Mason Myers
Ph.D. Student
Department of Biological Chemistry, University of Michigan
Medical School

Yan Zhang Lab

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Jun Hee Lee, Ph.D.
Associate Professor
Molecular & Integrative Physiology
Medical School

Lee Lab

Scientific interest video

We study the relationship between stress, aging and metabolism, focusing on the following projects: (1) Stress-inducible Sestrins and their role in age- and obesity-associated metabolic pathologies, (2) Biochemical mechanisms underlying physiological functions of Sestrins, (3) Pathogenetic mechanisms of how autophagy is abrogated in human diseases including non-alcoholic fatty liver disease (NAFLD) and movement disorders, (4) Stress-induced protein inclusions and RNA granules, (5) Single cell-level understanding of stress-induced transcriptome changes, and (6) Technology development for single-cell and subcellular studies of spatial transcriptome and proteome.

• What is the role of RNA in your research?
  We describe a new technology named Seq-Scope, which can examine RNA sequences in histological slide with a microscopic spatial resolution.

• Is there a layman image to explain your research?
  Current histological techniques can monitor only 2-3 genes at a time. Seq-Scope enables microscopic examination of gene expression for all genes in the genome.

• How did you become interested in this topic?
  We study gastrointestinal tissues (such as liver and colon) and their responses to stresses. The resolution of previous methods was not enough to approach the microscopic histopathological features important in these organs. To overcome the limitation, we worked on developing a completely new method.

• What brought you to the University of Michigan?
  I liked the collegial and supportive environment, in addition to the outstanding group of researchers.

• What advice would you give to students who’d like to get more involved in research?
  COVID-19 crisis and rapid vaccine development highlighted the importance of biomedical research. I strongly encourage you to dive into this field and make critical contributions.

• What profession other than your own would you enjoy, or what is your favorite hobby?
  I very much like my own profession. In the extra time, I enjoy playing with my son.

The post RNA Featured Researcher – Jun Hee Lee, Molecular & Integrative Physiology appeared first on Center for RNA Biomedicine.

Alyssa English, Ph.D.
Postdoctoral research fellow
Human Genetics, Medical School

Faculty-Mentor: Dr. Stephanie Moon

Moon Lab Website
Alyssa’s LinkedIn
Alyssa’s Twitter
Alyssa’s Google Scholar

Mutations in EIF2AK2, a crucial regulator of protein biosynthesis, memory storage, and synaptic plasticity, are associated with the genetic neurodevelopmental disorder Leukoencephalopathy, Developmental Delay, and Episodic Neurologic Regression (LEUDEN) syndrome through unclear mechanisms. I seek to determine the molecular mechanisms of disease-associated EIF2AK2 alleles by investigating its role in protein biosynthesis during stress, and neuronal development and function.

• How does RNA relate to your research interests, and why?
  RNA is central to my research. I study how mRNA localization and translation is controlled in the context of genetic diseases. More specifically, I study how mutations in key machinery responsible for coordinating the repression and derepression of translation affect the cell’s response to stress.

• How did you become interested in this topic?
  My Ph.D. research was focused on understanding the basic genetic mechanisms underlying adaptation to amino acid stress in yeast. For my postdoc, I was interested in seeking out training that would allow me to leverage my experience in basic genetics research to investigate topics more closely related to human health. I’m currently investigating the impact of clinically relevant genetic perturbations on the basic molecular mechanisms governing mRNA translation.

• Who/what brought you to science?
  The biological sciences have been an interest of mine that has grown over time. While I can’t pinpoint a specific moment that led me down this path, I’ve always enjoyed science courses the most.

• What brought you to the University of Michigan?
  Two things brought me here. First is the location. I grew up in Michigan and love that Ann Arbor is a small city with access to beautiful nature areas and is home to a world-class research institution. Second is the collaborative research community. Specifically, the Center for RNA Biomedicine and the Departments of Human Genetics and Neurology are highly collaborative, and it seemed like an excellent environment to tackle the questions I wanted to pursue during my postdoc.

• What are the main challenges/concerns to achieve your professional goals?
  The main challenge is the uncertainty involved in research. You can often go long periods of time without generating data that will lead to a publication. Since scientific success is often measured by publications, there is a lot of uncertainty with any new project and how it may impact your career going forward.

• What’s your favorite hobby?
  I enjoy spending time in the Michigan outdoors doing things like mushroom hunting, fishing, and mountain biking.

READ about Alyssa English’s scientific journey

The post RNA Featured Researcher – Alyssa English, Human Genetics appeared first on Center for RNA Biomedicine.

Sydney Rosenblum
Graduate Student
Program in Chemical Biology
Rackham Graduate School

Faculty-Mentor: Amanda Garner
Garner Lab

Broadly, I am interested in RNA and RNA-protein interactions as drug targets and using chemical biology to develop methods of probing or inhibiting those interactions.

• How does RNA relate to your research interests, and why?
  I am developing a cellular assay to enable the detection (or inhibition) of an RNA-protein interaction, which means RNA is central to my project. I am also developing a platform that allows us to monitor the interaction between a specific RNA sequence and a specific protein in the cell. With this technology I aim to discover small molecules that are capable of blocking this interaction, which is of interest as a drug target in several cancers.

• How did you become interested in this topic?
  In my undergraduate research I was introduced to the idea of chemical biology through the engineering of DNA polymerases capable of utilizing modified nucleotides, so in graduate school I searched for a lab that would allow me to continue exploring chemical biology and nucleic acids. The assay platform I have been developing during my PhD is a great example of leveraging biological systems using engineered proteins and biorthogonal chemistry to address gaps in technology related to studying RNA-protein interactions.

• Who/what brought you to science?
  My junior year of high school I was enrolled in a biotechnology class that introduced me to the idea of laboratory-based scientific research. Through this class I had the opportunity to intern with a local agricultural biotechnology company and I fell in love with the idea of applying scientific experimentation to solving real-world problems.

• What brought you to the University of Michigan?
  I joined the Program in Chemical Biology at the University of Michigan because of the diverse breadth of research opportunities and the collegial, collaborative environment.

• What are the main challenges/concerns to achieve your professional goals?
  At this point, my main challenge is pinpointing specific professional goals. I would love to be able to experience various careers and tackle diverse scientific problems.

• What’s your favorite hobby?
  Whenever possible I enjoy hiking and exploring the great outdoors and during the winter I like to quilt.

MORE ABOUT SYDNEY ROSENBLUM: “Building a better scientific world with hands-on science” 

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Rachel Torrez
Graduate Student, Ph.D. Candidate
Department of Medicinal Chemistry
College of Pharmacy

Faculty-Mentor: Dr. Amanda Garner and Dr. Melanie Ohi

Twitter: @torrez_rach
 Linkedin
Ohi Lab
Garner Lab

My research focuses on using cryogenic electron microscopy (cryo-EM) to study the structure and function of an enzyme called DICER1. DICER1 is a large, highly dynamic, multidomain protein that not only plays a crucial role in microRNA biogenesis, but also has been linked to tumor formation. Despite this direct connection to disease and demonstrated importance in proper microRNA maturation, little work has been done to structurally understand the underlying mechanism by which DICER1 performs its cleavage reaction. With more insight into the full-length structure of DICER1 bound to its pre-microRNA substrate, I hope to fill this gap in knowledge regarding this underlying mechanism.

• How does RNA relate to your research interests, and why?
  My research interests largely focus on better understand the how, why, and when of microRNA. How are mature strands of microRNA produced via the microRNA biogenesis pathway and how does DICER1 aid in the process. Why do mutations in DICER1 affect certain microRNAs? When do these mutations lead to downstream tumor/disease formation. Overall, the how, why, and when of microRNA are constantly guiding my research.

• Who/what brought you to science?
  Growing up I was always interested in science, but it was really my AP Chemistry teacher from high school who inspired and encouraged me to pursue science and research as a full-time career.

• What brought you to the University of Michigan?
  When first applying for Ph.D. programs I was still working in a chemistry focused lab. I wasn’t sure what type of research I wanted to pursue, but always knew I liked the idea of approaching science from multiple different points of view and fields of expertise. This is what brought me to the highly interdisciplinary programs at the University of Michigan and this mentality has also carried over into my research.

• What are the main challenges/concerns to achieve your professional goals?
  For me, finding the right mentors and collaborators is and will continue to be an important part in achieving my professional goals.

• What’s your favorite hobby?
  When not in the lab, I like to play ultimate frisbee and paint animal portraits (acrylicartist.net)

The post RNA Featured Researcher – Rachel Torrez, Medicinal Chemistry appeared first on Center for RNA Biomedicine.

Maha Hanafi, Ph.D.
Medicinal Chemistry, College of Pharmacy

Alumna, April 2021
Faculty-Mentor: Professor Nouri Neamati

LinkedIn: Maha Zidan

My research involves drug discovery where I focus on identifying novel anticancer agents for the treatment of various cancers especially pancreatic cancer being one of the most aggressive malignancies. I am always excited about my research and about medicinal chemistry as an interdisciplinary science that contributes to understanding complex diseases and to the development of effective therapeutics.

• How does RNA relate to your research interests, and why?
  Part of my research is performing RNA sequencing experiments to evaluate the response of anticancer agents and identify their mechanistic signature as well as potential target proteins/pathways.

• How did you become interested in this topic?
  The abundant information that we obtain from RNA sequencing that can guide our research and validate experimental findings.

• Who/what did bring you to science?
  My mother who is my role model had a huge impact on me, I was always impressed by how successful she is as a professor and a mother. From an early age I have been enthusiastic about science, especially medicine. I studied pharmacy and I was interested in understanding diseases and their targeted therapeutics so, I decided to pursue research in drug discovery hoping to contribute to finding a cure to devastating diseases like cancer.

• What did bring you to the University of Michigan?
  The interdisciplinary program at the University of Michigan that would allow for collaborative work and exposure to different research areas.

• What is your favorite hobby?
  I love taking pictures especially of nature. I’m always fascinated by the perfect sunset scenes. I also love food!

The post RNA Featured Researcher – Maha Hanafi, Ph.D., Medicinal Chemistry appeared first on Center for RNA Biomedicine.

Dawen Cai, Ph.D.
Associate Professor
Cell and Developmental Biology, Medical School
Biophysics, LS&A
Affiliated with Neuroscience Graduate Program, Medical School

Cai Lab
Michigan Expert

• What is the role of RNA in your research?
  We use scRNAseq to identify transcription factors that play critical roles in determining neuronal subtypes.

• Is there a layman image to explain your research?

Image shows genetic labeling of the type-II neuroblast and optic lobe lineages (white) in one hemisphere of the larval Drosophila brain. We generate targeted scRNA-seq datasets and combine in silico and in situ analysis to identify marker genes that specify cells derived from these two origins. mRNA in situ staining shows that mamo (yellow) and bi (magenta) are in the optic lobe derived cells, but dati (green) and lncRNA:cherub (cyan) are not.

• Who/what brought you to science? 
  Curiosity about how things work.

• What brought you to the University of Michigan?
  Graduated as a Ph.D. student in Biophysics

• What advice would you give to students who’d like to get more involved in research? 
  Keep asking “why.”

• Are there any opportunities for students to engage in your projects, currently or in the future? 
  Our lab has multiple positions opening to PhD students and postdoc fellows.
  • What skills would they need?
    General wet-lab and/or animal behavior training. Bioinformatics and/or quantitative image processing skills are desired.
  • What could they expect to learn?
    Interdisciplinary wet/dry lab skills, grant/paper writing, presentation, and critical thinking.

• What profession other than your own would you enjoy, or what is your favorite hobby? 
  Photography

The post RNA Featured Researcher – Dawen Cai, Cell & Developmental Biology, and Biophysics appeared first on Center for RNA Biomedicine.

Michelle Paulsen
Research Laboratory Specialist Intermediate
Bru-Seq Lab – Mats Ljungman Lab (Center for RNA Biomedicine core facility)
Radiation Oncology, Medical School

Website

• What is the role of RNA in your research?
  In the Ljungman Lab, RNA features predominantly as we developed the Bru-seq suite of techniques almost 20 years ago.  Bru-seq is a next generation sequencing technique that uses nascent RNA to assess RNA transcription, turnover, enhancers, splicing, as well as other RNA processes.  We work together with researchers all over the world on their Bru-seq projects as well as with major pharmaceutical companies.  We are also a part of the ENCODE project as a mapping center.

• Who/what brought you to science? 
  I’ve always been interested in science, but struggled with figuring out what career path to take.  After graduating with a Bachelor’s degree in biology, I applied for a job in a lab and somehow was hired, even with no experience.  I’ve learned a lot over the years and have been doing research now for over 25 years.

• What brought you to the University of Michigan?
  I’ve lived in Michigan my entire life so I was very familiar with the great reputation of the University and was happy to accept a position here.

• What advice would you give to students who’d like to get more involved in research? 
  Don’t be afraid of not having technical experience –  genuine curiosity and being willing to learn can take you far.  Also, mistakes happen and many times teach you more than your successes!

• Are there any opportunities for students to engage in your projects, currently or in the future?  
  Possibly, especially on the data analysis side of Bru-seq
  • What skills would they need?
    Familiarity with basic statistics and a willingness to learn.
    

• What profession other than your own would you enjoy, or what is your favorite hobby? 
  If I wasn’t in science, I would love to open a bakery!

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Arushi Varshney, Ph.D.
Computational Medicine and Bioinformatics
Medical School

Faculty-Mentor: Stephen C. J. Parker

Google scholar
LinkedIn 
Twitter

Through my research, I aim to better understand how predisposition to complex metabolic diseases such as type 2 diabetes (T2D) is encoded in our DNA. I employ computational and statistical approaches to analyze large high-throughput data sets on the genome, epigenome, and transcriptome from both bulk and single-cell platforms in disease-relevant tissues/cells to understand biological mechanisms of gene regulation.

• How does RNA relate to your research interests, and why?
  Information encoded in our DNA (genome) intricately percolates over layers of the epigenome, transcriptome, proteome and so on, to orchestrate disease mechanisms. Studying context-specific genetic regulation of RNA expression is critical in understanding disease mechanisms.

• Is there a layman image that could illustrate your research?
  Studying the genetic basis of complex disease is like assembling a jigsaw puzzle. Each piece represents information from diverse modalities and integrating this information together helps illustrate the molecular mechanisms in the cell.

• How did you become interested in this topic?
  As human genetics students we learn about the genetic basis of diseases. Many Mendelian diseases involve genetic variation that modify the structure or function of proteins. Such strong-effect genetic variants are usually quite rare. Complex diseases on the other hand are characterized by genetic variants that occur more frequently in the population, an each have modest or small effects. Most of such common variants affect participate in modulating the expression of genes. Studying intricate patterns of gene expression regulation by leveraging diverse and large molecular datasets got me interested in this topic.

• Who/what brought you to science?
  My mom was a high school physics teacher when I was young (she’s now principal), and I would often accompany her to the physics lab and hang out with the cool kids (:)), numerous field trips to science centers and museums and such and I always loved it. In many ways I was exposed to ideas and concepts that got me interested early on.

• What brought you to the University of Michigan?
  I arrived at the UM for my Ph.D.

• What are the main challenges/concerns to achieve your professional goals?
  This era of rapidly developing technology, advent of large human datasets and expanding computational capabilities is extremely exciting for computational biologists like me. At the same time, it is imperative to remain focused and detail oriented in our work, and always keep the main scientific questions clear in our minds.

• What’s your favorite hobby?
  I’m a plant lady – I love collecting and caring for plants. My small apartment has an absurd number of plants. I dream of having a lush garden one day.

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Becky Glineburg, Ph.D.
Postdoctorate
Neurology, Medical School

Faculty-Mentor: Peter Todd, M.D., Ph.D.

Google Scholar

I’m fascinated with how nucleic acid structure dictates various molecular pathways and mechanisms. Currently I’m investigating how GC-rich RNA repeat expansions promote an aberrant form of translation (RAN translation) and how this process contributes to neurodegenerative disease. I am also investigating how cellular stress regulates RAN translation in a number of neurodegenerative disease models.

How does RNA relate to your research interests, and why?
I study translation, so my entire research is based on how RNA structure promotes RAN translation in disease models.

How did you become interested in this topic?
In graduate school I studied DNA repair pathways and discovered that formation of various DNA repair intermediates influence DNA repair pathway choice. When I was looking for postdoc positions, I wanted to study another example of how nucleic acid structure can influence molecular pathways. When I came across Peter’s research on repeat expansion disorders and RAN translation I was immediately hooked.

Who/what brought you to science?
I’ve always been drawn to biology. When I was young this manifested as a love of animals and a desire to learn about their evolutionary adaptations. When I got older, I became interested in human genetic diseases and forensics. Eventually, I discovered most of my burning questions could be answered by understanding molecular biology, so that’s what’s kept me going since.

What brought you to the University of Michigan?
Honestly? A lake house. But when I started researching the breadth labs at Michigan I began to realize I hit the jackpot.

What are the main challenges/concerns to achieve your professional goals?
I absolutely love teaching and I have a tendency to put my students and trainees before my research. I want to eventually teach at a primarily undergraduate institution, but I know the road there requires a balance of both teaching and research.

What’s your favorite hobby?
I have a 15-month-old child, so I’ve forgotten what it’s like to have a hobby… but I probably enjoy photography, writing stupid poems or song parodies for my friends, and feeding farm and zoo animals (is that a hobby?) the most.

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