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Displaying 151 - 175 of 865

Chapter 4: Oxidatively induced DNA damage: Mechanisms and measurement

November 20, 2020
Author(s)
Miral M. Dizdar, Erdem Coskun, Gamze Tuna, Melis Kant, Pawel Jaruga
Oxidatively induced damage to DNA occurs in living organisms by endogenously or exogenously generated reactive species including free radicals. Mounting evidence suggests that this type of DNA damage plays an important role in the etiology of numerous

A Case Study of Medical Device Wireless Coexistence Evaluation

October 1, 2020
Author(s)
Mohamed Al-Kalaa, Joshua Guag, Seth Seidman, Yao Ma, Jason Coder
This article aims to provide a narrative for addressing wireless coexistence in medical devices to help medical device developers, test engineers, and regulatory affairs personnel throughout the device life cycle. Accordingly, we present a case-study

A NIST-Hosted Virtual Workshop on Measuring SARS-CoV-2 in Wastewater and Fecal Material: A Call for Standards

September 28, 2020
Author(s)
Sandra M. Da Silva, Paulina K. Piotrowski, Christina M. Jones, Stephanie L. Servetas, Nancy J. Lin, Katrice A. Lippa, Scott A. Jackson
The National Institute of Standards and Technology (NIST) has leveraged its expertise in chemical and biological metrology and standards development as well as its strong relationships with stakeholders to host a virtual workshop on June 16, 2020 that

A Diploid Assembly-based Benchmark for Variants in The Major Histocompatibility Complex

September 22, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Chen-Shan Chin, Qiandong Zeng, Alexander Dilthey, Tobias Marschall, Mikko Rautiainen, Erik Garrison, Shilpa Garg
Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5

THE GUT MICROBIOME AND XENOBIOTICS: IDENTIFYING KNOWLEDGE GAPS

July 1, 2020
Author(s)
Vicki L. Sutherland, Charlene A. McQueen, donna Mendrick, donna gulezian, Carl Cerniglia, Steven Foley, Samuel Forry, Sangeeta Khare, Xue Liang, Jose E. Manautou, Donald Tweedie, howard young, Alexander Aleksenkyo, frank burns, Rod Dietert, Katherine Karberg, alan wilson, connie chen
There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut

Improving patient outcomes with regenerative medicine: How to move the needle forward in cell manufacturing, standards, 3D bioprinting, AI enabled automation, education and training

June 17, 2020
Author(s)
Carl Simon, Josh Hunsberger, Claudia Zylberberg, Preveen Ramamoorthy, Thomas Tubon, Crystal Ruff, Ram Bedi, Kurt Gielen, Lynn Fisher, Jed Johnson, Priya Barankiak, Behzad Mahdavi, Michael Hadjisavas, Shannon Eaker, Cameron Miller
Regenerative Medicine Manufacturing Society (RMMS), is the first and only professional society dedicated specifically towards advancing manufacturing solutions for the field of regenerative medicine. RMMS' vision is to provide greater patient access to

Expression of a germline variant in the N-terminal domain of the human DNA glycosylase NTHL1 induces cellular transformation without impairing enzymatic function or substrate specificity

June 16, 2020
Author(s)
Carolyn G. Marsden, Pawel Jaruga, Erdem Coskun, Robyn L. Maher, David S. Pederson, Miral M. Dizdar, Joann B. Sweasy
Oxidatively-induced DNA damage, widely accepted as a key player in the onset of cancer, is predominantly repaired by base excision repair (BER). BER is initiated by DNA glycosylases, which locate and remove damaged bases from DNA. NTHL1 is a bifunctional

A robust benchmark for detection of germline large deletions and insertions

June 15, 2020
Author(s)
Justin Zook, Nathanael David Olson, Marc Salit, Fritz Sedlazeck
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a

Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen

June 9, 2020
Author(s)
David Gallagher, Roy A. Mariuzza, Brian G. Pierce, Daichao Wu, Ragul Gowthaman
Abstract Adoptive cell therapy (ACT) with tumor-specific T cells can mediate cancer regression. The main target of tumor-specific T cells are neoantigens arising from mutations in self-proteins. Although the majority of cancer neoantigens are unique to

Assembly and annotation of an Ashkenazi human reference genome

June 2, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Nathanael D. Olson, Steven L. Salzberg, Alaina Shumate, Aleksey V. Zimin, Daniela Puiu, Mihaela Pertea, Marc Salit
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

May 4, 2020
Author(s)
Justin M. Zook, Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Miten Jain, Benedict Paten
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and

Ion-beam radiation damage to DNA by investigation of free radical formation and base damage

March 1, 2020
Author(s)
Melis Kant, Pawel Jaruga, Erdem Coskun, Samuel Ward, Alexander Stark, David Becker, Amitav Adhikary, Michael Sevilla, Miral M. Dizdar
This work investigated the physicochemical processes and DNA base products involved in Ne-22 ion- beam (ca. 1.4 GeV) radiation damage to hydrated (12 waters/nucleotide) highly polymerized salmon sperm DNA. For this purpose, approximately 12 small (ca. 10

Measurement of PARP1 in human tissues by liquid chromatography tandem mass spectrometry

March 1, 2020
Author(s)
Erdem Coskun, Gamze Tuna, Pawel Jaruga, Alessandro Tona, Onur Erdem, Miral M. Dizdar
Poly(ADP ribose) polymerase 1 (PARP1) is a multifunctional DNA repair protein of the base excision repair pathway and plays a major role in the repair of DNA strand breaks and in replication and transcriptional regulation among other functions. Mounting

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di- heptamer macromolecular assembly

January 14, 2020
Author(s)
Xingjian Xu, Raquel Ruiz, Kaylin Adipietro, Christopher Peralta, Danya Ben-Hail, Kristen Varney, Mary Cook, Braden Roth, Paul Wilder, Thomas Cleveland, Alexander Grishaev, Heather Neu, Sarah Michel, Wenbo Yu, Dorothy Beckett, Richard Rustandi, Alex MacKerell, Amedee des Georges, Edwin Pozharski, David Weber
Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in

Measurement of Airborne Emissions from Extinguished Cigarettes: Final Report

December 16, 2019
Author(s)
Dustin G. Poppendieck
Three series of experiments were conducted in this study. First, studies were performed to the determine the relative distributions of the target chemicals in freshly smoked butts by analyzing six types of samples consisting of different parts of the butts
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