Studies

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Flis et al. (2025)

DOI: 10.1098/rsob.150042

Riedinger, Kristen; Bugher, Nicolette; Wardle, Annabella; Vandiver, Kathleen; Baskaran, Barathkumar; Michael, Zion; de Vera, Glen Andrew; Plata, Desiree

N-Nitrosodimethylamine (NDMA) is a probable human carcinogen that can be formed in drinking water treatment systems as a byproduct of chloramination and chlorination. Occurrence of NDMA and other N-nitrosamines in the United States has not been assessed at health-relevant levels (i.e., low to sub-ng/L concentrations) using sensitive analytical ...

Huntington MEA data for CureQ

Angel Nikolov

Tuberculosis (TB) is the world’s deadliest infection by number of lives claimed. Thus, novel vaccination and therapeutic strategies are urgently needed to limit the spread of TB. Historically, immunologists have made extensive efforts to potentiate cell-mediated immune responses to control Mycobacterium tuberculosis (Mtb). However, emerging data illustrate that the humoral immune system also plays a role in microbial control of Mtb. Antibodies targeted against surface structures ...

Angel Nikolov

Tuberculosis (TB) is the world’s deadliest infection by number of lives claimed. Thus, novel vaccination and therapeutic strategies are urgently needed to limit the spread of TB. Historically, immunologists have made extensive efforts to potentiate cell-mediated immune responses to control Mycobacterium tuberculosis (Mtb). However, emerging data illustrate that the humoral immune system also plays a role in microbial control of Mtb. Antibodies targeted against surface structures ...

Edward B. Irvine, Angel Nikolov, Mehak Z. Khan, Joshua M. Peters, Richard Lu, Jaimie Sixsmith, Aaron Wallace, Esther van Woudenbergh, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Patricia S. Grace, Galit Alter & Sarah M. Fortune

doi: https://doi.org/10.1101/2022.05.01.490220

Mounting evidence indicates that antibodies can contribute towards control of tuberculosis (TB). However, the underlying mechanisms ...

Krista M. Pullen, Ryan Finethy, Seung-Hyun B. Ko, Charlotte J. Reames, Christopher M. Sassetti, Douglas A. Lauffenburger

DOI: https://doi.org/10.1038/s41540-024-00487-6

Abstract:Numerous studies have identified similarities in blood transcriptomic signatures of mouse tuberculosis (TB) models and human disease phenotypes, such as type 1 interferon (IFN) production and innate immune cell activation, yet the pathophysiology observed in murine infection does not ...

Lee J. Pribyl, Jennifer E. Kay, Joshua J. Corrigan, Lindsay B. Volk, Monét Norales, Norah A. Owiti, Evan A. Kowal, Ishwar N. Kohale, Ilana S. Nazari, Matilda R. Swanson, Aimee C. Moise, Duanduan Ma, Stuart S. Levine, Emily Michelsen, Robert G. Croy, Timothy Ragan, Dorothea K. Torous, Svetlana L. Avlasevich, Stephen D. Dertinger, Sebastian E. Carrasco, Leona D. Samson, John M. Essigmann, Forest M. White, Bevin P. Engelward

DOI: https://www.biorxiv.org/content/10.1101/2025.10.01.679856v1 ...

Demo for multi electrode array study in the cureQ project

Considering parameter uncertainty explicitly by generating 50 models.

Vincent L. Butty, Pranav Patel, Stuart S. Levine

DOI:

Abstract: DNA labelling fluorescent dyes such as ethidium bromide have long been considered to be highly mutagenic during DNA replication. While recent studies have pushed back on this narrative, the intercalative nature of these dyes continues to raise the possibility that these dyes can induce mutations. The iconPCR instrument by n6tec uses fluorescent dyes to measure amplification in real time and to ...

Lindsay B Volk, Monét Norales, Callie Karjane, Joshua J Corrigan, Alper J Alcaraz, Lee J Pribyl, Nicolette A Bugher, Megan Blawas, Isabella Dulski, Einthavy Arunachalam, Nina Gubina, Emily Michelsen, Kannammai Pichappan, Natalya Yakimchuk, Matilda Swanson, Duanduan Ma, Stuart S Levine, Desiree L Plata, Robert G Croy, Leona D Samson, John M Essigmann, Carole L Yauk, Sebastian E Carrasco, Bevin P Engelward

Abstract: N-Nitrosodimethylamine (NDMA) is a probable human carcinogen found in ...

Nicolette A. Bugher, Jonathan W. Zheng, Annabella S. Wardle, William H. Green, and Desiree L. Plata

DOI:

Abstract: N-nitrosamines are a class of carcinogenic industrial pollutants that lack well-characterized physicochemical properties. Classical approaches to determine octanol-water partition coefficients (Kow) values are laborious, slow, and challenged by experimental error. Alternative methods include quantum chemical estimation (e.g., COSMO-RS), quantitative ...

Megan D. Maerz, Mohau S. Makatsa, Allison N. Bucsan, Matthew S. Sutton, Emma Bishop, Ziwei Tian, Erik D. Layton, Mario Roederer, Alex K. Shalek, Robert A. Seder, Thomas J. Scriba, Chuangqi Wang, Patricia A. Darrah, and Chetan Seshadri

DOI: https://doi.org/10.1016/j.xcrm.2025.102536

γδ T cells expressing a Vδ1/3+ T cell receptor are enriched at mucosal surfaces, but their role in protection against Mycobacterium tuberculosis (Mtb) is largely unknown. We used ...

Marie

todo ...

PPK was isolated and it was kinetically characterized in initial rate kinetic experiments. A rate equation was parameterized and used to simulate enzyme incubations

Fat quantification of 5 liver lobes (RML, LML, LLL, RL, CL) During the MRI sesssion at least one PRESS voxel was placed in each of those liver lobes to acquire PRESS data for later fat analysis. Acquisitions were without water suppression, so the fat peaks are relatively small.

The quantification was performed using lcmodel. The original MRI data are part of the MRI session assays (data files uploaded). Here you can find the additional analysis and the output of lcmodel: The "ps" in each exam ...

animals underwent a 60% PVL surgery and this MRI session was performed on post operation day 5 (POD5).

animals underwent a 60% PVL surgery and this MRI session was performed on post operation day 3 (POD3).

animals underwent a 60% PVL surgery and this MRI session was performed on post operation day 2 (POD2).

animals underwent a 60% PVL surgery and this MRI session was performed on post operation day 1 (POD1).

rats under control diet and no surgery to establish a baseline for fucntion, perfusion and fat content using MRI.

Elena Cambria, Adriana Blazeski, Eunkyung Clare Ko, Tran Thai, Shania Dantes, David A. Barbie, Sarah E. Shelton, Roger D. Kamm

https://www.biorxiv.org/content/10.1101/2025.01.10.632378v1

Abstract: Lung fibrosis, characterized by chronic and progressive scarring, has no cure. Hallmarks are the accumulation of myofibroblasts and extracellular matrix, as well as vascular remodeling. The crosstalk between myofibroblasts and vasculature is poorly understood, with ...