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https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#1
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107648/parp-1-controls-the-adipogenic-transcriptional-program-by-parylating-c-ebp%C3%AE-and-modulating-its-transcriptional-activity
#2
Xin Luo, Keun Woo Ryu, Dae-Seok Kim, Tulip Nandu, Carlos J Medina, Rebecca Gupte, Bryan A Gibson, Raymond E Soccio, Yonghao Yu, Rana K Gupta, W Lee Kraus
Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPβ's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28107554/inclusion-of-a-variable-rbe-into-proton-and-photon-plan-comparison-for-various-fractionation-schedules-in-prostate-radiation-therapy
#3
Jakob Ödén, Kjell Eriksson, Iuliana Toma-Dasu
PURPOSE: A constant relative biological effectiveness (RBE) of 1.1 is currently used in proton radiation therapy to account for the increased biological effectiveness compared to photon therapy. However, there is increasing evidence that proton RBE vary with the linear energy transfer (LET), the dose per fraction and the type of the tissue. Therefore, this study aims to evaluate the impact of disregarding variations in RBE when comparing proton and photon dose plans for prostate treatments for various fractionation schedules using published RBE models and several α/β assumptions...
January 20, 2017: Medical Physics
https://www.readbyqxmd.com/read/28107498/delineating-substrate-diversity-of-disparate-short-chain-dehydrogenase-reductase-from-debaryomyces-hansenii
#4
Arindam Ghatak, Nagakumar Bharatham, Anirudh P Shanbhag, Santanu Datta, Janani Venkatraman
Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus...
2017: PloS One
https://www.readbyqxmd.com/read/28105701/climate-change-and-alpine-stream-biology-progress-challenges-and-opportunities-for-the-future
#5
Scott Hotaling, Debra S Finn, J Joseph Giersch, David W Weisrock, Dean Jacobsen
In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities...
January 20, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28104755/n-glycosylation-of-human-sphingomyelin-phosphodiesterase-acid-like-3a-smpdl3a-is-essential-for-stability-secretion-and-activity
#6
Mathew Traini, Raani Kumaran, Morten Thaysen-Andersen, Maaike Kockx, Wendy Jessup, Leonard Kritharides
Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a recently identified phosphodiesterase, which is a secreted N -linked glycoprotein. SMPDL3A is highly homologous to acid sphingomyelinase (aSMase), but unlike aSMase can not cleave sphingomyelin. Rather, SMPDL3A hydrolyzes nucleotide tri- and diphosphates and their derivatives. While recent structural studies have shed light on these unexpected substrate preferences, many other aspects of SMPDL3A biology which may give insight into its function in vivo remain obscure...
January 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#7
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28103115/involvement-of-autophagy-in-nk-cell-development-and-function
#8
Alejandro López-Soto, José Manuel Bravo-San Pedro, Guido Kroemer, Lorenzo Galluzzi, Segundo Gonzalez
Natural killer (NK) cells are the prototypical members of the recently identified family of innate lymphoid cells (ILCs). Thanks to their cytotoxic and secretory functions, NK cells play a key role in the immune response to cells experiencing various forms of stress, including viral infection and malignant transformation. Autophagy is a highly conserved network of degradative pathways that participate in the maintenance of cellular and organismal homeostasis as they promote adaptation to adverse microenvironmental conditions...
January 19, 2017: Autophagy
https://www.readbyqxmd.com/read/28102122/advances-in-myeloid-like-cell-origins-and-functions-in-the-model-organism-drosophila-melanogaster
#9
Laure El Chamy, Nicolas Matt, Jean-Marc Reichhart
Drosophila has long served as a valuable model for deciphering many biological processes, including immune responses. Indeed, the genetic tractability of this organism is particularly suited for large-scale analyses. Studies performed during the last 3 decades have proven that the signaling pathways that regulate the innate immune response are conserved between Drosophila and mammals. This review summarizes the recent advances on Drosophila hematopoiesis and immune cellular responses, with a particular emphasis on phagocytosis...
January 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28101376/atpase-activity-tightly-regulates-reca-nucleofilaments-to-promote-homologous-recombination
#10
Bailin Zhao, Dapeng Zhang, Chengmin Li, Zheng Yuan, Fangzhi Yu, Shangwei Zhong, Guibin Jiang, Yun-Gui Yang, X Chris Le, Michael Weinfeld, Ping Zhu, Hailin Wang
Homologous recombination (HR), catalyzed in an evolutionarily conserved manner by active RecA/Rad51 nucleofilaments, maintains genomic integrity and promotes biological evolution and diversity. The structures of RecA/Rad51 nucleofilaments provide information critical for the entire HR process. By exploiting a unique capillary electrophoresis-laser-induced fluorescence polarization assay, we have discovered an active form of RecA nucleofilament, stimulated by ATP hydrolysis, that contains mainly unbound nucleotide sites...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28100803/a-new-cue-for-torpor-induction-charcoal-ash-and-smoke
#11
Clare Stawski, Julia Nowack, Gerhard Körtner, Fritz Geiser
Recent work has shown that the use of torpor for energy conservation increases after forest fires in heterothermic mammals, probably in response to the reduction of food. However, the specific environmental cues for this increased torpor expression remain unknown. It is possible that smoke and the novel substrate of charcoal and ash act as signals for an impending period of starvation requiring torpor. We therefore tested the hypothesis that the combined cues of smoke, a charcoal/ash substrate and food shortage will enhance torpor expression in a small forest-dwelling marsupial, the yellow-footed antechinus (Antechinus flavipes), because like other animals that live in fire-prone habitats they must effectively respond to fires to ensure survival...
January 15, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28100777/structure-activity-relationship-of-%C3%AE-mating-pheromone-from-the-fungal-pathogen-fusarium-oxysporum
#12
Stefania Vitale, Angélica Partida-Hanon, Soraya Serrano, Álvaro Martínez-Del-Pozo, Antonio Di Pietro, David Turrà, Marta Bruix
During sexual development, ascomycete fungi produce two types of peptide pheromones termed a and α. The α pheromone from the budding yeast Saccharomyces cerevisiae, a thirteen residue peptide which elicits cell cycle arrest and chemotropic growth, has served as paradigm for the interaction of small peptides with their cognate G protein-coupled receptors (GPCRs). However, no structural information is currently available for α pheromones from filamentous ascomycetes, which are significantly shorter and share almost no sequence similarity with the S...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100676/gene-body-chromatin-modification-dynamics%C3%A2-mediate-epigenome-differentiation-in%C3%A2-arabidopsis
#13
Soichi Inagaki, Mayumi Takahashi, Aoi Hosaka, Tasuku Ito, Atsushi Toyoda, Asao Fujiyama, Yoshiaki Tarutani, Tetsuji Kakutani
Heterochromatin is marked by methylation of lysine 9 on histone H3 (H3K9me). A puzzling feature of H3K9me is that this modification localizes not only in promoters but also in internal regions (bodies) of silent transcription units. Despite its prevalence, the biological significance of gene-body H3K9me remains enigmatic. Here we show that H3K9me-associated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing. Mutations in an Arabidopsis H3K9 demethylase gene IBM1 induce ectopic H3K9me2 accumulation in gene bodies, with accompanying severe developmental defects...
January 18, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28100022/mycorrhizal-specificity-does-not-limit-the-distribution-of-an-endangered-orchid-species
#14
Michael Waud, Rein Brys, Wouter Van Landuyt, Bart Lievens, Hans Jacquemyn
What factors determine the distribution of a species is a central question in ecology and conservation biology. In general, the distribution of plant species is assumed to be controlled by dispersal or environmentally controlled recruitment. For plant species which are critically dependent on mycorrhizal symbionts for germination and seedling establishment, specificity in mycorrhizal associations and availability of suitable mycorrhizal fungi can be expected to have a major impact on successful colonization and establishment, and thus ultimately on a species distribution...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100017/subspecies-delineation-amid-phenotypic-geographic-and-genetic-discordance-in-a-songbird
#15
Jennifer Walsh, Irby J Lovette, Virginia Winder, Chris S Elphick, Brian J Olsen, W Gregory Shriver, Adrienne I Kovach
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099784/investigating-the-extent-of-parallelism-in-morphological-and-genomic-divergence-among-lake-trout-ecotypes-in-lake-superior
#16
Alysse Perreault-Payette, Andrew M Muir, Frederick Goetz, Charles Perrier, Eric Normandeau, Pascal Sirois, Louis Bernatchez
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099772/exploring-the-symbiont-diversity-of-ancient-western-redcedars-arbuscular-mycorrhizal-fungi-of-long-lived-hosts
#17
Monika A Gorzelak, Brian J Pickles, Miranda M Hart
Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs, and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099770/cryptic-lineages-of-a-common-alpine-mayfly-show-strong-life-history-divergence
#18
Marie Leys, Irene Keller, Christopher T Robinson, Katja Räsänen
Understanding ecological divergence of morphologically similar but genetically distinct species ̶ previously considered as a single morphospecies ̶ is of key importance in evolutionary ecology and conservation biology. Despite their morphological similarity, cryptic species may have evolved distinct adaptations. If such ecological divergence is unaccounted for, any predictions about their responses to environmental change and biodiversity loss may be biased. We used spatio-temporally replicated field surveys of larval cohort structure and population genetic analyses (using nuclear microsatellite markers) to test for life history divergence between two cryptic lineages of the alpine mayfly Baetis alpinus in the Swiss Alps...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099117/casz1-loss-of-function-mutation-contributes-to-familial-dilated-cardiomyopathy
#19
Xing-Biao Qiu, Xin-Kai Qu, Ruo-Gu Li, Hua Liu, Ying-Jia Xu, Min Zhang, Hong-Yu Shi, Xu-Min Hou, Xu Liu, Fang Yuan, Yu-Min Sun, Jun Wang, Ri-Tai Huang, Song Xue, Yi-Qing Yang
BACKGROUND: The zinc finger transcription factor CASZ1 plays a key role in cardiac development and postnatal adaptation, and in mice, deletion of the CASZ1 gene leads to dilated cardiomyopathy (DCM). However, in humans whether genetically defective CASZ1 contributes to DCM remains unclear. METHODS: The coding exons and splicing junction sites of the CASZ1 gene were sequenced in 138 unrelated patients with idiopathic DCM. The available family members of the index patient harboring an identified CASZ1 mutation and 200 unrelated, ethnically matched healthy individuals used as controls were genotyped for CASZ1...
January 18, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28098310/a-computational-model-predicts-genetic-nodes-that-allow-switching-between-species-specific-responses-in-a-conserved-signaling-network
#20
Adriana T Dawes, David Wu, Karley K Mahalak, Edward M Zitnik, Natalia Kravtsova, Haiwei Su, Helen M Chamberlin
Cell signaling networks regulate a variety of developmental and physiological processes, and changes in their response to external stimuli are often implicated in disease initiation and progression. To elucidate how different responses can arise from conserved signaling networks, we have developed a mathematical model of the well-characterized Caenorhabditis vulval development network involving EGF, Wnt and Notch signaling that recapitulates biologically observed behaviors. We experimentally block a specific element of the EGF pathway (MEK), and find different behaviors in vulval development in two Caenorhabditis species, C...
January 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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