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https://www.readbyqxmd.com/read/29165646/development-and-application-of-a-recombination-based-library-versus-library-high-throughput-yeast-two-hybrid-rll-y2h-screening-system
#1
Fang Yang, Yingying Lei, Meiling Zhou, Qili Yao, Yichao Han, Xiang Wu, Wanshun Zhong, Chenghang Zhu, Weize Xu, Ran Tao, Xi Chen, Da Lin, Khaista Rahman, Rohit Tyagi, Zeshan Habib, Shaobo Xiao, Dang Wang, Yang Yu, Huanchun Chen, Zhenfang Fu, Gang Cao
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165610/gramene-2018-unifying-comparative-genomics-and-pathway-resources-for-plant-research
#2
Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D Stein, Robert Petryszak, Irene Papatheodorou, Paul J Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165593/funcoup-4-new-species-data-and-visualization
#3
Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L L Sonnhammer
This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165564/social-networks-as-a-tool-for-science-communication-and-public-engagement-focus-on-twitter
#4
Ignacio López-Goñi, Manuel Sánchez-Angulo
Social networks have been used to teach and engage people about the importance of science. The integration of social networks in the daily routines of Faculty and Scientists is strongly recommended to increase their personal brand, improve their skills, enhance their visibility, share and communicate science to society, promote scientific culture, and even as a tool for teaching and learning. Here we review the use of Twitter in Science and comment our previous experience on using this social network as a platform for a Massive Online Open Course (MOOC) in Spain and Latin America...
November 20, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29165461/synthesis-structures-and-magnetic-properties-of-two-chiral-mixed-valence-iron-ii-iii-coordination-networks
#5
Yun-Shan Xue, Xu Tan, Mengjie Zhou, Hua Mei, Yan Xu
Two rare chiral mixed-valence iron(ii,iii) coordination networks d-and l-{[Fe(II)FeO(BTC)3(DEF)3]·0.5H2O}n (d-1 and l-1) (H3BTC = 1,3,5-benzenetricarboxylic acid; DEF = N,N-diethylformamide) have been synthesized without any chiral auxiliary under the solvothermal conditions and structurally characterized by single crystal X-ray crystallography. Structural analysis indicates that these two polymers d-1 and l-1 are enantiomers. The only difference between d-1 and l-1 is that the framework of compound l-1 consists of left-handed double helical chains, while d-1 consists of right-handed double helical chains...
November 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29165444/low-temperature-crystallization-of-solution-derived-metal-oxide-thin-films-assisted-by-chemical-processes
#6
Iñigo Bretos, Ricardo Jiménez, Jesús Ricote, M Lourdes Calzada
Over the last few years the efforts devoted to the research on low-temperature processing of metal oxide thin films have increased notably. This has enabled the direct integration of metal oxide layers (amorphous semiconductors) on low-melting-point polymeric substrates for flexible electronic systems, which adds to the economic and environmental benefits of the use of these processes with reduced energy consumption. More challenging is the preparation of crystalline complex oxide films at temperatures compatible with their direct integration in flexible devices...
November 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/29165426/the-mitochondrial-upr-mechanisms-physiological-functions-and-implications-in-ageing
#7
REVIEW
Tomer Shpilka, Cole M Haynes
Mitochondrial function declines during ageing owing to the accumulation of deleterious mitochondrial genomes and damage resulting from the localized generation of reactive oxygen species, both of which are often exacerbated in diseases such as Parkinson disease. Cells have several mechanisms to assess mitochondrial function and activate a transcriptional response known as the mitochondrial unfolded protein response (UPR(mt)) when mitochondrial integrity and function are impaired. The UPR(mt) promotes cell survival and the recovery of the mitochondrial network to ensure optimal cellular function...
November 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29165314/towards-natural-mimetics-of-metformin-and-rapamycin
#8
Alexander Aliper, Leslie Jellen, Franco Cortese, Artem Artemov, Darla Karpinsky-Semper, Alexey Moskalev, Andrew G Swick, Alex Zhavoronkov
Aging is now at the forefront of major challenges faced globally, creating an immediate need for safe, widescale interventions to reduce the burden of chronic disease and extend human healthspan. Metformin and rapamycin are two FDA-approved mTOR inhibitors proposed for this purpose, exhibiting significant anti-cancer and anti-aging properties beyond their current clinical applications. However, each faces issues with approval for off-label, prophylactic use due to adverse effects. Here, we initiate an effort to identify nutraceuticals-safer, naturally-occurring compounds-that mimic the anti-aging effects of metformin and rapamycin without adverse effects...
November 15, 2017: Aging
https://www.readbyqxmd.com/read/29164943/a-global-perspective-on-religious-participation-and-suicide
#9
Ning Hsieh
Although sociological research in the Durkheimian tradition has generally accepted that religious involvement protects against suicide, few studies have examined this theoretical proposition outside Western industrialized settings. Using multilevel models to analyze data from the World Health Organization Mortality Database and the World Values Survey (1981-2007) across 42 countries in seven geographical-cultural regions, this study explores whether religious participation is more protective against suicide in some regions than others and, if so, why...
September 2017: Journal of Health and Social Behavior
https://www.readbyqxmd.com/read/29163774/integrative-analysis-of-novel-hypomethylation-and-gene-expression-signatures-in-glioblastomas
#10
Anan Yin, Amandine Etcheverry, Yalong He, Marc Aubry, Jill Barnholtz-Sloan, Luhua Zhang, Xinggang Mao, Weijun Chen, Bolin Liu, Wei Zhang, Jean Mosser, Xiang Zhang
Molecular and clinical heterogeneity critically hinders better treatment outcome for glioblastomas (GBMs); integrative analysis of genomic and epigenomic data may provide useful information for improving personalized medicine. By applying training-validation approach, we identified a novel hypomethylation signature comprising of three CpGs at non-CpG island (CGI) open sea regions for GBMs. The hypomethylation signature consistently predicted poor prognosis of GBMs in a series of discovery and validation datasets...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29163694/exploration-of-the-mechanism-of-colorectal-cancer-metastasis-using-microarray-analysis
#11
Shuo Chen, Yan Wang, Lin Zhang, Yinan Su, Mingqing Zhang, Juan Wang, Xipeng Zhang
The aim of the present study was to investigate the mechanism of metastasis in colorectal cancer (CRC) using microRNA (miRNA) and mRNA expression profiles. The mRNA and miRNA expression profiles of the GSE2509 and GSE56350 datasets were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were identified using the limma software package. The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29163453/an-integrated-insight-into-the-relationship-between-soil-microbial-community-and-tobacco-bacterial-wilt-disease
#12
Hongwu Yang, Juan Li, Yunhua Xiao, Yabing Gu, Hongwei Liu, Yili Liang, Xueduan Liu, Jin Hu, Delong Meng, Huaqun Yin
The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163229/cx43-isoform-gja1-20k-promotes-microtubule-dependent-mitochondrial-transport
#13
Ying Fu, Shan-Shan Zhang, Shaohua Xiao, Wassim A Basheer, Rachel Baum, Irina Epifantseva, TingTing Hong, Robin M Shaw
Connexin 43 (Cx43, encoded by GJA1) is a cell-cell communication gap junction protein expressed in all organ systems. It was recently found that GJA1 mRNA undergoes alternative translation to generate N-terminal truncated isoforms, of which GJA1-20k is the most abundant. Here we report a surprising finding that, unlike full length GJA1-43k, GJA1-20k has a strong tropism for mitochondria. Exploring function, we found that GJA1-20k appears to be an organelle chaperone and that overexpression of GJA1-20k is sufficient to rescue mitochondrial localization to the cell periphery upon exposure to hydrogen peroxide, which effectively limits the network fragmentation that occurs with oxidative stress...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29163099/a-computational-analysis-of-neural-mechanisms-underlying-the-maturation-of-multisensory-speech-integration-in-neurotypical-children-and-those-on-the-autism-spectrum
#14
Cristiano Cuppini, Mauro Ursino, Elisa Magosso, Lars A Ross, John J Foxe, Sophie Molholm
Failure to appropriately develop multisensory integration (MSI) of audiovisual speech may affect a child's ability to attain optimal communication. Studies have shown protracted development of MSI into late-childhood and identified deficits in MSI in children with an autism spectrum disorder (ASD). Currently, the neural basis of acquisition of this ability is not well understood. Here, we developed a computational model informed by neurophysiology to analyze possible mechanisms underlying MSI maturation, and its delayed development in ASD...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29162874/information-processing-in-the-nf-%C3%AE%C2%BAb-pathway
#15
Karolina Tudelska, Joanna Markiewicz, Marek Kochańczyk, Maciej Czerkies, Wiktor Prus, Zbigniew Korwek, Ali Abdi, Sławomir Błoński, Bogdan Kaźmierczak, Tomasz Lipniacki
The NF-κB pathway is known to transmit merely 1 bit of information about stimulus level. We combined experimentation with mathematical modeling to elucidate how information about TNF concentration is turned into a binary decision. Using Kolmogorov-Smirnov distance, we quantified the cell's ability to discern 8 TNF concentrations at each step of the NF-κB pathway, to find that input discernibility decreases as signal propagates along the pathway. Discernibility of low TNF concentrations is restricted by noise at the TNF receptor level, whereas discernibility of high TNF concentrations it is restricted by saturation/depletion of downstream signaling components...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29162819/exocytosis-coordinated-mechanisms-for-tip-growth-underlie-pollen-tube-growth-guidance
#16
Nan Luo, An Yan, Gang Liu, Jingzhe Guo, Duoyan Rong, Masahiro M Kanaoka, Zhen Xiao, Guanshui Xu, Tetsuya Higashiyama, Xinping Cui, Zhenbiao Yang
Many tip-growing cells are capable of responding to guidance cues, during which cells precisely steer their growth toward the source of guidance signals. Though several players in signal perception have been identified, little is known about the downstream signaling that controls growth direction during guidance. Here, using combined modeling and experimental studies, we demonstrate that the growth guidance of Arabidopsis pollen tubes is regulated by the signaling network that controls tip growth. Tip-localized exocytosis plays a key role in this network by integrating guidance signals with the ROP1 Rho GTPase signaling and coordinating intracellular signaling with cell wall mechanics...
November 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29162721/loss-of-%C3%AE-b-crystallin-function-in-zebrafish-reveals-critical-roles-in-the-development-of-the-lens-and-stress-resistance-of-the-heart
#17
Sanjay Mishra, Shu-Yu Wu, Alexandra W Fuller, Zhen Wang, Kristie L Rose, Kevin L Schey, Hassane S Mchaourab
Genetic mutations in the human small heat shock protein αB-crystallin have been implicated in autosomal cataracts and skeletal myopathies, including heart muscle diseases (cardiomyopathy). While these mutations lead to modulation of their chaperone activity in vitro, the in vivo functions of αB-crystallin in the maintenance of both lens transparency and muscle integrity remain unclear. This lack of information has hindered a mechanistic understanding of these diseases. To better define the functional roles of αB-crystallin, we generated loss-of-function zebrafish mutant lines by utilizing CRISPR/Cas9 system to specifically disrupt the two αB-crystallin genes, αBa and αBb We observed lens abnormalities in the mutant lines of both genes and the penetrance of the lens phenotype was higher in αBa than αBb mutants...
November 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29162416/crosstalk-complexities-between-auxin-cytokinin-and-ethylene-in-arabidopsis-root-development-from-experiments-to-systems-modelling-and-back-again
#18
REVIEW
Junli Liu, Simon Moore, Chunli Chen, Keith Lindsey
Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin and ethylene crosstalk...
November 18, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29162140/using-a-multi-state-learning-community-as-an-implementation-strategy-for-immediate-postpartum-long-acting-reversible-contraception
#19
Carla L DeSisto, Cameron Estrich, Charlan D Kroelinger, David A Goodman, Ellen Pliska, Christine N Mackie, Lisa F Waddell, Kristin M Rankin
BACKGROUND: Implementation strategies are imperative for the successful adoption and sustainability of complex evidence-based public health practices. Creating a learning collaborative is one strategy that was part of a recently published compilation of implementation strategy terms and definitions. In partnership with the Centers for Disease Control and Prevention and other partner agencies, the Association of State and Territorial Health Officials recently convened a multi-state Learning Community to support cross-state collaboration and provide technical assistance for improving state capacity to increase access to long-acting reversible contraception (LARC) in the immediate postpartum period, an evidence-based practice with the potential for reducing unintended pregnancy and improving maternal and child health outcomes...
November 21, 2017: Implementation Science: IS
https://www.readbyqxmd.com/read/29161597/sustainability-of-mega-water-diversion-projects-experience-and-lessons-from-china
#20
Min Yu, Chaoran Wang, Yi Liu, Gustaf Olsson, Chunyan Wang
Water availability and water demand are not evenly distributed in time and space. Many mega water diversion projects have been launched to alleviate water shortages in China. This paper analyzes the temporal and spatial features of 59 mega water diversion projects in China using statistical analysis. The relationship between nine major basins is measured using a network analysis method, and the associated economic, environmental and social impacts are explored using an impact analysis method. The study finds the development of water diversion has experienced four stages in China, from a starting period through to a period of high-speed development...
November 18, 2017: Science of the Total Environment
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