The RNA Transcript | August 14, 2023

Summer 2023

The RNA Transcript is published monthly during Summer 2023. Click here to review past editions to add to your summer reading list! Weekly publication will resume in September.

Seminars

RNA Collaborative Seminar

Zhejiang University (ZJU) Center for RNA Medicine

Lipid-based nanoparticles for organ selective mRNA delivery

Speaker Shuai Liu, PhD

Structure-based investigations of the working mechanisms underlying some specific non-coding RNA molecules

Speaker Aiming Ren, PhD

Moderator: Xin Li, PhD

Wednesday, August 16, 2023

10:00 AM ET

Zoom

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U-M RNA Innovation Seminar Series Returns in September

Title TBD (Updates will be posted at this link)

Graham Erwin, Ph.D.

Stanford Cancer Institute Postdoctoral Fellow

Department of Genetics

Stanford University

Monday, September 11, 2023

4:00 PM - 5:00 PM

BSRB ABC Seminar Rooms, Hybrid Link

This Month: Oral Defenses

U-M Oral Dissertations

RNA SOCIETY

Lexogen RNA Expertise Blog Series

Excellence is in Precision: PCR Add-on and Reamplification Kit V2

Our July 13, 2023 blog post focuses a new PCR Add-on and Reamplification Kit V2 that combines reagents for qPCR and library reamplification in one convenient kit.

Welcome to the LEXOGEN RNA EXPERTISE blog series, where we talk about various topics from the world of RNA and RNA-Seq, focusing on best practices, exciting applications, and more. 

April 2023

RNA Therapeutics: The Future is Bright

Inspired by the RNA journal's April 2023 special edition, we discuss the advantages of RNA therapeutics, concepts, and modes of action of different classes of RNA-based therapeutics. We also give a glimpse into the RNA therapeutics currently being evaluated in clinical trials or having received approval.

Job Postings

Postdoctoral Research Fellow and Graduate Research Assistants

Dr. Guizhi (Julian) Zhu Lab | University of Michigan

Dr. Guizhi (Julian) Zhu Lab in the Department of Pharmaceutical Sciences of University of Michigan has multiple full-time openings for Postdoctoral Research Fellow and Graduate Research Assistants.

With the overarching goal to develop novel and clinically translatable nucleic acid immunotherapeutics and vaccines, Zhu Lab's research interest lies at the interface of RNA/DNA/protein chemistry and engineering, immunology, and applied chemistry and biomaterials. Our current focus is to develop circRNA/mRNA/oligonucleotide immunotherapeutics/vaccines and their delivery systems for the prophylaxis or immunotherapy of cancer, infectious diseases, and autoimmune disorders. We have published 100 papers including recent research articles in Science Advances and Nature Communications. Learn more about Dr. Guizhi (Julian) Zhu.

Responsibilities: Lead research projects and work with the team on research projects, train junior graduate students and undergraduate students, writing manuscripts and assist in writing research proposals, and other duties required for regular lab management and research development.

Required Qualifications for Postdocs

• Candidates must hold a Ph.D. or equivalent degree in a relevant scientific discipline. Expertise in one or multiple of the following fields are desirable: nucleic acid chemistry/engineering/delivery, immunotherapy or vaccine development, gene editing, drug delivery, or related areas
• Strong motivation and down-to-earth attitude for scientific innovation and drug/vaccine/technology development
• Independent analytical and problem-solving skills: Ability to think critically, design experiments, analyze and interpret data, and troubleshoot experimental challenges
• Communication and teamwork: Excellent written and verbal communication skills and the ability to work collaboratively in a diverse team environment.

How to Apply

Interested Postdoc applicants please submit the following application materials to Dr. Guizhi Zhu guizhiz@umich.edu:

• CV
• A summary of previous research experience
• A brief statement of future research interests and career goals
• Contact information for three letters of reference

Prospective graduate students and research scientists are welcome to contact Dr. Zhu to discuss opportunities (guizhiz@umich.edu).

Additional information about the Zhu Lab and the University of Michigan Ann Arbor campus.

Research Technician and Post-Doctoral Research Fellow

Fred Hutchinson Cancer Center | The Lapointe Lab

The Lapointe Lab at the Fred Hutchinson Cancer Center is growing, and we are currently seeking to fill two positions: Research Technician and Post-Doctoral Research Fellow.

Research Technician:

This position is ideal for a recent graduate (bachelor’s degree) who wants to gain more research experience before pursuing graduate studies. When you join our group, we prioritize your continued development into an independent scientist.

Please follow this link for instructions on how to apply.

Post-Doctoral Research Fellow:

This position is ideal for a recent (or soon to be) Ph.D. graduate that is excited about RNA, translation, and/or viruses. When you join our group, we prioritize your continued development into an independent scientist.

Please follow this link for instructions on how to apply.

About:

The Lapointe lab is driven by questions that underly how human messenger RNAs (mRNAs) and the ribosome are regulated to determine when, where, and how much of a protein to synthesize.

Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. 

For more information contact the Employee Services Center at hrops@fredhutch.org or by calling 206-667-4700.

Research Technician - Yadavalli Lab

The Yadavalli lab at the Waksman Institute of Microbiology at Rutgers University (yadavallilab.org) is

looking for a full-time technician or research scientist to perform cutting-edge research in RNA biology

using high-throughput sequencing methods. We are seeking motivated candidates, who are enthusiastic

to train and build their skills in the generation of next-generation sequencing libraries. Our studies primarily

use bacteria, and we collaborate on several projects involving human cell lines, mice, and other model

organisms.

Knowledge and Experience

• Bachelor’s, master’s, or Ph.D. degree in biological sciences, genetics, biochemistry, or a related scientific field
• One or more years of molecular biology research experience is required
• Experience with high-throughput sequencing library preparations is highly desirable
• Good communication, meticulous organization and record-keeping, and computer literacy are required

Salary and benefits

• Range $40-80k, commensurate with experience and level of education
• Medical and dental insurance
• Retirement benefits
• Flexible times

Applicants should send a CV, transcript, and a list of references to Dr. Srujana Samhita Yadavalli at sam.yadavalli@rutgers.edu.

Postdoctoral Position - Maquat Lab

A postdoctoral position is open in the Maquat Lab at the University of Rochester Medical Center in Rochester, NY. Applicants should hold a PhD or MD/PhD degree(s) and have expertise in molecular, cellular, or structural biology to study one of a number of very exciting and ongoing projects, including but not limited to FMRP function in Fragile X Syndrome (FXS), newly defined effectors of nonsense-mediated mRNA decay, or the mechanistic coupling of transcription and RNA processing on chromatin and beyond. A background in neurobiology and/or stem-cell biology would facilitate the work on FXS (see, e.g., this article in the journal Nature), and a background in computational biology would facilitate all projects, but neither is required.  

Interested individuals should submit: 

1. A complete curriculum vitae
2. The names and email addresses of three references (applicants should state their relationship to each)
3. A description of RNA research experience, including experimental approaches and technologies with which the applicant has experience.  

The successful applicant will join a very productive, interactive lab and a lively, supportive RNA community that consists of more than 25 labs spanning the University of Rochester Medical Center and the adjacent Colleges of Arts, Sciences & Engineering. The Maquat lab offers an outstanding research environment, excellent opportunities to collaborate with basic scientists and clinicians, and a strong record of training postdocs for academic positions.

Please submit applications to: Liz at elizabeth_leverenz@urmc.rochester.edu 

Maquat Lab Website 

Center for RNA Biology

The University of Rochester is committed to diversity and equality in education and employment. EOE Minorities/Females/Protected Veterans/Disabled.

Research Assistant - Interdict Bio

Interdict Bio is a seed-stage biotech startup in San Francisco seeking a talented and motivated individual to join its biochemistry team and support its mission toward developing a novel small molecule therapeutics platform

for addressing historically undruggable targets.

This position is a fantastic opportunity to join a VC-funded early-stage biotech company, and to grow within a vibrant team dedicated to the discovery of innovative, targeted small molecule therapeutics. The ideal candidate will have experience in molecular/cellular biology and biochemistry, including mammalian cell culture, molecular cloning, and biochemical assays. Experience in recombinant protein expression/purification and stable cell line

generation is a plus, but not required. The ideal candidate will have strong interest in continued learning of cell biology techniques, as well as in vitro biochemical reconstitutions. The candidate will be immersed in several high-paced, exciting projects at the intersection of biochemistry, cell biology, and computational chemistry with opportunities to learn and grow in new directions.

Responsibilities:

• Participate in protein expression and purification to support biochemical reconstitution efforts
• Lead cloning efforts to establish cellular reporters for our biochemical platform and pipeline
• Manage workflows for generation of large quantities of both adherent and suspension human cell lines
• Optimize Western blotting techniques in various cell model systems
• Effectively collaborate with members of the biochemistry team to implement cellular assays into the broad biochemistry platform and pipeline
• Communicate scientific results through presentations and publications
• Contribute to lab organization and culture

Qualifications:

• B.A./B.S. in biochemistry, biology, molecular biology, or related field
• 2+ years of related wet-lab experience
• Expertise in protein/RNA biochemistry, including recombinant protein purification
• Hands-on experience in mammalian cell culture and molecular cloning; experience in qPCR is a plus
• Highly organized with excellent analytical skills and accurate documentation
• Excellent communication and collaboration skills
• Enthusiasm to learn and contribute to a multidisciplinary team

Contact: Anthony Schuller, Ph.D. | Associate Director – Biochemistry | Email: aschuller@interdictbio.com

Postdoctoral Position - Cooperman Laboratory

The Cooperman laboratory in the Chemistry Department of the University of Pennsylvania is seeking to recruit a postdoctoral student with a strong interest in understanding the mechanism and regulation of cytoplasmic eukaryotic protein synthesis. We have developed a highly purified, eukaryotic cell-free protein synthesis system and used it to determine the mechanism of initiating polypeptide elongation in an IRES- dependent system (Zhang et al., Elife 2016 5:e13429), measure the direct interaction of nonsense suppressor molecules with the protein synthesis machinery (Ng et al., ACS Med Chem Lett. 9:1285-1291), elucidate

the mechanisms of elongation and termination, differentiate between the mechanisms by which different nonsense suppressors stimulate readthrough of nonsense codons (Ng et al., PNAS 2021 118, e2020599118) and determine the precise mode of action of ataluren, the only nonsense suppressor currently in clinical use (Huang et al., Nature Comm. 2022 13: 2413). Our current efforts are focused on 1) determining the precise effects of epigenetic modification of mRNA and tRNA on polypeptide elongation and termination and 2) identifying new nonsense suppressors more potent than ataluren using high throughput screening (Ghelfi

et al., 2023 Biomolecules, 13, 242) and determining which patients are most likely to benefit from nonsense

suppressor treatment.

The successful applicant should be mechanistically oriented with expertise in biochemical and molecular

biological approaches. Experience with steady-state and pre-steady-state kinetics is a plus.

Qualifications include a recent Ph.D. in biochemistry, chemical biology, molecular biology, or a related

field and a strong interest in protein synthesis. Applicant must have a strong work ethic, communication &

organization skills, and a willingness to think about and learn new methodologies as the projects evolve.

Interested applicants should send a cover letter and CV with contact information for three references to

Barry Cooperman at cooprman@pobox.upenn.edu, (215) 898-6330.

News

Professor Nils Walter's Collegiate Professorship Lecture - Video

Dr. Nils Walter's Collegiate Professorship Lecture on May 8 discussed the opportunities that RNA will provide for us in the future.

In case you missed it, here is a recording.

Meetings

2023 Symposium for the University of Michigan Chemistry-Biology Interface Training Program | August 31, 2023

The Chemistry-Biology Interface Training Program at the University of Michigan is excited to announce the date and time for this year's annual symposium: 8:00 am - 4:30 pm on August 31, 2023. 

The symposium will focus on cutting-edge research conducted at the interface of chemistry and biology, with speakers from diverse backgrounds and research interests. This is an excellent opportunity for trainees to present their research through a poster session, network and connect with other trainees and researchers, and explore career paths through a diverse career panel.

Please click on the links below for symposium registration and poster abstract submission, further details and a schedule of events.

Registration and abstract submission (due August 24, 2023): submission form

Symposium details and schedule: event website

We hope you are able to join us! For more information contact kholton@umich.edu

Interacademy Conference Wurzburg, Germany September 20-22, 2023

"Microbiology: from single cell to microbiome and host” on September 20-22, 2023 in Würzburg, Germany.

This conference on molecular microbiology will be organized by the German National Academy of Sciences Leopoldina, the Académie des sciences, the Royal Society, and the Royal Swedish Academy of Sciences.

Hosted by the University of Würzburg and supported by the Helmholtz Institute Würzburg and the Krupp Foundation, the 2-day conference is the sequel to several successful and exceptionally well-attended Interacademy meetings on the topic that were held in Paris (2014) and London (2016).

For further information, including the line-up of our 22 outstanding speakers, as well as the registration and abstract submission process, please visit the Microbiology Conference 2023 website

Register by: July 31, 2023 (without abstract: end of August 2023).

We can accommodate up to 250 participants, so please try to register early. If you have any questions, please do not hesitate to contact us at stefanie.ziegler@helmholtz-hiri.de.

2023 RiboClub Annual Meeting: September 24-28

The RiboClub Annual Meeting aims at encouraging the exchange of ideas and stimulates collaborations between RNA biologists around the world. The meeting covers different topics related to the chemistry, structure and biology of RNA with emphasis on upcoming and debatable biological questions. In addition, every year the RiboClub puts the focus on a local or regional RNA group to highlight their efforts and introduce them to the international community.

The meeting format provides principal investigators the opportunity to present their point of views on the current state of knowledge and ignite the curiosity of young scientists. The meeting size and its format give ample opportunity for discussions and interactions, so bring your thinking hat to uncover the next big idea.

Registration fees are subsidized to encourage the participation of students and upcoming researchers. All laboratory members are invited to attend, listen to the presentations of leading scientists and participate in poster competition.

Annual Meeting September 24-28, 2023

Chéribourg Hotel, Orford, Quebec, Canada

Late Registration open through September

More Information: www.riboclub.org

Questions: riboclub@riboclub.org

International Conference on Nucleic Acid Immunity

October 26-28, 2023 | Dresden, Germany

The International Conference on Nucleic Acid Immunity, organized by the CRC/TRR237, will take place from October 26th to 28th, 2023 at the prestigious Deutsches Hygiene Museum in Dresden, Germany.

The conference aims to gather the world's top scientists to discuss the latest scientific advancements in the field. For further information, please visit our International Conference on Nucleic Acid Immunity website.

Registration is now open and involves the following steps:

1. Create a ConfTool account for our conference
2. Your account allows you to register and to submit an abstract.
3. Submit an abstract before or after your registration (submission deadline July 30th, 2023). Submitting an abstract is optional and not required for registration. We are eager to hear about your work and will provide a digital abstract book for the conference.
4. Register either as student (200€ | 300€), academic (350€ | 450€), or industry participant (800€ | 900€). The early bird registration period (first price) ends on September 17th. The late bird registration period (second price) ends on October 1st.

Conference Coordination: Bianca Weißbach (bianca.weissbach@ukdd.de)

Our members' publications are available through Altmetric. Queries are currently available: CRISPR, microRNA, molecule, RNA, RNA therapeutics, transcriptome, and translation.

Below are recent highlights.

Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S, What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome?, Molecular & Cellular Proteomics (2023), doi: https://doi.org/10.1016/j.mcpro.2023.100631.

Wilinski, D., Dus, M. "N6-adenosine methylation controls the translation of insulin mRNA." Nat Struct Mol Biol (2023) https://doi.org/10.1038/s41594-023-01048-x

Eid SA, Noureldein M, Kim B, Hinder LM, Mendelson FE, Hayes JM, Hur J, Feldman EL. Single-cell RNA-seq uncovers novel metabolic functions of Schwann cells beyond myelination. J Neurochem. 2023 Jun 16. doi: 10.1111/jnc.15877. Epub ahead of print. PMID: 37328915. https://onlinelibrary.wiley.com/doi/10.1111/jnc.15877

Mustoe AM, Weidmann CA, Weeks KM. Correction to "Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis". Acc Chem Res. 2023 Jun 20;56(12):1684. doi: 10.1021/acs.accounts.3c00304. Epub 2023 Jun 7. Erratum for: Acc Chem Res. 2023 Apr 4;56(7):763-775. PMID: 37283502. https://pubs.acs.org/doi/10.1021/acs.accounts.3c00304

Original Article, March 2023:

Mustoe AM, Weidmann CA, Weeks KM. Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis. Acc Chem Res. 2023 Apr 4;56(7):763-775. doi: 10.1021/acs.accounts.2c00782. Epub 2023 Mar 14. Erratum in: Acc Chem Res. 2023 Jun 20;56(12):1684. PMID: 36917683; PMCID: PMC10078950. https://pubs.acs.org/doi/10.1021/acs.accounts.2c00782

Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG. Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand. Nat Struct Mol Biol. 2023 Jun 1. doi: 10.1038/s41594-023-01002-x. Epub ahead of print. PMID: 37264140. https://www.nature.com/articles/s41594-023-01002-x

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

Katherine R. Harrison, Delaney Snead, Anna Kilts, Michelle L. Ammerman, Krista R. Wigginton medRxiv 2023.05.19.23290245; doi: https://doi.org/10.1101/2023.05.19.23290245

Communications Hub

Save the Date!

To share your news and comments, please contact

rna-communications@umich.edu