418,875 results match your criteria binding data

PsrA positively regulates the unsaturated fatty acid synthesis operon fabAB in Azotobacter vinelandii.

Microbiol Res 2021 Apr 29;249:126775. Epub 2021 Apr 29.

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México. Electronic address:

In Pseudomonas spp. PsrA, a transcriptional activator of the rpoS gene, regulates fatty acid catabolism by repressing the fadBA5 β-oxidation operon. In Azotobacter vinelandii, a soil bacterium closely related to Pseudomonas species, PsrA is also an activator of rpoS expression, although its participation in the regulation of lipid metabolism has not been analyzed. Read More

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Assay temperature affects corticosteroid-binding globulin and free corticosterone estimates across species.

Gen Comp Endocrinol 2021 May 5:113810. Epub 2021 May 5.

The Wildlife Biology Program, The University of Montana. 32 Campus Drive, HS 104, Missoula, MT 59801; Organismal Biology, Ecology, and Evolution, The University of Montana. 32 Campus Drive, HS 104, Missoula, MT 59801.

Glucocorticoid hormones are often measured to assess how organisms physiologically respond to challenges in their environment. In plasma, glucocorticoids circulate in two forms: bound to corticosteroid-binding globulins (CBG) or unbound (free). Measuring CBG allows us to estimate the amount of free glucocorticoids present in a plasma sample. Read More

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Biallelic mutations in RNF220 cause laminopathies featuring leukodystrophy, ataxia and deafness.

Brain 2021 May 8. Epub 2021 May 8.

Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.

Leukodystrophies are a heterogeneous group of rare inherited disorders that involve preferentially the white matter of the central nervous system (CNS). These conditions are characterized by a primary glial cell and myelin sheath pathology of variable etiology, which causes secondary axonal degeneration, generally emerging with disease progression. Whole exome sequencing performed in 5 large consanguineous nuclear families allowed to identify homozygosity for two recurrent missense variants affecting highly conserved residues of RNF220 as the causative event underlying a novel form of leukodystrophy with ataxia and sensorineural deafness. Read More

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Proteo3Dnet: a web server for the integration of structural information with interactomics data.

Nucleic Acids Res 2021 May 8. Epub 2021 May 8.

Université de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France.

Proteo3Dnet is a web server dedicated to the analysis of mass spectrometry interactomics experiments. Given a flat list of proteins, its aim is to organize it in terms of structural interactions to provide a clearer overview of the data. This is achieved using three means: (i) the search for interologs with resolved structure available in the protein data bank, including cross-species remote homology search, (ii) the search for possibly weaker interactions mediated through Short Linear Motifs as predicted by ELM-a unique feature of Proteo3Dnet, (iii) the search for protein-protein interactions physically validated in the BioGRID database. Read More

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Molecular mechanisms underlying the antidepressant actions of arketamine: beyond the NMDA receptor.

Mol Psychiatry 2021 May 7. Epub 2021 May 7.

Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, Japan.

The discovery of robust antidepressant actions exerted by the N-methyl-D-aspartate receptor (NMDAR) antagonist (R,S)-ketamine has been a crucial breakthrough in mood disorder research. (R,S)-ketamine is a racemic mixture of equal amounts of (R)-ketamine (arketamine) and (S)-ketamine (esketamine). In 2019, an esketamine nasal spray from Johnson & Johnson was approved in the United States of America and Europe for treatment-resistant depression. Read More

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Toll9 from functions as a pattern recognition receptor that shares features with Toll-like receptor 4 from mammals.

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

Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Insect Molecular Biology and Biotechnology, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China;

Toll/Toll-like receptors (TLRs) are key regulators of the innate immune system in both invertebrates and vertebrates. However, while mammalian TLRs directly recognize pathogen-associated molecular patterns, the insect Toll pathway is thought to be primarily activated by binding Spätzle cytokines that are processed from inactive precursors in response to microbial infection. Phylogenetic and structural data generated in this study supported earlier results showing that Toll9 members differ from other insect Tolls by clustering with the mammalian TLR4 group, which recognizes lipopolysaccharide (LPS) through interaction with myeloid differentiation-2 (MD-2)-like proteins. Read More

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Persistent spectral-based machine learning (PerSpect ML) for protein-ligand binding affinity prediction.

Sci Adv 2021 May 7;7(19). Epub 2021 May 7.

Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

Molecular descriptors are essential to not only quantitative structure-activity relationship (QSAR) models but also machine learning-based material, chemical, and biological data analysis. Here, we propose persistent spectral-based machine learning (PerSpect ML) models for drug design. Different from all previous spectral models, a filtration process is introduced to generate a sequence of spectral models at various different scales. Read More

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Cancer type-specific alterations in actin genes: Worth a closer look?

Int Rev Cell Mol Biol 2021 30;360:133-184. Epub 2021 Mar 30.

Department of Biomolecular Medicine, Ghent University, Gent, Belgium.

Actins form a strongly conserved family of proteins that are central to the functioning of the actin cytoskeleton partaking in natural processes such as cell division, adhesion, contraction and migration. These processes, however, also occur during the various phases of cancer progression. Yet, surprisingly, alterations in the six human actin genes in cancer studies have received little attention and the focus was mostly on deregulated expression levels of actins and even more so of actin-binding or regulatory proteins. Read More

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A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma.

BioData Min 2021 May 7;14(1):29. Epub 2021 May 7.

Department of Oncology, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.

Background: Hepatocellular carcinoma (HCC) is a disease with a high incidence and a poor prognosis. Growing amounts of evidence have shown that the immune system plays a critical role in the biological processes of HCC such as progression, recurrence, and metastasis, and some have discussed using it as a weapon against a variety of cancers. However, the impact of immune-related genes (IRGs) on the prognosis of HCC remains unclear. Read More

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The cytotoxic conjugate of highly internalizing tetravalent antibody for targeting FGFR1-overproducing cancer cells.

Mol Med 2021 May 7;27(1):46. Epub 2021 May 7.

Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, 50-383, Wroclaw, Poland.

Background: Antibody drug conjugates (ADCs) represent one of the most promising approaches in the current immuno-oncology research. The precise delivery of cytotoxic drugs to the cancer cells using ADCs specific for tumor-associated antigens enables sparing the healthy cells and thereby reduces unwanted side effects. Overexpression of fibroblast growth factor receptor 1 (FGFR1) has been demonstrated in numerous tumors and thereby constitutes a convenient molecular target for selective cancer treatment. Read More

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Increased hypospadias risk by rs3743104[G] in the southern Han Chinese population.

Aging (Albany NY) 2021 May 7;13. Epub 2021 May 7.

Department of Pediatric Urology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.

Hypospadias is a common congenital genitourinary malformation characterized by ventral opening of the urethral meatus. As a member of the bone morphogenic protein antagonist family, has been identified as associated with susceptibility to hypospadias in the European population. The present study was designed to elaborate on the mutual relationship between replicated single-nucleotide polymorphisms (SNPs) and hypospadias in Asia's largest case-control study in the Southern Han Chinese population involving 577 patients and 654 controls. Read More

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Internal loading of phosphate in rivers reduces at higher flow velocity and is reduced by iron rich sand application: an experimental study in flumes.

Water Res 2021 Apr 18;198:117160. Epub 2021 Apr 18.

Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001 Leuven, Belgium.

Many lowland regions are afflicted with high phosphorus (P) peaks in rivers during the summer months. Static incubations of sediments have shown that reductive dissolution of ferric iron (Fe(III)) minerals in the sediment explain these P peaks. This study was set up to identify if that mechanism also dominates in a dynamic system, thereby testing the roles of water flow velocity and sediment Fe/P ratio. Read More

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Characterization of Litopenaeus vannamei secreted protein acidic and rich in cysteine -like in WSSV infection.

J Invertebr Pathol 2021 May 4:107593. Epub 2021 May 4.

Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Shanghai Ocean University, Shanghai 201306.

Secreted protein acidic and rich in cysteine (SPARC) is an extracellular and non-structural glycoprotein. In shrimp, a significant function of SPARC in WSSV infection remains unclear. In this study, the full-length cDNA sequence of a secreted protein acidic and rich in cysteine -like was cloned from shrimp Litopenaeus vannamei (named as LvSPARC-L). Read More

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ERK1/2 kinases and dopamine D2 receptors participate in the anticonvulsant effects of a new derivative of benzoylpyridine oxime and valproic acid.

Eur J Pharmacol 2021 May 4:174150. Epub 2021 May 4.

Laboratory of Molecular Mechanisms of Biological Adaptation, Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 119991, Moscow, Russia. Electronic address:

Inhibition of the activity of extracellular signal-regulated kinases (ERK1/2) induced by the activation of the dopamine D2 receptor signalling cascade may be a promising pharmacological target. The aim of this work was to study the involvement of ERK1/2 and dopamine D2 receptor in the mechanism of the anticonvulsant action of valproic acid (VA) and a new benzoylpyridine oxime derivative (GIZH-298), which showed antiepileptic activity in different models of epilepsy. We showed that subchronic exposure to maximal electroshock seizures (MES) for 5 days reduced the density of dopamine D2 receptors in the striatum of mice. Read More

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Neural network strategies for plasma membrane selection in quantitative fluorescence microscopy images.

Biophys J 2021 May 4. Epub 2021 May 4.

Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore MD 21218. Electronic address:

In recent years there has been an explosion of fluorescence microscopy studies of live cells in the literature. The analysis of the images obtained in these studies often requires labor-intensive manual annotation to extract meaningful information. In this study, we explore the utility of a neural network approach to recognize, classify, and select plasma membranes in high resolution images, thus greatly speeding up data analysis and reducing the need for personnel training for highly repetitive tasks. Read More

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METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection.

Cell Rep 2021 May 3:109091. Epub 2021 May 3.

Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA. Electronic address:

It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining molecular mechanism. N-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Read More

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Microparticle-Based Biochemical Sensing Using Optical Coherence Tomography and Deep Learning.

ACS Nano 2021 May 7. Epub 2021 May 7.

Nokia Bell Labs, New Providence, New Jersey 07974 United States.

Advancing continuous health monitoring beyond vital signs to biochemistry will revolutionize personalized medicine. Herein, we report a biosensing platform to achieve remote biochemical monitoring using microparticle-based biosensors and optical coherence tomography (OCT). Stimuli-responsive, polymeric microparticles were designed to serve as freely dispersible biorecognition units, wherein binding with a target biochemical induces volumetric changes of the microparticle. Read More

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The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen .

RNA Biol 2021 May 7. Epub 2021 May 7.

Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223.

is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Read More

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SHAPE Directed Discovery of New Functions in Large RNAs.

Kevin M Weeks

Acc Chem Res 2021 May 7. Epub 2021 May 7.

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States.

ConspectusRNA lies upstream of nearly all biology and functions as the central conduit of information exchange in all cells. RNA molecules encode information both in their primary sequences and in complex structures that form when an RNA folds back on itself. From the time of discovery of mRNA in the late 1950s until quite recently, we had only a rudimentary understanding of RNA structure across vast regions of most messenger and noncoding RNAs. Read More

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Harmine targets inhibitor of DNA binding-2 and activator protein-1 to promote preosteoclast PDGF-BB production.

J Cell Mol Med 2021 May 7. Epub 2021 May 7.

Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.

Osteoporosis is one of the most common metabolic bone diseases affecting millions of people. We previously found that harmine prevents bone loss in ovariectomized mice via increasing preosteoclast platelet-derived growth factor-BB (PDGF-BB) production and type H vessel formation. However, the molecular mechanisms by which harmine promotes preosteoclast PDGF-BB generation are still unclear. Read More

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The Ca -binding protein sorcin stimulates transcriptional activity of the unfolded protein response mediator ATF6.

FEBS Lett 2021 May 7. Epub 2021 May 7.

Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion & Reproduction, Imperial College London, UK.

Sorcin is a calcium-binding protein involved in maintaining endoplasmic reticulum (ER) Ca stores. We have previously shown that overexpressing sorcin under the rat insulin promoter was protective against high fat diet-induced pancreatic beta cell dysfunction in vivo. Activating Transcription Factor 6 (ATF6) is a key mediator of the unfolded protein response (UPR) that provides cellular protection during the progression of ER stress. Read More

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Principles responsible for trace element concentrations in chronic kidney disease.

Clin Nephrol 2021 May 7. Epub 2021 May 7.

Derangements of trace elements often occur in patients with renal failure and play a crucial role in chronic kidney disease. The natural history of trace element deposition with worsening chronic kidney disease has been poorly described. Some essential trace elements may get wasted (e. Read More

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Defining functional variants associated with Alzheimer's disease in the induced immune response.

Brain Commun 2021 19;3(2):fcab083. Epub 2021 Apr 19.

Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.

Defining the mechanisms involved in the aetiology of Alzheimer's disease from genome-wide association studies alone is challenging since Alzheimer's disease is polygenic and most genetic variants are non-coding. Non-coding Alzheimer's disease risk variants can influence gene expression by affecting miRNA binding and those located within enhancers and within CTCF sites may influence gene expression through alterations in chromatin states. In addition, their function can be cell-type specific. Read More

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CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers.

Acta Naturae 2021 Jan-Mar;13(1):31-46

Institute of Gene Biology RAS, Moscow, 119334 Russia.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. Read More

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Removal of bisphenol A from aqueous media using a highly selective adsorbent of hybridization cyclodextrin with magnetic molecularly imprinted polymer.

R Soc Open Sci 2021 Mar 10;8(3):201604. Epub 2021 Mar 10.

Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Penang, Malaysia.

In this study, a unique magnetic molecularly imprinted polymer (MMIP) adsorbent towards bisphenol A (BPA) as a template molecule was developed by bulk polymerization using β-cyclodextrin (β-CD) as a co-monomer with methacrylic acid (MAA) to form MMIP MAA-βCD as a new adsorbent. β-CD was hybridized with MAA to obtain water-compactible imprinting sites for the effective removal of BPA from aqueous samples. Benzoyl peroxide and trimethylolpropane trimethacrylate were used as the initiator and cross-linker, respectively. Read More

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Released Myeloperoxidase Attenuates Neutrophil Migration and Accumulation in Inflamed Tissue.

Front Immunol 2021 20;12:654259. Epub 2021 Apr 20.

Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.

Neutrophil (PMN) recruitment to sites of insult is critical for host defense, however excessive PMN activity and tissue accumulation can lead to exacerbated inflammation and injury. Myeloperoxidase (MPO) is a PMN azurophilic granule enzyme, which together with HO, forms a powerful antimicrobial system designed to kill ingested bacteria. Intriguingly, in addition to intracellular killing of invading microorganisms and extracellular tissue damage due generation of ROS, soluble MPO has been directly implicated in modulating cellular responses and tissue homeostasis. Read More

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Molecular Dynamics Studies of Therapeutic Liquid Mixtures and Their Binding to Mycobacteria.

Front Pharmacol 2021 20;12:626735. Epub 2021 Apr 20.

Red Glead Discovery AB, Lund, Sweden.

Tuberculosis is an highly contagious disease still considered by the WHO as one of most infectious diseases worldwide. The therapeutic approach, used to prevent and treat tuberculosis targets the complex, comprises a combination of drugs administrated for long periods of time, which, in many cases, could cause several adverse effects and, consequently, low compliance of the patient to the treatment and drug-resistance. Therefore, therapeutic liquid mixtures formulated with anti-tuberculosis drugs and/or adjuvants in tuberculosis therapy are an interesting approach to prevent toxic effects and resistance to anti-tuberculosis drugs. Read More

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Intrasubunit and intersubunit steroid binding sites independently and additively mediate α1β2γ2L GABA receptor potentiation by the endogenous neurosteroid allopregnanolone.

Mol Pharmacol 2021 May 6. Epub 2021 May 6.

Anesthesiology, Washington University School of Medicine, United States

Prior work employing functional analysis, photolabeling, and X-ray crystallography have identified three distinct binding sites for potentiating steroids in the heteromeric GABA receptor. The sites are located in the membrane-spanning domains of the receptor at the β-α subunit interface ("Site I") and within the α ("Site II") and β subunits ("Site III"). Here, we have investigated the effects of mutations to these sites on potentiation of the rat α1β2γ2L GABA receptor by the endogenous neurosteroid allopregnanolone (3α5αP). Read More

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Drug Metab Dispos 2021 May 6. Epub 2021 May 6.

Genentech, A Member of the Roche Group, United States

Accurately predicting the pharmacokinetics of compounds that are transporter substrates has been notoriously challenging using traditional in vitro systems and physiologically based pharmacokinetic (PBPK) modeling. The objective of this study was to use PBPK modeling to understand the translational accuracy of data generated with human embryonic kidney (HEK)293 cells overexpressing the hepatic uptake transporters OATP1B1/3 with and without plasma, while accounting for transporter expression. Models of four OATP substrates, two with low protein binding (pravastatin and rosuvastatin) and two with high protein binding (repaglinide and pitavastatin) were explored, and the OATP in vitro data generated in plasma incubations were utilized for a plasma model, and in buffer incubations for a buffer model. Read More

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A novel computational framework for genome-scale alternative transcription units prediction.

Brief Bioinform 2021 May 6. Epub 2021 May 6.

School of Mathematics, Shandong University, Jinan 250200, China.

Alternative transcription units (ATUs) are dynamically encoded under different conditions and display overlapping patterns (sharing one or more genes) under a specific condition in bacterial genomes. Genome-scale identification of ATUs is essential for studying the emergence of human diseases caused by bacterial organisms. However, it is unrealistic to identify all ATUs using experimental techniques because of the complexity and dynamic nature of ATUs. Read More

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