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Bioscience

Search Publications

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Displaying 226 - 250 of 1242

Chromosome-scale, haplotype-resolved assembly of human genomes

December 7, 2020
Author(s)
Justin Zook, Shilpa Garg, Heng Li
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which

Crystal Structure of a Bivalent Antibody Fab Fragment

November 11, 2020
Author(s)
Salman Shahid, Mingming Gao, David Gallagher, Steven Foung, Zhen-Yong Keck, Thomas Fuerst, Roy Mariuzza
We determined the crystal structure to 1.8 Å resolution of the Fab fragment of an affinity- matured human monoclonal antibody (HC84.26.5D) that recognizes the E2 envelope glycoprotein of hepatitis C virus (HCV). Unlike conventional Fabs, which are

Conformational gating, dynamics and allostery in human monoacylglycerol lipase

October 28, 2020
Author(s)
Sergiy Tyukhtenko, Girija Rajarshi, Ioannis Karageorgos, Nikolai Zvonok, Kiran Vemuri, Jeffrey W. Hudgens, Xiaoyu Ma, Mahmoud L. Nasr, Alexandros Makriyannis, Kyle Anderson, Jason J. Guo, Gerhard Wagner
Inhibition of human Monoacylglycerol Lipase (hMGL) offers a novel approach for treating neurological diseases. The design of inhibitors, targeting active-inactive conformational transitions of the enzyme, can be aided by understanding the interplay between

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

Towards defining reference materials for extracellular vesicle size, concentration, refractive index and epitope abundance

September 24, 2020
Author(s)
Joshua Welsh, Edwin van der Pol, Britta Bettin, David Carter, An Hendrix, Metka Lenassi, Marc-Andre Langlois, Alicia Liorente, Arthur van de Nes, Rienk Nieuwland, Vera Tang, Kenneth Witwer, Jennifer Jones, Lili Wang
Accurate characterization of extracellular vesicles (EVs) is critical to explore their diagnostic and therapeutic applications. As the EV research field has developed, so too have the techniques used to characterize them. The development of reference

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

Lymphatic Vessel on a Chip with Capability for Exposure to Cyclic Fluidic Flow

September 7, 2020
Author(s)
Parinaz Fathi, Glenn E. Holland, Dipanjan Pan, Mandy B. Esch
Lymph nodes comprise a complex organ system that is essential in regulating the development of host immune responses. Due to the complexity of lymph nodes and the lack of animal models that can accurately replicate the lymphatic functionality of humans

An accurate and rapid single step protocol for enumeration of cytokine positive T lymphocytes

September 2, 2020
Author(s)
Deepa Rajagopal, Linhua Tian, Shiqiu Xiong, Hao-Wei Wang, Jonathan Campbell, Luisa Saraiva, S Vessillier
Activation of T lymphocytes leads to differentiation, characterized by the ability to induce production of cytokines. Accurate determination of cellular subsets that secrete particular cytokine(s) is therefore, a significant parameter for functional

Niche partitioning of microbial communities at an ancient vitrified hillfort: implications for vitrified radioactive waste disposal

August 30, 2020
Author(s)
Andrew Plymale, Jacqueline Wells, Carolyn Pearce, Colin Brislawn, Emily Graham, Tanya Cheeke, Jessica Allen, Sarah Fansler, Bruce Arey, Mark Bowden, Danielle Saunders, Vincent Danna, Kimberly Tyrrell, Jamie Weaver, Rolf Sjoblom, Rick L. Paul, John McCloy, Eva Hjarthner-Holdar, Mia Englund, Erik Ogenhall, David Peeler, Albert Kruger
A pre-Viking era vitrified hillfort, Broborg, provides a habitat analogue for disposed radioactive waste glass and shows strong niche partitioning among the organisms involved in glass alteration. Microbes cannot be eliminated from radioactive waste

Tissue Engineering Measurands

August 26, 2020
Author(s)
Greta Babakhanova, Carl Simon, Deepika Arora
A measurand is defined as the quantity that one intends to measure. As tissue engineering research translates into medical products, companies must prepare regulatory filings that contain many different types of measurement data that are collected about

Increasing the Coverage of a Mass Spectral Library of Milk Oligosaccharides Using a Hybrid- Search-Based Bootstrapping Method and Milks from a Wide Variety of Mammals

July 8, 2020
Author(s)
Concepcion A. Remoroza, Tytus D. Mak, Yuri A. Mirokhin, Sergey L. Sheetlin, Xiaoyu Yang, Stephen E. Stein, Power L. Michael, San Andres V. Joice, Yuxue Liang
This study significantly expands both the scope and method of identification for construction of a previously reported tandem mass spectral library of 74 human milk oligosaccharides (HMOs) derived from results of LC-MS/MS experiments. In the present work

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 Travis 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
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