My Way to RNA

In this section, we highlight the road taken by members of our CRSB community – as a way to inspire future students and staff towards Science, Technology, Engineering and Math (STEM) professions.

Jennifer Doudna

CRSB Founding Faculty Member

Erupting Scientific Interests
Jennifer Doudna grew up in Hawaii amidst the volcanoes, lush tropical forests, and remote beaches of Hilo. These natural wonders instilled in her an awe and appreciation of nature. Although her immediate and extended family had no scientists, Doudna first became interested in science in high school when she took her first chemistry class and participated in a science seminar series highlighting the chemistry of biological systems. Her parents, both academics in the humanities with avid interests in astronomy, geology, and evolution, encouraged her interests. They provided Doudna with science books, museum visits, and her first “hands-on” science experience—a summer studying worms and mushrooms in the laboratory of professor and family friend Don Hemmes, at the University of Hawaii (Hilo). After reading The Double Helix, James Watson’s account of his and Francis Crick’s discovery of the structure of DNA, Doudna was hooked on science and desired to delve deeper into the mysteries of the life sciences.

To indulge her scientific curiosity, Doudna studied chemistry at Pomona College (Claremont, CA) where she met several people who had a profound impact on her research career. These included chemistry professors Fred Grieman, whose passion for quantum mechanics was “infectious,” and Corwin Hansch, whose intensity and love for research was “inspirational.” Doudna began her first scientific research at Pomona, working in the laboratory of Sharon Panasenko, her undergraduate advisor. Panasenko was not only a superb scientist, said Doudna, but also led by example, showing that a woman could be successful in what some perceive as a male-dominated academic world. “It’s a challenging job, especially for women,” says Doudna. “The further along I get in my career, the more I see how important it is for young women to have supportive female mentors.” Doudna feels fortunate to have had a strong female ...

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Don Rio

CRSB Founding Faculty Member

I had an early interest in chemistry.  When I was 12, I went to the library and found the chemical formula for generating blackpowder (a mixture of salt peter, sulfur and charcoal), which I was able to successfully prepare in my basement and explode in my back yard.  I started college in engineering but found it boring, but again became interested in chemistry.  As an undergraduate at the University of Colorado, Boulder, I got involved in synthetic organic chemistry with a research project as a sophomore to synthesize housefly sex pheromone (which was biologically active when I brought it home to my apartment!).  It is likely I would have become a synthetic organic chemist, had it not been for a biochemistry course taught by Tom Cech in my junior year.  I got interested in nucleic acid chemistry as a junior, taking biochemistry and doing research in Tom Cech’s lab in the Chemistry Department at CU, Boulder.  His lab was small then and I got to work on my own project with him isolating precursor ribosomal RNA from Tetrahymena nuclei and performing electron microscopic analysis of RNA-DNA hybrids to map the ribosomal RNA transcription unit (R-loop mapping). led to the discovery of an intervening sequence or intron in the 26S ribosomal RNA gene. Subsequent work by Cech and colleagues showed the Tetrahymena rRNA intron could self-splice in vitro without the action of proteins – this was the discovery of catalytic RNA (and for this work Cech was awarded the 1989 Nobel Prize in Chemistry).  I next went on to graduate school where I studied eukaryotic transcriptional control and protein-DNA interactions of the T antigen protein using the mammalian tumor virus SV40 using biochemical methods and also the study of DNA-protein interactions in Bob Tjian’s lab.  My training in Cech’s lab working ...

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Lior Pachter

Faculty

I am a computational biologist working in genomics. My career began in comparative genomics, and initially I was interested in genome alignment, annotation, and the determination of conserved regions using phylogenetic methods. I contributed to the mouse, rat, chicken and fly genome sequencing consortia, and the pilot phase of the ENCODE project. More recently I’ve become focused on functional genomics, which includes answering questions about the function and interaction of DNA, RNA and protein products. I’m particularly interested in applications of high-throughput sequencing to RNA biology.

Genomics requires the development of algorithms, statistical methodology and mathematical foundations, and a major part of my research is therefore on methods. My views on the role of computational methods in genomics are explained in my keynote talk at the 2013 CSHL meeting on genome informatics titled “Stories from the Supplement”.

My interests are reflected in my appointments across different departments and colleges: Mathematics, Molecular & Cell Biology, and Electrical Engineering & Computer Science. My group includes students and postdocs from Computer Science, Mathematics, Bioengineering, Molecular and Cell Biology and Statistics.

I was born in Ramat Gan, Israel, and grew up in Pretoria, South Africa where I attended Pretoria Boys High School. After receiving a B.S. in Mathematics from Caltech in 1994, I left for MIT where I was awarded a PhD in applied mathematics in 1999. I then moved to the University of California at Berkeley where I was a postdoctoral researcher (1999-2001), assistant professor (2001-2005), associate professor (2005-2009), and am currently the Raymond and Beverly Sackler professor of computational biology at UC Berkeley and professor of mathematics and molecular and cellular biology with a joint appointment in computer science.
My research interests span the mathematical and biological sciences, and I have authored over 100 research articles in the areas of algorithms, combinatorics, ...

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James Lloyd

Post-Doctoral Researcher

I grew up in rural/costal Yorkshire, England and was a big fan of acting, history, science and science-fiction. Looking back at my childhood, my path into science almost seem obvious now but at the time I never saw the path in front of me. As a child I loved the character in films and TV shows who had the answers, who was the scientist. I idolised Egon Spengler in the Ghostbusters and Mr Spock in Star Trek over the more conventionally cooler Peter Venkman and Captain Kirk. I liked how they always solved the problem. They may not have known the answer at the outset but they knew how to get the answer to save the day. I thought that was so much more impressive than the traditional heros who would usually get the glory. But the thinker in the group was often the unsung hero and without them, there would be no happy ending. In high school I started to realise acting might not be for me and that science and university were options for me. Starting an undergraduate degree in Genetics at the University of York, UK, I wanted to join the fight against diseases like cancer but quickly I found that understanding how basic biological systems worked fascinated me. An interesting problem requires an interesting approach to solve it. Dr Simon Hardy introduced me at York to the interrupted gene problem and alternative splicing. This is where my love of RNA biology came from. The idea non-coding sequencing interrupt genes in eukaryotes and need to be recognised by the cell as non-coding and precisely removed really grabbed me. Then learning that this can be regulated so different cells remove different regions to change the coding potential depending on the cell type or environment (called alternative splicing) sealed ...

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