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Displaying 876 - 900 of 2355

Protein labeling in Escherichia coli with 2H, 13C and 15N

August 23, 2015
Author(s)
Zvi Kelman, Prasad T. Reddy
A number of structural biology techniques such as nuclear magnetic resonance (NMR) and small-angle neutron scattering (SANS) can be performed with proteins with nuclei at natural isotope abundance. However, the use of proteins labeled with heavy isotopes

svviz: a read viewer for validating structural variants

August 18, 2015
Author(s)
Noah Spies, Justin M. Zook, Marc L. Salit, Arend Sidow
We present svviz, a sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. This is accomplished by searching input bam(s) for potentially relevant reads, realigning them against the inferred

Evaluation of two mitochondrial DNA biomarkers for prostate cancer detection

August 17, 2015
Author(s)
Samantha D. Maragh, Steven P. Lund
BACKGROUND: A 3.4kb deletion (3.4kbΔ) in mitochondrial DNA (mtDNA) found in histologically normal prostate biopsy specimens has been reported to be a biomarker for the increased probability of prostate cancer. Increased mtDNA copy number is also reported

Small Molecule Inhibitors of 8-Oxoguanine DNA Glycosylase-1 (OGG1)

August 7, 2015
Author(s)
Pawel Jaruga, Erdem Coskun, M Miral Dizdar, Nathan Donley, Stephen Lloyd, Amanda McCullough
ABSTRACT The DNA base excision repair (BER) pathway, which utilizes DNA glycosylases to initiate repair of specific DNA lesions, is the major pathway for the repair of DNA damage induced by oxidation, alkylation, and deamination. Early results from

Isotopic Labeling of Proteins in Halobacterium salinarum

August 4, 2015
Author(s)
Thomas E. Cleveland, Zvi Kelman
It is often necessary to obtain isotopically labeled proteins containing 15N, 13C or 2H for NMR; and 2H for small-angle neutron scattering (SANS) or neutron diffraction studies. To achieve uniform isotopic labeling, protein expression is most commonly

Localization and Number of Au Nanoparticles in Optically Indexed Cells by FIB Tomography

August 2, 2015
Author(s)
Aric W. Sanders, Kavita M. Jeerage, Ann C. Chiaramonti Debay, Alexandra Curtin
Gold nanoparticles (GNPs) are gaining importance as therapeutic chemical delivery vehicles, medical diagnostic tools, phototherapeutic and contrast enhancement agents. GNPs are uniquely suited for these biological uses because of their chemical stability

Production, Purification and Characterization of 15N-Labeled DNA Repair Proteins as Internal Standards for Mass Spectrometric Measurements

July 26, 2015
Author(s)
Prasad T. Reddy, Pawel Jaruga, Bryant C. Nelson, Mark Lowenthal, Ann-Sofie Jemth, Olga Loseva, Erdem Coskun, Thomas Helleday, Miral M. Dizdar
Oxidatively induced DNA damage is caused in living organisms by a variety of damaging agents, resulting in the formation of a multiplicity of lesions, which are mutagenic and cytotoxic. Unless repaired by DNA repair mechanisms before DNA replication, DNA

Quantifying and Improving Clinical-grade Coverage and Accuracy using Augmented Exome Sequencing

July 16, 2015
Author(s)
Justin M. Zook, Anil Patwardhan, Marc L. Salit, Carlos Bustamante, Euan Ashley, Michael Snyder, John West, Richard Chen
Exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet accuracy and coverage in medically interpretable parts of the genome remains under-characterized. We evaluate recently developed exome sequencing platforms in the

Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics

July 7, 2015
Author(s)
Nathanael D. Olson, Steven P. Lund, Rebecca Colman, Jeffery T. Foster, Jason W. Sahl, James M. Schupp, Paul Keim, Jayne B. Morrow, Marc L. Salit, Justin M. Zook
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing

Applying Thymine Isostere 2,4-Difluoro-5-methylbenzene as an Assignment Tool and Probe of Purine-rich DNA Dynamics Using Proton NMR Spectroscopy

June 30, 2015
Author(s)
Robert G. Brinson, Jennifer T. Miller, Kahn Jason, Stuart F. Le Grice, John P. Marino
Proton assignment of NMR spectra of oligonucleotide duplexes can become difficult with increasing helical length due to cross peak overlap. Here we describe an alternative to 15N and 13C labeling that facilitates assignment via single site substitution
Displaying 876 - 900 of 2355
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