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Bioscience

Engineering/synthetic biology

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Displaying 26 - 50 of 53

Cotranscriptionally encoded RNA strand displacement circuits

March 23, 2022
Author(s)
Samuel Schaffter, Elizabeth Strychalski
Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions

The genotype-phenotype landscape of an allosteric protein

December 16, 2021
Author(s)
Drew S. Tack, Peter Tonner, Abe Pressman, Nathanael Olson, Eugenia Romantseva, Nina Alperovich, Olga Vasilyeva, David Ross, Sasha F. Levy
Allostery is a fundamental biophysical mechanism where the activity of a biomolecule is regulated by the binding of a ligand. Despite playing a central role in many biological processes, a quantitative understanding of allostery is lacking. To

The NIH Somatic Cell Genome Editing program

April 7, 2021
Author(s)
Samantha Maragh
The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more

Single-cell measurement of plasmid copy number and promoter activity

March 5, 2021
Author(s)
Bin Shao, Jayan Rammohan, Daniel Anderson, Nina Alperovich, David Ross, Christopher Voigt
We have developed a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of

Organizing genome engineering for the gigabase scale

February 9, 2021
Author(s)
Bryan A. Bartley, Jacob Beal, Jonathan R. Karr, Elizabeth Strychalski
Engineering an organism's entire genome enables large-scale changes in organization, function, and environmental interactions, with significant implications for industrial, medical, and environmental ap- plications broadly. Improvements to DNA synthesis

Cyberbiosecurity for biopharmaceutical products

February 8, 2021
Author(s)
Elizabeth Strychalski, Jennifer Mantla, Jayan Rammohan, Eugenia Romantseva, Reid D'Amico, Joel Welch, Leah R. Kauffman, Jim McCarthy, John E. Schiel, Jeffrey Baker, Kelley Rogers, Kelvin Lee

Probing Pluripotency Gene Regulatory Networks with Live Cell Imaging

September 20, 2020
Author(s)
Anne Plant, Michael Halter, Jeffrey R. Stinson
Live cell imaging uniquely enables the measurement of dynamic events in single cells, but it has not been used often in the study of gene regulatory networks. Network components can be examined in relation to one another by quantitative live cell imaging

Electron and x-ray focused beam-induced cross-linking in liquids: Toward rapid continuous 3D nanoprinting and interfacing using soft materials

September 15, 2020
Author(s)
Tanya Gupta, Evgheni Strelcov, Glenn Holland, Joshua D. Schumacher, Yang Yang, Mandy Esch, Vladimir Aksyuk, Patrick Zeller, Matteo Amati, Luca Gregoratti, Andrei Kolmakov
Additive fabrication of biocompatible 3D structures out of liquid hydrogel solutions has become pivotal technology for tissue engineering, soft robotics, biosensing, drug delivery etc. Electron and X-ray lithography are well suited to pattern nanoscopic

Measurement and Standardization Challenges for Exosome-Based Delivery Vectors

September 3, 2020
Author(s)
Bryant Nelson, Hao-Wei Wang, Samantha Maragh, Paul DeRose, Elzafir B. Elsheikh, Wyatt Vreeland, Ionita Ghiran, Jennifer Jones
Extracellular vesicles (EVs), and in particular exosomes, have the potential to revolutionize the development and efficient delivery of clinical therapeutics. In this Perspective, we focus on providing a brief introduction to the landscape of exosome-based

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

A Single Amino Acid Substitution Alters ClpS Binding Specificity

March 27, 2020
Author(s)
Christina Bergonzo, Jennifer A. Tullman, Kunal Dharmadhikari, Emily Samuels, Makenzie Christensen
ClpS is a small protein currently under development as a probe for detecting specific N-terminal amino acids of peptides. In order for ClpS to be used in this manner, it is important to understand the structural reasons for how and why ClpS recognizes

Improved stability of an engineered function using adapted bacterial strains

March 6, 2020
Author(s)
Drew S. Tack, Peter Tonner, Elena Musteata, David Ross, Vanya Paralanov
Engineering useful functions into cells is one of the primary goals of synthetic biology. However, engineering novel functions that remain stable for multiple generations remains a significant challenge. Here we report the importance of host fitness on the

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

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

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

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

Screening of Chemical Libraries Using a Yeast Model of Retinal Disease

September 25, 2019
Author(s)
Benjamin M. Scott
Retinitis pigmentosa (RP) is a degenerative retinal disease, often caused by mutations in the G protein-coupled receptor rhodopsin. The majority of pathogenic rhodopsin mutations cause rhodopsin to misfold, including P23H, disrupting its crucial ability to

EcoFAB: Advancing microbiome science through standardized fabricated ecosystems

June 21, 2019
Author(s)
Karsten Zengler, Kirsten Hofmockel, Scott Behie, Hans Bernstein, James Brown, Jos? Dinneny, Sheri Floge, Samuel Forry, Matthias Hess, Scott Jackson, Stephen Lindemann, Jennifer Pett-Ridge, Elizabeth Shank, Ophelia Venturelli, Matthew Wallenstein, Nitin Baliga, Christer Jansson, Trent Northen
Microbiome science is arguably the fastest-advancing research field in biology today. However, current efforts are largely focused on disparate and often irreproducible experimental systems. Here we present the results of a one-and-a-half-day workshop that

Targeting hMSC Response via Surface Carbonyl Groups, Contact Angle, and Protein Interactions

March 1, 2019
Author(s)
Max J. Lerman, Shinichiro N. Muramoto, Navein Arumugasaamy, Michael Van Order, Josephine Lembong, Anushka Gerald, John Gillen, John P. Fisher
Traditional 2D culture systems made of polystyrene (PS) require the addition of surface chemistry beyond the nominal phenyl groups present to facilitate and encourage cell adhesion. Determining the surface properties which enhance protein adhesion from
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