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Bioscience

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Displaying 101 - 125 of 1261

The complete sequence of a human Y chromosome

August 23, 2023
Author(s)
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah Hoyt, Dylan Taylor, Nathanael David Olson, Justin Zook, Adam Phillippy
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1,2,3. As a result, more than half of the Y chromosome is

A Draft Human Pangenome Reference

May 10, 2023
Author(s)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Erik Garrison, Tobias Marschall, Ira Hall, Heng Li, Benedict Paten
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the

Mechanical Regulation of Oral Epithelial Barrier Function

April 25, 2023
Author(s)
Eun Jin Lee, Paul Salipante, Anthony Kotula, Dana Graves, Stella Alimperti, Yoontae Kim
Epithelial cell function is modulated by mechanical forces imparted by the extracellular environment. The transmission of forces onto the cytoskeleton by modalities such as mechanical stress and matrix stiffness is necessary to address by the development

Toward a common standard for data and specimen provenance in life sciences

April 18, 2023
Author(s)
Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Muller, Markus Plass, Clare M Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Melanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki NAKAE, Isabelle PERSEIL, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio De Castillia, michael sussman, Jason Swedlow, Kurt Zatloukal, Joerg Geiger
Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by

Variant calling and benchmarking in an era of complete human genome sequences

April 14, 2023
Author(s)
Nathanael David Olson, Justin Wagner, Nathan Dwarshuis, Karen Miga, Marc L. Salit, Justin Zook
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of

The emerging landscape of single-molecule protein sequencing technologies

April 11, 2023
Author(s)
Zvi Kelman, John Marino
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe

Three-dimensional, label-free cell viability measurements in tissue engineering scaffolds using optical coherence tomography

March 14, 2023
Author(s)
Greta Babakhanova, Anant Agrawal, Deepika Arora, Allison Horenberg, Jagat Budhathoki, Joy Dunkers, Joe Chalfoun, Peter Bajcsy, Carl Simon Jr.
In the field of tissue engineering, 3D scaffolds and cells are often combined to yield constructs that are used as therapeutics to repair or restore tissue function in patients. Viable cells are required to achieve the intended mechanism of action for the

Variability in genome-engineering source materials: Consider your starting point

March 10, 2023
Author(s)
Simona Patange, Sierra Miller, Samantha Maragh
The presence and impact of variability in cells as the source material for genome engineering are important to consider for the design, execution and interpretation of outcomes of a genome-engineering process. Variability may be present at the genotype and

Micelle formation and phase separation of poloxamer 188 and preservative molecules in aqueous solutions studied by small angle X-ray scattering

March 1, 2023
Author(s)
Rachel Ford, Peter H. Gilbert, Richard Gillilan, Qingqiu Huang, Roisin Donnelly, Ken Qian, David Allen, Norman Wagner, Yun Liu
Multi-injection pharmaceutical products such as insulin must be formulated to prevent aggregation and microbial contamination. Small-molecule preservatives and nonionic surfactants such as poloxamer 188 (P188) are thus often employed in protein drug

Inhibition of human APE1 and MTH1 DNA repair proteins by dextran-coated g-Fe2O3 ultrasmall superparamagnetic iron oxide nanoparticles

February 28, 2023
Author(s)
Erdem Coskun, Pawel Jaruga, Miral M. Dizdar, Bryant C. Nelson, Neenu Singh, Leona Scanlan, Shareen Doak
Aim: To quantitatively evaluate the inhibition of human DNA repair proteins APE1 and MTH1 by dextran-coated γ-Fe2O3 ultrasmall superparamagnetic iron oxide nanoparticles (dUSPIONs). Materials & methods: Liquid chromatography–tandem mass spectrometry with

FixItFelix: improving genomic analysis by fixing reference errors

February 21, 2023
Author(s)
Sairam Behera, Jonathan LeFaive, Peter Orchard, Justin Zook, Fritz Sedlazeck
The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical

Biglycan regulates bone development and regeneration

February 16, 2023
Author(s)
Reut Shainer, Vardit Kram, Tina Kilts, Andrew Doyle, Inbal Shainer, Carl Simon Jr., Jinyang Zeng-Brouwers, Liliana Schaefer, Marian Young
Endochondral bone development and regeneration relies on activation and proliferation of periosteum derived cells (PDCs). Biglycan (Bgn), an extracellular matrix component, is known to be expressed in bone and cartilage, however little is known about its

Iron-sulfur clusters are involved in post-translational arginylation

January 28, 2023
Author(s)
Verna Van, Janae Brown, Corin R. O'Shea, Hannah Rosenbach, Ijaz Mohamed, Nna-Emeka Ejimogu, Toan Bui, Veronika Szalai, Kelly Chacon, Ingrid Span, Aaron T. Smith
Eukaryotic arginylation is an essential post-translational modification that both modulates protein stability and regulates protein half-life through the N-degron pathway. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA

Design and characterization of a protein fold switching network

January 26, 2023
Author(s)
David Travis Gallagher, Biao Ruan, Yanan He, Yingwei Chen, Eun Jung Choi, Yihong Chen, Dana Motabar, Tsega Solomon, Richard Simmerman, Thomas Kauffman, John Orban, Philip Bryan
Protein sequences encoding three common small folds (3-alpha, beta-grasp, and alpha/beta plait) were connected in a network of mutational pathways that intersect at high-identity sequences, termed nodes. The structures of proteins around nodes were
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