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https://www.readbyqxmd.com/read/27933070/transcriptional-responses-in-root-and-leaf-of-prunus-persica-under-drought-stress-using-rna-sequencing
#1
Najla Ksouri, Sergio Jiménez, Christina E Wells, Bruno Contreras-Moreira, Yolanda Gogorcena
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27931240/skeletal-muscle-characteristics-are-preserved-in-htert-cdk4-human-myogenic-cell-lines
#2
Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voit, Vincent Mouly, William Duddy
BACKGROUND: hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether genetic modification related to the cell cycle results in secondary effects that could undermine the validity of these cell models...
December 8, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27931210/ontological-security-and-connectivity-provided-by-pets-a-study-in-the-self-management-of-the-everyday-lives-of-people-diagnosed-with-a-long-term-mental-health-condition
#3
Helen Brooks, Kelly Rushton, Sandra Walker, Karina Lovell, Anne Rogers
BACKGROUND: Despite evidence that connecting people to relevant wellbeing-related resources brings therapeutic benefit, there is limited understanding, in the context of mental health recovery, of the potential value and contribution of pet ownership to personal support networks for self-management. This study aimed to explore the role of pets in the support and management activities in the personal networks of people with long-term mental health problems. METHODS: Semi-structured interviews centred on 'ego' network mapping were conducted in two locations (in the North West and in the South of England) with 54 participants with a diagnosis of a long-term mental health problem...
December 9, 2016: BMC Psychiatry
https://www.readbyqxmd.com/read/27930808/searching-the-mouse-genome-informatics-mgi-resources-for-information-on-mouse-biology-from-genotype-to-phenotype
#4
David R Shaw
The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mammalian Phenotype Ontology, and the Gene Ontologies...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27930677/de-novo-sequencing-and-comparative-analysis-of-schima-superba-seedlings-to-explore-the-response-to-drought-stress
#5
Bao-Cai Han, Wei Wei, Xiang-Cheng Mi, Ke-Ping Ma
Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress...
2016: PloS One
https://www.readbyqxmd.com/read/27927957/the-proteome-of-bloc-1-genetic-defects-identifies-the-arp2-3-actin-polymerization-complex-to-function-downstream-of-the-schizophrenia-susceptibility-factor-dysbindin-at-the-synapse
#6
Avanti Gokhale, Cortnie Hartwig, Amanda H Freeman, Ravi Das, Stephanie A Zlatic, Rachel Vistein, Amelia Burch, Guillemette Carrot, Arielle F Lewis, Sheldon Nelms, Dion K Dickman, Manojkumar A Puthenveedu, Daniel N Cox, Victor Faundez
: Proteome modifications downstream of monogenic or polygenic disorders have the potential to uncover novel molecular mechanisms participating in pathogenesis and/or extragenic modification of phenotypic expression. We tested this idea by determining the proteome sensitive to genetic defects in a locus encoding dysbindin, a protein required for synapse biology and implicated in schizophrenia risk. We applied quantitative mass spectrometry to identify proteins expressed in neuronal cells the abundance of which was altered after downregulation of the schizophrenia susceptibility factor dysbindin (Bloc1s8) or two other dysbindin-interacting polypeptides, which assemble into the octameric biogenesis of lysosome-related organelles complex 1 (BLOC-1)...
December 7, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27924297/datasets-for-the-validation-of-the-in-vivo-sirna-silencing-of-cd40-and-for-the-detection-of-new-markers-of-atherosclerosis-progression-in-apoe-deficient-mice
#7
Miguel Hueso, Laura De Ramon, Estanislao Navarro, Elia Ripoll, Josep M Cruzado, Josep M Grinyo, Joan Torras
Data presented in this Data in Brief article correspond to the article "in vivo" silencing of CD40 reduces progression of experimental atherogenesis through a NFκB/miR-125b axis and reveals new potential mediators in the pathogenesis of atherosclerosis" (M. Hueso, L. De Ramon, E. Navarro, E. Ripoll, J.M. Cruzado, J.M. Grinyo, J. Torras, 2016) [1]. Here, we describe the validation of the silencing of CD40 expression with a specific siRNA in ApoE(-/-) mouse aortas, and its systemic effects on splenic lymphocytic subpopulations as well as on the infiltration of aortic intima by F4/80(+), galectin-3(+) macrophages or by NF-κB(+) cells...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27924021/aagatlas-1-0-a-human-autoantigen-database
#8
Dan Wang, Liuhui Yang, Ping Zhang, Joshua LaBaer, Henning Hermjakob, Dong Li, Xiaobo Yu
Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924018/disgenet-a-comprehensive-platform-integrating-information-on-human-disease-associated-genes-and-variants
#9
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924016/bio-tds-bioscience-query-tool-discovery-system
#10
Etienne Z Gnimpieba, Menno S VanDiermen, Shayla M Gustafson, Bill Conn, Carol M Lushbough
Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923621/transcriptomic-analysis-of-gene-expression-profiles-of-stomach-carcinoma-reveal-abnormal-expression-of-mitotic-components
#11
Hongfei Tong, Jisheng Wang, Hui Chen, Zhaohong Wang, Henwei Fan, Zhonglin Ni
AIMS: In order to explore the etiology of gastric cancer on global gene expression level, we developed advanced bioinformatic analysis to investigate the variations of global gene expression and the interactions among them. MAIN METHODS: We downloaded the dataset GSE63288 from Gene Expression Omnibus (GEO) database which included 22 human gastric cancer and 22 healthy control samples. We identified the differential expression genes, and explored the Gene ontology (GO) and pathways of the differentially expressed genes...
December 3, 2016: Life Sciences
https://www.readbyqxmd.com/read/27922691/microarray-expression-profiles-of-genes-in-lung-tissues-of-rats-subjected-to-focal-cerebral-ischemia-induced-lung-injury-following-bone-marrow-derived-mesenchymal-stem-cell-transplantation
#12
Yue Hu, Liu-Lin Xiong, Piao Zhang, Ting-Hua Wang
Ischemia-induced stroke is the most common disease of the nervous system and is associated with a high mortality rate worldwide. Cerebral ischemia may lead to remote organ dysfunction, particular in the lungs, resulting in lung injury. Nowadays, bone marrow-derived mesenchymal stem cells (BMSCs) are widely studied in clinical trials as they may provide an effective solution to the treatment of neurological and cardiac diseases; however, the underlying molecular mechanisms remain unknown. In this study, a model of permanent focal cerebral ischemia-induced lung injury was successfully established and confirmed by neurological evaluation and lung injury scores...
December 6, 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#13
Jingyu Li, Zhengling Gao, Xingyu Wang, Hongbo Liu, Yan Zhang, Zhonghua Liu
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921231/the-cell-and-protoplasm-as-container-object-and-substance-1835-1861
#14
Daniel Liu
This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term "protoplasm" transformed from a botanical term of art in the 1840s to the so-called "living substance" and "the physical basis of life" two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form...
December 5, 2016: Journal of the History of Biology
https://www.readbyqxmd.com/read/27921076/yeast-2-hybrid-data-file-showing-progranulin-interactions-in-human-fetal-brain-and-bone-marrow-libraries
#15
Irmgard Tegeder
Progranulin deficiency in humans is associated with neurodegeneration. Its mechanisms are not yet fully understood. We performed a Yeast-2-Hybrid screen using human full-length progranulin as bait to assess the interactions of progranulin. Progranulin was screened against human fetal brain and human bone marrow libraries using the standard Matchmaker technology (Clontech). This article contains the full Y2H data table, including blast results and sequences, a sorted table according to selection criteria for likely positive, putatively positive, likely false and false preys, and tables showing the gene ontology terms associated with the likely and putative preys of the brain and bone marrow libraries...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27920753/neuroproteomics-and-systems-biology-approach-to-identify-temporal-biomarker-changes-post-experimental-traumatic-brain-injury-in-rats
#16
Firas H Kobeissy, Joy D Guingab-Cagmat, Zhiqun Zhang, Ahmed Moghieb, Olena Y Glushakova, Stefania Mondello, Angela M Boutté, John Anagli, Richard Rubenstein, Hisham Bahmad, Amy K Wagner, Ronald L Hayes, Kevin K W Wang
Traumatic brain injury (TBI) represents a critical health problem of which diagnosis, management, and treatment remain challenging. TBI is a contributing factor in approximately one-third of all injury-related deaths in the United States. The Centers for Disease Control and Prevention estimate that 1.7 million people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#17
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27918246/rice-leaf-transcriptional-profiling-suggests-a-functional-interplay-between-xanthomonas-oryzae-pv-oryzae-lipopolysaccharide-and-extracellular-polysaccharide-in-modulation-of-defense-responses-during-infection
#18
Anil Madhusoodana Girija, Bipin Kumar Kumar, Madhavi B Mylavarapu, Palaparthi Ramesh, Sridivya Vungarala, Hitendra Kumar Patel, Ramesh Sonti
Treatment of rice leaves with isolated Xanthomonas oryzae pv. oryzae lipopolysaccharide (LPS) induces the production of callose deposits, reactive oxygen species and enhanced resistance against subsequent bacterial infection. Expression profiling of X. oryzae pv. oryzae LPS treated rice (Oryza sativa ssp. indica) leaves showed that genes involved in the biosynthetic pathways for lignins, phenylpropanoids, chorismate, phenylalanine, salicylic acid and ethylene as well as a number of pathogenesis related proteins are up regulated...
December 5, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27917494/disturbing-sleep-and-sleepfulness-during-recovery-from-substance-dependence-in-residential-rehabilitation-settings
#19
Sarah Nettleton, Robert Meadows, Joanne Neale
There is evidence that poor sleep mitigates recovery from substance dependence and increases risk of relapse. However, to date research literature is located within biomedical, clinical and psychological paradigms. To complement the extant work, this article offers a sociological exploration of sleep in the context of recovery from dependence on alcohol and/or other drugs. Drawing on qualitative data generated through interviews with 28 men and women living in residential rehabilitation settings in England, we provide a detailed exploration of sleep practices focusing on how these are enacted throughout the night...
December 5, 2016: Sociology of Health & Illness
https://www.readbyqxmd.com/read/27917343/a-new-bioinformatic-insight-into-the-associated-proteins-in-psychiatric-disorders
#20
Wenlong Zhao, Wenjing Yang, Shuanglin Zheng, Qiong Hu, Ping Qiu, Xinghua Huang, Xiaoqian Hong, Fenghua Lan
BACKGROUND: Psychiatric diseases severely affect the quality of patients' lives and bring huge economic pressure to their families. Also, the great phenotypic variability among these patients makes it difficult to investigate the pathogenesis. Nowadays, bioinformatics is hopeful to be used as an effective tool for the diagnosis of psychiatric disorders, which can identify sensitive biomarkers and explore associated signaling pathways. METHODS: In this study, we performed an integrated bioinformatic analysis on 1945 mental-associated proteins including 91 secreted proteins and 593 membrane proteins, which were screened from the Universal Protein Resource (Uniport) database...
2016: SpringerPlus
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