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Bioscience

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Displaying 451 - 475 of 1250

Extensive sequencing of seven human genomes to characterize benchmark reference materials

June 7, 2016
Author(s)
Justin M. Zook, Jennifer H. McDaniel, David N. Catoe, Lindsay Harris, Marc L. Salit
The Genome in a Bottle Consortium hosted by the National Institute of Standards and Technology, (NIST), is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a

Measurement of DNA repair protein apurinic/apyrimidinic endonuclease 1 (APE1) in human tissues by liquid chromatography/tandem mass spectrometry with isotope dilution

June 5, 2016
Author(s)
Pawel Jaruga, Guldal Kirkali, Prasad T. Reddy, Alessandro Tona, Bryant C. Nelson, Li Mengxia, David M. Wilson III, Erdem Coskun, M Miral Dizdar
Introduction DNA repair proteins may be used as biomarkers in disease etiology and therapy. Thus, the accurate determination of DNA repair protein expression and genotype in human tissues is of fundamental importance. Apurinic/apyrimidinic endonuclease 1

Strategies for Achieving Measurement Assurance for Cell Therapy Products

June 1, 2016
Author(s)
Carl G. Simon Jr., Anne L. Plant, Sumona Sarkar, John T. Elliott, Sheng Lin-Gibson
Cell therapy products (CTPs) need quantitative, validated, and robust assays to support informed decision making during their development, manufacturing, and regulation. These products, the materials involved in their production and the methods for

DNA Damage and Repair in Cancer

May 26, 2016
Author(s)
M Miral Dizdar
Oxygen- and nitrogen-derived reactive species are constantly generated in living organisms by endogenous and exogenous sources. Reactions of reactive species such as free radicals with DNA cause the formation of multiple mutagenic and cytotoxic lesions

Large-scale Time-lapse Microscopy of Oct4 Expression in Human Embryonic Stem Cell Colonies

May 22, 2016
Author(s)
Kiran Bhadriraju, Michael Halter, Julien M. Amelot, Peter Bajcsy, Joe Chalfoun, Antoine Vandecreme, Barbara Mallon, Kye-yoon Park, John T. Elliott, Subhash Sista, Anne L. Plant
Identification of critical characteristics of therapeutically active cells, and quantification of those characteristics, are essential for assuring consistency and potency of cell therapy products. We have developed image analysis and visualization

Comparison of T1 measurement using ISMRM/NIST system phantom

May 9, 2016
Author(s)
Kathryn E. Keenan, Karl F. Stupic, Michael A. Boss, Stephen E. Russek, Thomas L. Chenevert, Pottumarthi V. Prasad, Wilburn E. Reddick, Jie Zheng, Peng Hu, Edward F. Jackson
We used the ISMRM/NIST system phantom to assess variations of T1 measurements across MRI systems at 1.5 T and 3 T, to determine the repeatability and reproducibility of the T1 measurements. This study demonstrates that T1 variations from NMR-measured value

A Roadmap for Regulatory Science Research for Next Generation Sequencing Informatics

April 20, 2016
Author(s)
Justin M. Zook, Marc L. Salit, Russ B. Altman, Arend Sidow, Rachel Goldfeder, Euan Ashley, Elizabeth Mansfield
The Precision Medicine Initiative (PMI) is a national effort in the United States “to enable a new era of medicine through research, technology, and policies that empower patients, researchers, and providers to work together toward development of

Engineered metal nanoparticles in the sub-nanomolar levels kill cancer cells

April 18, 2016
Author(s)
Yasmine C. Daniels, William A. MacCrehan, Shinichiro Muramoto, Gheorghe NMN Stan, Vitaly Vodyanoy, Oleg Pustovyy
Zinc and copper metal nanoparticles were produced from bulk metal rods by an underwater high-voltage discharge method. The metal nanoparticles, with estimated diameters of 1 nm to 2 nm, were determined to be more than 85 % non-oxidized. Exposure of rat RG2

Combined Effects of High-Dose Bisphenol A and Oxidizing Agent (KBrO3) on Cellular Microenvironment, Gene Expression, and Chromatin Structure of Ku70-deficient Mouse Embryonic Fibroblasts

April 15, 2016
Author(s)
Erdem Coskun, Pawel Jaruga, Miral M. Dizdar, Natalie Gassman, Samuel Wilson
Background: Exposure to the environmental endocrine disrupting chemical bisphenol A (BPA) has been reported to alter global gene expression, induce epigenetic modifications, and interfere with the complex regulatory networks of cells. In addition to these

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
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