592,443 results match your criteria domain

Comprehensive analysis of BTN3A1 in cancers: mining of omics data and validation in patient samples and cellular models.

FEBS Open Bio 2021 Jul 22. Epub 2021 Jul 22.

State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.

Butyrophilin 3A1 (BTN3A1), a major histocompatibility complex (MHC)-associated gene that encodes a membrane protein with 2 extracellular immunoglobulin domains and an intracellular B30.2 domain, is critical in T-cell activation and adaptive immune response. Here, the expression of BTN3A1 in cancers was analyzed in 8 databases comprising 86,733 patients of 33 cancers and the findings were validated in patient samples and cell models. Read More

View Article and Full-Text PDF

Genome-wide survey of the F-box/Kelch (FBK) members and molecular identification of a novel FBK gene TaAFR in wheat.

PLoS One 2021 22;16(7):e0250479. Epub 2021 Jul 22.

College of Life Sciences/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China.

F-box proteins play critical roles in plant responses to biotic/abiotic stresses. In the present study, a total of 68 wheat F-box/Kelch (TaFBK) genes, unevenly distributed across 21 chromosomes and encoding 74 proteins, were identified in EnsemblPlants. Protein sequences were compared with those of Arabidopsis and three cereal species by phylogenetic and domain analyses, where the wheat sequences were resolved into 6 clades. Read More

View Article and Full-Text PDF

Highly accurate protein structure prediction for the human proteome.

Nature 2021 Jul 22. Epub 2021 Jul 22.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally-determined structure. Here we dramatically expand structural coverage by applying the state-of-the-art machine learning method, AlphaFold, at scale to almost the entire human proteome (98. Read More

View Article and Full-Text PDF

Expanding DSD Phenotypes Associated with Variants in the DEAH-Box RNA Helicase DHX37.

Sex Dev 2021 Jul 22:1-9. Epub 2021 Jul 22.

Human Developmental Genetics Unit, CNRS UMR 3738, Institut Pasteur, Paris, France.

Missense variants in the RNA-helicase DHX37 are associated with either 46,XY gonadal dysgenesis or 46,XY testicular regression syndrome (TRS). DHX37 is required for ribosome biogenesis, and this subgroup of XY DSD is a new human ribosomopathy. In a cohort of 140 individuals with 46,XY DSD, we identified 7 children with either 46,XY complete gonadal dysgenesis or 46,XY TRS carrying rare or novel DHX37 variants. Read More

View Article and Full-Text PDF

Structural insights in galectin-1-glycan recognition: Relevance of the glycosidic linkage and the N-acetylation pattern of sugar moieties.

Bioorg Med Chem 2021 Jul 14;44:116309. Epub 2021 Jul 14.

Laboratorio de Bioquímica, Departamento de Biociencias, Facultad de Química, UdelaR, Gral. Flores, 2124, 11800 Montevideo, Uruguay. Electronic address:

Galectins, soluble lectins widely expressed intra- and extracellularly in different cell types, play major roles in deciphering the cellular glycocode. Galectin-1 (Gal-1), a prototype member of this family, presents a carbohydrate recognition domain (CRD) with specific affinity for β-galactosides such as N-acetyllactosamine (β-d-Galp-(1 → 4)-d-GlcpNAc), and mediate numerous physiological and pathological processes. In this work, Gal-1 binding affinity for β-(1 → 6) galactosides, including β-d-Galp-(1 → 6)-β-d-GlcpNAc-(1 → 4)-d-GlcpNAc was evaluated, and their performance was compared to that of β-(1 → 4) and β-(1 → 3) galactosides. Read More

View Article and Full-Text PDF

Leveraging unsupervised image registration for discovery of landmark shape descriptor.

Med Image Anal 2021 Jul 9;73:102157. Epub 2021 Jul 9.

Scientific Computing and Imaging Institute, 72 Central Campus Dr, University of Utah, Salt Lake City, Utah-84112, USA; School of Computing, 50 Central Campus Dr, University of Utah, Salt Lake City, Utah-84112, USA.

In current biological and medical research, statistical shape modeling (SSM) provides an essential framework for the characterization of anatomy/morphology. Such analysis is often driven by the identification of a relatively small number of geometrically consistent features found across the samples of a population. These features can subsequently provide information about the population shape variation. Read More

View Article and Full-Text PDF

A French survey on the lockdown consequences of COVID-19 pandemic in Parkinson's disease. The ERCOPARK study.

Parkinsonism Relat Disord 2021 Jul 13;89:128-133. Epub 2021 Jul 13.

Service de Neurologie, Centre Hospitalier Universitaire, Toulouse, France; France CHU de Toulouse, Université de Toulouse-Toulouse 3, INSERM, UMR1214 Toulouse NeuroImaging Centre "TONIC," Center of Excellence in Neurodegeneration (CoEN), NeuroToul, Centre Expert Parkinson de Toulouse, Centre d'Investigation Clinique CIC1436, NS-Park/FCRIN Network, Services de Neurologie et de Pharmacologie Clinique, UMR 1048 Institute for Cardiovascular Diseases, Toulouse, France.

Background: In 2020 the coronavirus disease 19 (COVID-19) pandemic imposed a total and sudden lockdown. We aimed to investigate the consequences of the first COVID-19 lockdown (mid-March - mid-April 2020) on motor and non-motor symptoms (NMS) in a cohort of French people with Parkinson's disease (PwP).

Methods: PwP were enrolled either by an on-line survey sent from the national France Parkinson association (FP) to reach the French community of PwP or as part of outpatients' telemedicine visits followed by an hospital-based Parkinson Expert Center (PEC). Read More

View Article and Full-Text PDF

Cross-domain associations between mathematical and narrative abilities in preschool-aged children.

J Exp Child Psychol 2021 Jul 19;212:105233. Epub 2021 Jul 19.

Crane Center for Early Childhood Research and Policy, The Ohio State University, Columbus, OH 43201, USA.

Both mathematical and narrative abilities are considered critical dimensions of children's kindergarten readiness skills and are emphasized in developmental standards and readiness assessments during the prekindergarten period. Yet, despite considerable opportunities available to educators to leverage potential cross-domain associations in their instruction, little is known about how component math skills are associated with narrative skills. The current study extends prior theoretical and empirical work on cross-domain associations by examining the extent to which component math skills, constituting a kindergarten readiness assessment battery, are associated with narrative comprehension skills in children aged 4-6 years. Read More

View Article and Full-Text PDF

Mig6 not only inhibits EGFR and HER2 but also targets HER3 and HER4 in a differential specificity: Implications for targeted esophageal cancer therapy.

Biochimie 2021 Jul 19. Epub 2021 Jul 19.

Department of Thoracic Surgery, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. Electronic address:

The human EGF receptor family plays pivotal roles in physiology and cancer, which contains four closely-related members: HER1/EGFR, HER2, HER3 and HER4. Previously, it was found that the mitogen-inducible gene 6 (Mig6) protein is a negative regulator of EGFR and HER2 by using its S1 segment to bind at the kinase dimerization interface. However, it is still unclear whether the S1 segment can also effectively target HER3 and HER4? Here, we performed a systematic investigation to address this issue. Read More

View Article and Full-Text PDF

Purification and characterization of an amyloidogenic repeat domain from the functional amyloid Pmel17.

Protein Expr Purif 2021 Jul 19:105944. Epub 2021 Jul 19.

Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States. Electronic address:

The pre-melanosomal protein (Pmel17) is a human functional amyloid that supports melanin biosynthesis within melanocytes. This occurs in the melanosome, a membrane-bound organelle with an acidic intraluminal pH. The repeat region of Pmel17 (RPT, residues 315-444) has been previously shown to form amyloid aggregates under acidic melanosomal conditions, but not under neutral cytosolic conditions, when expressed and purified using a C-terminal hexa-histidine tag (RPT-His). Read More

View Article and Full-Text PDF

Design and evaluation of GLP-1 receptor G-protein biased agonist with prolonged efficacy on diabetes.

Life Sci 2021 Jul 19:119844. Epub 2021 Jul 19.

Peking University Third Hospital, Beijing 100191, PR China. Electronic address:

Aim: Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have emerged as potent drug development target for treating diabetes and obesity. Here, we designed and evaluated novel long-acting GLP-1R G protein biased agonist with potent clinical application.

Main Methods: GLP-1R G-protein biased sequences were screened via a high-throughput autocrine-based strategy and then fused to Exendin (9-39). Read More

View Article and Full-Text PDF

DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study.

Biophys J 2021 Jul 19. Epub 2021 Jul 19.

Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany. Electronic address:

Linker histones (LH) bind to nucleosomes with their globular domain (gH) positioned in either an on- or an off-dyad binding mode. Here, we study the effect of the linker DNA (L-DNA) sequence on the binding of a full-length LH, Xenopus laevis H1.0b, to a Widom 601 nucleosome core particle (NCP) flanked by two 40 bp long L-DNA arms, by single-pair FRET spectroscopy. Read More

View Article and Full-Text PDF

TANGO1 marshals the early secretory pathway for cargo export.

Biochim Biophys Acta Biomembr 2021 Jul 19:183700. Epub 2021 Jul 19.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain. Electronic address:

TANGO1 protein facilitates the endoplasmic reticulum (ER) export of large cargoes that cannot be accommodated in 60 nm transport vesicles. It assembles into a ring in the plane of the ER membrane to create a distinct domain. Its lumenal portion collects and sorts folded cargoes while its cytoplasmic domains collar COPII coats, recruit retrograde COPI-coated membranes that fuse within the TANGO1 ring, thus opening a tunnel for cargo transfer from the ER into a growing export conduit. Read More

View Article and Full-Text PDF

PIP AQUAPORINS pH sensing is regulated by the length and charge of the C-terminal region.

FEBS J 2021 Jul 22. Epub 2021 Jul 22.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Argentina.

Plant PIP aquaporins play a central role in controlling plant water status. The current structural model for PIP pH-gating states that the main pH sensor is located in loopD and that all the mobile cytosolic elements participate in a complex interactions network that ensures the closed structure. However, the precise participation of the last part of the C-terminal domain (CT) in PIP pH-gating remains unknown. Read More

View Article and Full-Text PDF

Predicting mutant outcome by combining deep mutational scanning and machine learning.

Proteins 2021 Jul 22. Epub 2021 Jul 22.

Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel.

Motivation: Deep mutational scanning provides unprecedented wealth of quantitative data regarding the functional outcome of mutations in proteins. A single experiment may measure properties (e.g. Read More

View Article and Full-Text PDF

In-depth bioinformatic study of the cadherin 5 interactome in patients with thoracic aortic aneurysm unveils 8 novel biomarkers.

Eur J Cardiothorac Surg 2021 Jul 19. Epub 2021 Jul 19.

Department of Surgery and Cancer, Imperial College London, St Mary's Hospital, London, UK.

Objectives: Thoracic aortic aneurysm (TAA) is characterized by the dilation of the aorta and is associated with poor prognosis if not diagnosed and treated early. In this context, the identification of biomarkers regarding the TAA diagnosis, monitoring and prognosis is crucial. The purpose of the current study was to investigate the differential gene expression profile of the cadherin 5 (CDH5 or VE-Cadherin) gene network in patients with TAA, to propose novel biomarkers. Read More

View Article and Full-Text PDF

Validating the Michigan Hand Outcomes Questionnaire in patients with rheumatoid arthritis using Rasch analysis.

PLoS One 2021 22;16(7):e0254984. Epub 2021 Jul 22.

Section of Plastic Surgery, Michigan Medicine, Ann Arbor, Michigan, United States of America.

Introduction: The Michigan Hand Outcomes Questionnaire (MHQ) is a patient-reported outcome measure previously validated in patients with rheumatoid arthritis (RA) using classical test theory. Rasch analysis is a more rigorous method of questionnaire validation that has not been used to test the psychometric properties of the MHQ in patients with RA. The objective of this study is to evaluate the validity and reliability of the MHQ for measuring outcomes in patients with RA with metacarpophalangeal joint deformities. Read More

View Article and Full-Text PDF

Constitutive activation of NF-κB inducing kinase (NIK) in the mesenchymal lineage using Osterix (Sp7)- or Fibroblast-specific protein 1 (S100a4)-Cre drives spontaneous soft tissue sarcoma.

PLoS One 2021 22;16(7):e0254426. Epub 2021 Jul 22.

Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America.

Aberrant NF-κB signaling fuels tumor growth in multiple human cancer types including both hematologic and solid malignancies. Chronic elevated alternative NF-κB signaling can be modeled in transgenic mice upon activation of a conditional NF-κB-inducing kinase (NIK) allele lacking the regulatory TRAF3 binding domain (NT3). Here, we report that expression of NT3 in the mesenchymal lineage with Osterix (Osx/Sp7)-Cre or Fibroblast-Specific Protein 1 (FSP1)-Cre caused subcutaneous, soft tissue tumors. Read More

View Article and Full-Text PDF

Persistent homology as a new method of the assessment of heart rate variability.

PLoS One 2021 22;16(7):e0253851. Epub 2021 Jul 22.

Department of Hypertension and Diabetology, Medical University of Gdańsk, Gdańsk, Poland.

Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. Read More

View Article and Full-Text PDF

Ongoing global and regional adaptive evolution of SARS-CoV-2.

Proc Natl Acad Sci U S A 2021 Jul 2;118(29). Epub 2021 Jul 2.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;

Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. Read More

View Article and Full-Text PDF

COVID-19 reveals the urgent need to strengthen nursing informatics competencies: a view from Peru.

Inform Health Soc Care 2021 Jul 22:1-5. Epub 2021 Jul 22.

Facultad de Medicina Humana, Universidad Nacional José Faustino Sánchez Carrión, Huacho, Perú.

The COVID-19 pandemic requires an urgent action to transform health-care delivery and to promote research and capacity-building nursing programs. Specifically, many countries at the global level have described nursing informatics as an essential competence for nurse professionals. In Peru, nursing personnel represents the largest health workforce group and nursing informatics is still emerging, but the field appear to hold much promise. Read More

View Article and Full-Text PDF

Spectrum of BCR-ABL Mutations and Treatment Outcomes in Ethiopian Imatinib-Resistant Patients With Chronic Myeloid Leukemia.

JCO Glob Oncol 2021 Jul;7:1187-1193

Fred Hutchinson Cancer Research Center, Seattle, WA.

Purpose: Despite the successes achieved in chronic myeloid leukemia (CML) with tyrosine kinase inhibitor (TKI) therapy, resistance remains an obstacle. The most common mechanism of resistance is the acquisition of a point mutation in the BCR-ABL kinase domain. Few studies have reported African patients with CML in regard to such mutations. Read More

View Article and Full-Text PDF

Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks.

J Chem Inf Model 2021 Jul 22. Epub 2021 Jul 22.

iMolecule, Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.

Peptides and peptide-based molecules represent a promising therapeutic modality targeting intracellular protein-protein interactions, potentially combining the beneficial properties of biologics and small-molecule drugs. Protein-peptide complexes occupy a unique niche of interaction interfaces with respect to protein-protein and protein-small molecule complexes. Protein-peptide binding site identification resembles image object detection, a field that had been revolutionalized with computer vision techniques. Read More

View Article and Full-Text PDF

Cyclic, Hydrophobic Hexapeptide Fusahexin Is the Product of a Nonribosomal Peptide Synthetase in .

J Nat Prod 2021 Jul 22. Epub 2021 Jul 22.

Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK-9220 Aalborg, Denmark.

The plant pathogenic fungus is known to produce a wide array of secondary metabolites during plant infection. This includes several nonribosomal peptides. Recently, the fusaoctaxin (/9) and gramilin () gene clusters were shown to be induced by host interactions. Read More

View Article and Full-Text PDF

New Impedimetric Sandwich Immunosensor for Ultrasensitive and Highly Specific Detection of Spike Receptor Binding Domain Protein of SARS-CoV-2.

ACS Biomater Sci Eng 2021 Jul 22. Epub 2021 Jul 22.

Bioengineering Department, Faculty of Engineering, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey.

An impedance sensing platform-combined conducting nanocomposite layer was fabricated to develop an effective and rapid method for detection of coronavirus infection (COVID-19) specific spike receptor binding domain (RBD) protein, a precious antigen marker of COVID-19 disease. Coronavirus infection has spread globally and swiftly with major impacts on health, economy, and quality of life of communities. Fast and reliable detection of COVID-19 is a very significant issue for the effective treatment of this bad illness. Read More

View Article and Full-Text PDF

Data inaccessibility at sub-county scale limits implementation of manuresheds.

J Environ Qual 2021 Jul 22. Epub 2021 Jul 22.

Department of Agronomy, University of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53705.

The manureshed concept aims to rebalance surplus manure nutrients produced at animal feeding operations (sources) and the demands from nutrient-deficient croplands (sinks) to reduce negative environmental impacts and utilize nutrients more efficiently. Due to water quality implications, studies focused on this re-balancing have typically created domain boundaries that match a particular watershed. However, a majority of agricultural datasets that are used to inform these analyses - specifically, livestock populations - are only available at the county scale, which generally do not match watershed boundaries. Read More

View Article and Full-Text PDF

Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism.

Methods Mol Biol 2021 ;2353:37-50

Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, NJ, USA.

Iron-sulfur (Fe-S) clusters are among the oldest and most versatile cofactors present in all domains of life. Many bacterial and eukaryotic Fe-S proteins have been well-characterized, whereas the archaeal ones are less studied. Fe-S proteins are particularly abundant and play essential roles in methanogenic archaea. Read More

View Article and Full-Text PDF
January 2021

Brief Report: The Effectiveness of Hugging a Huggable Device Before Having a Conversation with an Unfamiliar Person for Autism Spectrum Disorders.

J Autism Dev Disord 2021 Jul 22. Epub 2021 Jul 22.

Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan.

Sensory overresponsivity (SOR) emerges before anxiety and positively predicts subsequent increasing levels of anxiety in individuals with autism spectrum disorder (ASD). Sensory seeking behavior occurs as compensation for SOR, and individuals may seek sensory input in one sensory domain to compensate for SOR. Tactile seeking behavior is sufficient to decrease social anxiety in communicating with unfamiliar people. Read More

View Article and Full-Text PDF

Landscape of EBV-positive gastric cancer.

Gastric Cancer 2021 Jul 22. Epub 2021 Jul 22.

Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, 1, Hikarigaoka, Fukushima, 960-1295, Japan.

Epstein-Barr virus-positive gastric cancer [EBV (+) GC] is associated with EBV infection and is one of the GC subtypes defined by the Cancer Genome Atlas. EBV (+) GC has several distinct genomic or epigenomic features and clinicopathological characteristics compared with other molecular subtypes of GC. Here, we summarize the unique features of EBV (+) GC including the clinical and histopathological features, and discuss associated genetic and epigenetic aberrations. Read More

View Article and Full-Text PDF

Identification and characterization of a novel virus associated with an eriophyid mite in extracts of fruit trees leaves.

Arch Virol 2021 Jul 22. Epub 2021 Jul 22.

United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Germplasm Quarantine Program, Beltsville, MD, USA.

Eriophyid mites are commonly found on the leaf surface of different plant species. In the present study, a novel virus associated with an eriophyid mite species was detected using high-throughput sequencing (HTS) of total RNA from fruit tree leaves, primarily growing under greenhouse conditions. The complete genome sequence was characterized using rapid amplification of cDNA ends followed by Sanger sequencing, revealing a genome of 8885 nucleotides in length. Read More

View Article and Full-Text PDF