Studies

_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, ...

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 ...

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) ...

The data / metadata will be available ** online** at the time of paper acceptance. If you would like access prior to acceptance, please reach out to Lindsay Volk: (lvolk@mit.edu)

Following on in silico and in vitro work, the effect of MCAD deficiency on CoA metabolism was investigated. Using a recently published HILIC-MS/MS method, free and acylated CoA species could be measured simultaneously in HepG2 MCAD-KO cells. The levels of CoA biosynthesis intermediates and total CoA was also characterised by HPLC in liver samples from MCAD-KO mice exposed to energetic stress (fasting adn cold). qPCR was applied to investigate changes in the CoA metabolism that might constitute ...

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 ...

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

...

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 ...

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 ...

*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 ...

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

DOI:

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 recapitulate some of the hallmarks of human ...

Satomi Hirose, Tatusya Osaki, Roger D. Kamm

Link to Publication: https://doi.org/10.1101/2024.06.28.601261

Abstract: Metastasis, the leading cause of cancer-related deaths, involves a complex cascade of events, including extravasation. Despite extensive research into metastasis, the mechanisms underlying extravasation remain unclear. Molecular targeted therapies have advanced cancer treatment, yet their efficacy is limited, prompting exploration into novel ...

Joshua M. Peters, Edward B. Irvine, Jacob M. Rosenberg, Marc H. Wadsworth II, Travis K. Hughes, Matthew Sutton, Sarah K. Nyquist, Joshua D. Bromley, Rajib Mondal, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Galit Alter, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Bryan D. Bryson

DOI: https://www.science.org/doi/10.1126/sciadv.adq8229

Intradermal Bacillus Calmette-Guérin (BCG) is the most widely administered vaccine, but it does not sufficiently ...

Files required for reproducibility of computational results. This include Docker file and python packages

Clock mutants for lhy-1/cca1-11, prr9/7, toc1, lux-4, elf3-1 were transformed with the genomic regions of the associated clock genes tagged with NanoLUC-3FLAG-10His. The tagged genomic constructs were transformed in the mutants using Agrobcterium ABI strain (kindly donated by Prof. Seth Davis University of York). T3 plants resistant to homozygous for BASTA resistance were phenotyped by luciferase imaging asessing period phenotype or plant architecture. Rescuing lines were then used for performing ...

Huu Tuan Nguyen, Nadia Gurvich, Mark Robert Gillrie, Giovanni Offeddu, Mouhita Humayun, Ellen L. Kan, Zhengpeng Wan, Mark Frederick Coughlin, Christie Zhang, Vivian Vu, Sharon Wei Ling Lee, Seng-Lai Tan, David Barbie, Jonathan Hsu, Roger D. Kamm

Link to Paper: https://www.sciencedirect.com/science/article/abs/pii/S0142961224002655

Abstract: Tumor-associated inflammation drives cancer progression and therapy resistance, often linked to the infiltration of ...

Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.

Link to Paper: https://doi.org/10.1038/s41564-024-01678-x

Abstract: Antibody features vary ...

Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn

Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3

Immunological ...

Short Name: P5_SxF_lav_ac Title: Detection of lavandulyl acetate in extracts of engineered fungi Description: Detection of lavandulyl acetate in extracts of engineered fungi (SxF) by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_SxF_lavandulol Title: Detection of lavandulol in SxF extracts Description: Detection of lavandulol in extracts of engineered fungi by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T33_MonoterpenoidsFungi

Investigation files _I_T32_CandidateGeneExpressionTesting