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Jamie McCann, Tae-Soo Jang, Jiri Macas, Gerald M Schneeweiss, Nicholas J Matzke, Petr Novák, Tod F Stuessy, José L Villaseñor, Hanna Weiss-Schneeweiss
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid...
March 19, 2018: Systematic Biology
Yanting Luo, Jianlin He, Xiguang Xu, Ming-An Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie
Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data...
March 2018: PLoS Computational Biology
Kohinoor M Darda, Emily E Butler, Richard Ramsey
Although humans show an involuntary tendency to copy other people's actions, which builds rapport between individuals, we do not copy actions indiscriminately. Instead, copying behaviors are guided by a selection mechanism, which inhibits some actions and prioritizes others. To date, the neural underpinnings of the inhibition of automatic imitation and differences between the sexes in imitation control are not well understood. Previous studies involved small sample sizes and low statistical power, which produced mixed findings regarding the involvement of domain-general and domain-specific neural architectures...
March 21, 2018: Journal of Cognitive Neuroscience
Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
BACKGROUND: Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss...
March 19, 2018: BMC Systems Biology
Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Jaewoo Kang
BACKGROUND: Drug combination therapy, which is considered as an alternative to single drug therapy, can potentially reduce resistance and toxicity, and have synergistic efficacy. As drug combination therapies are widely used in the clinic for hypertension, asthma, and AIDS, they have also been proposed for the treatment of cancer. However, it is difficult to select and experimentally evaluate effective combinations because not only is the number of cancer drug combinations extremely large but also the effectiveness of drug combinations varies depending on the genetic variation of cancer patients...
March 19, 2018: BMC Systems Biology
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
To understand the common gene expression patterns employed by P. placenta during lignocellulose degradation, we have retrieved genome wide transcriptome datasets from NCBI GEO database and analyzed using customized analysis pipeline. We have retrieved the top differentially expressed genes and compared the common significant genes among two different growth conditions. Genes encoding for cellulolytic (GH1, GH3, GH5, GH12, GH16, GH45) and hemicellulolytic (GH10, GH27, GH31, GH35, GH47, GH51, GH55, GH78, GH95) glycoside hydrolase classes were commonly up regulated among all the datasets...
2018: International Journal of Biological Sciences
Melissa L Sykes, Vicky M Avery
Using high throughput, high-content imaging, a proprietary library was screened against intracellular Trypanosoma cruzi amastigotes to identify compounds with novel activity against the parasite. Five inhibitors were discovered, which did not clear all of the parasites from 3T3 host cells following 48 hours exposure, and were identified as putative T. cruzi cytochrome P450 (TcCYP51) inhibitors. TcCYP51 inhibitors are not favourable for the drug discovery pipeline for treatment of Chagas Disease infection due to clinical and pre-clinical failures...
March 20, 2018: Scientific Reports
Ethan A G Baker, Jill L Wegrzyn, Uzay U Sezen, Taylor Falk, Patricia E Maloney, Detlev R Vogler, Annette Delfino-Mix, Camille Jensen, Jeffry Mitton, Jessica Wright, Brian Knaus, Hardeep Rai, Richard Cronn, Daniel Gonzalez-Ibeas, Hans A Vasquez-Gross, Randi A Famula, Jun-Jun Liu, Lara M Kueppers, David B Neale
Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors...
March 20, 2018: G3: Genes—Genomes—Genetics
Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells...
March 20, 2018: Genome Medicine
Luciano Rossetti
Luciano Rossetti, MD, Executive Vice President, Global Head of R&D at Merck KGaA, Darmstadt, Germany speaks to Laura Dormer, Commissioning Editor Luciano Rossetti, MD, is Executive Vice President, Global Head of R&D at Merck KGaA, Darmstadt, Germany, and a member of the Healthcare Executive Committee. As Global Head of R&D, Rossetti leads the strategy for Merck KGaA, Darmstadt, Germany's discovery and development efforts in healthcare. He joined Merck KGaA in July 2014, and has since led the acceleration of several key programs through the pipeline and advanced the innovation of Merck KGaA's discovery teams into development...
March 20, 2018: Neurodegenerative Disease Management
Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F Chen, Dong-Sheng Cao
BACKGROUND: With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important...
March 20, 2018: Journal of Cheminformatics
Thomas B Hansen
Non-coding RNA is an interesting class of gene regulators with diverse functionalities. One large subgroup of non-coding RNAs is the recently discovered class of circular RNAs (circRNAs). CircRNAs are conserved and expressed in a tissue and developmental specific manner, although for the vast majority, the functional relevance remains unclear. To identify and quantify circRNAs expression, several bioinformatic pipelines have been developed to assess the catalog of circRNAs in any given total RNA sequencing dataset...
2018: Frontiers in Cell and Developmental Biology
Hubert S Gabryś, Florian Buettner, Florian Sterzing, Henrik Hauswald, Mark Bangert
Purpose: The purpose of this study is to investigate whether machine learning with dosiomic, radiomic, and demographic features allows for xerostomia risk assessment more precise than normal tissue complication probability (NTCP) models based on the mean radiation dose to parotid glands. Material and methods: A cohort of 153 head-and-neck cancer patients was used to model xerostomia at 0-6 months (early), 6-15 months (late), 15-24 months (long-term), and at any time (a longitudinal model) after radiotherapy...
2018: Frontiers in Oncology
Carla Caballero, Sejal Mistry, Joe Vero, Elizabeth B Torres
The variability inherently present in biophysical data is partly contributed by disparate sampling resolutions across instrumentations. This poses a potential problem for statistical inference using pooled data in open access repositories. Such repositories combine data collected from multiple research sites using variable sampling resolutions. One example is the Autism Brain Imaging Data Exchange repository containing thousands of imaging and demographic records from participants in the spectrum of autism and age-matched neurotypical controls...
2018: Frontiers in Integrative Neuroscience
Ian M Boothroyd, Sam Almond, Fred Worrall, Rosemary K Davies, Richard J Davies
Natural gas pipelines are an important source of fugitive methane emissions in lifecycle greenhouse gas assessments but limited monitoring has taken place of UK pipelines to quantify fugitive emissions. This study investigated methane emissions from the UK high-pressure pipeline system (National Transmission System - NTS) for natural gas pipelines. Mobile surveys of CH4 emissions were conducted across four areas in the UK, with routes bisecting high-pressure pipelines (with a maximum operating pressure of 85bar) and separate control routes away from the pipelines...
February 28, 2018: Science of the Total Environment
Stephen J Fletcher, Mikael Boden, Neena Mitter, Bernard J Carroll
Summary: Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. Availability: The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license...
March 15, 2018: Bioinformatics
Wenbin Liu, Aimin Liu
With the exploitation of offshore oil and gas gradually moving to deep water, higher temperature differences and pressure differences are applied to the pipeline system, making the global buckling of the pipeline more serious. For unburied deep-water pipelines, the lateral buckling is the major buckling form. The initial imperfections widely exist in the pipeline system due to manufacture defects or the influence of uneven seabed, and the distribution and geometry features of initial imperfections are random...
2018: PloS One
Shihao Ran, Sebastian Berisha, Rupali Mankar, Wei-Chuan Shih, David Mayerich
Infrared (IR) spectroscopic microscopes provide the potential for label-free quantitative molecular imaging of biological samples, which can be used to aid in histology, forensics, and pharmaceutical analysis. Most IR imaging systems use broadband illumination combined with a spectrometer to separate the signal into spectral components. This technique is currently too slow for many biomedical applications such as clinical diagnosis, primarily due to the availability of bright mid-infrared sources and sensitive MCT detectors...
February 1, 2018: Biomedical Optics Express
Chang Xu
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications...
2018: Computational and Structural Biotechnology Journal
Magdalena Nüesch-Inderbinen, Katrin Zurfluh, Marc J A Stevens, Roger Stephan
OBJECTIVES: Carbapenem-resistant Klebsiella pneumoniae (CRKP) have emerged worldwide and represent a major threat to human health. Here, we report the genome sequence of K. pneumoniae 002SK2, an NDM-9 and CTX-M-15 producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone ST147. METHODS: Whole genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology RS2 reads (C4/P6 chemistry)...
March 15, 2018: Journal of Global Antimicrobial Resistance
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