The RNA Transcript, October 11, 2021 |
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Spark new ideas and catalyze energies
toward your next collaborative RNA grant proposal.
Grant Sprints create a space and time for collaboration and innovative thinking. They facilitate the concept, ideation, and grant writing process between experts from different fields. These brainstorming sessions are free, tailored to specific requests and goals, and offered to all our members. For detailed information and help on your next proposal, contact Martina Jerant (mjerant@umich.edu).
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Present your research at the international
RNA Collaborative Seminar Series
Application deadline, today, Monday, October 11
We are hosting an RNA Collaborative Seminar on Wednesday, January 26, 2022, at 4:00 pm ET. We are seeking self-nominations from Center members. To be considered, please contact Martina Jerant (mjerant@umich.edu) with your name, title, department, and a brief abstract by October 11, 2021. Postdocs and Junior Faculty are encouraged to apply.
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Monday, October 11, 1:00–2:00 pm ET, BSRB - ABC Seminar room | University of Michigan, Chromatin Club Seminar Series
"Prions - an extreme form of epigenetic inheritance"
"Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamin 1"
Trainee talk: Lindsay Moritz (Hammoud lab), Human Genetics
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Monday, October 11, 4:00–5:30 pm ET, 1640 Chemistry Dow Lab | University of Michigan, Department of Chemistry
"Integrative structural biology of telomerase"
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Tuesday, October 12, 10:00 am ET, ZOOM | German Research Foundation, Condensate Colloquium Series
"Condensate RNA-binding proteins act as matchmakers for protein complex assembly"
"Viscoelastic protein-RNA condensates with programmable mechanics"
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Tuesday, October 12, 12:00–1:00 pm ET, hybrid: 3330 MS I and ZOOM | University of Michigan, Department of Biological Chemistry
"Targeted DNA Integration Without Double-Strand Breaks Using CRISPR RNA-Guided Transposases"
Hosts: Yan Zhang and Nils Walter
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Wednesday, October 13, 12:00 pm ET | ZOOM | AAAS Seminar
"Improving hereditary cancer diagnostics using RNA sequencing: Lessons from a 43K patient study"
Rachid Karam, M.D., Ph.D., Ambry Genetics, Aliso Viejo, CA
Moderator: Jackie Oberst, Ph.D., Science/AAAS, Washington, DC
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Thursday, October 14, 12:00–3:00 pm ET, Zoom | University of Michigan, Protein Folding Diseases Initiative
"8th Annual Protein Folding Diseases Initiative Symposium"
Keynote speaker: Martin Kampmann, Ph.D., Associate Professor, UCSF, Investigator, Chan Zuckerberg Biohub, Paul G. Allen Distinguished Investigator, University of California, San Francisco.
Talks by Yang Zhang, Ph.D., Professor of Computational Medicine and Bioinformatics and Professor of Biochemistry, University of Michigan and Shyamal Mosalaganti, Ph.D., Assistant Professor in LSI, Cell and Developmental Biology and Biological Chemistry, University of Michigan.
Presentations will also be given by top three Young Investigators
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Thursday, October 14, 12:00 pm ET, hybrid, Forum Hall, Palmer Commons and ZOOM | University of Michigan, Life Sciences Institute Seminar Series
“The mitotic midbody is a novel class of RNA granule and unique extracellular vesicle necessary for intercellular communication”
Ahna Skop, Ph.D. Professor of Genetics University of Wisconsin-Madison
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Monday, October 18, 4:00 pm ET, ZOOM REGISTRATION | University of Michigan Center for RNA Biomedicine, RNA Innovation Seminar Series
“Imaging single-mRNA translation dynamics in living color”
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January 3–6, 2022, St. Petersburg, Florida | The RNA Society
6th Conference on Regulating with RNA in Bacteria & Archaea — CRISPR systems, small noncoding RNAs, riboswitches, transcriptomics, host-pathogen interactions, and more.
The deadline for early registration and submission of oral abstracts is October 31, 2021; poster abstracts will be accepted through November 15, 2021.
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For press releases and blog articles about your upcoming top journal publications, please
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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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Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor, KunalKhanna, Shankar Mandal, Aaron T.Blanchard, Muneesh Tewari, Alexander Johnson-Buck, Nils G.Walter, Biosensors and Bioelectronics, Volume 190, 15 October 2021, 113433, https://doi.org/10.1016/j.bios.2021.113433
Highlights:
• Amplification-free single-molecule kinetic fingerprinting identifies diverse disease biomarkers.
• A dynamic DNA nanosensor generates kinetic fingerprints via intramolecular single-molecule FRET.
• iSiMREPS in 10 s detects biomarkers with a limit of detection of ~3 fM in 1,000,000-fold WT excess.
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Long Noncoding RNAs in Plants, Wierzbicki A T, Blevins T, Świeżewski S, Annual Review of Plant Biology, Vol. 72:245-271 (Volume publication date June 2021)
Abstract: Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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G-CSF secreted by mutant IDH1 glioma stem cells abolishes myeloid cell immuno-suppression and enhances the efficacy of immunotherapy, Mahmoud S. Alghamri, Brandon L. McClellan, Ruthvik P. Avvari, Rohit Thalla, Stephen Carney, Margaret S. Hartlage, Santiago Haase, Maria Ventosa, Ayman Taher, Neha Kamran, Li Zhang, Syed Mohd Faisal, Felipe J. Núñez, María Belén Garcia-Fabiani, Wajd N. Al-Holou, Daniel Orringer, Shawn Hervey-Jumper, Jason Heth, Parag G. Patil, Karen Eddy, Sofia D. Merajver, Peter J. Ulintz, Joshua Welch, Chao Gao, Jialin Liu, Gabriel Núñez, Dolores Hambardzumyan, Pedro R. Lowenstein, Maria G. Castro, Science Advances, 29 Sep 2021, Vol 7, Issue 40, DOI: 10.1126/sciadv.abh3243
Abstract: Mutant isocitrate-dehydrogenase 1 (mIDH1) synthesizes the oncometabolite 2-hydroxyglutarate (2HG), which elicits epigenetic reprogramming of the glioma cells’ transcriptome by inhibiting DNA and histone demethylases. We show that the efficacy of immune-stimulatory gene therapy (TK/Flt3L) is enhanced in mIDH1 gliomas, due to the reprogramming of the myeloid cells’ compartment infiltrating the tumor microenvironment (TME). We uncovered that the immature myeloid cells infiltrating the mIDH1 TME are mainly nonsuppressive neutrophils and preneutrophils. Myeloid cell reprogramming was triggered by granulocyte colony-stimulating factor (G-CSF) secreted by mIDH1 glioma stem/progenitor-like cells. Blocking G-CSF in mIDH1 glioma–bearing mice restores the inhibitory potential of the tumor-infiltrating myeloid cells, accelerating tumor progression. We demonstrate that G-CSF reprograms bone marrow granulopoiesis, resulting in noninhibitory myeloid cells within mIDH1 glioma TME and enhancing the efficacy of immune-stimulatory gene therapy.
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Representation of molecules for drug response prediction, Xin An, Xi Chen, Daiyao Yi, Hongyang Li, Yuanfang Guan, Briefings in Bioinformatics, 2021; bbab393,
Abstract: ... This review is dedicated to the application of machine learning in drug response prediction. Specifically, we focus on molecular representations, which is a crucial element to the success of drug response prediction and other chemistry-related prediction tasks. We introduce three types of commonly used molecular representation methods, together with their implementation and application examples. This review will serve as a brief introduction of the broad field of molecular representations.
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