March 14, 2017: Guest Lecture Seminar
The Mouse Metabolic Phenotyping Center with the NIH West Coast Metabolomics Center proudly present
The Guest Lecture Seminar with Irwin J. Kurland, M.D., PhD.
Professor, Department of Medicine, Director of the Stable Isotope & Metabolomics Core Facility of the Diabetes Research Center
March 22, 2017 ~ Genome Center Auditorium ~ 10 – 11:30 a.m.
March 2, 2017: CMGI to Provide New Quantitative Image Analysis Services
The Center for Molecular and Genomic Imaging (CMGI) is pleased to announce an expansion of its imaging portfolio by adding Quantitative Image Analysis (QIA) services. QIA refers to the standardized extraction of meaningful, quantitative information from imaging data. It uses computational algorithms, instead of manual tasks performed by human users because the underlying tasks may be too complex or time consuming for humans, or the human visual system may not provide optimal detection capability for the task at hand.
“A question scientists are faced with is: are we getting the most amount of information we could from imaging data we collect? Most would agree that the answer is no. QIA allows us to precisely address this problem,” says Abhijit Chaudhari, CMGI Director.
For example, a study monitoring neurodegenerative changes requires extraction of the cortex of a rat brain from a 3D MRI scan. A person would typically manually outline the cortex from about 50 slices from the MRI scan. Even for an expert, this task can take 3-4 hours. Studies that require multiple scans of many animals over time become exorbitantly laborious, expensive, and potentially error-prone. Using a QIA method (image segmentation), the same task would take only minutes per animal scan, with little to no risk of error.
“The National Institutes of Health (NIH) recently defined two major cornerstones of scientific investigation: rigor and reproducibility. QIA methods, because of their minimal reliance on user error or variability, are inherently capable of providing reproducible results. I strongly believe that our QIA services will contribute toward enhancing the quality of scientific results of our investigators, and support the NIH mission,” says Dr. Chaudhari.
To spearhead the QIA services, Zachary T. Harmany, PhD, will join the center. Dr. Harmany has expertise in image reconstruction, processing, and analysis for biomedical research. He received a BS degree (magna cum laude, with honors) in Electrical Engineering and a BS degree (cum laude) in Physics from The Pennsylvania State University, and a PhD in Electrical and Computer Engineering from Duke University. Dr. Harmany’s past research has involved image and signal processing, machine learning, large-scale numerical optimization, and development of novel methods for processing, visualizing, and analyzing imaging data. He is also a member of the UC Davis Data Science Initiative, a multi-disciplinary collaborative effort to foster and promote research and education related to Data Science and Big Data.
The initiation of QIA services was made possible via the Campus Research Core Facilities Enhancement Funding Program administered by the UC Davis Office of Research. The services will be available to UC Davis investigators on a recharge basis from March 1, 2017.
February 28, 2017: MALDI Biotyper Service Coming to UC Davis
The Campus Mass Spectrometry Facilities is pleased to announce the upcoming MALDI Biotyperservice to the UC Davis research community. Biotyper is a relatively new, patented and FDA approved product which enables rapid (~5-10 min) identification of microbial organisms from microbial cultures using a MALDI mass spectrometer.
Once we have received training in the next few weeks, we will be offering this as both an open-access and single-sample service on our existing Bruker UltraFlextreme mass spectrometer. In addition to libraries for most common bacteria, we also have purchased libraries for fungi and mycobacteria.
Please use the link below to take a closer look at the flyer;
Contact Dr. Armann Andaya and William Jewell if you have any questions.
February 23, 2017 : Lattice Light Sheet Microscope Get’s Upgraded
The last two weeks have seen major upgrades to the Lattice Light Sheet Microscope in the MCB Light Microscopy Imaging Facility which should allow this microscope to now be used on a routine basis. This revolutionary design by Nobel Prize winner Eric Betzig — who is giving two Storer Lectures on campus this week — allows not-previously-possible long observations of living cells by applying extremely low doses of excitation light (illumination is only within the depth of focus of the observation lens). Very preliminary measurements in the MCB LM Imaging Facility last week showed photo-bleaching reduced in the range of 20 to 80-fold. This microscope is being developed for commercial release by a collaboration with Intelligent Imaging Innovations (3i) and the MCB LM Imaging Facility. UC-Davis was one of 10 sites initially chosen for this collaboration because of the very large number of biological model organisms in the College of Biological Sciences. This microscope is the only one of this design in an academic center west of Denver.
Images show the core optics of Lattice Light Sheet Microscope being moved to a new room and onto a larger optics table for the upgrades. This microscope now is also controlled by 3i’s “Slidebook” software, which makes the software interface much easier for regular users.
- Posted: February 10, 2017
Announcing a Bioinformatics Training Program Workshop
Feb. 23, 2017, 10 a.m. – noon
Location – UC Davis, Genome and Biomedical Sciences Facility Auditorium (GBSF Rm. 1005)
Contact – UC Davis Bioinformatics Core, email@example.com
This FREE workshop is intended for those who are interested in and are in the planning stages of conducting an experiment to study microbial communities using amplicon based methods (16S, ITS, etc.). Topics to be discussed will include:
The difference between Microbial Community Analysis and Metagenomics
Sample preparation, best practices
High throughput sequencing basics and choices
Microbial Community Analysis
Data cleanup and quality assurance
Assigning reads to organisms and counting
Analysis of the output
Downstream analysis/visualizations and tables
For more information, and to register, go to: https://registration.genomecenter.ucdavis.edu/events/microbial-workshopFeb2017/.
Posted: February 6, 2017
West Coast Metabolomics Center – Pilot and Feasibility Projects
The 2017 call for Pilot and Feasibility Proposals is open with a submission deadline of March 16, 2017.
The NIH executive committee decision is expected by June 2017.
Please, start working with the WCMC on your metabolic aims and service budgets for your 2017 submission.
Download the .
Submissions for maximum of $50,000 in metabolomic services.
One year maximum funding period
No salary support for investigator or investigator staff is permitted
No consumables or other financial support for the investigator’s lab is permitted.
The budget is for WCMC metabolomic services.
Consult with WCMC advanced laboratories about budget estimates.
Budget for WCMC advanced service laboratory staff will go in increments of 1-person months plus consumables needed to perform the project.
For additional criteria and considerations please visit their website:
Posted February 3, 2017
Video of the Informational Meeting on the NIH S10 Programs
Presented by: Julie A. Auger, Research Core Facilities Program
Posted: January 27, 2017
Applications for Pilot Project Proposals using Advanced Imaging Modalities
We are looking for pilot projects that seek to address novel research applications using advanced imaging modalities such as sample/tissue clearing, multiphoton, intravital, and super-resolution imaging. Information on the equipment and services available can be found at the HSDAIF website (http://www.vetmed.ucdavis.edu/advanced-imaging/index.cfm).
Purpose: The intent of the HSDAIF pilot project program is to provide an opportunity to develop new methodologies and obtain preliminary data with the goal of supporting new extramural funding applications. As such, funds may not be used to support established projects.
Eligibility requirements: Applicants must have Principal Investigator (PI) status or be supported by the PI (post-doctoral fellows, project scientists, and graduate students can apply but require the signature of their PI). Submissions from early career scientists and new users to the HSDAIF that are seeking preliminary data are particularly encouraged. This program is only open to NEW projects, with one submission per laboratory group. Members of the HSDAIF advisory board are not eligible to apply.
Funds available: Selected applications will be awarded $1000 in imaging time, with technical assistance available free of charge.
Application procedure: Applications should be no more than 2 pages single spaced 0.5 inch margins in Arial font size 11. Applications must include a project summary (one paragraph), specific aims, innovation, approach, future directions and intent to secure future extramural funding. All applications must be submitted as a single PDF by email to firstname.lastname@example.org by 5pm on March 3, 2017, including coversheet (pg.2).
Review Criteria and process: Applications will be reviewed by the director and facility manager of the HSDAIF and scored on an NIH scale of 1-10 based on (2) Scientific merit (scientific significance, approach, innovation), (2) technical innovation, (3) likelihood of the project producing preliminary data, (4) early stage investigator, (5) new HSDAIF user.
Selected applicants will be contacted by email. Projects can start on April 1, 2017 and must be completed by December 31, 2017.
For questions, more information, or technical consultation, contact Ingrid Brust-Mascher at email@example.com
Posted: November 22, 2016
Cellular and Molecular Imaging Core 3D Microscope Demonstration
The Cellular and Molecular Imaging Core in the Center for Health and the Environment will be hosting a microscope demonstration at CHE on December 9th. For additional information contact Patti Edwards.
Posted: September 9, 2016
Metabolomics Core: Pilot & Feasibility Program Applications sought.
The UC Davis Metabolomics core is establishing new services in stable isotope tracer and flux studies and is seeking a cohort of researchers with projects to assist in the development of these services. As such, they have released a call for Pilot & Feasibility Project Applications. Research areas may span biotechnology, agricultural research, cancer and biomedical studies, mechanisms in chemistry, pharmaceutical questions and other areas that involve small molecules. See the links for the Program Call and the Submission Form below for more information. Applications are due October 10, 2016.
The Pilot & Feasibility Program is funded by a recent investment in the Metabolomics Facility by the Research Core Facilities Program.
Posted: August 23, 2016
Research Core Facilities Program invests $2.1 million in designated facilities
The Research Core Facilities Program (RCFP), launched in 2015 by the Office of Research, is pleased to announce the recipients of $2.1 million in new funding to help strengthen the research infrastructure at UC Davis.
In its first year of operation, the RCFP developed the Campus Research Core Facilities Enhancement Funding Program to make strategic investments in shared research facilities. The goal of this program was to make funding available to support upgrades to instrumentation and the development of new research services to serve faculty, staff and students across the campus.
A request for proposals was issued in April 2016 to the 17 facilities that were recently designated as Campus Research Core Facilities (CRCF).
The following 11 proposals were approved for funding:
Short Term, High Impact Salary Support to Bring Two Fully-Funded, Game-Changing Microscopes Online, Light Microscopy Imaging Facility
Development and Implementation of Ultra-Long-Read Sequencing Protocols, DNA Technologies Core
Acquisition of an LC-Triple Quadrupole Mass Spectrometer for Open-Access Quantitative Analysis, Campus Mass Spectrometry Facility
Purchase of a New Cryoplatform for an Existing 600 MHz Nuclear Magnetic Resonance system, Nuclear Magnetic Resonance Facility
Request for Transmission Electron Microscope, BioEM Facility
Image Analysis Core for CMGI, Center for Molecular and Genomic Imaging
Applications Scientist to support new NIH Funded Orbitrap Fusion Mass Spectrometer, Proteomics Core
Operational Support for the Flow Cytometry Shared Resource, Flow Cytometry Shared Resource
Enhancing Keck Spectral Imaging Facility through Equipment Upgrade, Keck Spectral Imaging Facility
Establishing a UC Davis community for stable isotope tracer and cellular metabolism studies, Metabolomics Core
Acquisition of a Triple Quadropole ICP-MS for Advanced Research in the UC Davis Interdisciplinary Center for Plasma Mass Spectrometry, Interdisciplinary Center for Plasma Mass Spectrometry
A competitive review process was designed in close collaboration with the Research Core Advisory Council and the Academic Senate. Reviews of each proposal were conducted by at least three individual faculty, followed by a ranking of all proposals received during a panel discussion. Review criteria included a clear justification of how the proposed investment would strategically improve research infrastructure, accessibility and quality of service. In addition, facilities were required to demonstrate financial need for the requested resources.
The RCFP is now moving into its second full year of operations. The program anticipates a second call of applications for designating shared resource facilities that meet the established criteria. Another round of grants is also anticipated during the next fiscal year to meet the large demand for consolidated, high-quality research services for both on and off-campus users.
“It is tremendously gratifying to provide this first round of awards to our research core facilities that serve the largest number of faculty, staff and students across campus. These awards will significantly improve faculty competitiveness for extramural funding and will provide new opportunities for student training on state-of-the-art instrumentation,” said Harris Lewin, Vice Chancellor for Research.
“My congratulations and thanks to Director van Benthem, faculty and staff who worked so carefully and collaboratively to implement the strategic vision of this program.”
Posted: April 21, 2016
Imaging Flow Cytometry: Free Hands-on Workshop
When: May 2nd, all day (to sign up contact Katherine Ralston at firstname.lastname@example.org)
Where: MCB Imaging Core
What: Work with a specialist, one-on-one, run your own samples or discuss your potential applications
When: May 2nd, 9 am-4:30 pm (no sign-up required)
Where: GBSF Lobby
What: Learn about the new imaging cytometer now available in the MCB imaging core. Demo associated with the symposium “Game Changing Microscopy Across Biological Size Scales”
Posted: April 21, 2016
You are invited to the following event:
Monday, May 2, 2016 from 9:00 AM to 5:00 PM (PDT)
GBSF First Floor Auditorium
Davis, CA 95616
Join us for a day-long symposium to hear about the exciting new research being conducted on campus that is made possible with advanced light microscopy techniques. This event is open to the entire UC Davis scientific community to stimulate new collaborations and the exchange of ideas.
We hope you can make it! RSVP here.
MCB Imaging Core & HSD Advanced Imaging Facility
Posted: April 11, 2016
RNA-Seq Workshop – Library Preparation and Introduction to Data Analysis
May 10, 2016, 9 a.m. – May 12, 2016, 9 a.m. to 6 p.m.
Please see this page for the full information and the registration:
RNA-seq has revolutionized the way we address complex biological questions, allowing for differential gene expression, differential transcript analysis, as well as transcriptome assemblies. As sequencing output rapidly increases and sample numbers increase, library preparation becomes one of the major bottlenecks. This workshop provides comprehensive hands-on training in the preparation of high quality RNA-Seq libraries for the Illumina platform. Participants will generate two types of RNA-seq libraries: one using poly-A enrichment and one using ribo-depletion. The former protocol is preferred for high quality eukaryotic RNA samples. The latter is required for bacterial RNA-seq and fragmented RNA samples. Lectures will cover the entire workflow including sample QC/QA, as well as the basic principles of Illumina technology and considerations for experimental design meeting current publication standards. Approximately 6 hours will be spent on data analysis, presented by the Bioinformatics Core, and will include an introduction-to/demo-of RNA-seq data QA/QC, preprocessing, read mapping, gene counting as well as a hands-on-exercise on Differential Expression Analysis in R with previously computed gene counts tables.
Organizer – DNA Technologies Core
Launch of New Tool to Search for Instruments and Services
The Research Core Facilities Program has developed a dynamic database to assist researchers with finding instruments and services at laboratories across the campus. This tool provides inventory for over 450 devices and tests, searchable by keyword. The list of equipment will continue to grow as more facilities are added to the database.
Seventeen Labs Designated as Campus Research Core Facilities at UC Davis
The RCFP has initiated a process to designate certain laboratories across the university that provide shared research services as Campus Research Core Facilities. This designation provides a strategic platform to ensure state-of-the-art research capabilities are provided in a cost-efficient manner. The designated laboratories are expected to develop and represent best practices for core facility operation and emerge as centers of excellence for the university.Each lab designated as a Campus Research Core Facility will receive dedicated support from the program, including access to facility management software, marketing, and assistance with external contracting and negotiations. In addition, each facility is eligible for financial support for personnel and equipment. A list of the new designated CRCFs can be found here.The facilities were selected from 26 applications received in response to a campus-wide solicitation. An independent review panel consisting of faculty representing each college and professional school evaluated the applications. One key criterion for the core facilities is that they demonstrate a broad interdisciplinary impact, serving researchers from at least three colleges or professional schools.This initial group will serve as the model cohort in developing an improved support structure for shared research facilities at UC Davis. Opportunities for additional facilities to apply for the designation will be made available in the future.
Demo of Two Microscopes: Health Sciences District Advanced Imaging Facility – March 15-25. See the flier for technical details and to schedule a demo.
December 11, 2015: Save the date for a technical workshop:
“Preparing for Single Cell Genomics – Tips, Tricks and Secret Hacks to Improve your Success”
Friday December 11, 2015
UCDMC 10 a.m.-11:30a.m.
Davis 1:30 p.m.-3:30 p.m.
UC Davis Flow Cytometry Shared Resource
DNA Technologies Core at the UC Davis Genome Center
December 4, 2015: a Request for Application has been issued to apply for the designation of Campus Research Core Facility. Please follow this link for more information about the application and review process.
September 30, 2015: First meeting of the newly established Research Core Advisory Council (RCAC).