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Jingchao Chen, Hongjuan Huang, Shouhui Wei, Zhaofeng Huang, Xu Wang, Chaoxian Zhang
Glyphosate is an important non-selective herbicide that is commonly used worldwide. However, evolved glyphosate-resistant (GR) weeds significantly affect crop yields. Unfortunately, the mechanisms underlying resistance in GR weeds, such as goosegrass (Eleusine indica L.), an annual weed found worldwide, have not been fully elucidated. In this study, transcriptome analysis was conducted to further assess the potential mechanisms of glyphosate resistance in goosegrass. The RNA-seq libraries generated 24,597,462 clean reads...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Marzia Del Re, Elisa Biasco, Stefania Crucitta, Lisa Derosa, Eleonora Rofi, Cinzia Orlandini, Mario Miccoli, Luca Galli, Alfredo Falcone, Guido W Jenster, Ron H van Schaik, Romano Danesi
BACKGROUND: The androgen receptor splice variant 7 (AR-V7) is associated with resistance to hormonal therapy in castration-resistant prostate cancer (CRPC). Due to limitations of the methods available for AR-V7 analysis, the identification of a reliable detection method may facilitate the use of this biomarker in clinical practice. OBJECTIVE: To confirm AR-V7 as a predictor of resistance to hormonal therapy and develop a new approach to assess AR-V7 by highly sensitive digital droplet polymerase chain reaction (ddPCR) in plasma-derived exosomal RNA...
August 26, 2016: European Urology
Philip J Wilson, Stephen L R Ellison
BACKGROUND: Digital PCR (dPCR) is a technique for estimating the concentration of a target nucleic acid by loading a sample into a large number of partitions, amplifying the target and using a fluorescent marker to identify which partitions contain the target. The standard analysis uses only the proportion of partitions containing target to estimate the concentration and depends on the assumption that the initial distribution of molecules in partitions is Poisson. In this paper we describe a way to extend such analysis using the quantification cycle (Cq) data that may also be available, but rather than assuming the Poisson distribution the more general Conway-Maxwell-Poisson distribution is used instead...
October 12, 2016: BMC Bioinformatics
Sebastian Maciak, Katarzyna Michalak, Shiv D Kale, Pawel Michalak
Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F1 hybrids produced from reciprocal crosses between 2 sister species of Xenopus clawed frogs, X. muelleri and X. borealis, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant Xenopus species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition...
October 12, 2016: Cytogenetic and Genome Research
Ana Luiza Zaninotto, Jessica Elias Vicentini, Davi Jorge Fontoura Solla, Tatiana Tateishi Silva, Vinicius Monteiro de Paula Guirado, Fabrício Feltrin, Mara Cristina Souza de Lucia, Manoel Jacobsen Teixeira, Wellingson Silva Paiva
OBJECTIVE: Diffuse axonal injury (DAI) is prevalent in traumatic brain injury (TBI), and is often associated with poor outcomes and cognitive impairment, including memory deficits. Few studies have explored visual memory after TBI and its relationship to executive functioning. Executive functioning is crucial for remembering an object's location, operating devices, driving, and route finding. We compared visual memory performance via the Rey-Osterrieth Complex Figure (ROCF) test 6 and 12 months after DAI...
October 11, 2016: Acta Neuropsychiatrica
Takahiro Kishikawa, Motoyuki Otsuka, Takeshi Yoshikawa, Motoko Ohno, Keisuke Yamamoto, Natsuyo Yamamoto, Ai Kotani, Kazuhiko Koike
Pancreatic ductal adenocarcinoma (Pdac) is a malignancy with a poor prognosis due to difficulties in early detection. Although promising biomarkers are increasingly reported, such methods are not yet easy to apply clinically, mainly due to their low reproducibility or technical difficulties. In this study, we developed a convenient and sensitive method for quantifying aberrantly expressed satellite repeat RNAs in sera, which can be used to efficiently detect patients with Pdac. Here, we introduce a Tandem Repeat Amplification by nuclease Protection (TRAP) method combined with droplet digital PCR (ddPCR) to detect human satellite II (HSATII) RNAs, which are specifically expressed in human Pdacs at greater levels than normal tissues but are difficult to measure due to their repetitive sequences and irregularities...
June 2, 2016: JCI Insight
Yuta Aizawa, Akihide Koyama, Tomohiko Ishihara, Osamu Onodera, Akihiko Saitoh
BACKGROUND: Human parechovirus type 3 (HPeV3) is an emerging virus that causes sepsis and meningoencephalitis in neonates and young infants. Correct diagnosis of HPeV3 infection is critical in determining appropriate management and predicting patients' clinical course. Real-time reverse transcription PCR (RT-PCR) analysis of serum and/or cerebrospinal fluid (CSF) has been used to diagnose HPeV3 infection; however, the assay detection limits have not been fully evaluated. OBJECTIVES: We tested the hypothesis that droplet digital RT-PCR (RT-ddPCR)-a novel technique that precisely quantitates low-copy target genes by diluting and partitioning samples into compartments-increases the detection rate of HPeV3 RNA as compared with real-time RT-PCR...
September 23, 2016: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
Rachel V Purcell, John Pearson, Frank A Frizelle, Jacqueline I Keenan
Gut colonization with enterotoxigenic Bacteroides fragilis (ETBF) appears to be associated with the development of colorectal cancer. However, differences in carriage rates are seen with various testing methods and sampling sites. We compared standard PCR, SYBR green and TaqMan quantitative PCR (qPCR) and digital PCR (dPCR) in detecting the B. fragilis toxin (bft) gene from cultured ETBF, and from matched luminal and faecal stool samples from 19 colorectal cancer patients. Bland-Altman analysis found that all three quantitative methods performed comparably in detecting bft from purified bacterial DNA, with the same limits of detection (<1 copy/μl)...
September 30, 2016: Scientific Reports
D Fumagalli, T R Wilson, R Salgado, X Lu, J Yu, C O'Brien, K Walter, L Y Huw, C Criscitiello, I Laios, V Jose, D N Brown, F Rothé, M Maetens, D Zardavas, P Savas, D Larsimont, M J Piccart-Gebhart, S Michiels, M R Lackner, C Sotiriou, S Loi
BACKGROUND: Estrogen receptor-positive (ER+) breast cancers (BCs) constitute the most frequent BC subtype. The molecular landscape of ER+ relapsed disease is not well characterized. In this study, we aimed to describe the genomic evolution between primary (P) and matched metastatic (M) ER+ BCs after failure of adjuvant therapy. MATERIALS AND METHODS: A total of 182 ER+ metastatic BC patients with long-term follow-up were identified from a single institution. P tumor tissue was available for all patients, with 88 having matched M material...
October 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Alexander G Claxton, Ashley S Hammond, Julia Romano, Ekaterina Oleinik, Jeremy M DeSilva
Characterizing australopith pelvic morphology has been difficult in part because of limited fossilized pelvic material. Here, we reassess the morphology of an under-studied adult right ilium and pubis (Sts 65) from Member 4 of Sterkfontein, South Africa, and provide a hypothetical digital reconstruction of its overall pelvic morphology. The small size of the pelvis, presence of a preauricular sulcus, and shape of the sciatic notch allow us to agree with past interpretations that Sts 65 likely belonged to a female...
October 2016: Journal of Human Evolution
Martin Beránek, Zdeněk Fiala, Jan Kremláček, Ctirad Andrýs, Květoslava Hamáková, Vladimír Palička, Lenka Borská
Goeckerman therapy (GT) represents an effective treatment of psoriasis including a combination of pharmaceutical grade crude coal tar (CCT) and ultraviolet irradiation (UV-R). Coal tar contains a mixture of polycyclic aromatic hydrocarbons. The best known carcinogenic polyaromate - benzo[a]pyrene is metabolized into a highly reactive benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE). Glutathione S-transferase M1 (GSTM1) catalyses the conjugation of drugs, toxins and products of oxidative stress with glutathione. The aim of the study is to found possible associations between GSTM1 genotypes and the level of BPDE-DNA adducts in 46 psoriatic patients treated with GT...
August 29, 2016: Acta Medica (Hradec Králové)
Xiaoli Xu, Cheng Peng, Xiaofu Wang, Xiaoyun Chen, Qiang Wang, Junfeng Xu
This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators...
September 8, 2016: Transgenic Research
Wen Liang, Li Xu, Zhiwei Sui, Yan Li, Lanying Li, Yanli Wen, Chunhua Li, Shuzhen Ren, Gang Liu
BACKGROUND: The accuracy and metrology traceability of DNA quantification is becoming a critical theme in many fields, including diagnosis, forensic analysis, microorganism detection etc. Thus the research of DNA reference materials (RMs) and consistency of DNA quantification methods has attracted considerable research interest. RESULTS: In this work, we developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively...
2016: Chemistry Central Journal
Chiara Villa, Jo Buckberry, Niels Lynnerup
Age at death estimation of human skeletal remains is one of the key issues in constructing a biological profile both in forensic and archaeological contexts. The traditional adult osteological methods evaluate macroscopically the morphological changes that occur with increasing age of specific skeletal indicators, such as the cranial sutures, the pubic bone, the auricular surface of the ilium and the sternal end of the ribs. Technologies such as computed tomography and laser scanning are becoming more widely used in anthropology, and several new methods have been developed...
September 13, 2016: Journal of Anatomy
Liesbet Deprez, Philippe Corbisier, Anne-Marie Kortekaas, Stéphane Mazoua, Roxana Beaz Hidalgo, Stefanie Trapmann, Hendrik Emons
Digital PCR has become the emerging technique for the sequence-specific detection and quantification of nucleic acids for various applications. During the past years, numerous reports on the development of new digital PCR methods have been published. Maturation of these developments into reliable analytical methods suitable for diagnostic or other routine testing purposes requires their validation for the intended use. Here, the results of an in-house validation of a droplet digital PCR method are presented...
September 2016: Biomolecular Detection and Quantification
Fran Van Heuverswyn, Maria Karczmarczyk, Heinz Schimmel, Stefanie Trapmann, Hendrik Emons
Compared to other PCR technologies, digital PCR is a potentially highly accurate approach for the quantification of nucleic acid fragments. This study describes the impact of four experimental factors, namely primer and probe chemistry, PCR amplification target, duplexing, and template type, on the measurement results obtained by reverse transcription digital PCR (RT-dPCR) of viral RNA using influenza A virus as a model. Along conventional dual labelled probes (DLP), alternative primer and probe chemistries, including Zip Nucleic Acids (ZNAs), Locked Nucleic Acids (LNAs), and Scorpions(®), were compared with two RNA template types: i) total genomic RNA extracted from cell cultured influenza A and ii) a synthetically prepared RNA transcript (In vitro transcribed RNA)...
September 2016: Biomolecular Detection and Quantification
Ruurd C Verheul, Judith C T van Deutekom, Nicole A Datson
Antisense oligonucleotides (AONs) in clinical development for Duchenne muscular dystrophy (DMD) aim to induce skipping of a specific exon of the dystrophin transcript during pre-mRNA splicing. This results in restoration of the open reading frame and consequently synthesis of a dystrophin protein with a shorter yet functional central rod domain. To monitor the molecular therapeutic effect of exon skip-inducing AONs in clinical studies, accurate quantification of pre- and post-treatment exon skip levels is required...
2016: PloS One
Anja Perlich, Christoph Meinel
There is significant, unexploited potential to improve the patients' engagement in psychotherapy treatment through technology use. We develop Tele-Board MED (TBM), a digital tool to support documentation and patient-provider collaboration in medical encounters. Our objective is the evaluation of TBM's practical effects on patient-provider relationships and patient empowerment in the domain of talk-based mental health interventions. We tested TBM in individual therapy sessions at a psychiatric ward using action research methods...
2016: Studies in Health Technology and Informatics
Yang Zou, Peiwen Xu, Jie Li, Sexin Huang, Ming Gao, Ranran Kang, Xuan Gao, Yuan Gao
OBJECTIVE: To explore the clinical application of droplet digital PCR (ddPCR) for genetic testing and prenatal diagnosis of spinal muscular atrophy (SMA) with deletion of SMN1 gene exon 7. METHODS: A total of 138 clinical samples, including 121 peripheral blood, 13 amniotic fluid, 2 umbilical cord blood and 2 chorionic villi from 56 SMA families, were tested by both ddPCR and multiplex ligation-dependent probe amplification (MLPA). Results of the two approaches were analyzed with commercial software QuantaSoft (ddPCR) and Coffalyser (MLPA), respectively...
October 2016: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Tatsuo Ohira, Kazuko Sakai, Jun Matsubayashi, Naohiro Kajiwara, Masatoshi Kakihana, Masaru Hagiwara, Masaaki Hibi, Koichi Yoshida, Junichi Maeda, Keishi Ohtani, Toshitaka Nagao, Kazuto Nishio, Norihiko Ikeda
Next-generation sequencing (NGS) and digital polymerase chain reaction (PCR) technologies allow analysis of the mutational profile of circulating cell-free DNA (cfDNA) in individuals with advanced lung cancer. We have now evaluated the feasibility of cfDNA sequencing for mutation detection in patients with non-small cell lung cancer (NSCLC) at earlier stages. A total of 150 matched tumor and serum samples were collected from NSCLC patients at stages IA-IIIA. Amplicon sequencing with DNA extracted from tumor tissue detected frequent mutations in EGFR (37% of patients), TP53 (39%), and KRAS (10%), consistent with previous findings...
August 30, 2016: Cancer Science
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