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single cell pcr

Davina Gale, Andrew R J Lawson, Karen Howarth, Mikidache Madi, Bradley Durham, Sarah Smalley, John Calaway, Shannon Blais, Greg Jones, James Clark, Peter Dimitrov, Michelle Pugh, Samuel Woodhouse, Michael Epstein, Ana Fernandez-Gonzalez, Alexandra S Whale, Jim F Huggett, Carole A Foy, Gerwyn M Jones, Hadas Raveh-Amit, Karin Schmitt, Alison Devonshire, Emma Green, Tim Forshew, Vincent Plagnol, Nitzan Rosenfeld
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes...
2018: PloS One
Doaa Abdelmageed El Faham, Mohamed Amr Hussein Elnoury, Mona Ibraheim Morsy, Marwa Abdelmoneim El Shaer, Ghada Mohammed Nour Eldin, Osama Mahmoud Azmy
Low-level laser therapy (LLLT) has been used in photobiomodulation to promote healing, regenerate, and restore tissue function. Women with persistent thin endometrium were assumed to encounter diminished activity in the regenerative and functional capacity of their endometrium. The aim of this study was to examine the ability of LLLT in 635 nm wavelength to enhance the proliferation and gene expression of in vitro cultured endometrial cells. Single (SE) versus multiple exposures (ME) to LLLT were examined in the study groups and compared to controls...
March 15, 2018: Lasers in Medical Science
James W Checco, Guo Zhang, Wangding Yuan, Ke Yu, Siyuan Yin, Rachel H Roberts-Galbraith, Peter M Yau, Elena V Romanova, Jian Jing, Jonathan V Sweedler
Neuropeptides in several animals undergo an unusual post-translational modification: the isomerization of an amino acid residue from the L-stereoisomer to the D-stereoisomer. The resulting D-amino acid-containing peptide (DAACP) often displays higher biological activity than its all-L-residue analogue, with the D-residue being critical for function in many cases. However, little is known about the full physiological roles played by DAACPs and few studies have examined the interaction of DAACPs with their cognate receptors...
March 15, 2018: ACS Chemical Biology
Cosimo Cumbo, Luciana Impera, Crescenzio Francesco Minervini, Paola Orsini, Luisa Anelli, Antonella Zagaria, Nicoletta Coccaro, Giuseppina Tota, Angela Minervini, Paola Casieri, Claudia Brunetti, Antonella Russo Rossi, Elisa Parciante, Giorgina Specchia, Francesco Albano
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology...
February 16, 2018: Oncotarget
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
Katsuhito Matsuki, Daiki Kato, Masashi Takemoto, Yoshiaki Suzuki, Hisao Yamamura, Susumu Ohya, Hiroshi Takeshima, Yuji Imaizumi
Physiological functions of type 3 ryanodine receptors (RyR3) in smooth muscle (SM) tissues are not well understood, in spite of their wide expression. However, the short isoform of RyR3 is known to be a dominant negative variant (DN-RyR3), which may negatively regulate functions of both RyR2 and full length (FL)-RyR3 by forming hetero-tetramers. Here, functional roles of RyR3 in the regulation of Ca2+ signaling in mesenteric artery SM cells (MASMCs) were examined using RyR3 homozygous knockout mice (RyR3-/- )...
March 14, 2018: American Journal of Physiology. Cell Physiology
Meenakshi Mehrotra, Rajesh R Singh, Sanam Loghavi, Dzifa Yawa Duose, Bedia A Barkoh, Carmen Behrens, Keyur P Patel, Mark J Routbort, Scott Kopetz, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
A suitable clinical-grade platform is required for detection of somatic mutations with high sensitivity in cell-free DNA (cfDNA) of patients with solid tumors. In this study, we evaluated in parallel ultra-deep NGS with MassARRAY and allele-specific droplet digital PCR (ddPCR) for cfDNA genotyping and correlated cfDNA yield and mutation status with overall survival (OS) of patients. We assessed plasma samples from 46 patients with various advanced metastatic solid tumors and known mutations by deep sequencing using an Ampliseq cancer hotspot panel V2 on Ion Proton...
February 13, 2018: Oncotarget
Mohamad Assi, Nicolas Dauguet, Patrick Jacquemin
The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively...
2018: Frontiers in Physiology
F Wu, S Wu, X Gou
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer in adults. The aim of this study is to identify the biomarkers and potential molecular mechanisms of ccRCC. Three gene expression profiles and two miRNA expression profiles were downloaded from GEO database. A total of 330 up-regulated differentially expressed genes (DEGs), 545 down-regulated DEGs, 26 up-regulated differentially expressed miRNAs (DEMs) and 11 down-regulated DEMs were identified by GEO2R. The gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS software...
2018: Neoplasma
Husnain Ahmed, Jody Mays, Matti Kiupel, John R Dunn
A variety of techniques have been developed as diagnostic tools for the differential diagnosis of tumours produced by Marek's disease virus (MDV) from those induced by avian leukosis virus (ALV) and reticuloendotheliosis virus (REV). However, most current techniques are unreliable when used in formalin-fixed paraffin embedded (FFPE) tissues, which many times is the only sample type available for definitive diagnosis. A collection of tumours was generated by the inoculation of different strains of MDV, REV or ALV singularly or in combination...
March 13, 2018: Avian Pathology: Journal of the W.V.P.A
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
Patricia P Albani, Rachel Fleming
In forensic investigations, the identification of the cellular or body fluid source of biological evidence can provide crucial probative information for the court. Messenger RNA (mRNA) profiling has become a valuable tool for body fluid and cell type identification due to its high sensitivity and compatibility with DNA analysis. However, using a single marker to determine the somatic origin of a sample can lead to misinterpretation as a result of cross-reactions. While false positives may be avoided through the simultaneous detection of multiple markers per body fluid, this approach is currently limited by the small number of known differentially expressed mRNAs...
March 2018: Science & Justice: Journal of the Forensic Science Society
Zahra Tahmasebi Fard, Nahid Nafisi
BACKGROUND: Caveolae play a role in cell signal transduction, kinetic regulation of transport vesicles, and cellular physiology. In this study, we evaluated the role of caveolin-1 (CAV-1) genotypes in the risk of breast cancer. PATIENTS AND METHODS: We evaluated 6 single nucleotide polymorphisms of the CAV-1 gene in a sample size of 406 participants. Six polymorphisms-G32124A (rs3807992), T29107A (rs7804372), T28608A (rs3757733), G21985A (rs12672038), G14713A (rs3807987), and C521A (rs1997623)-were assessed using restriction fragment length polymorphism polymerase chain reaction...
January 31, 2018: Clinical Breast Cancer
Pavel Bashtrykov, Albert Jeltsch
Methylation of cytosine bases in DNA is one of the main epigenetic signals regulating gene expression and chromatin structure. The distribution of DNA methylation in the genome has a cell-type-specific pattern and can be modulated by internal or external stimuli. One of the most powerful approaches to investigate DNA methylation patterns is bisulfite conversion of the DNA followed by DNA sequencing, which allows to determine methylation patterns at a single-cytosine resolution. Here, we present a protocol for bisulfite DNA methylation analysis of targeted genomic regions using amplicon-based next-generation sequencing (NGS) on an Illumina sequencing system...
2018: Methods in Molecular Biology
MingXia Yu, Tao Cao, Dan Yu, Fusheng Huang
Genetic susceptibility to high mercury body burden has been suggested as an autism risk factor in children. Metallothionein III (MT3) is the brain-specific form of the metallothionein family, which plays a key role in metal metabolism. We therefore looked for genetic variations in the MT3 gene that might increase the predisposition to autism. DNA was extracted from 132 autistic children and 132 age and gender-matched unrelated controls. All the samples were analyzed for nine single nucleotide polymorphisms (SNPs) with minor allele frequency > 10% in the MT3 gene...
March 9, 2018: Neurotoxicity Research
Lunming Liu, Weifeng Shen, Zhihui Zhu, Jinxiong Lin, Qingxia Fang, Yeping Ruan, Huajun Zhao
Fulvestrant is the FDA-approved "pure anti-estrogen" agent for malignant breast cancer therapy. But endocrine resistance causes drug failure. A new approach is desired for fulvestrant-resistant breast cancer (FRBC) therapy. This study aims to find an effective approach to inhibit FRBC for patients with advanced breast cancer. MTT assay was first performed to detect the effect of inhibitors of c-ABL (imatinib) and EGFR (lapatinib) on FRBC cells. Microarray analysis was carried out to identify microRNA which is significantly changed between parental and FRBC cells...
March 6, 2018: Biochemical and Biophysical Research Communications
S Mashayekhi, H Saeidi Saedi, Z Salehi, S Soltanipour, E Mirzajani
Background microRNAs (miRNAs) are potentially involved in many physiopathological processes, including regulation of cell growth, differentiation, apoptosis and cancer. Single nucleotide polymorphisms of the genes encoding miRNAs can alter their expression and may influence cancer risks. This case-control study explored the relationship between three microRNA polymorphisms (miR-27a, miR-196a2 and miR -146a) and breast cancer (BC). Methods A total of 353 breast cancer cases and 353 controls were genotyped for miR-27a (rs895819), miR-196a2 (rs11614913) and miR -146a (rs2910164)...
March 9, 2018: British Journal of Biomedical Science
Athanasia Bletsa, Hisham Abdalla, Sigbjørn Løes, Ellen Berggreen
BACKGROUND: The lymphatic growth factors vascular endothelial growth factor (VEGF) -C and -D are important for maintenance and growth of lymphatic vessels (lymphangiogenesis), but their localization in human gingiva is unknown. This study investigated the expression of VEGF-C and -D in human gingiva and isolated human gingival fibroblasts (HGFs). In addition, the localization of their main receptor VEGFR-3 was explored. METHODS: Non-inflamed gingiva from 6 donors was used for immunohistochemistry or isolation of HGFs...
February 19, 2018: Journal of Periodontology
Rafael Taeho Han, Han-Byul Kim, Young-Beom Kim, Kyungmin Choi, Gi Yeon Park, Pa Reum Lee, JaeHee Lee, Hye Young Kim, Chul-Kyu Park, Youngnam Kang, Seog Bae Oh, Heung Sik Na
Recent studies have provided several lines of evidence that peripheral administration of oxytocin induces analgesia in human and rodents. However, the exact underlying mechanism of analgesia still remains elusive. In the present study, we aimed to identify which receptor could mediate the analgesic effect of intraperitoneal injection of oxytocin and its cellular mechanisms in thermal pain behavior. We found that oxytocin-induced analgesia could be reversed by d(CH2 )5 [Tyr(Me)2 ,Dab5 ] AVP, a vasopressin-1a (V1a) receptor antagonist, but not by desGly-NH2 -d(CH2 )5 [DTyr2 , Thr4 ]OVT, an oxytocin receptor antagonist...
March 2018: Korean Journal of Physiology & Pharmacology
Navin Sarin, Florian Engel, Florian Rothweiler, Jindrich Cinatl, Martin Michaelis, Roland Frötschl, Holger Fröhlich, Ganna V Kalayda
The major obstacle in the clinical use of the antitumor drug cisplatin is inherent and acquired resistance. Typically, cisplatin resistance is not restricted to a single mechanism demanding for a systems pharmacology approach to understand a whole cell's reaction to the drug. In this study, the cellular transcriptome of untreated and cisplatin-treated A549 non-small cell lung cancer cells and their cisplatin-resistant sub-line A549r CDDP2000 was screened with a whole genome array for relevant gene candidates...
March 7, 2018: International Journal of Molecular Sciences
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