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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/28107606/dishevelled-segment-polarity-protein-3-dvl3-a-novel-and-easily-applicable-recurrence-predictor-in-localized-prostate-adenocarcinoma
#2
Pil-Jong Kim, Ji Y Park, Hong-Gee Kim, Yong Mee Cho, Heounjeong Go
OBJECTIVE: To identify new biomarkers for the biochemical recurrence (BCR) of prostate adenocarcinoma. PATIENTS AND METHODS: Clinical information of 500 prostate adenocarcinoma patients and their 152 RNA-sequencing and protein-array data from The Cancer Genome Atlas (TCGA) were separated into a discovery-set and a validation-set. Each dataset was analyzed according to the Gleason grade groups reflecting BCR. The results obtained from the analysis using TCGA dataset were confirmed by immunohistochemistry analyses of the confirmation cohort composed of 395 localized prostate adenocarcinoma patients...
January 20, 2017: BJU International
https://www.readbyqxmd.com/read/28107589/serum-lincrna-p21-as-a-potential-biomarker-of-liver-fibrosis-in-chronic-hepatitis-b-patients
#3
Fujun Yu, Guangyao Zhou, Kate Huang, XuFei Fan, Guojun Li, Bicheng Chen, Peihong Dong, Jianjian Zheng
Serum long non-coding RNAs (lncRNAs) are emerging as promising biomarkers for various human diseases. The aim of this study was to investigate the feasibility of using serum long intergenic non-coding RNA-p21 (lincRNA-p21) as a biomarker for chronic hepatitis B patients. Serum lincRNA-p21 levels were quantified using real-time PCR in 417 CHB patients and 363 healthy controls. The promoter methylation level of lincRNA-p21 was detected using bisulfite-sequencing analysis in primary hepatic stellate cells (HSCs)...
January 20, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28107438/first-insights-into-the-subterranean-crustacean-bathynellacea-transcriptome-transcriptionally-reduced-opsin-repertoire-and-evidence-of-conserved-homeostasis-regulatory-mechanisms
#4
Bo-Mi Kim, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Inhye Ahn, Chi-Woo Lee, Joo-Lae Cho, Gi-Sik Min, Hyun Park
Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i...
2017: PloS One
https://www.readbyqxmd.com/read/28107426/identification-of-micrornas-in-response-to-drought-in-common-wild-rice-oryza-rufipogon-griff-shoots-and-roots
#5
Jing-Wen Zhang, Yan Long, Man-de Xue, Xing-Guo Xiao, Xin-Wu Pei
BACKGROUND: Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. RESULTS: In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where 'R' indicates the root tissue and 'L' indicates the shoot tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28107423/characterization-of-the-drug-resistance-profiles-of-patients-infected-with-crf07_bc-using-phenotypic-assay-and-ultra-deep-pyrosequencing
#6
Szu-Wei Huang, Wei-You Li, Wen-Hung Wang, Yu-Ting Lin, Chih-Hung Chou, Marcelo Chen, Hsien-Da Huang, Yen-Hsu Chen, Po-Liang Lu, Sheng-Fan Wang, Shinichi Oka, Yi-Ming Arthur Chen
The usefulness of ultra-deep pyrosequencing (UDPS) for the diagnosis of HIV-1 drug resistance (DR) remains to be determined. Previously, we reported an explosive outbreak of HIV-1 circulating recombinant form (CRF) 07_BC among injection drug users (IDUs) in Taiwan in 2004. The goal of this study was to characterize the DR of CRF07_BC strains using different assays including UDPS. Seven CRF07_BC isolates including 4 from early epidemic (collected in 2004-2005) and 3 from late epidemic (collected in 2008) were obtained from treatment-naïve patient's peripheral blood mononuclear cells...
2017: PloS One
https://www.readbyqxmd.com/read/28107419/a-new-israeli-tobamovirus-isolate-infects-tomato-plants-harboring-tm-22-resistance-genes
#7
Neta Luria, Elisheva Smith, Victoria Reingold, Ilana Bekelman, Moshe Lapidot, Ilan Levin, Nadav Elad, Yehudit Tam, Noa Sela, Ahmad Abu-Ras, Nadav Ezra, Ami Haberman, Liron Yitzhak, Oded Lachman, Aviv Dombrovsky
An outbreak of a new disease infecting tomatoes occurred in October-November 2014 at the Ohad village in Southern Israel. Symptomatic plants showed a mosaic pattern on leaves accompanied occasionally by narrowing of leaves and yellow spotted fruit. The disease spread mechanically and rapidly reminiscent of tobamovirus infection. Epidemiological studies showed the spread of the disease in various growing areas, in the South and towards the Southeast and Northern parts of the country within a year. Transmission electron microscope (TEM) analysis showed a single rod-like form characteristic to the Tobamovirus genus...
2017: PloS One
https://www.readbyqxmd.com/read/28107222/romidepsin-induced-hiv-1-viremia-during-effective-art-contains-identical-viral-sequences-with-few-deleterious-mutations
#8
Anni Winckelmann, Kirston Barton, Bonnie Hiener, Timothy E Schlub, Wei Shao, Thomas A Rasmussen, Lars Østergaard, Ole S Søgaard, Martin Tolstrup, Sarah Palmer
OBJECTIVE: To investigate the origin of the HIV-1 viremia induced by the latency-reversing agent romidepsin. DESIGN: Six individuals on suppressive antiretroviral therapy received romidepsin administered intravenously once weekly for three consecutive weeks. CD4+ T-cells were obtained at baseline, following the second and third romidepsin infusion, and 10 weeks after the final romidepsin treatment. METHODS: Single-genome sequencing of the env region was used to genetically characterize the virus from proviral DNA, the transcribed cell-associated RNA and the plasma RNA pool...
January 19, 2017: AIDS
https://www.readbyqxmd.com/read/28107200/variants-in-anril-gene-correlated-with-its-expression-contribute-to-myocardial-infarction-risk
#9
Jie Cheng, Meng-Yun Cai, Yu-Ning Chen, Zhi-Cheng Li, Sai-Sai Tang, Xi-Li Yang, Can Chen, Xinguang Liu, Xing-Dong Xiong
ANRIL (antisense non-coding RNA in the INK4 locus), located at the 9p21.3 locus, has been known to be closely associated with the risk of coronary artery disease (CAD). To date, studies of the 9p21.3 variants on CAD risk mainly focus on the non-coding region of ANRIL. However, the biological significance of the variants on ANRIL promoter and exons is still unknown. Here we investigate whether the variants on ANRIL promoter and exons have an effect on myocardial infarction (MI) risk, and further analyze the association of these variants with the expression of ANRIL transcript...
January 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28106924/incidence-clinicopathologic-features-and-fusion-transcript-landscape-of-translocation-renal-cell-carcinomas
#10
Marion Classe, Gabriel G Malouf, Xiaoping Su, Hui Yao, Erika J Thompson, Denaha J Doss, Valérie Grégoire, Julien Lenobin, Jean-Christophe Fantoni, Hélène Sudour-Bonnange, David Khayat, Sébastien Aubert, Nizar M Tannir, Xavier Leroy
AIMS: Translocation renal cell carcinoma (tRCC) is a rare subtype of kidney tumour characterized by translocations involving the transcription factor TFE3 or TFEB. tRCC was introduced into the World Health Organization classification in 2004, but much is still unknown about the natural history, clinicopathologic features, and outcomes of the disease. The aim of this study was to describe the landscape of fusion transcript in a large single-institution series of FISH confirmed tRCCs and then to confront it to morphological and clinical data...
January 20, 2017: Histopathology
https://www.readbyqxmd.com/read/28106800/frequency-and-pathological-phenotype-of-bovine-astrovirus-ch13-neuros1-infection-in-neurologically-diseased-cattle-towards-assessment-of-causality
#11
Senija Selimovic-Hamza, Céline L Boujon, Monika Hilbe, Anna Oevermann, Torsten Seuberlich
Next-generation sequencing (NGS) has opened up the possibility of detecting new viruses in unresolved diseases. Recently, astrovirus brain infections have been identified in neurologically diseased humans and animals by NGS, among them bovine astrovirus (BoAstV) CH13/NeuroS1, which has been found in brain tissues of cattle with non-suppurative encephalitis. Only a few studies are available on neurotropic astroviruses and a causal relationship between BoAstV CH13/NeuroS1 infections and neurological disease has been postulated, but remains unproven...
January 18, 2017: Viruses
https://www.readbyqxmd.com/read/28106375/acinetodin-and-klebsidin-rna-polymerase-targeting-lasso-peptides-produced-by-human-isolates-of-acinetobacter-gyllenbergii-and-klebsiella-pneumoniae
#12
Mikhail Metelev, Anatolii Arseniev, Leah B Bushin, Konstantin Kuznedelov, Tatiana O Artamonova, Ruslan Kondratenko, Mikhail Khodorkovskii, Mohammad R Seyedsayamdost, Konstantin Severinov
We report the bioinformatic prediction and structural validation of two lasso peptides, acinetodin and klebsidin, encoded by the genomes of several human-associated strains of Acinetobacter and Klebsiella. Computation of the three-dimensional structures of these peptides using NMR NOESY constraints verifies that they contain a lasso motif. Despite the lack of sequence similarity to each other or to microcin J25, a prototypical lasso peptide and transcription inhibitor from Escherichia coli, acinetodin and klebsidin also inhibit transcript elongation by the E...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28106309/transposable-elements-tes-contribute-to-stress-related-long-intergenic-noncoding-rnas-in-plants
#13
Dong Wang, Zhipeng Qu, Lan Yang, Qingzhu Zhang, Zhi-Hong Liu, Trung Do, David L Adelson, Zhen-Yu Wang, Iain Searle, Jian-Kang Zhu
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown...
January 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28106276/crispr-cas9-mediated-deletion-of-c1eis-inhibits-chicken-embryonic-stem-cell-differentiation-into-male-germ-cells-gallus-gallus
#14
Qisheng Zuo, Kai Jin, Yingjie Wang, Jiuzhou Song, Yani Zhang, Bichun Li
We previously found that C1EIS is preferentially expressed in Chicken spermatogonial stem cells (SSCs) by RNA sequencing (RNA-seq), so our current study focused on C1EIS's role in Chicken embryonic stem cells (ESCs) differentiation into male germ cells. We constructed a CRISPR/Cas9 vector targeting C1EIS. T7 endonuclease I (T7EI) digestion method and sequencing of TA cloning were used to detect the knock-out efficiency of the Single guide RNA (sgRNA) after the cas9/gRNA vector transfected into D fibroblasts 1(DF-1), ESCs and Chicken embryos...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28106101/the-systematic-analysis-of-coding-and-long-non-coding-rnas-in-the-sub-chronic-and-chronic-stages-of-spinal-cord-injury
#15
Raquel Cuevas-Diaz Duran, Han Yan, Yiyan Zheng, Xingfan Huang, Raymond Grill, Dong H Kim, Qilin Cao, Jia Qian Wu
Spinal cord injury (SCI) remains one of the most debilitating neurological disorders and the majority of SCI patients are in the chronic phase. Previous studies of SCI have usually focused on few genes and pathways at a time. In particular, the biological roles of long non-coding RNAs (lncRNAs) have never been characterized in SCI. Our study is the first to comprehensively investigate alterations in the expression of both coding and long non-coding genes in the sub-chronic and chronic stages of SCI using RNA-Sequencing...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105979/human-dental-pulp-stem-cells-are-more-effective-than-human-bone-marrow-derived-mesenchymal-stem-cells-in-cerebral-ischemic-injury
#16
Miyeoun Song, Jae-Hyung Lee, Jinhyun Bae, Youngmin Bu, Eun-Cheol Kim
We compared the therapeutic effects and mechanism of transplanted human dental pulp stem cells (hDPSCs) and human bonemarrow-derived mesenchymal stem cells (hMSCs) in a stroke model of rats and an <i>in vitro</i> ischemic model. Both hDPSCs- and hMSCs- intravenously injected rats 24&#8201;h after middle cerebral artery occlusion showed improved functional recovery and reduced infarct volume versus control rats, but the hDPSCs group showed greater reduction in infarct volume than hMSCs. The positive area for the endothelial cell marker was greater in the lesion boundary areas in the hDPSCs group than with hMSCs...
January 20, 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28105955/small-rna-profiles-in-soybean-primary-root-tips-under-water-deficit
#17
Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais-Brière, Andrew D Farmer, Gregory D May, Martin Crespi, Henry T Nguyen, Ramanjulu Sunkar
BACKGROUND: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#18
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#19
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105932/genes-of-susceptibility-to-early-neurodegenerative-changes-in-the-rat-retina-and-brain-analysis-by-means-of-congenic-strains
#20
Elena E Korbolina, Anna A Zhdankina, Anzhela Zh Fursova, Oyuna S Kozhevnikova, Natalia G Kolosova
BACKGROUND: There has been considerable interest in discovery of the genetic architecture of complex traits, particularly age-related neurodegenerative disorders. To predict disease risk and to understand its genetic basis in humans, it is necessary to study animal models. Our previous research on the accelerated-senescence OXYS strain has revealed two quantitative trait loci (QTLs) on rat chromosome 1 that are associated with early cataract and/or retinopathy as well as with behavioral abnormalities...
December 22, 2016: BMC Genetics
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