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https://www.readbyqxmd.com/read/29453065/transcriptomic-analysis-of-boron-hyperaccumulation-mechanisms-in-puccinellia-distans
#1
Saniye Elvan Öztürk, Mehmet Göktay, Canan Has, Mehmet Babaoğlu, Jens Allmer, Sami Doğanlar, Anne Frary
Puccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L -1 ) and elevated (500 mg L -1 ) boron levels in hydroponic solution...
February 12, 2018: Chemosphere
https://www.readbyqxmd.com/read/29445367/microbial-communities-and-diversities-in-mudflat-sediments-analyzed-using-a-modified-metatranscriptomic-method
#2
Yong-Wei Yan, Qiu-Yue Jiang, Jian-Gong Wang, Ting Zhu, Bin Zou, Qiong-Fen Qiu, Zhe-Xue Quan
Intertidal mudflats are land-sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29443014/recurrent-ret-gene-rearrangements-in-intraductal-carcinomas-of-salivary-gland
#3
Ilan Weinreb, Justin A Bishop, Simion I Chiosea, Raja R Seethala, Bayardo Perez-Ordonez, Lei Zhang, Yun-Shao Sung, Chun-Liang Chen, Adel Assaad, Bahram R Oliai, Cristina R Antonescu
Intraductal carcinoma (IC) is the World Health Organization designation for lesions previously called low-grade cribriform cystadenocarcinoma. The relationship of IC to salivary duct carcinoma (SDC) is controversial, but currently these are considered distinct entities. It is hypothesized that IC and SDC should have different genomic signatures that may be identifiable by next-generation sequencing. A total of 23 ICs were identified: 14 pure IC and 9 invasive carcinomas with an intraductal component. Five invasive carcinomas were subjected to next-generation paired-end RNA sequencing...
October 25, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29441981/long-non-coding-rna-sox4-promotes-proliferation-and-migration-by-activating-wnt-%C3%AE-catenin-signaling-pathway-in-osteosarcoma
#4
Zhoubin Tian, Guang Yang, Peng Jiang, Laibo Zhang, Jian Wang, Shui Sun
Osteosarcoma is a bone tumor without effective treatment in the world. Recently, long non-coding RNAs (lncRNAs) are considered as essential regulators in cancer progression. LncSox4 plays crucial roles in liver tumor-initiating cells self-renewal and tumor initiation. However, the effect of lncSox4 in osteosarcoma remains largely unclear. Quantitative real-time PCR (qRT-PCR) and Northern blot were performed to detect lncSox4 expressions in osteosarcoma. The functions of lncSox4 in osteosarcoma were determined using cell viability and migration assays...
September 1, 2017: Die Pharmazie
https://www.readbyqxmd.com/read/29434445/behind-the-curtain-of-non-coding-rnas-long-non-coding-rnas-regulating-hepatocarcinogenesis
#5
REVIEW
Aya El Khodiry, Menna Afify, Hend M El Tayebi
Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers worldwide. HCC is the fifth common malignancy in the world and the second leading cause of cancer death in Asia. Long non-coding RNAs (lncRNAs) are RNAs with a length greater than 200 nucleotides that do not encode proteins. lncRNAs can regulate gene expression and protein synthesis in several ways by interacting with DNA, RNA and proteins in a sequence specific manner. They could regulate cellular and developmental processes through either gene inhibition or gene activation...
February 7, 2018: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29431919/host-induced-gene-silencing-of-a-regulator-of-g-protein-signaling-gene-vdrgs1-confers-resistance-to-verticillium-wilt-in-cotton
#6
Jun Xu, Xinyu Wang, Yongqing Li, Jianguo Zeng, Guilin Wang, Chaoyang Deng, Wangzhen Guo
Verticillium wilt (VW), caused by soil-borne fungi of the genus Verticillium, is a serious disease affecting a wide range of plants and leading to a constant and major challenge to agriculture worldwide. Cotton (Gossypium hirsutum) is the world's most important natural textile fiber and oil crop. VW of cotton is a highly devastating vascular disease, however, few resistant germplasms have been reported in cotton. An increasing number of studies have shown that RNA interference (RNAi) based host-induced gene silencing (HIGS) is an effective strategy for improving plant resistance to pathogens by silencing genes essential for the pathogenicity of these pathogens...
February 12, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29424783/repeat-testing-of-low-level-hiv-1-rna-assay-performance-and-implementation-in-clinical-trials
#7
Kirsten White, Will Garner, Lilian Wei, Joseph J Eron, Lijie Zhong, Michael D Miller, Hal Martin, Andrew Plummer, Cecilia Tran-Muchowski, Kim Lindstrom, James Porter, David Piontkowsky, Angela Light, Heinz Reiske, Erin Quirk
OBJECTIVE: Assess the performance of HIV-1 RNA repeat testing of stored samples in cases of low-level viremia during clinical trials. DESIGN: Prospective and retrospective analysis of randomized clinical trial samples and reference standards. METHODS: To evaluate assay variability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test, v2.0, three separate sources of samples were utilized: the World Health Organization (WHO) HIV reference standard (assayed using 50 independent measurements at six viral loads <200 copies/ml), retrospective analysis of four to six aliquots of plasma samples from four clinical trial participants, and prospective repeat testing of 120 samples from participants in randomized trials with low-level viremia...
February 8, 2018: AIDS
https://www.readbyqxmd.com/read/29420906/development-of-an-indel-polymorphism-database-for-jute-via-comparative-transcriptome-analysis
#8
Zemao Yang, Zhigang Dai, Dongwei Xie, Jiquan Chen, Qing Tang, Chaohua Cheng, Ying Xu, Tingzhang Wang, Jianguang Su
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31...
February 8, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29420865/a-novel-approach-to-wildlife-transcriptomics-provides-evidence-of-disease-mediated-differential-expression-and-changes-to-the-microbiome-of-amphibian-populations
#9
Lewis J Campbell, S Austin Hammond, Stephen J Price, Manmohan D Sharma, Trenton W J Garner, Inanc Birol, Caren C Helbing, Lena Wilfert, Amber G F Griffiths
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R...
February 8, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29419284/dna-s-encounter-with-ultraviolet-light-an-instinct-for-self-preservation
#10
Adam Barlev, Dipankar Sen
Photochemical modification is the major class of environmental damage suffered by DNA, the genetic material of all free-living organisms. Photolyases are enzymes that carry out direct photochemical repair (photoreactivation) of covalent pyrimidine dimers formed in DNA from exposure to ultraviolet light. The discovery of catalytic RNAs in the 1980s led to the "RNA world hypothesis", which posits that early in evolution RNA or a similar polymer served both genetic and catalytic functions. Intrigued by the RNA world hypothesis, we set out to test whether a catalytic RNA (or a surrogate, a catalytic DNA) with photolyase activity could be contemplated...
February 8, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29415650/conservation-of-polypyrimidine-tract-binding-proteins-and-their-putative-target-rnas-in-several-storage-root-crops
#11
Kirtikumar R Kondhare, Amit Kumar, David J Hannapel, Anjan K Banerjee
BACKGROUND: Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth...
February 7, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29410498/knockdown-of-spry4-and-spry4-it1-inhibits-cell-growth-and-phosphorylation-of-akt-in-human-testicular-germ-cell-tumours
#12
Mrinal K Das, Kari Furu, Herman F Evensen, Øyvind P Haugen, Trine B Haugen
Testicular germ cell tumour (TGCT) is the most common cancer in young men in large parts of the world, but the aetiology is mainly unknown. Genome-wide association studies have so far identified about 50 susceptibility loci associated with TGCT, including SPRY4. SPRY4 has shown tumour suppressor activity in several cancer cells, such as lung and prostate, while it was found to act as an oncogene in ovarian cancer. An intronic region within the SPRY4 gene produces a long non-coding RNA, SPRY4-IT1, which has been reported to act as an oncogene in melanoma, breast cancer, and colorectal cancer, and as a tumour suppressor in lung cancer...
February 6, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29409859/rice-in-vivo-rna-structurome-reveals-rna-secondary-structure-conservation-and-divergence-in-plants
#13
Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao, Yiliang Ding
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa L.) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, for the first time we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N6-methyladenosine (m6A) modification tends to have less RNA structure in 3'UTR. GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation...
January 31, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29409309/daclatasvir-plus-asunaprevir-for-the-treatment-of-patients-with-hepatitis-c-virus-genotype-1b-infection-real-world-efficacy-changes-in-liver-stiffness-and-fibrosis-markers-and-safety
#14
Hye Won Lee, Se Rim Oh, Dong Yun Kim, Yechan Jeong, Seungtaek Kim, Beom Kyung Kim, Seung Up Kim, Do Young Kim, Sang Hoon Ahn, Kwang-Hyub Han, Jun Yong Park
Background/Aims: The treatment with daclatasvir plus asunaprevir (DCV+ASV) is associated with potent antiviral effects in patients with genotype 1b hepatitis C virus (HCV) infection. We investigated the real-world efficacy, changes in liver stiffness and noninvasive fibrosis markers, and the safety of DCV+ASV treatment in Korean patients. Methods: In total, 363 patients with chronic hepatitis C were treated with DCV+ASV between August 2015 and January 2017. Finally, we analyzed the data of 270 patients who were monitored for at least 12 weeks after the end of treatment...
February 8, 2018: Gut and Liver
https://www.readbyqxmd.com/read/29408647/whole-exome-mutational-and-transcriptional-landscapes-of-combined-hepatocellular-cholangiocarcinoma-and-intrahepatic-cholangiocarcinoma-reveal-molecular-diversity
#15
Zhen-Hao Liu, Bao-Feng Lian, Qiong-Zhu Dong, Han Sun, Jin-Wang Wei, Yuan-Yuan Sheng, Wei Li, Yixue Li, Lu Xie, Lei Liu, Lun-Xiu Qin
BACKGROUND: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). CHC is a distinct, albeit rare, subtype of PLC and is comprised of cells with histopathological features of both HCC and ICC. Several studies have focused on the mutation and expression landscapes of HCC and ICC...
January 31, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29405150/seroprevalence-risk-factors-and-genotype-distribution-for-hepatitis-c-infection-a-study-from-rural-hospital-in-maharashtra
#16
Satish Ramchandrra Patil, Kailash D Datkhile, M V Ghorpade, Supriya Satish Patil, Satish V Kakade
BACKGROUND AND OBJECTIVES: Hepatitis C is global health problem affecting a significant portion of the world's population. Available data in Western Maharashtra on seroprevalence, risk factors and genotype distribution are very limited. OBJECTIVES: The present study was carried out to estimate the seroprevalence, factors influencing transmission and distribution of genotype of hepatitis C virus (HCV) in a hospital-based population. MATERIALS AND METHODS: This was a cross-sectional, hospital-based study...
October 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29404420/limited-evidence-for-infection-of-urban-and-peri-urban-nonhuman-primates-with-zika-and-chikungunya-viruses-in-brazil
#17
Andres Moreira-Soto, Ianei de Oliveira Carneiro, Carlo Fischer, Marie Feldmann, Beate M Kümmerer, Nama Santos Silva, Uilton Góes Santos, Breno Frederico de Carvalho Dominguez Souza, Fernanda de Azevedo Liborio, Mônica Mafra Valença-Montenegro, Plautino de Oliveira Laroque, Fernanda Rosa da Fontoura, Alberto Vinicius Dantas Oliveira, Christian Drosten, Xavier de Lamballerie, Carlos Roberto Franke, Jan Felix Drexler
Chikungunya virus (CHIKV) and Zika virus (ZIKV) emerged in the Americas in 2013. Limited antigenic variability of CHIKV and ZIKV may restrict urban transmission cycles due to population protective immunity. In Africa, sylvatic transmission cycles involving nonhuman primates (NHP) are known for CHIKV and ZIKV, causing cyclic reemergence in humans. To evaluate whether sylvatic cycles can be expected in Latin America, we tested 207 NHP collected between 2012 and 2017 in urban and peri-urban settings in Brazil for infection with ZIKV and CHIKV...
January 2018: MSphere
https://www.readbyqxmd.com/read/29398222/analysis-of-evolutionarily-independent-protein-rna-complexes-yields-a-criterion-to-evaluate-the-relevance-of-prebiotic-scenarios
#18
Celia Blanco, Marco Bayas, Fu Yan, Irene A Chen
A central difficulty facing study of the origin of life on Earth is evaluating the relevance of different proposed prebiotic scenarios. Perhaps the most established feature of the origin of life was the progression through an RNA World, a prebiotic stage dominated by functional RNA. We use the appearance of proteins in the RNA World to understand the prebiotic milieu and develop a criterion to evaluate proposed synthetic scenarios. Current consensus suggests that the earliest amino acids of the genetic code were anionic or small hydrophobic or polar amino acids...
January 29, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29392896/the-emerging-role-of-long-non-coding-rna-in-spinal-cord-injury
#19
REVIEW
Zhongju Shi, Bin Pan, Shiqing Feng
Spinal cord injury (SCI) is a significant health burden worldwide which causes permanent neurological deficits, and there are approximately 17,000 new cases each year. However, there are no effective and current treatments that lead to functional recovery because of the limited understanding of the pathogenic mechanism of SCI. In recent years, the biological roles of long non-coding RNAs (lncRNAs) in SCI have attracted great attention from the researchers all over the world, and an increasing number of studies have investigated the regulatory roles of lncRNAs in SCI...
February 1, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29382904/evaluation-of-dried-blood-spot-samples-for-screening-of-hepatitis-c-and-human-immunodeficiency-virus-in-a-real-world-setting
#20
Sonia Vázquez-Morón, Pablo Ryan, Beatriz Ardizone-Jiménez, Dolores Martín, Jesus Troya, Guillermo Cuevas, Jorge Valencia, María A Jimenez-Sousa, Ana Avellón, Salvador Resino
Both hepatitis C virus (HCV) infection and human immunodeficiency virus (HIV) infection are underdiagnosed, particularly in low-income countries and in difficult-to-access populations. Our aim was to develop and evaluate a methodology for the detection of HCV and HIV infection based on capillary dry blood spot (DBS) samples taken under real-world conditions. We carried out a cross-sectional study of 139 individuals (31 healthy controls, 68 HCV-monoinfected patients, and 40 HCV/HIV-coinfected patients). ELISA was used for anti-HCV and anti-HIV antibody detection; and SYBR Green RT-PCR was used for HCV-RNA detection...
January 30, 2018: Scientific Reports
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