3,092 results match your criteria domains connected


Evolution of KIPPIS as a versatile platform for evaluating intracellularly functional peptide aptamers.

Sci Rep 2021 Jun 3;11(1):11758. Epub 2021 Jun 3.

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.

Chimeric proteins have been widely used to evaluate intracellular protein-protein interactions (PPIs) in living cells with various readouts. By combining an interleukin-3-dependent murine cells and chimeric proteins containing a receptor tyrosine kinase c-kit, we previously established a c-kit-based PPI screening (KIPPIS) system to evaluate and select protein binders. In the KIPPIS components, proteins of interest are connected with a chemically inducible helper module and the intracellular domain of the growth-signaling receptor c-kit, which detects PPIs based on cell proliferation as a readout. Read More

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RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements.

Viruses 2021 May 21;13(6). Epub 2021 May 21.

Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, 28049 Madrid, Spain.

Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Read More

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Prion-like proteins: From computational approaches to proteome-wide analysis.

FEBS Open Bio 2021 May 31. Epub 2021 May 31.

Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.

Prions are self-perpetuating proteins able to switch between a soluble state and an aggregated-and-transmissible conformation. These proteinaceous entities have been widely studied in yeast, where they are involved in hereditable phenotypic adaptations. The notion that such proteins could play functional roles and be positively selected by evolution has triggered the development of computational tools to identify prion-like proteins in different kingdoms of life. Read More

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Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation.

Protein Sci 2021 Jul 5;30(7):1467-1481. Epub 2021 Jun 5.

Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.

Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. Read More

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The physiological role of estrogen receptor functional domains.

Essays Biochem 2021 May 24. Epub 2021 May 24.

Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, United States.

Estrogen receptor (ER) is a member of the nuclear receptor superfamily whose members share conserved domain structures, including a DNA-binding domain (DBD) and ligand-binding domain (LBD). Estrogenic chemicals work as ligands for activation or repression of ER-mediated transcriptional activity derived from two transactivation domains: AF-1 and AF-2. AF-2 is localized in the LBD, and helix 12 of the LBD is essential for controlling AF-2 functionality. Read More

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Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters.

Proc Natl Acad Sci U S A 2021 May;118(21)

Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;

ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. Read More

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Chromatin architecture transitions from zebrafish sperm through early embryogenesis.

Genome Res 2021 Jun 18;31(6):981-994. Epub 2021 May 18.

Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. Read More

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Connectivity characterization of the mouse basolateral amygdalar complex.

Nat Commun 2021 05 17;12(1):2859. Epub 2021 May 17.

Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

The basolateral amygdalar complex (BLA) is implicated in behaviors ranging from fear acquisition to addiction. Optogenetic methods have enabled the association of circuit-specific functions to uniquely connected BLA cell types. Thus, a systematic and detailed connectivity profile of BLA projection neurons to inform granular, cell type-specific interrogations is warranted. Read More

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Structural basis for CD97 recognition of the decay-accelerating factor CD55 suggests mechanosensitive activation of adhesion GPCRs.

J Biol Chem 2021 May 13:100776. Epub 2021 May 13.

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. Electronic address:

The adhesion G protein-coupled receptor CD97 and its ligand complement decay-accelerating factor CD55 are important binding partners in the human immune system. Dysfunction in this binding has been linked to immune disorders such as multiple sclerosis and rheumatoid arthritis, as well as various cancers. Previous literatures have indicated that the CD97 includes three to five EGF domains at its N-terminus and these EGF domains can bind to the N-terminal SCR domains of CD55. Read More

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Transcription factor allosteric regulation through substrate coordination to zinc.

NAR Genom Bioinform 2021 Jun 3;3(2):lqab033. Epub 2021 May 3.

CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal.

The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. Read More

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Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2.

Biophys J 2021 May 10. Epub 2021 May 10.

Department of Physics, University of Cyprus, PO Box 20537, CY1678, Nicosia, Cyprus. Electronic address:

The coronavirus SARS-CoV-2, that is responsible for the COVID-19 pandemic, and the closely related SARS-CoV coronavirus enter cells by binding at the human angiotensin converting enzyme 2 (hACE2). The stronger hACE2 affinity of SARS-CoV-2 has been connected with its higher infectivity. In this work, we study hACE2 complexes with the receptor binding domains (RBDs) of the human SARS-CoV-2 and human SARS-CoV viruses, using all-atom molecular dynamics (MD) simulations and Computational Protein Design (CPD) with a physics-based energy function. Read More

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Multithreaded two-pass connected components labelling and particle analysis in ImageJ.

Authors:
Michael Doube

R Soc Open Sci 2021 Mar 3;8(3):201784. Epub 2021 Mar 3.

Department of Infectious Diseases and Public Health, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR.

Sequential region labelling, also known as connected components labelling, is a standard image segmentation problem that joins contiguous foreground pixels into blobs. Despite its long development history and widespread use across diverse domains such as bone biology, materials science and geology, connected components labelling can still form a bottleneck in image processing pipelines. Here, I describe a multithreaded implementation of classical two-pass sequential region labelling and introduce an efficient collision resolution step, '. Read More

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Perturbation of the peptidoglycan network and utilization of the signal recognition particle-dependent pathway enhances the extracellular production of a truncational mutant of CelA in Escherichia coli.

J Ind Microbiol Biotechnol 2021 May 6. Epub 2021 May 6.

Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea.

Caldicellulosiruptor bescii is the most thermophilic, cellulolytic bacterium known and has the native ability to utilize unpretreated plant biomass. Cellulase A (CelA) is the most abundant enzyme in the exoproteome of C. bescii and is primarily responsible for its cellulolytic ability. Read More

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Undoing the 'Nordic Paradox': Factors affecting rates of disclosed violence against women across the EU.

PLoS One 2021 5;16(5):e0249693. Epub 2021 May 5.

Division of Gender Studies and Sociology, School of Humanities, Education and Social Sciences, Örebro University, Örebro, Sweden.

Measuring violence against women raises methodological questions, as well as the wider question of how to understand violence and locate it in relation to a societal context. This is all the more relevant given that measurement of violence against women in the EU has made an interesting phenomenon apparent, the so-called 'Nordic Paradox', whereby prevalence is higher in more gender equal countries. This article examines this phenomenon by exploring a range of factors-methodological, demographic and societal-to contextualise disclosed levels of violence. Read More

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The psychometric network structure of mental health in eating disorder patients.

Eur Eat Disord Rev 2021 Jul 5;29(4):559-574. Epub 2021 May 5.

Department of Psychology, Health and Technology, Centre for eHealth and Wellbeing Research, University of Twente, Enschede, The Netherlands.

Objective: Psychometric network analysis has led to new possibilities to assess the structure and dynamics of psychiatric disorders. The current study focuses on mental health networks in patients with anorexia nervosa, bulimia nervosa, binge eating disorder and other specified eating disorders (EDs).

Method: Network analyses were applied with five mental health domains (emotional, psychological and social well-being, and general and specific psychopathology) among 905 ED patients. Read More

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Cognitive impairment after focal brain lesions is better predicted by damage to structural than functional network hubs.

Proc Natl Acad Sci U S A 2021 May;118(19)

Department of Psychiatry, Carver College of Medicine, Iowa City, IA 52242.

Hubs are highly connected brain regions important for coordinating processing in brain networks. It is unclear, however, which measures of network "hubness" are most useful in identifying brain regions critical to human cognition. We tested how closely two measures of hubness-edge density and participation coefficient, derived from white and gray matter, respectively-were associated with general cognitive impairment after brain damage in two large cohorts of patients with focal brain lesions (N = 402 and 102, respectively) using cognitive tests spanning multiple cognitive domains. Read More

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Behavioral Restriction Determines Left Attentional Bias: Preliminary Evidences From COVID-19 Lockdown.

Front Psychol 2021 9;12:650715. Epub 2021 Apr 9.

Department of Humanities, University of Naples Federico II, Naples, Italy.

During the COVID-19 lockdown, individuals were forced to remain at home, hence severely limiting the interaction within environmental stimuli, reducing the cognitive load placed on spatial competences. The effects of the behavioral restriction on cognition have been little examined. The present study is aimed at analyzing the effects of lockdown on executive function prominently involved in adapting behavior to new environmental demands. Read More

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Precise levels of the Drosophila adaptor protein Dreadlocks maintain the size and stability of germline ring canals.

J Cell Sci 2021 Apr 27;134(8). Epub 2021 Apr 27.

Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA.

Intercellular bridges are essential for fertility in many organisms. The developing fruit fly egg has become the premier model system to study intercellular bridges. During oogenesis, the oocyte is connected to supporting nurse cells by relatively large intercellular bridges, or ring canals. Read More

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Dilated Cardiomyopathy Mutations and Phosphorylation disrupt the Active Orientation of Cardiac Troponin C.

J Mol Biol 2021 Jun 24;433(13):167010. Epub 2021 Apr 24.

Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada; Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada. Electronic address:

Cardiac troponin (cTn) is made up of three subunits, cTnC, cTnI, and cTnT. The regulatory N-terminal domain of cTnC (cNTnC) controls cardiac muscle contraction in a calcium-dependent manner. We show that calcium-saturated cNTnC can adopt two different orientations, with the "active" orientation consistent with the 2020 cryo-EM structure of the activated cardiac thin filament by Yamada et al. Read More

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Effects of deep transcranial magnetic stimulation (dTMS) on cognition.

Neurosci Lett 2021 06 20;755:135906. Epub 2021 Apr 20.

National Institute of Mental Health, Topolová 748, Klecany, 25067, Czech Republic; Third Faculty of Medicine, Charles University, Ruská 87, Prague 10, 10100, Czech Republic. Electronic address:

Deep transcranial magnetic stimulation (dTMS) is a modern non-invasive brain stimulation method demonstrated as effective in the treatment of major depression and obsessive-compulsive disorder (OCD). This review aims to survey present knowledge concerning the cognitive function changes identified in dTMS research. A systematic literature search in PubMed and Google Scholar was performed and 23 out of 64 studies on dTMS and cognitive functioning were included in the review. Read More

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Ideological biases in social sharing of online information about climate change.

PLoS One 2021 23;16(4):e0250656. Epub 2021 Apr 23.

Department of Computer Science, University of Exeter, Exeter, Devon, United Kingdom.

Exposure to media content is an important component of opinion formation around climate change. Online social media such as Twitter, the focus of this study, provide an avenue to study public engagement and digital media dissemination related to climate change. Sharing a link to an online article is an indicator of media engagement. Read More

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Biolayer Interferometry: Protein-RNA Interactions.

Methods Mol Biol 2021 ;2263:351-368

Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.

RNA-binding proteins often contain multiple RNA-binding domains connected by short flexible linkers. This domain arrangement allows the protein to bind the RNA with greater affinity and specificity than would be possible with individual domains and sometimes to remodel its structure. It is therefore important to understand how multiple modules interact with RNA because it is the modular nature of these proteins which specifies their biological function. Read More

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January 2021

The Effects of Self-cleavage Intein-ELK16 Tag in the Transcript Steric Hindrance of IFN.

Indian J Clin Biochem 2021 Apr 30;36(2):159-166. Epub 2020 Jan 30.

Division of Genetics, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, 81746-73441 Iran.

Intervening proteins (Inteins) are identified as protein domains in a precursor protein structure. Inteins can excise itself from precursor protein and join the remaining portions which result in forming an active protein. In this study, the transcript expression level of recombinant human Interferon beta (rhIFNβ) connected to the self-cleavage Intein-ELK16 (LELELKLKLELELKLK) tag was measured by real-time PCR in HEK293T cell line. Read More

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Generation of Fluorescent Versions of Saccharomyces cerevisiae RPA to Study the Conformational Dynamics of Its ssDNA-Binding Domains.

Methods Mol Biol 2021 ;2281:151-168

Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.

Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that sequesters ssDNA and protects it from nucleolytic degradation. The RPA-ssDNA nucleoprotein acts as a hub to recruit over two dozen DNA metabolic enzymes onto ssDNA to coordinate DNA replication, repair, and recombination. RPA functions as a heterotrimer composed of RPA70, RPA32, and RPA14 subunits and has multiple DNA-binding and protein-interaction domains. Read More

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January 2021

What Can Network Science Tell Us About Phonology and Language Processing?

Top Cogn Sci 2021 Apr 9. Epub 2021 Apr 9.

Department of Psychology, University of Kansas.

Contemporary psycholinguistic models place significant emphasis on the cognitive processes involved in the acquisition, recognition, and production of language but neglect many issues related to the representation of language-related information in the mental lexicon. In contrast, a central tenet of network science is that the structure of a network influences the processes that operate in that system, making process and representation inextricably connected. Here, we consider how the structure found across phonological networks of several languages from different language families may influence language processing as we age and experience diseases that affect cognition during the typical and atypical acquisition of new words, during typical perception and production of speech in adults, and during language change over time. Read More

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Diffusion property and functional connectivity of superior longitudinal fasciculus underpin human metacognition.

Neuropsychologia 2021 Jun 1;156:107847. Epub 2021 Apr 1.

Shanghai Key Laboratory of Brain Functional Genomics, Key Laboratory of Brain Functional Genomics Ministry of Education, Shanghai Key Laboratory of Magnetic Resonance, Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China; Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China; NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China; Shanghai Changning Mental Health Center, China. Electronic address:

Metacognition as the capacity of monitoring one's own cognition operates across domains. Here, we addressed whether metacognition in different cognitive domains rely on common or distinct neural substrates with combined diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques. After acquiring DTI and resting-state fMRI data, we asked participants to perform a temporal-order memory task and a perceptual discrimination task, followed by trial-specific confidence judgments. Read More

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Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence.

Int J Mol Sci 2021 Mar 16;22(6). Epub 2021 Mar 16.

School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.

The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Read More

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Outpatient Virtual Visits and the "Right" Amount of Telehealth Going Forward.

Telemed J E Health 2021 Mar 31. Epub 2021 Mar 31.

Department of Emergency Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA.

An exponential increase in outpatient telehealth visits occurred early in the pandemic period that has been followed by volumes that, although lower than peak numbers, are substantially greater than the pre-pandemic period. This provided an opportunity to assess provider perceptions regarding the right prevalence going forward and key obstacles to achieving it. A 10-question survey was distributed to all outpatient providers within the Dartmouth-Hitchcock Health System. Read More

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Properties of FDA-approved small molecule phosphatidylinositol 3-kinase inhibitors prescribed for the treatment of malignancies.

Authors:
Robert Roskoski

Pharmacol Res 2021 Jun 26;168:105579. Epub 2021 Mar 26.

Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States. Electronic address:

The discovery of the phosphatidylinositol 3-kinase (PI 3-kinase) pathway was a major advance in understanding eukaryotic signal transduction. The high frequency of PI 3-kinase pathway mutations in many cancers stimulated the development of drugs targeting these oncogenic mutants. The PI 3-kinases are divided into three classes and Class I PI 3-kinases, which catalyze the phosphorylation of phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) to generate phosphatidylinositol-3,4,5-trisphosphate (PIP3), are the main subject of this review. Read More

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biotechnet Switzerland.

Chimia (Aarau) 2021 Mar;75(3):219-224

CSEM Landquart SA, Bahnhofstr. 1, CH-7302 Landquart.

The COVID-19 pandemic has raised in 2020 an unprecedented need for diagnostic testing, especially rapid testing, for SARS-CoV-2 infections. POC diagnostic tools, however, have clearly also importance in other domains such as oncology and women's health, because of the efficiency and convenience factors playing an increasingly important role in a mobile (and sometimes confined) and digitally connected world. Out of necessity, the 3 edition of the Swiss Symposium in POC Diagnostics, originally planned to take place at the La Poste Conference Center in Visp, was smoothly run with 170 engaged participants from science, industry and laboratory medicine. Read More

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