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https://www.readbyqxmd.com/read/28922823/de-novo-genome-assembly-of-camptotheca-acuminata-a-natural-source-of-the-anti-cancer-compound-camptothecin
#1
Dongyan Zhao, John P Hamilton, Gina M Pham, Emily Crisovan, Krystle Wiegert-Rininger, Brieanne Vaillancourt, Dean DellaPenna, C Robin Buell
Camptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28922759/transcriptomic-and-metabolomics-responses-to-elevated-cell-wall-invertase-activity-during-tomato-fruit-set
#2
Lei Ru, Sonia Osorio, Lu Wang, Alisdair R Fernie, John W Patrick, Yong-Ling Ruan
Fruit set is a developmental transition from ovaries to fruitlets that determines yield potential. Cell wall invertase (CWIN) is essential for fruit and seed set, but the underlying molecular basis remains elusive. We addressed this issue by using CWIN-elevated transgenic tomato, focusing on ovaries and fruitlets at 2 d before and after anthesis, respectively. RNAseq analyses revealed that ovaries and fruitlets exhibited remarkable differences in their transcriptomic responses to elevated CWIN activity. Ovaries 2 d before anthesis were far more responsive to elevated CWIN activity compared with the fruitlets...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922755/root-transcriptomic-responses-of-grafted-grapevines-to-heterogeneous-nitrogen-availability-depend-on-rootstock-genotype
#3
Noé Cochetel, Frédéric Escudié, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, Pierre-François Bert, Mindy Stephania Muñoz, Serge Delrot, Christophe Klopp, Nathalie Ollat, Virginie Lauvergeat
In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922415/rewiring-monocyte-glucose-metabolism-via-c-type-lectin-signaling-protects-against-disseminated-candidiasis
#4
Jorge Domínguez-Andrés, Rob J W Arts, Rob Ter Horst, Mark S Gresnigt, Sanne P Smeekens, Jacqueline M Ratter, Ekta Lachmandas, Lily Boutens, Frank L van de Veerdonk, Leo A B Joosten, Richard A Notebaart, Carlos Ardavín, Mihai G Netea
Monocytes are innate immune cells that play a pivotal role in antifungal immunity, but little is known regarding the cellular metabolic events that regulate their function during infection. Using complementary transcriptomic and immunological studies in human primary monocytes, we show that activation of monocytes by Candida albicans yeast and hyphae was accompanied by metabolic rewiring induced through C-type lectin-signaling pathways. We describe that the innate immune responses against Candida yeast are energy-demanding processes that lead to the mobilization of intracellular metabolite pools and require induction of glucose metabolism, oxidative phosphorylation and glutaminolysis, while responses to hyphae primarily rely on glycolysis...
September 18, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28921169/effects-of-acute-salt-stress-on-modulation-of-gene-expression-in-a-malaysian-salt-tolerant-indigenous-rice-variety-bajong
#5
Brandon Pei Hui Yeo, Mrinal Bhave, Siaw San Hwang
The small genome size of rice relative to wheat and barley, together with its salt sensitivity, make it an ideal candidate for studies of salt stress response. Transcriptomics has emerged as a powerful technique to study salinity responses in many crop species. By identifying a large number of differentially expressed genes (DEGs) simultaneously after the stress induction, it can provide crucial insight into the immediate responses towards the stressor. In this study, a Malaysian salt-tolerant indigenous rice variety named Bajong and one commercial rice variety named MR219 were investigated for their performance in plant growth and ion accumulation properties after salt stress treatment...
September 18, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28920844/identification-of-genes-involved-in-galactooligosaccharide-utilization-in-bifidobacterium-breve-strain-yit-4014t
#6
Hidetsugu Sotoya, Akira Shigehisa, Taeko Hara, Hoshitaka Matsumoto, Hiroshi Hatano, Takahiro Matsuki
Galactooligosaccharides (GOS) are mixed oligosaccharides that are mainly composed of galactosyllactoses (GLs), which include 3'-GL, 4'-GL, and 6'-GL. Data from numerous in vitro and in vivo studies have shown that GOS selectively stimulate the growth of bifidobacteria. Previously, we identified the gene locus responsible for 4'-GL utilization, but the selective routes of uptake and catabolism of 3'- and 6'-GL remain to be elucidated. In this study, we used differential transcriptomics to identify the utilization pathways of these GLs within the Bifidobacterium breve YIT 4014T strain...
September 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28920148/differential-gene-expression-profiles-and-alternative-isoform-regulations-in-gill-of-nile-tilapia-in-response-to-acute-hypoxia
#7
Hong Lian Li, Hao Ran Lin, Jun Hong Xia
Fish often encounters exposures to acute environmental hypoxia either spatially or temporally. Gill organ plays important roles in response to hypoxic stress in fish. Few studies focus on the molecular regulation mechanisms of gills under hypoxic stress. In this study, we investigated the transcriptomic response to 12-h acute hypoxia in gill of a hypoxia tolerant fish, Nile tilapia Oreochromis niloticus through RNA sequencing (RNA-Seq). We sequenced messenger RNA from three control samples and three hypoxia-treated samples...
September 18, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28920088/metabolic-and-transcriptomic-analysis-of-huntington-s-disease-model-reveal-changes-in-intracellular-glucose-levels-and-related-genes
#8
Gepoliano Chaves, Rıfat Emrah Özel, Namrata V Rao, Hana Hadiprodjo, Yvonne Da Costa, Zachary Tokuno, Nader Pourmand
Huntington's Disease (HD) is a neurodegenerative disorder caused by an expansion in a CAG-tri-nucleotide repeat that introduces a poly-glutamine stretch into the huntingtin protein (mHTT). Mutant huntingtin (mHTT) has been associated with several phenotypes including mood disorders and depression. Additionally, HD patients are known to be more susceptible to type II diabetes mellitus (T2DM), and HD mice model develops diabetes. However, the mechanism and pathways that link Huntington's disease and diabetes have not been well established...
August 2017: Heliyon
https://www.readbyqxmd.com/read/28920001/zoledronic-acid-inhibits-nfat-and-il-2-signaling-pathways-in-regulatory-t-cells-and-diminishes-their-suppressive-function-in-patients-with-metastatic-cancer
#9
Dhifaf Sarhan, Caroline Leijonhufvud, Shannon Murray, Kristina Witt, Christina Seitz, Majken Wallerius, Hanjing Xie, Anders Ullén, Ulrika Harmenberg, Elisabet Lidbrink, Charlotte Rolny, John Andersson, Andreas Lundqvist
Regulatory T cells (Treg) suppress anti-tumor immune responses and their infiltration in the tumor microenvironment is associated with inferior prognosis in cancer patients. Thus, in order to enhance anti-tumor immune responses, selective depletion of Treg is highly desired. We found that treatment with zoledronic acid (ZA) resulted in a selective decrease in the frequency of Treg that was associated with a significant increase in proliferation of T cells and natural killer (NK) cells in peripheral blood of patients with metastatic cancer...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28919881/genomic-and-transcriptomic-analysis-of-growth-supporting-dehalogenation-of-chlorinated-methanes-in-methylobacterium
#10
Pauline Chaignaud, Bruno Maucourt, Marion Weiman, Adriana Alberti, Steffen Kolb, Stéphane Cruveiller, Stéphane Vuilleumier, Françoise Bringel
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28919578/selectin-independent-adhesion-during-ovarian-cancer-metastasis
#11
Nadezhda A Khaustova, Diana V Maltseva, Leticia Oliveira-Ferrer, Christine Stürken, Karin Milde-Langosch, Julia A Makarova, Sergey Rodin, Udo Schumacher, Alexander G Tonevitsky
PURPOSE: Ovarian cancer (OvCa) progression mainly takes place by intraperitoneal spread. Adhesion of tumor cells to the mesothelial cells which form the inner surface of the peritoneum is a crucial step in this process. Cancer cells use in principle different molecules of the leukocyte adhesion cascade to facilitate adhesion. This cascade is initiated by selectin-ligand interactions followed by integrin - extracellular matrix protein interactions. Here we address the question whether all tumor cells predominantly employ selectin-dependent leukocyte-like adhesion cascade (SDAC) or whether they use integrin mediated adhesion for OvCa progression as well...
September 14, 2017: Biochimie
https://www.readbyqxmd.com/read/28918914/analysis-of-genomes-and-transcriptomes-of-hepatocellular-carcinomas-identifies-mutations-and-gene-expression-changes-in-the-transforming-growth-factor-beta-pathway-short-title-prognostic-significance-of-tgf-%C3%AE-signature-in-liver-cancer
#12
Jian Chen, Sobia Zaidi, Shuyun Rao, Jiun-Sheng Chen, Liem Phan, Patrizia Farci, Xiaoping Su, Kirti Shetty, Jon White, Fausto Zamboni, Xifeng Wu, Asif Rashid, Nagarajan Pattabiraman, Raja Mazumder, Anelia Horvath, Ray-Chang Wu, Shulin Li, Cuiying Xiao, Chu-Xia Deng, David A Wheeler, Bibhuti Mishra, Rehan Akbani, Lopa Mishra
BACKGROUND & AIMS: Development of hepatocellular carcinoma (HCC) is associated with alterations in the transforming growth factor beta (TGFβ) signaling pathway, which regulates liver inflammation and can have tumor suppressor or promoter activities. Little is known about the roles of specific members of this pathway at specific of HCC development. We took an integrated approach to identify and validate the effects of changes in this pathway in HCC and identify therapeutic targets. METHODS: We performed transcriptome analyses for a total of 488 HCCs that include data from The Cancer Genome Atlas...
September 14, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28918159/identification-of-circular-rna-in-the-bombyx-mori-silk-gland
#13
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Bombyx mori is an economically important holometabolous lepidopteran insect. In B. mori endogenous noncoding RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs play crucial biological functions in metamorphosis and sex determination. In addition, circular RNAs (circRNAs) have been recently identified as noncoding RNAs in most common model organisms and show potential as gene regulators. However, to date, there have been few studies on the circRNAs present in the B. mori genome conducted to date. Here, we identified 3916 circRNAs by deep circular transcriptome sequencing using the silk gland of B...
September 13, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28918038/strategies-for-in%C3%A2-vivo-screening-and-mitigation-of-hepatotoxicity-associated-with-antisense-drugs
#14
Piotr J Kamola, Klio Maratou, Paul A Wilson, Kay Rush, Tanya Mullaney, Tom McKevitt, Paula Evans, Jim Ridings, Probash Chowdhury, Aude Roulois, Ann Fairchild, Sean McCawley, Karen Cartwright, Nigel J Gooderham, Timothy W Gant, Kitty Moores, Stephen A Hughes, Mark R Edbrooke, Kenneth Clark, Joel D Parry
Antisense oligonucleotide (ASO) gapmers downregulate gene expression by inducing enzyme-dependent degradation of targeted RNA and represent a promising therapeutic platform for addressing previously undruggable genes. Unfortunately, their therapeutic application, particularly that of the more potent chemistries (e.g., locked-nucleic-acid-containing gapmers), has been hampered by their frequent hepatoxicity, which could be driven by hybridization-mediated interactions. An early de-risking of this liability is a crucial component of developing safe, ASO-based drugs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916813/genome-sequencing-reveals-metabolic-and-cellular-interdependence-in-an-amoeba-kinetoplastid-symbiosis
#15
Goro Tanifuji, Ugo Cenci, Daniel Moog, Samuel Dean, Takuro Nakayama, Vojtěch David, Ivan Fiala, Bruce A Curtis, Shannon J Sibbald, Naoko T Onodera, Morgan Colp, Pavel Flegontov, Jessica Johnson-MacKinnon, Michael McPhee, Yuji Inagaki, Tetsuo Hashimoto, Steven Kelly, Keith Gull, Julius Lukeš, John M Archibald
Endosymbiotic relationships between eukaryotic and prokaryotic cells are common in nature. Endosymbioses between two eukaryotes are also known; cyanobacterium-derived plastids have spread horizontally when one eukaryote assimilated another. A unique instance of a non-photosynthetic, eukaryotic endosymbiont involves members of the genus Paramoeba, amoebozoans that infect marine animals such as farmed fish and sea urchins. Paramoeba species harbor endosymbionts belonging to the Kinetoplastea, a diverse group of flagellate protists including some that cause devastating diseases...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916745/cadmium-effects-on-dna-and-protein-metabolism-in-oyster-crassostrea-gigas-revealed-by-proteomic-analyses
#16
Jie Meng, Wenxiong Wang, Li Li, Qi Yin, Guofan Zhang
Marine molluscs, including oysters, can concentrate high levels of cadmium (Cd) in their soft tissues, but the molecular mechanisms of Cd toxicity remain speculative. In this study, Pacific oysters (Crassostrea gigas) were exposed to Cd for 9 days and their gills were subjected to proteomic analysis, which were further confirmed with transcriptomic analysis. A total of 4,964 proteins was quantified and 515 differentially expressed proteins were identified in response to Cd exposure. Gene Ontology enrichment analysis revealed that excess Cd affected the DNA and protein metabolism...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916559/omics-analyses-of-trichoderma-reesei-cbs999-97-and-qm6a-indicate-a-relevance-of-female-fertility-for-cazyme-and-transporter-levels
#17
Doris Tisch, Kyle R Pomraning, James R Collett, Michael Freitag, Scott E Baker, Chia-Ling Chen, Paul Wei-Che Hsu, Yu Chien Chuang, Andre Schuster, Christoph Dattenböck, Eva Stappler, Michael Sulyok, Stefan Böhmdorfer, Josua Oberlerchner, Ting-Fang Wang, Monika Schmoll
The filamentous fungus Trichoderma reesei is predominantly found in the tropics, but also in more temperate regions, such as Europe and is widely known as producer of high amounts of plant cell wall degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from female sterile QM6a, but can cross sexually with QM6a. Transcriptome data for growth on cellulose showed that entire CAZyme families are consistently differentially regulated between these strains...
September 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28916376/transcriptome-profiling-of-the-plutella-xylostella-lepidoptera-plutellidae-ovary-reveals-genes-involved-in-oogenesis
#18
Lu Peng, Lei Wang, Yi-Fan Yang, Ming-Min Zou, Wei-Yi He, Yue Wang, Qing Wang, Liette Vasseur, Min-Sheng You
BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916360/trancriptome-profiles-of-amur-sturgeon-spleen-in-response-to-yersinia-ruckeri-infection
#19
Shaowu Li, Ying Zhang, Yongsheng Cao, Di Wang, Hongbai Liu, Tongyan Lu
Yersinia ruckeri (YR) is the causative agent of yersiniosis which has caused significant economic losses in fish culture worldwide, including in Amur sturgeon (Acipenser schrenckii) culture. To better understand the mechanism of the immune responses to YR in Amur sturgeon, the transcriptomic profiles of the spleens from YR-infected and non-infected groups were obtained using RNA-seq techniques. The de novo assemblies yielded totally 145 670 unigenes from the two libraries. The total numbers of transcripts in YR-infected and non-infected groups were from 110 893 to 147 336, with the mean length varying from 560 to 631 (N50: from 882 to 1083)...
September 12, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28915794/genome-sequence-of-the-ectophytic-fungus-ramichloridium-luteum-reveals-unique-evolutionary-adaptations-to-plant-surface-niche
#20
Bo Wang, Xiaofei Liang, Mark L Gleason, Rong Zhang, Guangyu Sun
BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS: The R...
September 15, 2017: BMC Genomics
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