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Bioscience

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Displaying 51 - 75 of 1261

Jointly benchmarking small and structural variant calls with vcfdist

October 2, 2024
Author(s)
Tim Dunn, Justin Zook, James Holt, Satish Narayanasamy
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a

Plug-and-play protein biosensors using aptamer-regulated in vitro transcription

September 12, 2024
Author(s)
Heonjoon Lee, Tian Xie, Byunghwa Kang, Xinjie Yu, Samuel Schaffter, Rebecca Schulman
Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers

Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

September 11, 2024
Author(s)
Ben Neely, Yasset Perez-Riverol, Magnus Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry–based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically

Multifaceted Neuroimaging Data Integration via Analysis of Subspaces

August 28, 2024
Author(s)
Andrew Ackerman, Zhengwu Zhang, Jan Hannig, Jack Prothero, J.S. Marron
Neuroimaging studies, such as the Human Connectome Project (HCP), often collect multifaceted and multi-block data to study the complex human brain. However, these data are often analyzed in a pairwise fashion, which can hinder our understanding of how

Optimizing Wastewater Surveillance: The Necessity of Standardized Reporting and Proficiency for Public Health

August 7, 2024
Author(s)
Ishi Keenum, Nancy Lin, Alshae Logan, Adam Gushgari, Nishita D'Souza4, Joshua Steele, Devrim Kaya, Lydia Gushgari
Wastewater-based surveillance (WBS) has emerged as a valuable tool for public health, allowing a greater understanding of disease prevalence in communities. With historical significance in monitoring polio transmission,1 WBS gained further prominence in

The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF

August 5, 2024
Author(s)
Joshua Klein, Henry Lam, Tytus Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels, Jim Shofstahl, Helge Hecht, Pierre-Alain Binz, Shin Kawano, Tim Van Den Bossche, Jeremy Carver, Ben Neely, Luis Mendoza, Tomi Suomi, Tine Claeys, Thomas Payne, Douwe Schulte, Zhi Sun, Nils Hoffmann, Yunping Zhu, Steffen Neumann, Andrew Jones, Nuno Bandeira, Juan Antonio Vizcaino, Eric Deutsch
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding

Metabolomics 2023 Workshop Report: Moving Toward Consensus on Best QA/QC Practices in LC-MS-Based Untargeted Metabolomics

July 9, 2024
Author(s)
Tracey Schock, Jonathan Mosley, Warwick Dunn, Julia Kuligowski, Matthew Lewis, Maria Monge, Candice Ulmer Holland, Dajana Vuckovic, Krista Zanetti
Introduction: During the Metabolomics 2023 conference, the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) presented a workshop focusing on key quality assurance and quality control (QA/QC) topic categories for LC-MS-based untargeted

Genome-wide profiling of genetic variation at tandem repeat from long reads

July 4, 2024
Author(s)
Helyaneh Jam, Justin Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal, Melissa Gymrek
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or

Investigation of the effect of peptide p5 targeting CDK5-p25 hyperactivity on Munc18-1(P67) regulating neuronal exocytosis using molecular simulations

July 2, 2024
Author(s)
Tejaswi Tammareddy, Walid Keyrouz, Ram Sriram, Harish Pant, Antonio Cardone, Jeffery Kluada
Munc18–1 is an SM (sec1/munc-like) family protein involved in vesicle fusion and neuronal exocytosis. Munc18–1 is known to regulate the exocytosis process by binding with closed- and open-state conformations of Syntaxin1, a protein belonging to the SNARE

Toward an International Standardisation Roadmap for Nanomedicine

June 12, 2024
Author(s)
Bryant C. Nelson, Gerrit Borchard, Luigi Calzolai, Fanny Caputo, Georges Favres, Fisicaro Fisicaro, Emeric Frejafon, Nazende Gunday-Tureli, Denis Koltsov, Caterina Minelli, Francois-Xavier Ouf, Jeremie Parot, Adriele Prina Mello, Shan Zou
The French National Measurement Institute (LNE) has initiated a series of events to identify priorities for test methods and their harmonisation that directly address regulatory needs in Nanomedicine. The workshop entitled "The International

Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry

June 4, 2024
Author(s)
Yuming Jiang, Devasahayam Rex, Dina Schuster, Ben Neely, German Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton Peters-Clarke, Susan Egbert, Simion Kreimer, Emma Doud, Oliver Cook, Amit Yadav, Muralidharan Vanuopadath, Martin Mayta, Anna Duboff, Nicholas Riley, Robert Moritz, Jesse Meyer
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed

Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (Zalophus californianus)

May 28, 2024
Author(s)
Gautam Ghosh, Ben Neely, Alison Bland, Emily Whitmer, Cara Field, Padraig Duignan, Michael Janech
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis have consistently increased. Currently there are no practical non-lethal clinical tests for the diagnosis of domoic acid toxicosis (DAT) that

Standards and Metrology for Viral Vectors as Molecular Tools: Outcomes from a CCQM Workshop

May 24, 2024
Author(s)
Janathan Campbell, Neil Almond, Y Bae, Ravneet Bhuller, Andrea Briones, S-Y CHO, Megan Cleveland, Thomas Cleveland, Francis Galaway, Hua-Jun He, U Herbrand, Jim Huggett, Sarah Kempster, Ibolya Kepiro, Afifa Khan, Edward Kwee, Wilson Li, Sheng Lin-Gibson, Luise Luckau, Caterina Minelli, M Ryadnov, I Searing, Lili Wang, Alexandra Whale, Julian Braybrook
Viral vectors are agents enabling gene transfer and genome editing and have widespread utility across the healthcare and biotechnology sectors. In January 2023, the International Bureau for Weights and Measures' Consultative Committee for Amount of

Recommendations on fit-for-purpose criteria to establish a quality management for microphysiological systems (MPS) and for monitoring of their reproducibility

May 14, 2024
Author(s)
David Pamies, Jason Ekert, Marie-Gabrielle Zurich, Olivier Frey, Sophie Werner, MONICA PIERGIOVANNI, Benjamin Freedman, Adrian Keong, Darwin Reyes-Hernandez, Hendrik Erfurth, Peter Loskill, Pelin Candarlioglu, Shan Wang, Thomas Hartung, Sandra Coecke, Glyn Stacey, Marcel Leist
Cell culture technology has seen great innovations and progress in the 21st centuryClassical single-cell and monolayer models have been replaced by more complex 3D models (e.g., reaggregates, spheroids, organoids) to improve the predictivity of in vitro

Important consideration when expressing mAbs in Escherichia coli

May 2, 2024
Author(s)
William Siegall, Zvi Kelman
Monoclonal antibodies (mAbs) are a driving force in the biopharmaceutical industry. The production of therapeutic mAbs is primarily done in mammalian cells, but recently there has been a push towards the use of alternative production hosts including

Nondestructive, Longitudinal, 3D Cell Viability Assessment in a Multi-well Plate System Using Electron Paramagnetic Resonance Oxygen Imaging

May 1, 2024
Author(s)
Safa Hameed, Navin Viswakarma, Eliyas Siddiqui, Greta Babakhanova, Carl Simon Jr., Boris Epel, Mrignayani Kotecha
Cell viability is an essential measurement for cell therapy, tissue engineered medical products (TEMPs), drug development, and many other biological processes and products. These systems rely on viable, healthy, and functional cells to work as intended

Mechanism of Action, Potency and Efficacy: Considerations for Cell and Gene Therapies

April 1, 2024
Author(s)
Carl Simon Jr., Anne L. Plant, Catherine Zander, Erich Bozenhardt, Christina Celluzzi, David Dobnik, Melanie Grant, John Hughes, Uma Lakshmipathy, Kok-Seong Lim, Laura Montgomery, Hesham Nawar, Thiana Nebel, Linda Peltier, James Sherley, Rouzbeh Taghizadeh, Eddie Tan, Sandrine Vessillier
One of the most challenging aspects of cell and gene therapy products (CGTPs) is defining mechanism of action (MOA), potency and efficacy of the product. This perspective examines these concepts and presents helpful ways to think about them through the

Quantitative and Standardized Pseudovirus Neutralization Assay for COVID-19

April 1, 2024
Author(s)
Jerilyn Izac, Edward Kwee, Adolfas Gaigalas, Lili Wang
COVID-19 is a global pandemic caused by the highly infectious SARS-CoV-2 virus. Efforts to combat SARS-CoV-2 infection include mass vaccination and development of monoclonal and convalescent plasma therapeutics that require precise measurements of

Comparison of N-glycopeptide to released N-glycan abundances and the influence of glycopeptide mass and charge state on N-linked glycosylation of IgG antibodies

March 7, 2024
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Tytus Mak, Sergey Sheetlin, Yuri Mirokhin, Zachary Goecker, Brian T. Cooper, Mark Lowenthal, Xiaoyu (Sara) Yang, Guanghui Wang, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary

Digital PCR for the Characterization of Reference Materials

February 14, 2024
Author(s)
Megan Cleveland, Hua-Jun He, Mojca Milavec, Young-Kyung Bae, Peter Vallone, Jim Huggett
Well characterized reference materials are essential to ensuring the harmonization and accuracy of nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non

Heart-on-a-Chip Systems: Disease Modeling and Drug Screening Applications

February 14, 2024
Author(s)
Derrick Butler, Darwin Reyes-Hernandez
Cardiovascular disease (CVD) is the leading cause of death worldwide, casting a substantial economic footprint and burdening the global healthcare system. Historically, pre-clinical CVD modeling and therapeutic screening has been performed using animal

Establishing a framework for best practices for quality assurance and quality control in untargeted metabolomics

February 12, 2024
Author(s)
Tracey Schock, Jonathan Mosley, Chris Beecher, Warwick Dunn, Julia Kuligowski, Matthew Lewis, Georgios Theodoridis, Candice Ulmer, Dajana Vuckovic, Ian Wilson, Krista Zanetti
Background: Quality assurance (QA) and quality control (QC) practices are key tenets that facilitate study and data quality across all applications of untargeted metabolomics. Such important practices will strengthen this field and accelerate its success
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