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Bioscience

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Displaying 376 - 400 of 1261

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

September 13, 2017
Author(s)
Alessandro Borgia, Wenwei Zheng, Karin Buholzer, Madeleine Borgia, Anja Schuler, Hagen Hoffman, Andrea Sorrano, Daniel Nettels, Klaus Gast, Alexander Grishaev, Robert Best, Benjamin Schuler
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing

Using metagenomic methods to detect organismal contaminants in microbial materials.

September 12, 2017
Author(s)
Nathanael D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin
High sensitivity methods as next generation sequencing and PCR are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require

Small molecule inhibitors of DNA glycosylases as potential drugs in cancer therapy

August 31, 2017
Author(s)
M Miral Dizdar, Aaron C. Jacobs, Nathan Donley, Marcus J. Calkins, Ajit Jadhav, Dorjbal Dorjsuren, David Maloney, Anton Simeonov, Pawel Jaruga, Erdem Coskun, Amanda K. McCullough, R. S. Lloyd
Statement of the Problem: Most chemotherapeutic agents kill cancer cells by damaging DNA. Cancer cells overexpress DNA repair proteins and thus increase DNA repair capacity that can cause resistance to therapy by removing DNA lesions before they become

A serum small molecule biosignature of radiation exposure from total body irradiated patients

August 21, 2017
Author(s)
Evagelia C. Laiakis, Evan L. Pannkuk, Siddheshwar Chauthe, Yi-Wen Wang, Ming Liang, Tytus Mak, Christopher A. Barker, Giuseppe Astarita, Albert J. Fornace
The potential of radiological accidents and nuclear terrorism have increased the need for development of new rapid biodosimetry methods. In addition, in a clinical setting the issue of an individual's radiosensitivity should be taken into consideration

Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.

August 6, 2017
Author(s)
Nathanael Olson, Chris M. Hill, Vistoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Todd J. Treangen, Mihai Pop
Metagenomic samples are snapshots of complex ecosystems at work. These samples often involve hundreds of bacteria from known and unknown species, contain multiple strain variants, and vary greatly both within and across environments. Many microbes found in

Genome-wide reconstruction of complex structural variants using read clouds

July 17, 2017
Author(s)
Noah Spies, Ziming Weng, Alex Bishara, Jennifer H. McDaniel, David N. Catoe, Justin M. Zook, Marc L. Salit, Robert B. West, Serafim Batzoglou, Arend Sidow
Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cloud approaches

Non-Uniform Sampling for All: More Spectral Quality, Less Measurement Time

June 30, 2017
Author(s)
Frank Delaglio, Gregory S. Walker, Kathleen A. Farley, Raman Sharma, Jeffrey C. Hoch, Luke Arbogast, Robert Brinson, John Marino
Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable tool in pharmaceutical science, with uses in drug discovery, development, and manufacturing. Non-Uniform Sampling (NUS) is an acquisition method for NMR experiments with two or more

Associations between perfluorinated alkyl acids measured in blood and ovarian follicular fluid and ovarian function in women undergoing assisted reproductive treatment

June 26, 2017
Author(s)
Jessica A. Cloy-McCoy, Jacqueline T. Bangma, Jessica L. Reiner, John Bowden, John Schnorr, Michael Slowey, Tom O'Leary, Louis J. Guillette, Benjamin B. Parrott
Endocrine disrupting contaminants, in combination with other environmental variables, are associated with altered reproductive health. Assisted reproductive technology (ART) procedures offer valuable opportunities to explore the connections between

The GAN exonuclease, or the flap endonuclease Fen1 and RNase HII are necessary for viability of Thermococcus kodakarensis.

June 13, 2017
Author(s)
Brett W. Burkhart, Lubomira Cubonova, Margaret R. Heider, John N. Reeve, Thomas J. Santangelo, Zvi Kelman
Many aspects of and factors required for DNA replication are conserved across all three Domains of life but there are some significant differences surrounding lagging strand synthesis. In Archaea a 5' to 3' exonuclease, related to both bacterial RecJ and

Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity

June 2, 2017
Author(s)
Prakash Kulkarni, Mohit Jolly, Dongya Jia, Steven Mooney, Ajay Bhargava, Luciane Kagohara, Yihong Chen, Pengyu Hao, Yanan He, Roberft Veltri, Alexander Grishaev, Keith Weninger, Herbert Levine, John Orban
Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a large fraction of the human proteome play important roles in numerous cellular functions. Prostate- Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of

Conformational Changes in Active and Inactive States of Human PP2C? characterized by Hydrogen/Deuterium Exchange-Mass Spectrometry

May 8, 2017
Author(s)
Sharlyn Mazur, Elyssia S. Gallagher, Subrata Debnath, Stewart R. Durell, Kyle Anderson, Lisa M. Jenkins, Ettore Appella, Jeffrey W. Hudgens
PPM serine/threonine protein phosphatases function in signaling pathways and require millimolar concentrations of Mn2+ or Mg2+ ions for activity. Whereas the crystal structure of human PP2Cα displayed two tightly bound Mn2+ ions in the active site, recent

FLOW CYTOMETER PERFORMANCE CHARACTERIZATION, STANDARDIZATION AND CONTROL

May 8, 2017
Author(s)
Hao-Wei Wang, Robert A. Hoffman
Flow cytometry is a widely used technique for the analysis of single cells and particles. It is an essential tool for immunological research, drug and device development, clinical trials, disease diagnosis, and therapy monitoring. However, the measurements

A novel measure and significance testing in data analysis of cell image segmentation

April 20, 2017
Author(s)
Jin Chu Wu, Michael W. Halter, Raghu N. Kacker, John T. Elliott, Anne L. Plant
Background: Cell image segmentation (CIS) is an essential part of quantitative imaging of biological cells. Designing a performance measure and conducting significance testing are critical for evaluating and comparing the CIS algorithms for image-based

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

April 3, 2017
Author(s)
Meghan C. Burke, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Sanford P. Markey, Stephen E. Stein, Jenny Heidbrink Thompson, Christopher Larkin
We present a mass spectral library based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a ‘hybrid’ method since it combines matching both ion m/z and mass losses. The
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