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https://www.readbyqxmd.com/read/29346773/dual-role-for-dsba-in-attacking-and-targeted-bacterial-cells-during-type-vi-secretion-system-mediated-competition
#1
Giuseppina Mariano, Laura Monlezun, Sarah J Coulthurst
Incorporation of disulfide bonds into proteins can be critical for function or stability. In bacterial cells, the periplasmic enzyme DsbA is responsible for disulfide incorporation into many extra-cytoplasmic proteins. The type VI secretion system (T6SS) is a widely occurring nanomachine that delivers toxic effector proteins directly into rival bacterial cells, playing a key role in inter-bacterial competition. We report that two redundant DsbA proteins are required for virulence and for proper deployment of the T6SS in the opportunistic pathogen Serratia marcescens, with several T6SS components being subject to the action of DsbA in secreting cells...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346752/epitranscriptomic-m6a-regulation-of-axon-regeneration-in-the-adult-mammalian-nervous-system
#2
Yi-Lan Weng, Xu Wang, Ran An, Jessica Cassin, Caroline Vissers, Yuanyuan Liu, Yajing Liu, Tianlei Xu, Xinyuan Wang, Samuel Zheng Hao Wong, Jessica Joseph, Louis C Dore, Qiang Dong, Wei Zheng, Peng Jin, Hao Wu, Bin Shen, Xiaoxi Zhuang, Chuan He, Kai Liu, Hongjun Song, Guo-Li Ming
N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single-base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury...
January 17, 2018: Neuron
https://www.readbyqxmd.com/read/29346730/2d-spectroscopy-is-being-used-to-address-core-scientific-questions-in-biology-and-materials-science
#3
Megan Petti, Justin P Lomont, Michał Maj, Martin T Zanni
Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photo-synthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy...
January 18, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29346729/electronic-interactions-in-iminophosphorane-superbase-complexes-with-carbon-dioxide
#4
Francesca Ingrosso, Manuel F Ruiz-Lopez
Iminophosphoranes or phosphazenes are an important class of compounds with increasing use in synthetic organic chemistry as neutral organic superbases exhibiting low nucleophilicity. Their electronic structure and therefore their properties strongly depend on substitution but there have been very few theoretical studies devoted to this topic, and more specifically to the formation of electron donor-acceptor complexes of iminophosphoranes with electrophiles. In this work, we have investigated the interaction with carbon dioxide at different ab initio levels...
January 18, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29346720/nanoscale-control-of-molecular-self-assembly-induced-by-plasmonic-hot-electron-dynamics
#5
Sabrina Simoncelli, Yi Li, Emiliano Cortes, Stefan A Maier
Self-assembly processes allow designing and creating complex nanostructures using molecules as building blocks and surfaces as scaffolds. This autonomous driven construction is possible due to a complex thermodynamic balance of molecule-surface interactions. As such, nanoscale guidance and control over this process is hard to achieve. Here we use the highly localized light-to-chemical-energy conversion of plasmonic materials to spatially cleave Au-S bonds on pre-determined locations within a single nanoparticle, enabling a high degree of control over this archetypal system for molecular self-assembly...
January 18, 2018: ACS Nano
https://www.readbyqxmd.com/read/29346652/toward-rational-antibody-design-recent-advancements-in-molecular-dynamics-simulations
#6
Takefumi Yamashita
Because antibodies have become an important therapeutic tool, rational antibody design is a challenging issue involving various science and technology fields. From the computational aspect, many types of design-assist methods have been developed, but their accuracy is not fully satisfactory. Because of recent advancements in computational power, molecular dynamics (MD) simulation has become a helpful tool to trace the motion of proteins and to characterize their properties. Thus, MD simulation has been applied to various systems involving antigen-antibody complexes and has been shown to provide accurate insight into antigen-antibody interactions and dynamics at an atomic resolution...
January 15, 2018: International Immunology
https://www.readbyqxmd.com/read/29346583/datamed-an-open-source-discovery-index-for-finding-biomedical-datasets
#7
Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu
Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium...
January 13, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29346445/transcriptome-analysis-of-skin-fibroblasts-with-dominant-negative-col3a1-mutations-provides-molecular-insights-into-the-etiopathology-of-vascular-ehlers-danlos-syndrome
#8
Nicola Chiarelli, Giulia Carini, Nicoletta Zoppi, Marco Ritelli, Marina Colombi
Vascular Ehlers-Danlos syndrome (vEDS) is a dominantly inherited connective tissue disorder caused by mutations in the COL3A1 gene that encodes type III collagen (COLLIII), which is the major expressed collagen in blood vessels and hollow organs. The majority of disease-causing variants in COL3A1 are glycine substitutions and in-frame splice mutations in the triple helix domain that through a dominant negative effect are associated with the severe clinical spectrum potentially lethal of vEDS, characterized by fragility of soft connective tissues with arterial and organ ruptures...
2018: PloS One
https://www.readbyqxmd.com/read/29346370/structure-function-and-control-of-the-human-musculoskeletal-network
#9
Andrew C Murphy, Sarah F Muldoon, David Baker, Adam Lastowka, Brittany Bennett, Muzhi Yang, Danielle S Bassett
The human body is a complex organism, the gross mechanical properties of which are enabled by an interconnected musculoskeletal network controlled by the nervous system. The nature of musculoskeletal interconnection facilitates stability, voluntary movement, and robustness to injury. However, a fundamental understanding of this network and its control by neural systems has remained elusive. Here we address this gap in knowledge by utilizing medical databases and mathematical modeling to reveal the organizational structure, predicted function, and neural control of the musculoskeletal system...
January 2018: PLoS Biology
https://www.readbyqxmd.com/read/29346265/halfway-between-2d-and-animal-models-are-3d-cultures-the-ideal-tool-to-study-cancer-microenvironment-interactions
#10
REVIEW
Jessica Hoarau-Véchot, Arash Rafii, Cyril Touboul, Jennifer Pasquier
An area that has come to be of tremendous interest in tumor research in the last decade is the role of the microenvironment in the biology of neoplastic diseases. The tumor microenvironment (TME) comprises various cells that are collectively important for normal tissue homeostasis as well as tumor progression or regression. Seminal studies have demonstrated the role of the dialogue between cancer cells (at many sites) and the cellular component of the microenvironment in tumor progression, metastasis, and resistance to treatment...
January 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29346114/or-net-a-service-oriented-architecture-for-safe-and-dynamic-medical-device-interoperability
#11
Martin Kasparick, Malte Schmitz, Björn Andersen, Max Rockstroh, Stefan Franke, Stefan Schlichting, Frank Golatowski, Dirk Timmermann
Modern surgical departments are characterized by a high degree of automation supporting complex procedures. It recently became apparent that integrated operating rooms can improve the quality of care, simplify clinical workflows, and mitigate equipment-related incidents and human errors. Particularly using computer assistance based on data from integrated surgical devices is a promising opportunity. However, the lack of manufacturer-independent interoperability often prevents the deployment of collaborative assistive systems...
January 18, 2018: Biomedizinische Technik. Biomedical Engineering
https://www.readbyqxmd.com/read/29346058/how-much-do-we-spend-creating-historical-estimates-of-public-health-expenditures-in-the-united-states-at-the-federal-state-and-local-levels
#12
Jonathon P Leider, Beth Resnick, David Bishai, F Douglas Scutchfield
The United States has a complex governmental public health system. Agencies at the federal, state, and local levels all contribute to the protection and promotion of the population's health. Whether the modern public health system is well situated to deliver essential public health services, however, is an open question. In some part, its readiness relates to how agencies are funded and to what ends. A mix of Federalism, home rule, and happenstance has contributed to a siloed funding system in the United States, whereby health agencies are given particular dollars for particular tasks...
January 18, 2018: Annual Review of Public Health
https://www.readbyqxmd.com/read/29346037/development-of-an-ultrasensitive-pcr-assay-for-polycyclic-musk-determination-in-fish
#13
Xiaohan Zhang, Huisheng Zhuang
Polycyclic musks (PCMs) in the aquatic environment and organisms have become an emerging environmental issue because of their potential risk. The most used method for polycyclic musk determination is gas chromatography-mass spectrometry (GC-MS) with different sample extractions, which are somewhat expensive to operate, complex and laborious. In this study, a novel and ultrasensitive real-time polymerase chain reaction (PCR) assay with multiple signal amplification of carboxylic-DNA by gold nanoparticle-polyamidoamine conjugation (Au-PAMAM) was developed for determining polycyclic musks in fish...
January 18, 2018: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/29345953/micro-to-nanoscale-engineering-of-surface-precipitates-using-reconfigurable-contact-lines
#14
Prasenjit Kabi, Swetaprovo Chaudhuri, Saptarshi Basu
Nanoscale engineering has traditionally adopted the chemical route of synthesis or opto-chemical techniques like lithography requiring large process times, expensive equipment and an inert environment. Directed self-assembly using evaporation of nanocolloidal droplet can be a potential low-cost alternative across various industries ranging from semiconductors to biomedical systems. It is relatively simple to scale and re-orient the evaporation driven internal flow field in an evaporating droplet which can direct dispersed matter into functional agglomerates...
January 18, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29345927/embedded-multireference-coupled-cluster-theory
#15
David James Coughtrie, Robin Giereth, Daniel Kats, Hans-Joachim Werner, Andreas Köhn
Internally contracted multireference coupled cluster (icMRCC) theory is embedded within multireference perturbation theory (MRPT) to calculate energy differences in large strongly correlated systems. The embedding scheme is based on partitioning the orbital spaces of a complete active space self consistent field (CASSCF) wave function, with the truncated virtual space constructed by transforming selected projected atomic orbitals (PAOs). MRPT is applied to the environment using a subtractive embedding approach, that also allows for multilayer embedding...
January 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29345924/domain-based-local-pair-natural-orbital-version-of-mukherjee-s-state-specific-coupled-cluster-method
#16
Jiri Brabec, Jakub Lang, Masaaki Saitow, Jiri Pittner, Frank Neese, Ondrej Demel
This article reports development of a local variant of Mukherjee's state specific multireference coupled cluster method based on the domain-based pair natural orbital approach (DLPNO-MkCC). The current implementation is restricted to connected single and double excitations and model space with up to biexcited references. The performance of the DLPNO-MkCCSD was tested on calculations of tetramethyleneethane. The results show that above 99.9% of correlation energy was recovered, with respect to the conventional MkCC method...
January 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29345775/versatile-modes-of-cooperative-b-h-bond-activation-reactions-in-ruthenium-carbene-complexes-addition-ring-opening-and-insertion
#17
Scharf T Lennart, Julia Weismann, Kai-Stephan Feichtner, Felix Lindl, Viktoria H Gessner
Cooperative B-H bond activation reactions with thio- and iminophosphoryl tethered ruthenium carbene complexes are reported. The complexes show surprisingly different reactivities towards the commonly employed boranes CatBH, PinBH and BH3∙LB as a result of different modes of metal ligand cooperation. While the iminophosphoryl system allows for selective 1,2-addition of the B-H bond across the Ru=C double bond, the sulfur analogue only delivers the 1,2-addition product for CatBH, while activation of BH3 and PinBH lead to further insertion reactions in one or more sides of the Ru-C-P-S-ring...
January 18, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29345638/molecular-mechanism-of-promoter-opening-by-rna-polymerase-iii
#18
Matthias K Vorländer, Heena Khatter, Rene Wetzel, Wim J H Hagen, Christoph W Müller
RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29345617/loss-of-functional-bap1-augments-sensitivity-to-trail-in-cancer-cells
#19
Krishna Kalyan Kolluri, Constantine Alifrangis, Neelam Kumar, Yuki Ishii, Stacey Price, Magali Michaut, Steven Williams, Syd Barthorpe, Howard Lightfoot, Sara Busacca, Annabel Sharkey, Zhenqiang Yuan, Elizabeth K Sage, Sabarinath Vallath, John Le Quesne, David A Tice, Doraid Alrifai, Sylvia von Karstedt, Antonella Montinaro, Naomi Guppy, David A Waller, Apostolos Nakas, Robert Good, Alan Holmes, Henning Walczak, Dean A Fennel, Mathew Garnett, Francesco Iorio, Lodewyk Wessels, Ultan McDermott, Samuel M Janes
Malignant mesothelioma (MM) is poorly responsive to systemic cytotoxic chemotherapy and invariably fatal. Here we describe a screen of 94 drugs in 15 exome-sequenced MM lines and the discovery of a subset defined by loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1) that demonstrate heightened sensitivity to TRAIL (tumour necrosis factor-related apoptosis-inducing ligand). This association is observed across human early passage MM cultures, mouse xenografts and human tumour explants...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29345589/neonatal-systemic-thrombosis-an-updated-overview
#20
Salvatore Santo Signorelli, Gea Oliveri Conti, Angelo Claudio Molinari, Martino Ruggieri, Alfina Grasso, Margherita Ferrantea
Thromboembolic disease is a complex disorder with a multifactorial aetiology and a severe outcome. In newborns and children it may be missed or diagnosed late, thus worsening the prognosis. The neonatal disease is different from the disorder affecting older children and adults. However, scant epidemiological data and few randomised clinical trials regarding paediatric patients are available, and treatment recommendations are largely based on adult guidelines. Younger patients then have several decades over which they will suffer from the complications of thrombosis and risk of a new thrombotic episode...
January 16, 2018: Current Vascular Pharmacology
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