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https://www.readbyqxmd.com/read/28432092/a-genome-wide-investigation-on-biofilm-formation-in-bacillus-cereus
#1
Fang Yan, Yiyang Yu, Kevin Gozzi, Yun Chen, Jian-Hua Guo, Yunrong Chai
Bacillus cereus is a soil-dwelling Gram-positive bacterium capable of forming structured multicellular communities, or biofilms. However, the regulatory pathways controlling biofilm formation are less well understood in B. cereus In this work, we developed a method to study B. cereus biofilms formed at the air-liquid interface. We applied two genome-wide approaches, random transposon insertion mutagenesis to identify genes that are potentially important for biofilm formation, and transcriptome analyses by RNA-seq to characterize genes that are differentially expressed in B...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431977/transcriptome-comparison-reveals-insights-into-muscle-response-to-hypoxia-in-blunt-snout-bream-megalobrama-amblycephala
#2
Bo-Xiang Chen, Shao-Kui Yi, Wei-Feng Wang, Yan He, Yan Huang, Ze-Xia Gao, Hong Liu, Wei-Min Wang, Huan-Ling Wang
The economic and biological significance of blunt snout bream (Megalobrama amblycephala) makes this species important to explore the underlying molecular mechanism of hypoxia response. In the present study, we compared the transcriptional responses to serious hypoxia in skeletal muscle among hypoxia tolerant (MT), sensitive (MS) and control (without hypoxia treatment, MC) M. amblycephala obtained according to the time difference of losing balance after hypoxia treatment. A total of 88,200,889 clean reads were generated and assembled into 44,493 unigenes...
April 18, 2017: Gene
https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#3
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431510/delayed-response-to-cold-stress-is-characterized-by-successive-metabolic-shifts-culminating-in-apple-fruit-peel-necrosis
#4
Nigel E Gapper, Maarten L A T M Hertog, Jinwook Lee, David A Buchanan, Rachel S Leisso, Zhangjun Fei, Guiqin Qu, James J Giovannoni, Jason W Johnston, Robert J Schaffer, Bart M Nicolaï, James P Mattheis, Christopher B Watkins, David R Rudell
BACKGROUND: Superficial scald is a physiological disorder of apple fruit characterized by sunken, necrotic lesions appearing after prolonged cold storage, although initial injury occurs much earlier in the storage period. To determine the degree to which the transition to cell death is an active process and specific metabolism involved, untargeted metabolic and transcriptomic profiling was used to follow metabolism of peel tissue over 180 d of cold storage. RESULTS: The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using antioxidant (diphenylamine; DPA) or rendered insensitive to ethylene using 1-methylcyclopropene (1-MCP) beginning between 30 and 60 days of storage...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28431015/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#5
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430144/a-systems-biology-approach-using-transcriptomic-data-reveals-genes-and-pathways-in-porcine-skeletal-muscle-affected-by-dietary-lysine
#6
Taiji Wang, Jean M Feugang, Mark A Crenshaw, Naresh Regmi, John R Blanton, Shengfa F Liao
Nine crossbred finishing barrows (body weight 94.4 ± 6.7 kg) randomly assigned to three dietary treatments were used to investigate the effects of dietary lysine on muscle growth related metabolic and signaling pathways. Muscle samples were collected from the longissimus dorsi of individual pigs after feeding the lysine-deficient (4.30 g/kg), lysine-adequate (7.10 g/kg), or lysine-excess (9.80 g/kg) diet for five weeks, and the total RNA was extracted afterwards. Affymetrix Porcine Gene 1.0 ST Array was used to quantify the expression levels of 19,211 genes...
April 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28429252/analysis-of-global-gene-expression-profiles-during-the-flowering-initiation-process-of-lilium%C3%A2-%C3%A3-%C3%A2-formolongi
#7
Yu-Fan Li, Ming-Fang Zhang, Meng Zhang, Gui-Xia Jia
The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70...
April 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28429075/toward-personalized-management-in-bladder-cancer-the-promise-of-novel-molecular-taxonomy
#8
REVIEW
Marie-Lisa Eich, Lars Dyrskjøt, George J Netto
Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer...
April 21, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#9
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428821/genome-wide-search-for-candidate-genes-for-yeast-robustness-improvement-against-formic-acid-reveals-novel-susceptibility-trk1-and-positive-regulators-and-resistance-haa1-regulon-determinants
#10
Sílvia F Henriques, Nuno P Mira, Isabel Sá-Correia
BACKGROUND: Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS: This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28428793/transcriptomics-targeted-metabolomics-and-gene-expression-of-blackberry-leaves-and-fruits-indicate-flavonoid-metabolic-flux-from-leaf-to-red-fruit
#11
Enrique Gutierrez, Ana García-Villaraco, José A Lucas, Ana Gradillas, F Javier Gutierrez-Mañero, Beatriz Ramos-Solano
Blackberries (Rubus spp.) are among the high added value food products relevant for human health due to the increasing evidence of the beneficial effects of polyphenols, which are very abundant in these fruits. Interestingly, these compounds also play a role on plant physiology, being especially relevant their role in plant defense against biotic and abiotic stress. Hence, we hypothesize that since blackberry fruits have high amounts of flavonols and anthocyanins, leaves would also have high amounts of these compounds, and can be studied as a source of active molecules; furthermore, leaf synthesis would support their high contents in fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428792/identification-of-candidate-genes-and-biosynthesis-pathways-related-to-fertility-conversion-by-wheat-ktm3315a-transcriptome-profiling
#12
Jiali Ye, Yang Duan, Gan Hu, Xingxia Geng, Gaoming Zhang, Pengjiao Yan, Zihan Liu, Lingli Zhang, Xiyue Song
The Aegilops kotschyi thermo-sensitive cytoplasmic male sterility (K-TCMS) system may facilitate hybrid wheat (Triticum aestivum L.) seed multiplication and production. The K-TCMS line is completely male sterile during the normal wheat-growing season, whereas its fertility can be restored in a high-temperature environment. To elucidate the molecular mechanisms responsible for male sterility/fertility conversion and candidate genes involved with pollen development in K-TCMS, we employed RNA-seq to sequence the transcriptomes of anthers from K-TCMS line KTM3315A during development under sterile and fertile conditions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428780/genomic-and-transcriptomic-insights-into-calcium-carbonate-biomineralization-by-marine-actinobacterium-brevibacterium-linens-bs258
#13
Yuying Zhu, Ning Ma, Weihua Jin, Shimei Wu, Chaomin Sun
Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca(2+) concentration. To disclose the mechanisms of biomineralization, the genome of B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28428441/selective-glucocorticoid-receptor-modulators-sgrms-delay-castrate-resistant-prostate-cancer-growth
#14
Jacob Kach, Tiha M Long, Phillip Selman, Eva Y Tonsing-Carter, Maria A Bacalao, Ricardo R Lastra, Larischa de Wet, Shane Comiskey, Marc Gillard, Calvin VanOpstall, Diana C West, Wen-Ching Chan, Donald Vander Griend, Suzanne D Conzen, Russell Z Szmulewitz
Increased glucocorticoid receptor (GR) expression and activity following androgen blockade can contribute to castration-resistant prostate cancer (CRPC) progression. Therefore, we hypothesized that GR antagonism will have therapeutic benefit in CRPC. However, the FDA-approved nonselective, steroidal GR antagonist, mifepristone, lacks GR specificity, reducing its therapeutic potential. Here we report that two novel non-steroidal and highly selective GR modulators (SGRMs), CORT118335 and CORT108297, have the ability to block GR activity in prostate cancer (PC) and slow CRPC progression...
April 20, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28427951/uncovering-the-immune-responses-of-apis-mellifera-ligustica-larval-gut-to-ascosphaera-apis-infection-utilizing-transcriptome-sequencing
#15
Dafu Chen, Rui Guo, Xijian Xu, Cuiling Xiong, Qin Liang, Yanzhen Zheng, Qun Luo, Zhaonan Zhang, Zhijian Huang, Dhiraj Kumar, Weijun Xi, Xuan Zou, Min Liu
Honeybees are susceptible to a variety of diseases, including chalkbrood, which is capable of causing huge losses of both the number of bees and colony productivity. This research is designed to characterize the transcriptome profiles of Ascosphaera apis-treated and un-treated larval guts of Apis mellifera ligustica in an attempt to unravel the molecular mechanism underlying the immune responses of western honeybee larval guts to mycosis. In this study, 24, 296 and 2157 genes were observed to be differentially expressed in A...
April 18, 2017: Gene
https://www.readbyqxmd.com/read/28427347/comparative-transcriptomics-of-mountain-pine-beetle-pheromone-biosynthetic-tissues-and-functional-analysis-of-cyp6de3
#16
J A Nadeau, J Petereit, R L Tillett, K Jung, M Fotoohi, M MacLean, S Young, K Schlauch, G J Blomquist, C Tittiger
BACKGROUND: The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a highly destructive pest of pine forests in western North America. During flight to a new host tree and initiation of feeding, mountain pine beetles release aggregation pheromones. The biosynthetic pathways of these pheromones are sex-specific and localized in the midgut and fat body, but the enzymes involved have not all been identified or characterized. RESULTS: We used a comparative RNA-Seq analysis between fed and unfed male and female MPB midguts and fat bodies to identify candidate genes involved in pheromone biosynthesis...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28427185/transcriptional-landscape-of-human-cancers
#17
Mengyuan Li, Qingrong Sun, Xiaosheng Wang
The homogeneity and heterogeneity in somatic mutations, copy number alterations and methylation across different cancer types have been extensively explored. However, the related exploration based on transcriptome data is lacking. In this study we explored gene expression profiles across 33 human cancer types using The Cancer Genome Atlas (TCGA) data. We identified consistently upregulated genes (such as E2F1, EZH2, FOXM1, MYBL2, PLK1, TTK, AURKA/B and BUB1) and consistently downregulated genes (such as SCARA5, MYOM1, NKAPL, PEG3, USP2, SLC5A7 and HMGCLL1) across various cancers...
March 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426704/population-effect-model-identifies-gene-expression-predictors-of-survival-outcomes-in-lung-adenocarcinoma-for-both-caucasian-and-asian-patients
#18
Guoshuai Cai, Feifei Xiao, Chao Cheng, Yafang Li, Christopher I Amos, Michael L Whitfield
BACKGROUND: We analyzed and integrated transcriptome data from two large studies of lung adenocarcinomas on distinct populations. Our goal was to investigate the variable gene expression alterations between paired tumor-normal tissues and prospectively identify those alterations that can reliably predict lung disease related outcomes across populations. METHODS: We developed a mixed model that combined the paired tumor-normal RNA-seq from two populations. Alterations in gene expression common to both populations were detected and validated in two independent DNA microarray datasets...
2017: PloS One
https://www.readbyqxmd.com/read/28425640/profiling-of-the-silica-induced-molecular-events-in-lung-epithelial-cells-using-the-rna-seq-approach
#19
Judy Y W Chan, Joseph C C Tsui, Patrick T W Law, Winnie K W So, Doris Y P Leung, Michael M K Sham, Stephen K W Tsui, Carmen W H Chan
Silicosis is a prolonged, irreversible and incurable occupational disease, and there is a significant number of newly diagnosed cases every year in Hong Kong. Due to the long latency of the disease, the diagnosis can be missed until detailed clinical examination at a later stage. For a better control of this deadly disease, detailing the pro-inflammatory and fibrotic events in the macrophage would be instrumental in understanding the pathogenesis of the disease and essential for the significant biomarkers discovery...
April 20, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28425468/transcriptome-analysis-of-mango-mangifera-indica-l-fruit-epidermal-peel-to-identify-putative-cuticle-associated-genes
#20
Julio C Tafolla-Arellano, Yi Zheng, Honghe Sun, Chen Jiao, Eliel Ruiz-May, Miguel A Hernández-Oñate, Alberto González-León, Reginaldo Báez-Sañudo, Zhangjun Fei, David Domozych, Jocelyn K C Rose, Martín E Tiznado-Hernández
Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq...
April 20, 2017: Scientific Reports
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