Studies

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 ...

_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, ...

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

Short Name: TransientLPPSCPPS Title: Transient expression of lavandulyl pirophosphate synthase (LPPS) and chrysanthemyl pirophhosphate synthase (CPPS) Description: The purpose of this study is to perform the transient expression of LPPS and CPPS gene for the production of lavandulol and chrysanthemol, respectively. Production is measured by GCMS of samples. Raw Data: pISA Study creation date: 2021-12-03 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution ...

Short Name: P5_PhContentPlants Title: Quantification of total moth pheromone contents in SxP Description: Quantification of the total pheromone content in SxPv1.2 plants Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_PhEmissionPlants Title: Quantification of the pheromone emitted by SxP plants Description: Quantification of the quantity of pheromone emitted by SxPv1.2 plants by volatile collection and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T24_phero

Short Name: P5_EAGresponse Title: Electrophysiological response of moths to SxP extracts Description: Electrophysiological response of Sesamia nonagrioides males to selected fractions of the SxPv1.2 extracts Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P1_ConstExp_Pdigitatum Title: Constitutive expression of moth pheromone pathway in Penicillium digitatum. Description: For this Proof of Concept, the three enzymes of the moth pheromones route were assembled in TUs using fungal promoters and terminators, and transformed into Penicillium digitatum. Pheromone production of the selected transformants will be assessed via GC-MS. Raw Data: pISA Study creation date: 2020-18-04 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez ...

Short Name: P5_SxFliquids Title: Pheromone detection in liquid extracts of SxF Description: Pheromone detection in liquid extracts of modified filamentous fungi (SxF) by liquid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_SxFmycelia Title: Pheromone detection in SxF mycelial biomass Description: Pheromone detection in the mycelial biomass of modified filamentous fungi by solid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T23_SxF

Investigation files _I_T22_SxPv2

Short Name: P1_TransgenicStableSxPv2 Title: Generation of Sexy Plant version 2: transgenic plants with the moth sex pheromones biosynthetic pathway genes regulated by synthetic promotors. Description: The purpose of this study is to generate transgenic stable lines of Nicotiana benthamiana plants ready to express the moth sex pheromone biosynthetic pathway in a regulable way. The moth sex pheromones biosynthetic pathway genes are regulated by synthetic promotors, so in a basal state, the plants ...

Investigation files _I_T12_CuInducible

Short Name: P1_TransientExp_Nb Title: Agroinfiltration of copper inducible system in Nicotiana benthamiana Description: The copper inducible dCasEV was tested transiently in Nicotiana benthamiana leaves together with the moth pheromone pathway under the regulation of the synthetic promoters created in T11 Raw Data: https://zenodo.org/communities/susphire/search?page=1&size=20 pISA Study creation date: 2020-10-28 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative ...

Investigation files _I_T11_dCas9SynProm

Short Name: P1_SynProm_Nbenthamiana Title: Transient expression in Nicotiana benthamiana of the synthetic promoters developed Description: Different A1 and A2 Different A1 and A2 promoter pieces were designed containing as much random sequence as possible, and the target sequence for the guideRNA 1 of SlDFR promoter. In the same way, some minimal promoters containing only the TATA-Box signal and the 5'UTR region were designed as "core promoter" pieces. Different synthetic promoters were then ...

Short Name: P4_Pcitri_tr1tr2combo Title: Combining tr1 and tr2 P. citri de novo transcriptomes into one transcriptome set Description: Production of one set of transcripts that will be easier for the readers of the planned publication Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_tr2 Description: Study of P. citri transcriptome data from SUSPHIRE and mealybug.org RNA-Seq datasets Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_genomes Title: Mealybug genome queries for pheromone biosynthesis genes Description: Survey of the available mealybug genomes for potential sex pheromone biosynthesis genes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_genome Title: P. citri SUSPHIRE samples mapping to genome and differential gene expression analysis Description: Illumina reads from virgin and mated female Pcitri samples were mapped to P. citri genome available at mealybug.org (ensembl) Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_genome_extSamples Title: P. citri all available samples mapping to genome and differential gene expression analysis Description: Illumina reads from all available P. citri samples (SUSPHIRE, Edinburgh and SRA) were mapped to P. citri genome available at mealybug.org (ensembl) Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_IsoSeq Title: P citri Iso-Seq transcriptome generation and search for new sex pheromone biosynthesis genes Description: PacBio IsoSeq transcriptome sequencing and data analysis Raw Data: SRR15093694 Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation: _I_T3.1_mealybug project: _p_SUSPHIRE Short Name: P4_Pcitri_tr Title: P. citri transcriptome study Description: We are interested in certain mealybugs both because they are important pests and very difficult to control but because their sex pheromones are irregular terpenoids, which are (a) very cool molecules and (b) extremely difficult and expensive to make using chemistry.In our project, we will be doing comparative transcriptomics of virgin and mated females to attempt to ...

Investigation files _I_T31_mealybug

Short Name: P3_expressionEcoli Title: Expression of IDS candidates in E. coli Description: IDS candidate sequences are expressed in E. coli and tested for enzyme activities Raw Data: Principal investigator: Heribert Warzecha License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_AdPathGenes Title: Additional search for genes involved in P citri sex pheromone production pathway Description: Search for additional pathway genes using coexpression etc Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_IDScandidates Title: Generation of the candidate list for cis and trans IDS enzymes from P. citri Description: From the P. citri genome and both de novo transcriptome assembly versions we mined homologues of trans(PF00348, IPR000092) and cis (PF01255, IPR001441) IDS enzymes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Glucose-6-phosphate dehydrogenase (G6PDH), the enzyme that catalyzes the first step of the oxidative pentose phosphate (OPP) pathway, plays a key role in this process. G6PDH is produced at the onset of nitrogen starvation but remains inactive in dormant cells, only to be rapidly reactivated when nitrogen is restored. In this study, we investigated the mechanisms underlying this enzymatic regulation and found that G6PDH inactivation is primarily due to the accumulation of inhibitory metabolites. ...

In a well with a total volume of 250 µL, the following components are added: 219 µL of 0.1 M TEA buffer, pH 7.5 1 µL of L-LDH (550 U.mL-1) 10 µL of NADH (10 mg.mL-1) 20 µL of the sample to be assayed

The initial absorbance (Ainitial) was measured at 340 nm, followed by the introduction of the Li-HPA sample solution, whether diluted or not. After stabilization, the final absorbance (Afinal) was measured. The concentration of Li-HPA was determined using the equation: ...

Michelle Chen, Elliot I. Corless, Bevin P. Engelward, Timothy M. Swager

Link to Paper: https://pubs.acs.org/doi/full/10.1021/acsomega.4c03959

Agglutination of liquid Janus emulsions creates optical signals that can be detected and quantified. This study reports the detection and quantitation of Interleukin-6 (IL-6) using emulsions functionalized at the water-organic interface with engineered hyperthermophilic affinity proteins (rcSso7d) derived from ...

Jessica C. Beard, Chi-Hsien Wang, Arun Sridharan, Robert G. Croy, John M. Essigmann, Timothy M. Swager

Link to Paper: https://doi.org/10.1021/acssensors.4c00927

N-Nitrosamines are contaminants found throughout the environment, including in drinking water, and many nitrosamines are likely potent carcinogens. Correspondingly, there is need for rapid and cost-effective in-field detection methods that can provide timely information about their contamination ...

Shu Wang, Amy J Myers, Edward B Irvine, Chuangqi Wang, Pauline Maiello, Mark A Rodgers, Jaime Tomko, Kara Kracinovsky, H. Jacob Borish, Michael C Chao, Douaa Mugahid, Patricia A. Darrah, Robert A. Seder, Mario Roederer, Charles A Scanga, Philana Ling Lin, Galit Alter, Sarah M Fortune, JoAnne L Flynn, Douglas A Lauffenburger

Paper Link: https://doi.org/10.1101/2024.04.13.589359

Link to Model Validation Datasets: https://fairdomhub.org/studies/1198

Abstract: ...

Utilization of enzyme assays to investigate PGM variants from Synechocystis

Abstract The enzyme Glucose-1-phosphate adenylyltransferase (GlgC, EC:2.7.7.27) catalyses the first step in glycogen synthesis by converting glucose-1-phosphate into ADP-Glucose, which is added in turn to a growing glycogen chain by glycogen synthases. Thus far, the in vitro study of GlgC were mainly performed using colorimetric or radiolabel-based phosphate release assays, limiting the option for analysing this reaction. With this work, we present a novel in vitro continuous assay coupling the ...

Giovanni S. Offeddu#, Elena Cambria#, Sarah E. Shelton, Kristina Haase, Zhengpeng Wan, Luca Possenti, Huu Tuan Nguyen, Mark R. Gillrie, Dean Hickman, Charles G. Knutson, and Roger D. Kamm

Abstract: Desmoplasia in breast cancer leads to heterogeneity in physical properties of the tissue, resulting in disparities in drug delivery and treatment efficacy among patients, thus contributing to high disease mortality. Personalized in vitro breast cancer models hold ...

Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*

Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...

Caylin G. Winchell, Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins, Michael Chase, Hannah P. Gideon, Kush V. Patel, Joshua D. Bromley, Andrew W. Simonson, Roisin Floyd-O’Sullivan, Marc Wadsworth, Jacob M. Rosenberg, Rockib Uddin, Travis Hughes, Ryan J. Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A. Scanga, Joshua Mattila, Sarah M. Fortune, Alex K. Shalek, Philana Ling Lin, JoAnne L. Flynn; CD8+ lymphocytes are critical for early ...

Huu Tuan Nguyen, Nicholas Pietraszek, Sarah E. Shelton, Kwabena Arthur, Roger D. Kamm

Link to Paper:

Abstract: Significance: Accurate cell segmentation and classification in 3 dimensional (3D) images are vital for studying live cell behavior and drug responses in 3D tissue culture. Evaluating diverse cell populations in 3D cell culture over time necessitates non-toxic staining methods, as specific fluorescence tags may not be suitable and immunofluorescence ...

Edward B. Irvine, Joshua M. Peters, Richard Lu, Patricia S. Grace, Jaimie Sixsmith, Aaron Wallace, Matthew Schneider, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Esther van Woudenbergh, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Galit Alter, Sarah M. Fortune doi: https://doi.org/10.1101/2022.05.01.490220

Novel vaccination and therapeutic strategies are urgently needed to mitigate the tuberculosis (TB) epidemic. While extensive efforts have focused ...

Jing Ge, Le P. Ngo, Simran Kaushal, Ian J. Tay, Elina Thadhani, Jennifer E. Kay, Patrizia Mazzucato, Danielle N. Chow, Jessica L. Fessler, David M. Weingeist, Robert W. Sobol, Leona D. Samson, Scott R. Floyd, Bevin P. Engelward,*

Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439179/

DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have ...

Norah Owiti, Joshua Corrigan, Lee Pribyl, Jennifer Kay, Bevin Engelward

https://doi.org/10.3390/ijms231911776

The comet assay is a versatile assay for detecting DNA damage in eukaryotic cells. The assay can measure the levels of various types of damage, including DNA strand breaks, abasic sites and alkali-sensitive sites. Furthermore, the assay can also be modified to include purified DNA glycosylases so that alkylated and oxidized bases can be detected. The ...

Edward B Irvine, Patricia A Darrah, Shu Wang, Chuangqi Wang, Ryan P McNamara, Mario Roederer, Robert A Seder, Douglas A Lauffenburger, JoAnne L Flynn, Sarah M Fortune, Galit Alter

https://doi.org/10.1101/2023.07.31.551245

Altering the route of Bacille Calmette-Guérin (BCG) immunization from low-dose intradermal vaccination to high-dose intravenous (IV) vaccination resulted in a high level of protection against Mycobacterium tuberculosis ( Mtb ) infection, ...

HSD11B1 was inhibited in human subcutaneous and omental adipose tissue, and the effect on oxygenated adrogen metabolism was studied.

Surface plots showing the computational analysis of combined HSD11B1/AKR1C3 ratios and HSD11B1 inhibition.

HSD11B1 was inhibited by CBX and the effect of the inhibition on Cortisone and 11KA4 conversion by HSD11B1/AKR1C3 incubations were measured.

PFK-1 and PFK-2 were cloned and expressed in E. coli, purified, and kinetically characterised in terms of substrates and allosteric regulators.

HSD11B1 and AKR1C3 transfected cells were mixed at difefrent ratios and effects on cortisone conversion (Fig. 2B) and 11KT production (Fig. 2C) were measured and simulated.

Emmanouil Angelidakis, Sophia Chen, Shun Zhang, Zhengpeng Wan, Roger D. Kamm, Sarah E. Shelton

Link to Paper: https://doi.org/10.1002/adhm.202202984

A bidirectional association exists between metastatic dissemination and the hypercoagulable state associated with many types of cancer. As such, clinical studies have provided evidence that markers associated with elevated levels of coagulation and fibrinolysis correlate with decreased patient survival. However, ...

Sequence data for European Nucleotide Archive (ENA ) https://www.ebi.ac.uk/ena/

Metabolomics data a for Metabolight DB

Proteomics data for PRIDE, UniProt and others

Lauren Baugh, Brittany A. Goods, Juan S. Gnecco, Yunbeen Bae, Michael Retchin, Constantine N. Tzouanas, Megan Loring, Keith Isaacson, Alex K. Shalek, Douglas Lauffenburger, Linda Griffith

https://www.medrxiv.org/content/10.1101/2022.01.29.22269829v1

Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes ...

Juan S. Gnecco, Alexander Brown, Kira Buttrey, Clara Ives, Brittany A. Goods, Lauren Baugh, Victor Hernandez-Gordillo, Megan Loring, Keith Isaacson, Linda G. Griffith

https://doi.org/10.1101/2021.09.30.462577

The human endometrium undergoes recurring cycles of growth, differentiation, and breakdown in response to sex hormones. Dysregulation of epithelial-stromal communication during hormone cycles is linked to myriad gynecological disorders for which treatments ...

Chemical named entity recognition (NER) is a significant pre-processing task in natural language processing. Identification and extraction of chemical entities from biomedical literature and entities linking to the knowledge base are essential steps for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we ...

Biomedical pre-trained language models (BioPLMs) have been achieving state-of-the-art results for various biomedical text mining tasks. However, prevailing fine-tuning approaches naively train BioPLMs on targeted datasets without considering the class distributions. This is problematic, especially with dealing with imbalanced biomedical gold-standard datasets for named entity recognition (NER). Regardless of the high-performing SOTA fine-tuned NER models, they are biased towards other (O) tags ...

Hannah P.Gideon, Travis K.Hughes, Constantine N.Tzouanas, Marc H.WadsworthII, Ang AndyTu, Todd M.Gierahn, Joshua M.Peters, Forrest F.Hopkins, Jun-RongWei, Conner Kummerlowe, Nicole L.Grant, Kievershen Nargan, Jia YaoPhuah, H. JacobBorish, Pauline Maiello, Alexander G.White, Caylin G.Winchell, Sarah K.Nyquist, Sharie Keanne C.Ganchua, Amy Myers, Kush V.Patel, Cassaundra L.Ameel, Catherine T.Cochran, Samira Ibrahim, Jaime A.Tomko, Lonnie JamesFrye, Jacob ...

Irene Hu and Harold Hemond

https://doi.org/10.3390/

Aquatic eddy covariance (AEC) is an in situ technique for measuring fluxes in marine and freshwater systems based on the covariance of velocity and concentration measurements. Here, development of a fast multiple-channel sensor (FACT) enables the use of AEC for measurement of benthic fluxes of fluorescent dissolved organic material, salt, and heat at three distinct sites in Massachusetts, USA, including the ...

Jennifer E. Kay, Joshua J. Corrigan, Amanda L. Armijo, Ilana S. Nazari, Ishwar N. Kohale, Dorothea K. Torous, Svetlana L. Avlasevich, Robert G. Croy, Dushan N. Wadduwage, Sebastian E. Carrasco, Stephen D. Dertinger, Forest M. White, John M. Essigmann, Leona D. Samson, Bevin P. Engelward

doi: https://doi.org/10.1101/2021.01.12.426356

Link to all of the Imaging done in this study: https://omero.mit.edu/webclient/?show=project-153 ...

Thiel BA, Worodria W, Nalukwago S, Nsereko M, Sanyu I, Rejani L, Zawedde J, Canaday DH, Stein CM, Chervenak KA, Malone LL, Kiyemba R, Silver RF, Johnson JL, Mayanja-Kizza H, Boom WH. Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resist versus those who develop latent Mycobacterium tuberculosis infection. PLoS One. 2021 Apr 9;16(4):e0249477. doi: 10.1371/journal.pone.0249477. PMID: 33836031; PMCID: PMC8034721.

Abstract: ...

Induced fit docking studies of the dinitroaniline parent trifluraline and the newly designed dinitroaniline-etherphospholipid hybrids against different potential binding sites in monomeric and multimeric kinetoplastid tubulin receptors.

This study includes the experimental data for model validation and the model predictions of that data set.

This study includes the experimental data for model validation and the model predictions of that data set.

Haosheng Feng, Shao-Xiong Lennon Luo, Robert G Croy, John M. Essigmann, Timothy M. Swager

https://doi.org/10.1039/D2DT03848J

Cu(I) from tetrakis(acetonitrile)copper(I) hexafluorophosphate ([Cu(MeCN)4]PF6) was complexed with five structurally related phosphines containing N-heterocycles. The interactions between the resulting complexes and some N-nitrosamines were studied using X-ray crystallography as well as emission spectroscopy. Upon complexation, three ...

Amanda L. Armijo, Pennapa Thongaram, Bogdan I. Fedeles, Judy Yau, Jennifer E Kay, Joshua J. Corrigan, Marisa Chancharoen, Supawadee Chawanthayatham, Leona D. Samson, Sebastian E. Carrasco, Bevin P. Engelward, James G. Fox, Robert G. Croy & John M. Essigmann

DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA ...

Sequence and electrostatic potential analyses to identify sites in tubulins that differ between dinitroaniline-sensitive and dinitroaniline-resistant species.

A minimal metadata template for high content screening experiments in microscopy. The template is compliant with REMBI (Recommended Metadata for Biological Images) and the ISA framework (Investigations, Studies and Assays).

Here you will find guidelines for filling in MIHCSME metadata templates, as well as examples of published HCS studies that use MIHCSME.

This study describes the results of a survey on enrichment analysis tool usage and provenance reporting for a corpus of SARS-CoV2 data.

This study investigates the citations of reproducible vs. not reproducible papers and is based on 328 published models, classified by Tiwari et al. based on their reproducibility are analyzed in this study. Hypothese testing is performed using a flexible Bayesian approach for a complete assessment of posteriors. The approach handels outliers via a non-central t distribution. Results show that reproducible papers are significantly more citet between 2013 and 2020, i.e. 10 years after the introduction ...

This study contains the singele nuclei data analysis part of the Bl6 and Rag2del comparison. Here, we used Seurat, harmony, and monocle for an in-depth analysis.