Proteomics Metabolomics Mass Spectrometry
Current RG Studies
Jenn Page (Chair) - University of California, San Francisco
Channabasavaiah Gurumurthy (Co-Chair) - University of Nebraska Medical Center
Pawel Bialk - Gene Editing Institute
Kym Delventhal (EB liaison) - HHMI Janelia
Jenn Page - University of California - San Francisco
Shondra Pruett-Miller - St. Jude Children's Research Hospital
Studies
Current Study:
Dear ABRF community,
Genome Editing Research Group (GERG) is pleased to invite interested researchers to participate in its research study.
The GERG study: Generating cell lines containing specific point mutations using CRISPR-Cas9 is a frequent request for genome engineering core facilities. In this study, we set out to compare the efficiency of point mutation generation using CRISPR with Cas9, Cas12a/Cpf1, and prime editing. This will be a multi-center study to evaluate the application of these newer tools for routine use at core facility laboratories to develop genome-edited cell lines.
Current status of the project: The experimental plan is completely designed, and the necessary reagents are procured. The experiments are being initiated at 5 independent laboratories.
What are we seeking from you? We hope to conduct this study at a greater number of laboratories, preferably up to 10. A larger number of participants and experiments will help evaluate the systems more robustly.
Participation details: We will provide the details of the cell culture experiments involving transfection, including all the necessary reagents and protocols. As a participant laboratory, you will do the cell culture experiments, collect samples, and ship them to a central laboratory for analysis. The central laboratory will perform the downstream experiments (such as NGS and other methods), and the data will be analyzed.
Benefits of participating in the study: We intend to publish the results, preferably in a peer-reviewed open-access journal. Researcher/s from the participating laboratories will have a chance to be included as authors in the article.
To get started or if you need more information: Contact abrf@abrf.org
We look forward to your participation!
Best Regards,
GERG
------------------------
GERG 2019 Study
Recent advances in genome engineering are allowing scientists to better understand biology by precisely deleting, editing, or tagging genomic DNA. The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas) system was first used to edit mammalian cells in 2013 and has grown in popularity ever since. Multiple guideRNA and Cas9 reagent formats can be used for editing cells. In this study, we compared three popular methods: 1. a plasmid expressing both the guideRNA and Cas9, 2. Cas9 protein combined with a synthetic single guideRNA, and 3. Cas9 combined with a 2-part guideRNA. In addition, the CRISPR/Cas system can be delivered to cells via lipofection or nucleofection transfection methods. This study aims to compare the efficiency of gene editing outcomes at 3 different genomic targets, 3 unique guideRNA reagent formats, and 2 delivery method across multiple labs. For the 2018 GERG study, the group performed a pilot study and found that the results varied considerably across the 4 sites. Three possible sources of the variation are: 1. researchers had different levels of experience with the different methods 2. the provided protocols (from the companies) were challenging to understand, and 3. each researcher only performed one replicate. In 2019, we wrote a standard protocol and repeated the experiments multiple times to more accurately evaluate the reproducibility of these methods. Determining which CRISPR reagent format is the most reproducible and has the highest gene editing outcomes will be beneficial for core facilities or research labs getting started with genome editing.
Results were presented in a poster at ABRF 2020: GERG Study 2019-2020: Reproducibility of indel formation rates by comparing guideRNA format and delivery method
GERG 2018 Reproducibility Study
In 2018, GERG initiated a study to evaluate the reproducibility of indel formation rates by comparing guideRNA format and cell delivery methods across multiple labs. Various configurations of guideRNA and Cas9 components can be used for editing cells. A few options include: a plasmid expressing both the guideRNA and Cas9, Cas9 protein combined with a synthetic single guideRNA, and Cas9 combined with a synthetic 2-part guideRNA. In addition, delivering these components to cells can be done using lipofection or nucleofection transfection methods. In the GERG 2017 survey (CRISPR/Cas9 Methods: Preferences from the Field), plasmid format and lipofection delivery were favored among cell culture users. Meanwhile, RNP format for the guideRNA and Cas9 is gaining in popularity in combination with nucleofection delivery. This study aims to evaluate cutting efficiency at 3 different guideRNA targets based on the guideRNA format and delivery method across multiple labs. Determining which method or format is the most reproducible will be beneficial. Core facilities or research labs getting started with genome editing could use these results as a benchmark for optimizing their own protocols.
Results were presented in a presentation at ABRF 2019: Reproducibility of indel formation rates by comparing guideRNA format and delivery method
Results were also presented in a poster at ABRF 2019: Reproducibility of indel formation rates by comparing guideRNA format and delivery method
GERG Survey 2017
The Genome Editing Research Group surveyed users of the CRISPR/Cas9 technology to help establish an understanding of preferred methods being used. As new core facilities are being formed to support the CRISPR/Cas9 technology, or existing cores have adapted their services to fit the technology into their workflows, considering what other cores are using is important. Questions regarding preferred guideRNA design tools, format of reagents, mutation analysis methods, and other relevant topics were included.
The collected data can be viewed here: https://www.surveymonkey.com/results/SM-ZBM5L6768/
Results were summarized in a poster and presented at ABRF 2018: CRISPR/Cas9 Methods: Preferences from the Field
| Name | Organization (during membership) | Member | Chair | Co-Chair |
| Channabasavaiah Gurumurthy | University of Nebraska Medical Center | 03-15 | 03-15 to 04-17 | |
| Kym Delventhal | Stowers Institute for Medical Research | 03-15 | 04-17 to 05-19 | |
| TJ Craddick | Georgia Institute of Technology, Emory University | 03-15 to 12-16 | ||
| Vittorio Sebastiano | Standford University | 05-15 to 12-16 | ||
| Eric Kmiec | Gene Editing Institute | 09-15 | ||
| Shondra Pruett-Miller | Washington University, St. Jude Children's Research Hospital | 12-15 | ||
| Timothy Dahlem | University of Utah | 07-16 | ||
| Elizabeth Sergison | Dartmouth College | 05-17 | 05-19 | 04-18 to 05-19 |
| Gerald Marsischky | Independent Consultant | 02-17 | ||
| Maureen Regan | University of Illinois at Chicago | 09-18 | 05-19 |
Questions or interest in joining an ABRF research group? Contact us!
- Benjamin Abrams - University of California Santa Cruz
- Constadina Arvanitis - Northwestern University
- Linda Callahan - University of Rochester Medical Center
- Richard Cole - Wadsworth Center
- Natalia Dworak - University of Virginia
- Joseph Dragavon - University of Colorado
- Corinne Esquibel - Van Andel Institute
- Kari Herrington - University of California, San Francisco
- Michelle Itano - University of North Carolina
- Justine Kigenyi (EB liaison) - Kansas University Medical Center
- Soyeon Kim - University of California, San Francisco
- Kristopher Kubow - James Madison University
- DeLaine Larsen - University of California, San Francisco
- Guillermo Marques - University of Minnesota
- Arvydas Matiukas - SUNY Upstate Medical University
- Valeria Mezzano, NYU School of Medicine
- Thomas Pengo - University of Minnesota
- Josh Rappoport - Boston College
- Mark Sanders - University of Minnesota
- Jian Wei Tay - University of Colorado
- Erika Wee - Cold Spring Harbor Laboratory
3D Image Analysis Tools and Reproducibility Event
Wednesday, April 27, 2022
Workshop breakout session recordings:
Nearly 100 attendees participated in this session on 3D image analysis tools and how they can help improve reproducibility, hosted by the Light Microscopy Research Group.
This event was centered around the LMRG’s ongoing study of reproducibility in 3D image analysis in which we seek to characterize and identify sources of (ir)reproducibility in 3D segmentation. Representatives from several major 3D analysis platforms walked attendees through how to segment and analyze the images from our study and discussed how their platforms support reproducible image analysis.
This program was targeted to people who are interested in learning more about a specific image analysis platform, learning how to use an image analysis tool better, and/or learning about how reproducibility is addressed by these platforms.
If you have questions about the LMRG study, please contact LMRG member Jessica Hornick for more information.
New LMRG Study - Volunteers Needed!
The Light Microscopy Research Group of the ABRF is launching a study to assess reproducibility in quantitative image analysis and needs YOUR help! We are seeking volunteers to segment 3D fluorescence microscope image sets and provide us with both their analysis and their analysis strategy. Our goal is not to find novel segmentation algorithms, but to compare segmentation results and strategies across a broad cross-section of volunteer analysts.
You can help by analyzing one (or more!) images for us! We need participants from all levels of image analysis experience. Everyone can participate - from students to core directors to image analysis experts. See our study website to find-out more: https://sites.google.com/view/lmrg-image-analysis-study
November 2020 ABRF LMRG/Industry Partner Discussion
The Light Microscopy Research Group and Corporate Relations Committee organized a conversation between light microscopy user groups and corporate partners, including Leica, Nikon, Olympus and Zeiss. This conversation provided an opportunity for each company to explain how they are being impacted by the COVID-19 pandemic and how they are adapting to the evolving needs of their customers.
Date: 11/18/2020
Time: 1:00-2:30 EST
View session recording.
Participants:
Ben Abrams, ABRF Light Microscopy Research Group and Corporate Relations Committee member, Director - Life Science Microscopy Facility Univ. of California Santa Cruz
Rich Cole, ABRF 2020 President, Light Microscopy Research Group member, Director - Advanced Light Microscopy & Image Analysis Core, New York State Dept. of Health Wadsworth Center
Joshua Rappoport, ABRF Light Microscopy Research Group member, Executive Director - Research Infrastructure at Boston College, Secretary – Core Technologies for Life Sciences
Michelle Itano, Director, UNC Neuroscience Microscopy Core Facility
Leica:
Greg Eppink General Manager Microscopy
Ryan Hrejsa, Senior Marketing Manager
Nikon:
Mike Gallo, General Manager, Service
Mike Johnson, Senior Regional Manager, Sales
Lynne Chang, Senior Marketing Manager
Olympus:
Shane Andrews, Manager, Sales Research Market, Life Science, Olympus Corporation of the Americas Scientific Solutions Group
Kerry Israel, Manager, Marketing Communications, Life Science, Olympus Corporation of the Americas Scientific Solutions Group
Zeiss:
Joseph Huff, Head of Marketing, North America, Zeiss Research Microscopy Solutions
Rosey Manser, Head of Business Development for Core Facilities
Studies
Activities
| 1) | ABRF2014 LMRG Group and CCMA Travel Award Winners - Richard Cole, John Russ, and Claire Brown (2,464K) - CCMA Travel Award Winners (1,934K) |
| 2) | ABRF2013 LMRG Photo - ABRF2013 LMRG Photo |
| 3) | ABRF 12 RG group photo - 2012 Meeting Group Photo |
| 4) | ABRF 12 RG intro talk - LMRG 2012 Overview Talk |
| 5) | ABRF 12 RG data talk - Study #2 Presentation (7,190K) |
| 6) | Proteomics workshop-- Get on Your Way to Microproteomics with laser Microdissection - Proteomics - Sarah Baxter |
| 7) | Proteomics workshop-- Sample prep - Tissue Proteomics Sample Preparation Leica Talk |
| 8) | ABRF 11 LMRG group photo - View Document (3,315K) |
| 9) | ABRF 11 RG talk - View Document (13,284K) |
| 10) | ABRF 2010 talk - View Document (4,643K) |
| 11) | Talk for ABRF 09 - View Document (10,567K) |
Protocols
| 1) | This is a paper written by Cole and Brown and gives a lot of background on how to measure point spread functions, why you may want to measure them, how to prepare bead slides and then a detailed protocol for setting up the instrument and measuring and interpreting the PSF. This article should be looked at first before referring to the specific protocols for the individual microscope platforms. - Nature Protocols Paper (1,371K) |
| 2) | PSF Protocol Leica SP5 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Leica SP5 |
| 3) | PSF Protocol Nikon A1 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Nikon A1 |
| 4) | PSF Protocol Olympus FV1000 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Olympus FV1000 |
| 5) | PSF Protocol Zeiss 510 - Measuring the PSF with the 0.175 um green fluorescent bead sample using the AIM software. - PSF Protocol Zeiss 510 |
| 6) | Spectral Accuracy Protocol Leica SP5 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. - Spectral Accuracy Protocol Leica SP5 |
| 7) | Spectral Accuracy Protocol Olympus FV1000 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. - Spectral Accuracy Protocol Olympus FV1000 |
| 8) | Spectral Accuracy Protocol Zeiss 710 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. Uses the ZEN software. - Spectral Accuracy Protocol Zeiss 710 (261K) |
| 9) | Spectral Accuracy Protocol Zeiss 510 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. Uses the AIM software. - Spectral Accuracy Protocol Zeiss 510 |
| 10) | Spectral Separation Accuracy Protocol Leica SP5 - Protocol for spectral separation testing of software un-mixing with double orange stained beads. - Spectral Separation Accuracy Protocol Leica SP5 - Bead Core Spectra Text File - Bead Ring Spectra Text File - Bead Core Spectra lsf File (12K) - Bead Ring Spectra lsf File (9K) |
| 11) | Protocol for testing the spectral separation accuracy of the Olympus FV1000. - Spectral Separation Protocol Olympus FV1000 (1,133K) |
| 12) | Study #1 Laser Stability, Alignment and Co-registration Protocol - Study #1 Laser Stability, Alignment and Co-registr |
| 13) | Improved GFP imaging in live cells - Improved GFP imaging in live cells |
Publications
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Microsc and Microanal. 2013 Dec;19(6):1653-68.
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Microsc Microanal. 2011 Aug;17(4):598-606.
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Nature Protocols 6 (2011):1929
| Member Name | Organization | Details |
|---|---|---|
| Pamela Scott Adams | Trudeau Institute | Ad hocEB Liaison: 02/09 - 03/10 |
| Carol J Bayles | Cornell University | Member: 04/08 - 05/15 |
| Claire M Brown | McGill University | Chair: 03/11 - 04/15 Member: 09/10 - 03/18 |
| Lisa Cameron | Duke University | Member |
| Richard Cole | Wadsworth Center | Chair: 03/08 - 03/11 |
| Arnold M. Falick | HHMI-UC Berkeley | Ad hocEB Liaison: 03/08 - 02/09 |
| Paul Furcinitti | UMass Medical School | Member: 05/13 - 12/14 |
| Anne-Marie Girard | Center for Genome Research and Biocomputing, Oregon State University | Member: 02/10 - 05/15 |
| William G Hendrickson | Univ. of Illinois, Chicago | EB Liaison: 09/13 - 04/14 |
| Jessica Hornick | Northwestern University | Member through 12/22 |
| Karen R Jonscher | University of Colorado Denver | Ad hocEB: 04/10 - 03/13 |
| Gary Laevsky | Princeton University | Member: 01/17-04/19 |
| Karen Martin | West Virginia University | Member: 12/08 - 05/15 |
| George McNamara | U Miami | Member: 06/11 - 03/13 Ad hoc: 03/13 - 12/14 |
| Kary Oakleaf | Molecular Probes, Life Technologies | Member: 06/13 - 12/14 |
| Cynthia Opansky | Blood Center of Wisconsin | Member: 02/09 - 12/13 |
| James Powers | Indiana University | Member through 12/22 |
| Joshua Rappoport | Northwestern University | Member: 03/15-01/19 |
| Katherine Schulz | Blood Center of Wisconsin | Member: 03/09 - 04/13 |
| Robert F. Stack | Wadsworth Center NYSDOH | Member: 02/09 - 03/11 |
| Marc Thibault | Ecole Polytechnique | Member: 06/11 - 03/14 |
| Erika Wee | McGill University | Chair: 04/15 - 05/18 |
| Frances Weis-Garcia | Memorial Sloan Kettering Cancer Center | EB Liaison: 05/14 - 04/15 |
Questions or interest in joining an ABRF research group? Contact us!
Metabolomics (MRG)
Metabolomics Research Group 2022 Study
- Compound Identification –
Consistent and accurate compound identification is a major challenge for LC/MS based metabolomics. The presence of multiple isomeric compounds, matrix effects, low and varying analyte concentration, and in source fragmentation and adduct formation are major contributing factors to this challenge. A combination of accurate mass MS1, MS2 fragmentation, and retention time (RT) of external standards is frequently used to provide a high confidence, though unconfirmed, compound identification. However, given this information (MS1, MS2, RT) it is unclear how much compound identification success will vary from lab to lab. The aim of this study is to quantify inter-personal and inter-lab variability of compound identification.
The target population of this study are PIs, trainees, and professional staff of metabolomics laboratories. More than one participant from each lab can participate so we can assess not only inter- but also intra-lab variability of compound identification accuracy.
The study participants are provided with two datasets. They have the option to return results for only one dataset or both datasets.
he study material can be downloaded as a single Zip file: https://osf.io/xbgc5/download. It consists of an Excel spreadsheet including instructions and a survey (MRG_CompoundID study.xlsx) and two mzML data files (MS1.mzML and ddMS2.mzML). The Excel file is used for returning results by email.
IMPORTANT: All results are submitted anonymously, identified only by an 8-digit identification number that you select.
Please return your results to mrgabrf2022@gmail.com no later than December 31, 2022.
If you have any questions please contact Ryan Sheldon or Chris Turck.
Mission
The aims of the Metabolomics Research Group are a) to educate research scientists and resource facilities in the analytical approaches and management of data resulting from comprehensive metabolite studies and b) to promote the science and standardization of metabolomic analyses for a variety of applications. Group efforts will also include conducting surveys and organizing sessions at the annual ABRF meeting to explore the current state of the art in the field and the organization of research studies.
Questions or interest in joining an ABRF research group? Contact us!
Metabolomics is the comprehensive profiling of metabolites and other small molecules. The large structural diversity of these compounds makes both comprehensive profiling and identification challenging. The major platforms are NMR and mass spectrometry, particularly LC/MS and GC/MS. There is currently a great variety of approaches, including untargeted profiling, targeted approaches, and fluxomics. Both semi-quantitative and quantitative approaches can be used. Challenges include identification of metabolites and how they change in relation to a biological perturbation (e.g. drug, diet, disease) and determining the biological significance of these changes. The Metabolomics Research Group consists of members from academic core and research laboratories, industrial analytical laboratories and providers of metabolomic services, analytical standards and instrumentation.
- Ryan Sheldon (Chair) - Van Andel Institute
- Amrita K. Cheema - Georgetown University
- Caroline Chidley - University of Massachusetts Chan Medical School
- Daniel Cuthbertson - Agilent Technologies
- Maryam Goudarzi - Sciex
- Tytus Mak - NIST
- Magnus Palmblad - Leiden University Medical Center
- Reza Salek - International Agency for Research on Cancer
- Chris W. Turck - Max Planck Institute of Psychiatry
- Sue Weintraub (Executive Board Liaison) - University of Texas Health Science Center at San Antonio
1. The Metabolomics Research Group has conducted another survey study to collect data on the current use of metabolomics technologies in core and research laboratories. Questions are designed to elicit responses concerning the current level of interest in the field of metabolomics. For those already offering/practicing metabolomics technologies we wanted to find out what instrumentation is used, types of application, etc.
A similar survey was conducted by the Metabolomics Research Group 10 years ago. Of particular interest was how the practice of metabolomics in core and research laboratories has changed over a decade. What technologies are used and what are the bottlenecks in the field?
- MRG2020 Survey Study Results
2. The Metabolomics Research Group has organized and finished its second study with a focus on strategies for the analysis of metabolomics data collected with high resolution mass spectrometry. Results of the study were presented at the ABRF 2017 conference in San Diego, CA. A manuscript summarizing the study has been accepted for publication in a Metabolites Special Issue.
- MRG2016 Study Results
- MRG2016 Study Announcement
3. The Metabolomics Research Group's second study focused on strategies for the analysis of metabolomics data collected with high resolution mass spectrometry. For study details and materials please consult the Instructions and Bioshare Data
repository.
4. The Metabolomics Research Group has organized and finished its first Research Study. Results of the study were presented at the ABRF 2014 conference in Albuquerque, NM. A manuscript summarizing the MRG study results has been accepted for publication in JBT.
- MRG2013 Study Announcement
- MRG2013 Amrita Cheema Presentation
- MRG2013 Study Results (18K)
5. The MRG has conducted a survey to collect data on the current use of metabolomics technologies in core facilities. Questions were designed to elicit responses concerning the current level of interest in the field of metabolomics, and for those already offering a metabolomics service to find out what instrumentation is used, types of application, etc. The results of the survey were presented at the ABRF2010 meeting during the MRG session.
1) MRG member Amrita Cheema's presentation at ABRF 2021
- ABRF Metabolomics Research Group Survey Study
2) MRG member Amrita Cheema's presentation at ABRF 2017
- ABRF Metabolomics Research Group Data Analysis Study
3) MRG member Amrita Cheema's presentations at ABRF2016
- Metabolomics: Challenges and Opportunities
4) The NIH ‘Common Funds Metabolomics Program’ held its first annual meeting in Ann Arbor, Michigan September 27-29, 2013 at Michigan Regional Comprehensive Metabolomics Research Core (MRC2). The program currently supports a variety of initiatives for increasing national capacity in metabolomics including three ‘Regional Comprehensive Metabolomics Research Cores’ (RCMRC), a ‘Data Repository and Coordination Center’ (DRCC), technology development, education and training grants and several administrative supplements. More information on initiatives can be obtained at http://commonfund.nih.gov/Metabolomics.
- Metabolomics Annual Program Meeting
5) MRG member Amrita Cheema's presentation at ABRF2013
- Applications of Metabolomics to Bio-medical research
6) MRG members Bill Wikoff, Vladimir Tolstikov and John Asara presented details on ongoing MRG Study, metabolomics core laboratories and research projects at ABRF2011.
- Bill Wikoff Presentation
- Vladimir Tolstikov Presentation
7) William Wikoff of the MRG organized a Satellite Workshop entitled 'An Introduction to Metabolomics' at ABRF2011. The workshop was intended for the scientist who wants an introduction to metabolomics, with an emphasis on practical, mass spectrometry-based approaches. The entire process of metabolomics, from study design to data processing and analysis was presented. Topics included: types of detectors and their relative merits for specific metabolomics applications(including standard and specialized instruments), methods for sample extraction peak integration, data alignment, software, and data analysis with an emphasis on selecting straightforward approaches appropriate for a given problem. Approaches to biomarker discovery and metabolomics in drug discovery were discussed and a review of selected case studies from the literaturewereincluded.
- ABRF2011 Satellite Workshop
8) The newly formed 'Metabolomics Research Group' held its first session at ABRF2010. Presentation topics included survey results and metabolomics core facilities.
- Chris Turck Presentation
- Tom O'Connell Presentation (3,731K)
- Pavel Aronov Presentation (628K)
- Vladimir Tolstikov Presentation (2,608K)
9) Bill Wikoff (MRG chair) organized the ‘Metabolomics Scientific Session’ at ABRF2010. Three prominent scientists in the field spoke about technologies and applications.
- Bill Wikoff Presentation
- Oliver Fiehn Presentation
- David Wishart Presentation
- Chris Beecher Presentation
| 1) | A positivenegative ion–switching, targeted mass spectrometry– based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue - Targeted metabolomics platform |
| 2) | Validated high quality automated metabolome analysis of Arabidopsis Thaliana leaf disks - Arabidopsis Thaliana metabolome analysis |
| 3) | Small molecule metabolite extraction strategy for improving LC/MS detection - Small molecule metabolite extraction (1,587K) |
| Member Name | Organization | Details |
|---|---|---|
| Dr. Pavel Aronov | Stanford University | Member: 03/09 - 03/12 |
| Dr. John M Asara | Beth Israel Deaconess Medical Center | Member: 03/10 - 03/15 |
| Stephen Brown | Member: - 3/15 | |
| Dr. Christopher Colangelo | Primary Ion | EB Liaison: 03/15 - 03/18 |
| Dr. Nathan Dodder | NIST | Member: 03/09 - 03/10 |
| Dr. Brenda Kesler | Thermo Fisher Scientific | Member: 03/09 - 02/11 |
| Dr Thomas Neubert | New York Univ Sch of Med | Member: 03/14 - 03/15 Liaison: 03/13 - 03/14 |
| Dr Thomas M. O'Connell | University of North Carolina | Member: 03/09 - 11/10 |
| Dr. Andrew Patterson | Penn State University | Member: 04/14 - 03/17 |
| Dr. Brett S Phinney | Proteomics Core UC Davis Genome Center | EB Liaison: 02/11 - 03/12 |
| Prof. Vladimir Shulaev | University of North Texas | Member: 03/10 - 03/13 |
| Jack Simpson | EB Liaison: 04/12 - 03/13 | |
| Dr. Vladimir V. Tolstikov | UC Davis Genome Center | Member: 03/09 - 05/12 |
| Chris W Turck | Max Planck Institute of Psychiatry | Ad hoc: 02/11 - 05/12 EB Liaison: 03/10 - 02/11 |
| Baljit Kaur Ubhi | Sciex | Member through 12/21 |
| Dr. William R. Wikoff | University of California, Davis | Chair: 03/10 - 05/12 Member: 03/09 - 03/10 Member: 05/12 - 03/13 |
Questions or interest in joining an ABRF research group? Contact us!
Metagenomics and Microbiome (MMRG)
Mission
Many of the Members on the MMRG have been involved in microbiome analysis for over 20 years and have a strong appreciation for the field. They are dedicated and understand the needs of this new and exciting field that continues to grow at an exponential rate.
Call for Members:
The ABRF Microbiome and Metagenomics Research Group (MMRG) is seeking to expand its membership. The research group focuses on both general and special topics in all aspects of microbiome sciences including study design, surveys, lab methods and results, disruptive technologies, and commercial product characterization. We are seeking new members who have bandwidth to contribute to our study topic.
Please join our exciting and rewarding research team. Contact us to learn how you can join the MMRG ....
The ABRF Metagenomics and Microbiome Research Group is composed of Core lab managers, bench scientists, and bioinformaticists. The goals of the MMRG will be to establish and evaluate techniques that core laboratory operators, directors, managers, and users commonly ask. Initial studies include assembling microbial standards and to characterize shortcomings of current metagenomic techniques. this includes optimizing DNA extraction protocols, library synthesis methods for different NGS platforms and developing best approaches for bioinformatics. The development of bacterial cocktails includes working with specific vendors in the field to establish a bacterial counting platform (similar to simple low cost mammalian cell counters) that can be used for low cost, high speed bacterial cell counting as needed for both research and clinical metagenomic quality control requirements. This enumeration device will be validated against standard techniques such as flow cytometry, Microscopic, and LSC techniques. Development of a fixation technique that preserves DNA and RNA without cell leakage is also required. We intend to work very closely with the appropriate vendor of the field to help advance this technology.
- Scott Tighe (Co-Chair) - Vermont Cancer Center
- Ravi Ranjan (Co-Chair) - University of Massachusetts Amherst
- Ebrahim Afshinnekoo - Weill Cornell Medical College
- Nadim Ajami - Baylor University
- Don A. Baldwin - MicroPath ID Diagnostics
- Nathan J. Bivens - University of Missouri
- Russ Carmical - UTMB - Galveston
- Christina Cartaciano - University of Michigan
- Sridar Chittur - SUNY Albany (Executive Board liaison)
- Caryn Evilia - Idaho State University
- Stefan J. Green - University of Illinois at Chicago - DNAS Facility
- Ian Herriott - University of Alaska Fairbanks
- Jessica Hoffman – Vermont Cancer Center
- Joshua R. Hyman –University of Wisconsin - Madison
- Sarah Johnson - Georgetown University
- Samantha Joye - University of Georgia
- Kevin Knudtson - University of Iowa
- Jodie Lee (Ad hoc) - Qiagen
- Shawn Levy - HudsonAlpha Institute for Biotechnology
- Christian Lytle – Giesel School of Medicine at Dartmouth
- Christopher E. Mason - Weill Cornell Medical College
- Lisa Mattei, The CHOP Microbiome Center
- Ken McGrath - Australian Genome Research Facility
- Dev Mittar – ATCC Microbiology Systems
- Natalia G. Reyero Vinas - Mississippi State University
- Rachid Ounit – University of California, Riverside
- Matthew L. Settles - University of Idaho
- Alexander J. Spicer – Sheffield Hallam University
- Kelley Thomas - Hubbard Center for Genome Studies
Ongoing 2021-2022:
Estimating the lowest DNA input for mitigating confounding contaminants in library preparation kit used for shotgun metagenomics
2019 - 2020
Evaluation of rapid DNA library preparation kit for shotgun metagenomics studies
(Phased out due to COVID-19)
The study aimed to evaluate and benchmark the performance of rapid DNA library kits for shotgun metagenomics. The general criteria for kits evaluated in this study was based on - variable range of input DNA, enzymatic or transposase-based fragmentation method, one bead clean-up. We also planned to prep libraries using TE or MQ water to establish baseline data for negative controls and the “kitome”. With this study the MGRG aimed to provide a platform to compare the kits for - efficiency, reproducibility, total time, quality, sequencing outcomes, using known DNA known standards, which will be beneficial to the research community.
2020 ABRF Annual Meeting: Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrity.
2017 ABRF Annual Meeting. McIntyre A. Life at the Extreme: The ABRF Metagenomics Research Group. Implementing New Standards in Metagenomics and the Extreme Microbiome Project.
2016 ABRF Annual Meeting. Baldwin DA. Life at the Extreme: The ABRF Metagenomics Research Group. Implementing New Standards in Metagenomics and the Extreme Microbiome Project.
The 2103 NARG study evaluated many DNA extraction techniques against specific bacteria. Results describe the efficiency of each technique.
Presentation from the 2014 ABRF Metagenomics session describing proper use of controls for metagenomics studies
Poster MGRG and XMP - Albany New York
2015 MGRG poster: Life at the extreme.
2020 ABRF Annual Meeting, Tighe S. Close Encounters of the Third Kind Circumventing the Effects of Extraterrestrial DNA.
2019 ABRF Annual Meeting, Tighe S. Characterizing the Whole Cell Microbial Reference Standard using RNA and DNA-Sequencing.
2017 Current Innovations for Metagenomics used in Antarctica.
2017 Straight up, with a Twist: Innovative Enzyme Cocktail to Improve DNA extractions of Metagenomic Samples
2017 An automated low-volume, high-throughput library prep for studying bacterial genomes.
2017 Metagenomic Analysis using the MinION Nanopore Sequencer.
2017 Metasub-"Metagenomics Across the World's Cities.
2016 Standardizing Metagenomics: a Novel Class I Microbial Reference Standard and Improved DNA Extraction Using a Multicomponent Enzyme Reagent.
2015 Development of New Standards for Metagenomics and the Extreme Microbiome Project (XMP).
2014 Challenges and Controls in Metagenomics
| Extreme Microbiome Project Website - View Document |
| The Pathomap project is authored by many of the MGRG members - View Document |
2019 Tighe S. Metagenomics Research Group Study: Characterizing The Whole Cell Microbial Reference Standard Using RNA and DNA-Sequencing. J Biomol Tech. 2019 Dec;30(Suppl):S55.
2017 Mason CE, Tighe S. Focus on Metagenomics. J Biomol Tech. 2017 Apr;28(1):1.
2017 Tighe S, et al., Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). J Biomol Tech. 2017 Apr;28(1):31-39
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