Biology Research labs
(L to R) Farhana Runa, PhD; Elizabeth Ortiz; Matthew Wallace;
DEVELOPMENTAL ONCOGENE LAB
Progression of cancers in the breast, pancreas and liver involve tumor cell proliferation, therapy resistance and metastatic dissemination to distant tissues – there is a strong correlation between these events and poor patient survival (Wang et al. 2019 BMC Cancer). Notably, many signaling pathways and molecular/cellular mechanisms that control normal tissue homeostasis and repair are reactivated and/or dysregulated during the progression of solid tumors. My research laboratory aims to identify and elucidate how cell intrinsic and extrinsic factors regulate cancer metastasis and therapy resistance, and whether these mechanisms may also control normal tissue repair processes. Ultimately, our goal is to develop novel strategies to diagnose cancers earlier and treat disease progression more effectively.
Two- and three-dimensional in vitro/ex vivo cell systems, primary patient samples, molecular biology, live-cell microscopy, multiplexing single-cell immunofluorescence, flow cytometry, RNAseq, bioinformatics and preclinical vertebrate animal models.
(L to R): Alagu Subramanian; Emily York; Jacob Bailey; Lydia Allabaugh; Michelle Pujols; Santha Rangananthan, PhD; Sam Davis; Joe Taube, PhD; Tolu Ojo; Charli Worth; Juli Watkins; Haleigh Parker; Kayla Haberman; Adhwaitha Nambiar; Maya Cappellino; Jenna Tobin
Not Pictured: Alison Whitley
EPIGENETICS AND CANCER LAB
Outgrowth of disseminated metastases is the major cause of mortality in cancer patients. In the Taube lab, we are investigating the molecular pathways and cellular properties which enable primary tumor cells to metastasize. In normal tissues, epithelial cells form a well-structured barrier using a variety of adhesion molecules. However, aberrant activation of a conserved cellular program, termed epithelial-mesenchymal transition (EMT), facilitates the separation of epithelial cells from this tissue. When EMT occurs in epithelial tumors, the probability of metastatic dissemination is increased. Our current work is focused on uncovering the regulatory mechanisms which facilitate EMT in both normal and cancerous settings, describing the specific targets and roles of these regulatory mechanisms and testing small molecule inhibitors of these proteins to ultimately lead to novel therapeutic strategies.
Molecular biology, live-cell microscopy, CRISPR, immunofluorescence, flow cytometry, RNAseq, bioinformatics and preclinical vertebrate animal models.
(L to R) Prabin Dhungana; Bryan King; Cheolho Sim, PhD; Ryan Wei
Not pictured: Tatyana Martynova
VECTOR BIOLOGY LAB
The Sim lab has two major focuses for research: Photoperiodic diapause and sex determination in the mosquito Culex pipiens. Insect diapause is a physiologically dynamic state of arrested development caused by interpretation of the short days of late summer and early fall. We have uncovered a role for insulin signaling and the forkhead transcription factor (FOXO) in regulating diapause in Cx. pipiens. Although we are gaining a clearer picture of the hormonal pathways underlying diapause in Cx. pipiens, we still do not know how any animal is able to measure and interpret daylength. Accordingly, there is a critical need to determine how animals translate environmental signals into molecular regulators so that we can fully understand how mosquitoes and other animals properly time their growth and reproduction to coincide with favorable environmental conditions and alter their physiology to survive harsh season.
RNAi, insect cell culture, microscopy, western blot, microinjection, qRT-PCR
(L to R Backrow): (Isaac Montgomery; Trent Rothell; Aadil Sheikh; James Lotter; Colin Scano; Ankan Choudhury, PhD
(L to R Frontrow) Ella von Dohlen; Sudili Fernando; Madhur Wyatt; Leigh Greathouse, PhD; Kaitlin Tremble; Lauren Crowhurst; Alea Brummel; Allison Jung
Not pictured: Julia Xu
DIET, MICROBIOME, AND CANCER RISK LAB
Our research group is dedicated to illuminating the intricate relationship between diet and the microbiome and their effects on cancer development and treatment, with a focus on colorectal cancer. Our goals encompass three key objectives: 1.) Identifying dietary factors that influence the microbiome and their impact on colon cancer. 2.) Elucidating the fundamental mechanisms governing communication between microbiota and the host. 3.) Developing dietary and microbial classifiers to enhance patient stratification for colon cancer treatment. Our aim is to uncover dietary factors and microbial targets, enabling the creation of clinical tools that effectively prevent colon cancer development and significantly reduce associated morbidity and mortality.
- 16s rRNA sequencing and analysis.
- Isolation and characterization of bacterial outer membrane vesicles.
- Growth and characterization of anaerobic bacteria.
- Animation of polymicrobial communities in a continuous reactor.
- Dietary intervention study design in humans focused on interaction with the gut microbiome.
- Dietary pattern analysis.
- Colon organoid generation and maintenance.
(L to R): Raquel Guerrero; Princesa Alvarez; Hunter Martin; Patrick Ortiz; Chris Kearney, PhD; Mik Young, PhD; Anusha Paul Raj; Toslim Mahmud, PhD
TARGETED PATHOGEN CONTROL LAB
Our focus is on developing methods for specifically controlling gastrointestinal pathogens without disturbing the rest of the microbiome. We are currently using antimicrobial peptides fused to guide sequences which bind to a target protein on surface of the targeted bacterium. We are able to eliminate an infection of H. pylori within 5 days in a mouse model using a single dose of a probiotic bacterium engineered to secrete the guided antimicrobial peptide (Microbiology Spectrum, in press). We are expanding this technology to other pathogenic bacteria and are interested in studying the mechanism of this specificity.
Genetic engineering, ligation independent cloning systems
Protein production in E. coli expression systems
Protein purification, FPLC
BSL2 bacterial culture
Flow cytometry, confocal microscopy
VECTOR-BORNE DIESEASES LAB
Vector-borne diseases are a persistent global health threat. A plethora of questions remain about the evolutionary changes that occur within a vector-borne disease system in settings of recent mosquito vector invasions and range expansions. Understanding how mosquito vectors adapt to new environments with different climates, landscapes, and anthropogenic forces can inform models of future spread. Furthermore, understanding the compatibility between invasive vectors and local parasite populations before and after invasions is crucial for predicting the impact of invasions on local malaria epidemiology. Our research program explores these topics using genomic analysis of natural vector and parasite populations. Currently, we are investigating the invasion of malaria vector An. stephensi in Africa and the Arabian Peninsula. Using several -omic approaches, we work on understanding An. stephensi’s evolutionary history, the development of insecticide resistance, patterns of local adaptation, coevolutionary and molecular interactions between invasive vector and local Plasmodium strains. We are also investigating the utility of Aedes genomic data sets for predicting An. stephensi emergence and spread. Finally, we evaluate and design field executable approaches for molecular surveillance of the invasion.
Sequence analysis (targeted, genome-wide), evolutionary genetic analysis (phylogenetic, population genetics), basic bioinformatics, nextgen sequencing library preparation, DNA/ RNA extractions, PCR, gel electrophoresis
(L to R Backrow): Shittu Oluwatosin; Amelia Wickham; Noah Flood; Ashish Anand, PhD; Aaron Wright, PhD; Harrison Hall
(L to R Frontrow): Whitney Garcia, PhD; LaRae Hudson; Chinenye Nwike; Laura Truong; Kamila Montenegro; Isabelle Russo; Sara Farahani
Not Pictured: Bryana Trejo
MICROBIOME MECHANISMS AND BIOLOGICAL CONSEQUENCES LAB
The Wright group investigates host-microbiome-environment interactions with functional resolution at the molecular scale. The Wright group performs interdisciplinary research in microbiology, chemical biology, systems biology, and functional multi-omics to study protein function and protein-small molecule interactions in host-associated microbes and microbiomes, and directly in host organisms. Towards mechanistic understanding of host-microbe-environment interaction mechanisms, we are focused on:
- Identifying and validating the mechanisms of drug and xenobiotic metabolism in the gut microbiome
- Determining the impact of chemical exposures during development on the gut microbiome
- Characterizing microbial mechanisms of mucin & carbohydrate deconstruction, particularly in irritable bowel diseases and in response to chemical exposures
- Mapping phenotypic outcomes to molecular determinants of biochemical activity
- Developing novel chemical biology and multi-omics methodologies to enable discoveries in biology at the molecular scale with functional resolution
Microbiology / microbiome sciences, anaerobic microbiology, genomics, metabolomics, proteomics, chemical probes, organic synthesis, protein labeling, protein expression
(L to R Backrow): Dhivya Rajamanickam; Heidi Pullmann-Lindsley; Matthew Cooke
(L to R Middlerow): Ben Turnley; John Boyi; Ava Miller; Nathan Truong; Jason Pitts, PhD
(L to R Frontrow): Caleb Hemphill; Duncan Crosby
ARTHROPOD SENSORY BIOLOGY LAB
Our lab investigates the molecular and sensory neuronal mechanisms that are critical to the life histories of insects and other arthropods of medical and agricultural importance. Of particular interest are the pathways that contribute to chemical- and temperature-oriented behaviors such as host-seeking, nectar feeding, and oviposition site selection. Our major objective is to understand complex biological systems by employing a range of techniques including gene expression, neurophysiology, and animal responses to sensory stimuli.
(L to R): Bessie Kebaara, PhD; Lauren Jaramillo; Ethan Blasdel; Xinyi Zhang; Ethan Blasdel; Sunday Olaniyan; Elizabeth John; Q Carrol
Not Pictured: Jana Chao; Xavier Juarez-Jacinto; Alice Qiu
THE NONSENSE LAB
We are interested in how the environment controls the regulation of gene expression at the messenger RNA level. Specifically, we investigate the recognition and targeting of natural mRNAs by the nonsense-mediated mRNA decay (NMD) pathway using the model eukaryote Saccharomyces cerevisiae. NMD is an evolutionarily conserved mRNA decay pathway that recognizes and degrades mRNAs that prematurely terminate translation. Our goal is to understand the recognition and targeting of natural mRNAs by NMD and determine the physiological consequences that result from the degradation of specific natural mRNAs. Currently, we are investigating the regulation of natural mRNAs involved in biometal homeostasis and toxic metal detoxification by the pathway.
Yeast microbiology, molecular Biology, RNA techniques, Northern Blotting.
(L to R): Abby Smason, Brittany Carnathan; Jasmine Stovall; Alex Hoke; Jaylen Powell; Thad Scott PhD; Isabelle Anderson; Caleb Robbins, PhD; Sara Coppellotti; Rhea Bogarapu
LIMNOLOGY AND AQUATIC BIOGEOCHEMISTRY LAB
The Scott lab conducts research on the reciprocal relationship between aquatic microorganisms (phytoplankton, bacterioplankton, periphyton) and their chemical environment across spatiotemporal scales from populations to ecosystems. Our work involves both basic and applied questions such as the role of diazotrophs in controlling the nitrogen pool of lakes and the causes and effects of harmful algal blooms, respectively. We are interested in applying limnology to understand general ecological patterns and processes in nature, and to understand how microbial biogeochemistry impacts human welfare through water quality.
Phytoplankton isolation and culturing, Membrane Inlet Mass Spectrometry (MIMS), phytoplankton identification, chlorophyll-a extractions, cyano-toxin quantification, DNA extraction, sediment coring, ecosystem stoichiometry analyses, dissolved and total nutrient analysis, ecological forecasting, having fun on a boat
(L to R): Malcolm Macleod; Lacy Miller; Steve Powers, PhD; Luke Day
GLOBAL CHANGE AND AQUATIC ECOSYTEM ANALYSIS LAB
High-speed mapping of water quality in lakes and rivers with sensor-equipped boats, analysis of biological and chemical influences on water color, distributed sensor networks, Github collaboration, R/Rstudio, time series modeling, geospatial analysis.
Bear Bear Bear
BEAR BEAR BEAR LAB
Bear bear bear bear bear
Picking berries, catching fish, climbing trees