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Bioscience

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Displaying 251 - 275 of 1242

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

Mass Spectral Library of Acylcarnitines Derived from Human Urine

April 8, 2020
Author(s)
Xinjian Yan, Sanford Markey, Ramesh Marupaka, Qian Dong, Brian T. Cooper, Yuri Mirokhin, William E. Wallace, Stephen Stein
We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC–MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of

Highland games: A benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences

April 6, 2020
Author(s)
John E. Schiel, Coffman Jon, Bruno Marques, Griesbach Jan, Ambrose Williams, Gisela Ferreira, Rushd Khalaf, David Roush, Charles Haynes
Biopharmaceutical product and process development does not yet take advantage of predictive computational modeling to nearly the degree seen in industries based on smaller molecules. To assess and advance progress in this area, spirited coopetition was

Quantitative Bright-Field Microscopy Combined with Deep Neural Networks Predict Live Tissue Function

February 29, 2020
Author(s)
Carl Simon, Nicholas J. Schaub, Petru S. Manescu, Sarala Padi, Mylene Simon, Peter Bajcsy, Nathan A. Hotaling, Joe Chalfoun, Mohamed Ouladi, Qin Wan, Kapil Bharti, Ruchi Sharma
Progressive increases in the number of cell therapies in the preclinical and clinical phases has prompted the need for reliable and non-invasive assays to validate transplant function in clinical biomanufacturing. Here, we developed a robust

HIV-1 gp120-CD4-Induced Antibody Complex Elicits CD4 Binding Site-Specific Antibody Response in Mice

February 17, 2020
Author(s)
Andrey Galkin, Yajing Chen, Sijy O'Dell, Roderico Acevedo, James Steinhardt, Yimeng Wang, Richard Wilson, Chi-I Chiang, Alexander Grishaev, John Mascola, Yuxing Li
Elicitation of broadly neutralizing Ab (bNAb) responses toward the conserved HIV-1 envelope (Env) CD4 binding site (CD4bs) by vaccination is an important goal for vaccine development and yet to be achieved. The outcome of previous immunogenicity studies

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

Implications of DNA Damage and DNA Repair on Human Diseases

January 10, 2020
Author(s)
Bryant C. Nelson, M Miral Dizdar
Cellular DNA damage is implicated in the etiology and progression of many different types of human disorders and diseases. Much of the current research in the DNA damage field is devoted towards understanding the mechanisms and biological implications of

Quantifying protein aggregation kinetics using electrospray differential mobility analysis

January 5, 2020
Author(s)
Kaleb J. Duelge, Jeremie Parot, Vincent A. Hackley, Michael R. Zachariah
Protein aggregation is a significant concern in bioprocessing and end use applications. Here the thermal aggregation kinetics of bovine serum albumin (BSA) and α-chymotrypsinogen A (α- chymo) were measured over a range of concentrations and temperatures by

Strategies for Development of a Next-Generation Protein Sequencing Platform

January 1, 2020
Author(s)
Nicholas Callahan, Jennifer A. Tullman, John Marino, Zvi Kelman
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e. antibodies), both of which require a priori knowledge of the sample. A non

Establishing Standards and Methods for Qualification and Validation of New Particle Measurement Technologies

November 12, 2019
Author(s)
Srivalli Telikepalli, Dean C. Ripple, Kurt D. Benkstein, Kristen L. Steffens, Michael J. Carrier, Christopher B. Montgomery
Numerous particle sizing and counting methods exist for measuring particles in the submicrometer, subvisible, and visible size range. This article will briefly describe some key aspects that need to be considered for the most commonly used methods in order

Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite

November 7, 2019
Author(s)
Dan Bearden, David A. Sheen, Yamil Simon, Bruce A. Benner Jr., Werickson Fortunato de Carvalho Rocha, Niksa Blonder, Katrice A. Lippa, Richard Beger, Laura Schnackenberg, Jinchun Sun, Khyati Mehta, Amrita Cheema, Haiwei Gu, Ramesh Marupaka, Nagana Gowda, Daniel Raftery
There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the

Selective spin inversion in solution by magic field cross polarization

November 1, 2019
Author(s)
Joel Tolman, Luke Arbogast
A pulsed element is proposed allowing the selective inversion of a single 1H nucleus, without regard to the presence of other degenerate 1H nuclei, provided that it is coupled to a heteronuclear spin with adequate chemical shift resolution in a 2D

Characterization of the internal translation initiation region in monoclonal antibodies expressed in Escherichia coli

October 11, 2019
Author(s)
Erik M. Leith, William Brad O'Dell, Na Ke, Colleen McClung, Mehmet Berkmen, Christina Bergonzo, Robert G. Brinson, Zvi Kelman
Monoclonal antibodies (mAbs) represent an important platform for the development of biotherapeutic products. While most mAbs are produced in mammalian cells, there are several examples of mAbs made in Escherichia coli, including therapeutic fragments. When

NIST Fatty Acid Quality Assurance Program 2017 Final Report

October 1, 2019
Author(s)
Bruce A. Benner Jr., Jacolin A. Murray
At the request of the National Institutes of Health’s (NIH’s) Office of Dietary Supplements (ODS) and in conjunction with the Centers for Disease Control and Prevention (CDC), in 2017 the National Institute of Standards and Technology (NIST) conducted the

Pumpless Microfluidic Devices for Generating Healthy and Diseased Endothelia

September 27, 2019
Author(s)
Yang Yang, Parinaz Fathi, Glenn Holland, Dipanjan Pan, Nam Wang, Mandy Esch
We have developed a pumpless cell culture platform that can recirculate small amounts of cell culture medium (400 µL) in a unidirectional or bidirectional flow pattern. The device produces an average wall shear stress of up to 0.587 Pa ± 0.006 Pa without
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