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Bioscience

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Displaying 476 - 500 of 1261

Inhibitors of DNA glycosylases as potential therapeutic drugs in cancer

April 4, 2016
Author(s)
M Miral Dizdar, Aaron C. Jacobs, Nathan Donley, Ajit Jadhav, Dorjbal Dorjsuren, David Maloney, Anton Simeonov, Pawel Jaruga, Erdem Coskun, Amanda K. McCullough, R. S. Lloyd
Ionizing radiation and most chemotherapeutic agents kill tumor cells by damaging DNA. The efficacy of DNA-damaging agents may be influenced by increased DNA repair capacity in tumors that results from overexpression of DNA repair proteins. Inhibition of

Genetic circuit design automation

April 1, 2016
Author(s)
Alec Nielsen, Bryan Der, Jonghyeon Shin, Prashant Vaidyanathan, Douglas Densmore, Vanya M. Paralanov, Elizabeth Strychalski, David J. Ross, Christopher Voigt
Computation can be performed in living cells using DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We

Design and synthesis of a minimal bacterial genome

March 25, 2016
Author(s)
Elizabeth A. Strychalski, Clyde A. Hutchinson III, Ray-Yuan Chuang, Vladimir Noskov, Nacyra Assad-Garcia, Tom J. Deerinck, Mark H. Ellisman, John Gill, Krishna Kannan, Bogumil J. Karas, Li Ma, James F. Pelletier, Zhi-Qing Qi, Alexander Richter, Lijie Sun, Yo Suzuki, Billyana Tsvetanova, Kim S. Wise, Hamilton O. Smith, John I. Glass, Chuck Merryman, Daniel G. Gibson, J. C. Venter
We used whole-genome design and complete chemical synthesis to minimize the 1079–kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon

SMALL MOLECULE INHIBITORS OF DNA GLYCOSYLASES AS POTENTIAL DRUGS IN CHEMO- AND RADIOTHERAPIES

March 19, 2016
Author(s)
M Miral Dizdar, Aaron C. Jacobs, Nathan Donley, Marcus J. Calkins, Ajit Jadhav, Dorjbal Dorjsuren, David Maloney, Anton Simeonov, Amanda K. McCullough, R S. Lloyd, Erdem Coskun, Pawel Jaruga
Introduction: Ionizing radiation and most chemotherapeutic agents kill tumor cells by damag-ing DNA. The efficacy of DNA-damaging agents may be influenced by increased DNA repair capacity in tumors that results from overexpression of DNA repair proteins

Automation of Antimicrobial Activity Screening

March 12, 2016
Author(s)
Samuel P. Forry, Meggan C. Madonna, Daneli Lopez-Perez, Nancy J. Lin, Madeleine D. Pasco
ABSTRACT: Manual and automated methods were compared for routine screening of compounds for antimicrobial activity. Automation generally accelerated assays and required less user intervention while producing comparable results. Automated protocols were

Clinical Implications of Technical Performance in Medical Genome Sequencing

March 2, 2016
Author(s)
Justin M. Zook, James Priest, Rachel Goldfeder, Megan Grove, Daryl Waggott, Matthew Wheeler, Euan Ashley, Marc L. Salit
As next-generation sequencing is becoming routinely applied to clinical care, the predictive characteristics and limitations of whole exome and whole genome sequencing need to be well-understood. The Genome in a Bottle Consortium has recently published a

Method Validation and Standards in Hydrogen/Deuterium Exchange Mass Spectrometry

March 1, 2016
Author(s)
Jeffrey W. Hudgens, Richard Y. Huang, Emma D'Ambro
The chapter examines method validation and measurement standards for measuring protein dynamics by hydrogen/deuterium exchange mass spectrometry. Topics examined include the rationale for a reference measurement system for HDX-MS, attaining high accuracy

THE PROFICIENCY TEST (PILOT) REPORT OF THE GLOBAL MICROBIAL IDENTIFIER INITIATIVE YEAR 2014

March 1, 2016
Author(s)
Nathanael D. Olson, Rene S. Hendriksen, Susanne K. Pedersen, Mette V. Larsen, Jamie N. Pedersen, Oksana Lukjancenko, Rolf S. Kaas, Pimlapas Leekitcharoenphon, Lasse Bergmark, Inge M. Hansen, Vitali Sintchenko, William J. Wolfgang, Henrik T. Westh, Jacob Moran-Gilad, Isabel Cuesta, Angel Zaballos, Brian Beck, Anthony Underwood, Errol Strain, James Pettengill

Quantitative Flow Cytometry Measurements in Antibody Bound per Cell Based on CD4 Reference

February 12, 2016
Author(s)
Lili Wang, Heba Degheidy, Fatima Abbasi, Howard Mostowski, Gerald Marti, Steven R. Bauer, Robert Hoffman, Adolfas K. Gaigalas
Multicolor flow cytometer assays are with fluorescently labeled antibodies routinely used in clinical laboratories to measure the cell number of specific immunophenotypes and to estimate expression levels of specific receptors/antigens either on the cell

A Description of the Clinical Proteomics Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

February 10, 2016
Author(s)
Jeri S. Roth, Paul A. Rudnick, Sanford Markey, Yuri Mirokhin, Xinjian Yan, Dmitrii Tchekhovskoi, Stephen Stein, Nathan J. Edwards, Ratna R. Thangudu, Karen A. Ketchum, Christopher R. Kinsinger, Mehdi Mesri, Henry Rodriguez
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics datasets from the mass spectrometric interrogation of tumor samples previously studied by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and

Dioctyl sodium sulfosuccinate (DOSS; CAS #577-11-7) a major component of the dispersant COREXIT is an obesogen

January 20, 2016
Author(s)
Alexis M. Temkin, Robert R. Bowers, Margaret E. Magaletta, Steven Holshouser, Adriana Maggi, Paolo Ciana, Louis J. Guillette Jr., John Bowden, John E. Baatz, Demetri D. Spyropoulos, John Kucklick
Background: Product safety testing typically involves lethal toxicity assessments, which likely miss long- term health impacts. Optimizing long-term product safety is critical for widespread chemical use. The obesity epidemic exemplifies a condition based

SVClassify: a method to use multiple datasets to classify candidate structural variants into true positives and false positives

January 16, 2016
Author(s)
Justin M. Zook, Hemang M. Parikh, Desu Chen, Hariharan K. Iyer, Marc L. Salit, Wolfgang Losert
The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). While high-quality benchmark small variant calls have recently been developed by the Genome in a Bottle Consortium, no

ASTM Workshop on Standards & Measurements for Tissue Engineering Scaffolds

January 1, 2016
Author(s)
Carl G. Simon Jr., John Test, Michael Yaszemski, Reto Luginbuehl, Anthony Ratcliffe, Paul Tomlins
A “Workshop on Standards & Measurements for Tissue Engineering Scaffolds” was held on May 21, 2013 and was sponsored by the American Society of Testing and Materials International (ASTM International) in Indianapolis, IN. The purpose of the workshop was to

QUANTITY: An Isobaric Tag for Quantitative Glycomics

November 30, 2015
Author(s)
Shuang Yang, Meiyao Wang, Lijun Chen, Illarion Turko, Karen W. Phinney, Shuwei Li
We describe the design and synthesis of a novel set of iso-baric tags for quantitative glycan profiling, which will have broad applications in carbohydrate based biomarker dis-covery, therapeutic protein characterization, and vaccine development.

Gold Nanoparticle Quantitation by Whole Cell Tomography

November 13, 2015
Author(s)
Aric W. Sanders, Kavita M. Jeerage, Cindi Schwartz, Alexandra Curtin, Ann C. Chiaramonti Debay
Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized

MEASUREMENT OF DNA REPAIR PROTEINS IN RELATION TO DISEASE BIOMARKERS AND DRUG DEVELOPMENT

November 7, 2015
Author(s)
Erdem Coskun, Pawel Jaruga, Leona D. Scanlan, Alessandro Tona, Mark S. Lowenthal, Prasad T. Reddy, M Miral Dizdar, Ann-Sofie Jemth, Olga Loseva, Thomas Helleday
Introduction: In aerobic organisms, intracellular metabolism and exogenous sources such as ionizing radiation and carcinogenic compounds generate reactive species including free radicals derived from either oxygen or nitrogen. Oxidative stress thereby

DNA Extraction and DNA Damage Measurement in the Nematode Caenorhabditis elegans

November 1, 2015
Author(s)
Leona D. Scanlan, Pawel Jaruga, Sanem Hosbas Coskun, Jamie L. Almeida, David N. Catoe, Jennifer McDaniel, Miral M. Dizdar
Little is known about endogenous DNA damage in the nematode. In this work, we standardized the growth of the nematode in two different growth media (axenic CeHR supplemented with 20% milk and S-basal with E. coli), and developed a novel high-salt, phenol
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