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https://www.readbyqxmd.com/read/28220596/quantitative-pcr-is-a-valuable-tool-to-monitor-performance-of-dna-encoded-chemical-library-selections
#1
Yizhou Li, Gunther Zimmermann, Jörg Scheuermann, Dario Neri
Phage-display libraries and DNA-encoded chemical libraries (DECL) represent useful tools for the isolation of specific binding molecules out of large combinatorial sets of compounds. In both methods, specific binders are recovered at the end of affinity capture procedures, using target proteins of interest immobilized on a solid support. However, while the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DNA-encoded chemical library selections...
February 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28220459/-how-would-you-call-this-in-english-being-reflective-about-translations-in-international-cross-cultural-qualitative-research
#2
Esther Helmich, Sayra Cristancho, Laura Diachun, Lorelei Lingard
INTRODUCTION: Medical education researchers increasingly collaborate in international teams, collecting data in different languages and from different parts of the world, and then disseminating them in English-language journals. Although this requires an ever-present need to translate, it often occurs uncritically. With this paper we aim to enhance researchers' awareness and reflexivity regarding translations in qualitative research. METHODS: In an international study, we carried out interviews in both Dutch and English...
February 20, 2017: Perspectives on Medical Education
https://www.readbyqxmd.com/read/28220154/dna-display-of-folded-rna-libraries-enabling-rna-selex-without-reverse-transcription
#3
I S MacPherson, J S Temme, I J Krauss
A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription...
February 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28219123/identification-of-core-gene-networks-and-hub-genes-associated-with-progression-of-nonalcoholic-fatty-liver-disease-by-rna-sequencing
#4
Kikuko Hotta, Masataka Kikuchi, Takuya Kitamoto, Aya Kitamoto, Yuji Ogawa, Yasushi Honda, Takaomi Kessoku, Kaori Kobayashi, Masato Yoneda, Kento Imajo, Wataru Tomeno, Akihiro Nakaya, Yutaka Suzuki, Satoru Saito, Atsushi Nakajima
AIM: Nonalcoholic fatty liver disease (NAFLD) progresses because of the interaction between numerous genes. Thus, we performed weighted gene co-expression network analysis to identify core gene networks and key genes associated with NAFLD progression. METHODS: We enrolled 39 patients with mild NAFLD (fibrosis stages 0 to 2) and 21 with advanced NAFLD (fibrosis stages 3 or 4). Total RNA was extracted from frozen liver biopsies, and sequenced to capture a large dynamic range of expression levels...
February 20, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28217240/microfluidics-cell-sample-preparation-for-analysis-advances-in-efficient-cell-enrichment-and-precise-single-cell-capture
#5
REVIEW
Liang Huang, Shengtai Bian, Yinuo Cheng, Guanya Shi, Peng Liu, Xiongying Ye, Wenhui Wang
Single cell analysis has received increasing attention recently in both academia and clinics, and there is an urgent need for effective upstream cell sample preparation. Two extremely challenging tasks in cell sample preparation-high-efficiency cell enrichment and precise single cell capture-have now entered into an era full of exciting technological advances, which are mostly enabled by microfluidics. In this review, we summarize the category of technologies that provide new solutions and creative insights into the two tasks of cell manipulation, with a focus on the latest development in the recent five years by highlighting the representative works...
January 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28213217/selective-enrichment-of-glycopeptides-phosphopeptides-using-fe3o4-au-b-oh-2-mtio2-core-shell-microspheres
#6
Dongpo Xu, Guoquan Yan, Mingxia Gao, Chunhui Deng, Xiangmin Zhang
In this work, the bifunctional Fe3O4@Au-B(OH)2@mTiO2 core-shell core-shell microspheres were designed and synthesized for the selective enrichment of glycopeptides/ phosphopeptides. Due to the bifunctional property of the titanium dioxide and the boronic acid group, the microspheres were successfully applied to the enrichment of phosphopeptides and glycopeptides, evaluated by capturing phosphopeptides from tryptic digestion of model phosphoprotein bovine β-casein diluted to 2.0pgμL(-1) (8.0×10(-17)molμL(-1)) and glycopeptides from tryptic digestion of model glycoprotein horseradish peroxidase (HRP) diluted to 80pgμL(-1) (2...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213213/titanium-iv-ion-modified-covalent-organic-frameworks-for-specific-enrichment-of-phosphopeptides
#7
Heping Wang, Fenglong Jiao, Fangyuan Gao, Yayao Lv, Qiong Wu, Yan Zhao, Yehua Shen, Yangjun Zhang, Xiaohong Qian
To date, plenty of new alternative materials for phosphopeptides enrichment prior to mass spectrometry (MS) analysis appear, especially immobilized metal ion affinity chromatography (IMAC) materials. The variable combinations with different metal ions, chelating ligands and solid supports offer full of optionality for IMAC. However, further improvement was predicted by the tedious and complex synthetic process. In this work, a novel covalent organic framework (COF)-based IMAC material (denoted TpPa-2-Ti(4+)) was prepared simply by direct immobilizing Ti (IV) into TpPa-2 COFs without any extra chelating ligands...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28212540/expression-of-met-in-circulating-tumor-cells-correlates-with-expression-in-tumor-tissue-from-advanced-stage-lung-cancer-patients
#8
Marius Ilie, Edith Szafer-Glusman, Véronique Hofman, Elodie Long-Mira, Rebecca Suttmann, Walter Darbonne, Catherine Butori, Salomé Lalvée, Julien Fayada, Eric Selva, Wei Yu, Charles-Hugo Marquette, David S Shames, Elizabeth Punnoose, Paul Hofman
Given the difficulty in obtaining adequate tissue in NSCLC, we investigated the utility of circulating tumor cells (CTCs) for MET status assessment in NSCLC patients. We used two platforms for CTC capture, and assessed MET expression in CTCs and matched-bronchial biopsies in patients with advanced-stage III/IV lung adenocarcinoma. Baseline peripheral blood was collected from 256 advanced-stage III/IV NSCLC patients from Genentech clinical trials, and from 106 patients with advanced-stage III/IV lung adenocarcinoma treated at the Department of Pneumology, Pasteur Hospital, Nice...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28208267/highly-selective-capture-surfaces-on-medical-wires-for-fishing-tumor-cells-in-whole-blood
#9
Frank D Scherag, Robert Niestroj-Pahl, Solveigh Krusekopf, Klaus Lücke, Thomas Brandstetter, Jürgen Rühe
The detection of circulating tumor cells (CTCs) in the blood of cancer patients is a challenging task. CTCs are, especially at the early stages of cancer development, extremely rare cells hidden in a vast background of regular blood cells. We describe a new strategy for the isolation of CTCs from whole blood. The key component is a medical wire coated with a multilayer assembly that allows highly specific capture of EpCAM (epithelial cell adhesion molecule) positive CTCs from blood. The assembly is generated in a layer-by-layer fashion through photochemically induced C,H insertion reactions and consists of a protective layer, which shields the contacting solution from the metal, a protein resistant layer, which prevents nonspecific interactions with proteins and a layer containing the EpCAM antibodies...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28207535/an-investigation-of-obesity-susceptibility-genes-in-northern-han-chinese-by-targeted-resequencing
#10
Yili Wu, Weijing Wang, Wenjie Jiang, Jie Yao, Dongfeng Zhang
Our earlier genome-wide linkage study of body mass index (BMI) showed strong signals from 7q36.3 and 8q21.13. This case-control study set to investigate 2 genomic regions which may harbor variants contributed to development of obesity.We employed targeted resequencing technology to detect single nucleotide polymorphisms (SNPs) in 7q36.3 and 8q21.13 from 16 individuals with obesity. These were compared with 504 East Asians in the 1000 Genomes Project as a reference panel. Linkage disequilibrium (LD) block analysis was performed for the significant SNPs located near the same gene...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28202276/a-possible-co2-leakage-event-can-the-marine-microbial-community-be-recovered
#11
A R Borrero-Santiago, E Bautista-Chamizo, T Á DelValls, I Riba
Bacterial communities have been studied to a much lesser degree than macrofauna in the case of a CO2 release. The resistance capacity of marine bacteria is well known, but their possible responses and their ability to recover after a CO2 release has not been investigated. Therefore, this work evaluated the responses of a marine bacterial community after 96h of CO2 exposure under diverse pH treatments (7.8 as control without CO2, 7.0, 6.5, and 6.0) and 24h after CO2 exposure. Results showed that the respiration activity and the diversity of the community were affected in all pH treatments...
February 12, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28202223/filtration-based-enrichment-of-circulating-tumor-cells-from-all-prostate-cancer-risk-groups
#12
Julius Adebayo Awe, Jeff Saranchuk, Darrel Drachenberg, Sabine Mai
OBJECTIVE: To combine circulating tumor cell (CTC) isolation by filtration and immunohistochemistry to investigate the presence of CTCs in low, intermediate, and high-risk prostate cancer (PCa). CTCs isolated from these risk groups stained positive for both cytokeratin and androgen receptors, but negative for CD45. PATIENTS AND METHODS: Blood samples from 41 biopsy confirmed patients with PCa at different clinical stages such as low, intermediate, and high risk were analyzed...
February 12, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28192936/generic-hybrid-ligand-binding-assay-liquid-chromatography-high-resolution-mass-spectrometry-based-workflow-for-multiplexed-human-immunoglobulin-g1-quantification-at-the-intact-protein-level-application-to-preclinical-pharmacokinetic-studies
#13
Christian Lanshoeft, Sarah Cianférani, Olivier Heudi
The quantitative analysis of human immunoglobulin G1 (hIgG1) by mass spectrometry is commonly performed using surrogate peptides after enzymatic digestion. Since some limitations are associated with this approach, a novel workflow is presented by hybridizing ligand binding assay (LBA) with liquid chromatography-high-resolution mass spectrometry (LC-HRMS) for hIgG1 quantification directly at the intact protein level. Different hIgG1s, including a [(13)C]-labeled version used as internal standard, were immuno-enriched from rat serum with a fully automated platform based on streptavidin coated tips and a biotinylated mouse anti-hIgG capture antibody targeting the fragment crystallizable region followed by overnight deglycosylation prior to LC-HRMS analysis...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28188833/metabolomic-profiling-of-lung-function-in-costa-rican-children-with-asthma
#14
Rachel S Kelly, Yamini Virkud, Rachel Giorgio, Juan C Celedón, Scott T Weiss, Jessica Lasky-Su
BACKGROUND: The development of novel therapeutics and treatment regimens for the management of asthma is hindered by an incomplete understanding of its heterogeneous nature and pathophysiology. Metabolomics can provide an integrated and global profile of a biological system in a dysregulated state, making it a valuable tool to identify biomarkers along the disease development pathway and to understand the biological mechanisms driving that pathway. METHODS: Liquid Chromatography-Mass spectrometry metabolomic profiling was conducted on plasma samples provided at recruitment for 380 children with asthma from the 'Genetic Epidemiology of Asthma in Costa Rica Cohort'...
February 7, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28188526/multi-lectin-affinity-chromatography-for-separation-identification-and-quantitation-of-intact-protein-glycoforms-in-complex-biological-mixtures
#15
Sarah M Totten, Majlinda Kullolli, Sharon J Pitteri
Protein glycosylation is considered to be one of the most abundant post-translational modifications and is recognized for playing key roles in cellular functions. Aberrant N-linked glycosylation has been associated with several human diseases and has prompted the development and constant improvement of analytical tools to separate, characterize, and quantify glycoproteins in complex mixtures extracted from various biological samples (such as blood and tissue). Lectins, or carbohydrate-binding proteins, have been used as valuable tools for enriching for glycoproteins and selecting for specific types of glycosylation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28183795/med12-is-recurrently-mutated-in-middle-eastern-colorectal-cancer
#16
Abdul K Siraj, Tariq Masoodi, Rong Bu, Poyil Pratheeshkumar, Nasser Al-Sanea, Luai H Ashari, Alaa Abduljabbar, Samar Alhomoud, Fouad Al-Dayel, Fowzan S Alkuraya, Khawla S Al-Kuraya
OBJECTIVE: Colorectal cancer (CRC) is a common cancer and a leading cause of cancer deaths. Previous studies have identified a number of key steps in the evolution of CRC but our knowledge of driver mutations in CRC remains incomplete. Recognising the potential of studying different human populations to reveal novel insights in disease pathogenesis, we conducted genomic analysis of CRC in Saudi patients. DESIGN: In the discovery phase of the study, we conducted whole genome sequencing of tumour and corresponding germline DNA in 27 patients with CRC...
February 9, 2017: Gut
https://www.readbyqxmd.com/read/28177221/highly-selective-and-repeatable-surface-enhanced-resonance-raman-scattering-detection-for-epinephrine-in-serum-based-on-interface-self-assembled-2d-nanoparticles-arrays
#17
Binbin Zhou, Xiaoyun Li, Xianghu Tang, Pan Li, LiangBao Yang, Jinhuai Liu
Target analyte detection in complex system with high selectivity and repeatability is crucial to analytical technology and science. Here we present a two-dimensional (2D) surface-enhanced resonance Raman scattering (SERRS) platform, which takes advantage of self-assembled of Au nanoparticles (Au NPs) arrays at cyclohexane/water interface, for detecting trace Epinephrine (EP) in the serum. To realize sensitive and selective detection of EP in complex system, Au NPs is modified with -nitriloacetic acid and Fe(NO3)3 to form the Au NP-(Fe-NTA) sensor, as consequence, EP can be rapidly captured by sen-sor on the surface of Au NPs, then delivered at cyclohexane/water interface...
February 8, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28166506/collaborative-random-faces-guided-encoders-for-pose-invariant-face-representation-learning
#18
Ming Shao, Yizhe Zhang, Yun Fu
Learning discriminant face representation for pose-invariant face recognition has been identified as a critical issue in visual learning systems. The challenge lies in the drastic changes of facial appearances between the test face and the registered face. To that end, we propose a high-level feature learning framework called ''collaborative random faces (RFs)-guided encoders'' toward this problem. The contributions of this paper are three fold. First, we propose a novel supervised autoencoder that is able to capture the high-level identity feature despite of pose variations...
February 1, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28164404/mysterious-decomposition-of-alkoxyphosphonium-chlorides-postulated-involvement-of-the-hcl2-anion-and-its-capture-in-the-solid-state
#19
Kirill Nikitin, Helge Müller-Bunz, Jimmy Muldoon, Declan G Gilheany
P-Alkoxyphosphonium (AP) chlorides were generated by reacting P-chlorophosphonium chlorides with alcohols. Their well-known spontaneous Arbuzov-type collapse leading to phosphine oxides was studied and its rate found to be dependent on a number of factors in an unexpected fashion: it is inversely proportional to the initial concentration and it shows strong dependence on the acidity of the media but is not very sensitive to the presence of base. To explain these observations, we evoke a self-inhibition model with the formation of the less nucleophilic hydrodichloride anion HCl2 in solution...
February 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28159918/protein-drug-target-activation-homogeneity-in-the-face-of-intra-tumor-heterogeneity-implications-for-precision-medicine
#20
Erika Maria Parasido, Alessandra Silvestri, Vincenzo Canzonieri, Claudio Belluco, Maria Grazia Diodoro, Massimo Milione, Flavia Melotti, Ruggero De Maria, Lance Liotta, Emanuel F Petricoin, Mariaelena Pierobon
INTRODUCTION: Recent studies indicated tumors may be comprised of heterogeneous molecular subtypes and incongruent molecular portraits may emerge if different areas of the tumor are sampled. This study explored the impact of intra-tumoral heterogeneity in terms of activation/phosphorylation of FDA approved drug targets and downstream kinase substrates. MATERIAL AND METHODS: Two independent sets of liver metastases from colorectal cancer were used to evaluate protein kinase-driven signaling networks within different areas using laser capture microdissection and reverse phase protein array...
December 15, 2016: Oncotarget
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