Summer REU Program:
Re-IMAGiNE Life, Exploring Function through Adaptation

2022 REU dates: May 23 – July 29

The UA REU application site is open, click here!

Applications require one reference letter from a professor to be complete. Letters are to be sent to Dr. Julie Olson (jolson@ua.edu) and Dr. Michael McKain (mrmckain@ua.edu) by March 15, 022.

Final day to submit an application is March 8, 2022.
Reference letters are accepted until March 15, 2022.

Application review starts on March 16, 2022 and will continue until all positions are filled.

 

Understanding how genomic and environmental variation are integrated to give rise to complex traits via adaptation is one of the key challenges in biology. Although a wealth of genotypic and phenotypic data regarding how organisms respond under varying environmental conditions is now available, integrating this information into functional and predictive models of evolution continues to be challenging.The focus of this REU site is Re-IMAGiNE Life, Exploring Function through Adaptation. This topic encompasses a wide variety of subdisciplines within biology and creates opportunities for lab and/or field-based, hands-on research by undergraduate students to explore the interplay of genomes, phenotypes, and environments at all levels of biological organization.

Plant material ground in mortar Ciesla lab Plant extract in flask

Program highlights

  • 10-week research training opportunity
  • Students conduct individual research projects designed by faculty within the Department of Biological Sciences at the University of Alabama
  • Weekly academic and professional development programs
  • $6,000 stipend
  • Paid on-campus housing
  • $150 weekly food allowance
  • Up to $600 relocation stipend

Students who would benefit from this experience

  • Motivated students interested in learning more about what can be done with a degree in the life sciences
  • Students considering graduate school
  • Students within historically underrepresented groups, those with non-traditional backgrounds and academic paths, veterans, and first-generation college students are encouraged to apply

Requirements for eligibility

  • No prior research experience is needed but priority will be given to students who have completed at least one course in biology or a related discipline
  • Undergraduates who will be enrolled at a 2- or 4-year college or university in fall of 2022
  • United States citizens or permanent residents (requirement of NSF)
  • Applicants should be 18 years of age by May 23, 2022

What should students expect?

  • Robust training in modern and integrative scientific techniques
  • Full time work commitment for the 10-week period
  • Professional development, trips to local research centers, and networking with peers and faculty
  • Opportunities to present and/or publish their findings
  • Experience working in the labs of UA faculty

 


Faculty Mentors and Projects

 

Dr. Carla Atkinson
Adaptation of freshwater mussels to varying water temperatures

Carla Atkinson

Freshwater mussels are filter-feeders, so their feeding improves water quality and clarity. However, how mussels may adapt to changes in stream temperature and chemistry as a result of global climate change is not known. The REU student will measure filtration rates in multiple native species in temperature-controlled laboratory trials. In addition, they will assist with an in-stream transplant experiement to examine how growth rates and gut microbial communities respond to varying abiotic conditions. The student will collect mussels from local rivers, tag and measure mussels, grow and maintain algal cultures, perform thermal acclimations and data analyses, and will have the opportunity to interact with local and European collaborators.

 


 

Dr. Guy Caldwell
Neurobehavioral analysis of epigenetic factors regulating organismal response to neurodegeneration

Guy A. Caldwell

Closely related and even identical individuals exhibit variations in their ability to adapt to genetic and environmental stresses. Resilience to neurodegeneration will be examined in C. elegans, in which we have developed models to investigate factors influencing Parkinson’s and Alzheimer’s disease (PD, AD). Using RNA interference (RNAi), automated tracking of animal behavior, and microscopy, the REU student will conduct quantitative behavioral analysis experiments of specific genes that are modified by epigenetic regulation to discern phenotypes associated with dysfunctional dopamine or glutamate neurons, as associated with models of PD or AD.

 


 

Dr. Kim Caldwell
An environmental exposure that induces neuron cell death via ferroptosis

Kim Caldwell

Streptomyces venezuelae (S. ven) produces a secondary metabolite that can either extend or shorten lifespan, depending upon concentration. Similarly, neurons die at concentrations that shorten lifespan. Using transcriptomic profiling methods following S.ven metabolite-induced C. elegans, genes associated with oxidative stress response pathways were activated, which suggests that the metabolite triggers cellular redox changes. Cellular adaptation to environmental exposures are not well understood, so the REU student will examine several transcriptomic candidates using RNAi, along with S. ven exposure, a fluorescent indicator to evaluate the role of S. ven in neuronal cell death, and also perform a lifespan analysis in C. elegans.

 


 

Genetic analysis of temporal responses to RNA virus infection in insects

Stanislava Chtarbanova

Insects are exposed in their native environment to a myriad of pathogenic microorganisms, including viruses, and mount potent innate immune responses to protect themselves. However, how such adaptations have evolved in the course of insect ontogeny is not well understood. Using the model organism Drosophila melanogaster and a combination of classic genetic and molecular approaches, the REU student will investigate the role of selected candidate genes in age-dependent responses to infection with an insect BSL-1 RNA virus.

 

 


 

Dr. Lukasz Cielsa
Phytochemical profile changes of edible plants in response to environmental changes

Lukasz Ciesla

Compelling evidence suggests that diet rich in vegetables, fruit and herbs can prevent or delay the onset of numerous chronic diseases. These beneficial effects are often ascribed to plant phytochemicals, which are often produced in response to environmental factors such as drought, UV radiation or pesticides. Using techniques such as high-performance liquid chromatography, high-resolution mass spectrometry, and cryogenic nuclear magnetic resonance imaging, the REU student will evaluate the molecular mechanism of action of phytochemicals and their profiles under varying environmental factors.

 


 

Dr. Kaleb Heinrich

IMAGiNE biology education research

Kaleb Heinrich

The REU student will engage in the scholarship of teaching and learning with a focus on curricular development of functional genomics and/or organismal adaptations in a dynamic environment. Inquiry based lessons/labs will be developed, in conjunction with assessments to be used in undergraduate biology courses that incorporate evidence-based teaching and diversity, equity, and inclusivity practices. Materials will also align with the core concepts and competencies for biology education identified in the AAAS Vision and Change report (2011).

 

 


 

Dr. Melanie Higgins
N-glycan degradation in Actinobacteria

Melanie Higgins

Microbes have evolved many mechanisms to utilize glycans, the most abundant and diverse natural biopolymers, as sources of carbon and energy. Recently, it was discovered that certain gut- and soil-dwelling Actinobacteria have distinct polysaccharide utilization loci likely dedicated to degrading diverse N-glycan structures.  Although these loci share common core genes, they differ in genes that encode for auxiliary glycan degrading enzymes. The REU student will learn and apply in vitro protein biochemistry and structural biology studies of the different auxiliary enzymes to better understand if and how they contribute to distinct N-glycan metabolism profiles between gut- and soil-dwelling bacteria.

 


 

Dr. Matthew Jenny
Molecular mechanisms of tolerance and adaptation to environmental pollutants

Matthew Jenny

As a result of climate change, aquatic organisms are routinely being exposed to warmer temperatures that results in significant cellular stress.  Freshwater unionid mussels are one of the most imperiled group of aquatic organisms and a better understanding of how mussel species respond and adapt to environmental changes will greatly improve conservation and restoration efforts.  To compare the different responses to thermal stress among unionid species with different life-history strategies, the REU student will participate in mesocosm studies this summer in which up to four different unionid species will be exposed to a gradient of thermal challenges over the course of six weeks. During this time, metabolic and physiological measurements will be performed on the mussels. At the completion of the six-week thermal challenge, the REU student will have the opportunity to participate in the collection and analysis of several cellular and molecular biomarkers, including those for energy storage, changes in aerobic versus anaerobic respiration, cellular antioxidant assessment and changes in gene expression.

 


 

Dr. Brandon Kim
Analysis of microbial gene networks at the blood-brain interface

Brandon KimGroup B Streptococcus and Neisseria meningitidis are pathogenic bacteria that are able to cross the highly specialized blood-brain barrier and cause bacterial meningitis. To date, little is known about how these pathogens adapted their transcriptomes to interact with the blood-brain barrier. Using RNAseq data from the transcriptomes of both pathogens, the REU student will identify potential targets for gene knockout prior to performing allelic exchange mutagenesis and screening. Cell based assays to test the ability of the mutant(s) to interact with the blood-brain barrier will follow.

 


 

Dr. Michael McKain
Impacts of polyploid genome diploidization on the invasive potential of a grass species

Michael McKainPolyploidy is a common phenomenon in flowering plants and has been identified as a potential promotor of invasiveness. After polyploidy, genomes undergo diploidization that includes the loss of duplicated genes, reorganization of chromosomes, changes in expression patterns and other processes. The patterns of diploidization are likely a combination of stochastic and predetermined factors that, when coupled with natural selection, lead to lineage-specific variation. The REU student will use field work, genomics, and computational biology to investigate how diploidization has varied across populations and lineages of the allotetraploid species Sorghum halpenese as it spread across the US.

 


 

Dr. Julie Olson
Factors that increase the expression of secondary metabolites in environmental bacteria

Julie B. OlsonMany species of bacteria produce secondary metabolites, providing an advantage to the producing organism. However, other than entering stationary phase or exhaustion of a required nutrient, the environmental conditions that induce secondary metabolite formation in these organisms are not well understood. The REU student will investigate the effect of different environmental conditions (e.g., temperature, pH) on the production and diversity of secondary metabolites using a combination of microbiological cultivation methods, bioassays, and molecular genetic techniques.

 


 

Dr. Katrina Ramonell
Identification of protein targets involved in Arabidopsis defense responses

Katrina RamonellThe ubiquitin proteasome system is responsible for the regulation of critical cellular processes through the selective degradation of proteins. In Arabidopsis, the ATL protein family of ubiquitin E3 ligases, has been shown to play an integral role in plant defense against microbial pathogens. However, the protein targets of these E3 ligases remain largely unidentified. The REU student will perform a screen of an in-house 3X coverage Arabidopsis cDNA bimolecular fluorescence complementation library to identify potential interacting protein partners of ATL family E3 ligases that are involved in plant defense responses. This project will involve the use of microbiological cultivation methods, molecular biological techniques and confocal imaging microscopy.

 


 

Dr. Laura Reed
Examination of the evolutionary processes shaping metabolic regulation of homeostasis

Laura ReedUsing the model organism Drosophila melanogaster, the REU student will use bioinformatics and genomics to analyze the molecular evolution of gene regulation in the insulin signaling pathway. Additional laboratory experiments will be performed to test how the evolution of gene regulation relates to the robustness of metabolic regulation across diets, exercise, or other dimensions of environmental variation.