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https://www.readbyqxmd.com/read/27914159/-molecular-mechanisms-for-adhesion-and-colonization-of-human-gastric-mucosa-by-helicobacter-pylori-and-its-clinical-implications
#1
REVIEW
Elisabete Coelho, Ana Magalhães, Mário Dinis-Ribeiro, Celso A Reis
INTRODUCTION: Helicobacter pylori infection is very prevalent worldwide and is associated with the progression of the gastric carcinogenesis cascade, being one of the main risk factors for the development of gastric carcinoma. Several factors are determinant for the infection and for the development of gastric disease, including environmental factors, host genetic factors and virulence factors of the bacteria. MATERIAL AND METHODS: In this review, we present an overview of the current knowledge on the determinants of the infection and on the recently described molecular mechanisms of Helicobacter pylori adhesion to the gastric mucosa, as well as its possible future therapeutic application...
August 2016: Acta Médica Portuguesa
https://www.readbyqxmd.com/read/27914124/atypical-neonatal-marfan-syndrome-with-p-glu1073lys-mutation-of-fbn1-the-first-case-in-korea
#2
Ju Sun Heo, Joo Young Song, Eun Young Choi, Eun Hee Kim, Ji Hee Kim, So Eun Park, Ji Hyun Jeon
Neonatal Marfan syndrome (nMFS) is considered to be on the most severe end of the spectrum of type I fibrillinopathies. The common features of nMFS include ascending aortic dilatation, severe mitral and/or tricuspid valve insufficiency, ectopia lentis, arachnodactyly, joint contractures, crumpled ear, loose skin, and pulmonary emphysema.We describe a newborn male diagnosed with nMFS. He presented several atypical features, such as diaphragmatic eventration, severe hydronephrosis with hydroureter, and dilated cisterna magna...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914115/molecular-phylogeny-and-taxonomy-of-a-new-freshwater-hymenostomatid-from-northeastern-china-with-the-establishment-of-a-new-genus-anteglaucoma-gen-n-protista-ciliophora-oligohymenophorea
#3
Xuming Pan, Zihan Shi, Chundi Wang, William A Bourland, Ying Chen, Weibo Song
The morphology, infraciliature and SSU rDNA sequence of a new freshwater hymenostomatid ciliate, Anteglaucoma harbinensis gen. nov., spec. nov., collected from a farmland pond in Harbin, China, were investigated. The new genus Anteglaucoma is characterized as follows: small to medium-sized Glaucomidae with oral apparatus in anterior one-third of cell; paroral membrane composed of almost longitudinally arranged dikinetids; three adoral membranelles nearly equal in length and arranged almost longitudinally in parallel; silverline pattern tetrahymenid...
November 7, 2016: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/27914109/bcor-upregulation-in-a-poorly-differentiated-synovial-sarcoma-with-ss18l1-ssx1-fusion-a-pathologic-and-molecular-pitfall
#4
Yu-Chien Kao, Yun-Shao Sung, Lei Zhang, Samuel Kenan, Samuel Singer, William D Tap, David Swanson, Brendan C Dickson, Cristina R Antonescu
The diagnosis of poorly differentiated synovial sarcoma (PD-SS) may be challenging due to overlapping morphologic features with other undifferentiated round cell sarcomas (URCS). Particularly relevant is the histologic overlap and shared BCOR overexpression between a subset of SS and URCS with various BCOR genetic abnormalities. Here we report a case of PD-SS lacking the canonical SS18-SSX gene fusion, but showing strong BCOR immunoreactivity and BCOR gene abnormalities by FISH which were misinterpreted as a URCS with BCOR gene rearrangements...
December 3, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27914103/-click-on-the-alkynylated-carbon-quantum-dots-an-efficient-surface-functionalization-for-specific-biosensing-and-bioimaging
#5
Mingxuan Gao, Lin Yang, Yi Zheng, Xiaoxi Yang, Hongyan Zou, Jing Han, Zexi Liu, Yuanfang Li, Cheng Zhi Huang
Surface functionalization is an essential prerequisite for wide and specific applications of nanoparticles such as photoluminescent (PL) carbon quantum dots (CQDs), but still remains as a major challenge. In this report, alkynylated CQDs, which were prepared at first from carboxyl-rich CQDs through amidation with propargylamine in the presence of 1,1'-carbonyldiimidazole, were efficiently modified with azido molecular beacon DNA through copper(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC). As the proof of concept, the DNA-modified CQDs was then bonded with 5-nm gold nanoparticles (AuNPs) through gold-sulfur bond...
December 3, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27914089/generating-and-purifying-fab-fragments-from-human-and-mouse-igg-using-the-bacterial-enzymes-ides-speb-and-kgp
#6
Jonathan Sjögren, Linda Andersson, Malin Mejàre, Fredrik Olsson
Fab fragments are valuable research tools in various areas of science including applications in imaging, binding studies, removal of Fc-mediated effector functions, mass spectrometry, infection biology, and many others. The enzymatic tools for the generation of Fab fragments have been discovered through basic research within the field of molecular bacterial pathogenesis. Today, these enzymes are widely applied as research tools and in this chapter, we describe methodologies based on bacterial enzymes to generate Fab fragments from both human and mouse IgG...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914083/antibody-guided-molecular-imaging-of-infective-endocarditis
#7
Kenneth L Pinkston, Peng Gao, Kavindra V Singh, Ali Azhdarinia, Barbara E Murray, Eva M Sevick-Muraca, Barrett R Harvey
In this protocol, we describe the application of using a high affinity monoclonal antibody generated against the major pilin protein component of the pilin structure of Enterococcus faecalis as a PET imaging agent for enterococcal endocarditis detection. The anti-pilin -mAb 64Cu conjugate was able to specifically label enterococcal endocarditis vegetation in vivo in a rodent endocarditis model. By targeting pili, a covalently linked surface antigen extending from the bacterial surface, we provided evidence that gram-positive pilin represent a logical surface antigen to define or target an infectious agent for molecularly guided imaging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914074/common-challenges-in-studying-the-structure-and-function-of-bacterial-proteins-case-studies-from-helicobacter-pylori
#8
Daniel A Bonsor, Eric J Sundberg
Employing biophysical and structural methods is a powerful way to elucidate mechanisms of molecular recognition in bacterial pathogenesis. Such studies invariably depend on the production of pure, folded and stable proteins. Many proteins that can be expressed recombinantly ultimately fail to meet one or more of these criteria. The cag proteins from Helicobacter pylori form a secretion system that delivers the oncoprotein, CagA, into human gastric epithelial cells through an interaction between CagL and host cell integrins, where it can cause gastric adenocarcinoma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914069/protein-based-strategies-to-identify-and-isolate-bacterial-virulence-factors
#9
Rolf Lood, Inga-Maria Frick
Protein-protein interactions play important roles in bacterial pathogenesis. Surface-bound or secreted bacterial proteins are key in mediating bacterial virulence. Thus, these factors are of high importance to study in order to elucidate the molecular mechanisms behind bacterial pathogenesis. Here, we present a protein-based strategy that can be used to identify and isolate bacterial proteins of importance for bacterial virulence, and allow for identification of both unknown host and bacterial factors. The methods described have among others successfully been used to identify and characterize several IgG-binding proteins, including protein G, protein H, and protein L...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#10
Armando Jerome de Jesus, Hang Yin
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#11
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#12
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#13
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#14
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914013/inhibitory-effect-of-homocysteine-on-rat-neural-stem-cell-growth-in-vitro-is-associated-with-reduced-protein-levels-and-enzymatic-activities-of-aconitase-and-respiratory-complex-iii
#15
Xu-Mei Zhang, Ya-Qian Zhao, Hai Yan, Huan Liu, Guo-Wei Huang
Increased blood plasma concentration of the sulphur amino acid homocysteine (Hcy) is considered as an independent risk factor of the neurodegenerative diseases. However, the detailed molecular mechanisms by which Hcy leads to neurotoxicity have yet to be clarified. Recent research has suggested that neurotoxicity of Hcy may involve negative regulation of neural stem cell (NSC) proliferation. In the current study, primary NSCs were isolated from neonatal rat brain hippocampus and the inhibition in cell growth was observed after exposure to l50 μM and 500 μM L-Hcy...
December 2, 2016: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/27914009/serum-response-factor-srf-ablation-interferes-with-acute-stress-associated-immediate-and-long-term-coping-mechanisms
#16
Annemarie Zimprich, Gabi Mroz, Christopher Meyer Zu Reckendorf, Sofia Anastasiadou, Philip Förstner, Lillian Garrett, Sabine M Hölter, Lore Becker, Jan Rozman, Cornelia Prehn, Birgit Rathkolb, Kristin Moreth, Wolfgang Wurst, Thomas Klopstock, Martin Klingenspor, Jerzy Adamski, Eckhard Wolf, Raffi Bekeredjian, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe de Angelis, Bernd Knöll
Stress experience modulates behavior, metabolism, and energy expenditure of organisms. One molecular hallmark of an acute stress response is a rapid induction of immediate early genes (IEGs) such as c-Fos and Egr family members. IEG transcription in neurons is mediated by the neuronal activity-driven gene regulator serum response factor (SRF). We show a first role of SRF in immediate and long-lasting acute restraint stress (AS) responses. For this, we employed a standardized mouse phenotyping protocol at the German Mouse Clinic (GMC) including behavioral, metabolic, and cardiologic tests as well as gene expression profiling to analyze the consequences of forebrain-specific SRF deletion in mice exposed to AS...
December 2, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27914004/hybrid-receptor-bound-mm-gbsa-per-residue-energy-based-pharmacophore-modelling-enhanced-approach-for-identification-of-selective-lta4h-inhibitors-as-potential-anti-inflammatory-drugs
#17
Patrick Appiah-Kubi, Mahmoud Soliman
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity...
December 2, 2016: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27913954/the-anti-inflammatory-activities-of-two-major-withanolides-from-physalis-minima-via-acting-on-nf-%C3%AE%C2%BAb-stat3-and-ho-1-in-lps-stimulated-raw264-7-cells
#18
Rui-Jun Li, Cai-Yun Gao, Chao Guo, Miao-Miao Zhou, Jun Luo, Ling-Yi Kong
Physalis minima has been traditionally used as a folk herbal medicine in China for the treatment of many inflammatory diseases. However, little is known about its anti-inflammatory constituents and associated molecular mechanisms. In our study, withaphysalin A (WA) and 2, 3-dihydro-withaphysalin C (WC), two major withanolide-type compounds, were obtained from the anti-inflammatory fraction of P. minima. Both WA and WC significantly inhibited the production of nitrite oxide (NO), prostaglandin E2 (PGE2), and several pro-inflammatory cytokines, such as interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α) in lipopolysaccharide (LPS)-activated RAW264...
December 2, 2016: Inflammation
https://www.readbyqxmd.com/read/27913951/stereolithography-based-3d-printed-pillar-plates-that-minimizes-fluid-transfers-during-enzyme-linked-immunosorbent-assays
#19
Justin D McCallen, Alison Schaefer, Phoebe Lee, Loretta Hing, Samuel K Lai
Enzyme linked immunosorbent assay (ELISA) is one of the most popular and indispensable tools in molecular biology. Despite numerous advances in ELISA methods that markedly improve the sensitivity and throughput of detection, a hallmark of all ELISA continues to be repeated pipetting of fluids that is not only cumbersome but can easily introduce errors or contaminations. Robotics, despite obvious advantages, remains expensive. Here, we designed and produced cheap "pillar plates" using stereolithography-based 3D printing that can be readily inserted into conventional 96- and 384- well plates and serve as the substrate for ELISA...
December 2, 2016: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/27913919/a-critical-overview-on-the-biological-and-molecular-features-of-red-and-processed-meat-in-colorectal-carcinogenesis
#20
REVIEW
Arunan Jeyakumar, Lakal Dissabandara, Vinod Gopalan
A recent investigation by the World Health Organisation (WHO) has found that the consumption of processed meat and potentially red meat promotes carcinogenesis and can increase the risk of colorectal cancer. This literature review aims to summarise both the red and processed meat molecules associated with colorectal carcinogenesis and investigate their relationship with the pathogenic process of colorectal cancer. Literature relating to the carcinogenic effect of red and processed meat molecules was critically reviewed...
December 2, 2016: Journal of Gastroenterology
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