The RNA Transcript | July 17, 2023

Summer 2023

The RNA Transcript will be published monthly during Summer 2023. Watch your inbox the week of August 14 for the next issue. And click here to review past editions to add to your summer reading list! Weekly publication will resume in September.

Seminars

U-M RNA Innovation Seminar

Seminars will return in September 2023.

Watch for announcements in upcoming issues of The RNA Transcript, or visit the Events Calendar on the website.

RNA Collaborative Seminar

MD Anderson Center for RNA Interference and Non-Coding RNAs

Enhanced vesicles for nucleotide delivery for cancer therapy

Speaker: Sara Corvigno, Ph.D.

Aptamer chimera for therapeutic delivery

Speaker: Paola Amero, Ph.D.

Moderator: Gabriel Lopez-Berestein, MD

Wednesday, July 19, 2023

4:00 PM ET

Zoom

_______________________________________



RiboClub Sherbrooke

Mammalian aminoacyl-tRNA Synthetases in mRNA translation and beyond

Speaker: Haissi Cui, PhD

Exploring how biomolecular condensates can regulate mRNA decay

Speaker: Marc Fabian, PhD

Moderator: Sherif Abou Elela

Wednesday, August 2, 2023

4 PM ET

Zoom



This Week: Oral Defenses

U-M Oral Dissertation

For more information and to view the full schedule of upcoming U-M Oral Defenses, please visit: https://rackham.umich.edu/navigating-your-degree/oral-defense-dates/

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

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 the link for instructions how to apply:  https://careers-fhcrc.icims.com/jobs/25654/job

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 the link for instructions how to apply:  https://careers-fhcrc.icims.com/jobs/25653/job

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., https://www.nature.com/articles/s41556-020-00618-1), 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: https://www.urmc.rochester.edu/labs/Maquat-Lab/ 

Center for RNA Biology: http://www.urmc.rochester.edu/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.

Postdoctoral Position - Walter Laboratory | Application Deadline August 1

Postdoctoral:

A postdoctoral position is available in the Nils Walter laboratory at the University of Michigan, Chemistry Department. We are particularly interested in an enthusiastic team member who has experience working with cell culture, neurodegenerative diseases, as well as RNA or single molecule tools as our two main areas of excellence.

Information about the Walter laboratory can be found here: https://sites.lsa.umich.edu/walter-lab/

Job Requirements: Ph.D. in Chemistry, Biophysics, Cell Biology, Biochemistry, or Molecular Biology; related research experience in neurodegenerative diseases such as ALS, RNA biology, single-molecule fluorescence microscopy, enzymology, next-generation sequencing, or

spectroscopy is a plus. The ideal candidate will be a conscientious, responsible, and collaborative individual interested in becoming a member of a dynamic, engaged team of postdoctoral fellows, graduate and undergraduate students; have excellent organizational skills; and can communicate effectively with a wide range of people with diverse backgrounds. Postdoctoral Research Fellows in the Walter laboratory are expected to show leadership in

their projects and sub-groups, and in mentoring graduate and undergraduate students working alongside them to answer important biological questions; they will also be excited to communicate their newest findings in publications and presentations.

How to Apply: Interested applicants should email a cover letter outlining their specific interest in the position as well as any skills and experiences that directly relate to the description above, an up-to-date CV, and contact information for three references directly to Dr. Nils G. Walter

(nwalter@umich.edu).

Application Deadline: August 1, 2023

Projected State Date: Fall 2023

Employment: Full-time, 12-month appointment term

Michigan Pioneer Fellows Program | Deadline August 4

Pioneer Fellows Program:

The Michigan Pioneer Fellows program at the University of Michigan provides exceptional postdoctoral scholars with a unique, multidisciplinary community focused on nurturing & launching truly innovative scientists into groundbreaking careers.

In this highly competitive "super-postdoc" program, fellows receive funding to pursue independent research, as well as strong mentorship, skill-building & additional resources.

This partnership between the U-M Life Science Institute, Medical School, College of Pharmacy, & College of LSA, is designed to enhance the research program of the entire life sciences enterprise across the university & to help train & develop the next generation of scientific leaders.

The 2023 Timeline:

April 17: Open for submission

August 4: Deadline for application

Appointment start date is flexible

For more information about the program & how to apply, visit: Pioneerfellows.umich.edu

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

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 conference website www.microbiology2023.de

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 website https://www.trr237.uni-muenchen.de/meeting/index.html

Registration is now open and involves the following steps:

1. Create a ConfTool account for our conference here: https://www.conftool.com/nucleic-acid-immunity-2023/
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 Altmetrics. Queries are currently available: CRISPR, microRNA, molecule, RNA, RNA therapeutics, transcriptome, and translation.

Below are recent highlights.

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 https://doi.org/10.1101/2023.05.19.23290245

To share your news and comments, please contact

rna-communications@umich.edu