Read by QxMD icon Read

Target sequencing

Fanwei Dai, Zhenjiang Wang, Zhiyi Li, Guoqing Luo, Yi Wang, Cuiming Tang
The aim of this work was to gain insights into the molecular mechanisms and dynamics of the mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides infection. A transcriptomic and proteomic study was carried out based on RNA sequencing and isobaric tags for relative and absolute quantification analysis, respectively. These data were then validated using quantitative real-time PCR and multiple reaction monitoring assays. Comparative analyses revealed that 9.0% of the transcriptome and 20.8% of the proteome were differentially regulated after C...
October 10, 2018: Journal of Proteomics
P Mancini, G Bonanno Ferraro, M Iaconelli, E Suffredini, B Valdazo-González, S Della Libera, M Divizia, G La Rosa
AIMS: Human Sapoviruses (HSaVs) are etiological agents of sporadic cases and outbreaks of acute gastroenteritis in humans of all ages. Evidence of worldwide distribution of HSaV has been documented, however little is known about HSaV circulation in Italy. To study their occurrence and genetic diversity a nation-wide environmental surveillance was undertaken. METHODS AND RESULTS: One hundred sixty-six raw sewage samples, collected from 16 wastewater treatment plants throughout Italy, were processed and analysed by a RT-nested-PCR targeting the capsid region, followed by amplicon sequencing...
October 13, 2018: Journal of Applied Microbiology
Nasr Alrabadi, Natasha Gibson, Kendra Curless, Liang Cheng, Matthew Kuhar, Shaoxiong Chen, Simon J P Warren, Ahmed K Alomari
Dedifferentiated metastatic melanoma can pose a significant diagnostic challenge, especially if the history of primary melanoma is not known or is remote. BRAF and NRAS mutations are common melanoma driver mutations that are usually sequenced to evaluate for treatment targets. We evaluated whether BRAF and NRAS mutational testing could contribute to the diagnosis of dedifferentiated metastatic melanoma when immunostains are negative. Seven patients with melanoma who had an additional diagnosis of poorly differentiated sarcoma with negative melanocytic immunostains were tested for BRAF and NRAS mutations...
October 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Ana M Bolivar, Rajyalakshmi Luthra, Meenakshi Mehrotra, Wei Chen, Bedia A Barkoh, Peter Hu, Wei Zhang, Russell R Broaddus
There is currently no blood-based marker in routine use for endometrial cancer patients. Such a marker could potentially be used for early detection, but it could also help to track tumor recurrence following hysterectomy. This is important, as extra-vaginal recurrence of endometrial endometrioid adenocarcinoma is usually incurable. This proof-of-principle study was designed to determine if tumor-associated mutations could be detected in cell-free DNA from the peripheral blood of early and late stage endometrial endometrioid carcinoma patients...
October 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Chang S Chan, Saurabh V Laddha, Peter W Lewis, Matthew S Koletsky, Kenneth Robzyk, Edaise Da Silva, Paula J Torres, Brian R Untch, Janet Li, Promita Bose, Timothy A Chan, David S Klimstra, C David Allis, Laura H Tang
The commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. We genotyped 64 PanNETs and found 58% carry ATRX, DAXX, and MEN1 mutations (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis to reveal two distinct subgroups with one consisting entirely of A-D-M mutant PanNETs. Two genes differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs...
October 12, 2018: Nature Communications
Mengxin Lu, Qiangqiang Ge, Gang Wang, Yongwen Luo, Xiaolong Wang, Wei Jiang, Xuefeng Liu, Chin-Lee Wu, Yu Xiao, Xinghuan Wang
Cold-inducible RNA binding protein (CIRBP) has been reported to be associated with distinct tumorigenesis. In this study, we investigated the role of CIRBP in human bladder cancer (BCa), indicating that CIRBP is overexpressed in BCa tissues and cell lines to promote proliferation and migration. Moreover, CIRBP could induce expression of HIF-1α via binding to the 3'-UTR of its mRNA to increase the mRNA stability in BCa cells. Furthermore, we demonstrated that PTGIS is a HIF-1α targeted gene, a major regulator in hypoxic cancer progression by activating transcription of various oncogenes...
October 12, 2018: Cell Death & Disease
Adrienne Tin, Yong Li, Jennifer A Brody, Teresa Nutile, Audrey Y Chu, Jennifer E Huffman, Qiong Yang, Ming-Huei Chen, Cassianne Robinson-Cohen, Aurélien Macé, Jun Liu, Ayşe Demirkan, Rossella Sorice, Sanaz Sedaghat, Melody Swen, Bing Yu, Sahar Ghasemi, Alexanda Teumer, Peter Vollenweider, Marina Ciullo, Meng Li, André G Uitterlinden, Robert Kraaij, Najaf Amin, Jeroen van Rooij, Zoltán Kutalik, Abbas Dehghan, Barbara McKnight, Cornelia M van Duijn, Alanna Morrison, Bruce M Psaty, Eric Boerwinkle, Caroline S Fox, Owen M Woodward, Anna Köttgen
Elevated serum urate levels can cause gout, an excruciating disease with suboptimal treatment. Previous GWAS identified common variants with modest effects on serum urate. Here we report large-scale whole-exome sequencing association studies of serum urate and kidney function among ≤19,517 European ancestry and African-American individuals. We identify aggregate associations of low-frequency damaging variants in the urate transporters SLC22A12 (URAT1; p = 1.3 × 10-56 ) and SLC2A9 (p = 4.5 × 10-7 )...
October 12, 2018: Nature Communications
Beimi Cui, Qiaona Pan, David Clarke, Marisol Ochoa Villarreal, Saima Umbreen, Bo Yuan, Weixing Shan, Jihong Jiang, Gary J Loake
Nitric oxide (NO) orchestrates a plethora of incongruent plant immune responses, including the reprograming of global gene expression. However, the cognate molecular mechanisms remain largely unknown. Here we show a zinc finger transcription factor (ZF-TF), SRG1, is a central target of NO bioactivity during plant immunity, where it functions as a positive regulator. NO accumulation promotes SRG1 expression and subsequently SRG1 occupies a repeated canonical sequence within target promoters. An EAR domain enables SRG1 to recruit the corepressor TOPLESS, suppressing target gene expression...
October 12, 2018: Nature Communications
Deepanshi Mishra, Gita Satpathy, Rohan Chawla, Pradeep Venkatesh, Nishat Hussain Ahmed, Subrat Kumar Panda
BACKGROUND: Endophthalmitis, a sight-threatening intraocular infection, can be of postsurgical, post-traumatic or endogenous origin. Laboratory diagnosis-based appropriate therapy can be vision-saving. Conventional culture-based laboratory diagnosis takes time and lacks sensitivity. In this study a broad-range PCR assay was assessed against conventional and automated culture methods in vitreous specimens for accurate microbiological diagnosis. AIMS: To use broad-range PCR assay targeting 16S ribosomal RNA (rRNA) region of bacteria and to assess its performance vis-à-vis conventional and automated culture methods in the laboratory diagnosis of endophthalmitis...
October 12, 2018: British Journal of Ophthalmology
Bethany J Madison, Kathleen A Clark, Niraja Bhachech, Peter Hollenhorst, Barbara J Graves, Simon L Currie
Many different transcription factors (TFs) regulate gene expression in a combinatorial fashion, often by binding in close proximity to each other on composite cis-regulatory DNA elements. Here we investigated how ETS TFs bind with the AP1 TFs JUN-FOS at composite DNA-binding sites. DNA-binding ability with JUN-FOS correlated with the phenotype of ETS proteins in prostate cancer. We found that the oncogenic ETS related gene (ERG) and ETS variant (ETV) 1/4/5 subfamilies co-occupy ETS-AP1 sites with JUN-FOS in vitro, whereas JUN-FOS robustly inhibited DNA binding by the tumor suppressors ETS homologous factor (EHF) and SAM pointed domain-containing ETS TF (SPDEF)...
October 12, 2018: Journal of Biological Chemistry
R Gautam, D Price, C W Revie, I A Gardner, R Vanderstichel, L Gustafson, K Klotins, M Beattie
Infectious salmon anaemia (ISA) can be a serious viral disease of farmed Atlantic salmon (Salmo salar). A tool to rank susceptible farms based on the risk of ISA virus (ISAv) infection spread from infectious farms after initial incursion or re-occurrence in an endemic area, can help guide monitoring and surveillance activities. Such a tool could also support the response strategy to contain virus spread, given available resources. We developed a tool to rank ISAv infection risks using seaway distance and hydrodynamic information separately and combined...
November 1, 2018: Preventive Veterinary Medicine
Michela Zamboni, Donato Civitareale
In non-small lung cancer, the expression of the transcription factor TTF-1/Nkx2.1 correlates with the presence of EGFR mutations, therefore TTF-1/Nkx2.1 expression is used to optimize an EGFR testing strategy and to guide clinical treatment. We investigate the molecular mechanisms underlying the functional connection between EGFR and TTF-1/Nkx2.1 gene expression in lung adenocarcinoma. Using the H1975 cell line as a non-small cell lung cancer model system and short hairpin RNA, we have selected clones with TTF-1/Nkx2...
October 9, 2018: Biochemical and Biophysical Research Communications
Paola Fortis, Roberta Ronchi, Valeria Velardo, Elena Calzolari, Elisabetta Banco, Lorella Algeri, Maria Simonetta Spada, Giuseppe Vallar
Spatial neglect is a debilitating disorder frequently observed after damage to the right cerebral hemisphere. Previous investigations have revealed that prism adaptation (PA) therapy can lead to improvements in neglect-related symptoms. In the typical PA protocol patients repeatedly point toward a visual target while wearing prism goggles. A few years ago, a novel PA procedure, involving a variety of more "ecological" visuo-motor activities during adaptation, less repetitive than a sequence of pointings, was introduced by our research group, and shown to be able to improve neglect-related symptoms to the same extent as the standard pointing task...
September 18, 2018: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
Alireza Neshani, Reza Kamali Kakhki, Mojtaba Sankian, Hosna Zare, Amin Hooshyar Chichaklu, Mahsa Sayyadi, Kiarash Ghazvini
BACKGROUND: The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test. METHODS: A specific target was identified using modified genome comparison method and an in-house PCR test was designed...
October 12, 2018: BMC Infectious Diseases
Sung Hyun Hwang, Woo Young Kwon, Hyunmin Eun, Sehan Jeong, Jun Seok Park, Kwang Jin Kim, Hyung Joo Kim, Sang Hyun Lee, Kyungmoon Park, Jeong-Jun Yoon, Yung-Hun Yang, Ki Soo Park
A simple, sequence-specific DNA detection method, utilizing a fluorescent 2-aminopurine (2-AP) nucleobase analogue-containing split G-quadruplex as the key detection component, is described. In the sensor, the 2-AP-containing G-quadruplex is split into two segments and linked to a target-specific overhang sequence. The separate G-quadruplex sequences form an active G-quadruplex structure only in the presence of a complementary target DNA, which leads to a significant increase in the intensity of fluorescence from the 2-AP fluorophore...
October 12, 2018: Artificial Cells, Nanomedicine, and Biotechnology
Ying Li, Chao Zhang, Luwei Qin, Dong Li, Guangyuan Zhou, Dejian Dang, Shuaiyin Chen, Tiantian Sun, Rongguang Zhang, Weidong Wu, Yuanlin Xi, Yuefei Jin, Guangcai Duan
Enterovirus 71 (EV71) is the main pathogen of severe hand-foot-mouth disease (HFMD). Long non-coding RNAs (lncRNAs) are recognized as pivotal factors during the pathogenesis of viral infection. However, the critical functions of lncRNAs in EV71⁻host interactions have not been characterized. Here, for the first time, we performed global transcriptome analysis of lncRNA and mRNA expression profiles in EV71-infected human rhabdomyosarcoma (RD) cells and skeletal muscle of mice using second-generation sequencing...
October 11, 2018: Viruses
Yang Ji, Peilin Chen, Jing Chen, Kayla K Pennerman, Xiaoyu Liang, Haidong Yan, Sifan Zhou, Guangyan Feng, Chengran Wang, Guohua Yin, Xinquan Zhang, Yuanbin Hu, Linkai Huang
Drought stress is a global problem, and the lack of water is a key factor that leads to agricultural shortages. MicroRNAs play a crucial role in the plant drought stress response; however, the microRNAs and their targets involved in drought response have not been well elucidated. In the present study, we used Illumina platform ( and combined data from miRNA, RNA, and degradome sequencing to explore the drought- and organ-specific miRNAs in orchardgrass ( Dactylis glomerata L.) leaf and root...
October 11, 2018: International Journal of Molecular Sciences
Neven Maksemous, Robert A Smith, Heidi G Sutherland, Hugo Sampaio, Lyn R Griffiths
Although the clinical use of targeted gene sequencing-based diagnostics is valuable, whole-exome sequencing has also emerged as a successful diagnostic tool in molecular genetics laboratories worldwide. Molecular genetic tests for episodic ataxia type 2 (EA2) usually target only the specific calcium channel gene ( CACNA1A ) that is known to cause EA2. In cases where no mutations are identified in the CACNA1A gene, it is important to identify the causal gene so that more effective treatment can be prioritized for patients...
October 11, 2018: International Journal of Molecular Sciences
Jing Wang, Cong Zhou, Yuanyuan Xiao, Hongqian Liu
RATIONALE: Retinitis pigmentosa (RP) is a group of clinically and genetically heterogeneous diseases; X-linked retinitis pigmentosa (XLRP) is the most serious type. Mutations in RP GTPase regulator (RPGR) account for over 70% of patients with XLRP. PATIENT CONCERNS: We report a Chinese family with RP, 5 males presented with night blindness and decreased vision, and 8 females showed different severities of myopia. DIAGNOSES: Targeted exome capture sequencing was performed in 2 affected males, which revealed a novel variant (NM_000328...
October 2018: Medicine (Baltimore)
Hai-Xia Chen, Yan-Song Liu, Xiu-Jie Zhang
OBJECTIVE: Systematic tracking of microRNA (miRNA) targets remains a challenge. In our work, we aimed to use TargetScore to investigate the potential targets of miRNA203 and miRNA-146a in psoriasis by integrating miRNA overexpression information and sequence data, and to further uncover the functions of miRNA203 and miRNA-146a in psoriasis. METHODS: This was a case-control bioinformatics analysis using already published microarray data of psoriasis. We calculated targetScores by combining log fold-change and sequence scores obtained from TargetScan context score, probabilities of conserved targeting, and derived the distribution of targetScores...
October 2018: Medicine (Baltimore)
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"