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https://www.readbyqxmd.com/read/29145154/a-pipeline-for-proteome-scale-identification-and-studies-on-hormone-sensitive-lipases-in-mycobacterium-tuberculosis
#1
Durairaj Sherlin, Sharmila Anishetty
Hormone sensitive lipases (HSLs) play an important role in the survival of M. tuberculosis during dormancy. They help in the utilization of fatty acids from stored lipids. The objective of the current study was to identify all HSLs from the proteome of M. tuberculosis H37Rv. We have developed a novel HSL identification pipeline, based on amino acid sequence homology, presence of conserved motifs and other sequence features deciphered from known HSL dataset. Through this pipeline, we identified 10 proteins as putative HSLs in M...
November 7, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29144203/suppression-or-activation-of-immune-responses-by-predicted-secreted-proteins-of-the-soybean-rust-pathogen-phakopsora-pachyrhizi
#2
Mingsheng Qi, James P Grayczyk, Janina M Seitz, Youngsill Lee, Tobias I Link, Doil Choi, Kerry F Pedley, Ralf T Voegele, Thomas J Baum, Steven A Whitham
Rust fungi, such as the soybean rust pathogen Phakopsora pachyrhizi, are major threats to crop production. They form specialized haustoria that are hyphal structures intimately associated with host-plant cell membranes. These haustoria have roles in acquiring nutrients and secreting effector proteins that manipulate host immune systems. Functional characterization of effector proteins of rust fungi is important for understanding mechanisms that underlie their virulence and pathogenicity. Hundreds of candidate effector proteins have been predicted for rust pathogens, but it is not clear how to prioritize these effector candidates for further characterization...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29143810/next-generation-pacemakers-from-small-devices-to-biological-pacemakers
#3
REVIEW
Eugenio Cingolani, Joshua I Goldhaber, Eduardo Marbán
Electrogenesis in the heart begins in the sinoatrial node and proceeds down the conduction system to originate the heartbeat. Conduction system disorders lead to slow heart rates that are insufficient to support the circulation, necessitating implantation of electronic pacemakers. The typical electronic pacemaker consists of a subcutaneous generator and battery module attached to one or more endocardial leads. New leadless pacemakers can be implanted directly into the right ventricular apex, providing single-chamber pacing without a subcutaneous generator...
November 16, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/29140767/genomic-medicine-without-borders-which-strategies-should-developing-countries-employ-to-invest-in-precision-medicine-a-new-fast-second-winner-strategy
#4
Konstantinos Mitropoulos, David N Cooper, Christina Mitropoulou, Spiros Agathos, Jürgen K V Reichardt, Fatima Al-Maskari, Wasun Chantratita, Ambroise Wonkam, Collet Dandara, Theodora Katsila, Catalina Lopez-Correa, Bassam R Ali, George P Patrinos
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29140531/an-update-on-sorfs-org-a-repository-of-small-orfs-identified-by-ribosome-profiling
#5
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140523/sequential-coiling-assisted-deployment-of-flow-diverter-for-treatment-of-fusiform-middle-cerebral-artery-aneurysms
#6
Abdulrahman Y Alturki, Philip G R Schmalz, Christopher S Ogilvy, Ajith J Thomas
BACKGROUND AND IMPORTANCE: Fusiform intracranial aneurysms remain challenging lesions to treat. These aneurysms have historically required bypass procedures or clip remodeling constructs for cure. Recently, endovascular specialists have reported experience with flow diversion for complex fusiform aneurysms of the vertebrobasilar system, with mixed results. Vascular anatomy for anterior circulation fusiform aneurysms may make these lesions more amenable to flow diversion and embolization procedures; however, published experience with these techniques is lacking...
November 11, 2017: Operative Neurosurgery (Hagerstown, Md.)
https://www.readbyqxmd.com/read/29140462/data-portal-for-the-library-of-integrated-network-based-cellular-signatures-lincs-program-integrated-access-to-diverse-large-scale-cellular-perturbation-response-data
#7
Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J Cooper, John P Turner, Dušica Vidovic, Michele Forlin, Tanya T Kelley, Alessandro D'Urso, Bryce K Allen, Denis Torre, Kathleen M Jagodnik, Lily Wang, Sherry L Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Mahi, Marcin Pilarczyk, Nicholas Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C Schürer
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138298/first-insights-into-the-diverse-human-archaeome-specific-detection-of-archaea-in-the-gastrointestinal-tract-lung-and-nose-and-on-skin
#8
Kaisa Koskinen, Manuela R Pausan, Alexandra K Perras, Michael Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth Schmitz, Christine Moissl-Eichinger
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29138089/rapid-two-step-dipole-inversion-for-susceptibility-mapping-with-sparsity-priors
#9
Christian Kames, Vanessa Wiggermann, Alexander Rauscher
Quantitative susceptibility mapping (QSM) is a post-processing technique of gradient echo phase data that attempts to map the spatial distribution of local tissue magnetic susceptibilities. To obtain these maps, an ill-posed field-to-source inverse problem must be solved to remove non-local magnetic field perturbations. Current state-of-the-art algorithms which aim to solve the dipole inversion problem are plagued by the trade-off between reconstruction speed and accuracy. A two-step dipole inversion algorithm is proposed to bridge this gap...
November 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/29136907/ultrasonic-based-membrane-aided-sample-preparation-of-urine-proteomes
#10
Jemmyson Romário Jesus, Hugo M Santos, H López-Fernández, Carlos Lodeiro, Marco Aurélio Zezzi Arruda, J L Capelo
A new ultrafast ultrasonic-based method for shotgun proteomics as well as label-free protein quantification in urine samples is developed. The method first separates the urine proteins using nitrocellulose-based membranes and then proteins are in-membrane digested using trypsin. The enzymatic digestion process is accelerated from overnight to four minutes using a sonoreactor ultrasonic device. Overall, the sample treatment pipeline comprising protein separation, digestion and identification is done in just 3h...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136819/alteration-in-the-liver-metabolome-of-rats-with-metabolic-syndrome-after-treatment-with-hydroxytyrosol-a-mass-spectrometry-and-nuclear-magnetic-resonance-based-metabolomics-study
#11
Ioanna Dagla, Dimitra Benaki, Eirini Baira, Nikolaos Lemonakis, Hemant Poudyal, Lindsay Brown, Anthony Tsarbopoulos, Alexios-Leandros Skaltsounis, Emmanouel Mikros, Evagelos Gikas
Metabolic syndrome (MetS) represents a group of abnormalities that enhances the risk for cardiovascular disease, diabetes and stroke. The Mediterranean diet seems to be an important dietary pattern, which reduces the incidence of MetS. Hydroxytyrosol (HT) - a simple phenol found in olive oil - has received increased attention for its antioxidant activity. Recently, the European Foods Safety Authority (EFSA) claimed that dietary consumption of HT exhibits a protective role against cardiovascular disease. In this study, an experimental protocol has been setup, including isolated HT administration in a diet induced model of MetS in young Wistar rats, in order to find out whether HT has a protective effect against MetS...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136663/phylogenic-inference-using-alignment-free-methods-for-applications-in-microbial-community-surveys-using-16s-rrna-gene
#12
Yifei Zhang, Alexander V Alekseyenko
The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data...
2017: PloS One
https://www.readbyqxmd.com/read/29136644/developmentally-regulated-internal-transcription-initiation-during-meiosis-in-budding-yeast
#13
Sai Zhou, Rolf Sternglanz, Aaron M Neiman
Sporulation of budding yeast is a developmental process in which cells undergo meiosis to generate stress-resistant progeny. The dynamic nature of the budding yeast meiotic transcriptome has been well established by a number of genome-wide studies. Here we develop an analysis pipeline to systematically identify novel transcription start sites that reside internal to a gene. Application of this pipeline to data from a synchronized meiotic time course reveals over 40 genes that display specific internal initiations in mid-sporulation...
2017: PloS One
https://www.readbyqxmd.com/read/29136216/the-eukaryotic-linear-motif-resource-2018-update
#14
Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Manjeet Kumar, András Zeke, Benjamin Lang, Benoit Bely, Lucía B Chemes, Norman E Davey, Ziqi Deng, Francesca Diella, Clara-Marie Gürth, Ann-Kathrin Huber, Stefan Kleinsorg, Lara S Schlegel, Nicolás Palopoli, Kim V Roey, Brigitte Altenberg, Attila Reményi, Holger Dinkel, Toby J Gibson
Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#15
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29136000/point-cloud-registration-from-local-feature-correspondences-evaluation-on-challenging-datasets
#16
Tomas Petricek, Tomas Svoboda
Registration of laser scans, or point clouds in general, is a crucial step of localization and mapping with mobile robots or in object modeling pipelines. A coarse alignment of the point clouds is generally needed before applying local methods such as the Iterative Closest Point (ICP) algorithm. We propose a feature-based approach to point cloud registration and evaluate the proposed method and its individual components on challenging real-world datasets. For a moderate overlap between the laser scans, the method provides a superior registration accuracy compared to state-of-the-art methods including Generalized ICP, 3D Normal-Distribution Transform, Fast Point-Feature Histograms, and 4-Points Congruent Sets...
2017: PloS One
https://www.readbyqxmd.com/read/29135912/a-statistical-study-on-the-effect-of-hydrostatic-pressure-on-metastable-pitting-corrosion-of-x70-pipeline-steel
#17
Zixuan Yang, Bo Kan, Jinxu Li, Lijie Qiao, Alex A Volinsky, Yanjing Su
Hydrostatic pressure effects on pitting initiation and propagation in X70 steel are investigated by evaluating metastable pitting probability using electrochemical methods and immersion corrosion tests in containing chlorine ion solution. Potentiodynamic tests indicated that hydrostatic pressure can decrease the breakdown potential and lead to a reduced transpassivity region. Metastable test results revealed that hydrostatic pressure can increase metastable pitting formation frequency and promote stabilization of metastable pitting growth...
November 14, 2017: Materials
https://www.readbyqxmd.com/read/29134624/challenges-for-training-translational-researchers-in-the-era-of-ubiquitous-data
#18
Russ B Altman
Our ability to collect data at every stage of the translational pipeline creates great opportunities for formulating hypotheses both "upstream" (towards clinical implementation) and "downstream" (back to basic discovery). Translational researchers therefore must integrate information at multiple scales to both generate and test hypotheses-to some extent they must all be comfortable with the basics of "big data" analyses. This increased focus on data-driven science requires an understanding of basic experimental and clinical data collection-understanding that likely cannot efficiently be gathered through traditional apprenticeship models...
November 14, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29134599/phage-genome-annotation-using-the-rast-pipeline
#19
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh, Robert Edwards
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134153/hgtsim-a-simulator-for-horizontal-gene-transfer-hgt-in-microbial-communities
#20
Weizhi Song, Kerrin Steensen, Torsten Thomas
The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets...
2017: PeerJ
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