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https://www.readbyqxmd.com/read/29045404/transcriptomic-responses-of-biomphalaria-pfeifferi-to-schistosoma-mansoni-investigation-of-a-neglected-african-snail-that-supports-more-s-mansoni-transmission-than-any-other-snail-species
#1
Sarah K Buddenborg, Lijing Bu, Si-Ming Zhang, Faye D Schilkey, Gerald M Mkoji, Eric S Loker
BACKGROUND: Biomphalaria pfeifferi is highly compatible with the widespread human-infecting blood fluke Schistosoma mansoni and transmits more cases of this parasite to people than any other snail species. For these reasons, B. pfeifferi is the world's most important vector snail for S. mansoni, yet we know relatively little at the molecular level regarding the interactions between B. pfeifferi and S. mansoni from early-stage sporocyst transformation to the development of cercariae. METHODOLOGY/PRINCIPAL FINDINGS: We sought to capture a portrait of the response of B...
October 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29040625/rise-a-database-of-rna-interactome-from-sequencing-experiments
#2
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yucheng T Yang, Qiangfeng Cliff Zhang
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast...
October 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040619/sublethal-effects-of-the-neonicotinoid-insecticide-thiamethoxam-on-the-transcriptome-of-the-honey-bees-hymenoptera-apidae
#3
Teng-Fei Shi, Yu-Fei Wang, Fang Liu, Lei Qi, Lin-Sheng Yu
Neonicotinoid insecticides are now the most widely used insecticides in the world. Previous studies have indicated that sublethal doses of neonicotinoids impair learning, memory capacity, foraging, and immunocompetence in honey bees (Apis mellifera, Linnaeus) (Hymenoptera: Apidae). Despite these, few studies have been carried out on the molecular effects of neonicotinoids. In this study, we focus on the second-generation neonicotinoid thiamethoxam, which is currently widely used in agriculture to protect crops...
October 11, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29036633/rna-sequencing-of-brassica-napus-reveals-cellular-redox-control-of-sclerotinia-infection
#4
Ian J Girard, Chaobo Tong, Michael G Becker, Xingyu Mao, Junyan Huang, Teresa de Kievit, W G Dilantha Fernando, Shengyi Liu, Mark F Belmonte
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathogen interactions at the molecular level, we have yet to fully understand the biological processes and underlying gene regulatory networks responsible for determining disease outcomes. Using global RNA sequencing, we profiled gene activity at the first point of infection on the leaf surface 24 hours after pathogen exposure in susceptible (B...
September 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036529/itsonedb-a-comprehensive-collection-of-eukaryotic-ribosomal-rna-internal-transcribed-spacer-1-its1-sequences
#5
Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034472/protective-effects-of-curcumin-against-aflatoxicosis-a-comprehensive-review
#6
REVIEW
Mohammad Mohajeri, Behzad Behnam, Arrigo F G Cicero, Amirhossein Sahebkar
Aflatoxicosis is a deleterious medical condition that results from aflatoxins (AFs) or ochratoxins (OTs). Contamination with these toxins exerts detrimental effects on the liver, kidneys, reproductive organs, and also on immunological and cardiovascular systems. Aflatoxicosis is closely associated with overproduction of reactive oxygen species (ROS) as key contributors to oxidative and nitrosative stress responses, and subsequent damages to lipids, proteins, RNA, and DNA. The main target organ for AF toxicity is the liver, where DNA adducts, degranulation of endoplasmic reticulum, increased hepatic lipid peroxide, GSH depletion, mitochondrial dysfunction, and reduction of enzymatic and non-enzymatic antioxidants are manifestations of aflatoxicosis...
October 16, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29033905/a-review-on-the-applications-of-next-generation-sequencing-technologies-as-applied-to-food-related-microbiome-studies
#7
REVIEW
Yu Cao, Séamus Fanning, Sinéad Proos, Kieran Jordan, Shabarinath Srikumar
The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29032634/prevalence-of-hepatitis-c-infection-and-its-associated-factors-in-healthy-adults-without-identifiable-route-of-transmission
#8
Ngai Sze Wong, Cheuk Kwong Lee, Siu Cheung Ng, Hoi Kei Wong, Denise P C Chan, Shui Shan Lee
While hepatitis C virus (HCV) infection is long known to be associated with parenteral exposure, the specific route of transmission is not identified in a proportion of infected patients. Taking blood donors as the surrogate of healthy adults in the community in Hong Kong, we identified 91 HCV infected donors (≤0.02% positive rate) in 2014-2016, of whom 46 were recruited in a mixed method study to examine their transmission routes. A majority (75%) of the recruited donors were HCV RNA positive, with the predominant subtypes being 1b and 6a...
October 15, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/29028266/circpro-an-integrated-tool-for-the-identification-of-circrnas-with-protein-coding-potential
#9
Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen
Summary: Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5' caps or 3' polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027387/safety-and-efficacy-of-ziagen-abacavir-sulfate-in-hiv-infected-korean-patients
#10
Heawon Ann, Ki Hyon Kim, Hyun Young Choi, Hyun Ha Chang, Sang Hoon Han, Kye Hyung Kim, Jin Soo Lee, Yeon Sook Kim, Kyung Hwa Park, Young Keun Kim, Jang Wook Sohn, Na Ra Yun, Chang Seop Lee, Young Wha Choi, Yil Seob Lee, Shin Woo Kim
BACKGROUND: Abacavir is a widely-used nucleoside reverse transcriptase inhibitor for the treatment of human immunodeficiency virus (HIV) infection. Mandatory postmarketing surveillance was conducted in Korea to monitor the safety and evaluate the effectiveness of Ziagen® (abacavir sulfate 300 mg; ViiV Healthcare, Middlesex, UK). MATERIALS AND METHODS: An open-label, multi-center, non-interventional postmarketing surveillance study was conducted from June 2010 to June 2016 to monitor the safety and effectiveness of Ziagen across 12 hospitals in Korea...
September 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/29023590/de-novo-assembly-and-analysis-of-the-transcriptome-of-rumex-patientia-l-during-cold-stress
#11
Jianxin Liu, Yongqing Xu, Liguo Zhang, Wei Li, Zhenxue Cai, Fei Li, Mu Peng, Fenglan Li, Baozhong Hu
BACKGROUND: Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. patientia under normal and cold conditions to evaluate how it responds to cold stress. RESULTS: After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28989747/molecular-trade-offs-in-rna-ligases-affected-the-modular-emergence-of-complex-ribozymes-at-the-origin-of-life
#12
Nisha Dhar, Marc S Weinberg, Richard E Michod, Pierre M Durand
In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing...
September 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28986523/bagging-nearest-neighbor-prediction-independence-test-an-efficient-method-for-nonlinear-dependence-of-two-continuous-variables
#13
Yi Wang, Yi Li, Xiaoyu Liu, Weilin Pu, Xiaofeng Wang, Jiucun Wang, Momiao Xiong, Yin Yao Shugart, Li Jin
Testing dependence/correlation of two variables is one of the fundamental tasks in statistics. In this work, we proposed an efficient method for nonlinear dependence of two continuous variables (X and Y). We addressed this research question by using BNNPT (Bagging Nearest-Neighbor Prediction independence Test, software available at https://sourceforge.net/projects/bnnpt/). In the BNNPT framework, we first used the value of X to construct a bagging neighborhood structure. We then obtained the out of bag estimator of Y based on the bagging neighborhood structure...
October 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28985305/genome-sequencing-and-comparative-genomics-reveal-the-potential-pathogenic-mechanism-of-cercospora-sojina-hara-on-soybean
#14
Xuming Luo, Jidong Cao, Junkai Huang, Zongyi Wang, Zhengyan Guo, Yihua Chen, Shumei Ma, Jun Liu
Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C...
September 18, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28983675/efficacy-and-safety-of-sofosbuvir-plus-ribavirin-for-treatment-of-cirrhotic-patients-with-genotype-4-hepatitis-c-virus-in-real-life-clinical-practice
#15
Sherief Abd-Elsalam, Mohamed Sharaf-Eldin, Shaimaa Soliman, Asem Elfert, Rehab Badawi, Youssef K Ahmad
Egypt has the highest hepatitis C virus (HCV) prevalence in the world. Sofosbuvir is a new highly effective drug for treatment of HCV infection. Compared to previous treatments, sofosbuvir-based regimens provide a higher cure rate, fewer side effects, and a two- to fourfold reduced duration of therapy. The aim of this study was to evaluate the antiviral efficacy, safety, and tolerability of sofosbuvir plus ribavirin in Egyptian patients with liver cirrhosis due to chronic HCV infection. We studied 2400 cirrhotic Egyptian patients with chronic HCV infection who were treated with dual therapy with sofosbuvir and ribavirin for 24 weeks...
October 5, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28981779/the-osabf1-transcription-factor-improves-drought-tolerance-by-activating-the-transcription-of-cor413-tm1-in-rice
#16
Chunyu Zhang, Cong Li, Jun Liu, Yandong Lv, Chunsheng Yu, Hongyu Li, Tao Zhao, Bin Liu, Jianhua Zhang
Water deprivation causes substantial losses in crop yields around the world. In this study, we show that when overexpressed in transgenic rice (Oryza sativa), the bZIP transcription factor OsABF1 confers distinctly different drought-tolerance phenotypes when tethered to the transcriptional activator VP16 versus the transcriptional repressor EAR. We performed chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) assays on transgenic rice lines and determined that OsABF1 binds to DNA sequences containing an ACGT core motif...
July 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28981563/identification-of-genes-related-to-high-royal-jelly-production-in-the-honey-bee-apis-mellifera-using-microarray-analysis
#17
Hongyi Nie, Xiaoyan Liu, Jiao Pan, Wenfeng Li, Zhiguo Li, Shaowu Zhang, Shenglu Chen, Xiaoqing Miao, Nenggan Zheng, Songkun Su
China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees...
October 2, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28978863/myeloid-neoplasms-in-the-world-health-organization-2016-classification
#18
Norio Asou
In the 2016 revision of the World Health Organization (WHO) classification, the categories of myeloid neoplasms have not been revised significantly from the 2008 fourth edition. However, recent discovery of molecular abnormalities provides a new perspective regarding the diagnostic and prognostic markers. In myeloproliferative neoplasms, the identification of CALR gene mutation, in addition to the JAK2 and MPL mutations, has impacted the diagnostic criteria. In myelodysplastic syndromes and acute myeloid leukemia, in addition to alterations in the transcription factors and signal transduction pathways, discovery of gene mutations in the epigenetic regulators that are involved in DNA methylation, histone modification, cohesin complex, and RNA splicing, by comprehensive genetic analyses, has improved our understanding of the pathobiology of these diseases...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28978701/processing-of-potato-spindle-tuber-viroid-pstvd-rnas-in-yeast-a-nonconventional-host
#19
Dillon Friday, Priyadarshini Mukkara, Robert A Owens, Tilman Baumstark, Michael F Bruist
Potato spindle tuber viroid (PSTVd) is a circular, single-stranded, noncoding RNA plant pathogen that is a useful model for the processing of noncoding RNA in eukaryotes. Infective PSTVd circles are replicated via an asymmetric rolling circle mechanism to form linear multimeric RNAs. An endonuclease cleaves these into monomers; a ligase seals these into mature circles. All eukaryotes may have such enzymes for processing noncoding RNA. As a test, we investigated the processing of three PSTVd RNA constructs in the yeast Saccharomyces cerevisiae...
October 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28976967/a-viral-sm-class-rna-base-pairs-with-mrnas-and-recruits-micrornas-to-inhibit-apoptosis
#20
Carlos Gorbea, Tim Mosbruger, Demián Cazalla
Viruses express several classes of non-coding RNAs; the functions and mechanisms by which most of these act are unknown. Herpesvirus saimiri, a γ-herpesvirus that establishes latency in the T cells of New World primates and has the ability to cause aggressive leukaemias and lymphomas in non-natural hosts, expresses seven small nuclear uracil-rich non-coding RNAs (called HSURs) in latently infected cells. These HSURs associate with Sm proteins, and share biogenesis and structural features with cellular Sm-class small nuclear RNAs...
October 12, 2017: Nature
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