224,012 results match your criteria Biophysics Nagoya-shi Japan[Journal]


De novo glycan structural identification from mass spectra using tree merging strategy.

Comput Biol Chem 2019 Mar 30;80:217-224. Epub 2019 Mar 30.

Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Motivation: Glycans are large molecules with specific tree structures. Glycans play important roles in a great variety of biological processes. These roles are primarily determined by the fine details of their structures, making glycan structural identification highly desirable. Read More

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http://dx.doi.org/10.1016/j.compbiolchem.2019.03.015DOI Listing

STIM1 structure-function and downstream signaling pathways.

Cell Calcium 2019 Apr 8;80:101-102. Epub 2019 Apr 8.

Institute of Biophysics, Johannes Kepler University Linz, Life Science Center, Gruberstrasse 40, 4020 Linz, Austria. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01434160193000
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http://dx.doi.org/10.1016/j.ceca.2019.01.004DOI Listing
April 2019
1 Read

Differential Expression of HMGA1 and HMGA2 in pituitary neuroendocrine tumors.

Mol Cell Endocrinol 2019 Apr 15. Epub 2019 Apr 15.

Laboratory of Experimental Endocrinology - LEEx, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Brazil; Graduate Program in Endocrinology, Faculty of Medicine, Federal University of Rio de Janeiro, Brazil; Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Brazil. Electronic address:

Defining biomarkers for invasive pituitary neuroendocrine tumors (PitNETs) is highly desirable. The high mobility group A (HMGA) proteins are among the most widely expressed cancer-associated proteins. Indeed, their overexpression is a frequent feature of human malignancies, including PitNETs. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03037207193011
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http://dx.doi.org/10.1016/j.mce.2019.04.010DOI Listing
April 2019
1 Read

βC1 protein encoded in geminivirus satellite concertedly targets MKK2 and MPK4 to counter host defense.

PLoS Pathog 2019 Apr 18;15(4):e1007728. Epub 2019 Apr 18.

State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.

Plant viruses have evolved multiple strategies to overcome host defense to establish an infection. Here, we identified two components of a host mitogen-activated protein kinase (MAPK) cascade, MKK2 and MPK4, as bona fide targets of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNV). βC1 interacts with the kinase domain of MKK2 and inhibits its activity. Read More

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http://dx.doi.org/10.1371/journal.ppat.1007728DOI Listing

Three novel compound heterozygous IL12RB1 mutations in Chinese patients with Mendelian susceptibility to mycobacterial disease.

PLoS One 2019 18;14(4):e0215648. Epub 2019 Apr 18.

Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China.

Mendelian Susceptibility to Mycobacterial Diseases (MSMD) is a primary immunodeficiency disease (PID) characterized by variable susceptibility to weakly virulent mycobacteria (Bacille Calmette-Guerin, BCG) and various intramacrophagic bacteria, fungi, parasites. Mycobacterial disease generally begins in childhood, more rarely during adolescence and adulthood. The pathogenesis of MSMD is the inherited impaired production of interferon gamma (IFN-γ) or inadequate response to it. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215648PLOS

In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine.

PLoS One 2019 18;14(4):e0215508. Epub 2019 Apr 18.

Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.

Brain-derived neurotrophic factor (BDNF) plays an important role in neurogenesis and synapse formation. The V66M is the most prevalent BDNF mutation in humans and impairs the function and distribution of BDNF. This mutation is related to several psychiatric disorders. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215508PLOS

Reply to "Letter to the Editor: Two of the significant omissions from a 'general' model of respiratory energy transduction".

J Appl Physiol (1985) 2019 Apr;126(4):1172

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1152/japplphysiol.01055.2018DOI Listing

Actions developed by the Brazilian Physiological Society to promote women's participation in science.

Adv Physiol Educ 2019 Jun;43(2):199-206

Instituto do Coração, University of São Paulo , São Paulo , Brazil.

Here we described two activities related to Women in Science: one main conference and one symposium, both developed during the Annual Congress of the Brazilian Physiological Society, which were held within the XXXIII Annual Meeting of the Federation of Brazilian Experimental Biology Societies, from September 3-6, 2018, in Campos do Jordão (SP/Brazil). This conference and the symposium were among the most popular activities of the congress. This is important because the activities addressed important issues, including the fact that only 29% of the worlds' researchers are women, and women have difficulty progressing in a scientific career. Read More

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http://dx.doi.org/10.1152/advan.00216.2018DOI Listing

RNA dynamics by NMR.

Chembiochem 2019 Apr 17. Epub 2019 Apr 17.

Karolinska Institute, Medical Biochemistry and Biophysics, Scheeles Väg 2, 17177, Stockholm, SWEDEN.

An ever-increasing number of functional RNAs require mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new Nuclear Magnetic Resonance (NMR) methods have been developed to elucidate these dynamics in RNA with atomic resolution. Read More

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http://dx.doi.org/10.1002/cbic.201900072DOI Listing

TNRC6 proteins modulate hepatitis C virus replication by spatially regulating the binding of miR-122/Ago2 complexes to viral RNA.

Nucleic Acids Res 2019 Apr 18. Epub 2019 Apr 18.

Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

The liver-specific microRNA, miR-122, is an essential host factor for replication of the hepatitis C virus (HCV). miR-122 stabilizes the positive-strand HCV RNA genome and promotes its synthesis by binding two sites (S1 and S2) near its 5' end in association with Ago2. Ago2 is essential for both host factor activities, but whether other host proteins are involved is unknown. Read More

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http://dx.doi.org/10.1093/nar/gkz278DOI Listing

Lipid-independent control of endothelial and neuronal TRPC3 channels by light.

Chem Sci 2019 Mar 15;10(9):2837-2842. Epub 2019 Jan 15.

Gottfried Schatz Research Center - Biophysics , Medical University of Graz , Neue Stiftingtalstraße 6/D/04 , 8010 Graz , Austria . Email:

Lipid-gated TRPC channels are highly expressed in cardiovascular and neuronal tissues. Exerting precise pharmacological control over their activity in native cells is expected to serve as a basis for the development of novel therapies. Here we report on a new photopharmacological tool that enables manipulation of TRPC3 channels by light, in a manner independent of lipid metabolism and with higher temporal precision than lipid photopharmacology. Read More

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http://dx.doi.org/10.1039/c8sc05536jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427946PMC

Label-free target identification reveals oxidative DNA damage as the mechanism of a selective cytotoxic agent.

Chem Sci 2019 Mar 19;10(12):3449-3458. Epub 2019 Feb 19.

CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , Seoul 08826 , Korea.

Phenotypic screening can not only identify promising first-in-class drug candidates, but can also reveal potential therapeutic targets or neomorphic functions of known proteins. In this study, we identified target proteins of SB2001, a cytotoxic agent that acts specifically against HeLa human cervical cancer cells. Because SB2001 lacks chemical modification sites, label-free target identification methods including thermal stability shift-based fluorescence difference in two-dimensional gel electrophoresis (TS-FITGE) and thermal proteome profiling (TPP) were applied to characterize its mechanism of action. Read More

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http://dx.doi.org/10.1039/c8sc05465gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438152PMC

Global small-angle scattering data analysis of inverted hexagonal phases.

J Appl Crystallogr 2019 Apr 28;52(Pt 2):403-414. Epub 2019 Mar 28.

University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, 8010 Graz, Austria.

A global analysis model has been developed for randomly oriented, fully hydrated, inverted hexagonal (H) phases formed by many amphiphiles in aqueous solution, including membrane lipids. The model is based on a structure factor for hexagonally packed rods and a compositional model for the scattering length density, enabling also the analysis of positionally weakly correlated H phases. Bayesian probability theory was used for optimization of the adjustable parameters, which allows parameter correlations to be retrieved in much more detail than standard analysis techniques and thereby enables a realistic error analysis. Read More

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http://dx.doi.org/10.1107/S1600576719002760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448687PMC

LLGL2 rescues nutrient stress by promoting leucine uptake in ER breast cancer.

Nature 2019 Apr 17. Epub 2019 Apr 17.

Department of Medicine, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.

Drosophila Lgl and its mammalian homologues, LLGL1 and LLGL2, are scaffolding proteins that regulate the establishment of apical-basal polarity in epithelial cells. Whereas Lgl functions as a tumour suppressor in Drosophila, the roles of mammalian LLGL1 and LLGL2 in cancer are unclear. The majority (about 75%) of breast cancers express oestrogen receptors (ERs), and patients with these tumours receive endocrine treatment. Read More

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http://www.nature.com/articles/s41586-019-1126-2
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http://dx.doi.org/10.1038/s41586-019-1126-2DOI Listing
April 2019
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Direct detection of bacteremia by exploiting host-pathogen interactions of lipoteichoic acid and lipopolysaccharide.

Sci Rep 2019 Apr 17;9(1):6203. Epub 2019 Apr 17.

Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States.

Bacteremia is a leading cause of death in sub-Saharan Africa where childhood mortality rates are the highest in the world. The early diagnosis of bacteremia and initiation of treatment saves lives, especially in high-disease burden areas. However, diagnosing bacteremia is challenging for clinicians, especially in children presenting with co-infections such as malaria and HIV. Read More

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http://dx.doi.org/10.1038/s41598-019-42502-5DOI Listing

Author Correction: Resistance training regulates gene expression of molecules associated with intramyocellular lipids, glucose signaling and fiber size in old rats.

Sci Rep 2019 Apr 17;9(1):6383. Epub 2019 Apr 17.

Graduate program of Rehabilitation Sciences, University of Brasilia, Distrito Federal, Brazil.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. Read More

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http://dx.doi.org/10.1038/s41598-019-42462-wDOI Listing

Development and Application of a Functional Human Esophageal Mucosa Explant Platform to Eosinophilic Esophagitis.

Sci Rep 2019 Apr 17;9(1):6206. Epub 2019 Apr 17.

Division of Allergy & Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.

There is an increasing prevalence of esophageal diseases but intact human tissue platforms to study esophageal function, disease mechanisms, and the interactions between cell types in situ are lacking. To address this, we utilized full thickness human donor esophagi to create and validate the ex vivo function of mucosa and smooth muscle (n = 25). Explanted tissue was tested for contractile responses to carbachol and histamine. Read More

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http://dx.doi.org/10.1038/s41598-019-41147-8DOI Listing

A role of the 53BP1 protein in genome protection: structural and functional characteristics of 53BP1-dependent DNA repair.

Aging (Albany NY) 2019 Apr 17. Epub 2019 Apr 17.

Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic.

Nuclear architecture plays a significant role in DNA repair mechanisms. It is evident that proteins involved in DNA repair are compartmentalized in not only spontaneously occurring DNA lesions or ionizing radiation-induced foci (IRIF), but a specific clustering of these proteins can also be observed within the whole cell nucleus. For example, 53BP1-positive and BRCA1-positive DNA repair foci decorate chromocenters and can appear close to nuclear speckles. Read More

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http://dx.doi.org/10.18632/aging.101917DOI Listing

A genome-wide haploid genetic screen identifies heparan sulfate-associated genes and the macropinocytosis modulator TMED10 as factors supporting vaccinia virus infection.

J Virol 2019 Apr 17. Epub 2019 Apr 17.

Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands

Vaccinia virus is a promising viral vaccine and gene delivery candidate, and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to Modified Vaccinia Virus Ankara (MVA). Read More

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http://dx.doi.org/10.1128/JVI.02160-18DOI Listing

In vivo assembly and trafficking of olfactory Ionotropic Receptors.

BMC Biol 2019 Apr 17;17(1):34. Epub 2019 Apr 17.

Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland.

Background: Ionotropic receptors (IRs) are a large, divergent subfamily of ionotropic glutamate receptors (iGluRs) that are expressed in diverse peripheral sensory neurons and function in olfaction, taste, hygrosensation and thermosensation. Analogous to the cell biological properties of their synaptic iGluR ancestors, IRs are thought to form heteromeric complexes that localise to the ciliated dendrites of sensory neurons. IR complexes are composed of selectively expressed 'tuning' receptors and one of two broadly expressed co-receptors (IR8a or IR25a). Read More

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http://dx.doi.org/10.1186/s12915-019-0651-7DOI Listing

Tri-Cyclic Nucleobase Analogs and their Ribosides as Substrates of Purine-Nucleoside Phosphorylases. II Guanine and Isoguanine Derivatives.

Molecules 2019 Apr 16;24(8). Epub 2019 Apr 16.

Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.

Etheno-derivatives of guanine, -methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,-etheno-guanine and 1,-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from , while -methyl-,3-etheno-guanine exhibited moderate activity vs. Read More

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http://dx.doi.org/10.3390/molecules24081493DOI Listing

Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.

J Mol Biol 2019 Apr 14. Epub 2019 Apr 14.

International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland. Electronic address:

Specificity engineering is challenging, and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evolution approach to the engineering of a dimeric, blunt end cutting restriction enzyme NlaIV (GGN/NCC). Read More

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http://dx.doi.org/10.1016/j.jmb.2019.04.010DOI Listing

Calcium-Activated Chloride Channels in Newly Differentiating Mouse Lens Fiber Cells and Their Role in Volume Regulation.

Invest Ophthalmol Vis Sci 2019 Apr;60(5):1621-1629

Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, Chicago, Illinois, United States.

Purpose: Chloride channels have been proposed to play an important role in the regulation of lens volume. Unfortunately, little information is available about the molecular identity of these channels or how they are regulated in the lens due to the difficulties in isolating mouse fiber cells. Recently, our laboratory has developed a new technique for isolating these cells by using transgenic mouse lenses that lack both Cx50 and Cx46. Read More

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http://dx.doi.org/10.1167/iovs.19-26626DOI Listing

Optical Coherence Tomography Angiography in Mice: Quantitative Analysis After Experimental Models of Retinal Damage.

Invest Ophthalmol Vis Sci 2019 Apr;60(5):1556-1565

Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada.

Purpose: We implemented optical coherence tomography angiography (OCT-A) in mice to: (1) develop quantitative parameters from OCT-A images, (2) measure the reproducibility of the parameters, and (3) determine the impact of experimental models of inner and outer retinal damage on OCT-A findings.

Methods: OCT-A images were acquired with a customized system (Spectralis Multiline OCT2). To assess reproducibility, imaging was performed five times over 1 month. Read More

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http://dx.doi.org/10.1167/iovs.18-26441DOI Listing

Consistent elicitation of cross-clade HIV-neutralizing responses achieved in guinea pigs after fusion peptide priming by repetitive envelope trimer boosting.

PLoS One 2019 17;14(4):e0215163. Epub 2019 Apr 17.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.

The vaccine elicitation of broadly neutralizing responses is a central goal of HIV research. Recently, we elicited cross-clade neutralizing responses against the N terminus of the fusion peptide (FP), a critical component of the HIV-entry machinery. While the consistency of the elicited cross-clade neutralizing responses was good in mice, it was poor in guinea pigs: after seven immunizations comprising either envelope (Env) trimer or FP coupled to a carrier, serum from only one of five animals could neutralize a majority of a cross-clade panel of 19 wild-type strains. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215163PLOS

Neuroprotection During Infection Is Related To the Release of Neurotrophic Factors BDNF and NGF.

J Parasitol 2019 Apr;105(2):313-320

1   Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon s/no. Vale do Canela, Salvador-BA, 40110-902, Brazil.

is a parasite that infects many animal species and has tropism for various tissues, particularly the nervous system, where it generally remains in cysts. Under infection, glial cells activate immune responses by a Th2 profile, suggesting an immunologically privileged environment that controls parasite proliferation, with neuronal preservation. In this study, we investigated the role of soluble neurotrophic factors released by glial cells on neuronal integrity during infection in vitro. Read More

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April 2019
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Role of KASH domain lengths in the regulation of LINC complexes.

Mol Biol Cell 2019 Apr 17:mbcE19020079. Epub 2019 Apr 17.

Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, United States.

The LINC complex is formed by the conserved interactions between SUN and KASH domain proteins, providing a physical coupling between the nucleoskeleton and cytoskeleton that mediates the transfer of physical forces across the nuclear envelope. The LINC complex can perform distinct cellular functions by pairing various KASH domain proteins with the same SUN domain protein. For example, In , SUN protein UNC-84 binds to two KASH proteins UNC-83 and ANC-1 to mediate nuclear migration and anchorage, respectively. Read More

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https://www.molbiolcell.org/doi/10.1091/mbc.E19-02-0079
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http://dx.doi.org/10.1091/mbc.E19-02-0079DOI Listing
April 2019
1 Read

How Cerebellar Motor Learning Keeps Saccades Accurate.

J Neurophysiol 2019 Apr 17. Epub 2019 Apr 17.

Physiology/Biophysics, Univ. of Washington, United States.

The neuronal substrate underlying the learning of a sophisticated task has been difficult to study. However, the advent of a behavioral paradigm that deceives the saccadic system into thinking it is making an error has allowed the mechanisms of the adaptation that corrects this error to be revealed in a primate. The neural elements that fashion the command signal for the generation of accurate saccades involve subcortical structures in the brainstem and cerebellum. Read More

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https://www.physiology.org/doi/10.1152/jn.00781.2018
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http://dx.doi.org/10.1152/jn.00781.2018DOI Listing
April 2019
1 Read

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

J Comput Chem 2019 Apr 17. Epub 2019 Apr 17.

Los Alamos National Laboratory, Los Alamos, New Mexico.

The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long-range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.25840
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http://dx.doi.org/10.1002/jcc.25840DOI Listing
April 2019
2 Reads

Saline extract from Malpighia emarginata DC leaves showed higher polyphenol presence, antioxidant and antifungal activity and promoted cell proliferation in mice splenocytes.

An Acad Bras Cienc 2019 8;91(1):e20190916. Epub 2019 Apr 8.

Department of Antibiotics, Biosciences Centre, Federal University of Pernambuco, Av. Prof. Artur de Sá, s/n, 50740-520 Recife, PE, Brazil.

Currently, the research of new natural compounds with biological potential demonstrates great ethnopharmacological importance. In this study, we evaluated the biological properties promoted by saline extract from Malpighia emarginata DC leaves, whose objective is to evaluate the antioxidant, antimicrobial and cytotoxicity potential. Phytochemical characterization was performed by UPLC-MS chromatography to identify the chemical compounds. Read More

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http://dx.doi.org/10.1590/0001-3765201920180358DOI Listing

7.0T ultrahigh-field MRI directly visualized the pedunculopontine nucleus in Parkinson's disease patients.

Clinics (Sao Paulo) 2019 15;74:e573. Epub 2019 Apr 15.

Department of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Xicheng District, Beijing, 100053, P.R., China.

Objectives: The pedunculopontine nucleus (PPN) is considered a promising new target for neurostimulation in Parkinson's disease (PD) patients with postural instability and gait disturbance that is refractory to other treatment modalities. However, the PPN is typically difficult to visualize with magnetic resonance imaging (MRI) at clinical field strengths, which greatly limits the PPN as a viable surgical target for deep brain stimulation (DBS). Thus, the aim of this study is to directly visualize the PPN based on 7. Read More

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http://dx.doi.org/10.6061/clinics/2019/e573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456917PMC
April 2019
1 Read

Three-dimensional Therapy Needle Applicator Segmentation for Ultrasound-guided Focal Liver Ablation.

Med Phys 2019 Apr 17. Epub 2019 Apr 17.

Department of Medical Biophysics.

Purpose: Minimally invasive procedures, such as microwave ablation, are becoming first-line treatment options for early-stage liver cancer due to lower complication rates and shorter recovery times than conventional surgical techniques. Although these procedures are promising, one reason preventing widespread adoption is inadequate local tumour ablation leading to observations of higher local cancer recurrence compared to conventional procedures. Poor ablation coverage has been associated with two-dimensional (2D) ultrasound (US) guidance of the therapy needle applicators and has stimulated investigation into the use of three-dimensional (3D) US imaging for these procedures. Read More

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http://dx.doi.org/10.1002/mp.13548DOI Listing

Obstructive sleep apnea, nighttime arousals, and leukocyte telomere length: The Multi-Ethnic Study of Atherosclerosis (MESA).

Sleep 2019 Apr 17. Epub 2019 Apr 17.

Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School.

Study Objectives: Sleep disturbances and sleep apnea are associated with increased vulnerability to age-related disease, altering molecular pathways affecting biological aging. Telomere length captures one component of biological aging. We evaluated whether objectively assessed sleep and sleep apnea relate to leukocyte telomere length (LTL) in the Multi-Ethnic Study of Atherosclerosis (MESA). Read More

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https://academic.oup.com/sleep/advance-article/doi/10.1093/s
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http://dx.doi.org/10.1093/sleep/zsz089DOI Listing
April 2019
1 Read

The Measurement of Volume Change by Capillary Dilatometry.

Authors:
Peter C Kahn

Protein Sci 2019 Apr 16. Epub 2019 Apr 16.

Department of Biochemistry & Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901.

Capillary dilatometry enables direct measurement of changes in volume, an extensive thermodynamic property. The results provide insight into the changes in hydration that occur upon protein folding, ligand binding and the interactions of proteins with nucleic acids and other cellular components. Often the entropy change arising from release of hydrating solvent provides the main driving force of a binding reaction. Read More

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http://dx.doi.org/10.1002/pro.3626DOI Listing

Facile measurement of protein stability and folding kinetics using a nano differential scanning fluorimeter.

Protein Sci 2019 Apr 16. Epub 2019 Apr 16.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India.

With advancements in high-throughput generation of phenotypic data on mutant proteins, it has become important to individually characterise different proteins or their variants rapidly and with minimal sample consumption. We have made use of a nano Differential Scanning Fluorimetric device, from NanoTemper technologies, to rapidly carry out isothermal chemical denaturation and measure folding/unfolding kinetics of proteins and compared these to corresponding data obtained from conventional spectrofluorimetry. We show that using sample volumes ten-fifty fold lower than with conventional fluorimetric techniques, one can rapidly and accurately measure thermodynamic and kinetic stability, as well as folding/unfolding kinetics. Read More

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http://dx.doi.org/10.1002/pro.3622DOI Listing

Structure Elucidation of Macrolide Antibiotics Using MS Analysis and Deuterium Labelling.

J Am Soc Mass Spectrom 2019 Apr 16. Epub 2019 Apr 16.

Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.

The 14- and 16-membered macrolide antibiotics are an important structural class. Ubiquitously produced by a number of bacterial strains, namely actinomycetes, purification and structure elucidation of the wide array of analogs is challenging, both for discovery efforts and methodologies to monitor for byproducts, metabolites, and contaminants. Collision-induced dissociation mass spectrometry offers an attractive solution, enabling characterization of mixtures, and providing a wealth of structural information. Read More

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http://dx.doi.org/10.1007/s13361-019-02210-wDOI Listing
April 2019
1 Read

Quantitative and Qualitative Improvement of Low-Count [Ga]Citrate and [Y]Microspheres PET Image Reconstructions Using Block Sequential Regularized Expectation Maximization Algorithm.

Mol Imaging Biol 2019 Apr 15. Epub 2019 Apr 15.

Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, 94143-0946, USA.

Purpose: There are several important positron emission tomography (PET) imaging scenarios that require imaging with very low photon statistics, for which both quantitative accuracy and visual quality should not be neglected. For example, PET imaging with the low photon statistics is closely related to active efforts to significantly reduce radiation exposure from radiopharmaceuticals. We investigated two examples of low-count PET imaging: (a) imaging [Y]microsphere radioembolization that suffers the very small positron emission fraction of Y-90's decay processes, and (b) cancer imaging with [Ga]citrate with uptake time of 3-4 half-lives, necessary for visualizing tumors. Read More

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http://dx.doi.org/10.1007/s11307-019-01347-0DOI Listing

Quantitative Phenotyping of Cell-Cell Junctions to Evaluate ZO-1 Presentation in Brain Endothelial Cells.

Ann Biomed Eng 2019 Apr 15. Epub 2019 Apr 15.

Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA.

The selective permeability of the blood-brain barrier (BBB) is controlled by tight junction-expressing brain endothelial cells. The integrity of these junctional proteins, which anchor to actin via zonula occludens (e.g. Read More

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http://dx.doi.org/10.1007/s10439-019-02266-5DOI Listing

Absolute basophil count is associated with time to recurrence in patients with high-grade T1 bladder cancer receiving bacillus Calmette-Guérin after transurethral resection of the bladder tumor.

World J Urol 2019 Apr 16. Epub 2019 Apr 16.

Department of Clinical Medicine and Surgery, Federico II University of Naples, Naples, Italy.

Background: Basophils, eosinophils and monocytes may be involved in BCG-induced immune responses and be associated with outcomes of bladder cancer patients receiving intravesical BCG. Our objective was to explore the association of baseline counts of basophils, eosinophils and monocytes with outcomes of patients with high-grade T1 bladder cancer receiving a standard course of intravesical BCG.

Methods: We retrospectively reviewed medical records of patients with primary T1 HG/G3 bladder cancer. Read More

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http://dx.doi.org/10.1007/s00345-019-02754-2DOI Listing

Erratum: Author Correction: Human motor cortex relies on sparse and action-specific activation during laughing, smiling and speech production.

Commun Biol 2019 8;2:128. Epub 2019 Apr 8.

1Medical AI Lab, Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, 79106 Germany.

[This corrects the article DOI: 10.1038/s42003-019-0360-3.]. Read More

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http://dx.doi.org/10.1038/s42003-019-0404-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453910PMC

Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction.

PeerJ 2019 8;7:e6700. Epub 2019 Apr 8.

Centre for Ecology and Evolution in Microbial model Systems-EEMiS, Linnaeus University, Kalmar, Sweden.

Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g. Read More

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http://dx.doi.org/10.7717/peerj.6700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6459318PMC

Cross-talk between ER stress and mitochondrial pathway mediated adriamycin-induced testicular toxicity and DA-9401 modulate adriamycin-induced apoptosis in Sprague-Dawley rats.

Cancer Cell Int 2019 4;19:85. Epub 2019 Apr 4.

1Department of Urology, Institute for Medical Sciences, Chonbuk National University Medical School-Biomedical Research and Institute and Clinical Trial Center for Medical Devices, Chonbuk National University Hospital, Jeonju, 54907 Republic of Korea.

Background: DA-9401 was prepared as a mixture of Chinese medicinal herb extracts from roots of Morinda officinalis How (Rubiaceae), outer scales of L. (Liliceae) and seeds of Cuscuta chinensis Lamark (Convolvulaceae). The present study was designed to investigate the possible protective role of DA-9401 in adriamycin (ADR)-induced testicular toxicity associated with oxidative stress, endoplasmic reticulum (ER) stress, and apoptosis. Read More

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http://dx.doi.org/10.1186/s12935-019-0805-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450013PMC
April 2019
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Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.

Nat Chem Biol 2019 May 15;15(5):472-479. Epub 2019 Apr 15.

Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.

Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Read More

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http://dx.doi.org/10.1038/s41589-019-0267-9DOI Listing

Quality and quantity control of gene expression by nonsense-mediated mRNA decay.

Nat Rev Mol Cell Biol 2019 Apr 16. Epub 2019 Apr 16.

Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.

Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. Read More

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http://www.nature.com/articles/s41580-019-0126-2
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http://dx.doi.org/10.1038/s41580-019-0126-2DOI Listing
April 2019
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An innate interaction between IL-18 and the propeptide that inactivates its precursor form.

Sci Rep 2019 Apr 16;9(1):6160. Epub 2019 Apr 16.

Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.

Uncontrolled secretion of mature interleukin (IL)-1β and IL-18 is responsible for severe autoinflammatory or autoimmune disorders and various allergic diseases. Here we report an intramolecular interaction between IL-18 and its propeptide, which is proteolytically removed from its precursor proIL-18 during maturation. The intramolecular interaction was recapitulated intermolecularly using recombinant propeptide. Read More

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http://www.nature.com/articles/s41598-019-42661-5
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http://dx.doi.org/10.1038/s41598-019-42661-5DOI Listing
April 2019
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Designed Mutations Alter the Binding Pathways of an Intrinsically Disordered Protein.

Sci Rep 2019 Apr 16;9(1):6172. Epub 2019 Apr 16.

Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.

Many cellular functions, including signaling and regulation, are carried out by intrinsically disordered proteins (IDPs) binding to their targets. Experimental and computational studies have now significantly advanced our understanding of these binding processes. In particular, IDPs that become structured upon binding typically follow a dock-and-coalesce mechanism, whereby the docking of one IDP segment initiates the process, followed by on-target coalescence of remaining IDP segments. Read More

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http://www.nature.com/articles/s41598-019-42717-6
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http://dx.doi.org/10.1038/s41598-019-42717-6DOI Listing
April 2019
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RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation.

Sci Rep 2019 Apr 16;9(1):6171. Epub 2019 Apr 16.

Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.

Aberrant expression, dysfunction and particularly aggregation of a group of RNA-binding proteins, including TDP-43, FUS and RBM45, are associated with neurological disorders. These three disease-linked RNA-binding proteins all contain at least one RNA recognition motif (RRM). However, it is not clear if these RRMs contribute to their aggregation-prone character. Read More

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http://www.nature.com/articles/s41598-019-42367-8
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http://dx.doi.org/10.1038/s41598-019-42367-8DOI Listing
April 2019
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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 Apr 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. Read More

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019
2 Reads

MPSSS impairs the immunosuppressive function of cancer-associated fibroblasts via the TLR4-NF-κB pathway.

Biosci Rep 2019 Apr 16. Epub 2019 Apr 16.

Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

The polysaccharides MPSSS was extracted from and has been reported to effectively inhibit tumor growth and to eliminate the function of myeloid-derived immune suppressor cell-mediated T cell inhibition, thus improving the efficacy of cancer therapy. The exploration of how MPSSS affects the functions of CAFs (cancer associated fibroblasts) will provide a new perspective for understanding the antitumor effects of MPSSS. In this study, prostate CAFs were selected as target cells to study whether MPSSS affected cell proliferation and function. Read More

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http://dx.doi.org/10.1042/BSR20182171DOI Listing

Intracellular calcium dysregulation in autism spectrum disorder: An analysis of converging organelle signaling pathways.

Biochim Biophys Acta Mol Cell Res 2018 Nov 9;1865(11 Pt B):1718-1732. Epub 2018 Aug 9.

Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA; UCI Center for Autism Research and Translation, School of Medicine, University of California, Irvine, Irvine, CA, USA; Department of Pediatrics, Section of Human Genetics and Genomics, University of California, Irvine, Irvine, CA, USA. Electronic address:

Autism spectrum disorder (ASD) is a group of complex, neurological disorders that affect early cognitive, social, and verbal development. Our understanding of ASD has vastly improved with advances in genomic sequencing technology and genetic models that have identified >800 loci with variants that increase susceptibility to ASD. Although these findings have confirmed its high heritability, the underlying mechanisms by which these genes produce the ASD phenotypes have not been defined. Read More

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http://dx.doi.org/10.1016/j.bbamcr.2018.08.003DOI Listing
November 2018