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https://www.readbyqxmd.com/read/27916435/analytical-validation-of-androgen-receptor-splice-variant-7-detection-in-a-clinical-laboratory-improvement-amendments-clia-laboratory-setting
#1
Parvez M Lokhandwala, Stacy L Riel, Lisa Haley, Changxue Lu, Yan Chen, John Silberstein, Yezi Zhu, Gang Zheng, Ming-Tseh Lin, Christopher D Gocke, Alan W Partin, Emmanuel S Antonarakis, Jun Luo, James R Eshleman
Patients with castration-resistant prostate cancer (CRPC) often are treated with drugs that target the androgen receptor (AR) ligand-binding domain. Constitutively active AR splice variant 7 (AR-V7) lacks the ligand-binding domain and, if detected in circulating tumor cells, may be associated with resistance to these agents. We validated an AR-V7 assay in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. Circulating tumor cells were isolated, and mRNA was reverse-transcribed into cDNA...
December 1, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27910951/molecular-imaging-with-engineered-physiology
#2
Mitul Desai, Adrian L Slusarczyk, Ashley Chapin, Mariya Barch, Alan Jasanoff
In vivo imaging techniques are powerful tools for evaluating biological systems. Relating image signals to precise molecular phenomena can be challenging, however, due to limitations of the existing optical, magnetic and radioactive imaging probe mechanisms. Here we demonstrate a concept for molecular imaging which bypasses the need for conventional imaging agents by perturbing the endogenous multimodal contrast provided by the vasculature. Variants of the calcitonin gene-related peptide artificially activate vasodilation pathways in rat brain and induce contrast changes that are readily measured by optical and magnetic resonance imaging...
December 2, 2016: Nature Communications
https://www.readbyqxmd.com/read/27908122/static-polarizabilities-for-excited-states-within-the-spin-conserving-and-spin-flipping-equation-of-motion-coupled-cluster-singles-and-doubles-formalism-theory-implementation-and-benchmarks
#3
Kaushik D Nanda, Anna I Krylov
We present the theory and implementation for calculating static polarizabilities within the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) framework for electronically excited states and its spin-flip variant. We evaluate the second derivatives of the EOM-CCSD Lagrangian with respect to electric-field perturbations. The relaxation of reference molecular orbitals is not included. In our approach, the wave function amplitudes satisfy the 2n + 1 rule and the amplitude-response Lagrange multipliers satisfy the 2n + 2 rule...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#4
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27891726/everyday-conversation-in-dementia-a-review-of-the-literature-to-inform-research-and-practice
#5
REVIEW
Jacqueline Kindell, John Keady, Karen Sage, Ray Wilkinson
BACKGROUND: There has been increasing interest in dementia care in recent years, including how practitioners, service providers and society in general can help individuals to live well with the condition. An important aspect to this is provision of advice to ensure conversation partners effectively support the person with dementia in conversation. AIMS: To provide a descriptive review of the literature examining everyday conversation in dementia in order to inform practice and research...
November 27, 2016: International Journal of Language & Communication Disorders
https://www.readbyqxmd.com/read/27889474/the-von-willebrand-factor-a1-collagen-iii-interaction-is-independent-of-conformation-and-type-2-von-willebrand-disease-phenotype
#6
Venkata R Machha, Alexander Tischer, Laurie Moon-Tasson, Matthew Auton
The blood von Willebrand factor (VWF) mediates platelet adhesion to injured vessels by sequestering platelets from blood flow and depositing them to collagen and other exposed subendothelial matrix proteins. This process of capturing platelets to facilitate formation of platelet plugs occurs through transient interactions with platelet glycoprotein Ibα via the VWF A1 domain which also binds collagen. Using a conformationally diverse collection of natively folded and mutation-induced misfolded von Willebrand disease (VWD) variants, we test a recently proposed affinity up-regulation hypothesis which states that collagen binding changes the conformation of the A1 domain to a high-affinity GPIbα binding competent state...
November 24, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27887824/reconstructing-a-long-term-record-of-microcystins-from-the-analysis-of-lake-sediments
#7
A Zastepa, Z E Taranu, L E Kimpe, J M Blais, I Gregory-Eaves, R W Zurawell, F R Pick
Based on an analysis of sediment cores from Baptiste Lake (Alberta, Canada), we quantified century-scale trends in cyanobacteria and cyanotoxins, and identified possible drivers of toxigenic cyanobacteria. We measured concentrations of microcystins and pigments preserved in the sediment as proxies of toxigenic cyanobacteria and phytoplankton communities, respectively, while fossil diatom assemblages were used to infer past nutrient concentrations. Microcystins were detected in older sediments (ca. 1800s), pre-dating any significant alteration to the watershed...
November 22, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27885684/interference-free-mass-spectrometric-detection-of-capillary-isoelectric-focused-proteins-including-charge-variants-of-a-model-monoclonal-antibody
#8
Jens Hühner, Kevin Jooß, Neusüß Christian
CIEF represents an elegant technique especially for the separation of structural similar analytes, whereas MS is a state of the art instrumentation for the identification and characterization of biomolecules. The combination of both techniques can be realized by hyphenating CIEF with CZE-ESI-MS applying a mechanical valve. During the CZE step, the remaining ESI-interfering components of the CIEF electrolyte are separated from the analytes prior to MS detection. In this work, a multiple heart-cut approach is presented expanding our previous single heart-cut concept resulting in a dramatical reduction of analysis time...
November 25, 2016: Electrophoresis
https://www.readbyqxmd.com/read/27882723/an-in-depth-understanding-of-biomass-recalcitrance-using-natural-poplar-variants-as-the-feedstock
#9
Xianzhi Meng, YUnqiao Pu, Chang Geun Yoo, Mi Li, Garima Bali, Doh-Yeon Park, Erica Gjersing, Mark Davis, Muchero Wellington, Gerald Tuskan, Timothy Tschaplinski, Arthur Jonas Ragauskas
In an effort to better understand and overcome biomass recalcitrance, six natural poplar variants were selected as the feedstock. Compositional analysis and physicochemical characterizations of these poplars were performed using different analytical techniques and the correlations between these physicochemical properties and enzymatic hydrolysis yield were investigated. Gel permeation chromatography (GPC) and 13C NMR were used to determine the degree of polymerization (DP) and crystallinity index (CrI) of cellulose, and the results along with the sugar release study indicated that cellulose DP likely played a more important role in enzymatic hydrolysis...
November 23, 2016: ChemSusChem
https://www.readbyqxmd.com/read/27882339/surface-plasmon-resonance-biosensing-of-the-monomer-and-the-linked-dimer-of-the-variants-of-protein-g-under-mass-transport-limitation
#10
Hiroshi Imamura, Shinya Honda
This article presented the data related to the research article entitled "Calibration-free concentration analysis for an analyte prone to self-association" (H. Imamura, S. Honda, 2017) [1]. The data included surface plasmon resonance (SPR) responses of the variants of protein G with different masses under mass transport limitation. The friction factors of the proteins analyzed by an ultracentrifugation were recorded. Calculation of the SPR response of the proteins was also described.
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27872164/functional-consequences-of-b-repeat-sequence-variation-in-the-staphylococcal-biofilm-protein-aap-deciphering-the-assembly-code
#11
Catherine L Shelton, Deborah G Conrady, Andrew B Herr
Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated Accumulation-Associated Protein (Aap), via zinc-mediated self-assembly of its B-repeat region. This region contains up to 17 nearly-identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids...
November 21, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27871843/considerations-when-using-next-generation-sequencing-for-genetic-diagnosis-of-long-qt-syndrome-in-the-clinical-testing-laboratory
#12
Hyojin Chae, Jiyeon Kim, Gun Dong Lee, Woori Jang, Joonhong Park, Dong Wook Jekarl, Yong Seog Oh, Myungshin Kim, Yonggoo Kim
BACKGROUND: Congenital long-QT syndrome (LQTS) is a potentially lethal cardiac electrophysiologic disorder characterized by QT interval prolongation and T-wave abnormalities. At least 13 LQTS-associated genes have been reported, but the high cost and low throughput of conventional Sanger sequencing has hampered the multi-gene-based LQTS diagnosis in clinical laboratories. METHODS: We developed an NGS (next-generation sequencing)-based targeted gene panel for 13 LQTS genes using the Ion PGM platform, and a cohort of 36 LQTS patients were studied for characterization of analytical performance specifications...
November 18, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27870944/application-of-single-molecule-amplification-and-resequencing-technology-for-broad-surveillance-of-plasma-mutations-in-patients-with-advanced-lung-adenocarcinoma
#13
Zheng Wang, Gang Cheng, Xiaohong Han, Xinlin Mu, Yuhui Zhang, Di Cui, Chang Liu, Li Zhang, Zaiwen Fan, Lingyun Ma, Li Yang, Jing Di, David S Cram, Yuankai Shi, Dongge Liu
Liquid biopsy to access the circulating tumor DNA is a promising surrogate for invasive tumor genotyping. We designed a multiplex assay based on circulating single-molecule amplification and resequencing technology (cSMART) to simultaneously detect and quantitate hot spot EGFR, KRAS, BRAF, ERBB2, and ALK plasma DNA variants in 103 patients with advanced lung adenocarcinoma. In validation studies using an analytical mutation standard, the sensitivity of the assay for EGFR mutation detection was at least 0.1% and specificity was 100%...
November 18, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27863262/in-silico-proficiency-testing-for-clinical-next-generation-sequencing
#14
REVIEW
Eric J Duncavage, Haley J Abel, John D Pfeifer
Quality assurance for clinical next-generation sequencing (NGS)-based assays is difficult given the complex methods and the range of sequence variants such assays can detect. As the number and range of mutations detected by clinical NGS assays has increased, it is difficult to apply standard analyte-specific proficiency testing (PT). Most current proficiency testing challenges for NGS are methods-based PT surveys that use DNA from reference samples engineered to harbor specific mutations that test both sequence generation and bioinformatics analysis...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27862490/symptom-clusters-in-patients-receiving-hemodialysis-a-systematic-review-of-observational-studies
#15
REVIEW
Xiaoyi Cao, Lang Tian, Lin Chen
AIMS AND OBJECTIVES: To systematically review the common composition and the analytical methods performed to derive symptom clusters in patients receiving hemodialysis, and to examine their common predictive and outcome variables. BACKGROUND: Patients receiving hemodialysis may suffer from multiple and interactive symptoms simultaneously, which may impact their mortality, morbidity and quality of life. The composition of these symptom clusters varies depending on the different assessment tools, the variant evaluation timing points and the various statistical methodologies...
November 10, 2016: Journal of Clinical Nursing
https://www.readbyqxmd.com/read/27856697/caenorhabditis-elegans-daf-2-as-a-model-for-human-insulin-receptoropathies
#16
David A Bulger, Tetsunari Fukushige, Sijung Yun, Robert K Semple, John A Hanover, Michael W Krause
Human exome sequencing has dramatically increased the rate of identification of diseaseassociated polymorphisms. However, examining the functional consequences of those variants has created an analytic bottleneck. Insulin-like signaling in Caenorhabditis elegans has long provided a model to assess consequences of human insulin signaling mutations, but this has not been evaluated in the context of current genetic tools. We have exploited strains derived from the Million Mutation Project and gene editing to explore further the evolutionary relationships and conservation between the human and C...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27854017/analytical-ultracentrifuge-analysis-of-nucleosomes-assembled-from-recombinant-acid-extracted-hplc-purified-histones
#17
Manjinder S Cheema, Juan Ausió
The accumulating discoveries of new posttranslational modifications (PTMs) and the increasing relevance of histone variants within the frame of epigenetics demand the availability of methods for a rapid and efficient nucleosome reconstitution to analyze their structural and functional implications. Here we describe a method suitable for this purpose, starting from bacterially expressed histones, solubilized by acid and purified by reversed-phase high-performance liquid chromatography. This method allows the preparation of micrograms to milligram amounts of in vitro-assembled nucleosomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27852342/on-studying-ageism-in-long-term-care-a-systematic-review-of-the-literature
#18
José Manuel Sousa de São José, Carla Alexandra Filipe Amado
BACKGROUND: Ageism in long-term care is pervasive, but it is not easy to define, to identify and to fight it in practice. These difficulties could be overcome if we develop research capable to conceptualize, detect, measure, and understand the multidimensionality and complexity of ageism. Nevertheless, to achieve this, it is fundamental to know how ageism in long-term care has been previously studied. METHODS: This paper systematically reviews studies on ageism in long-term care services published before October 2015 and indexed in Web of Science, PubMed, and Social Care Online electronic databases...
November 17, 2016: International Psychogeriatrics
https://www.readbyqxmd.com/read/27846814/lack-of-direct-evidence-for-natural-selection-at-the-candidate-thrifty-gene-locus-ppargc1a
#19
Murray Cadzow, Tony R Merriman, James Boocock, Nicola Dalbeth, Lisa K Stamp, Michael A Black, Peter M Visscher, Phillip L Wilcox
BACKGROUND: The gene PPARGC1A, in particular the Gly482Ser variant (rs8192678), had been proposed to be subject to natural selection, particularly in recent progenitors of extant Polynesian populations. Reasons include high levels of population differentiation and increased frequencies of the derived type 2 diabetes (T2D) risk 482Ser allele, and association with body mass index (BMI) in a small Tongan population. However, no direct statistical tests for selection have been applied. METHODS: Using a range of Polynesian populations (Tongan, Māori, Samoan) we re-examined evidence for association between Gly482Ser with T2D and BMI as well as gout...
November 15, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27836695/clinical-validation-of-a-next-generation-sequencing-genomic-oncology-panel-via-cross-platform-benchmarking-against-established-amplicon-sequencing-assays
#20
Sabah Kadri, Bradley C Long, Ibro Mujacic, Chao J Zhen, Michelle N Wurst, Shruti Sharma, Nadia McDonald, Nifang Niu, Sonia Benhamed, Jigyasa Tuteja, Tanguy Seiwert, Kevin White, Megan E McNerney, Carrie Fitzpatrick, Y Lynn Wang, Larissa V Furtado, Jeremy P Segal
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations...
November 8, 2016: Journal of Molecular Diagnostics: JMD
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