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Viola Krukenberg, Dietmar Riedel, Harald R Gruber-Vodicka, Pier Luigi Buttigieg, Halina E Tegetmeyer, Antje Boetius, Gunter Wegener
The sulfate-dependent, anaerobic oxidation of methane (AOM) is an important sink for methane in marine environments. It is carried out between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) living in syntrophic partnership. In this study, we compared the genomes, gene expression patterns and ultrastructures of three phylogenetically different microbial consortia found in hydrocarbon-rich environments under different temperature regimes: ANME-1a/HotSeep-1 (60°C), ANME-1a/Seep-SRB2 (37°C) and ANME-2c/Seep-SRB2 (20°C)...
February 22, 2018: Environmental Microbiology
Hülya Kaya, Henrik Hasman, Jesper Larsen, Marc Stegger, Thor Bech Johannesen, Rosa Lundbye Allesøe, Camilla Koldbæk Lemvigh, Frank Møller Aarestrup, Ole Lund, Anders Rhod Larsen
Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCC mec ), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCC mec is less trivial because of its heterogeneity...
January 2018: MSphere
Gergely Ivády, László Madar, Erika Dzsudzsák, Katalin Koczok, János Kappelmayer, Veronika Krulisova, Milan Macek, Attila Horváth, István Balogh
BACKGROUND: Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis...
February 21, 2018: BMC Genomics
Lennard Glaeser, Joerg Henes, Ina Kötter, Wichard Vogel, Lothar Kanz, Reinhild Klein
OBJECTIVES: To evaluate the effect of autologous stem cell transplantation (aSCT) on antibody (ab) reactivity towards linear epitopes of topoisomerase-I (topo-I/Scl70) in patients with systemic sclerosis (SSc) and to correlate antibody reactivities with clinical outcome after aSCT. METHODS: Fourteen anti-topo-I/Scl70-positive SSc-patients were analysed before and after non-myeloablative aSCT. Five patients showed ongoing good response (group 1), 9 had primarily responded but later relapsed or did not respond (group 2)...
February 13, 2018: Clinical and Experimental Rheumatology
Devi Gunasekera, James C Zimring, Kathleen P Pratt
BACKGROUND: Kell is a glycoprotein expressed on red blood cells (RBCs). Its K and k variants contain either Met (K antigen) or Thr (k antigen) at Position 193, respectively. Development of anti-K after K-mismatched antigen exposure via blood transfusions or pregnancy can destroy RBCs, leading to hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. The immunogenicity of overlapping 15-mer Kell peptides with M193 or T193 at every possible position was investigated previously...
February 20, 2018: Transfusion
Cao Zhen, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
Motivation: The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date...
February 15, 2018: Bioinformatics
Jinzhu Ma, Yuhua Wei, Limeng Zhang, Xintong Wang, Di Yao, Daolong Liu, Wei Liu, Simiao Yu, Yongzhong Yu, Zhijun Wu, Liquan Yu, Zhanbo Zhu, Yudong Cui
PURPOSE: To explore an epitope-based vaccine against Staphylococcus aureus, we screened the epitopes in the N2N3 subdomain of fibronectin-binding protein A (FnBPA) as a surface component of S. aureus. METHODOLOGY: We expressed N2N3 proteins and prepared monoclonal antibodies (mAbs) against N2N3 by the hybridoma technique, before screening the B-cell epitopes in N2N3 using a phage-displayed random 12-mer peptide library with these mAbs against N2N3. Finally, we analysed the characters of the screened epitopes using immunofluorescence and an S...
January 18, 2018: Journal of Medical Microbiology
Ana S Peinetti, Helena Ceretti, Martín Mizrahi, Graciela A González, Silvana A Ramírez, Félix G Requejo, Javier M Montserrat, Fernando Battaglini
Polyvalent gold nanoparticle oligonucleotide conjugates are subject of intense research. Even though 2nm diameter AuNPs have been previously modified with DNA, little is known about their structure and electrochemical behavior. In this work, we examine the influence of different surface modification strategies on the interplay between the meso-organization and the molecular recognition properties of a 27-mer DNA strand. This DNA strand is functionalized with different sulfur-containing moieties and immobilized on 2nm gold nanoparticles confined on a nanoporous alumina, working the whole system as an electrode array...
February 9, 2018: Bioelectrochemistry
Rafal Tokarz, Nischay Mishra, Teresa Tagliafierro, Stephen Sameroff, Adrian Caciula, Lokendrasingh Chauhan, Jigar Patel, Eric Sullivan, Azad Gucwa, Brian Fallon, Marc Golightly, Claudia Molins, Martin Schriefer, Adriana Marques, Thomas Briese, W Ian Lipkin
Tick-borne diseases are the most common vector-borne diseases in the United States, with serology being the primary method of diagnosis. We developed the first multiplex, array-based assay for serodiagnosis of tick-borne diseases called the TBD-Serochip. The TBD-Serochip was designed to discriminate antibody responses to 8 major tick-borne pathogens present in the United States, including Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Borrelia miyamotoi, Ehrlichia chaffeensis, Rickettsia rickettsii, Heartland virus and Powassan virus...
February 16, 2018: Scientific Reports
Mudsser Azam, Arif Tasleem Jan, Ashutosh Kumar, Kehkashan Siddiqui, Aftab Hossain Mondal, Qazi Mohd Rizwanul Haq
Escalating burden of antibiotic resistance that has reached new heights present a grave concern to mankind. As the problem is no longer confined to clinics, we hereby report identification of a pandrug resistant Escherichia coli isolate from heavily polluted Delhi stretch of river Yamuna, India. E. coli MRC11 was found sensitive only to tobramycin against 21 antibiotics tested, with minimum inhibitory concentration values >256μg/mL for amoxicillin, carbenicillin, aztreonam, ceftazidime and cefotaxime. Addition of certain heavy metals at higher concentrations were ineffective in increasing susceptibility of E...
February 12, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
Ricardo Dias, Natércia F Brás, Iva Fernandes, Maria Pérez-Gregório, Nuno Mateus, Victor Freitas
Celiac Disease (CD) is now recognized as a worldwide epidemic. Although a gluten free diet usually induces clinical improvements within days or weeks, adhering to this routine is still troublesome. Therefore, new solutions are needed for quality-of-life improvement of CD patients. The present work intends to bring molecular and thermodynamic insights on the ability of green tea epigalhocatechin-3-gallate (EGCG) to interact and modulate the bioavailability of a major CD immunodominant peptide (32-mer). Characterization of peptide binding was assessed by means of both 1D and 2D 1 H NMR experiments, ITC and Molecular Dynamics simulations...
February 12, 2018: International Journal of Biological Macromolecules
Amir Tajbakhsh, Mehdi Rezaee, Petri T Kovanen, Amirhossein Sahebkar
Atherosclerosis is a dynamic and progressive inflammatory process in the intimal layer of large and medium-sized arteries, and it is the major contributor to the atherosclerotic cardiovascular disease (ACVD), the leading cause of death worldwide. In an atherosclerotic plaque, phagocytosis of apoptotic cells occurs through an intricate process designated efferocytosis. Defective efferocytosis has emerged as a causal factor in the etiopathogenesis of atherosclerosis and its progression into overt ACVD. Both specialized phagocytes (macrophages and dendritic cells) and non-specialized cells with phagocytic capabilities (smooth muscle and endothelial cells) are involved in the efferocytotic process...
February 11, 2018: Pharmacology & Therapeutics
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
Prashant Pandey, Michael A Bender, Rob Johnson, Rob Patro, Bonnie Berger
Motivation: k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure...
February 15, 2018: Bioinformatics
Divya Nayar, Nico F A van der Vegt
Water-mediated hydrophobic interactions play an important role in self-assembly processes, aqueous polymer solubility, and protein folding, to name a few. Cosolvents affect these interactions however the implications for hydrophobic polymer collapse and protein folding equilibria are not well-understood. This study examines cosolvent effects on the hydrophobic collapse equilibrium of a generic 32-mer hydrophobic polymer in urea, trimethylamine-N-oxide (TMAO), and acetone aqueous solutions using molecular dynamics simulations...
February 14, 2018: Journal of Physical Chemistry. B
Chao Wang, Shuai Xia, Peiyu Zhang, Tianhong Zhang, Weicong Wang, Yangli Tian, Guangpeng Meng, Shibo Jiang, Keliang Liu
The hexameric α-helical coiled-coil formed between the C-terminal and N-terminal heptad repeat (CHR and NHR) regions of class I viral fusion proteins plays an important role in mediating the fusion of the viral and cellular membranes and provides a clear starting point for molecular mimicry that drives viral fusion inhibitor design. Unfortunately, such peptide mimicry of the short α-helical region in the CHR of Middle East respiratory syndrome coronavirus (MERS-CoV) spike protein has been thwarted by the loss of the peptide's native α-helical conformation when taken out of the parent protein structure...
February 14, 2018: Journal of Medicinal Chemistry
Guoan Zhang, Meng Wang, Hongli Zhao, Wen Cui
Axl receptor tyrosine kinase (hereafter Axl) is a member of the tyrosine-protein kinase receptor Tyro3, Axl and proto-oncogene tyrosine-protein kinase Mer family of receptor tyrosine kinases, possessing multiple different functions in normal cells. Axl is overexpressed and activated in numerous different human cancer types, triggering several signaling pathways and enhancing tumor progression. The present review assesses previous studies on the function of Axl in non-small cell lung cancer (NSCLC). Axl is overexpressed in the tumor tissues of a number of patients with NSCLC and is associated with poorer clinical outcomes; it promotes NSCLC tumor growth, invasion/metastasis, drug resistance and the epithelial-mesenchymal transition, thus providing a survival advantage to tumor cells...
March 2018: Oncology Letters
Guoan Zhang, Xia Kong, Meng Wang, Hongli Zhao, Sha Han, Ronghang Hu, Jian Huang, Wen Cui
Esophageal squamous cell carcinoma (ESCC) is a common cancer in China and certain other parts of the world with a dismal prognosis for affected patients. AXL is a member of the TYRO3-AXL-MER family of receptor tyrosine kinases, and has been revealed to be an important mediator of epithelial-mesenchymal transition (EMT) in several types of cancer. However, to the best of our knowledge, its function in EMT in ESCC cells has not yet been examined. The present study employed two independent ESCC mRNA profile datasets and revealed that AXL is associated with several EMT markers...
February 2018: Oncology Letters
Alexander Pichugin, Stasya Zarling, Leah Perazzo, Patrick Emmet Duffy, Hidde Lolke Ploegh, Urszula Krzych
We recently identified novel Plasmodium berghei (Pb) liver stage (LS) genes that as DNA vaccines significantly reduce Pb LS parasite burden (LPB) in C57Bl/6 (B6) mice through a mechanism mediated, in part, by CD8 T cells. In this study, we sought to determine fine antigen (Ag) specificities of CD8 T cells that target LS malaria parasites. Guided by algorithms for predicting MHC class I-restricted epitopes, we ranked sequences of 32 Pb LS Ags and selected ~400 peptides restricted by mouse H-2Kb and H-2Db alleles for analysis in the high-throughput method of caged MHC class I-tetramer technology...
2018: Frontiers in Immunology
Eduardo Peris, Robert H Crabtree
Pincers, tridentate ligands that prefer a meridional geometry, are a rising class because of their distinctive combination of properties. They permit a good level of control on the nature of the coordination sphere by holding the donor groups in a predictable arrangement. Some groups, such as an aryl or a pyridine, that would normally be easily lost as monodentate ligands, become reliably coordinated, especially if they form the central donor unit of the three. Many pincer complexes show exceptional thermal stability, a property that is particularly prized in homogeneous catalysis where they can permit high temperature operation...
February 12, 2018: Chemical Society Reviews
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