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https://www.readbyqxmd.com/read/28333072/detection-of-circulating-tumor-cells-using-negative-enrichment-immunofluorescence-and-an-in-situ-hybridization-system-in-pancreatic-cancer
#1
Yu Xu, Tai Qin, Jing Li, Xiuchao Wang, Chuntao Gao, Chao Xu, Jihui Hao, Jingcheng Liu, Song Gao, He Ren
Pancreatic cancer (PC) is the most lethal type of gastrointestinal cancer, and early detection and monitoring is an urgent problem. Circulating tumor cells (CTCs) are emerging as a non-invasive biomarker for tumor detection. However, the low sensitivity is a main problem in the traditional CellSearch System for detecting CTCs, especially in patients with PC. In this study, we used negative enrichment (NE), immunofluorescence and in situ hybridization (FISH) of chromosome 8 (NE-iFISH) to capture and identify CTCs in PC patients...
March 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28330894/targeted-enrichment-for-pathogen-detection-and-characterization-in-three-felid-species
#2
Justin S Lee, Ryan S Mackie, Thomas Harrison, Basir Shariat, Trey Kind, Timo Kehl, Martin Löchelt, Christina Boucher, Sue VandeWoude
Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application detecting low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While prior studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting has not yet been evaluated...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28324158/the-influence-of-sex-and-diet-on-the-characteristics-of-hibernation-in-syrian-hamsters
#3
Marie Trefna, Maaike Goris, Cynthia M C Thissen, Vera A Reitsema, Jojanneke J Bruintjes, Edwin L de Vrij, Hjalmar R Bouma, Ate S Boerema, Robert H Henning
Research on deep hibernators almost exclusively uses species captured from the wild or from local breeding. An exception is Syrian hamster (Mesocricetus auratus), the only standard laboratory animal showing deep hibernation. In deep hibernators, several factors influence hibernation quality, including body mass, sex and diet. We examined hibernation quality in commercially obtained Syrian hamsters in relation to body mass, sex and a diet enriched in polyunsaturated fatty acids. Animals (M/F:30/30, 12 weeks of age) were obtained from Harlan (IN, USA) and individually housed at 21 °C and L:D 14:10 until 20 weeks of age, followed by L:D 8:16 until 27 weeks...
March 21, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28318465/lunch-at-the-library-examination-of-a-community-based-approach-to-addressing-summer-food-insecurity
#4
Janine S Bruce, Monica M De La Cruz, Gala Moreno, Lisa J Chamberlain
OBJECTIVE: To examine a library-based approach to addressing food insecurity through a child and adult summer meal programme. The study examines: (i) risk of household food insecurity among participants; (ii) perspectives on the library meal programme; and (iii) barriers to utilizing other community food resources. DESIGN: Quantitative surveys with adult participants and qualitative semi-structured interviews with a sub-sample of adult participants. SETTING: Ten libraries using public and private funding to serve meals to children and adults for six to eight weeks in low-income Silicon Valley communities (California, USA) during summer 2015...
March 20, 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/28315738/pulmonary-sarcomatoid-carcinomas-commonly-harbor-either-potentially-targetable-genomic-alterations-or-high-tumor-mutational-burden-as-observed-by-comprehensive-genomic-profiling
#5
Alexa B Schrock, Shuyu D Li, Garrett M Frampton, James Suh, Eduardo Braun, Ranee Mehra, Steven Buck, Jose A Bufill, Nir Peled, Nagla Abdel Karim, Cynthia Hsieh, Manuel Doria, James Knost, Rong Chen, Sai-Hong Ignatius Ou, Jeffrey S Ross, Philip J Stephens, Paul Fishkin, Vincent A Miller, Siraj M Ali, Balazs Halmos, Jane J Liu
BACKGROUND: Pulmonary sarcomatoid carcinoma (PSC) is a high-grade non-small cell lung carcinoma (NSCLC) characterized by poor prognosis and resistance to chemotherapy. Development of targeted therapeutic strategies for PSC has been hampered due to limited and inconsistent molecular characterization. METHODS: Hybrid-capture based comprehensive genomic profiling (CGP) was performed on DNA from 15,867 FFPE NSCLCs including 125 PSCs (0.8%). Tumor mutational burden (TMB) was calculated from 1...
March 15, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28302159/a-data-driven-approach-links-microglia-to-pathology-and-prognosis-in-amyotrophic-lateral-sclerosis
#6
Johnathan Cooper-Knock, Claire Green, Gabriel Altschuler, Wenbin Wei, Joanna J Bury, Paul R Heath, Matthew Wyles, Catherine Gelsthorpe, J Robin Highley, Alejandro Lorente-Pons, Tim Beck, Kathryn Doyle, Karel Otero, Bryan Traynor, Janine Kirby, Pamela J Shaw, Winston Hide
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that lacks a predictive and broadly applicable biomarker. Continued focus on mutation-specific upstream mechanisms has yet to predict disease progression in the clinic. Utilising cellular pathology common to the majority of ALS patients, we implemented an objective transcriptome-driven approach to develop noninvasive prognostic biomarkers for disease progression. Genes expressed in laser captured motor neurons in direct correlation (Spearman rank correlation, p < 0...
March 16, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28302059/correspondence-of-d-melanogaster-and-c-elegans-developmental-stages-revealed-by-alternative-splicing-characteristics-of-conserved-exons
#7
Ruiqi Gao, Jingyi Jessica Li
BACKGROUND: We report a statistical study to find correspondence of D. melanogaster and C. elegans developmental stages based on alternative splicing (AS) characteristics of conserved cassette exons using modENCODE RNA-seq data. We identify "stage-associated exons" to capture the AS characteristics of each stage and use these exons to map pairwise stages within and between the two species by an overlap test. RESULTS: Within fly and worm, adjacent developmental stages are mapped to each other, i...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28293947/water-solubilizing-hydrophobic-znaginse-zns-qds-with-tumor-targeted-crgd-sulfobetaine-pima-histamine-ligands-via-a-self-assembly-strategy-for-bioimaging
#8
Tao Deng, Yanan Peng, Rong Zhang, Jie Wang, Jie Zhang, Yueqing Gu, Dechun Huang, Dawei Deng
Exploring the organic-to-aqueous phase transfer of quantum dots (QDs) is significant for achieving their versatile applications in biomedical fields. In this thematic issue, surface modification, size control, and biocompatibility of QDs and QDs-based nanocomposites are core problems. Herein, the new highly fluorescent tumor-targeted QDs-clusters consisting of ZnAgInSe/ZnS (ZAISe/ZnS) QDs and sulfobetaine-PIMA-histamine (SPH) polymer with the ανβ3 integrin receptor cyclic RGD (c-RGD) were developed via ligand exchange and an accompanying self-assembly process...
March 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#9
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28291231/targeted-deep-sequencing-of-flowering-regulators-in-brassica-napus-reveals-extensive-copy-number-variation
#10
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod J Snowdon
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28288384/bulk-production-and-evaluation-of-high-specific-activity-186g-re-for-cancer-therapy-using-enriched-186-wo3-targets-in-a-proton-beam
#11
Tara Mastren, Valery Radchenko, Hong T Bach, Ethan R Balkin, Eva R Birnbaum, Mark Brugh, Jonathan W Engle, Matthew D Gott, James Guthrie, Heather M Hennkens, Kevin D John, Alan R Ketring, Marina Kuchuk, Joel R Maassen, Cleo M Naranjo, F Meiring Nortier, Tim E Phelps, Silvia S Jurisson, D Scott Wilbur, Michael E Fassbender
INTRODUCTION: Rhenium-186g (t1/2 = 3.72 d) is a β(-) emitting isotope suitable for theranostic applications. Current production methods rely on reactor production by way of the reaction (185)Re(n,γ)(186g)Re, which results in low specific activities limiting its use for cancer therapy. Production via charged particle activation of enriched (186)W results in a (186g)Re product with a higher specific activity, allowing it to be used more broadly for targeted radiotherapy applications. This targets the unmet clinical need for more efficient radiotherapeutics...
March 3, 2017: Nuclear Medicine and Biology
https://www.readbyqxmd.com/read/28287571/merging-ion-concentration-polarization-between-juxtaposed-ion-exchange-membranes-to-block-the-propagation-of-the-polarization-zone
#12
Minyoung Kim, Hyunjoon Rhee, Ji Yoon Kang, Tae Song Kim, Rhokyun Kwak
The ion concentration polarization (ICP) phenomenon is one of the most prevailing methods to preconcentrate low-abundance biological samples. The ICP induces a noninvasive region for charged biomolecules (i.e., the ion depletion zone), and targets can be preconcentrated on this region boundary. Despite the high preconcentration performances with ICP, it is difficult to find the operating conditions of non-propagating ion depletion zones. To overcome this narrow operating window, we recently developed a new platform for spatiotemporally fixed preconcentration...
February 23, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28282148/alterations-in-the-salivary-proteome-and-n-glycome-of-sj%C3%A3-gren-s-syndrome-patients
#13
Steven C Hall, Maria E Hassis, Katherine E Williams, Matthew E Albertolle, Akraporn Prakobphol, Andrew B Dykstra, Megan Laurance, Katherine Ona, Richard K Niles, Namrata Prasad, Matthew Gormley, Caroline H Shiboski, Lindsey A Criswell, H Ewa Witkowska, Susan J Fisher
We used isobaric mass tagging (iTRAQ) and lectin affinity capture mass spectrometry (MS)-based workflows for global analyses of parotid saliva (PS) and whole saliva (WS) samples obtained from patients diagnosed with primary Sjögren's Syndrome (pSS) who were enrolled in the Sjögren's International Collaborative Clinical Alliance (SICCA) as compared to two control groups. The iTRAQ analyses revealed up- and down-regulation of numerous proteins that could be involved in the disease process (e.g., histones) or attempts to mitigate the ensuing damage [e...
March 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28273892/identifying-differentially-coexpressed-module-during-hiv-disease-progression-a-multiobjective-approach
#14
Sumanta Ray, Ujjwal Maulik
Microarray analysis based on gene coexpression is widely used to investigate the coregulation pattern of a group (or cluster) of genes in a specific phenotype condition. Recent approaches go one step beyond and look for differential coexpression pattern, wherein there exists a significant difference in coexpression pattern between two phenotype conditions. These changes of coexpression patterns generally arise due to significant change in regulatory mechanism across different conditions governed by natural progression of diseases...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28273065/complex-multi-enhancer-contacts-captured-by-genome-architecture-mapping
#15
Robert A Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C A Kraemer, Mita Chotalia, Sheila Q Xie, Mariano Barbieri, Inês de Santiago, Liron-Mark Lavitas, Miguel R Branco, James Fraser, Josée Dostie, Laurence Game, Niall Dillon, Paul A W Edwards, Mario Nicodemi, Ana Pombo
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation)...
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28267323/a-dna-templated-aptamer-probe-for-identification-of-target-proteins
#16
Wenjing Bi, Xue Bai, Fan Gao, Congcong Lu, Ye Wang, Guijin Zhai, Shanshan Tian, Enguo Fan, YuKui Zhang, Kai Zhang
Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and non-covalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-crosslinking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another comple-mentary DNA with a photo-active group and reporter group was modified as capture probe (CP)...
March 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28266533/catch-and-release-of-target-cells-using-aptamer-conjugated-electroactive-zwitterionic-oligopeptide-sam
#17
Junko Enomoto, Tatsuto Kageyama, Tatsuya Osaki, Flavia Bonalumi, Francesca Marchese, Alfonso Gautieri, Elena Bianchi, Gabriele Dubini, Chiara Arrigoni, Matteo Moretti, Junji Fukuda
Nucleic acid aptamers possess attractive features such as specific molecular recognition, high-affinity binding, and rapid acquisition and replication, which could be feasible components for separating specific cells from other cell types. This study demonstrates that aptamers conjugated to an oligopeptide self-assembled monolayer (SAM) can be used to selectively trap human hepatic cancer cells from cell mixtures containing normal human hepatocytes or human fibroblasts. Molecular dynamics calculations have been performed to understand how the configurations of the aptamers are related to the experimental results of selective cell capture...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28266176/quantitative-method-for-analysis-of-tobacco-specific-n-nitrosamines-in-mainstream-cigarette-smoke-by-using-heart-cutting-two-dimensional-liquid-chromatography-with-tandem-mass-spectrometry
#18
Min Chen, Leijun Wang, Huizhong Dong, Xi Shao, Da Wu, Baizhan Liu, Xiangmin Zhang, Chaoying Chen
A heart-cutting two dimensional liquid chromatography coupled with tandem mass spectrometry method was developed for the analysis of tobacco-specific nitrosamines at low concentration level in Virginia-type cigarette smoke. A strong cation exchange column was utilized for the first dimensional separation, which effectively removed acidic and neutral components in the smoke, followed by a reversed phase liquid chromatography coupled with tandem mass spectrometric analysis. To capture components of the tobacco-specific nitrosamines in the effluent on the trapping column, a compensating pump was applied for on-line dilution and pH adjustment during the period of the tobacco-specific nitrosamines fraction transferring and enrichment...
March 7, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28250207/capturing-goats-documenting-two-hundred-years-of-mitochondrial-dna-diversity-among-goat-populations-from-britain-and-ireland
#19
Lara M Cassidy, Matthew D Teasdale, Seán Carolan, Ruth Enright, Raymond Werner, Daniel G Bradley, Emma K Finlay, Valeria Mattiangeli
The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing...
March 2017: Biology Letters
https://www.readbyqxmd.com/read/28245896/an-improved-barcoded-oligonucleotide-primers-based-next-generation-sequencing-approach-for-direct-identification-of-viral-pathogens-in-clinical-specimens
#20
Chun Hua Wang, Kai Nie, Yi Zhang, Ji Wang, Shuai Feng Zhou, Xin Na Li, Hang Yu Zhou, Shun Xiang Qi, Xue Jun Ma
OBJECTIVE: To provide a feasible and cost-effective next-generation sequencing (NGS) method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. METHODS: Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure: reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide (random hexamer or non-ribosomal hexanucleotide) primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline...
January 2017: Biomedical and Environmental Sciences: BES
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