The RNA Transcript, September 7, 2020 |
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Dear Colleagues,
While the COVID-19 pandemic has been causing major disruptions as well as many inconveniences, it also offers some new opportunities; perhaps now is the most opportune time to make new interpersonal connections, start new scientific collaborations, and broaden one’s horizons by learning from others. Through our activities below, we aim to support the community of U-M RNA scientists, to help us lead the solutions to the most pressing and transformative biological and medical needs as exemplified by the positive-strand, single-stranded RNA virus SARS-CoV-2. We are here to support you in connecting and creating synergies that lead to innovative research across disciplines, yielding collaborative grants and impactful research, as follows:
• An outstanding series of RNA Innovation Seminars featuring high-profile US and international scientists, enabled by the ability to bring them to campus remotely. Depending on the individual speaker’s time zone, seminars will take place on Mondays at 9:00 am or 4:00 pm.
• The Student and Postdoc Council is resuming its Journal Club that will highlight papers of upcoming speakers. Meetings take place Thursdays at 4:00 pm.
• The international RNA Collaborative Seminar Series, which now links 16 RNA research centers throughout the US and the world, will continue every other Wednesday at 4:00 pm through the fall.
• By the end of September, you will receive an electronic version of our first annual magazine, RNA Translated, that focuses on RNA viruses research at the U-M. The magazine also serves an annual report that features the Center’s achievements for the 2019-20 period.
• As always, we will send The RNA Transcript every Monday morning, to help you plan your week and keep you informed of the Center’s for RNA Biomedicine members’ achievements.
• We invite you to also join us on Twitter, @umichrna.
We welcome back our community from the summer break and ask you to share your accomplishments with us and the RNA community: please contact Martina Jerant, Center Manager, or Elisabeth Paymal, Public Relations Specialist.
We’re looking forward to this most unusual semester, since together - we solve!
Nils G. Walter and Mats Ljungman
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Wednesday, September 9, 4:00–5:00 pm |
Moderator: Mats Ljungman, Ph.D
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"Same Same Different: Single cell RNAseq identifies conserved and divergent features of mammalian spermatogenesis"
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Justin Colacino, Ph.D. "Single cell transcriptomic profiling to understand breast stem cell heterogeneity in development and cancer disparities"
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Wednesday, September 9, 1:30– 3:00 pm | MIDAS Faculty Research Pitch
Join the very first MIDAS faculty research pitch session. Find out about exciting data science research that is happening at U-M, explore collaboration opportunities and student research opportunities. Faculty members will each give a 3-minute lightning talk, and there will be a 30-minute networking session. All U-M faculty, staff and students are welcome to attend.
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“A small RNA based innate immune system”
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A line up of outstanding RNA scientists from the US and around the world. All times are EDT.
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Monday, September 21, 4:00 pm, Andrey Krasilnikov, Penn State
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Monday, September 28, 9:00 am, Hiroaki Suga, University of Tokyo, Japan
- Monday, October 5, 4:00 pm, Chase Weidmann, Washington University School of Medicine in St. Louis
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Monday, October 19, 4:00 pm, Gene Yeo, University of California, San Diego
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Monday, October 26, 9:00 am, Aleksandra Filipovska, University of Western Australia, Australia
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Monday, November 9, 9:00 am, Jeff Twiss, University of South Carolina
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Monday, November 16, 4:00 pm, Michelle Hastings, Chicago Medical School, Rosalind Franklin University of Medicine and Science
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Monday, December 7, 4:00 pm, John Mattick, Garvin Institute of Medical Research, RNA Biology and Plasticity Lab, Darlinghurst, Australia
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Monday, December 14, 4:00 pm, Narry Kim, Seoul National University
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Monday, January 25, 2021, 4;00 pm, Elena Conti, Max Planck Institute of Biochemistry, Germany
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Our members' publications are available through Altmetric. Five queries are currently available: "RNA," "microRNA," "Transcriptome," "Translation," and "Molecule." Please make sure to have at least one of these key words in your title or abstract. Below are recent highlights.
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Direct kinetic fingerprinting and digital counting of single protein molecules, Tanmay Chatterjee, Achim Knappik, Erin Sandford, Muneesh Tewari, Sung Won Choi, William B. Strong, Evan P. Thrush, Kenneth J. Oh, Ning Liu, Nils G. Walter, and Alexander Johnson-Buck, PNAS, August 31, 2020 https://doi.org/10.1073/pnas.2008312117
Illustration: Kinetic fingerprinting with dynamically binding fluorescent antibodies (cyan with red glowing orb) distinguishes between the repetitive binding to a specific target protein (left) and the less repetitive nonspecific binding to other proteins (right) captured on a surface using conventional IgG antibodies (blue Y-shaped molecules, bottom). The highly specific single-molecule detection of this approach provides approximately 100-fold higher sensitivity than conventional protein detection assays such as ELISA.
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Taken together, these findings suggest that C-terminal sequences outside of the repeat region may alter the behavior and toxicity of dipeptide repeat proteins derived from GGGGCC repeats.
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T Paulsen, Brian Magnuson, Mats Ljungman, Daeyoon Park, Chi Zhang, Zachary T Campbell, Aaron C Goldstrohm and Peter L Freddolino, RNA, a publication of The RNA Society, August 4, 2020, doi:10.1261/rna.077362.120
By integrating our results with prior knowledge, we developed a ‘rulebook’ of key contextual features that differentiate functional vs. non-functional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
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Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics, MiYang, Francesca Petralia, ZhiLi, Hongyang Li, Weiping Ma, Xiaoyu Song, Sunkyu Kim, Heewon Lee, Han Yu, Bora Lee, Seohui Bae, Eunji Heo, Jan Kaczmarczyk, Piotr Stępniak, Michał Warchoł, Thomas Yu, Anna P. Calinawan, Paul C.Boutros, et al., Cell Systems, Volume 11, Issue 2, 26 August 2020, Pages 186-195.e9, https://doi.org/10.1016/j.cels.2020.06.013
Highlights
- Crowdsourcing of methods to predict (phospho)proteins from DNA and RNA
- Unbiased assessment uncovers best practices
- Proteins in metabolic pathways and complexes best and worst predicted, respectively
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Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change, Ameya P.Jalihal, Sethuramasundaram Pitchiaya, LanboXiao, Pushpinder Bawa, Xia Jiang, Karan Bedi, Abhijit Parolia, Marcin Cieslik, Mats Ljungman, Arul M. Chinnaiyan, Nils G.Walter, Molecular Cell (2020),
A pink cell experiences a gradient of salt levels, depicted as crystals. In response to changes in external salt levels, “clouds” of protein form by phase separation. These protect against the dehydrating effects of salt.
Our illustration made the cover of Molecular Cell!
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Postdoctoral Fellowship at Bio-Rad, Ann Arbor, MI
Bio-Rad is seeking an independent scientist in Biochemistry for a 12-month Postdoctoral Fellowship in the Technology Development Group. You will be a key contributor innovating molecular biology solutions and workflows for Bio-Rad’s new suite of Digital Biology tools. These platforms will be leveraged to change the world’s ability to resolve disease biology with unprecedented resolution, ease, and speed.
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Study abroad at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, Germany
HIRI is the first research institution worldwide to specifically investigate the role of RNA in infection processes. Our goal is to exploit the enormous potential of RNA as a diagnostic, preventive and therapeutic agent in the development of new strategies to combat infectious diseases.
This call closes on October 11
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