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https://www.readbyqxmd.com/read/29045845/revealing-the-determinants-of-widespread-alternative-splicing-perturbation-in-cancer
#1
Yongsheng Li, Nidhi Sahni, Rita Pancsa, Daniel J McGrail, Juan Xu, Xu Hua, Jasmin Coulombe-Huntington, Michael Ryan, Boranai Tychhon, Dhanistha Sudhakar, Limei Hu, Michael Tyers, Xiaoqian Jiang, Shiaw-Yih Lin, M Madan Babu, Song Yi
It is increasingly appreciated that alternative splicing plays a key role in generating functional specificity and diversity in cancer. However, the mechanisms by which cancer mutations perturb splicing remain unknown. Here, we developed a network-based strategy, DrAS-Net, to investigate more than 2.5 million variants across cancer types and link somatic mutations with cancer-specific splicing events. We identified more than 40,000 driver variant candidates and their 80,000 putative splicing targets deregulated in 33 cancer types and inferred their functional impact...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045754/genomic-studies-of-local-adaptation-in-natural-plant-populations
#2
Victoria L Sork
Local adaptation arises as a result of selection by the local environment favoring phenotypes that enhance fitness. Geographic patterns of phenotypic variation are in part due to this selective process. Classically, the genetic basis of those phenotypes has been studied in plant populations using a quantitative genetic approach in which plants from different source populations are grown in common environments, in reciprocal transplant experiments, or in studies across a wide geographic and environmentally heterogeneous area...
October 14, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29045649/understanding-evolutionary-impacts-of-seasonality-an-introduction-to-the-symposium
#3
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
October 16, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29045542/bacterial-artificial-chromosomes-as-recombinant-reporter-constructs-to-investigate-gene-expression-and-regulation-in-echinoderms
#4
Katherine M Buckley, Ping Dong, R Andrew Cameron, Jonathan P Rast
Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions...
October 17, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29045534/evaluation-of-variable-selection-methods-for-random-forests-and-omics-data-sets
#5
Frauke Degenhardt, Stephan Seifert, Silke Szymczak
Machine learning methods and in particular random forests are promising approaches for prediction based on high dimensional omics data sets. They provide variable importance measures to rank predictors according to their predictive power. If building a prediction model is the main goal of a study, often a minimal set of variables with good prediction performance is selected. However, if the objective is the identification of involved variables to find active networks and pathways, approaches that aim to select all relevant variables should be preferred...
October 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29045465/identifying-protein-complex-by-integrating-characteristic-of-core-attachment-into-dynamic-ppi-network
#6
Xianjun Shen, Li Yi, Xingpeng Jiang, Tingting He, Jincai Yang, Wei Xie, Po Hu, Xiaohua Hu
How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes...
2017: PloS One
https://www.readbyqxmd.com/read/29045433/integrated-mrna-and-microrna-transcriptome-analyses-reveal-regulation-of-thermal-acclimation-in-gymnocypris-przewalskii-a-case-study-in-tibetan-schizothoracine-fish
#7
Cunfang Zhang, Chao Tong, Fei Tian, Kai Zhao
Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways...
2017: PloS One
https://www.readbyqxmd.com/read/29045401/genome-wide-snps-reveal-the-drivers-of-gene-flow-in-an-urban-population-of-the-asian-tiger-mosquito-aedes-albopictus
#8
Thomas L Schmidt, Gordana Rašić, Dongjing Zhang, Xiaoying Zheng, Zhiyong Xi, Ary A Hoffmann
Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Aedes albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes...
October 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29045151/dynamic-blue-light-inducible-t7-rna-polymerases-opto-t7rnaps-for-precise-spatiotemporal-gene-expression-control
#9
Armin Baumschlager, Stephanie K Aoki, Mustafa Khammash
Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold...
October 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29044927/knock-out-of-histamine-receptor-h3-alters-adaptation-to-sudden-darkness-and-monoamine-levels-in-the-zebrafish
#10
Henri A J Puttonen, Maria Sundvik, Svetlana Semenova, Yukako Shirai, Yu-Chia Chen, Pertti Panula
AIM: Histamine receptor H3 has substantial neuropharmacological potential. Currently, knock-out models of this receptor have been investigated only in mice. We characterized the expression of this receptor in the zebrafish and generated a zebrafish histamine receptor H3 knock-out line. Using this model, we studied the role of histamine receptor H3 in important behaviours. We also analyzed the effect of histamine receptor H3 knock-out on monoaminergic systems, which has not been thoroughly studied in any animal model...
October 16, 2017: Acta Physiologica
https://www.readbyqxmd.com/read/29044887/quantitative-mapping-of-genetic-similarity-in-human-heritable-diseases-by-shared-mutations
#11
Huiying Zhao, Yuedong Yang, Yutong Lu, Matthew Mort, David N Cooper, Zhiyi Zuo, Yaoqi Zhou
Many genetic diseases exhibit considerable epidemiological comorbidity and common symptoms, which provokes debate about the extent of their etiological overlap. The rapid growth in the number of known disease-causing mutations in the Human Gene Mutation Database (HGMD) has allowed us to characterise genetic similarities between diseases by ascertaining the extent to which identical genetic mutations are shared between diseases. Using this approach, we show that 41.6% of disease pairs in all possible pairs (42, 083) exhibit a significant sharing of mutations (P-value < 0...
October 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/29044796/social-traits-social-networks-and-evolutionary-biology
#12
David N Fisher, Andrew G McAdam
The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships, and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness...
October 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29044773/integrated-analysis-of-microrna-and-mrna-expression-profiles-in-the-rat-spinal-cord-under-inflammatory-pain-conditions
#13
Chien Cheng Liu, Jiin Tsuey Cheng, Tien Yui Li, Ping Heng Tan
Recent studies using microarray-based approaches have demonstrated that microRNAs (miRNAs) are involved in pain processing pathways. However, a significant proportion of computational predictions of miRNA targets are false-positive interactions. To increase the chance of identifying biologically relevant targets, we performed an integrated analysis of both miRNA and mRNA expression profiles in the rat spinal cord during complete Freund's adjuvant (CFA)-induced inflammatory pain. We generated miRNA and mRNA arrays from the same corresponding samples on Days 5 and 14 after CFA injection...
October 17, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29044557/rice-phytoglobin-regulate-responses-under-low-mineral-nutrients-and-abiotic-stresses-in-arabidopsis-thaliana
#14
Alka Shankar, Joel Lars Fernandes, Kanwaljeet Kaur, Manisha Sharma, Suman Kundu, Girdhar K Pandey
Just like animals, plants also contain haemoglobins (known as phytoglobins in plants). Plant phytoglobins (Pgbs) have been categorized into six different classes viz. Phytogb0 (Pgb0), Phytogb1 (Pgb1), Phytogb2 (Pgb2), SymPhytogb (sPgb), Leghemoglobin (Lb) and Phytogb3 (Pgb3). Among the 6 Phytogbs, sPgb and Lb have been functionally characterized and the understanding of roles of other Pgbs is still evolving. In our present study, we have explored the function of two rice Pgbs (OsPgb1.1 and OsPgb1.2). OsPgb1...
October 17, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29044468/matchmaker-exchange
#15
Nara L M Sobreira, Harindra Arachchi, Orion J Buske, Jessica X Chong, Ben Hutton, Julia Foreman, François Schiettecatte, Tudor Groza, Julius O B Jacobsen, Melissa A Haendel, Kym M Boycott, Ada Hamosh, Heidi L Rehm
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29044196/exercise-and-high-fat-feeding-remodel-transcript-metabolite-interactive-networks-in-mouse-skeletal-muscle
#16
Joaquín Pérez-Schindler, Aditi Kanhere, Lindsay Edwards, J William Allwood, Warwick B Dunn, Simon Schenk, Andrew Philp
Enhanced coverage and sensitivity of next-generation 'omic' platforms has allowed the characterization of gene, metabolite and protein responses in highly metabolic tissues, such as, skeletal muscle. A limitation, however, is the capability to determine interaction between dynamic biological networks. To address this limitation, we applied Weighted Analyte Correlation Network Analysis (WACNA) to RNA-seq and metabolomic datasets to identify correlated subnetworks of transcripts and metabolites in response to a high-fat diet (HFD)-induced obesity and/or exercise...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044146/dissecting-the-underlying-pharmaceutical-mechanism-of-chinese-traditional-medicine-yun-pi-yi-shen-tong-du-tang-acting-on-ankylosing-spondylitis-through-systems-biology-approaches
#17
Duoli Xie, Lin Huang, Guanghui Zhao, Yiran Yu, Jiawei Gao, Haichang Li, Chengping Wen
Traditional Chinese Medicine (TCM) has been served as complementary medicine for Ankylosing Spondylitis (AS) treatment for a long time. Yun-Pi-Yi-Shen-Tong-Du-Tang (Y-Y-T) is a novel empirical formula designed by Prof. Chengping Wen. In this study, a retrospective investigation supported efficacy of Y-Y-T and then we deciphered the underlying molecular mechanism of the efficacy. Herbal ingredients and targeting proteins were collected from TCMID. PPI networks were constructed to further infer the relationship among Y-Y-T, drugs used for treating AS, differentially expressed genes of AS patients and AS disease proteins...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043294/integrating-networks-and-comparative-genomics-reveals-retroelement-proliferation-dynamics-in-hominid-genomes
#18
Orr Levy, Binyamin A Knisbacher, Erez Y Levanon, Shlomo Havlin
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29043084/multi-species-genetic-connectivity-in-a-terrestrial-habitat-network
#19
Robby R Marrotte, Jeff Bowman, Michael G C Brown, Chad Cordes, Kimberley Y Morris, Melanie B Prentice, Paul J Wilson
BACKGROUND: Habitat fragmentation reduces genetic connectivity for multiple species, yet conservation efforts tend to rely heavily on single-species connectivity estimates to inform land-use planning. Such conservation activities may benefit from multi-species connectivity estimates, which provide a simple and practical means to mitigate the effects of habitat fragmentation for a larger number of species. To test the validity of a multi-species connectivity model, we used neutral microsatellite genetic datasets of Canada lynx (Lynx canadensis), American marten (Martes americana), fisher (Pekania pennanti), and southern flying squirrel (Glaucomys volans) to evaluate multi-species genetic connectivity across Ontario, Canada...
2017: Movement Ecology
https://www.readbyqxmd.com/read/29042584/the-role-of-chromatin-density-in-cell-population-heterogeneity-during-stem-cell-differentiation
#20
Mahdi Golkaram, Jiwon Jang, Stefan Hellander, Kenneth S Kosik, Linda R Petzold
We incorporate three-dimensional (3D) conformation of chromosome (Hi-C) and single-cell RNA sequencing data together with discrete stochastic simulation, to explore the role of chromatin reorganization in determining gene expression heterogeneity during development. While previous research has emphasized the importance of chromatin architecture on activation and suppression of certain regulatory genes and gene networks, our study demonstrates how chromatin remodeling can dictate gene expression distribution by folding into distinct topological domains...
October 17, 2017: Scientific Reports
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