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Spotlights 2022

 

wbaker

December 2022 Spotlight
Dr. Wendy Baker

I was trained as an analytical chemist at TAMU with a focus on surface science but have happily spent the last 12 years doing various types of biological research at UTMB.  I’ve used triple resonance NMR to study the HIV-1 RNA transport molecule Rev, searched for biomarkers for hepatocellular carcinoma using 1H NMR and nanoflow TQMS, and investigated the reliability of a portable thrombosis detector for warfarin therapy patients.  Currently I’m working under the guidance of Dr. Catherine Schein and Dr. Werner Braun to develop a computationally designed protein vaccine which will confer immunity against multiple alphaviruses.

I get a kick out of being in the lab, learning about different areas of biology, being helpful to others, and mastering new analytical techniques.  I’m a mother of two spirited teenage girls (and way too many cats), voracious reader, vegetarian cooking enthusiast, and lover of the great outdoors.  If you see me strolling around campus on an afternoon tea/sunshine break feel free to say hello.

 

portraits-2018-khin-khine-zar-mon

November 2022 Spotlight
Dr. Khine Kai Mon

I am a postdoc fellow in Dr. Linda Kenney’s lab and joined UTMB in the year 2020. Being a microbiologist, I was always intrigued by microbes and their versatile lifestyle. More specifically, I am fascinated by the intricate interplay between the host and pathogen with reciprocal influence on each other during disease progression. To fully understand the pathogenesis of microbes, it is important to investigate and unravel the complexity of host-microbe interactions that affect the overall health status of animals and humans. In my Ph.D. work at UC Davis, I examined the interplay of trios: host, pathogen, as well as gut microbiota in the chicken host during Salmonella infection through multi-omics technologies. My graduate work elucidated both molecular and cellular mechanisms that contributed to the colonization persistence of Salmonella in the gut of young chicks. Building upon my previous experience working with chicken and Salmonella pathogen, my current research work focuses on unraveling the full mechanistic insight on tumor colonization and accumulation by Salmonella Typhimurium using a unique chick embryo chorioallantoic membrane (CAM) model. The overall aim is to develop the CAM model as a robust experimental platform for identifying key bacterial virulence factors that promote anti-tumor activity for the future development of therapeutic strains for bacterial-mediated cancer therapy.

Dr. Chen (2)

October 2022 Spotlight
Dr. Yunfeng Chen

My research focus is mechanobiology and vascular biology. We study the adhesion and mechano-sensing of vascular cells like platelets and neutrophils, and how these events go wrong in diseases. Eventually, we aim to come up with groundbreaking strategies to interfere with cell mechanobiological functions for treating diseases, abiding the concept of 'mechano-medicine'.

I always loved biology and medical science. Although my undergraduate major was mechanics because I was quite good at it, I explored whether mechanics can be connected with biology, and I was thrilled to find that there is actually such a field named "mechanobiology". So upon receiving my bachelor's degree, I joined Georgia Tech and started to study mechanobiology, which was the beginning of my research career. I hope that one day I can develop 'mechano-medicines' to treat diseases that are currently untreatable and improve human health.

I love watching movies and playing video games. I also enjoy spending time with my family. I am a lyric writer in Chinese. I have written more than 50 lyrics, and co-produced several songs, which were launched in multiple platforms.

You can find out more about our lab and research at: https://scsb.utmb.edu/labgroups/chen/welcome     @YunfengChen2

 

Feinberg_Headshot (2)

September 2022 Spotlight
Mandi Feinberg

I am beginning my fourth year as a PhD candidate in the Molecular Biophysics track of BCMB in Dr. Kay Choi’s lab. My research interests are in virology and structural biology. I got involved in research during undergrad at Virginia Commonwealth University through a Phage Discovery course where I isolated a mycobacterium phage from a soil sample. Visualizing my phage via electron microscopy was one of the most fascinating and rewarding experiences and little did I realize that it was the start of my career in structural biology. My current research focuses on determining the mechanism for synthesis of the West Nile virus genome. I am utilizing biophysical assays and X-ray crystallography to determine the structures and interactions of the viral polymerase (NS5) with the RNA promoter (stem-loop A) structure at the beginning of the 5’ untranslated region of the viral RNA genome.

My love of science extends outside the lab to my love of baking. There are many days where you might be able to find some baked goods or bread outside the lab. If I am not in the lab or baking, you can usually catch me at the island brewery or taking too many photos of my cat, Franklin, named after one of my favorite scientists. You can follow me on twitter @MandiFeinberg!

 

Henock

August 2022 Spotlight
Dr. Henock Deberneh

I joined UTMB as a postdoctoral fellow at the beginning of this year. My career started in Addis Ababa, Ethiopia, as A computer engineer. I completed my Ph.D. in South Korea with a major in information and communication engineering. I am interested in the medical application of machine learning and data science. Currently, I conduct my research within professor Rovshan Sadygov’s research lab. Our research focuses on the theoretical development of bioinformatics and statistical approaches to address challenges posed in biological inferences from high-throughput proteomics data. We have developed software that can quantify protein turnover rates and visualize the depletion of the mass isotopomers. The visualization tool can be used to validate spectral errors in mass spec data. Furthermore, the software has improved the number of quantified peptides significantly as compared to the previous version. Currently, we are working on implementing the alignment of chromatographic surfaces in the presence of metabolic labeling. The alignment information will be used for peak detection and quantification of peptides that have been fragmented and identified in some, but not all, experiments. This method will be used to address the missing value problem in protein turnover studies and will improve the power analysis of degradation rate constant estimation.

 

Yiyang Tommy Zhou

July 2022 Spotlight
Dr. Yiyang Tommy Zhou

I am a research scientist in Department of Biochemistry and Molecular Biology. My research interest is molecular virology. I started my journal with viruses when I was a graduate student in Baylor University. My Ph.D. work is around the development of a plant-based vaccine platform which uses a plant virus capsid to “trans-coat” an animal virus RNA. Fascinated by the nature of viruses, I joined UTMB 5 years ago in Dr. Andrew Routh group. My current research focuses on using and developing next generation sequencing tools to understand the molecular interactions inside virus particles (such as RNA-capsid interactions and RNA-RNA interactions) as well as the interactions between virus and host cells. These dynamic interactions ultimately dictate virus structure features, their biological functions, and the direction of evolution. I work with a wide range of viruses, from a model virus (the mighty Flock House virus!) to important human pathogens (CHIKV, HIV-1, SARS-CoV-2 etc.). You can find more about my research on Twitter@TommyGottaGo.

Just like the dynamic life cycle of a virus, I too enjoy a dynamic lifestyle in my spare time: both the active (i.e. chasing and being chased by my dog) and the peaceful (letting my cat sit on my lap and being sucked into a vacuum of time).

 

June 2022 Spotlight
Dr. Krishna Rajarathnam

I am a Professor in the Department of Biochemistry and Molecular Biology and started my career in UTMB as an assistant professor more than 20 years ago. We are interested in the very early events of how the host immune system responds to microbial infection. In particular, my lab studies the molecular mechanisms by which chemokines, a family of inflammatory proteins, orchestrate leukocyte migration from the blood to the infected tissue to eliminate the pathogens. We address these questions at a molecular, cellular, and systems level, using tools and methods in protein biochemistry and engineering, solution biophysics, computational biology, solution NMR spectroscopy, and animal models. You can find more about our work at our website (https://bmb.utmb.edu/people/faculty/bios/rajarathnam).

 

May 2022 Spotlight
Valerie Rodecap

Valerie is the Director of Business Operations and works closely with Dr. Mariano Garcia-Blanco toward the mission of the department.  Her scope includes supporting Faculty, Staff and Students in their research and education and maintaining successful operations in the department.   She serves as a liaison with Provost Office, Faculty Relations, HR, and the Graduate School of Biomedical Sciences for various processes along with many other administrative matters.  Valerie is from Kansas and has past professional experiences from working in an investment brokerage firm, as well as clinic and hospital settings.  She has been in the BMB for 6 years.   Valerie enjoys her career at UTMB and especially in BMB because it is motivating to be a part of a goal driven department that strives to be the best and recognizes the outstanding talent of our faculty and staff which makes everything, we do here meaningful.

 

April 2022 Spotlight
Dr. Andy (Andrzej) Kudlicki

I am a computational biologist, interested in various aspects of transcriptional and epigenetic regulation in disease and development. I joined UTMB in 2009, after a postdoc in UT Southwestern in Dallas, TX. My effort is divided between original research at BMB and collaborative projects conducted within the Informatics Service Center at the Institute for Translational Sciences.

The long-term goal of my research is to understand how and why transcription factor binding sites are selected and how chromatin modifications are directed to specific sites, depending on the time, cell type and environmental factors. In human and other vertebrates, the numbers of metameric segments in each region of the spine, as well as the total number of vertebrae are highly conserved, for example almost all mammals have exactly seven cervical vertebrae. The identity of body segments depends on the Hox transcription factors, that are in turn controlled by chromatin modifications, but it has been unknown how chromatin state is regulated in a robust, segment-specific manner.

 I have discovered a regulatory element (HRC3 motif) that is responsible for recruiting histone demethylases to the correct loci, and I have proposed a mechanism that allows cells to obtain and store the segmental information in digital form, and to produce a pattern of chromatin accessibility that in turn regulates Hox gene expression. The finding explains how counting of segments is performed by the developing embryo, and how the numbers are encoded in the genome. My model of segmental identity allows correctly predicting the numbers of segments in a vertebrate using only sequence information; it also resolves the 40-year-old enigma of the function of temporal and spatial collinearity of Hox genes.

Currently, I am working on expanding the model of segmental identity into a more complete theory that explains multiple aspects of evolutionary developmental biology. I am exploring a connection between this process and certain diseases, including Huntington's Disease, and autosomal dominant Spinocerebellar ataxias. Before I became a computational biologist, I used to do research in astrophysics, working on motions of clusters of galaxies and estimating the total mass of the Universe. When I am not in the lab, you might find me windsurfing on Galveston Bay, taking night-time photographs, or playing at a local bridge tournament. (Twitter @aanzelm)

Dr. White

March 2022 Spotlight
Dr. Mark White

My major interests include developing the tools of Structural Biology, the pursuit of novel macromolecular structures and complexes, and their functional analysis. I employ single crystal x-ray crystallography and solution macromolecular small angle x-ray scattering (BioSAXS) to determine the structure and function of macromolecules, their complexes, and inhibitors. In varied structural collaborations I have studied: a number of flavivirus proteins, the DNA packaging motor assembly used by Phage, the assembly of amyloid and self-assembling nanoparticle fibrils, structural changes to the cAMP-binding proteins CRP and EPAC, domain assembly in synaptic proteins, protein-DNA interactions, cytochrome P450 inhibition, and the repurposing of drugs to target the SARS-CoV-2 nsp13 helicase. While crystallography offers high resolution detail of a molecule and its interactions many structural studies are limited by the possible: the study of static structures. BioSAXS opens up an avenue to the study of dynamic and even unstructured molecules of almost any size, from disaccharides to viral particles. At it’s simplest the assembly, oligomerization state, or domain organization can be confirmed, determined, or modeled. At its most complex the distribution of multiple conformational states may be determined.  BioSAXS offers a tool for the validation of Molecular Dynamics simulations, which in reciprocity provides molecular models for the analysis of SAXS data. BioSAXS analysis is a powerful addition to any structural study, be it crystallography, electron microscopy, or NMR.

 

February 2022 Spotlight
Dr. Yu-Hsiu (Eric) Wang

I am from Taiwan and I’m a Research Assistant Professor in the Department of Biochemistry and Molecular Biology. I carry out my research within the Dr. Michael Sheetz’ research group. Fascinated by the world of phosphoinositide lipids, I developed a great interest in the signaling of phosphoinositide lipids not only in the plasma membrane but also in the nucleus, which involves early DNA damage signaling, genotoxic stress sensing and RNA processing. My research focus sits on the dynamics and molecular basis of nuclear lipid signaling in early DNA damage repair. Tumor suppressor p53, which was discovered as a nuclear phosphoinositide-binding partner in 2019, also became an important part of my study. In collaboration with Dr. David Lane, who discovered p53 in 1979, we characterized a transcription-independent activity of p53 which involves rapid damaged DNA sensing and correlates with its tumor suppressive function. My ultimate goal is to characterize nuclear lipid biology and understand how lipids regulate protein functions in the nucleus. I believe this knowledge will provide us a different handle in fighting genome instability, cancer and relevant diseases.

As a microscopist, I enjoy photography, filming and editing. The sunrise and sunset at Galveston beach is amazing.

 

M_Ward

January 2022 Spotlight
Dr. Michelle Ward

I joined BMB and UTMB as an Assistant Professor in 2020. My lab is interested in understanding the mechanisms of global transcriptional regulation, and the control of tissue-specific gene expression in the context of cardiovascular development, stress and disease. We consider variation between human individuals as well as variation between species to tackle this problem using induced pluripotent stem cell and next-generation sequencing technologies. My research journey started in Cape Town, and continued on via Cambridge and Chicago – I broke the string of cities starting with “C” when starting at UTMB! I do enjoy working on an island and being able to look out at the gulf and palm trees every day though. You can find out more about our lab and research here (https://www.ward-lab.org/) or follow me on Twitter (@michelle_c_ward).