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https://www.readbyqxmd.com/read/28938599/a-pathways-based-prediction-model-for-classifying-breast-cancer-subtypes
#1
Tong Wu, Yunfeng Wang, Ronghui Jiang, Xinliang Lu, Jiawei Tian
Breast cancer is highly heterogeneous and is classified into four subtypes characterized by specific biological traits, treatment responses, and clinical prognoses. We performed a systemic analysis of 698 breast cancer patient samples from The Cancer Genome Atlas project database. We identified 136 breast cancer genes differentially expressed among the four subtypes. Based on unsupervised clustering analysis, these 136 core genes efficiently categorized breast cancer patients into the appropriate subtypes. Functional enrichment based on Kyoto Encyclopedia of Genes and Genomes analysis identified six functional pathways regulated by these genes: JAK-STAT signaling, basal cell carcinoma, inflammatory mediator regulation of TRP channels, non-small cell lung cancer, glutamatergic synapse, and amyotrophic lateral sclerosis...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938057/outbreak-of-drepanopeziza-fungus-in-aspen-forests-and-variation-in-stand-susceptibility-leaf-functional-traits-compensatory-growth-and-phenology
#2
Anson C Call, Samuel B St Clair
In the spring of 2015, a severe outbreak of the necrotrophic pathogen Drepanopeziza (also known as Marssonina) spread across large portions of aspen (Populus tremuloides Michx.) forests in the western United States. Among adjacent stands, some were diseased and others were not. Drepanopeziza infection in diseased aspen stands stimulated compensatory growth of second-flush leaves at the top of the canopy. These patterns of infection provided an opportunity to characterize associations of pathogen infection and leaf functional traits...
September 1, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28938055/photosynthetic-phenological-variation-may-promote-coexistence-among-co-dominant-tree-species-in-a-madrean-sky-island-mixed-conifer-forest
#3
D L Potts, R L Minor, Z Braun, G A Barron-Gafford
Across much of western North America, forests are predicted to experience a transition from snow- to rain-dominated precipitation regimes due to anthropogenic climate warming. Madrean sky island mixed conifer forests receive a large portion of their precipitation from summertime convective storms and may serve as a lens into the future for snow-dominated forests after prolonged warming. To better understand the linkage between physiological traits, climate variation, and the structure and function of mixed conifer forests, we measured leaf photosynthetic (A) responses to controlled variation in internal CO2 concentration (Ci) to quantify interspecific phenological variation in A/Ci-derived ecophysiological traits among ponderosa pine (Pinus ponderosa Lawson and C...
September 1, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28937814/comparative-analyses-of-phenotypic-trait-covariation-within-and-among-populations
#4
Kathryn S Peiman, Beren W Robinson
Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28936944/bacterial-endosymbionts-master-modulators-of-fungal-phenotypes
#5
Sarah J Araldi-Brondolo, Joseph Spraker, Justin P Shaffer, Emma H Woytenko, David A Baltrus, Rachel E Gallery, A Elizabeth Arnold
The ecological modes of fungi are shaped not only by their intrinsic features and the environment in which they occur, but also by their interactions with diverse microbes. Here we explore the ecological and genomic features of diverse bacterial endosymbionts-endohyphal bacteria-that together are emerging as major determinants of fungal phenotypes and plant-fungi interactions. We first provide a historical perspective on the study of endohyphal bacteria. We then propose a functional classification of three main groups, providing an overview of their genomic, phylogenetic, and ecological traits...
September 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28936744/cardiac-telocyte-derived-exosomes-and-their-possible-implications-in-cardiovascular-pathophysiology
#6
Mirca Marini, Lidia Ibba-Manneschi, Mirko Manetti
Among cardiac interstitial cells, the recently described telocytes (TCs) display the unique ability to build a supportive three-dimensional network formed by their very long and thin prolongations named telopodes. Cardiac TCs are increasingly regarded as pivotal regulators in intercellular signaling with multiple cell types, such as cardiomyocytes, stem/progenitor cells, microvessels, nerve endings, fibroblasts and immune cells, thus converting the cardiac stromal compartment into an integrated system that may drive either heart development or maintenance of cardiac homeostasis in post-natal life...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28936643/climate-variability-affects-the-germination-strategies-exhibited-by-arid-land-plants
#7
Sarah Barga, Thomas E Dilts, Elizabeth A Leger
Spatial and temporal environmental variability can lead to variation in selection pressures across a landscape. Strategies for coping with environmental heterogeneity range from specialized phenotypic responses to a narrow range of conditions to generalist strategies that function under a range of conditions. Here, we ask how mean climate and climate variation at individual sites and across a species' range affect the specialist-generalist spectrum of germination strategies exhibited by 10 arid land forbs. We investigated these relationships using climate data for the western United States, occurrence records from herbaria, and germination trials with field-collected seeds, and predicted that generalist strategies would be most common in species that experience a high degree of climate variation or occur over a wide range of conditions...
September 21, 2017: Oecologia
https://www.readbyqxmd.com/read/28935893/trap-diversity-and-character-evolution-in-carnivorous-bladderworts-utricularia-lentibulariaceae
#8
Anna Sofia Westermeier, Andreas Fleischmann, Kai Müller, Bastian Schäferhoff, Carmen Rubach, Thomas Speck, Simon Poppinga
Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935391/extracellular-vesicles-released-by-mesenchymal-like-prostate-carcinoma-cells-modulate-emt-state-of-recipient-epithelial-like-carcinoma-cells-through-regulation-of-ar-signaling
#9
Ihsan Y El-Sayed, Ahmad Daher, Damien Destouches, Virginie Firlej, Enis Kostallari, Pascale Maillé, Eric Huet, Nathaline Haidar-Ahmad, Guido Jenster, Alexandre de la Taille, Raghida Abou Merhi, Stéphane Terry, Francis Vacherot
Extracellular vesicles released from cancer cells may play an important role in cancer progression by shuttling oncogenic information into recipient cells. However, our knowledge is still fragmentary and there remain numerous questions regarding the mechanisms at play and the functional consequences of these interactions. We have recently established a mesenchymal-like prostate cancer cell line (22Rv1/CR-1; Mes-PCa). In this study, we assessed the effects of the extracellular vesicles released by these cells on recipient androgen-dependent epithelial VCaP prostate cancer cells...
September 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28935211/sustained-molecular-pathology-across-episodes-and-remission-in-major-depressive-disorder
#10
Enzo Scifo, Mohan Pabba, Fenika Kapadia, Tianzhou Ma, David A Lewis, George C Tseng, Etienne Sibille
BACKGROUND: Major depressive disorder (MDD) is a debilitating mental illness and a major cause of lost productivity worldwide. MDD patients often suffer from life-long recurring episodes of increasing severity, reduced therapeutic response, and shorter remission periods, suggesting the presence of a persistent and potentially progressive pathology. METHODS: Subgenual anterior cingulate cortex postmortem samples from four MDD cohorts (single episode, n = 20; single episode in remission, n = 15; recurrent episode, n = 20; and recurrent episode in remission, n = 15), and one control cohort (n = 20) were analyzed by mass spectrometry-based proteomics (n = 3630 proteins) combined with statistical analyses...
August 18, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28934612/measuring-and-modeling-for-the-assessment-of-the-genetic-background-behind-cognitive-processes-in-donkeys
#11
Francisco Javier Navas, Jordi Jordana, José Manuel León, Ander Arando, Gabriela Pizarro, Amy Katherine McLean, Juan Vicente Delgado
New productive niches can offer new commercial perspectives linked to donkeys' products and human therapeutic or leisure applications. However, no assessment for selection criteria has been carried out yet. First, we assessed the animal inherent features and environmental factors that may potentially influence several cognitive processes in donkeys. Then, we aimed at describing a practical methodology to quantify such cognitive processes, seeking their inclusion in breeding and conservation programmes, through a multifactorial linear model...
September 14, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28934490/number-of-inadvertent-rna-targets-for-morpholino-knockdown-in-danio-rerio-is-largely-underestimated-evidence-from-the-study-of-ser-arg-rich-splicing-factors
#12
Marine Joris, Marie Schloesser, Denis Baurain, Marc Hanikenne, Marc Muller, Patrick Motte
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934485/detecting-gene-subnetworks-under-selection-in-biological-pathways
#13
Alexandre Gouy, Joséphine T Daub, Laurent Excoffier
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934397/a-modifier-of-huntington-s-disease-onset-at-the-mlh1-locus
#14
Jong-Min Lee, Michael J Chao, Denise Harold, Kawther Abu Elneel, Tammy Gillis, Peter Holmans, Lesley Jones, Michael Orth, Richard H Myers, Seung Kwak, Vanessa C Wheeler, Marcy E MacDonald, James F Gusella
Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in HTT. Many clinical characteristics of HD such as age at motor onset are determined largely by the size of HTT CAG repeat. However, emerging evidence strongly supports a role for other genetic factors in modifying the disease pathogenesis driven by mutant huntingtin. A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome 3...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28933792/a-common-haplotype-containing-functional-cacna1h-variants-is-frequently-coinherited-with-increased-tpsab1-copy-number
#15
Jonathan J Lyons, Stephanie C Stotz, Jack Chovanec, Yihui Liu, Katie L Lewis, Celeste Nelson, Thomas DiMaggio, Nina Jones, Kelly D Stone, Heejong Sung, Leslie G Biesecker, Michael A Colicos, Joshua D Milner
PurposeCaV3.2 signaling contributes to nociception, pruritus, gastrointestinal motility, anxiety, and blood pressure homeostasis. This calcium channel, encoded by CACNA1H, overlaps the human tryptase locus, wherein increased TPSAB1 copy number causes hereditary α-tryptasemia. Germ-line CACNA1H variants may contribute to the variable expressivity observed with this genetic trait.MethodsTryptase-encoding sequences at TPSAB1 and TPSB2, and TPSG1 and CACNA1H variants were genotyped in 46 families with hereditary α-tryptasemia syndrome...
September 21, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28933692/a-quantitative-hypermorphic-cngc-allele-confers-ectopic-calcium-flux-and-impairs-cellular-development
#16
David M Chiasson, Kristina Haage, Katharina Sollweck, Andreas Brachmann, Petra Dietrich, Martin Parniske
The coordinated control of Ca(2+) signaling is essential for development in eukaryotes. Cyclic nucleotide-gated channel (CNGC) family members mediate Ca(2+) influx from cellular stores in plants(1-4). Here we report the unusual genetic behavior of a quantitative gain-of-function CNGC mutation (brush) in Lotus japonicus resulting in a leaky tetrameric channel. brush resides in a cluster of redundant CNGCs encoding subunits which resemble metazoan voltage-gated potassium (Kv1-Kv4) channels in assembly and gating properties...
September 21, 2017: ELife
https://www.readbyqxmd.com/read/28932898/differential-effects-of-chaperones-on-yeast-prions-current-view
#17
REVIEW
Andrew G Matveenko, Yury A Barbitoff, Lina Manuela Jay-Garcia, Yury O Chernoff, Galina A Zhouravleva
Endogenous yeast amyloids that control heritable traits and are frequently used as models for human amyloid diseases are termed yeast prions. Yeast prions, including the best studied ones ([PSI (+)] and [URE3]), propagate via intimate interactions with molecular chaperones. Different yeast prions exhibit differential responses to changes in levels, functionality or localization of the components of chaperone machinery. Here, we provide additional data confirming differential effects of chaperones (and specifically, Hsp40s) on yeast prions and summarize current knowledge of the mechanisms underlying chaperone specificities...
September 20, 2017: Current Genetics
https://www.readbyqxmd.com/read/28932233/three-key-sub-leaf-modules-and-the-diversity-of-leaf-designs
#18
Le Li, Zeqing Ma, Ülo Niinemets, Dali Guo
Earth harbors a highly diverse array of plant leaf forms. A well-known pattern linking diverse leaf forms with their photosynthetic function across species is the global leaf economics spectrum (LES). However, within homogeneous plant functional groups such as tropical woody angiosperms or temperate deciduous woody angiosperms, many species can share a similar position in the LES but differ in other vital leaf traits, and thus function differently under the given suite of environmental drivers. How diverse leaves differentiate from each other has yet to be fully explained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28931887/multiple-stressor-effects-on-marine-infauna-responses-of-estuarine-taxa-and-functional-traits-to-sedimentation-nutrient-and-metal-loading
#19
J I Ellis, D Clark, J Atalah, W Jiang, C Taiapa, M Patterson, J Sinner, J Hewitt
Sedimentation, nutrients and metal loading to coastal environments are increasing, associated with urbanization and global warming, hence there is a growing need to predict ecological responses to such change. Using a regression technique we predicted how maximum abundance of 20 macrobenthic taxa and 22 functional traits separately and interactively responded to these key stressors. The abundance of most taxa declined in response to sedimentation and metal loading while a unimodal response was often associated with nutrient loading...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931629/selinene-volatiles-are-essential-precursors-for-maize-defense-promoting-fungal-pathogen-resistance
#20
Yezhang Ding, Alisa Huffaker, Tobias G Köllner, Philipp Weckwerth, Christelle A M Robert, Joseph L Spencer, Alexander E Lipka, Eric A Schmelz
To ensure food security, maize (Zea mays) is a model crop for understanding useful traits underlying stress resistance. In contrast to foliar biochemicals, root defenses limiting the spread of disease remain poorly described. To better understand below-ground defenses in the field, we performed root metabolomic profiling and uncovered unexpectedly high levels of the sesquiterpene volatile β-selinene and the corresponding non-volatile antibiotic derivative, β-costic acid. The application of metabolite-based quantitative trait loci (mQTL) mapping using bi-parental populations, genome wide association studies, and near-isogenic lines (NILs) enabled the identification of terpene synthase 21 (ZmTps21) on chromosome 9 as a β-costic acid pathway candidate gene...
September 20, 2017: Plant Physiology
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