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Yipeng Du, Zichao Zhai, Ying Li, Ming Lu, Tanxi Cai, Bo Zhou, Lei Huang, Taotao Wei, Tingting Li
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins in low abundance or absent in specific biological samples. To circumvent these problems, we developed a computational method to predict lysine acylation, including acetylation, malonylation, succinylation, and glutarylation. The prediction algorithm integrated flanking primary sequence determinants and evolutionary conservation of acylated lysine, as well as multiple protein functional annotation features including gene ontology, conserved domains and protein-protein interactions...
October 24, 2016: Journal of Proteome Research
Ian Vincent McGonigle
Ethnopharmacologists are scientists and anthropologists that study indigenous medicines and healing practices, and who often develop new therapies and medicines for wider use. Ethnopharmacologists do fieldwork with indigenous peoples in traditional societies, where they encounter a wide range of cultural values and varying ideas about the nature of property relations. This poses difficulties for protecting indigenous intellectual property and for making just trade agreements. This Note reviews the legal issues relevant to the protection of indigenous resources in ethnopharmacology trade agreements, and suggests that recent developments in anthropology and the social study of science could be instructive in furthering the legal discourse and in providing policy directions...
April 2016: Journal of Law and the Biosciences
Zhao Li, Guanghui Hu, Xiangfeng Liu, Yao Zhou, Yu Li, Xu Zhang, Xiaohui Yuan, Qian Zhang, Deguang Yang, Tianyu Wang, Zhiwu Zhang
Originating in a tropical climate, maize has faced great challenges as cultivation has expanded to the majority of the world's temperate zones. In these zones, frost and cold temperatures are major factors that prevent maize from reaching its full yield potential. Among 30 elite maize inbred lines adapted to northern China, we identified two lines of extreme, but opposite, freezing tolerance levels-highly tolerant and highly sensitive. During the seedling stage of these two lines, we used RNA-seq to measure changes in maize whole genome transcriptome before and after freezing treatment...
2016: Frontiers in Plant Science
Baoyu Huang, Linlin Zhang, Xueying Tang, Guofan Zhang, Li Li
Alternative splicing (AS) is thought to enhance transcriptome diversity dramatically and play an important role in stress adaptation. While well studied in vertebrates, AS remains poorly understood in invertebrates. Here, we used high-throughput RNA-sequencing data to perform a genome-wide survey of AS in the Pacific oyster (Crassostrea gigas), an economically important mollusk that is cultivated worldwide. This analysis identified 8223 AS events corresponding to 4480 genes in the Pacific oyster, suggesting that about 16 % of oyster multiexonic genes undergo AS...
October 22, 2016: Marine Biotechnology
Christine Altmann, Verica Vasic, Stefanie Hardt, Juliana Heidler, Annett Häussler, Ilka Wittig, Mirko H H Schmidt, Irmgard Tegeder
BACKGROUND: Peripheral nerve injury is a frequent cause of lasting motor deficits and chronic pain. Although peripheral nerves are capable of regrowth they often fail to re-innervate target tissues. RESULTS: Using newly generated transgenic mice with inducible neuronal progranulin overexpression we show that progranulin accelerates axonal regrowth, restoration of neuromuscular synapses and recovery of sensory and motor functions after injury of the sciatic nerve...
October 22, 2016: Molecular Neurodegeneration
Julia Engelhorn, Franziska Turck
Genome-wide analyses of chromatin factor-binding sites or histone modification localization generate lists of up to several thousand potential target genes. For many model organisms, large annotation databases are available to help with the characterization and classification of genomic datasets. The term meta-analysis has been coined for this type of multi-database comparison. In this chapter, we describe a workflow to perform a transcriptional and functional analysis of genome-wide target genes. Sources of transcription data and clustering tools to subdivide genes according to their expression pattern are described...
2017: Methods in Molecular Biology
Erica Borgstrom
This review will outline various ways in which the notion of 'social death' can be understood, and how they can be related to clinical practice. The idea of social death is used to analytically represent how someone can be identified and treated as if they are ontologically deficient - meaning that they are not seen as being 'fully human.' This impacts on their position within society and how they are interacted with. This review will consider three examples of social death - often distinguished from physical or biological death - that are important for clinical practice: loss of agency and identity; treating people as if they are already dead; and, rituals and bereavement...
October 20, 2016: QJM: Monthly Journal of the Association of Physicians
Juliet Richetto, Renaud Massart, Ulrike Weber-Stadlbauer, Moshe Szyf, Marco A Riva, Urs Meyer
BACKGROUND: Prenatal exposure to infectious or inflammatory insults increases the risk of neurodevelopmental disorders. Using a well-established mouse model of prenatal viral-like immune activation, we examined whether this pathological association involves genome-wide DNA methylation differences at single nucleotide resolution. METHODS: Prenatal immune activation was induced by maternal treatment with the viral mimetic polyriboinosinic-polyribocytidylic acid in middle or late gestation...
August 12, 2016: Biological Psychiatry
Gloria Isani, Enea Ferlizza, Aurora Cuoghi, Elisa Bellei, Emanuela Monari, Barbara Bianchin Butina, Carolina Castagnetti
Characterisation of the physiologic equine amniotic fluid (AF) proteome is a prerequisite to study its changes during diseases and discover new biomarkers. The aim of this study was to identify by a proteomic approach the most abundant proteins of equine AF. AF samples were collected at parturition from 24 healthy mares that delivered healthy foals. All samples were subjected to sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) on 4-12% gels. A pool of the 24 samples, after SDS-PAGE, was cut in 25 slices, trypsin-digested and analysed by mass spectrometry (MS) for protein identification...
October 11, 2016: Animal Reproduction Science
Chaoyun Hao, Zhiqiang Xia, Rui Fan, Lehe Tan, Lisong Hu, Baoduo Wu, Huasong Wu
BACKGROUND: Piper nigrum L., or "black pepper", is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora capsici, and genetic improvement of black pepper is essential for combating foot rot diseases. However, little is known about the mechanism of anti- P. capsici in black pepper. The molecular mechanisms underlying foot rot susceptibility were studied by comparing transcriptome analysis between resistant (Piper flaviflorum) and susceptible (Piper nigrum cv...
October 21, 2016: BMC Genomics
Jianjun Niu, Yong Lin, Pingguo Liu, Yiwen Yu, Chenghao Su, Xiaomin Wang
Long non-coding RNAs are involved with development and progression of cancer, and the advance of microarray technology allows the researchers to investigate the complete expression profile of lncRNA in various kinds of sample. We enrolled 5 male primary HCC cases with chronic HBV infection and the HCC and normal tissues have been obtained during the resection surgery. After total RNA extraction, the lncRNA microarray analysis was conducted to determine the lncRNA and mRNA expression signals. 612 lncRNAs and 1,064 mRNAs were significantly up-regulated in HCC tissue while 656 lncRNAs and 1,532 mRNAs were down-regulated in HCC tissues...
October 18, 2016: Oncotarget
Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
Yongsheng Bai, Lizhong Ding, Steve Baker, Jenny M Bai, Ethan Rath, Feng Jiang, Jianghong Wu, Hui Jiang, Gary Stuart
BACKGROUND: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples. Moreover, a deep investigation of miRNA-mRNA target and biological relationships across multiple cancer types by integrating web-based analysis has not been thoroughly conducted...
October 6, 2016: BMC Bioinformatics
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
Tahar Ait-Ali, Ivan Díaz, Ferran Soldevila, Esmeralda Cano, Yanli Li, Alison D Wilson, Bruno Giotti, Alan L Archibald, Enric Mateu, Laila Darwich
Little is known about the host factor in the response to PRRSV vaccination. For this purpose, piglets were immunized with a commercial PRRSV-live vaccine and classified as high responders (HR) or low responders (LR) as regards to the frequencies of virus-specific IFN-γ-secreting cells. Six weeks post vaccination, PBMCs isolated from three individuals with the most extreme responses in each HR and LR groups and 3 unvaccinated controls, were either stimulated with phytohaemagglutinin, challenged with the vaccine or mock treated for 24 h, prior conducting transcriptional studies, gene ontology and pathway analyses...
October 20, 2016: Veterinary Research
Xiangrui Li, Fangmei Zhang, Brad Coates, Yunhui Zhang, Xuguo Zhou, Dengfa Cheng
MicroRNAs (miRNAs) are short single-stranded non-coding RNAs that regulate gene expression, particularly during development. In this study, 345 miRNAs were identified from the English green aphid, Sitobion avenae (F.), of which 168 were conserved and 177 were S. avenae-specific. Quantitative comparison of miRNA expression levels indicated that 16 and 12 miRNAs were significantly up-regulated in winged and wingless S. avenae small RNA libraries, respectively. Differential expression of these miRNAs was confirmed by real-time quantitative RT-PCR validation...
October 20, 2016: Scientific Reports
Yuan Yao, Jin Shang, Weilin Song, Qiyue Deng, Huan Liu, Yue Zhou
This article contains relevant data of the research article titled Global profiling of the gene expression and alternative splicing events during the hypoxia-regulated chondrogenic differentiation in human cartilage endplate-derived stem cells (Yao et al., 2016) [1]. The data show global profiling of the DEGs (Differentially expressed genes) and AS (Alternative splicing) events during the hypoxia-regulated chondrogenesis of CESCs (human cartilage endplate-derived stem cells) by using Affymetrix Human Transcriptome Array 2...
June 2016: Data in Brief
Azam Moshtaghi, Md Lifat Rahi, Viet Tuan Nguyen, Peter B Mather, David A Hurwood
BACKGROUND: Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. METHODS: To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology...
2016: PeerJ
Daniel V Guebel, Néstor V Torres
Motivation: In the brain of elderly-healthy individuals, the effects of sexual dimorphism and those due to normal aging appear overlapped. Discrimination of these two dimensions would powerfully contribute to a better understanding of the etiology of some neurodegenerative diseases, such as "sporadic" Alzheimer. Methods: Following a system biology approach, top-down and bottom-up strategies were combined. First, public transcriptome data corresponding to the transition from adulthood to the aging stage in normal, human hippocampus were analyzed through an optimized microarray post-processing (Q-GDEMAR method) together with a proper experimental design (full factorial analysis)...
2016: Frontiers in Aging Neuroscience
D S Fleming, J E Koltes, E R Fritz-Waters, M F Rothschild, C J Schmidt, C M Ashwell, M E Persia, J M Reecy, S J Lamont
BACKGROUND: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation...
October 19, 2016: BMC Genomics
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