Daily Calendar – Genomics

Events - Daily

<< March 25, 2013 >>

Monday, March 25
Roman Stocker, MIT, Spying on the lives of marine microbes: From biophysics to ecology At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment. New technologies, including microfluidics and high-speed video microscopy, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology, and enabling a deeper understanding of the biophysical mechanisms underpinning these behaviors. I will illustrate this 'quantitative natural history approach' to microbial ecology by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) sub-micrometer imaging of single cells at up to thousand frames per second, demonstrating that marine bacteria have a unique mode of swimming, exploiting a mechanical buckling instability of their flagellum to reorient; and (ii) microfluidic experiments that capture the dramatic chemotactic abilities of marine bacteria, including bacterial pathogens storming towards the roiling surface of their coral hosts. Through these examples, I aim to illustrate how we can use direct visualization to learn about the biophysical mechanisms and the ecological implications of the behaviors of the smallest of life forms. Joseph Henry Room, Jadwin Hall · 12:00 p.m.– 1:00 p.m.
Gene-Wei Li, UCSF, A quantitative view of the bacterial proteome https://sites.google.com/site/geneweili/about-me Protein biosynthesis is the biggest consumer of cellular energy during proliferation. The composition of the proteome is therefore tightly regulated in order to achieve efficient use of ribosome. At UCSF, I have made several key discoveries revealing how bacteria precisely control the speed of protein synthesis. First, I found that, contrary to current dogma, translation rate in vivo is independent of codon usage. Instead, pervasive ribosome pausing throughout the transcriptome is driven by internal Shine-Dalgarno sequences. This observation provides critical insights into the selection of coding sequences. Second, by developing a method to quantify the absolute rate of protein synthesis for nearly all genes in bacteria, I showed that many proteins have precisely controlled expression levels that quantitatively reflect their functions and the cell's physiology. This set of methods and genome-wide data provides a unique way to broadly characterize many specific cellular processes, from design principles of transcriptional regulation to metabolic pathways. Carl Icahn Lab 101 · 4:15 p.m.– 5:15 p.m.

Monday, March 25

Roman Stocker, MIT, Spying on the lives of marine microbes: From biophysics to ecology
At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment. New technologies, including microfluidics and high-speed video microscopy, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology, and enabling a deeper understanding of the biophysical mechanisms underpinning these behaviors. I will illustrate this 'quantitative natural history approach' to microbial ecology by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) sub-micrometer imaging of single cells at up to thousand frames per second, demonstrating that marine bacteria have a unique mode of swimming, exploiting a mechanical buckling instability of their flagellum to reorient; and (ii) microfluidic experiments that capture the dramatic chemotactic abilities of marine bacteria, including bacterial pathogens storming towards the roiling surface of their coral hosts. Through these examples, I aim to illustrate how we can use direct visualization to learn about the biophysical mechanisms and the ecological implications of the behaviors of the smallest of life forms.
Joseph Henry Room, Jadwin Hall · 12:00 p.m.– 1:00 p.m.

Gene-Wei Li, UCSF, A quantitative view of the bacterial proteome
https://sites.google.com/site/geneweili/about-me

Protein biosynthesis is the biggest consumer of cellular energy during proliferation. The composition of the proteome is therefore tightly regulated in order to achieve efficient use of ribosome. At UCSF, I have made several key discoveries revealing how bacteria precisely control the speed of protein synthesis. First, I found that, contrary to current dogma, translation rate in vivo is independent of codon usage. Instead, pervasive ribosome pausing throughout the transcriptome is driven by internal Shine-Dalgarno sequences. This observation provides critical insights into the selection of coding sequences. Second, by developing a method to quantify the absolute rate of protein synthesis for nearly all genes in bacteria, I showed that many proteins have precisely controlled expression levels that quantitatively reflect their functions and the cell's physiology. This set of methods and genome-wide data provides a unique way to broadly characterize many specific cellular processes, from design principles of transcriptional regulation to metabolic pathways.
Carl Icahn Lab 101 · 4:15 p.m.– 5:15 p.m.

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