Cores Newsletter July 2023

Luca Comai Elected to the National Academy of Sciences

Luca Comai, a distinguished professor at the University of California, Davis, has recently been elected to the National Academy of Sciences (NAS), one of the most prestigious honors a scientist can achieve. The NAS announced the election of 120 members and 23 international members on May 2nd, including three professors from UC Davis.

Capsule Captures First Look Inside Digestion in Healthy People

Using a specially designed capsule, researchers can now voyage through the digestive system, collecting new data about digestion and microorganisms. The work by a team including researchers at the University of California, Davis, Stanford University and Envivo Bio Inc., is published May 10, 2023 in Nature and Nature Metabolism.

UPCOMING COURSES

Introduction to Python for Bioinformatics

Jul 10-14, 2023 @ 2:00pm - 5:00pm

Enhance your bioinformatics knowledge with this five-part online workshop in Introduction to Python. Python is a programming language that is used widely in the creation of many bioinformatics software.

International Summer Sessions in Metabolomics 2023

Aug 21 - Sep 1, 2023 @ 9:00am - 5:00pm

Learn about metabolomics and enhance your research skills in our two-week summer session. Join us for an immersive learning experience and gain insights from top experts in the field. Register now and take the next step towards advancing your career in metabolomics!

2023 Hands on Proteomics Short Course

Aug 28 - Sep 1, 2023 @ 8:00am - 3:00pm

This introductory proteome analysis workshop is designed to expose participants to current methodologies in sample preparation, Liquid chromatography - Tandem mass spectrometry and data analysis in the field of mass spectrometry-based proteomics. Image

Bits & Bites #05: Identification of unknown compounds in untargeted metabolomics using freely available software

Sep 7, 2023 @ 9:00am - 5:00pm

This short course will provide an overview of the current status of compound ID in metabolomics, participants will learn how to use freely available in silico fragmentation tools.

Introduction to the Command Line for Bioinformatics

Sep 11-15, 2023 @ 2:00pm - 5:00pm

Get off to a good start in bioinformatics with this three-part online workshop in the use of the command line interface.

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MESSAGE FROM THE CORES

West Coast Metabolomics Center

The WCMC Metabolomics Core Facility recently attended the ASMS 2023 conference in Houston, TX, and presented the following presentations:

QA/QC for Untargeted Metabolomics in a Large Core Lab: Current Best Practices and Innovative Strategies - Oral by Uri Keshet, Technical Director

Comparing Targeted LC-MS/MS and Untargeted GC-MS for the analysis of Kynurenine Pathway in Plasma Samples - Poster by Luis Valdiviez, Lab Manager and GC-MS Team Leader

Combined GC-TOF-MS and LC-TOF-MS/MS Untargeted Metabolomics Yields Insight into Pathophysiology of Parkinson’s Disease - Poster by Jeremiah Wells, Untargeted LC-MS Team Leader

We were delighted to read your positive feedback in the Research Core Facilities Survey results and we are grateful for the suggestions for improvement. We are diligently working on enhancing our turnaround time to meet the significant demand for our services. We wish to thank you for your patience and support.

Please don't hesitate to contact us for information on the presentations or with any other questions or requests, at metabolomics@ucdavis.edu.

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Proteomics Core

Join us for an immersive and informative introductory proteome analysis workshop! Led by UC Davis faculty and renowned external specialists, this weeklong course is specially designed to introduce participants to the latest methodologies in sample preparation, liquid chromatography, tandem mass spectrometry, and data analysis within the dynamic field of mass spectrometry-based proteomics. Don't miss this incredible opportunity to expand your knowledge and skills in proteomics! Mark your calendars for August 28th - September 1st. For more information and to register, visit our webpage.

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Bioinformatics Core

The Bioinformatics Core is announcing a call for applications for pilot projects in multi-omics and spatial multi-omics. This grant aims to support data analysis and integration of multi-omics data provided by researchers, from raw data to publication-quality visualizations. Please visit our webpage for information on how to apply.

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DNA Technologies & Expression Analysis Core

Out with the Old, in with the New!

Ten months after purchasing one of the first AVITI sequencers manufactured by Element Biosciences, the DNA Technologies Core has acquired a second AVITI instrument. This sequencer is capable of running the new 'Cloudbreak' chemistry, reducing run times from 48 to 36 hours for a PE150 run, while a PE75 run will take less than 24 hours. After testing, the Core's original AVITI will be upgraded to enable Cloudbreak. Both machines will then be capable of running PE300 runs when the 600-cycle kit becomes available later in 2023. For more details, please see our introduction to Aviti sequencing webpage.

A consequence of ever cheaper sequencing is that other technologies become less attractive. After 15 faithful years, the Illumina iScan is being retired from the Core. This scanner has imaged hundreds of Infinium chips, each with thousands of SNP genotypes, and the technology still has relevance (it's the backbone of 23andMe and other ancestry testing services). SNP genotyping will continue to be represented in the Core via the Fluidigm EP1 system.

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