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Marzena Wojciechowska, Krzysztof Sobczak, Piotr Kozlowski, Saam Sedehizadeh, Agnieszka Wojtkowiak-Szlachcic, Karol Czubak, Robert Markus, Anna Lusakowska, Anna Kaminska, J David Brook
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs...
April 12, 2018: Scientific Reports
Xiaojuan Wang, Jie Gu, Hua Gao, Xun Qian, Haichao Li
The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR) to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs) at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase ( intI1 ) gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3-V4 regions using MiSeq sequencing...
April 10, 2018: International Journal of Environmental Research and Public Health
Gian Paolo Caviglia, Maria Lorena Abate, Francesco Tandoi, Alessia Ciancio, Antonio Amoroso, Mauro Salizzoni, Giorgio Maria Saracco, Mario Rizzetto, Renato Romagnoli, Antonina Smedile
BACKGROUND & AIMS: The accurate diagnosis of occult HBV infection (OBI) requires the demonstration of HBV DNA in liver biopsies of HBsAg-negative subjects. However, in clinical practice a latent OBI is deduced by the finding of the antibody to the HB-core antigen (anti-HBc). We investigated the true prevalence of OBI and the molecular features of intrahepatic HBV in anti-HBc-positive subjects. METHODS: The livers of 100 transplant donors (median age 68.2 years; 64 males, 36 females) positive for anti-HBc at standard serologic testing, were examined for total HBV DNA by nested-PCR and for the HBV covalently closed circular DNA (HBV cccDNA) with an in-house droplet digital PCR assay (ddPCR) (Linearity: R2 = 0...
April 2, 2018: Journal of Hepatology
Katherine T W Lee, Vinod Gopalan, Alfred K Lam
Somatic copy-number alterations are commonly found in cancer and play key roles in activating oncogenes and deactivating tumor suppressor genes. Digital polymerase chain reaction is an effective way to detect the changes in copy number. In esophageal adenocarcinoma, detection of somatic copy-number alterations could predict the prognosis of patients as well as the response to therapy. This chapter will review the methods involved in digital polymerase chain reaction for the research or potential clinical applications in esophageal adenocarcinoma...
2018: Methods in Molecular Biology
Michael B Cooley, Diana Carychao, Lisa Gorski
Pathogen contamination of surface water is a health hazard in agricultural environments primarily due to the potential for contamination of crops. Furthermore, pathogen levels in surface water are often unreported or under reported due to difficulty with culture of the bacteria. The pathogens are often present, but require resuscitation, making quantification difficult. Frequently, this leads to the use of quantitative PCR targeted to genes unique to the pathogens. However, multiple pathogen types are commonly in the same water sample, both gram + and gram -, leading to problems with DNA extraction...
2018: Frontiers in Microbiology
Yu Yang, Liang Li, Hui Yang, Xiaying Li, Xiujie Zhang, Junfeng Xu, Dabing Zhang, Wujun Jin, Litao Yang
The accurate monitoring and quantification of genetically modified organisms (GMOs) are key points for the implementation of labelling regulations, and a certified reference material (CRM) acts as the scaleplate for quantifying the GM contents of foods/feeds and evaluating a GMO analytical method or equipment. Herein, we developed a series of CRMs for transgenic rice event G6H1, which possesses insect-resistant and herbicide-tolerant traits. Three G6H1 CRMs were produced by mixing seed powders obtained from homozygous G6H1 and its recipient cultivar Xiushui 110 at mass ratios of 49...
March 27, 2018: Journal of Agricultural and Food Chemistry
Shigeo Yamaguchi, Shin Takahashi, Kaoru Mogushi, Yuki Izumi, Yumi Nozaki, Tadashi Nomizu, Yoichiro Kakugawa, Takanori Ishida, Noriaki Ohuchi, Chikashi Ishioka, Shunsuke Kato
Purpose: TP53 signature has a robust predictive performance for prognosis in early-stage breast cancer, but the experiment that reported this relied on public microarray data and fresh-frozen samples. Before TP53 signature can be used in a clinical setting, a simple and low-cost diagnostic system using formalin-fixed paraffin-embedded (FFPE) samples is needed. New treatments based on the biological characteristics of TP53 signature are expected to follow. Experimental Design: TP53 signature was evaluated in 174 FFPE early breast cancer specimens using digital quantification via the nCounter technique (NanoString)...
March 6, 2018: Oncotarget
Yuwen Luo, Yao Li
This study aims to develop a new method for the detection of KRAS mutations related to colorectal cancer in cfDNA, and to evaluate the sensitivity and accuracy of the detection. We designed a method of cfDNA based KRAS detection by droplets digital PCR (ddPCR). The theoretical performance of the method is evaluated by reference standard and compared to the ARMS PCR method. Two methods, ddPCR and qPCR, were successfully established to detect KRAS wild type and 7 mutants. Both methods were validated using plasmid standards and actual samples...
March 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Wenjun Tong, Xiangchen Li, Yunyun Huo, Lu Zhang, Ying Cao, Entao Wang, Weimin Chen, Shiheng Tao, Gehong Wei
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA...
March 16, 2018: Systematic and Applied Microbiology
Federico Cunha, Soo Jin Jeon, Rodolfo Daetz, Achilles Vieira-Neto, Jimena Laporta, K Casey Jeong, Anthony F Barbet, Carlos A Risco, Klibs N Galvão
Metritis is caused by polymicrobial infection; however, recent metagenomic work challenges the importance of known pathogens such as Escherichia coli and Trueperella pyogenes while identifying potential new pathogens such as Bacteroides pyogenes, Porphyromonas levii and Helcococcus ovis. This study aims to quantify known and emerging uterine pathogens, and to evaluate their association with metritis and fever in dairy cows. Metritis was diagnosed at 6 ± 2 days postpartum, a uterine swab was collected and rectal temperature was measured...
March 16, 2018: Theriogenology
Hua-Jun He, Erica V Stein, Paul DeRose, Kenneth D Cole
We compared different methods (absorbance, fluorescent dye-binding, and digital PCR) for measuring the concentrations of human genomic DNA from cultured cells and absorbance measurements of a synthetic DNA oligonucleotide. NIST Standard Reference Material (SRM) 2082, a pathlength absorbance standard, was used to benchmark the absorbance measurements done with microvolume spectrophotometers and a microvolume plate reader. Control absorbance values were measured on a high accuracy spectrophotometer and a NIST calibrated pathlength cuvette...
February 1, 2018: BioTechniques
Tanya C Do, Stephen J Kerr, Anchalee Avihingsanon, Saowaluk Suksawek, Supalak Klungkang, Taweesak Channgam, Christoph C Odermatt, Wirach Maek-A-Nantawat, Kiat Ruxtungtham, Jintanat Ananworanich, Victor Valcour, Peter Reiss, Ferdinand W Wit
Objectives: To assess cognitive performance and psychomotor impairment in an HIV-positive cohort, well-suppressed on combination antiretroviral therapy (cART), in an Asian resource-limited setting. Methods: Cross-sectional sociodemographic and cognitive data were collected in 329 HIV-positive and 510 HIV-negative participants. Cognitive performance was assessed using the International HIV Dementia Scale (IHDS), Montreal Cognitive Assessment (MoCA), WAIS-III Digit Symbol, Trail Making A, and Grooved Pegboard (both hands)...
January 1, 2018: Journal of Virus Eradication
David L Duewer, Margaret C Kline, Erica L Romsos, Blaza Toman
The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI)...
March 19, 2018: Analytical and Bioanalytical Chemistry
Katherine Ting-Wei Lee, Vinod Gopalan, Farhadul Islam, Riajul Wahab, Afraa Mamoori, Cu-Tai Lu, Robert Anthony Smith, Alfred King-Yin Lam
GAEC1 (gene amplified in oesophageal cancer 1) is a transforming oncogene with tumorigenic potential observed in both oesophageal squamous cell carcinoma and colorectal cancer. Nonetheless, there has been a lack of study done on this gene to understand how this gene exert its oncogenic properties in cancer. This study aims to identify novel mutation sites in GAEC1. To do so, seventy-nine matched colorectal cancers were tested for GAEC1 mutation via Sanger sequencing. The mutations noted were investigated for the correlations with the clinicopathological parameters of the patients with the cancer...
March 13, 2018: European Journal of Cell Biology
Natascia De Lucia, Silvio Peluso, Alessandro Roca, Cinzia Valeria Russo, Marco Massarelli, Giovanna De Michele, Luigi Di Maio, Elena Salvatore, Giuseppe De Michele
Objective: In visuo-constructional tasks, patients may reproduce drawings near-to or superimposed on a model, showing the so-called "Closing-in" (CI), often ascribed to a defect in inhibitory control. CI has been described in neurological conditions, but no studies have explored CI in Huntington's disease (HD), a neurodegenerative disorder often involving the frontal cortical-subcortical circuits. We searched for the occurrence of CI in HD patients and systematically investigated its correlates to find a clinical marker of the frontal/executive dysfunctions in the early examination of HD patients...
March 15, 2018: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
Arun Gupta, Pratima Murthy, Shobini Rao
Chronic use of mind altering substances can lead to a wide variety of neuropsychological deficits, affecting the domains of attention, learning, memory, reasoning. Executive functions such as working memory, cognitive flexibility and inhibitory control may specifically be impaired. These deficits can impact engagement in effective psychosocial interventions. Mild to moderate cognitive dysfunction may not be picked up in routine clinical examination or through commonly used tests like the mini-mental state examination (MMSE)...
February 2018: Indian Journal of Psychiatry
Kathryn B Manheimer, Nihir Patel, Felix Richter, Joshua Gorham, Angela C Tai, Jason Homsy, Marko T Boskovski, Michael Parfenov, Elizabeth Goldmuntz, Wendy K Chung, Martina Brueckner, Martin Tristani-Firouzi, Deepak Srivastava, Jonathan G Seidman, Christine E Seidman, Bruce D Gelb, Andrew J Sharp
Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs)...
March 11, 2018: Human Mutation
Carolyn Kincade, Lindsay McHutchion, Johan Wolfaardt
The present report describes the digital design of patient-specific milled abutments for the retention of osseointegrated facial prostheses by using digital technology. Patient imaging including surface scans of the patient's head, scans of the patient's definitive cast, and digitally designed prosthesis prototypes were combined to create a digital simulation of the patient. Using this simulation, patient-specific abutments were digitally designed, printed in 3-dimensions (3D), and finally copy-milled in titanium...
March 8, 2018: Journal of Prosthetic Dentistry
Marzia Del Re, Riccardo Marconcini, Giulia Pasquini, Eleonora Rofi, Caterina Vivaldi, Francesco Bloise, Giuliana Restante, Elena Arrigoni, Chiara Caparello, Maria Grazia Bianco, Stefania Crucitta, Iacopo Petrini, Enrico Vasile, Alfredo Falcone, Romano Danesi
BACKGROUND: PD-L1 expression in tumour tissues is widely used to select patients to receive anti-PD-1/PD-L1 antibodies, but data are lacking on the correlation of plasma PD-L1 levels with the effect of treatments. METHODS: To investigate the association between PD-L1 mRNA in plasma-derived exosomes and response to nivolumab and pembrolizumab in patients with melanoma (n=18) and NSCLC (n=8), blood was obtained at time point 0 and after 2 months. Exosomal PD-L1 mRNA was measured by digital droplet PCR...
March 6, 2018: British Journal of Cancer
Alessandra Ruggiero, Alessandro Cozzi-Lepri, Apostolos Beloukas, Douglas Richman, Saye Khoo, Andrew Phillips, Anna Maria Geretti
Background: Persistence of plasma HIV-1 RNA during seemingly effective antiretroviral thereapy (ART) is incompletely understood. Using an ultrasensitive assay, this cross-sectional study investigated residual plasma HIV-1 RNA in subjects maintained on firstline ART with continuous viral load suppression <50 copies/mL for ≤15 years without recognized viral load blips or treatment interruptions and explored its relationship with the duration of suppressive ART, efavirenz concentrations in plasma, 2-LTR circular HIV-1 DNA (2-LTRc DNA) in peripheral blood mononuclear cells, and cellular (CD4 plus CD26/CD38/CD69; CD8 plus CD38/HLA-DR/DP/DQ) and soluble (sCD14, sCD27, sCD30, IL-6) markers of immune activation in peripheral blood...
February 2018: Open Forum Infectious Diseases
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