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Integrative genomics

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https://www.readbyqxmd.com/read/28918530/exogenous-and-endogenous-increase-in-fungal-ggpp-increased-fungal-taxol-production
#1
Sameh S M Soliman, Kareem A Mosa, Ali A El-Keblawy, Mohamed I Husseiny
Taxol is an anticancer identified in both endophytic fungus and its host plant. Plant Taxol is a diterpenoid with geranylgeranyl diphosphate (GGPP) mediates the biosynthesis of its terpenoid moiety. Previous report has suggested that fungal Taxol may require terpenoid pathway for its biosynthesis. Here in this study, feeding a Taxol-producing endophytic fungus (Paraconiothyrium SSM001) with terpenoid precursors including isopentenyl pyrophosphate (IPP, isoprene) and GGPP enhanced Taxol production threefold and fivefold, respectively, compared to the control...
September 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28916934/cohort-research-in-omics-and-preventive-medicine
#2
Yi Shen, Sheng Zhang, Jie Zhou, Jiajia Chen
Cohort studies are observational studies in which the investigator determines the exposure status of subjects and then follows them for subsequent outcomes. The incidence of outcomes is observed in the exposed group and compared with that in a nonexposed group. Recently, new epidemiologic strategies have encouraged cohort research information exchange and cooperation to improve the cognition of disease etiology, such as case-cohort design and nested case-control study, which is available for "omics" data. Meanwhile, large-scale cohort studies using a prospective multiple design and long follow-ups have explored some of the challenges in preventive medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916644/subset-and-tissue-defined-stat5-thresholds-control-homeostasis-and-function-of-innate-lymphoid-cells
#3
Alejandro V Villarino, Giuseppe Sciumè, Fred P Davis, Shigeru Iwata, Beatrice Zitti, Gertraud W Robinson, Lothar Hennighausen, Yuka Kanno, John J O'Shea
Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we demonstrate that the signal-dependent transcription factor (TF) STAT5 is critical for accumulation of all known ILC subsets in mice and reveal a hierarchy of STAT5 dependency for populating lymphoid and nonlymphoid tissues. We apply transcriptome and genomic distribution analyses to define a STAT5 gene signature in natural killer (NK) cells, the prototypical ILC subset, and provide a systems-based molecular rationale for its key functions downstream of IL-15...
September 15, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28916376/transcriptome-profiling-of-the-plutella-xylostella-lepidoptera-plutellidae-ovary-reveals-genes-involved-in-oogenesis
#4
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/28915836/changes-in-dna-methylation-in-na%C3%A3-ve-t-helper-cells-regulate-the-pathophysiological-state-in-minimal-change-nephrotic-syndrome
#5
Yasuko Kobayashi, Akira Aizawa, Takumi Takizawa, Katsuhide Igarashi, Izuho Hatada, Hirokazu Arakawa
BACKGROUND: DNA methylation plays a crucial role in regulating transcription, and changes in DNA methylation affect gene expression and disease development. Minimal change nephrotic syndrome (MCNS) has been reported to involve immunological disturbances. Since the characteristic features of the disease include recurrent relapse and sex and age preference, the disease pathogenesis may be partly related to epigenetic changes. However, little is known about these changes. METHODS: We analyzed genome-wide DNA methylation using the microarray-based integrated analysis of methylation by isoschizomers method...
September 15, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28915671/integration-of-alv-into-ctdspl-and-ctdspl2-genes-in-b-cell-lymphomas-promotes-cell-immortalization-migration-and-survival
#6
Shelby Winans, Alyssa Flynn, Sanandan Malhotra, Vidya Balagopal, Karen L Beemon
Avian leukosis virus induces tumors in chickens by integrating into the genome and altering expression of nearby genes. Thus, ALV can be used as an insertional mutagenesis tool to identify novel genes involved in tumorigenesis. Deep sequencing analysis of viral integration sites has identified CTDSPL and CTDSPL2 as common integration sites in ALV-induced B-cell lymphomas, suggesting a potential role in driving oncogenesis. We show that in tumors with integrations in these genes, the viral promoter is driving the expression of a truncated fusion transcript...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915660/mass-spectrometry-based-assay-for-the-molecular-diagnosis-of-glioma-concomitant-detection-of-chromosome-1p-19q-codeletion-and-idh1-idh2-and-tert-mutation-status
#7
Chiara Pesenti, Leda Paganini, Laura Fontana, Emanuela Veniani, Letterio Runza, Stefano Ferrero, Silvano Bosari, Maura Menghi, Giovanni Marfia, Manuela Caroli, Rosamaria Silipigni, Silvana Guerneri, Silvia Tabano, Monica Miozzo
The World Health Organization recently revised the diagnosis of glioma, to integrate molecular parameters, including IDH mutations and codeletion (loss of heterozygosity; LOH) of chromosome arms 1p/19q, into the definitions of adult glioma histological subtypes. Mutations in the TERT promoter may also be useful for glioma diagnosis and prognosis. The integration of molecular markers into routine diagnosis requires their rapid and reliable assessment. We propose a MassARRAY (MS)-based test that can identify 1p/19q codeletion using quantitative SNP genotyping and, simultaneously, characterize hotspot mutations in the IDH1, IDH2, and TERT genes in tumor DNA...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915622/genomic-analysis-integrated-whole-exome-sequencing-of-neuroblastomas-identifies-genetic-mutations-in-axon-guidance-pathway
#8
Yuanyuan Li, Miki Ohira, Yong Zhou, Teng Xiong, Wen Luo, Chao Yang, Xiangchun Li, Zhibo Gao, Rui Zhou, Yohko Nakamura, Takehiko Kamijo, Yasuhiko Kaneko, Takeshi Taketani, Junichi Ueyama, Tatsuro Tajiri, Hongyan Zhang, Jian Wang, Huanming Yang, Ye Yin, Akira Nakagawara
Neuroblastoma (NB) is a childhood solid malignant tumor originating from precursor cells of the peripheral nervous system. We have previously established a risk classification system based on DNA copy number profiles. To further explore the pathogenesis of NBs in distinct risk groups, we performed whole-exome sequencing analysis of 57 primary and 7 recurrent/metastatic tumors with unique chromosomal aberration profiles as categorized by our genomic sub-grouping system. Overall, a low frequency of somatic mutations was found...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915241/the-relative-contribution-of-dna-methylation-and-genetic-variants-on-protein-biomarkers-for-human-diseases
#9
Muhammad Ahsan, Weronica E Ek, Mathias Rask-Andersen, Torgny Karlsson, Allan Lind-Thomsen, Stefan Enroth, Ulf Gyllensten, Åsa Johansson
Associations between epigenetic alterations and disease status have been identified for many diseases. However, there is no strong evidence that epigenetic alterations are directly causal for disease pathogenesis. In this study, we combined SNP and DNA methylation data with measurements of protein biomarkers for cancer, inflammation or cardiovascular disease, to investigate the relative contribution of genetic and epigenetic variation on biomarker levels. A total of 121 protein biomarkers were measured and analyzed in relation to DNA methylation at 470,000 genomic positions and to over 10 million SNPs...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28914267/developing-a-common-framework-for-evaluating-the-implementation-of-genomic-medicine-interventions-in-clinical-care-the-ignite-network-s-common-measures-working-group
#10
Lori A Orlando, Nina R Sperber, Corrine Voils, Marshall Nichols, Rachel A Myers, R Ryanne Wu, Tejinder Rakhra-Burris, Kenneth D Levy, Mia Levy, Toni I Pollin, Yue Guan, Carol R Horowitz, Michelle Ramos, Stephen E Kimmel, Caitrin W McDonough, Ebony B Madden, Laura J Damschroder
PurposeImplementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing Genomics in Practice (IGNITE) Network's efforts to promote (i) a broader understanding of genomic medicine implementation research and (ii) the sharing of knowledge generated in the network.MethodsTo facilitate this goal, the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide its approach to identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross-network analyses...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28913952/new-age-ideas-about-age-old-sex-separating-meiosis-from-mating-could-solve-a-century-old-conundrum
#11
Michael Brandeis
Ever since Darwin first addressed it, sexual reproduction reigns as the 'queen' of evolutionary questions. Multiple theories tried to explain how this apparently costly and cumbersome method has become the universal mode of eukaryote reproduction. Most theories stress the adaptive advantages of sex by generating variation, they fail however to explain the ubiquitous persistence of sexual reproduction also where adaptation is not an issue. I argue that the obstacle for comprehending the role of sex stems from the conceptual entanglement of two distinct processes - gamete production by meiosis and gamete fusion by mating (mixis)...
September 14, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28913805/real-time-pcr-for-the-detection-of-precise-transgene-copy-number-in-wheat
#12
Angelica Giancaspro, Agata Gadaleta, Antonio Blanco
Despite the unceasing advances in genetic transformation techniques, the success of common delivery methods still lies on the behavior of the integrated transgenes in the host genome. Stability and expression of the introduced genes are influenced by several factors such as chromosomal location, transgene copy number and interaction with the host genotype. Such factors are traditionally characterized by Southern blot analysis, which can be time-consuming, laborious, and often unable to detect the exact copy number of rearranged transgenes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28912832/unique-organization-and-unprecedented-diversity-of-the-bacteroides-pseudobacteroides-cellulosolvens-cellulosome-system
#13
Olga Zhivin, Bareket Dassa, Sarah Moraïs, Sagar M Utturkar, Steven D Brown, Bernard Henrissat, Raphael Lamed, Edward A Bayer
BACKGROUND: (Pseudo) Bacteroides cellulosolvens is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the B. cellulosolvens genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28912487/cscape-a-tool-for-predicting-oncogenic-single-point-mutations-in-the-cancer-genome
#14
Mark F Rogers, Hashem A Shihab, Tom R Gaunt, Colin Campbell
For somatic point mutations in coding and non-coding regions of the genome, we propose CScape, an integrative classifier for predicting the likelihood that mutations are cancer drivers. Tested on somatic mutations, CScape tends to outperform alternative methods, reaching 91% balanced accuracy in coding regions and 70% in non-coding regions, while even higher accuracy may be achieved using thresholds to isolate high-confidence predictions. Positive predictions tend to cluster in genomic regions, so we apply a statistical approach to isolate coding and non-coding regions of the cancer genome that appear enriched for high-confidence predicted disease-drivers...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912341/the-role-of-blm-helicase-in-homologous-recombination-gene-conversion-tract-length-and-recombination-between-diverged-sequences-in-drosophila
#15
Henry A Ertl, Daniel P Russo, Noori Srivastava, Joseph T Brooks, Thu N Dao, Jeannine R LaRocque
DNA double-strand breaks (DSBs) are a particularly deleterious class of DNA damage that threatens genome integrity. DSBs are repaired by three pathways: non-homologous end joining (NHEJ), homologous recombination (HR), and single-strand annealing (SSA). Drosophila melanogaster Blm (DmBlm) is the ortholog of Saccharomyces cerevisiae SGS1 and human BLM, and has been shown to suppress crossovers in mitotic cells and repair mitotic DNA gaps via HR. To further elucidate the role of DmBlm in repair of a simple DSB, and in particular recombination mechanisms, we utilized the DR-white and DR-white...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912125/blm-helicase-regulates-dna-repair-by-counteracting-rad51-loading-at-dna-double-strand-break-sites
#16
Dharm S Patel, Sarah M Misenko, Joonyoung Her, Samuel F Bunting
The BLM gene product, BLM, is a RECQ helicase that is involved in DNA replication and repair of DNA double-strand breaks by the homologous recombination (HR) pathway. During HR, BLM has both pro- and anti-recombinogenic activities, either of which may contribute to maintenance of genomic integrity. We find that in cells expressing a mutant version of BRCA1, an essential HR factor, ablation of BLM rescues genomic integrity and cell survival in the presence of DNA double-strand breaks. Improved genomic integrity in these cells is linked to a substantial increase in the stability of RAD51 at DNA double-strand break sites and in the overall efficiency of HR...
September 14, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28911628/antifungal-activity-of-momordica-charantia-seed-extracts-toward-the-pathogenic-fungus-fusarium-solani-l
#17
Shuzhen Wang, Yongliang Zheng, Fu Xiang, Shiming Li, Guliang Yang
Momordica charantia L., a vegetable crop with high nutritional value, has been used as an antimutagenic, antihelminthic, anticancer, antifertility, and antidiabetic agent in traditional folk medicine. In this study, the antifungal activity of M. charantia seed extract toward Fusarium solani L. was evaluated. Results showed that M. charantia seed extract effectively inhibited the mycelial growth of F. solani, with a 50% inhibitory rate (IC50) value of 108.934 μg/mL. Further analysis with optical microscopy and fluorescence microscopy revealed that the seed extract led to deformation of cells with irregular budding, loss of integrity of cell wall, as well as disruption of the fungal cell membrane...
October 2016: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28911331/dynamic-dna-methylation-reconfiguration-during-seed-development-and-germination
#18
Taiji Kawakatsu, Joseph R Nery, Rosa Castanon, Joseph R Ecker
BACKGROUND: Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared time-series methylomes of dry and germinating seeds to publicly available seed development methylomes...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911330/extensive-transcriptomic-and-epigenomic-remodelling-occurs-during-arabidopsis-thaliana-germination
#19
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G Lewsey, James Whelan
BACKGROUND: Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911120/phirex-a-programmable-and-red-light-regulated-protein-expression-switch-for-yeast
#20
Lena Hochrein, Fabian Machens, Katrin Messerschmidt, Bernd Mueller-Roeber
Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiReX is based on the combination of a customizable synTALE DNA-binding domain, the VP64 activation domain and the light-sensitive dimerization of the photoreceptor PhyB and its interacting partner PIF3 from Arabidopsis thaliana...
September 6, 2017: Nucleic Acids Research
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