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https://www.readbyqxmd.com/read/28723116/integrated-magnetic-bead-quantum-dot-immunoassay-for-malaria-detection
#1
Chloe Kim, Gwendolyn Hoffmann, Peter C Searson
Malaria persists as a disease of high morbidity and mortality due to improper diagnosis, overuse of drugs, rapidly evolving drug resistant parasites, and poor disease monitoring. The two common tests used in developing countries, microscopic examination of Glemsa slides and rapid diagnostic tests (RDTs), have limitations associated with variability in specificity and sensitivity, and qualitative outcome. Here we report on an immunoassay using magnetic beads for capture and quantum dots for detection of histidine-rich protein 2 (HRP2)...
June 23, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722675/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#2
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28720682/reducing-artifactual-egfr-t790m-mutations-in-dna-from-formalin-fixed-paraffin-embedded-tissue-by-use-of-thymine-dna-glycosylase
#3
Hongdo Do, Ramyar Molania, Paul L Mitchell, Rita Vaiskunaite, John D Murdoch, Alexander Dobrovic
BACKGROUND: False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28720421/assessment-of-the-hiv-1-reservoir-in-cd4-regulatory-t-cells-by-a-droplet-digital-pcr-based-approach
#4
Gábor Artúr Dunay, Anastasia Solomatina, Silke Kummer, Anja Hüfner, Julia Katharina Bialek, Johanna Maria Eberhard, Eva Tolosa, Joachim Hauber, Julian Schulze Zur Wiesch
The relative contribution of regulatory T cells (Treg) as reservoir of HIV-1 in patients on chronic antiretroviral therapy is unclear to date. The aim of the current study was to assess the total HIV DNA burden and replication competent viral reservoir in Treg in comparison to central and effector memory cells (Tcm and Tem). Peripheral blood mononuclear cells were obtained from 10 HIV patients treated with antiretroviral therapy and one HIV elite controller. Droplet Digital PCR (ddPCR) was used to quantify total HIV DNA loads in FACS sorted CD4+ Treg (CD25+CD127lo) as compared with Tcm (CD45RO+CCR7+) and Tem (CD45RO+CCR7-)...
July 15, 2017: Virus Research
https://www.readbyqxmd.com/read/28714107/the-braf-and-nras-mutation-prevalence-in-dermoscopic-subtypes-of-acquired-naevi-reveals-constitutive-mapk-pathway-activation
#5
J M Tan, L N Tom, K Jagirdar, D Lambie, H Schaider, R A Sturm, H P Soyer, M S Stark
BACKGROUND: Acquired naevi can have unique dermoscopic patterns that correspond to distinct microanatomical growth patterns. Previous studies on acquired naevi stratified according to dermoscopic pattern, focused on the frequency of somatic BRAF mutations, whereas NRAS mutations remained to be elucidated. OBJECTIVES: To investigate the BRAF and NRAS mutation prevalence and activation of the MAPK pathway in distinct dermoscopic subtypes of acquired naevi. METHODS: Common mutations present in BRAF and NRAS were assessed in 40 globular, reticular, and peripheral rim of globules (PG) subtypes of acquired naevi from 27 participants (19 male, 8 female; mean age 46...
July 17, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28711990/assessment-of-braf-v600e-mutation-in-pulmonary-langerhans-cell-histiocytosis-in-tissue-biopsies-and-bronchoalveolar-lavages-by-droplet-digital-polymerase-chain-reaction
#6
Clémence Pierry, Charline Caumont, Elodie Blanchard, Camille Brochet, Gael Dournes, Audrey Gros, Thomas Bandres, Séverine Verdon, Marion Marty, Hugues Bégueret, Jean-Philippe Merlio
The neoplastic nature of pulmonary Langerhans cell histiocytosis (PLCH) is still debated. As the detection of BRAF (V600E) and MAP2K1 mutations in patients with PCLH is now considered for such assessment, the aim of our study was to evaluate digital droplet polymerase chain reaction (ddPCR) in PCLH diagnosis. We retrospectively analyzed BRAF(V600E) detection in a cohort of 42 PCLH tissues and 18 bronchoalveolar lavages (BALs) by ddPCR, immunohistochemistry, high-resolution melting PCR (HRM), and next-generation sequencing (NGS)...
July 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28711173/presymptomatic-diagnosis-of-spinal-muscular-atrophy-through-newborn-screening
#7
Yin-Hsiu Chien, Shu-Chuan Chiang, Wen-Chin Weng, Ni-Chung Lee, Ching-Jie Lin, Wu-Shiun Hsieh, Wang-Tso Lee, Yuh-Jyh Jong, Tsang-Ming Ko, Wuh-Liang Hwu
OBJECTIVE: To demonstrate the feasibility of presymptomatic diagnosis of spinal muscular atrophy (SMA) through newborn screening (NBS). STUDY DESIGN: We performed a screening trial to assess all newborns who underwent routine newborn metabolic screening at the National Taiwan University Hospital newborn screening center between November 2014 and September 2016. A real-time polymerase chain reaction (RT-PCR) genotyping assay for the SMN1/SMN2 intron 7 c.888+100A/G polymorphism was performed to detect homozygous SMN1 deletion using dried blood spot (DBS) samples...
July 12, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28701865/processed-panax-ginseng-sun-ginseng-inhibits-the-differentiation-and-proliferation-of-3t3-l1-preadipocytes-and-fat-accumulation-in-caenorhabditis-elegans
#8
Hyejin Lee, Jinhee Kim, Jun Yeon Park, Ki Sung Kang, Joeng Hill Park, Gwi Seo Hwang
BACKGROUND: Heat-processed ginseng, sun ginseng (SG), has been reported to have improved therapeutic properties compared with raw forms, such as increased antidiabetic, anti-inflammatory, and antihyperglycemic effects. The aim of this study was to investigate the antiobesity effects of SG through the suppression of cell differentiation and proliferation of mouse 3T3-L1 preadipocyte cells and the lipid accumulation in Caenorhabditis elegans. METHODS: To investigate the effect of SG on adipocyte differentiation, levels of stained intracellular lipid droplets were quantified by measuring the oil red O signal in the lipid extracts of cells on differentiation Day 7...
July 2017: Journal of Ginseng Research
https://www.readbyqxmd.com/read/28694163/mice-maintain-predominantly-maternal-g%C3%AE-s-expression-throughout-life-in-brown-fat-tissue-bat-but-not-other-tissues
#9
Olta Tafaj, Steven Hann, Ugur Ayturk, Matthew L Warman, Harald Jüppner
The murine Gnas (human GNAS) locus gives rise to Gαs and different splice variants thereof. The Gαs promoter is not methylated thus allowing biallelic expression in most tissues. In contrast, the alternative first Gnas/GNAS exons and their promoters undergo parent specific methylation, which limits transcription to the non-methylated allele. Pseudohypoparathyroidism type Ia (PHP1A) or type Ib (PHP1B) are caused by heterozygous maternal GNAS mutations suggesting that little or no Gαs is derived in some tissues from the non-mutated paternal GNAS thereby causing hormonal resistance...
July 8, 2017: Bone
https://www.readbyqxmd.com/read/28692535/effect-of-cmv-and-ebv-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#10
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: Eighty biopsies from left and right colon (n=63) and terminal ileum (n = 17) were collected from 19 HIV-infected and 22 HIV-uninfected subjects. Levels of cytomegalovirus (CMV) and Epstein Barr Virus (EBV) DNA were measured by droplet-digital (dd)PCR. Mucosal gene expression was measured via multiplex-assay. Microbiome analysis was performed using bacterial 16S-rDNA-pyrosequencing...
July 7, 2017: AIDS
https://www.readbyqxmd.com/read/28692472/quantification-of-immune-dysregulation-by-next-generation-polymerase-chain-reaction-to-improve-sepsis-diagnosis-in-surgical-patients
#11
Raquel Almansa, Alicia Ortega, Ana Ávila-Alonso, Maria Heredia-Rodríguez, Silvia Martín, Diana Benavides, Marta Martín-Fernandez, Lucia Rico, César Aldecoa, Jesús Rico, Iñigo López de Cenarruzabeitia, Juan Beltrán de Heredia, Esther Gomez-Sanchez, Marta Aragón, Cristina Andrés, Dolores Calvo, David Andaluz-Ojeda, Pilar Liu, Francisco Blanco-Antona, Lydia Blanco, Jose Ignacio Gómez-Herreras, Eduardo Tamayo, Jesus F Bermejo-Martin
OBJECTIVES: To quantify immunological dysfunction in surgical patients with presence/absence of sepsis using a droplet digital polymerase chain reaction (ddPCR) transcriptomic analysis. The study also aims to evaluate this approach for improving identification of sepsis in these patients. BACKGROUND: Immune dysregulation is a central event in sepsis. Quantification of the expression of immunological genes participating in the pathogenesis of sepsis could represent a new avenue to improve its diagnosis...
July 7, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28691397/cyanidin-3-glucoside-increases-whole-body-energy-metabolism-by-upregulating-brown-adipose-tissue-mitochondrial-function
#12
Yilin You, Xiaoxue Yuan, Xiaomeng Liu, Chen Liang, Minghui Meng, Yuanyuan Huang, Xue Han, Jielong Guo, Yu Guo, Chenglong Ren, Qianwen Zhang, Xiangyu Sun, Tingting Ma, Guojie Liu, Wanzhu Jin, Weidong Huang, Jicheng Zhan
SCOPE: Obesity develops when energy intake exceeds energy expenditure. Promoting brown adipose tissue (BAT) formation and function increases energy expenditure and may protect against obesity. Cyanidin-3-glucoside (C3G) is an anthocyanin compound which occurs naturally in many fruits and vegetables. In this study, we investigated the effect and mechanism of C3G on the prevention of obesity. METHODS AND RESULTS: Db/db mice received C3G dissolved in drinking water for 16 weeks; Drinking water served as the vehicle treatment...
July 10, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28691390/an-improved-digital-polymerase-chain-reaction-protocol-to-capture-low-copy-kras-mutations-in-plasma-cell-free-dna-by-resolving-subsampling-issues
#13
REVIEW
Yusuke Ono, Ayumu Sugitani, Hidenori Karasaki, Munehiko Ogata, Reo Nozaki, Junpei Sasajima, Tomoki Yokochi, Shingo Asahara, Kazuya Koizumi, Kiyohiro Ando, Katsunori Hironaka, Tsutomu Daito, Yusuke Mizukami
Genetic alterations responsible for the initiation of cancer may serve as immediate biomarkers for early diagnosis. Plasma levels of cell-free DNA (cfDNA) in cancer patients are higher than those in healthy individuals, however, the major technical challenge for the widespread implementation of cfDNA genotyping as a diagnostic tool is the insufficient sensitivity and specificity of detecting early-stage tumors that shed low amounts of cfDNA. To establish a protocol for ultrasensitive droplet digital polymerase chain reaction (ddPCR) for quantification of low-frequency alleles within a limited cfDNA pool, two-step multiplex ddPCR targeting eight clinically relevant mutant KRAS variants was examined...
July 10, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28687414/ovarian-expression-and-localization-of-clathrin-cltc-components-in-cutthroat-trout-oncorhynchus-clarki-evidence-for-cltc-involvement-in-endocytosis-of-vitellogenin-during-oocyte-growth
#14
Hiroko Mizuta, Yuji Mushirobira, Jun Nagata, Takashi Todo, Akihiko Hara, Benjamin J Reading, Craig V Sullivan, Naoshi Hiramatsu
To evaluate potential involvement of clathrin in endocytosis of vitellogenin (Vtg) by teleost oocytes, cDNAs encoding clathrin heavy chain (cltc) were cloned from ovaries of cutthroat trout. Quantitative PCR revealed three types of cltc (cltc-a1, cltc-a2, cltc-b) to be expressed in 10 different tissues including the ovary. The cltc-a1 alone exhibited a significant decrease in ovarian expression during vitellogenesis; this was correlated with a corresponding decrease in transcripts encoding the major Vtg receptor (Vtgr)...
July 4, 2017: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/28683077/dna-isolation-protocol-effects-on-nuclear-dna-analysis-by-microarrays-droplet-digital-pcr-and-whole-genome-sequencing-and-on-mitochondrial-dna-copy-number-estimation
#15
Elizabeth Nacheva, Katya Mokretar, Aynur Soenmez, Alan M Pittman, Colin Grace, Roberto Valli, Ayesha Ejaz, Selina Vattathil, Emanuela Maserati, Henry Houlden, Jan-Willem Taanman, Anthony H Schapira, Christos Proukakis
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol...
2017: PloS One
https://www.readbyqxmd.com/read/28681063/circulating-tumour-dna-for-monitoring-treatment-response-to-anti-pd-1-immunotherapy-in-melanoma-patients
#16
Atsuko Ashida, Kaori Sakaizawa, Hisashi Uhara, Ryuhei Okuyama
Anti-programmed cell death-1 (anti-PD-1) antibody shows high therapeutic efficacy in patients with advanced melanoma. However, assessment of its therapeutic activity can be challenging because of tumour enlargement associated with intratumoural inflammation. Because circulating tumour DNA (ctDNA) correlates with tumour burden, we assessed the value of ctDNA levels as an indicator of tumour changes. Quantification of ctDNA (BRAFmutant or NRASmutant) levels by droplet digital PCR in 5 patients with BRAF or NRAS mutant melanoma during the treatment course showed dynamic changes corresponding to radiological and clinical alterations...
July 6, 2017: Acta Dermato-venereologica
https://www.readbyqxmd.com/read/28679689/two-different-mutually-exclusively-distributed-tp53-mutations-in-ovarian-and-peritoneal-tumor-tissues-of-a-serous-ovarian-cancer-patient-indicative-for-tumor-origin
#17
Nyamdelger Sukhbaatar, Anna Bachmayr-Heyda, Katharina Auer, Stefanie Aust, Simon Deycmar, Reinhard Horvat, Dietmar Pils
High-grade serous ovarian cancer (HGSOC) is characterized by a TP53 mutation rate of up to 96.7% and associated with a more aggressive tumor biology. The origin of HGSOC is thought to arise either from fallopian tube secretory cells or the ovarian surface epithelium/inclusion cysts, the former with more evidence. Peritoneal tumor spread is heterogeneous, either excessive in the peritoneum (with miliary appearance) or more confined to the ovaries with only few (bigger and exophytically growing) peritoneal implants...
July 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28673857/development-and-application-of-a-reverse-transcriptase-droplet-digital-pcr-rt-ddpcr-for-sensitive-and-rapid-detection-of-japanese-encephalitis-virus
#18
Xulong Wu, Hua Lin, Shijie Chen, Lu Xiao, Miao Yang, Wei An, Yin Wang, Xueping Yao, Zexiao Yang
Japanese encephalitis (JE) is one of the most common zoonoses caused by Japanese encephalitis virus (JEV). Droplet digital PCR (ddPCR) is a novel sensitive, accurate method that enables absolute quantitation without the need for calibration curves. The aim of this study was to develop a RT-ddPCR method to detect JEV, and to compare its sensitivity with real-time TaqMan RT-PCR by analysis of clinical samples. The methods of JEV real-time RT-PCR and RT-ddPCR were established and optimal reaction conditions were confirmed...
June 30, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28672891/osteogenic-potency-of-dedifferentiated-fat-cells-isolated-from-elderly-people-with-osteoporosis
#19
Wei Hao, Chuanqiang Jiang, Ming Jiang, Tian Wang, Xin Wang
Mature adipocytes are the major cell type in adipose tissue. This study aimed to explore the osteogenic potency of dedifferentiated fat cells obtained from osteoporotic patients (opDFATs) in vitro and in vivo. Mature adipocytes and adipose-derived stem cells (opASCs) were harvested from subcutaneous adipose tissue. Mature adipocytes were dedifferentiated to produce opDFATs by the ceiling culture method. OpDFATs were osteogenically induced in vitro with opASCs as a control. Cell growth, alkaline phosphatase (ALPase) activity and cell mineralization were determined, and expression levels of osteogenesis-specific genes (collagen I, osteocalcin and bone sialoprotein) were analyzed using quantitative reverse transcription polymerase chain reaction...
July 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28670746/hpv-circulating-tumor-dna-to-monitor-the-efficacy-of-anti-pd-1-therapy-in-metastatic-squamous-cell-carcinoma-of-the-anal-canal-a-case-report
#20
Luc Cabel, François-Clément Bidard, Vincent Servois, Wulfran Cacheux, Pascale Mariani, Emanuela Romano, Mathieu Minsat, Ivan Bieche, Fereshteh Farkhondeh, Emmanuelle Jeannot, Bruno Buecher
Squamous cell carcinoma of the anal canal (SCCA) is a rare HPV-associated cancer with limited sensitivity to standard chemotherapy. In a phase 2 study, nivolumab, an anti PD-1 immune checkpoint inhibitor, demonstrated significant efficacy as single-agent therapy in metastatic SCCA patients. Nevertheless, imaging assessment by standard RECIST criteria of the efficacy of immune therapy can be difficult in some patients due to tumor immune cell infiltration, and biomarkers of treatment efficacy are needed. We have previously developed a quantitative droplet digital PCR (ddPCR) technique to detect HPV circulating tumor DNA (HPV ctDNA), with excellent sensitivity and specificity...
July 3, 2017: International Journal of Cancer. Journal International du Cancer
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