Biophysics Seminars

Upcoming Seminars:

April 24th, 2014, 10:30AM - 11:30AM

Dr. Chongli Yuan from Purdue University will visit our biophysics program.
 

Previous Seminars (Spring 2014):

March 20th, 2014, 10:30AM - 11:30AM

Dr. Liping Xiong From George Washington University (Prof. Ganhui Lan's group)
Title:
An optimal energy dissipation strategy of the MinCDE oscillator in regulating symmetric bacterial cell division
Abstract:
Rod-like bacterial cells utilize a MinCDE system to locate the cytokinesis machinery to mid-cell for symmetric cell division. In Escherichia coli, this regulation is implemented through the pole-to-pole oscillation of the Min proteins. State-of-art experimental approaches have identified the involved bio-molecules and most of their interactions, based on which several dynamic models have been developed and have successfully explained the emergence of the oscillatory phenomenon. However, a more fundamental understanding of this bio-oscillator’s dissipative nature and its relation to the regulatory function is lacking. Here, we address this problem by studying the energetics of the MinCDE reaction network in E. coli. We derive the mathematical expression for the network’s energy dissipation and relate it to a previously defined regulatory “performance”. Our results indicate that, unlike the stationary sensory adaptation systems whose regulatory performance can be monotonically improved to their upper limits by higher energy dissipation, the MinCDE oscillator has a more complicated performance-to-cost relation: energy is required to drive the oscillation but excess energy dissipation could reduce its regulatory performance. We further show that to achieve optimal performance, most of the energy from ATP hydrolysis has to be strategically assigned to the MinE-aided MinD release and the MinD immobilization steps. These discoveries suggest an optimal dissipation strategy in the MinCDE oscillatory system and imply that E. coli cells live within this optimal regime.
 

Feb 27th, 2014, 10:30AM - 11:30AM

Dr. Jun Zhu, Core Director, DNA Sequencing and Computational Biology Core, NIH
Title:
Transcriptome analysis by NGS: From the start to the end and beyond
Abstract:
One fundamental question in gene expression regulation is the transcriptome diversity and plasticity. The complexity of mammalian transcriptome may be resulting from distinct and yet interconnected mechanisms, such as alternative usage of transcriptional start sites (TSSs) and polyadenylation sites, and alternative pre-mRNA splicing. Our group has recently developed several genome-wide techniques, such as PEAT and PA-seq, to investigate the regulated transcriptional initiation and alternative polyadenylation events. In addition, we recently uncovered that global intron retention may serve as a novel mechanism to control gene expression during T cell activation. Together, these studies help to better characterize eukaryotic transcriptome in a more comprehensive fashion.
 

Feb 6th, 2014, 10:30AM - 11:30AM

Dr. Xinxin Quan, NIH
Title:
Gene Expression signature and involved signaling pathways of CD133+ tumor Initiating Cells in Human Squamous Cell Carcinoma of skin
Abstract:
Tumor initiating cells (TICs) of skin squamous cell carcinoma (SCC) have speculated as the major cancer stem cell population causing metastasis and drug resistance; however, their molecular signatures and cellular functions have not been well understood. Here, a small percentage of CD133+ cell population enriched for TICs was isolated by sorting with multiple cell surface markers from primary human SCC tumors. These cells contain cancer stem cell features as demonstrated by in vitro spheroid formation and in vivo tumor generation. Gene signatures of the distinct CD133+ subset were profiled by comparing with CD133- cancer cells by microarray, and further verified by Nanostring gene expression assay. Several top ranked pathways are analyzed by GeneGo and IPA. And their biological functions related to maintain cancer stem cell population were studied in details.
 

Jan 30th, 2014, 10:30AM - 11:30AM

Dr. Weiyang ShiTongji University, China
Title:
Exploring marine invertebrates as new models for genomics studies
Abstract:
We are interested in studying the genetic and epigenetic regulation of early embryonic development. The past decade has seen an explosion of sequencing technologies and many non-traditional model organisms have become accessible to functional genomic studies. Here I will discuss our efforts using two marine invertebrates, the Urochordate ascidian Ciona intestinalis and the mollusk pacific oyster Crassostrea gigas, to understand how gene networks and epigenetic modifications control embryogenesis. Ciona is a close relative to the vertebrates and many genomic features and developmental pathways are conserved. We investigated the gene regulatory network that underlies notochord convergent extension in Ciona embryogenesis and identified novel regulators for this morphogenetic process. We also carried out analysis of non-coding RNAs in Ciona and developed an algorithm to identify microRNAs from NGS data. The NGS study also led to the discovery of a new class of non-coding RNAs that are super enriched in Ciona but widely observed in other organisms. The oyster represents a large yet under studied group of protostomes, the Lophotrochozoans, that differ from the traditional Ecdysozoan models like fly and worm. We will discuss two ongoing projects in the lab. First is using time-course transcriptome data to identify developmental hourglass during oyster development. The second project aims to elucidate the epigenetic changes during the transition of zygotic gene activation and explore their roles for later development.
 

Jan 29th, 2014, 10:30AM - 11:30AM

Dr. Eric Hoffman, Director, Research Center for Genetic Medicine, Children's National Medical Center, Professor and Chairman, Department of Integrative Systems Biology, George Washington University
Title:
Defining the systems biology of the chronic inflammatory state: (Why we need to 'get local' into the tissue microenvironment)
Abstract:
We are interested in studying the genetic and epigenetic regulation of early embryonic development. The past decade has seen an explosion of sequencing technologies and many non-traditional model organisms have become accessible to functional genomic studies. Here I will discuss our efforts using two marine invertebrates, the Urochordate ascidian Ciona intestinalis and the mollusk pacific oyster Crassostrea gigas, to understand how gene networks and epigenetic modifications control embryogenesis. Ciona is a close relative to the vertebrates and many genomic features and developmental pathways are conserved. We investigated the gene regulatory network that underlies notochord convergent extension in Ciona embryogenesis and identified novel regulators for this morphogenetic process. We also carried out analysis of non-coding RNAs in Ciona and developed an algorithm to identify microRNAs from NGS data. The NGS study also led to the discovery of a new class of non-coding RNAs that are super enriched in Ciona but widely observed in other organisms. The oyster represents a large yet under studied group of protostomes, the Lophotrochozoans, that differ from the traditional Ecdysozoan models like fly and worm. We will discuss two ongoing projects in the lab. First is using time-course transcriptome data to identify developmental hourglass during oyster development. The second project aims to elucidate the epigenetic changes during the transition of zygotic gene activation and explore their roles for later development.