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https://www.readbyqxmd.com/read/28918092/growth-rate-dependent-regulation-of-trna-level-and-charging-in-bacillus-licheniformis
#1
Iolanda Ferro, Klaus Liebeton, Zoya Ignatova
Cellular growth crucially depends on protein synthesis and the abundance of translational components. Among them, aminoacyl-tRNAs play a central role in biosynthesis and shape the kinetics of mRNA translation, thus influencing protein production. Here, we used microarray-based approaches to determine the charging levels and tRNA abundance of Bacillus licheniformis. We observed an interesting cross-talk among tRNA expression, charging pattern and growth rate. For a large subset of tRNAs, we found a co-regulated and augmented expression at high growth rate...
September 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28916633/systems-genetics-identifies-a-co-regulated-module-of-liver-micrornas-associated-with-plasma-ldl-cholesterol-in-murine-diet-induced-dyslipidemia
#2
Alisha R Coffey, Tangi L Smallwood, Jody Albright, Kunjie Hua, Matt Kanke, Daniel Pomp, Brian J Bennett, Praveen Sethupathy
Chronically altered levels of circulating lipids, termed dyslipidemia, is a significant risk factor for a number of metabolic and cardiovascular morbidities. MicroRNAs (miRNAs) have emerged as important regulators of lipid balance, have been implicated in dyslipidemia, and have been proposed as candidate therapeutic targets in lipid-related disorders including atherosclerosis. A major limitation of most murine studies of miRNAs in lipid metabolic disorders is that they have been performed in just one (or very few) inbred strains, such as C57BL/6...
September 15, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28911113/mcbiclust-a-novel-algorithm-to-discover-large-scale-functionally-related-gene-sets-from-massive-transcriptomics-data-collections
#3
Robert B Bentham, Kevin Bryson, Gyorgy Szabadkai
The potential to understand fundamental biological processes from gene expression data has grown in parallel with the recent explosion of the size of data collections. However, to exploit this potential, novel analytical methods are required, capable of discovering large co-regulated gene networks. We found current methods limited in the size of correlated gene sets they could discover within biologically heterogeneous data collections, hampering the identification of multi-gene controlled fundamental cellular processes such as energy metabolism, organelle biogenesis and stress responses...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911111/combinatorial-ensemble-mirna-target-prediction-of-co-regulation-networks-with-non-prediction-data
#4
Jason A Davis, Sita J Saunders, Martin Mann, Rolf Backofen
MicroRNAs (miRNAs) are key regulators of cell-fate decisions in development and disease with a vast array of target interactions that can be investigated using computational approaches. For this study, we developed metaMIR, a combinatorial approach to identify miRNAs that co-regulate identified subsets of genes from a user-supplied list. We based metaMIR predictions on an improved dataset of human miRNA-target interactions, compiled using a machine-learning-based meta-analysis of established algorithms. Simultaneously, the inverse dataset of negative interactions not likely to occur was extracted to increase classifier performance, as measured using an expansive set of experimentally validated interactions from a variety of sources...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28905321/network-analysis-of-mpo-and-other-relevant-proteins-involved-in-diabetic-foot-ulcer-and-other-diabetic-complications
#5
Mathew Saumya, E K Subin, T V Suchithra
Network analysis and visualization of genes are very important to understand large complex biological data in a better manner. Large data on genes and proteins in the biological systems are analyzed on the occurrence, interactions, co-expression, and co-regulations of various genes. Here we have visualized the genes involved in type 1 diabetes (T1D), type 2 diabetes (T2D), and foot ulcer condition to put light on the corrective measures to the problem of impaired healing. The goal of this study was to identify the important genes involved in the pathogenesis of diabetes complications and foot ulcer and its association with the free radical-producing enzyme, the myeloperoxidase (MPO)...
September 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28902867/analysis-of-the-relationship-between-coexpression-domains-and-chromatin-3d-organization
#6
María E Soler-Oliva, Jose A Guerrero-Martínez, Valentina Bachetti, Jose C Reyes
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs...
September 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28900192/comparative-transcriptome-analysis-of-axillary-buds-in-response-to-the-shoot-branching-regulators-gibberellin-a3-and-6-benzyladenine-in-jatropha-curcas
#7
Jun Ni, Mei-Li Zhao, Mao-Sheng Chen, Bang-Zhen Pan, Yan-Bin Tao, Zeng-Fu Xu
Cytokinin (CK) is the primary hormone that positively regulates axillary bud outgrowth. However, in many woody plants, such as Jatropha curcas, gibberellin (GA) also promotes shoot branching. The molecular mechanisms underlying GA and CK interaction in the regulation of bud outgrowth in Jatropha remain unclear. To determine how young axillary buds respond to GA3 and 6-benzyladenine (BA), we performed a comparative transcriptome analysis of the young axillary buds of Jatropha seedlings treated with GA3 or BA...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28898255/molecular-and-biochemical-characterization-of-a-potato-collection-with-contrasting-tuber-carotenoid-content
#8
Maria Sulli, Giuseppe Mandolino, Monica Sturaro, Chiara Onofri, Gianfranco Diretto, Bruno Parisi, Giovanni Giuliano
After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum) and diploid (S. phureja and S. chacoense) genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2) gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP) recessive allele...
2017: PloS One
https://www.readbyqxmd.com/read/28892078/detection-of-dysregulated-protein-association-networks-by-high-throughput-proteomics-predicts-cancer-vulnerabilities
#9
John D Lapek, Patricia Greninger, Robert Morris, Arnaud Amzallag, Iulian Pruteanu-Malinici, Cyril H Benes, Wilhelm Haas
The formation of protein complexes and the co-regulation of the cellular concentrations of proteins are essential mechanisms for cellular signaling and for maintaining homeostasis. Here we use isobaric-labeling multiplexed proteomics to analyze protein co-regulation and show that this allows the identification of protein-protein associations with high accuracy. We apply this 'interactome mapping by high-throughput quantitative proteome analysis' (IMAHP) method to a panel of 41 breast cancer cell lines and show that deviations of the observed protein co-regulations in specific cell lines from the consensus network affects cellular fitness...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28886026/population-fba-predicts-metabolic-phenotypes-in-yeast
#10
Piyush Labhsetwar, Marcelo C R Melo, John A Cole, Zaida Luthey-Schulten
Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media...
September 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28884952/soluble-dietary-fiber-reduces-trimethylamine-metabolism-via-gut-microbiota-and-co-regulates-host-ampk-pathways
#11
Qian Li, Tao Wu, Rui Liu, Min Zhang, Ruijun Wang
SCOPE: Evidence from animal experiments and clinical medicine suggest that high dietary fiber intake, followed by gut microbiota-mediated fermentation, decreases trimethylamine (TMA) metabolism, the mechanism of which, however, remains unclear. The objective of this analysis was to evaluate, using mice fed with red meat, the effects of soluble dietary fiber (SDF) intervention on TMA metabolism. METHODS AND RESULTS: Low- or high-dose soluble dietary fiber (SDF) from natural wheat bran (LN and HN, low- and high-dose natural SDF), fermented wheat bran (LF and HF, low- and high-dose fermented SDF), and steam-exploded wheat bran (LE and HE, low- and high-dose exploded SDF groups) were used to examine whether SDF interventions in mice fed with red meat can alter TMA and trimethylamine N-oxide (TMAO) metabolism by gut microbial communities in a diet-specific manner...
September 8, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28883458/genetic-correlations-reveal-the-shared-genetic-architecture-of-transcription-in-human-peripheral-blood
#12
Samuel W Lukowski, Luke R Lloyd-Jones, Alexander Holloway, Holger Kirsten, Gibran Hemani, Jian Yang, Kerrin Small, Jing Zhao, Andres Metspalu, Emmanouil T Dermitzakis, Greg Gibson, Timothy D Spector, Joachim Thiery, Markus Scholz, Grant W Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
Transcript co-expression is regulated by a combination of shared genetic and environmental factors. Here, we estimate the proportion of co-expression that is due to shared genetic variance. To do so, we estimated the genetic correlations between each pairwise combination of 2469 transcripts that are highly heritable and expressed in whole blood in 1748 unrelated individuals of European ancestry. We identify 556 pairs with a significant genetic correlation of which 77% are located on different chromosomes, and report 934 expression quantitative trait loci, identified in an independent cohort, with significant effects on both transcripts in a genetically correlated pair...
September 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28882591/the-poz-zf-transcription-factor-znf131-is-implicated-as-a-regulator-of-kaiso-mediated-biological-processes
#13
Shaiya C Robinson, Nickett S Donaldson-Kabwe, Anna Dvorkin-Gheva, Joseph Longo, Lloyd He, Juliet M Daniel
Znf131 belongs to the family of POZ-ZF transcription factors, but, in contrast to most other characterized POZ-ZF proteins that function as transcriptional repressors, Znf131 acts as a transcriptional activator. Znf131 heterodimerizes with the POZ-ZF protein Kaiso, which itself represses a subset of canonical Wnt target genes, including the cell cycle regulator Cyclin D1. Herein, we report a possible role for Znf131 in Kaiso-mediated processes. Notably, we found that Znf131 associates with several Kaiso target gene promoters, including that of CCND1...
September 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28873253/tomexpress-a-unified-tomato-rna-seq-platform-for-visualization-of-expression-data-clustering-and-correlation-networks
#14
Mohamed Zouine, Elie Maza, Anis Djari, Mattieu Lauvernier, Pierre Frasse, Abdelaziz Smouni, Julien Pirrello, Mondher Bouzayen
The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA-Seq data visualization and data mining. To avoid major biases that can result from the use of different mapping and statistical processing methods, RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence and post-processed using the same pipeline with accurate parameters. Following the calculation of the number of counts per gene in each RNA-Seq sample, a communal global normalization method was applied to all expression values...
September 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28871548/studying-individual-plant-aox-gene-functionality-in-early-growth-regulation-a-new-approach
#15
Birgit Arnholdt-Schmitt, Vinod Kumar Patil
AOX1 and AOX2 genes are thought to play different physiological roles. Whereas AOX1 is typically expected to associate to stress and growth responses, AOX2 was more often found to be linked to development and housekeeping functions. However, this view is questioned by several adverse observations. For example, co-regulated expression for DcAOX1 and DcAOX2a genes was recently reported during growth induction in carrot (Daucus carota L.). Early expression peaks for both genes during the lag phase of growth coincided with a critical time point for biomass prediction, a result achieved by applying calorespirometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28871546/a-driving-bioinformatics-approach-to-explore-co-regulation-of-aox-gene-family-members-during-growth-and-development
#16
José Hélio Costa, Birgit Arnholdt-Schmitt
The alternative oxidase (AOX) gene family is a hot candidate for functional marker development that could help plant breeding on yield stability through more robust plants based on multi-stress tolerance. However, there is missing knowledge on the interplay between gene family members that might interfere with the efficiency of marker development. It is common view that AOX1 and AOX2 have different physiological roles. Nevertheless, both family member groups act in terms of molecular-biochemical function as "typical" alternative oxidases and co-regulation of AOX1 and AOX2 had been reported...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28869592/reconstruction-of-enhancer-target-networks-in-935-samples-of-human-primary-cells-tissues-and-cell-lines
#17
Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T S Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S L Cheng, Kevin Y Yip
We propose a new method for determining the target genes of transcriptional enhancers in specific cells and tissues. It combines global trends across many samples and sample-specific information, and considers the joint effect of multiple enhancers. Our method outperforms existing methods when predicting the target genes of enhancers in unseen samples, as evaluated by independent experimental data. Requiring few types of input data, we are able to apply our method to reconstruct the enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, which constitute by far the largest set of enhancer-target networks...
September 4, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28867346/germline-stem-cell-activity-is-sustained-by-sall4-dependent-silencing-of%C3%A2-distinct-tumor-suppressor-genes
#18
Ai-Leen Chan, Hue M La, Julien M D Legrand, Juho-Antti Mäkelä, Michael Eichenlaub, Mia De Seram, Mirana Ramialison, Robin M Hobbs
Sustained spermatogenesis in adult males and fertility recovery following germ cell depletion are dependent on undifferentiated spermatogonia. We previously demonstrated a key role for the transcription factor SALL4 in spermatogonial differentiation. However, whether SALL4 has broader roles within spermatogonia remains unclear despite its ability to co-regulate genes with PLZF, a transcription factor required for undifferentiated cell maintenance. Through development of inducible knockout models, we show that short-term integrity of differentiating but not undifferentiated populations requires SALL4...
September 12, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28865032/regulation-of-skeletal-myoblast-differentiation-by-drebrin
#19
Robert S Krauss
Myoblast differentiation is a complex process. As myoblasts differentiate into myofibers, they acquire a cell type-specific transcriptional program, irreversibly exit the cell cycle, and dramatically change their morphology. The morphological changes include cell elongation, alignment, and fusion into syncytial myofibers. Several lines of evidence suggest that these events may be co-regulated. However, the mechanisms that coordinate major alterations in a cell's transcriptome and its shape are not well understood...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28861105/interplay-between-light-and-plant-hormones-in-the-control-of-arabidopsis-seedling-chlorophyll-biosynthesis
#20
REVIEW
Xiaoqin Liu, Yue Li, Shangwei Zhong
Chlorophyll biosynthesis is one of the most important cellular processes and is essential for plant photosynthesis. After germination under the soil, dark-grown seedlings are etiolated and accumulate the chlorophyll precursor protochlorophyllide (Pchlide) in cotyledons. Upon exposure to light, Pchlide is rapidly converted to chlorophyll to initiate photoautotrophic growth. In this light-regulated de-etiolation process, multiple endogenous phytohormones are also involved. Although the co-regulation of seedling greening by light and hormones has long been observed, recent studies greatly advanced our understanding of their interplay by identifying the key components connecting these pathways...
2017: Frontiers in Plant Science
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