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https://www.readbyqxmd.com/read/28548560/microalgal-oil-from-schizochytrium-sp-prevents-hfd-induced-abdominal-fat-accumulation-in-mice
#1
Jinhui Yu, Yong Ma, Jie Sun, Liyuan Ran, Youwei Li, Ning Wang, Tao Yu, Wenting Gao, Wenbin Jia, Rujiao Jiang, Meihua Guo, Yuping Bi, Yingjie Wu
OBJECTIVE: Dietary n-3 polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acids (EPA) and docosahexaenoic acid (DHA), are proved to be effective in obesity reduction. Microalgal oil (MO) is an important alternative source of n-3 PUFAs that effectively alleviates obesity. The aim of the present study was to explore the anti-obesity effects of microalgal oil from Schizochytrium sp. (SMO) and to compare the effects of 2 SMOs (SMO1 and SMO2) with different levels of purity of n-3 PUFAs on high fat diet (HFD)-induced obesity in male C57BL/6J mice...
May 26, 2017: Journal of the American College of Nutrition
https://www.readbyqxmd.com/read/28546538/droplet-digital-pcr-versus-qpcr-for-gene-expression-analysis-with-low-abundant-targets-from-variable-nonsense-to-publication-quality-data
#2
Sean C Taylor, Genevieve Laperriere, Hugo Germain
Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28540249/liquid-biopsies-for-bladder-cancer
#3
EDITORIAL
Douglas G Ward, Richard T Bryan
The development of accurate urinary biomarkers for the non-invasive detection of urothelial bladder cancer (UBC) could transform patient pathways by reducing reliance on cystoscopy, and the identification of highly prognostic (or even predictive) biomarkers could better guide patient management. A number of approaches are being utilised to address these challenges in both urinary- and plasma-borne tumour DNA (tDNA), so-called "liquid biopsies". Next generation sequencing (NGS) and droplet digital PCR (ddPCR) allow detection of very low levels of such tDNA amongst a large excess of non-tumour DNA, the former permitting large mutation panels to be assessed and the latter potentially identifying ultrarare mutant alleles yet restricted for multiplexing...
April 2017: Translational Andrology and Urology
https://www.readbyqxmd.com/read/28539377/dietary-starch-intake-modifies-the-relation-between-copy-number-variation-in-the-salivary-amylase-gene-and-bmi
#4
Gull Rukh, Ulrika Ericson, Johanna Andersson-Assarsson, Marju Orho-Melander, Emily Sonestedt
Background: Studies have shown conflicting associations between the salivary amylase gene (AMY1) copy number and obesity. Salivary amylase initiates starch digestion in the oral cavity; starch is a major source of energy in the diet.Objective: We investigated the association between AMY1 copy number and obesity traits, and the effect of the interaction between AMY1 copy number and starch intake on these obesity traits.Design: We first assessed the association between AMY1 copy number (genotyped by digital droplet polymerase chain reaction) and obesity traits in 4800 individuals without diabetes (mean age: 57 y; 60% female) from the Malmö Diet and Cancer Cohort...
May 24, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28529628/cross-platform-comparison-of-four-leading-technologies-for-detecting-egfr-mutations-in-circulating-tumor-dna-from-non-small-cell-lung-carcinoma-patient-plasma
#5
Ting Xu, Xiaozheng Kang, Xiaofang You, Liang Dai, Dequan Tian, Wanpu Yan, Yongbo Yang, Hongchao Xiong, Zhen Liang, Grace Q Zhao, Shengrong Lin, Ke-Neng Chen, Guobing Xu
Analysis of circulating tumor DNA (ctDNA) is emerging as a powerful tool for guiding targeted therapy and monitoring tumor evolution in patients with non-small cell lung cancer (NSCLC), especially when representative tissue biopsies are not available. Here, we have compared the ability of four leading technology platforms to detect epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, T790M and G719X) in ctDNA from NSCLC patients. Two amplification refractory mutation systems (cobas-ARMS and ADx-ARMS), a droplet digital polymerase chain reaction (ddPCR) and a next-generation sequencing (Firefly NGS) platform were included in the comparison...
2017: Theranostics
https://www.readbyqxmd.com/read/28529033/high-throughput-characterization-of-hiv-1-reservoir-reactivation-using-a-single-cell-in-droplet-pcr-assay
#6
Robert W Yucha, Kristen S Hobbs, Emily Hanhauser, Louise E Hogan, Wildaliz Nieves, Mehmet O Ozen, Fatih Inci, Vanessa York, Erica A Gibson, Cassandra Thanh, Hadi Shafiee, Rami El Assal, Maja Kiselinova, Yvonne P Robles, Helen Bae, Kaitlyn S Leadabrand, ShuQi Wang, Steven G Deeks, Daniel R Kuritzkes, Utkan Demirci, Timothy J Henrich
Reactivation of latent viral reservoirs is on the forefront of HIV-1 eradication research. However, it is unknown if latency reversing agents (LRAs) increase the level of viral transcription from cells producing HIV RNA or harboring transcriptionally-inactive (latent) infection. We therefore developed a microfluidic single-cell-in-droplet (scd)PCR assay to directly measure the number of CD4(+) T cells that produce unspliced (us)RNA and multiply spliced (ms)RNA following ex vivo latency reversal with either an histone deacetylase inhibitor (romidepsin) or T cell receptor (TCR) stimulation...
May 4, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28527094/circulating-tumor-dna-measurement-by-picoliter-droplet-based-digital-pcr-and-vemurafenib-plasma-concentrations-in-patients-with-advanced-braf-mutated-melanoma
#7
Fanny Garlan, Benoit Blanchet, Nora Kramkimel, Alicja Puszkiel, Jean-Louis Golmard, Gaelle Noe, Nicolas Dupin, Pierre Laurent-Puig, Michel Vidal, Valerie Taly, Audrey Thomas-Schoemann
BACKGROUND: Circulating tumor DNA (ctDNA) has been reported as a prognostic marker in melanoma. In BRAF V600-mutant melanoma, a plasma under-exposure to vemurafenib could favor emerging resistance but no biological data are available to support this hypothesis. OBJECTIVE: We aimed to investigate the relationship between vemurafenib plasma concentrations and the ctDNA plasma concentration during follow-up of BRAF-mutated melanoma patients. PATIENTS AND METHODS: Eleven patients treated with single-agent vemurafenib for advanced BRAF V600-mutant melanoma were analyzed in an exploratory monocentric study...
May 19, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/28525638/glucokinase-gene-may-be-a-more-suitable-target-than-the-insulin-gene-for-detection-of-beta-cell-death
#8
J Sklenarova, L Petruzelkova, S Kolouskova, J Lebl, Z Sumnik, O Cinek
Detection and quantification of unmethylated circulating insulin (INS) DNA presumably released from beta cells has been previously used for assessing their destruction. As the targets within the INS gene suffer from suboptimal specificity, we sought to improve the assay parameters by using the glucokinase gene (GCK) tissue-specific pancreatic promoter.The amount of methylated and unmethylated GCK DNA was measured using a droplet PCR assay, and compared with the previously published INS-targeted assay. The method was tested using synthetic target sequences and DNA from pancreatic islets, blood, brain, kidney, large intestine, liver, lung, small intestine and stomach...
May 18, 2017: Endocrinology
https://www.readbyqxmd.com/read/28522907/droplet-digital-pcr-for-quantification-of-itga6-in-a-stool-mrna-assay-for-the-detection-of-colorectal-cancers
#9
Elizabeth Herring, Shigeru Kanaoka, Éric Tremblay, Jean-François Beaulieu
AIM: To investigate the use of droplet digital polymerase chain reaction (ddPCR) for detecting host mRNA markers in stools as a non-invasive test for colorectal cancer screening. METHODS: ddPCR and quantitative PCR were compared side by side for their performance in the detection of ITGA6 and ITGA6A transcripts in stool samples obtained from patients with various types of colorectal lesions (advanced adenomas and stage II-IV colorectal cancers) and control (patients displaying no pathological findings) using duplex TaqMan reactions for both methods...
April 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28515773/building-a-multipurpose-insertional-mutant-library-for-forward-and-reverse-genetics-in-chlamydomonas
#10
Xi Cheng, Gai Liu, Wenting Ke, Lijuan Zhao, Bo Lv, Xiaocui Ma, Nannan Xu, Xiaoling Xia, Xuan Deng, Chunlei Zheng, Kaiyao Huang
BACKGROUND: The unicellular green alga, Chlamydomonas reinhardtii, is a classic model for studying flagella and biofuel. However, precise gene editing, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system, is not widely used in this organism. Screening of random insertional mutant libraries by polymerase chain reaction provides an alternate strategy to obtain null mutants of individual gene. But building, screening, and maintaining such a library was time-consuming and expensive...
2017: Plant Methods
https://www.readbyqxmd.com/read/28499138/human-pegivirus-1-in-the-csf-of-patients-with-hiv-associated-neurocognitive-disorder-hand-may-be-derived-from-blood-in-highly-viraemic-patients
#11
Diana Hardie, Heidi Smuts
BACKGROUND: Human pegivirus-1 (HPgV-1) infection in the brain has not been extensively examined and its association with disease remains unconfirmed. In a high throughput sequencing study to look for infectious agents that could play a role in HIV-associated neurocognitive disorder (HAND), this virus was detected in 3 of 8 CSF samples. OBJECTIVES: To determine the significance of this finding, additional patients were screened and the viral load and viral diversity in blood and CSF were examined...
April 6, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28497651/harnessing-the-power-of-digital-droplet-pcr-to-conduct-real-world-microbial-competitions
#12
Helen A Murphy
The budding yeast, Saccharomyces cerevisiae, has a long and storied history as a model organism for genetic, cellular and molecular biological research. More recently, researchers have sought to understand the ecology and evolution of its sister species, Saccharomyces paradoxus, in part to put our vast knowledge of the model yeast into its natural context (Replansky et al. ). However, the research tools have been limited, and most investigations into natural populations have either been descriptions of patterns of biogeography or taken the organism back into the laboratory for mating, growth and competition assays (Kuehne et al...
May 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28494459/influence-of-bovine-serum-lipids-and-fetal-bovine-serum-on-the-expression-of-cell-surface-markers-in-cultured-bovine-preadipocytes
#13
Mansur A Sandhu, Sandra Jurek, Susanne Trappe, Martin Kolisek, Gerhard Sponder, Jörg R Aschenbach
To establish the influence of fetal bovine serum (FBS) and bovine serum lipids (BSL) on cell differentiation marker expression, bovine adipose-derived stem cells from subcutaneous tissue were incubated for 14 days in 4 types of differentiation media containing 10% FBS and 10 µL/mL BSL (TRT-1), no FBS and 10 µL/mL of BSL (TRT-2), 10% FBS and no BSL (TRT-3), or no supplements (TRT-4). Cells were subjected to Nile red staining, immunocytochemistry (CD73, CD90, CD105, DLK1, FabP4), and quantitative real-time PCR (CD73, CD90, CD105, FabP4)...
May 12, 2017: Cells, Tissues, Organs
https://www.readbyqxmd.com/read/28490568/noninvasive-detection-of-f8-int22h-related-inversions-and-sequence-variants-in-maternal-plasma-of-hemophilia-carriers
#14
Irena Hudecova, Peiyong Jiang, Joanna Davies, Y M Dennis Lo, Rezan A Kadir, Rossa W K Chiu
Direct detection of F8 and F9 sequence variants in maternal plasma of hemophilia carriers has been demonstrated by microfluidics digital PCR. Noninvasive prenatal assessment of the most clinically relevant group of sequence variants among hemophilia patients, namely those involving int22h-related inversions disrupting the F8 gene, poses additional challenges due to its molecular complexity. We investigated the use of droplet digital PCR (ddPCR) and targeted massively parallel sequencing (MPS) for maternal plasma DNA analysis to noninvasively determine fetal mutational status in pregnancies at risk for hemophilia...
May 10, 2017: Blood
https://www.readbyqxmd.com/read/28489996/cancer-associated-mutations-in-endometriosis-without-cancer
#15
Michael S Anglesio, Nickolas Papadopoulos, Ayse Ayhan, Tayyebeh M Nazeran, Michaël Noë, Hugo M Horlings, Amy Lum, Siân Jones, Janine Senz, Tamer Seckin, Julie Ho, Ren-Chin Wu, Vivian Lac, Hiroshi Ogawa, Basile Tessier-Cloutier, Rami Alhassan, Amy Wang, Yuxuan Wang, Joshua D Cohen, Fontayne Wong, Adnan Hasanovic, Natasha Orr, Ming Zhang, Maria Popoli, Wyatt McMahon, Laura D Wood, Austin Mattox, Catherine Allaire, James Segars, Christina Williams, Cristian Tomasetti, Niki Boyd, Kenneth W Kinzler, C Blake Gilks, Luis Diaz, Tian-Li Wang, Bert Vogelstein, Paul J Yong, David G Huntsman, Ie-Ming Shih
BACKGROUND: Endometriosis, defined as the presence of ectopic endometrial stroma and epithelium, affects approximately 10% of reproductive-age women and can cause pelvic pain and infertility. Endometriotic lesions are considered to be benign inflammatory lesions but have cancerlike features such as local invasion and resistance to apoptosis. METHODS: We analyzed deeply infiltrating endometriotic lesions from 27 patients by means of exomewide sequencing (24 patients) or cancer-driver targeted sequencing (3 patients)...
May 11, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28487054/reduced-cost-chlamydia-trachomatis-specific-multiplex-real-time-pcr-diagnostic-assay-evaluated-for-ocular-swabs-and-use-by-trachoma-research-programmes
#16
Robert Butcher, Jo Houghton, Tamsyn Derrick, Athumani Ramadhani, Beatriz Herrera, Anna R Last, Patrick A Massae, Matthew J Burton, Martin J Holland, Chrissy H Roberts
INTRODUCTION: Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct), is the leading infectious cause of preventable blindness. Many commercial platforms are available that provide highly sensitive and specific detection of Ct DNA. However, the majority of these commercial platforms are inaccessible for population-level surveys in resource-limited settings typical to trachoma control programmes. We developed two low-cost quantitative PCR (qPCR) tests for Ct using readily available reagents on standard real-time thermocyclers...
May 6, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28485163/microarray-profiling-defines-circulating-micrornas-associated-with-myelodysplastic-syndromes
#17
M Dostalova Merkerova, A Hrustincova, Z Krejcik, H Votavova, E Ratajova, J Cermak, M Belickova
Circulating microRNAs (miRNAs) are non-coding RNAs secreted into body fluids, and aberrant levels of these miRNAs correlate with diseases of various origins, making them highly potential clinical biomarkers. We investigated the spectrum of circulating miRNAs in the plasma of myelodysplastic syndrome (MDS) patients to identify miRNAs showing discriminatory levels in the patients with different prognosis. Plasma samples were analyzed with microarrays to define miRNA profiles, and the deregulated miRNAs were further studied using droplet digital PCR...
May 9, 2017: Neoplasma
https://www.readbyqxmd.com/read/28484715/plasma-circulating-tumor-dna-levels-for-the-monitoring-of-melanoma-patients-landscape-of-available-technologies-and-clinical-applications
#18
REVIEW
Benoit Busser, Julien Lupo, Lucie Sancey, Stéphane Mouret, Patrice Faure, Joel Plumas, Laurence Chaperot, Marie Thérèse Leccia, Jean Luc Coll, Amandine Hurbin, Pierre Hainaut, Julie Charles
Melanoma is a cutaneous cancer with an increasing worldwide prevalence and high mortality due to unresectable or metastatic stages. Mutations in BRAF, NRAS, or KIT are present in more than 60% of melanoma cases, but a useful blood-based biomarker for the clinical monitoring of melanoma patients is still lacking. Thus, the analysis of circulating tumor cells (CTCs) and/or cell-free circulating tumor DNA (ctDNA) analysis from blood (liquid biopsies) appears to be a promising noninvasive, repeatable, and systemic sampling tool for detecting and monitoring melanoma...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28483527/immuno-pcr-with-digital-readout
#19
Hendrik Schröder, Maximilian Grösche, Michael Adler, Mark Spengler, Christof M Niemeyer
Immuno-PCR (IPCR) combines the versatile ELISA antigen detection with ultrasensitive PCR signal amplification, thereby enabling the highly sensitive detection of a broad range of targets with a typically very large dynamic detection range. The quantification of the antigen is usually achieved by real-time PCR, which provides a correlation between the target concentration and amplified DNA marker. We here report on the implementation of digital droplet PCR as a means for direct quantification of DNA copies to enable the highly sensitive detection of protein biomarkers...
May 5, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28477149/current-and-emerging-applications-of-droplet-digital-pcr-in-oncology
#20
REVIEW
Susana Olmedillas-López, Mariano García-Arranz, Damián García-Olmo
The clinical management of cancer has evolved in recent years towards more personalized strategies that require a comprehensive knowledge of the complex molecular features involved in tumor growth and evolution, and the development of drug resistance mechanisms leading to disease progression. Droplet digital PCR (ddPCR) has become one of the most accurate and reliable tools for the examination of genetic alterations in a wide variety of cancers because of its high sensitivity and specificity. ddPCR is currently being applied for absolute allele quantification, rare mutation detection, analysis of copy number variations, DNA methylation, and gene rearrangements in different kinds of clinical samples...
May 5, 2017: Molecular Diagnosis & Therapy
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