The work was started by Tannia Lau during her PhD thesis in Scott Lokey’s lab. For her project, machine learning methods were explored for analyzing cytological profiling screen data from macrophages, collected in the CSC. This is a very hot topic for high content screening. So while Tannia had since graduated and moved to a career in industry at Eli Lilly & Co, we were excited to validate and investigate the hits from her screen, and get it over the finish line to publication. To do this, we employed the new wetlab capabilities of the revamped CSC. These follow-up studies benefitted from the versatility of the acoustic dispenser, image quality and intuitive quantification tools of the confocal imager, accuracy of the new bulk dispenser, and speed of the new plate washer. The two phases of the project were presented by Tannia and Beverley at the annual Society for Laboratory Automation Sciences. We continue to use these methods in our ongoing studies in natural product drug discovery with the HiFAN team, and welcome collaborators or customers to inquire about having your own samples run through image cytometry for immune-modulating compounds.
We are excited to announce the 6 winning proposals for seed funds:
Shaheen Sikandar, “Elucidating the role of vascular mimicry in breast cancer metastasis.” This project is lead by graduate student Isobel Fetter.
Vicki Auerbuch Stone, “Identifying inhibitors of the bacterial PAP I polyadenylase.” This project is led by graduate student Karen Hug.
Manel Camps, “Identification of bioactive compounds interfering with plasmid maintenance” – read more here. This project is led by graduate student Christina Egami.
Angela Brooks, “Investigating how [a gene of interest] alters stress granule response in HBECs.” This project is led by graduate student Cindy Liang.
Are you interested in the advantages of high throughput robotically-controlled assays and screens? Do you want to use our “Lamborghini of confocal microscopes” for live cells, organoids, or other imaging studies? Or perhaps you have an application for our freshly purchased chemical compound collections? Well, you’re in luck because, thanks to a donation from the Office of Research, the CSC is welcoming in-house applications for seed funds to facilitate exciting new projects!
—The Application Process—
Applications are done via this Google form. Awards will be announced by November 20, 2023. Following award notice, the team will meet (professor, trainee, and CSC staff), the experiment details will be agreed upon, and a formal quote for the planned work will be generated. The experiments may then commence immediately, subject to the availability of the trainee and CSC staff, and the funds must be expended by May 31, 2024.
—Eligibility—
The applicant must either be a UCSC professor, or a current member of a UCSC professor’s research lab, who has prior permission from the professor to fill out the form. The project must be assigned to a member of the professor’s lab, who will get trained during the course of the experiments, and who will be primarily responsible for planning and executing the experiments, taking notes, and analyzing the results, with the assistance of CSC staff. Individuals can make multiple submissions for consideration.
—Budget—
Awards within the range of $2,000 – $10,000 may be requested. We anticipate awarding 5-10 awards.
The seed funds will be applied to offset recharges incurred at the CSC. This includes recharges for staff time, instrument time, bioinformatics workstations, and compound libraries. The awardee will be allowed to charge a total of less than 20% of the award for purchases of disposables (microplates, reagents, solvents) associated with the proposed experiments.
The award will not cover other projects, follow-up studies, experiments otherwise not described in the application, recharges for other facilities, or salary for the trainees involved.
Depending on the complexity of the project, the seed fund could be enough to cover assay development/pilot experiment and a medium-scale screen. If you already have an assay working, the seed funds could cover a high throughput screen. We offer robots to automate sample prep, multiple analytical mechanisms, and different types of compound libraries.
We welcome any questions about our resources, workflows, and prices to help you develop your application.
We’re hosting an event all about plate reader assays. Please come with your questions to ask the experts! We’ll have a short presentation starting around 12 (from myself and some field application scientists from Revvity) and lots of time for discussion, ending around 2pm. This may be a great opportunity to come get guidance for your seed fund application! Please register so we can get a lunch headcount and all registrants get a 15% discount on kit purchases from Revvity!
In case you’d like to see my slides from today’s talk invited to the Western Association of Core Directors. You’ll likely have to download the .PPT file locally, as the file is too big to preview on the browser. Enjoy!
Thanks to our brilliant summer intern, Kenny, we now have a CSC YouTube channel@UCSC_ChemicalScreeningCenter with several captioned training videos! These will serve as a starting point for new trainees and a refresher for previous trainees. Each piece of equipment has its own playlist, so select to watch the video most relevant to the task you wish to perform. Feel free to comment below with which video you would like to see us make next!
The Grand (Re) Opening Celebration & Research Symposium on May 5, 2023 was a marvelous success. Thank you to everyone who came, interacted, presented research, or showcased technologies.
The event was held in the beautiful University Center venue. Scott Lokey and Phil Crews presented some entertaining stories from the beginnings of the CSC. We also had on stage Paul Koch, the Dead of the PBSci division.
Trainees flaunted their research success with talks, posters, and a number of fun prizes. Trainee talks were given by Aswad Khadilkar, Jaru Taechalertpaisarn, and Cindy Liang. The first place poster prize was tied between Tilini Wijeratne and Peter Ngoi, and third place was awarded to Nadia Dzhanbekova. Recognized for their excellence in High Throughput Technology were instrument users Matylda Zietek, Priya Crosby, Jaru Taechalertpaisarn, Matt Loven, Jackson Baumgartner, Adam Lentz, and Akshar Lohith.
We had a lovely catered party at the end of the day, where we heard from Cynthia Larive, Chancellor of the University, who recognized the ways that the CSC supports inspiring, high impact research that improves lives for the better.
Thank you to Jack Lee for being our photographer for the symposium!
We also want to thank our industry sponsors, primarily Perkin Elmer, whose donation funded the majority of the event. We also had vendor tables from Agilent BioTek and BioLegend. We also thank our internal symposium sponsors, the Office of Research; the PBSci Division Dean’s Office; Department of Chemistry & Biochemistry; Department of Molecular, Cellular, and Developmental Biology; Department of Microbiology and Environmental Toxicology; and the Biomolecular Engineering department within Baskin Engineering.
Last but not least, we thank QB3 and the UCSC Physical and Biological Sciences Division for ongoing support of the CSC daily operations.
“Rabbitts provides one-on-one training for students and other new users of the center’s facilities. Lokey said the focus on training sets the UCSC center apart from other screening centers.
“It’s valuable experience for the students, and the symposium will give them an opportunity to showcase what they’ve been doing,” he said.”
Full article: https://news.ucsc.edu/2023/04/csc-symposium.html
Ben Abrams, academic/research staff – Life Sciences Microscopy Center. The UCSC Life Sciences Microscopy Center Has Tools for Your Research Nadia Dzhanbekova, graduate student – Seth Rubin. Chemical Library Screening to Identify Novel Molecular Mechanisms Behind Cell Cycle Arrest Sahar Hosseinzadeh, graduate student – John MacMillan. Identification of Selective Cytotoxins for Non-Small Cell Lung Cancer Cell Lines Karen Hug, graduate student – Victoria Auerbuch Stone. Disruption of the Yersinia pseudotuberculosis T3SS primes bacteria for envelope stress Rachel Jacobson, Senior Director Research – Spring Discovery. Using Machine Learning to Harness the Complexities of Inflammasome Biology for Novel Drug Discovery *Aswad Khadilkar, academic/research staff – John MacMillan. Assigning Mechanism of Action To Natural Products In Multiple Biological Contexts Using Gene Expression And Phenotypic Screening Methods Established By The HIFAN Program *Cindy Liang, graduate student – Angela Brooks. Pairing phenotypic assays with direct RNA sequencing to understand U2AF1 S34F and cigarette smoke’s functional role in lung cancer Akshar Lohith, PhD Candidate – Scott Lokey and John MacMillan. Advancing Cell Profiling to cover a broad phenotypic space and determine the mechanism of action of diverse perturbations
Poster session 2
Gabe Mitchell, industry. Open Innovation @ NITD: targeting the host-pathogen interface during microbial infection Joseph Morris, lab of Tyler Johnson, Dominican University of California. In Vivo Evaluation of Zampanolide & Thermolysis Reveals Cytotoxicity of Hemi-Aminal Side Chain & Delayed Binding Mode of Dactylolide Samuel Mussetter, undergraduate student – Crews Lab.Further Evaluation of a Bicyclic Pyrazolines as a 15-Lipoxygenase V-Type Activators – Scrutizining Their 3D Properties Peter Ngoi, graduate student – Seth Rubin. Structural basis for E2F1 Recognition by E3 Ligase SCF-CyclinF Beverley Rabbitts, core director of CSC. High content screening and machine learning for identifying novel natural product modulators of the innate immune response. Francesco Rubbo, industry researcher – Spring Discovery. A Benchmark Dataset for Phenotypic Compound Similarity in Inflammasomes Screens
Diksha Sharma, graduate student – Carrie Partch. Small-molecule screening:PASsing the binding test *Jaru Taechalertpaisarn, post-doc – Scott Lokey. Discovery of Novel Active Macrocyclic Peptides Through Permeable-First Perspective Tilini Wijeratne, graduate student – Seth Rubin. B-Myb association with DNA is regulated by its Negative regulatory domain and Cdk phosphorylation Kevin Yang, graduate student – Scott Lokey. Development and Characterization of Passively Cell-Permeable RNA-Binding Cyclic Peptides
*=giving a talk (plus or minus poster) with this title. The rest are posters only.
