Lab group – August 2018
Top row from left: Anton Alenko, Vadim Patsalo, Matthew J. Salie, Olivier Duss, John Hammond
Middle row from left: Luigi D’Ascenzo, Lili K. Doerfel, Yisong Deng, Galina Stepanyuk, Anna Popova
Bottom row from left: Katrina Schreiber, James R. Williamson, Jessica Rabuck-Gibbons, Ning Li


James R. Williamson, Ph.D. – Professor

For those interested in joining our Lab, please visit the OPEN POSITIONS page for more information!

Farshad Abdollah-Nia, Ph.D., Postdoctoral Associate

I am interested in understanding how bacterial cells manage the production of proteins, as well as the flux of metabolites in different growth conditions. I use mass spectrometry to quantify protein levels on a cell-wide scale in E. coli. Then I apply mathematical models that describe the dynamics of large groups of proteins. These models help us understand global resource allocation strategies in cells and enable us to predict the growth and the makeup of the cells in various environments.

Anshul Chaudhary, Ph.D., Postdoctoral Associate

I am focusing on understanding ribosome biogenesis. RNA helicases play various roles in ribosome biogenesis; however, it is unclear how most RNA helicases interact with intermediates of ribosome assemblies. SrmB is a DEAD-box helicase that operates early in the ribosome assembly process. To provide a structural and functional view of SrmB, DEAD-box helicase for ribosome assembly, this study uses a range of biochemical, biophysical, and X-ray/cryo-electron techniques.

Luigi D’Ascenzo, Ph.D., Postdoctoral Fellow

I am currently working on realizing a “molecular movie” of the ribosome biogenesis, integrating simulations and 3D modelling with experimental data. In parallel, I am developing novel tools for mass spectrometry data analysis with heavy isotope labelling, focusing on the investigation of modifications in ribosomal RNA and on proteomics analysis of prokaryotes.
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Lili K. Doerfel, Ph.D., Postdoctoral Fellow

I am studying ribosome assembly in vitro. This allows to severely perturb ribosome assembly e.g. by deleting essential proteins or adding inhibitory molecules and thus enables to explore the plasticity of the assembly pathway and its regulatory network. Using a combination of a functional assay, quantitative mass spectrometry and single particle cryo-electron microscopy the structure of assembly intermediates can be correlated with the r-protein content and the activity of the particle. Moreover, I aim to correlate co-transcriptional rRNA processing and rRNA folding to the sequential binding of ribosomal proteins and the transient action of ribosome assembly factors thereby achieving kinetic insight into the assembly process.


     John Hammond, Ph.D., Staff Scientist

I am interested in the assembly, function, and structure of viral/host ribonucleoprotein complexes. Of late, we have been studying the assembly of a nuclear export complex required for HIV-1 replication, as well as understanding the assembly of the HIV-1 virus. This work uses a variety of biochemical, biophysical and cellular biology techniques to provide a universal structural and functional view of these RNP processes.

Vadim Patsalo, Ph.D., Staff Scientist

I aim to understand and quantitatively predict bacterial resource allocation. Cells execute such gene-expression strategies during both steady-state growth and dynamic adaptations to changing environments, such as the sudden onset of stress. Measuring physiological, metabolic, and gene-expression parameters, we work to establish a systematic biophysical comprehension of the cell.

Anna Popova, Ph.D., Staff Scientist

I am particularly fond of rRNA modifications! All different kinds, found in bacteria, yeast, and human cells. Using modern mass spectrometry tools, I can identify and quantify relative abundance of RNA modifications in mature ribosomes and the intermediates. This quantitative approach proved to be effective in understanding modifications as part of the ribosome biogenesis process.
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Jessica Rabuck-Gibbons, Ph.D., Postdoctoral Associate

I am interested in exploring the structure of heterogeneous RNA/protein complexes in vivo and expanding biophysical characterization methodologies. Currently, I am working on understanding ribosome biogenesis in vivo. After depleting E. coli of a ribosomal protein of interested, I use a combination of quantitative mass spectrometry with isotope labeling and single particle cryo-electron microscopy to understand the composition and structure of the ribosome assembly intermediates.
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Katrina Schreiber, Administrative Manager

Analytical and detail-oriented professional with experience coordinating, planning, and supporting daily operational and administrative functions within the Williamson Laboratory and in support of Dr. Williamson’s executive obligations. I come from a lengthy background of management roles in research and healthcare, with 16+ combined years at TSRI, and plan to continue my lifelong pursuit of assisting my colleagues, so they can focus on what they do best…science!

Lincoln Scott, Ph.D., Visiting Investigator

I am interested in the chemo-enzymatic synthesis of isotopically labeled nucleotides and nucleotide analogs. These compounds are used in a variety of NMR and mass spectrometry based biophysical studies of RNA and RNA-protein complexes. This work has led to the formation of Cassia LLC, a company that prepares isotopically labeled primary metabolites for the biophysical research community.
Cassia, LLC
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Kai Sheng, Graduate Student

I was trained as a chemical biologist during my undergraduate research, developing methodology in protein modifications and its applications in therapeutics. I also had one year working with Floyd Romesberg, exploring the exciting semi-synthetic organism. Now I turned my research interest to ribosomes, one of the most beautiful, sophisticated and meanwhile complex systems in biology. I am now using the in vitro ribosome assembly assay to screen inhibitors which are specific for the assembling process.

Anne Zhou, Graduate Student

I am working on elucidating stepwise Gag assembly process in the presence of both lipids and RNAs. To accomplish this goal, we are looking into using nanodisc combined with single molecule TIRF technology to facilitate our observations. We aim to investigate how Gag comes into association with viral RNA and membrane lipids, how different Gag or RNA mutations would affect the assembly process, and how membrane lipids composition may play a role and to what extent.

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