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Search Publications

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Displaying 276 - 300 of 1242

Measurement of Oxidatively Induced DNA Damage in Caenorhabditis elegans with High-Salt DNA Extraction and Isotope-Dilution Mass Spectrometry

August 27, 2019
Author(s)
Leona D. Scanlan, Pawel Jaruga, Sanem Hosbas Coskun, Christopher Sims, Shannon Hanna, Jamie L. Almeida, David N. Catoe, Bryant C. Nelson, Miral M. Dizdar, Erdem Coskun
Caenorhabditis elegans (C. elegans) is used as a medical and systems toxicity model organism for environmental and developmental assays that include high-throughput methods and genetic studies. However, little is known about background levels of

Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis

August 18, 2019
Author(s)
Yamil Simon, Ramesh Marupaka, Xinjian Yan, Yuxue Liang, Kelly H. Telu, Yuri Mirokhin, Stephen E. Stein
A large fraction of ions observed in electrospray liquid chromatography–mass spectrometry (LC–ESI-MS) experiments of biological samples remain unidentified. One of the main reasons for this is that spectral libraries of pure compounds fail to account for

Analysis of Different Computational Techniques for Calculating the Polarizability Tensors of Stem Cells with Realistic Three-Dimensional Morphologies

July 15, 2019
Author(s)
Jack F. Douglas, Beatriz Betancourt, Somen Baidya, Ahmed M. Hassan, Waleed Al-Shaikhli, Edward J. Garboczi
In living systems, it is frequently stated that form follows function by virtue of evolutionary pressures on organism development, but in the study of how functions emerge at the cellular level, function often follows form. We study this chicken versus egg

Mass spectrometry enumeration of filamentous M13 bacteriophage

July 2, 2019
Author(s)
Tingting Wang, Ai Nguyen, Linwen Zhang, Illarion Turko
In the last decade, filamentous M13 bacteriophage has emerged into numerous biotechnological applications as a promising nontoxic and self-assembling biomaterial with specific binding properties. This raises a question about its upscale production that

genomeview - an extensible python-based genomics visualization engine

June 26, 2019
Author(s)
Noah Spies, Justin Zook, Marc L. Salit, Arend Sidow
Visual inspection and analysis is integral to quality control, hypothesis generation, methods development and validation of genomic data. The richness and complexity of genomic data necessitates customized visualizations highlighting specific features of

Interlaboratory study to validate a STR profiling method for intraspecies identification of mouse cell lines

June 20, 2019
Author(s)
Jamie L. Almeida, Aleksandra Dakic, Karin Kindig, Maikan Kone, Deborah L. Letham, Scott Langdon, Ruth Peat, Jayamalini Holding-Pillai, Erin Hall, Mark Ladd, Megan Shaffer, Heath Berg, Jinliang Li, Georges Wigger, Steven P. Lund, Carolyn R. Steffen, Barbara Fransway, Bob Geraghty, Manuela Natoli, Beth Bauer, Susanne M. Gollin, Dale Lewis, Yvonne A. Reid
The Consortium for Mouse Cell Line Authentication was formed to validate Short Tandem Repeat (STR) markers for intraspecies identification of mouse cell lines. The STR profiling method is a multiplex polymerase chain reaction (PCR) assay comprised of

Development of Protein-Like Reference Material for Semi-Quantitatively Monitoring Visible Proteinaceous Particles in Biotherapeutics

June 17, 2019
Author(s)
Srivalli Telikepalli, Kristen Gonzalez, Sonia Dragulin-Otto, Dean C. Ripple, Michael J. Carrier, M Khan
Visual inspection of biotherapeutics is required at various stages of drug production and manufacturing to ensure quality and consistency of drug products. Inherent particles, composed of aggregated protein from the drug-product, may potentially pose

Workshop 13: Building Measurement Assurance in Flow Cytometry

June 17, 2019
Author(s)
Lili Wang, Stephen Perfetto, Robert Hoffman, John T. Elliott, Sheng Lin-Gibson, Steven Bauer, Heba Degheidy, Judith Arcidiacono, Litwin Virginia
Two workshops were held to identify measurement challenges and potential solutions for building measurement assurance for flow cytometry. This report summarizes key findings, including the need for high quality reagents, reference standards or materials

Workshop 9: Control Cells or Not

June 17, 2019
Author(s)
Paul Wallace, Jonni S. Moore, Derek Jones, Litwin Virginia, Lili Wang, Yanli Liu
"Control Cells or Not" was an educational workshop that used surveys, lectures, and discussions to identify problems and solutions related to using commercially available control cell products and lab-developed approaches. Collective efforts are proposed

High-coverage, long-read sequencing of Chinese trio reference samples

June 14, 2019
Author(s)
Justin M. Zook, Nathanael D. Olson, Marc L. Salit, Aaron Wenger, Chunlin Xiao, Robert Sebra
Genome In a Bottle (GIAB) is a consortium hosted by the National Institute of Standards and Technology whose primary objective is the development and characterization of human genomic reference materials. The consortium includes representatives from

Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization

May 30, 2019
Author(s)
Ella Mihailescu, Mirco Sorci, Jolita Seckute, Vitalii I. Silin, Janet Hammer, B. Scott Perrin, Jorge Hernandez, Nedzada Smajic, Akritee Shrestha, Kimberly Bogadardus, Alexander Greenwood, Riqiang Fu, Jack Blazyk, Richard W. Pastor, Linda Nicholson, Georges Belfort, Myriam Cotten
Piscidins are histidine-enriched antimicrobial peptides that interact with lipid bilayers as amphipathic alpha-helices. Their activity at acidic and basic pH in vivo makes them promising templates for biomedical applications. This study focuses on p1 and

Structural Insights into DNA-Stabilized Silver Clusters

May 10, 2019
Author(s)
Danielle Schultz, Robert G. Brinson, Fahriye N. Sari, Jeffrey Fagan, Christina Bergonzo, Nancy Lin, Joy Dunkers
The structure and dynamics of Ag complexes derived from single stranded DNA (ssDNA) is less understood than their double stranded (dsDNA) counterparts despite their great promise as fluorescent biological probes and sensors. In this work, we seek new

Strategies for robust and accurate measurement of nanomaterial bioaccumulation

April 17, 2019
Author(s)
Elijah J. Petersen, Monika Mortimer, Robert Burgess, Richard Handy, Shannon Hanna, Kay Ho, Monique E. Johnson, Susana Louriero, Selck Henriette, Janeck Scott-Fordsmand, David Spurgeon, Jason Unrine, Nico van den Brink, Ying Wang, Jason White, Patricia Holden
One of the key components for environmental risk assessment of engineered nanomaterials (ENMs) is data on bioaccumulation potential. Accurately measuring bioaccumulation can be critical for regulatory decision making regarding material hazard and risk, and

Ligand-based stability changes in duplex DNA measured with a microscale electrochemical platform

April 12, 2019
Author(s)
Sarah M. Robinson, Zuliang Shen, Jon R. Askim, Christopher B. Montgomery, Herman O. Sintim, Stephen Semancik
Development of technologies for rapidly screening the thermal stability of DNA secondary structures and the effects on stability for binding of small molecule drugs is important to the drug discovery process. In this report, we describe the capabilities of

An open resource for accurately benchmarking small variant and reference calls

April 1, 2019
Author(s)
Justin M. Zook, Jennifer H. McDaniel, Marc L. Salit, Nathanael D. Olson, Justin M. Wagner
Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to

Best practices for benchmarking germline small-variant calls in human genomes

March 11, 2019
Author(s)
Justin M. Zook, Marc L. Salit
Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant- calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part

Engineering ClpS for Selective and Enhanced N-terminal Amino Acid Binding

March 1, 2019
Author(s)
Jennifer A. Tullman, Zvi Kelman, John P. Marino
One of the central challenges in the development of single-molecule protein sequencing technologies is achieving high-fidelity, sequential recognition and detection of specific amino acids that comprise the peptide sequence. An approach towards achieving
Displaying 276 - 300 of 1242
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