Public programs at UCMP : UCMP's annual short course

Unraveling the Genome: What we've learned and why it matters

The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism, whether it be a bacterium, a honey bee, or a chimpanzee. Unraveling and comparing genomes informs our understanding of evolution, biodiversity, conservation, and the very essence of life. From the basics of genome sequencing to horizontal gene transfer and jumping genes, this short course focused on what we have learned and why it matters.

The 2013 UCMP Short Course was dedicated to the memory of Mary Jane Holmes, a local teacher who looked forward every year to a new topic that would stimulate her thinking and energize her teaching.
This short course was cosponsored by the Berkeley Natural History Museums (BNHM) and Science@Cal.

Saturday, February 23, 2013
9:00 am to 3:30 pm





Welcome, logistics, and introduction by Lisa White


Setting the stage — Dave Lindberg


What if we could sequence everything?
Jeffrey Boore, CEO of Genome Project Solutions and Adjunct Professor, UC Berkeley
The fantastic drop in cost and increase in throughput of DNA sequencing has created a remarkable new tool for biological research. Genomics research is revolutionizing one field after another, including cancer biology, biofuels production, evolutionary biology, and agricultural improvements. Whereas we were struggling a few years ago just to determine DNA sequence, we are now awash in a flood of data. The challenge today and to be highlighted in the talk is to find ways to creatively address important scientific questions with the DNA sequencing.
Download Jeffrey's Powerpoint presentation.


Reverse ecology: Population genomics, divergence and adaptation
John W. Taylor, Professor, Department of Plant and Microbial Biology, UC Berkeley
Branching points in the Tree of Life originate from population divergence and subsequent adaptation to changing environments whether, fungi, human, or other organism. Reverse ecology is the use of population genomics to find genes involved in adaptation of newly diverged populations. The talk will highlight specific use of genomic sequencing to determine the many individuals of the fungus, Neurospora crassa, and revelations of recently diverged populations and evidence of natural selection and adaptation.
Download John's presentation (pdf).


Simple animals, complex genomes: How comparative genomics shows how similar we are to sponges, sea anemones, and multicellular pancakes
Mansi Srivastava, Postdoctoral Researcher, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology
Once the human genome project concluded, the technology developed for sequencing the human genome opened up the possibility of looking into the genomes of many other organisms. Srivastava will highlight the key insights that have emerged from comparative genomic studies of sponges, sea anemones, and an enigmatic animal lineage called the placozoans. A major focus of the talk will be the idea of a "toolkit" of genes that the first animals to emerge over 650 million years ago encoded in their genomes. Srivastava will end by discussing how surprises in comparative genomic analyses have generated new hypotheses that might explain the difference in complexity between humans and "simpler" animals.
Download Mansi's Powerpoint presentation.


Break for lunch (on your own)


Secrets of the genome: Employing new sequencing technologies to learn about high altitude living and human adaptation
Emilia Huerta-Sanchez, Postdoctoral Researcher, Department of Integrative Biology, UC Berkeley
Imagine living in the Tibetan Plateau, which is often described as one of the harshest environments in the world, characterized by extreme cold and extreme altitude. Many of us could not readily settle in such extreme conditions. Native Tibetans, however, have managed to cope and prosper in this extreme environment. Highlights of their adaptations will be discussed, and detecting and characterizing natural selection in human populations as clear examples of human evolution will be presented.
Download Emilia's presentation (pdf).


Genetic biodiversity, the tree of life, and conservation
Rob DeSalle, Curator, Sackler Institute of Comparative Genomics at the American Museum of Natural History
The role of genomics in modern systematics and an understanding of the relationships of organisms on this planet will be discussed. The basic methods for tree construction at the genomic level and the application of the approach to understanding the genetic makeup and biodiversity in major groups of organisms will also be detailed.
Download Rob's Powerpoint presentation.


Open questions

About the speakers

Jeffrey Boore is the CEO of Genome Project Solutions and an Adjunct Professor at UC Berkeley. He holds a PhD in Biology from the University of Michigan. He was previously Head of Evolutionary Genomics (and currently a guest researcher) at the Department of Energy Joint Genome Institute (at Lawrence Berkeley National Lab) where he was instrumental in guiding the transition from a human genome sequencing to a comparative genomics facility and in establishing the Community Sequencing Program.

Rob DeSalle is a Curator in the Sackler Institute of Comparative Genomics at the American Museum of Natural History (AMNH). He leads a group of researchers working on molecular systematics, molecular evolution, population and conservation genetics, and evolutionary genomics of a wide array of life forms ranging from viruses, bacteria, corals, and plants, to all kinds of insects, reptiles, and mammals. Rob holds Adjunct Professor positions at Columbia University and the City University of New York, and is a Distinguished Professor in Residence at New York University.

Emilia Huerta-Sanchez is a postdoctoral researcher in the Department of Integrative Biology at UC Berkeley in the lab of Professor Rasmus Nielsen. She received her PhD in Applied Mathematics in 2008 from Cornell University. She spends most of her time analyzing human genomes to understand how evolutionary processes have shaped human genetic variation within the Center of Theoretical and Evolutionary Genomics in the Nielsen lab.

Mansi Srivastava is a postdoctoral researcher at the Whitehead Institute for Biomedical Research at MIT. In 2009 she received her PhD in Molecular and Cell Biology at UC Berkeley while completing research on the genomes and embryos of early animal lineages such as sea anemones and sponges to learn about early animal evolution. At MIT she is studying how regenerative mechanisms have evolved in animals. To this end, she is developing a species of acoel worms as a new model for molecular genetic studies of regeneration.

John W. Taylor is a Professor in the Department of Plant and Microbial Biology at UC Berkeley. Currently, he is President of the International Mycological Association and a founding co-Director of Berkeley’s Computational Genomics Resource Lab. He has received awards for excellence in teaching from the Mycological Society of America and the College of Natural Resources at Berkeley.

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