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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 ...
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 ...
Submitter: Jake Schissel
Investigation: IMPAcTB
Assays: All Metadata, Antibody Challenge - Metadata, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Survivability Restriction Assay - Data Linked, ELISA - Data Linked, Glycosylation Assay - Data Linked, Library Prep - Metadata, Luminex - Data Linked, Patient Visit - Metadata, Single Cell Clustering Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Extraction - Metadata
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 ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Survivability Restriction Assay: Validation Data - Data Attached, Cell Extraction: Validation Data - Metadata, Gene Expression Analysis: Training Data - Data Linked, Gene Expression Analysis: Validation Data - Data Linked, Library Prep: Training Data - Metadata, Library Prep: Validation Data - Metadata, PCR: Validation Data - Data Attached, RNA Extraction: Validation Data - Metadata, Short Read Sequencing: Training Data - Data Linked, Short Read Sequencing: Validation Data - Data Linked, Tissue Collection: Training Data - Metadata, TransCompR Cross Species Modeling - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, DNA Adduct Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Gene Expression Analysis - Data Linked, Imaging - Data Linked, Imaging Analysis - Data Linked, Library Creation - Metadata, Mouse Challenge - Metadata, Phosphoproteomics Analysis - Data Linked, Short Read Sequencing - Data Linked, Spatial Transcriptomics - Data Linked, Spatial Transcriptomics Analysis - Data Linked, Tissue Collection - Metadata, Western Blot - Data Linked, Western Blot Analysis - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, DNA Extraction - Metadata, GPT Assay - Data Linked, Genome Alignment - Data Linked, Imaging Analysis - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mutational Spectra Analysis - Data Linked, Protein Extraction - Metadata, RNA Isolation - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata, Tissue Imaging - Data Linked, Tissue Sectioning - Metadata, Western Blot - Data Linked, Western Blot Analysis - Data Linked
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 ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, FCS Analysis - Data Linked, Flow Cytometry - Data Linked, Library Creation - Metadata, Mass Cytometry - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Marie
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 ...
Nina Gubina, Lindsay B. Volk, Anna Dormitzer, Emily Michelsen, Lee J. Pribyl, Joshua J. Corrigan, Esha Dalvie, Amanda L. Armijo, Nicolette A. Bugher, Kayla Shonvisky, Monét Norales, Desiree L. Plata, Bevin P. Engelward, Robert G. Croy, John M. Essigmann, Bogdan I. Fedeles
DOI:
Abstract: N-Nitrosodimethylamine (NDMA) is an animal and probable human carcinogen. Here DNA adduct and high-resolution mutational spectra were correlated following administration of ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, Chemical Challenge - Metadata, DNA Extraction - Metadata, ELISA - Data Linked, GPT Assay - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mutational Spectra Analysis - Data Linked, PCR - Data Linked, RNA Extraction - Metadata, RaDR - Data Linked, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Abiola F. Ogunsola, Rocky Lai, Kelly Cavallo, Gillian L. Beamer, and Samuel M. Behar
DOI:
Abstract: Vaccine development for tuberculosis is a global priority. Our studies using Collaborative Cross (CC) mice show that genetic diversity influences the efficacy of BCG, the most widely used TB vaccine. BCG vaccination of CC042 mice reduces their lung bacillary burden and increases their survival following low-dose aerosol Mycobacterium tuberculosis infection ...
Mohau S. Makatsa, Emma Bishop, Allison N. Bucsan, Matthew Sutton, Chelsea Lehman, Molly Robertson, Krystle K.Q. Yu, Joshua M. Peters, Bryan D. Bryson, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Chetan Seshadri
DOI: https://doi.org/10.1016/j.mucimm.2025.10.011
Abstract: Intravenous (IV) vaccination with Bacillus Calmette–Guerin (BCG) mediates sterilizing immunity against Mycobacterium tuberculosis (Mtb) in rhesus macaques but the cellular mechanisms ...
Andrew W Simonson, Michael C Chao, Luke E Hood, Rachel A Donlan, Forrest Hopkins, Michael R Chase, Andrew J Vickers, Alanna Callendrello, Edwin Klein, H Jacob Borish, Marshall Malin, Pauline Maiello, Charles A Scanga, Philana Ling Lin, Sarah M Fortune, JoAnne L Flynn
DOI: https://doi.org/10.1101/2025.07.08.663727
Immunological memory elicited either through previous or ongoing M. tuberculosis (Mtb) infection provides a critical mechanism by which hosts protect ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Library Prep - Metadata, PET-CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Marie Floryan, Elena Cambria, Adriana Blazeski, Mark F. Coughlin, Zhengpeng Wan, Giovanni Offeddu, Vinayak Vinayak, Aayush Kant, Vivek Shenoy, Roger D. Kamm
DOI:
Abstract: The incorporation of a functional perfusable microvascular network (MVN) is a common requirement for most organ on-chip-models. Long-term perfusion of MVNs is often required for the maturation of organ phenotypes and disease pathologies and to model the transport of cells and drugs entering ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: All Metadata, Cell Extraction - Metadata, Cytokine Luminex - Data Linked, Gene Expression Analysis - Data Linked, Library Prep - Metadata, MVN Imaging Analysis - Data Linked, Mass Spectrometry Proteomics - Data Linked, Microfluidic Network Formation - Metadata, Microfluidic Network Imaging - Data Linked, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, Short Read Sequencing - Data Linked
_Andrew W. Simonson, Joseph J. Zeppa, Allison N. Bucsan, Michael C. Chao, Supriya Pokkali, Forrest Hopkins, Michael R. Chase, Andrew J. Vickers, Matthew S. Sutton, Caylin G. Winchell, Amy J. Myers, Cassaundra L. Ameel, Ryan Kelly, Ben Krouse, Luke E. Hood, Jiaxiang Li, Chelsea C. Lehman, Megha Kamath, Jaime Tomko, Mark A. Rodgers, Rachel Donlan, Harris Chishti, H. Jacob Borish, Edwin Klein, Charles A. Scanga, Sarah Fortune, Philana Ling Lin, Pauline Maiello, Mario Roederer, Patricia A. Darrah, ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Bacterial Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Library Prep - Metadata, PET-CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Ze Gong, Koen van den Dries, Rodrigo A. Migueles-Ramírez, Paul W. Wiseman, Alessandra Cambi & Vivek B. Shenoy
DOI: https://doi.org/10.1038/s41467-023-38598-z
Abstract: Immune cells, such as macrophages and dendritic cells, can utilize podosomes, mechanosensitive actin-rich protrusions, to generate forces, migrate, and patrol for foreign antigens. Individual podosomes probe their microenvironment through periodic protrusion and retraction cycles (height ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: All Metadata, Dendritic Cell Preparation - Metadata, Imaging Analysis - Data Linked, Live Cell Imaging - Data Linked, Modeling - Data Linked
Kathryn M. Yammine, Sophia Mirda Abularach, Michael Xiong, Seo-yeon Kim, Agata A. Bikovtseva, Vincent L. Butty, Richard P. Schiavoni, John F. Bateman, Shireen R. Lamandé, and Matthew D. Shoulders
A dbGaP Submission is underway and metadata will be updated at the completion of submission. The remaining of the data and metadata are available here.
DOI: 10.1101/2024.11.07.622468.
Abstract:
Objectives Mutations in the procollagen-II gene (COL2A1) ...
Submitter: Charles Demurjian
Investigation: Shoulders Lab Individual Publications
Assays: All Metadata, Cell Imaging - Data Linked, Gene Expression Analysis - Data Linked, LC - MS/MS (Proteomics) - Data Linked, Library Creation - Metadata, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, Short Read Sequencing - Data Linked, iPSC Culture and Chondronoid Formation - Metadata
Oleksandr Chepizhkoa, Josep-Maria Armengol-Colladob, Stephanie Alexander, Esther Wagenae, Bettina Weigelin, Luca Giomi, Peter Friedl, Stefano Zapperi,Caterina A. M. La Porta
DOI: https://doi.org/10.1073/pnas.2414009121
Abstract: Cancer metastasis involves the collective migration of cancer cells in confined space, a problem that has been widely investigated in vitro. Here, we quantify the flow patterns of cancer cell as they invade tissue space and deform ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: All Metadata, Imaging Analysis - Data Linked, Intravital Microscopy
Luay M Almassalha 1 2, Marcelo Carignano 2 3, Emily Pujadas Liwag 2 4, Wing Shun Li 2 3 5, Ruyi Gong 2 3, Nicolas Acosta 2 3, Cody L Dunton 2 3, Paola Carrillo Gonzalez 2 3, Lucas M Carter 2 4, Rivaan Kakkaramadam 2 4, Martin Kröger 6, Kyle L MacQuarrie 7 8, Jane Frederick 2 3, I Chae Ye 2 3, Patrick Su 2 3, Tiffany Kuo 2 4, Karla I Medina 2 4, Josh A Pritchard 2 3, Andrew Skol 7, Rikkert Nap 2 3, Masato Kanemaki 9 10 11, Vinayak Dravid 5 12 13 14 15, Igal Szleifer 2 3 12, Vadim Backman 2 3 ...
Patricia S. Grace, Joshua M. Peters, Jaimie Sixsmith, Richard Lu, Corinne Luedeman, Brooke A. Fenderson, Andrew Vickers, Matthew D. Slein, Edward B. Irvine, Tanya McKitrick, Mo-Hui Wei, Richard D. Cummings, Aaron Wallace, Lisa A. Cavacini, Alok Choudhary, Megan K. Proulx, Christopher Sundling, Gunilla Källenius, Rajko Reljic, Joel D. Ernst, Arturo Casadevall, Camille Locht, Abraham Pinter, Christopher M. Sasseti, Bryan D. Bryson, Sarah M. Fortune, Galit Alter
...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: ADCD Analysis - Data Linked, ADFP Analysis - Data Linked, All Metadata, Antibody Dependent Complement Deposition - Data Linked, Antibody Dependent Functional Profiling - Data Linked, Bacterial Survivability Restriction Assay - Data Linked, Cell Extraction - Metadata, Cell Sorting – Data Linked, ELISA Assay - Data Linked, FC-Receptor Binding Assay - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Mouse Challenge – Metadata, Short Read Sequencing - Data Linked, Single Cell Clustering - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection – Metadata, Western Blot - Data Linked
Joshua M. Peters, Hannah P. Gideon, Travis K. Hughes, Cal Gunnarson, Pauline Maiello, Douaa Mugahid, Sarah K. Nyquist, Joshua D. Bromley, Paul C. Blainey, Beth F. Junecko, Molly L. Nelson, Douglas A. Lauffenburger, Philana Ling Lin, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Joshua T. Mattila, Bryan D. Bryson
DOI: https://www.biorxiv.org/content/10.1101/2024.05.24.595747v1.full
Additional Datasets:
- More Metadata associated with these NHPs exists ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Cell Isolation - Metadata, Gene Expression Analysis - Data Linked, Immunohistochemistry - Data Linked, Library Creation - Metadata, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Owen Leddy, Yufei Cui, Ryuhjin Ahn, Lauren Stopfer, Elizabeth Choe, Do Hun Kim, Malte Roerden, Stefani Spranger, Bryan D. Bryson & Forest M. White
DOI: https://www.nature.com/articles/s41596-024-01076-x#Sec43
Abstract: Vaccines and immunotherapies that target peptide–major histocompatibility complexes (peptide–MHCs) have the potential to address multiple unmet medical needs in cancer and infectious disease. Designing vaccines and immunotherapies to target ...
Submitter: Charles Demurjian
Investigation: CSBC
Assays: All Metadata, ImmunoPeptideomics - Data Linked, Sample Processing - Metadata, SureQuant Analysis - Data Linked
*Tigist Y Tamir 1,2,3,6, Shreya Chaudhary 1,6, Annie X Li 1,6, Sonia E Trojan 1,4,6 3 , Cameron T Flower 1,2,5,6, Paula Vo 7 , Yufei Cui 1,3,6, Jeffrey C Davis1,4,6, Rachit S Mukkamala 1,3,6 4 , Francesca N Venditti 1,6, Alissandra L Hillis 8 , Alex Toker 8 , Matthew G Vander Heiden 1,2,4,6,7 5 , Jessica B Spinelli 9 , Norman J Kennedy 9 , Roger J Davis 9 , and *Forest M White 1,2,3,5,6
Image
DOI: https://www.biorxiv.org/content/10.1101/2024.08.28.609894v1.full
Abstract: Coordination of adaptive ...
Zhewen Guo, Haosheng Feng, Timothy Swager
DOI: https://pubs.acs.org/doi/10.1021/acssensors.4c02462
Abstract: Herein, we present the development and evaluation of a molecularly imprinted polymer (MIP) sensor for the sensitive and selective detection of N-nitrosodimethylamine (NDMA) in aqueous environments. MIP coatings over electrochemically active electrodes enable NDMA detection with a notably low detection limit of 1.16 ppb. Our findings demonstrate that the ...
Megan K. Proulx, Christine D. Wiggins, Charlotte J. Reames, Claire Wu, Michael C. Kiritsy, Patricia Grace, Clare M. Smith, Cecelia S. Lindestam Arlehamn, Galit Alter, Douglas A. Lauffenburger, Christopher M. Sassetti
Training Data for the Model: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267774
Abstract: While control of Mycobacterium tuberculosis (Mtb) infection is generally understood to require a Th1-immune response and IFN secretion, infection ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: CITESEQ Analysis - Data Linked, Cell Isolation - Metadata, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Histology - Data Linked, Library Prep - Metadata, Model Validation - Data Linked, Pathogen Challenge and Antibody Depletion - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
