Studies

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 ...