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https://www.readbyqxmd.com/read/28636641/development-of-a-range-of-fluorescent-reagentless-biosensors-for-atp-based-on-malonyl-coenzyme-a-synthetase
#1
Renée Vancraenenbroeck, Simone Kunzelmann, Martin R Webb
The range of ATP concentrations that can be measured with a fluorescent reagentless biosensor for ATP has been increased by modulating its affinity for this analyte. The ATP biosensor is an adduct of two tetramethylrhodamines with MatB from Rhodopseudomonas palustris. Mutations were introduced into the binding site to modify ATP binding affinity, while aiming to maintain the concomitant fluorescence signal. Using this signal, the effect of mutations in different parts of the binding site was measured. This mutational analysis revealed three variants in particular, each with a single mutation in the phosphate-binding loop, which had potentially beneficial changes in ATP binding properties but preserving a fluorescence change of ~3-fold on ATP binding...
2017: PloS One
https://www.readbyqxmd.com/read/28636372/surface-desorption-dielectric-barrier-discharge-ionization-mass-spectrometry
#2
Hong Zhang, Jie Jiang, Na Li, Ming Li, Yingying Wang, Jing He, Hong You
A variant of dielectric-barrier discharge named surface desorption dielectric-barrier discharge ionization (SDDBDI) mass spectrometry was developed for high-efficiency ion transmission and high spatial resolution imaging. In SDDBDI, a tungsten nanotip and the inlet of the mass spectrometer are used as electrodes, and a piece of cover slip is used as a sample plate as well as an insulating dielectric barrier, which simplifies the configuration of instrument and thus the operation. Different from volume dielectric-barrier discharge (VDBD), the microdischarges are generated on the surface at SDDBDI, and therefore the plasma density is extremely high...
June 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28630524/a-martingale-analysis-of-first-passage-times-of-time-dependent-wiener-diffusion-models
#3
Vaibhav Srivastava, Samuel F Feng, Jonathan D Cohen, Naomi Ehrich Leonard, Amitai Shenhav
Research in psychology and neuroscience has successfully modeled decision making as a process of noisy evidence accumulation to a decision bound. While there are several variants and implementations of this idea, the majority of these models make use of a noisy accumulation between two absorbing boundaries. A common assumption of these models is that decision parameters, e.g., the rate of accumulation (drift rate), remain fixed over the course of a decision, allowing the derivation of analytic formulas for the probabilities of hitting the upper or lower decision threshold, and the mean decision time...
April 2017: Journal of Mathematical Psychology
https://www.readbyqxmd.com/read/28622622/characterization-of-drug-load-variants-in-a-thiol-linked-antibody-drug-conjugate-using-multidimensional-chromatography
#4
Jonathan J Gilroy, Catherine M Eakin
The biological complexity associated with biotherapeutics such as antibody-drug conjugates (ADCs) requires extensive characterization to ensure product quality consistency, safety, and efficacy. ADCs generated via partial reduction of antibody interchain disulfide bonds result in a distribution of variants containing 0-8 conjugated drugs. Hydrophobic interaction chromatography (HIC) is a key analytical technique used to separate drug load variants of thiol linked ADCs and to calculate the average drug-to-antibody molar ratio (DAR)...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28616206/a-systematic-review-and-meta-analysis-of-genetic-association-studies-for-the-role-of-inflammation-and-the-immune-system-in-diabetic-nephropathy
#5
Maria Tziastoudi, Ioannis Stefanidis, Georgios M Hadjigeorgiou, Konstantinos Stravodimos, Elias Zintzaras
Background: Despite the certain contribution of metabolic and haemodynamic factors in diabetic nephropathy (DN), many lines of evidence highlight the role of immunologic and inflammatory mechanisms. To elucidate the contribution of the immune system in the development of DN, we explored the contribution of gene variants (polymorphisms) in relevant pathophysiologic pathways. Methods: We selected six major pathways related to immune response from the Kyoto Encyclopaedia of Genes and Genomes database and thereafter we traced all available genetic association studies (GASs) involving gene variants in these pathways from PubMed and HuGE Navigator...
June 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28598898/a-99mtc-labelled-scfv-antibody-fragment-that-binds-to-prostate-specific-membrane-antigen
#6
Saima Nawaz, Gregory E D Mullen, Philip J Blower, James R Ballinger
INTRODUCTION: Prostate-specific membrane antigen (PSMA) is an extensively studied antigen for imaging prostate cancer. We prepared a single-chain variable fragment (scFv) of J591, a monoclonal antibody that recognises an external epitope of PSMA, incorporating a His-tag for labelling with Tc tricarbonyl, and evaluated its binding using human PCa cell lines. METHODS: J591(scFv) was expressed in HEK-293T cells and purified by metal ion affinity chromatography, followed by size exclusion chromatography...
June 8, 2017: Nuclear Medicine Communications
https://www.readbyqxmd.com/read/28592645/inbred-strain-variant-database-isvdb-a-repository-for-probabilistically-informed-sequence-differences-among-the-collaborative-cross-strains-and-their-founders
#7
Daniel Oreper, Yanwei Cai, Lisa M Tarantino, Fernando Pardo-Manuel de Villena, William Valdar
The Collaborative Cross (CC) is a panel of recently established multiparental recombinant inbred mouse strains. For the CC, as for any multiparental population (MPP), effective experimental design and analysis benefit from detailed knowledge of the genetic differences between strains. Such differences can be directly determined by sequencing, but until now whole-genome sequencing was not publicly available for individual CC strains. An alternative and complementary approach is to infer genetic differences by combining two pieces of information: probabilistic estimates of the CC haplotype mosaic from a custom genotyping array, and probabilistic variant calls from sequencing of the CC founders...
June 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28591459/simulating-head-recovery-and-intermittent-discharge-in-free-flowing-wells
#8
Ferenc Székely
Modeling of the head recovery (buildup) in and intermittent operation of flowing wells lacks rigorous analytical tools. Presently different methods are applied in discharging and recovery phases. The presented reliable approximate solution considers a continuous free flow process and time variant screen loss parameters. The latter are temporarily set to large value to prevent inflow into the well bore during the single recovery or in repeated shut down periods. This method is called as screen loss control or SLC technique and is verified by means of comparative analysis with the constant rate pumping-recovery test simulated in leaky aquifer...
June 7, 2017: Ground Water
https://www.readbyqxmd.com/read/28587503/sense-of-responsibility-in-icu-end-of-life-decision-making-relatives-experiences
#9
Ranveig Lind
BACKGROUND: Relatives of intensive care unit patients who lack or have reduced capacity to consent are entitled to information and participation in decision-making together with the patient. Practice varies with legislation in different countries. In Norway, crucial decisions such as withdrawing treatment are made by clinicians, usually morally justified to relatives with reference to the principle of non-maleficence. The relatives should, however, be consulted about whether they know what the patient would have wished in the situation...
January 1, 2017: Nursing Ethics
https://www.readbyqxmd.com/read/28586760/clinical-mutational-profiling-of-1006-lung-cancers-by-next-generation-sequencing
#10
Peter B Illei, Deborah Belchis, Li-Hui Tseng, Doreen Nguyen, Federico De Marchi, Lisa Haley, Stacy Riel, Katie Beierl, Gang Zheng, Julie R Brahmer, Frederic B Askin, Christopher D Gocke, James R Eshleman, Patrick M Forde, Ming-Tseh Lin
Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2-5% in 33 (4.3%) mutations and 2-10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations...
May 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28573082/electrospray-modifications-for-advancing-mass-spectrometric-analysis
#11
Anil Kumar Meher, Yu-Chie Chen
Generation of analyte ions in gas phase is a primary requirement for mass spectrometric analysis. One of the ionization techniques that can be used to generate gas phase ions is electrospray ionization (ESI). ESI is a soft ionization method that can be used to analyze analytes ranging from small organics to large biomolecules. Numerous ionization techniques derived from ESI have been reported in the past two decades. These ion sources are aimed to achieve simplicity and ease of operation. Many of these ionization methods allow the flexibility for elimination or minimization of sample preparation steps prior to mass spectrometric analysis...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28557600/integration-of-technical-bioinformatic-and-variant-assessment-approaches-in-the-validation-of-a-targeted-next-generation-sequencing-panel-for-myeloid-malignancies
#12
Mariam Thomas, Mahadeo A Sukhai, Tong Zhang, Roozbeh Dolatshahi, Djamel Harbi, Swati Garg, Maksym Misyura, Trevor Pugh, Tracy L Stockley, Suzanne Kamel-Reid
CONTEXT: - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes...
June 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28557599/validation-of-oncopanel-a-targeted-next-generation-sequencing-assay-for-the-detection-of-somatic-variants-in-cancer
#13
Elizabeth P Garcia, Alissa Minkovsky, Yonghui Jia, Matthew D Ducar, Priyanka Shivdasani, Xin Gong, Azra H Ligon, Lynette M Sholl, Frank C Kuo, Laura E MacConaill, Neal I Lindeman, Fei Dong
CONTEXT: - The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. OBJECTIVE: - To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. DESIGN: - OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology...
June 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28555559/-bisalbuminemia-a-rare-variant-of-albumin
#14
Carla Garcez, Susana Carvalho
INTRODUCTION: Bisalbuminemia is a qualitative disorder of albumin and it is defined by the coexistence in the same individual of two types of serum albumin with different electrophoretic mobility. There are two forms: hereditary and permanent, or acquired and transient. CASE REPORT: Girl, 17-years-old, referenced to the hospital consult after incidental finding of bisalbuminemia detected in plasma protein electrophoresis performed within the investigation of diminished muscular tone in the lower limbs...
April 28, 2017: Acta Médica Portuguesa
https://www.readbyqxmd.com/read/28550058/whole-genome-and-core-genome-multilocus-sequence-typing-and-single-nucleotide-polymorphism-analyses-of-listeria-monocytogenes-associated-with-an-outbreak-linked-to-cheese-united-states-2013
#15
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28549280/protocols-for-the-analytical-characterization-of-therapeutic-monoclonal-antibodies-i-non-denaturing-chromatographic-techniques
#16
Alexandre Goyon, Valentina D'Atri, Balazs Bobaly, Elsa Wagner-Rousset, Alain Beck, Szabolcs Fekete, Davy Guillarme
Size-, charge- and hydrophobicity-related variants of a biopharmaceutical product have to be deeply characterized for batch consistency and for the assessment of immunogenicity and safety effects. Size exclusion chromatography (SEC) and ion exchange chromatography (IEX) are considered as the gold standard for the analysis of high molecular weight species (HMWS) and charge-related variants, respectively. Hydrophobic interaction chromatography (HIC) has drawn renewed attention to monitor the small drug payload distribution in the cysteine-linked antibody-drug conjugates (ADC)...
May 11, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#17
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree among themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28543614/capillarys-2-flex-piercing-analytical-performance-assessment-according-to-clsi-protocols-for-hba1c-quantification
#18
Radhouene Doggui, Chaïma Abdelhafidh Sahli, Wassef Lotfi Aissa, Maroua Hammami, Maha Ben Sedrine, Rahma Mahjoub, Khemais Zouaoui, Rim Daboubi, Hajer Siala, Taieb Messaoud, Amina Bibi
HbA1c is used for monitoring diabetic balance. In this paper we report an assessment of the analytical performances of Capillarys 2 Flex Piercing (C2FP) for HbA1c measurement using CE (Capillary Electrophoresis). CLSI (Clinical and Laboratory Standard Institute) protocols are used for the evaluation of apparatus performances: precision, linearity, method comparison, truness and common interferences. HbA1c CVs average in intra-assay was 1.6% between run imprecision CV ranged from0.1 to 1.8%. The linearity was demonstrated between 4...
May 19, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28542587/seminal-plasma-induces-inflammation-and-enhances-hiv-1-replication-in-human-cervical-tissue-explants
#19
Andrea Introini, Stéphanie Boström, Frideborg Bradley, Anna Gibbs, Axel Glaessgen, Annelie Tjernlund, Kristina Broliden
The most immediate and evident effect of mucosal exposure to semen in vivo is a local release of proinflammatory mediators accompanied by an influx of leukocytes into the female genital mucosa (FGM). The implication of such response in HIV-1 transmission has never been addressed due to limitations of currently available experimental models. Using human tissue explants from the uterine cervix, we developed a system of mucosal exposure to seminal plasma (SP) that supports HIV-1 replication. Treatment of ectocervical explants with SP resulted in the upregulation of inflammatory and growth factors, including IL-6, TNF, CCL5, CCL20, CXCL1, and CXCL8, and IL1A, CSF2, IL7, PTGS2, as evaluated by measuring protein levels in explant conditioned medium (ECM) and gene expression in tissue...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28535921/out-of-field-in-vivo-dosimetry-using-tld-in-sabr-for-primary-kidney-cancer-involving-mixed-photon-fields
#20
P Lonski, S Keehan, S Siva, D Pham, R D Franich, M L Taylor, T Kron
PURPOSE: To assess out-of-field dose using three different variants of LiF thermoluminescence dosimeters (TLD) for ten patients who underwent stereotactic ablative body radiotherapy (SABR) for primary renal cell carcinoma (RCC) and compare with treatment planning system (TPS) dose calculations. METHODS AND MATERIALS: Thermoluminescent dosimeter (TLD) measurements were conducted at 20, 30, 40 and 50cm from isocentre on ten patients undergoing SABR for primary RCC...
May 2017: Physica Medica: PM
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