Publication of our cytological profiling in macrophages

Our article was the cover-featured, first-listed research paper in the January 15 issue of ChemBioChem.

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.

Tannia’s PhD research was funded in 2019-2020 by a prestigious NIH F31 Kirschstein-NRSA fellowship, building upon her prior work supported by UCSC’s Initiative for Maximizing Student Development, a Navajo Scholarship, and Society for the Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS). We are grateful to these programs for continuing to support work of excellent trainees like Tannia.

The cover of ChemBioChem with a painting of a macrophage and floating chemical structures.

6 seed grants awarded

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.
  • Seth Rubin, “BMyb-MuvB inhibitor screen.” This project is led by graduate students Peter Ngoi and Nadia (Nadezhda) Dzhanbekova.
  • Ali Shariati, “Enhancing reprogramming  through a chemo-RNA approach.” This project is led by postdoctoral fellow Estefania Sanchez-Vasquez.

Seed fund application deadline extended to noon Thursday, November 2

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.

a droplet is formed with a sunset background and Santa Cruz beach/cave in the foreground.
Oil on Canvas by Beverley Rabbitts.

Lunch and Learn on October 26

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!

a flyer with info on the event 12-2pm PSB240 sponsored by Revvity. QR code to register link is in the blurb.

CSC is now on YouTube

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!

a screenshot of our YouTube channel showing four playlists

CSC Symposium is in the UCSC news

newscenter screenshot with the article title and picture of users at the microscope

“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

Research in Progress Presentations at the 2023 CSC Symposium

Poster session 1

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 CSCHigh 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.

Who’s Who at the 2023 CSC Symposium

We hope you will enjoy this networking opportunity!

External academic guests:

Michelle Arkin, Distinguished Professor of Pharmaceutical Chemistry at UCSF.
Ramiro Alejandro Tomasi, Assistant Professor of Buccal Pathology at National University of Cordoba, Argentina.
Tyler Johnson, Associate Professor of Natural Sciences and Mathematics at Dominican U of CA.
Joseph Morris, researcher in the lab of Tyler Johnson at Dominican U of CA)
Mary West, Core Facility Director for the Cell and Tissue Analysis Facility (CTAF) and High-Throughput Screening Facility (HTSF).
~~Attn: CSC trainees…The HTSF is recruiting to hire a new screening facility manager!~~
Pingping He, Core Facility Manager for the High-Throughput Screening Facility (HTSF).
Deepa Sridharan, Project Scientist for the High-Throughput Screening Facility (HTSF).

Industry guests:

Maddalena Adorno, CEO & Co-Founder at Dorian Therapeutics. LinkedIn
Asheley Bailey, Advanced Technology Account Executive at CDW. LinkedIn
Rachel Bright, Alliance Management and Business Development at Gilead Sciences. LinkedIn
Alix Chan, Lead Scientist at Genentech. LinkedIn
*Paul Fielder, Vice President of Biomarker Development at Genentech. LinkedIn
*David Greenberg, Account Manager at Axion Biosystems. LinkedIn
Maureen Hillenmeyer, CEO & Founder of Hexagon Bio, Inc. LinkedIn
Kelly Huggins, Director of Technology & Strategic Alliances, Therapeutic Discovery at Amgen. LinkedIn
*Tannia Lau, Research Scientist, Genetic Medicine at Eli Lilly. LinkedIn
Gabriel Mitchel, Senior Innovation Scholar, Novartis Institutes for BioMedical Research (NIBR). LinkedIn
Gregory Notte, Executive Director of Medicinal Chemistry at Gilead. LinkedIn
*Cameron Pye,Co-Founder at Unnatural Products. LinkedIn
Francesco Rubbo, Staff Machine Learning Scientist at Spring Discovery. LinkedIn
*Josh Schwoshert, Co-Foudner at Unnatural Products. LinkedIn
Shuhei Tomimoto, Sr. Manager at Ono Pharmaceuticals. LinkedIn

*=UCSC Alum

Vendor tables:

Agilent Technologies
Diana Bogorodskaya, Sales & Business Development. LinkedIn

PerkinElmer
Marc Guerra, Sales Specialist, In Vivo. LinkedIn
Chananat Klomsiri, Sr. Discovery Reagent Sales Specialist. LinkedIn
Bill Ortiz, Principal Sales Specialist, plate readers. LinkedIn

BioLegend (affiliated with Perkin Elmer)
Anisha Madhav. LinkedIn
Robert Adams, Sr. Marketing Coordinator – Trade Shows and Events. LinkedIn

UCSC Faculty attending:

Chemistry and Biochemistry
Phillip Crews, Chem Biochem (emeritus)
Timothy Johnstone
Joseph Konopelski (emeritus)
Scott Lokey, Chem Biochem & Faculty Director of the CSC
John MacMillan, Chem Biochem & VCR
Glenn Millhauser, Chem Biochem & Dept Chair
Seth Rubin, Chem Biochem
Laura Sanchez, Chem Biochem

Molecular, Cellular, and Developmental Biology
Bradley Colquitt
Sharma Upasna
Martha Zuniga

Microbiology and Environmental Toxicology
Vicki Auerbuch Stone, Assoc Faculty Director of the CSC
Karen Ottemann
Michael Patnode

Engineering
Angela Brooks
Daniel Kim
Shelbi Russell
Ali Yanik, Electrical & Computer Engineering

Earth & Planetary Sciences Department
Paul Koch, PBSci Dean

And many more registrants!

CSC Symposium Agenda for May 5

10 AM REGISTRATION

Coffee available in the Bojwani room. Come check out the vendor tables in the Rotunda: Perkin Elmer, Agilent/BioTek, and BioLegend.

10:30-12:30 MORNING SESSION

10:30 AM Land acknowledgement, Vicki Auerbuch Stone, Professor of Microbiology & Environmental Toxicology and CSC Associate Director. Click for more info about the land acknowledgement.

10:31 AM Welcome, Glenn Millhauser, Head of Chemistry & Biochemistry Department

10:35 AM Opening plenary, Scott Lokey, Professor of Chemistry & Biochemistry and Faculty Director of the CSC
“UCSC CSC – a Rich and Varied History”

11:00 AM Tools & technologies update, Beverley Rabbitts, CSC Director of Operations
“Welcome to a New Era at the Fully Revamped CSC”

11:15 AM Research in progress: Jaru Taechalertpaisarn, CSC user from Scott Lokey’s lab
“Discovery of Novel Active Macrocyclic Peptides Through Permeable-First Perspective”

11:30 PM Research in progress: Aswad Khadilkar, CSC user from John MacMillan’s lab
“Assigning Mechanism of Action To Natural Products In Multiple Biological Contexts Using Gene Expression And Phenotypic Screening Methods Established By The HIFAN Program”

11:45 AM Morning keynote, Maureen Hillenmeyer, Founder and CEO of Hexagon Bio
“From academia to biotech startup: Launching a drug discovery company using new approaches in computation and automation”

12:30-1:30 PM NETWORKING LUNCH AND POSTER SESSION

12:30-1:00 PM First session – Poster presenters with last names A-L:
Abrams, Cech, Dzhanbekova, Hosseinzadeh, Hug, Jacobson, Johnson, Khadilkar, Liang, Lohith

1:00 PM-1:30 PM Second session – Poster presenters with last names M-Z:
Morris, Mitchell, Mueller, Ngoi, Rabbitts, Rubbo, Sharma, Taechalertpaisarn, Wijeratne, Yang

1:30-3:30 AFTERNOON SESSION

1:30 PM Invited faculty talk: Phil Crews, Distinguished Professor of Chemistry & Biochemistry
“Sponge Derived Molecule Discovery, Adventures of The Three Amigos Using the UCSC CSC”

2 PM Research in progress: Cindy Liang, CSC user from Angela Brooks’s lab
“Pairing Phenotypic Assays with Direct RNA Sequencing to Understand U2AF1 S34F and Cigarette Smoke’s Functional Role in Lung Cancer”

2:15 PM Research in progress: Gerd Mueller, CSC user from Seth Rubin’s lab
“Mechanisms of cell cycle-dependent gene regulation”

2:30 PM Presentation from our sponsor, Robert Graves, Field Applications Scientist, Perkin Elmer
“Phenotypic profiling by Cell Painting and fast confocal imaging with the Opera Phenix Plus High-Content Screening System”

2:35 PM Expression of gratitude, poster prizes, and awards, Beverley Rabbitts and Scott Lokey

2:40 PM Afternoon keynote, Michelle Arkin, UC San Francisco
“Looking for the Middle Way – Innovation and Application in Academic Drug Discovery”

3:25 PM Closing remarks, Paul Koch, Distinguished Professor of Earth & Planetary Sciences and Dean of the Division of Physical & Biological Sciences

 

Our industry sponsors will have the following vendor tables available throughout the day for education and networking:

PerkinElmer High Content, reagents and supplies, automation, plate readers, and bioinformatics (3 tables).

BioLegend Antibodies, proteins, and kits (1 table).

Agilent BioTek liquid handling (1 table).

We also thank our symposium sponsors at UCSC: 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.

We also would like to thank the following supporters of the Chemical Screening Center: the Santa Cruz branch of the California Institute for Quantitative Biosciences (QB3) and the UCSC Physical and Biological Sciences Division. We are grateful for their ongoing financial support for our daily operations, which supplements user fees to keep our staff paid and our instruments running!

the logo for QB3 at UC Santa Cruz