Enhancing Research, Rigor and Reliability
Issue 1, November 2022
Featured
Flow Cytometry Core Facility – ISAC Recognized Outstanding Shared Resource Lab
FCCF is one of ten labs to become recognized in 2022. The recognition program is supported by the International Society of Advancement of Cytometry (ISAC) and is intended to promote sustained achievement of excellence in SRL operations while acknowledging these accomplishments, financial benefits, and access to development opportunities. This will be a valuable endorsement for UVA investigators utilizing the flow cytometry core and future funding of new technologies within the FCCF.
Services & Technology
Advanced Microscopy Core
AMF recently purchased Zeiss Lightsheet 7 Microscope for multiview imaging of living and optically cleared specimens up to 2cm in size at subcellular resolution given any refractive index between 1.33 – 1.58. Microscope allows live cell imaging thanks to the sample chamber providing heating, cooling and CO2 supply. https://med.virginia.edu/advanced-microscopy-facility/equipment/lightsheet-microscopy/
Molecular Electron Microscopy Core
The Molecular Electron Microscopy Core (MEMC) is offering structure modeling using the artificial intelligence program AlphaFold. The MEMC can generate AlphaFold models of large proteins and protein complexes that are unavailable in the public database. The MEMC can also assist with interpretation of the models and experimental design using AlphaFold. Below is model of a receptor in complex with a heterotrimeric G protein. The model is colored by confidence score (dark blue: high-confidence to red: low-confidence).
Bioinformatics Core
Bioinformatics core in collaboration with GATC has developed and optimized a new single-cell analysis pipeline for the single-cell library prepared by the Parse Bioscience protocol https://www.parsebiosciences.com/technology). Parse Bioscience protocol “harness the power of combinatorial barcoding” allows users to sequence a few hundred thousand cells in one experiment. Bioinformatics core has also optimized and added a new popular trajectory analysis pipeline PHATE (https://www.nature.com/articles/s41587-019-0336-3) to the existing single cell data analysis pipeline for “visualizing structure and transitions in high-dimensional single-cell biological data”.
Biomolecular Analysis Facility
The BAF Core now offers SEC-FPLC as a service in the Shared Instrument section with the addition of an AKTA Pure 25L system and a 5mm x 15cm column capable of separating proteins in the 10-600kDa range. The service can be accessed in iLab under the HPLC/FPLC project (you can choose either type of separation). The new system can accommodate various types and lengths of columns so users can provide their own and we will work with them.
https://uva.corefacilities.org/sc/3485/biomolecular-analysis-facility/?tab=services
Biorepository and Tissue Research Facility
BTRF has successfully launched NanoString GeoMx Digital Spatial Profiler (DSP) Service.NanoString GeoMx DSP, an advanced analytic platform to our instrumentation portfolio via an ETF purchase. The GeoMx DSP enables spatially resolved, high-plex (10s -10,000s) digital quantitation of proteins and mRNA in tissue. The distribution of protein or gene expression can be visualized across multiple tissue compartments. It also provides a complete analyses system for identifying biomarkers and pathway analyses to understand disease mechanisms of action and identify novel targets. To find out more please visit: BTRF November Newsletter
Spatial Biology Core
Isoplexis for Single-Cell Secretome Analysis
Isoplexis allows single-cell secretome analysis by monitoring multiple cytokines at high intensity. The platform offers a variety of panels for humans and mice, and you can track more than 30 cytokines simultaneously. We can analyze 30,000 cells per chip from different sources: PBMC, processed tissue, urine, or other biological fluids. Cells can be doubly labeled and monitored in real time individually.
For more information contact Dr. Ana de Oliveira, SBC Core Director ak4yj@virginia.edu
Spatial Biology Core
The stem cell culture lab is backIf you have plans to start a project using iPSC technology or keep on with an ongoing project, we can provide scientific support and appropriate facilities for cell culture. Also, we made a partnership with STEMCELL Technologies, which will also provide scientific support and promotional prices in the first months of the project.
For more information contact Dr. Ana de Oliveira, SBC Core Director ak4yj@virginia.edu
Spatial Biology Core
New Technology – Multiplex Analysis – Single-Cell Resolution
The ZellScannerOne from Canopy can marker more them 20 markers using an optical imaging method based on staining and bleaching cycles that allow multiplexed imaging. The Spatial Analysis predicts morphological features associated with biomarker expression in target tissue sections in a single-cell resolution. Resolution = 500 microns per pixel . It is applicable to Fresh Frozen Tissue, FFPE, TMA and Suspension Cells from any biological fluid.
To find out more please visit: SBC November Newsletter
Genetically Engineered Murine Model Core
The Mouse Line Cryopreservation Service Has Returned to Business as UsualThe GEMM paused its cryopreservation service for Sept and Oct due to the supply-chain caused delay in delivery by the manufacturer of a newly purchased liquid nitrogen storage dewar. For those labs that have been waiting for cryopreserving their mouse lines, please resume submitting requests in iLab and transferring mice via CCM. We have purchased a larger dewar that hopefully will meet the need for cryopreservation for years.
Read more: GEMM November Newsletter
People
Advanced Microscopy Facility – New Director
Dr. Sijie Hao joined Advanced Microscopy Facility as a Core Director at the end of September.Dr. Hao received his PhD in Bioengineering from Pennsylvania State University. Before coming to UVA Dr. Hao was a Core Facilities Manager at University of Maryland (College Park, MD). https://med.virginia.edu/advanced-microscopy-facility/contact/
Exercise Physiology Core Lab – Welcome Back Shannon Wells
The EPCL welcomes (back) a new (former) staff member. Shannon Wells, M.Ed returned to the EPCL August 2022 after a 6 year hiatus to focus on her family. Now that her little ones Henry and Emma are in 1st grade and kindergarten, Shannon was ready to come back to work. She replaces Nicole Huebner, who moved to Atlanta in June. The EPCL also welcomes a new graduate research assistant Jeison De Guzman. Jeison is a graduate student in Exercise Physiology and hopes to begin medical school fall 2023.
Molecular Imaging Core – Director Search
Dr. Stuart Berr is stepping down from the Director of Molecular Imaging Core position end of January 2023. We are actively recruiting candidates for this position. Two candidates will visit UVA to give a seminars. To find out more please visit: https://med.virginia.edu/core-facilities/seminar-announcements/
Seminars & Workshops
Flow Cytometry Core Facility – Cell Sorting Course
The Sony MA900 Cell Sorter is up and running and can be scheduled in ilab. The UVA Flow Core is now offering users to perform their own sorts on the new Sony MA900. This will allow you to sort without the need to schedule or wait for flow core staff availability and perform afterhours sorts if needed. For unassisted cell sorting we require a one-day cell sorting course, didactic and hands on, followed by one or two one-on-one training with flow core staff.Course description can be found on our website https://med.virginia.edu/flow-cytometry-facility/flow-cytometry-training-courses/
Advanced Microscopy Facility – Instrument of the Month Workshop
The Instrument of the Month workshop highlights one of the state-of-the-art microscopes hosted by AMF. The workshop lasts one day and is held on the first Friday of each month. The morning session features a lecture covering fundamental concepts such as fluorescence microscopy, sample preparation, and imaging data analysis, as well as advanced microscopy applications such as tissue clearing, TIRF, spectral unmixing, two-photon, lightsheet, and super-resolution. The afternoon session consists of hands-on operating activities of the Instrument of the Month to reinforce learning. The workshop uses a small-group approach to provide opportunities for better participation and more individualized feedback and support. Contact us today to sign up for the workshop. Send your specific inquiries to AMF to learn more details.
Other Announcements
Biorepository and Tissue Research Facility
After carefully analyzing increased materials and overhead costs 2021-2022, we’ve made the decision to increase our prices on all items by 5%. This change will go into effect on November 1st, 2022. We appreciate our customers and are grateful for the business they do with us.
Genome Analysis and Technology Core
Dr. Sol-Church from the Genome Analysis and Technology Core launched a new Single Cell Genomics User Group to accelerate single cell research at UVA. Katia’s goal will be to integrate the flow core preparative and Bioinformatics core analytical pipelines and provide unique educational and method sharing/collaborations opportunities to the UVA scientists. The inaugural user group meeting took place in Sept and was attended by more than 60 individuals. An overview of the GATC single cell services and highlights of research performed by core users was presented. Experts from 10X genomics and BioLegend presented their latest release in reagents for single cell transcriptomics and new technologies available for spatial transcriptomics. For more information please contact Dr. Sol-Church ks5uq@virginia.eduIf you’re interested, you can join using this link:https://join.slack.com/t/singlecellomicsatuva/shared_invite/zt-1g95xv97k-Yls0dcVPbEfBnHiurlE1yA.
Cores
Advanced Microscopy FacilityBioinformatics CoreBiomolecular Analysis FacilityBiomolecular Magnetic Resonance FacilityBiorepository and Tissue Research FacilityExercise Physiology Core LaboratoryCenter for Human Therapeutics cGMPFlow Cytometry Core FacilityGenome Analysis and Technology CoreGenetically Engineered Murine Model (GEMM) CoreMolecular Electron Microscopy CoreMolecular Imaging CoreMolecular Immunologic & Translational Sciences (MITS) CoreMolMartRadiochemistry CoreResearch Histology Core