol 2021 Apr 23;79:125797. Epub 2021 Apr 23.

Division of Earth Environmental System Science, Pukyong National University, Busan 48513, Republic of Korea; Department of Oceanography, Pukyong National University, Busan 48513, Republic of Korea. Electronic address:

During daily monitoring in Yongho Bay off Busan, Korea in 2019, an isolate of the dinoflagellate genus Heterocapsa was established in clonal culture. Light and electron microscopic examination revealed that the isolate was ellipsoid in shape, exhibiting a thecal plate arrangement (Po, cp, X, 5', 3a, 7″, 6c, 5s, 5‴, 2'''') consistent with most other Heterocapsa species. A large, elongated nucleus was positioned on the left side of the cell, a single reticulate chloroplast was located peripherally, and a single, starch-sheathed, spherical pyrenoid was present in the episome or near the cingulum. Read More

View Article and Full-Text PDF

Role of nuclear localization in the regulation and function of T-bet and Eomes in exhausted CD8 T cells.

Cell Rep 2021 May;35(6):109120

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

The transcription factors T-bet and Eomesodermin (Eomes) regulate CD8 T cell exhaustion through undefined mechanisms. Here, we show that the subcellular localization of T-bet and Eomes dictate their regulatory activity in exhausted T cells (Ts). Ts had a higher ratio of nuclear Eomes:T-bet than memory T cells (Ts) during chronic lymphocytic choriomeningitis virus (LCMV) infection in preclinical cancer models and in human tumors. Read More

View Article and Full-Text PDF

Using an Ensemble to Identify and Classify Macroalgae Antimicrobial Peptides.

Interdiscip Sci 2021 May 12. Epub 2021 May 12.

Marine and Freshwater Research Centre (MFRC), Galway-Mayo Institute of Technology (GMIT), Galway, Ireland.

The rapid spread of multi-drug resistant microbes has lead researchers to discover natural alternative remedies such as antimicrobial peptides (AMPs). In the first line of defense, AMPs display a broad spectrum of potent activity against multi-resistant pathogenic bacteria, viruses, fungi, and even cancer. AMPs can be further characterised into families according to amino acid composition, secondary structure, and function. Read More

View Article and Full-Text PDF

Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.

Hum Genet 2021 May 12. Epub 2021 May 12.

Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Intermediate-sized insertions are one of the structural variants contributing to genome diversity. However, due to technical difficulties in identifying them, their importance in disease pathogenicity and gene expression regulation remains unclear. We used whole-genome sequencing data of 174 Japanese samples to characterize intermediate-sized insertions using a highly-accurate insertion calling method (IMSindel software and joint-call recovery) and obtained a catalogue of 4254 insertions. Read More

View Article and Full-Text PDF

Antibacterial Performance of a Streptomyces spectabilis Strain Producing Metacycloprodigiosin.

Curr Microbiol 2021 May 12. Epub 2021 May 12.

Medicine Research Institute, HuBei University of Science and Technology, Xianning, 437000, China.

After separation of bacterial colonies on solid plates, purification, and screening through the agar cup-plate method, an antibiotic-resistant bacterial isolate was obtained, and named strain L20190601, the 16S rRNA gene sequence data of strain L20190601 to GenBank, NCBI have provided GenBank accession number MW931615. 16S rRNA gene sequencing revealed that this isolate was highly similar to a number of Streptomyces species. Among them, the homology with S. Read More

View Article and Full-Text PDF

Clustering FunFams using sequence embeddings improves EC purity.

Bioinformatics 2021 May 12. Epub 2021 May 12.

TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany.

Motivation: Classifying proteins into functional families can improve our understanding of protein function and can allow transferring annotations within one family. For this, functional families need to be "pure", i.e. Read More

View Article and Full-Text PDF

Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction.

Bioinformatics 2021 May 12. Epub 2021 May 12.

Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea.

Motivation: Characterizing drug-protein interactions is crucial to the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without human trial and error. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Read More

View Article and Full-Text PDF

CrepHAN: Cross-species prediction of enhancers by using hierarchical attention networks.

Bioinformatics 2021 May 12. Epub 2021 May 12.

Department of Computer Science and Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Rd., Shanghai 200240, China.

Motivation: Enhancers are important functional elements in genome sequences. The identification of enhancers is a very challenging task due to the great diversity of enhancer sequences and the flexible localization on genomes. Till now, the interactions between enhancers and genes have not been fully understood yet. Read More

View Article and Full-Text PDF

Os(II)-Bridged Polyarginine Conjugates: The Additive Effects of Peptides in Promoting or Preventing Permeation in Cells and Multicellular Tumor Spheroids.

Inorg Chem 2021 May 12. Epub 2021 May 12.

School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.

The preparation of two polyarginine conjugates of the complex Os(II) [bis-(4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine)] [Os-(R)] ( = 4 and 8; = 10 and 18) is reported, to explore whether the R8 peptide sequence that promotes cell uptake requires a contiguous amino acid sequence for membrane permeation or if this can be accomplished in a linearly bridged structure with the additive effect of shorter peptide sequences. The conjugates exhibit NIR emission centered at 754 nm and essentially oxygen-insensitive emission with a lifetime of 89 ns in phosphate-buffered saline. The uptake, distribution, and cytotoxicity of the parent complex and peptide derivatives were compared in 2D cell monolayers and a three-dimensional (3D) multicellular tumor spheroid (MCTS) model. Read More

View Article and Full-Text PDF

An update on emerging therapeutics to combat COVID-19.

Basic Clin Pharmacol Toxicol 2021 May 11. Epub 2021 May 11.

Division of Veterinary Parasitology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S Pura-181102, J & K, India.

Background: The COVID-19 pandemic has demanded effective therapeutic protocol from researchers and clinicians across the world. Currently, a large amount of primary data have been generated from several preclinical studies. At least 300 clinical trials are underway for drug repurposing against COVID-19; the clinician needs objective evidence-based medication to treat COVID-19. Read More

View Article and Full-Text PDF

DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery.

Adv Sci (Weinh) 2021 05 8;8(9):2004958. Epub 2021 Mar 8.

Center for Precision Health School of Biomedical Informatics The University of Texas Health Science Center at Houston (UTHealth) Houston TX 77030 USA.

Approximately 15% of human cancers are estimated to be attributed to viruses. Virus sequences can be integrated into the host genome, leading to genomic instability and carcinogenesis. Here, a new deep convolutional neural network (CNN) model is developed with attention architecture, namely DeepVISP, for accurately predicting oncogenic virus integration sites (VISs) in the human genome. Read More

View Article and Full-Text PDF

Historical effective population size of North American hoary bat () and challenges to estimating trends in contemporary effective breeding population size from archived samples.

PeerJ 2021 19;9:e11285. Epub 2021 Apr 19.

U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, United States of America.

Background: Hoary bats () are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Read More

View Article and Full-Text PDF

Molecular evolution and SSRs analysis based on the chloroplast genome of .

Ecol Evol 2021 May 20;11(9):4786-4802. Epub 2021 Mar 20.

College of Life Sciences South China Agricultural University Guangzhou China.

Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of , and . Read More

View Article and Full-Text PDF

The feasibility of Gazefinder under 12 months of age infants.

Sci Rep 2021 May 11;11(1):10009. Epub 2021 May 11.

Department of Pediatrics, Shimane University Faculty of Medicine, 89-1, Enya-cho, Izumo, Shimane, 693-8501, Japan.

Eye-tracking to evaluate gaze patterns has developed as an assessment tool for children with autism spectrum disorder (ASD). Gazefinder is one of Eye-tracking devices and few studies have investigated whether it can measure the gaze data of infants under 12 months of age. We conducted a prospective cross-sectional study from April 2019 to March 2020 in a periodic health checkup in Ohchi County, Shimane, Japan. Read More

View Article and Full-Text PDF

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions.

Sci Rep 2021 May 11;11(1):9999. Epub 2021 May 11.

Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA.

The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. Read More

View Article and Full-Text PDF

Variation in selective constraints along the Plasmodium life cycle.

Infect Genet Evol 2021 May 8:104908. Epub 2021 May 8.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA. Electronic address:

Plasmodium parasites, the cause of malaria, have a complex life cycle, infecting alternatively vertebrate hosts and female Anopheles mosquitoes and going through intra- and extra-cellular development in several organs of these hosts. Most of the ~5000 protein-coding genes present in Plasmodium genomes are only expressed at specific life stages, and different genes might therefore be subject to different selective pressures depending on the biological activity of the parasite and its microenvironment at this point in development. Here, we estimate the selective constraints on the protein-coding sequences of all annotated genes of rodent and primate Plasmodium parasites and, using data from scRNA-seq experiments spanning many developmental stages, analyze their variation with regard to when these genes are expressed in the parasite life cycle. Read More

View Article and Full-Text PDF

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.

J Microbiol Methods 2021 May 8:106235. Epub 2021 May 8.

Scotland's Rural College, Edinburgh, UK. Electronic address:

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Read More

View Article and Full-Text PDF

Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments.

PLoS One 2021 11;16(5):e0247541. Epub 2021 May 11.

Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America.

Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that "write" these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. Read More

View Article and Full-Text PDF

A Multimodality-Contribution-Aware TripNet for Histologic Grading of Hepatocellular carcinoma.

IEEE/ACM Trans Comput Biol Bioinform 2021 May 11;PP. Epub 2021 May 11.

Hepatocellular carcinoma (HCC) is a type of primary liver malignant tumor with a high recurrence rate and poor prognosis even undergoing resection or transplantation. Accurate discrimination of the histologic grades of HCC plays a critical role in the management and therapy of HCC patients. In this paper, we discuss a deep learning-based diagnostic model for HCC histologic grading with multimodal Magnetic Resonance Imaging (MRI) images to overcome the problem of limited well-annotated data and extract the discriminated fusion feature referring to the clinical diagnosis experience of radiologists. Read More

View Article and Full-Text PDF

Subchondral bone length in knee osteoarthritis: A deep learning derived imaging measure and its association with radiographic and clinical outcomes.

Arthritis Rheumatol 2021 May 11. Epub 2021 May 11.

Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA, 02118.

Objective: Develop a bone shape measure that reflects the extent of cartilage loss and bone flattening in knee osteoarthritis (OA) and test it against estimates of disease severity.

Methods: A fast region-based convolutional neural network was trained to crop the knee joints in sagittal dual-echo steady state MRI sequences obtained from the Osteoarthritis Initiative (OAI). Publicly available annotations of the cartilage and menisci were used as references to annotate the tibia and the femur in 61 knees. Read More

View Article and Full-Text PDF

Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae.

J Zhejiang Univ Sci B 2021 May;22(5):366-382

Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of and in the rice, , sorghum, maize, and foxtail millet genomes. Read More

View Article and Full-Text PDF

Planococcus soli sp. nov., isolated from antarctic soil.

Antonie Van Leeuwenhoek 2021 May 11. Epub 2021 May 11.

Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 100081, Beijing, People's Republic of China.

A novel bacterial strain, designated C23, was isolated from a soil sample obtained from King George Island, Antarctica. Phenotypic, phylogenetic, chemotaxonomic and molecular analyses were performed on the new isolate. Strain C23 formed orange colonies on agar plates and was Gram-stain-positive. Read More

View Article and Full-Text PDF

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.

Nat Genet 2021 May 10. Epub 2021 May 10.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.

As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of 'genomic contact tracing'-that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. Read More

View Article and Full-Text PDF

Determination of a microRNA signature of protective kidney ischemic preconditioning originating from proximal tubules.

Sci Rep 2021 May 10;11(1):9862. Epub 2021 May 10.

Wales Kidney Research Unit, School of Medicine, College of Biomedical & Life Sciences, Cardiff University, Heath Park Campus, Cardiff, CF14 4XN, UK.

Ischemic preconditioning (IPC) is effective in limiting subsequent ischemic acute kidney injury in experimental models. MicroRNAs are an important class of post-transcriptional regulator and show promise as biomarkers of kidney injury. We evaluated the time- and dose-dependence of benefit from IPC in a rat model of functional (bilateral) ischemia-reperfusion injury (IRI). Read More

View Article and Full-Text PDF

Novel functional sequences uncovered through a bovine multiassembly graph.

Proc Natl Acad Sci U S A 2021 May;118(20)

Animal Genomics, Eidgenössische Technische Hochschule (ETH) Zürich, 8315 Zürich, Switzerland.

Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. Read More

View Article and Full-Text PDF

Vps34 and TOR Kinases Coordinate mRNA Translation in the presence or absence of Ire1-dependent Splicing.

Mol Cell Biol 2021 May 10. Epub 2021 May 10.

Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI-53211, USA

In the budding yeast an mRNA, called , exists in a translationally repressed form in the cytoplasm. Under conditions of cellular stress, such as when unfolded proteins accumulate inside the endoplasmic reticulum (ER), an RNase Ire1 removes an intervening sequence (intron) from the mRNA by non-conventional cytosolic splicing. Removal of the intron results in translational de-repression of mRNA and production of a transcription factor that activates expressions of many enzymes and chaperones to increase the protein-folding capacity of the cell. Read More

View Article and Full-Text PDF

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.

J Mol Biol 2021 May 24;433(11):166895. Epub 2021 Feb 24.

Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany. Electronic address:

Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. Read More

View Article and Full-Text PDF

Simultaneous learning of individual microRNA-gene interactions and regulatory comodules.

BMC Bioinformatics 2021 May 10;22(1):237. Epub 2021 May 10.

Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA.

Background: MicroRNAs (miRNAs) function in post-transcriptional regulation of gene expression by binding to target messenger RNAs (mRNAs). Because of the key part that miRNAs play, understanding the correct regulatory role of miRNAs in diverse patho-physiological conditions is of great interest. Although it is known that miRNAs act combinatorially to regulate genes, precise identification of miRNA-gene interactions and their specific functional roles in regulatory comodules remains a challenge. Read More

View Article and Full-Text PDF

Identification of the conserved long non-coding RNAs in myogenesis.

BMC Genomics 2021 May 10;22(1):336. Epub 2021 May 10.

Data Sciences and Computational Biology Centre, Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, Manesar, 122413, Haryana, India.

Background: Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Read More

View Article and Full-Text PDF

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples.

BMC Bioinformatics 2021 May 10;22(1):236. Epub 2021 May 10.

DKMS Life Science Lab, Dresden, Germany.

Background: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation.

Results: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies-the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing-to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. Read More

View Article and Full-Text PDF