REU: Bioenergy Systems

Study Bioenergy! The research of today for the solutions of tomorrow.

For information contact

Dr. Paul Blum
Charles Bessey Professor of Biology
402-472-2769
pblum1@unl.edu

Julie McManamey
REU Support Staff
402-472-7665
julie.mcmanamey@unl.edu

2016 Bioenergy Systems REU scholars touring Sheldon Power Station.
2016 Bioenergy Systems REU scholars touring Sheldon Power Station.

Application Dates

Nov 15 2016 App opens
February 1 Priority deadline
March 1 App closes
April 1 Decisions complete

Program Dates

June 4 2017 Arrival day
June 5 Program begins
August 9 Program ends
August 10 Departure day

Who should apply


Related fields

  • Biology
  • Biochemistry
  • Microbiology
  • Molecular Biology
  • Plant Science

Applications are encouraged from students with sophomore standing or higher and a GPA of 3.0 or higher.

Eligibility

Participation in the Nebraska Summer Research Program is limited to students who meet the following criteria:
  • U.S. Citizen or Permanent Resident
  • Current undergraduate with at least one semester of coursework remaining before obtaining a bachelor's degree

See Eligibility for more information.

How to apply

Follow the application steps to submit the following materials.

About the Program

One of the greatest challenges facing 21st-century society is finding a sustainable energy supply. Energy is the basis for a large portion of the global economy and we are currently primarily dependent on nonrenewable fossil fuels. Not only are reserves dwindling, but nonrenewable fossil fuels also contribute significantly to pollution and climate change. With adequate research and proper implementation, plants, algae, and other microorganisms have great potential to help address the energy crisis.

UNL’s Integrated Development of Bioenergy Systems REU is funded by NSF and administered by the School of Biological Sciences. We collaborate with faculty mentors within five departments as well as the Center for Plant Science Innovation to provide diverse research opportunities with laboratories covering a wide spectrum of bioenergy research topics. You are matched with a faculty mentor and participate actively in the design and implementation of a ten-week research project in order to contribute new knowledge to sustainable energy systems.

Bioenergy REU Scholars researching algae as a biofuel
Bioenergy REU Scholars researching algae as a biofuel

Bioenergy seminars, a group writing project and touring a local power plant provide opportunities to exchange ideas with other students, researchers, and faculty. The program offers graduate school and professional development seminars as well as social and recreational activities.  

Benefits

  • Competitive stipend: $5,250
  • Suite-style room and meal plan
  • Travel expenses to and from Lincoln
  • Campus parking and/or bus pass
  • Full access to the Campus Recreation Center and campus library system
  • Wireless internet access

Learn more about academic and financial benefits.

Events

  • Campus and department orientation
  • Department seminars and presentations
  • Professional development workshops (e.g., applying to graduate school, taking the GRE)
  • Welcome picnic
  • Day trip to Omaha's Henry Doorly Zoo
  • Canoe and camping trip
  • Research symposium

Mentors and Projects

Dr. Audrey Atkin School of Biological Sciences

Co-regulated Gene Networks

The Atkin lab studies RNA biology with a particular emphasis on regulation of gene expression using eukaryotic model systems.

Dr. Paul Blum School of Biological Sciences

Energy Metabolism in Thermophiles, Algae and Fungi

Diverse microbes are being engineered to improve synthesis of renewable energy and chemical feedstocks such as cellulosic ethanol, biohydrogen, and chemical intermediates.

Dr. Nicole Buan Department of Biochemistry

Metabolic Engineering of Methane Production by Anaerobic Archaea

Natural gas provides up to 50% of all US domestic energy needs. It is primarily composed of methane and is an important fuel for transportation, heat, and generating electricity. Methane-producing archaea (methanogens) are naturally-occurring microbes found in the environment that can make methane from renewable biomass. The Buan lab is focused on engineering methanogens by manipulating the electron transport system to produce organisms that are suitable for industrial-scale production of methane as a renewable energy source.

Dr. Edgar Cahoon Department of Biochemistry & Center for Plant Science Innovation

Metabolic Engineering and Functional Genomics of Oilseed Crops for Improved Oil Content and

We conduct research to modify lipid metabolism in oilseeds and algae to increase the oil content and improve fatty acid composition of vegetable oils for biofuels and biobased lubricants. Our research encompasses the use of metabolic engineering and synthetic biology for improvement oil and seed co-product traits in crops such as soybean and camelina. The research not only is aimed at outcomes to address world energy needs but also at providing basic insights into plant and algal fatty acid biosynthetic and metabolic pathways and their regulation.

Dr. Heriberto Cerutti School of Biological Sciences & Center for Plant Science Innovation

Algae as Model Systems for Oil Biosynthesis and Biofuel Production

We are interested in improving, by genetic, genomic and biochemical means, the capability of algae to accumulate oil in order to create a reliable and sustainable source for the production of next generation biofuels. Undergraduate students participating in these projects will have the opportunity to learn a variety of biochemistry, molecular biology and bioinformatics techniques; participate in the design, execution and interpretation of experiments; and contribute to publication in scientific journals.

Dr. Steve Harris Department of Plant Pathology & Center for Plant Science Innovation

Chemical Signaling in Fungi as a Potential Source for Biofuels

Fungi utilize an array of chemical signals to coordinate growth, morphogenesis, and development. Because these signals are related to biofuels and other high-value compounds (e.g., butanol, farnesol), we are interested in learning how they are synthesized and in understanding their mechanisms of action. Current projects will focus on the use of functional genomic screens.

Dr. Joshua Herr Department of Plant Pathology & Center for Plant Science Innovation

Genome sequencing of growth promoting bacterial endophytes of bioenergy plants

Summer REU projects will consist of a two-part "wet-lab” and “dry-lab” exercise to sequence the genome of a plant growth promoting bacterial isolated from bioenergy plants.  Each student will select a pre-cultured bacterial isolate from our culture collection, will grow the isolate in culture, and will extract and prepare DNA for sequencing.  After DNA sequencing takes place, the student will use computational methods to assemble, quality assess, and annotate genes, potentially determining the microbial mode of action on plant growth.  Finally, each student will author a peer-reviewed publication for the journal Genome Announcements which will describe their process.

Dr. Robert Hutkins Department of Food Science and Technology

Modulation of the gut microbiota by prebiotics

The Hutkins Lab studies bacteria important in human health and in fermented foods. The lab is particularly interested in understanding factors that affect persistence of probiotic lactic acid bacteria and bifidobacteria in the gastrointestinal tract. Specifically, we are focused on establishing the molecular basis for metabolism of prebiotic oligosaccharides and how these prebiotics shift the intestinal microbiota in humans and animals. We are also interested in the anti-adherence properties of oligosaccharides against intestinal pathogens and the molecular mechanisms involved in pathogen binding to the surface of host cells.

Dr. Kenneth Nickerson School of Biological Sciences

Physiological Aspects of Quorum Sensing in Eukaryotes

Our lab studies bacterial, fungal, and algal systems. Active areas of research include: fungal dimorphism in Candida albicans and Ceratocystis ulmi; farnesol as a quorum sensing molecule (QSM) produced by C. albicans; farnesol's mode of action as a QSM and as a virulence factor; anaerobic growth of C. albicans; urea metabolism in C. albicans and other fungi; biotinylated histones in C. albicans; chlamydospore formation in C. albicans; high cell density QSMs from diatoms and other algae; detergent resistance in algae; and microbial ecology of alkaline lakes in Western Nebraska.

Dr. Wei Niu Department of Chemical & Biomolecular Engineering

Microbial synthesis of chemicals from renewable feedstocks

Microorganisms are natural chemical factories at micrometer scale. The Niu lab focuses on applying systems metabolic engineering principles and synthetic biology tools to microbial hosts, such as E. coli and yeast, to achieve the microbial syntheses of diverse molecules ranging from biofuel to high value-added pharmaceutical intermediates. Students will be exposed to both wet-lab techniques, such as molecular cloning and protein purification, and computational tools for data analysis.

Dr. Wayne Riekhof School of Biological Sciences

Lipid biology, biochemistry and molecular biology of algae

Research in my lab focuses on using microbial eukaryotic model organisms as systems to study various aspects of lipid metabolism, including membrane lipid and fatty acid trafficking between organelles, the regulation of membrane lipid and triglyceride synthesis, and the regulation of lipid droplet assembly and morphology. 

Dr. Rebecca Roston Department of Biochemistry & Center for Plant Science Innovation

Stress-triggered membrane remodeling as a learning platform for energy production in land plants

Formation and maintenance of the photosynthetic membrane and the responses of membranes to severe stresses are studied. These topics are relevant to improving crop engineering strategies resulting in healthier, more stable crop production. Students will have the opportunity to use techniques from basic plant growth to lipid quantification using gas chromatography and everything in between.

Dr. Rajib Saha Department of Chemical & Biomolecular Engineering

In Silico Aided Metabolic Engineering of Actinobacillus succinogenes for Production of Succinate

Prerequisites: http://engineering.unl.edu/chme/faculty/rajib-saha/

Actinobacillus succinogenes is a facultative anaerobe with higher productivity and ability to grow on a broader range of sugars including glucose and xylose. Rafieenia has developed a small-scale metabolic model by including the central carbon metabolism and tested different ratios of glucose and xylose as substrates and also the effect of blocking acetate formation on succinic acid production. Although this strain has been utilized to remove CO2 from biogas and subsequently convert it to succinic acid, its full metabolic potential still remains to be explored. To this end, we will fist construct a genome-scale model (GSM) for A. succinogenes using a semi-automatic pipeline in the SEED database. The GSM will subsequently be curated, gap-filled, and incorporated with the estimated growth and non-growth associated ATP (GAM & NGAM) requirements. Next, we plan to characterize its metabolic capabilities on a system-level and, subsequently, apply computational strain design techniques to propose nonintuitive genetic intervention strategies to overproduce succinic acid by fixating CO2 from biogas, while the strain is growing on xylose.

Dr. James Schnable Department of Agronomy & Horticulture & Center for Plant Science Innovation

Comparing the genomes and phenomes of grain crops in response to abiotic stresses

Using a combination of high throughput sequencing, comparative genomic and computer-vision based phenotyping, the Schnable lab works on developing new techniques to identify genetic differences between related crop species, and link specific changes in gene sequence or gene regulation to variation in abiotic stress tolerance between maize (corn) a highly productive but relatively stress sensitive crop and closely related species with higher levels of stress tolerance including other crop species such as sorghum and pearl millet, as well as wide species such as Paspalum vaginatum (a salt tolerant species that can grow right on the beach).

Dr. James Van Etten Department of Plant Pathology & Center for Plant Science Innovation

Pathogens of Algae

Research in the Van Etten laboratory focuses on the isolation and characterization of large (encode more than 400 proteins) icosahedral, dsDNA-containing, plaque-forming viruses that infect certain unicellular, eukaryotic chlorella-like green algae. These viruses are ubiquitous in fresh water from all over the world. In addition to being pathogens, the algal viruses are a source of elements (e.g., promoters) for genetically modifying algae for biofuels.

Dr. Karrie Weber School of Biological Sciences & Department of Earth & Atmospheric Sciences

Rock and the Role of Microorganisms in the Environment

Microorganisms are capable of utilizing a diversity of energy sources in the environment as such their metabolism has contributed to the production of bioenergy. Research in the Weber laboratory assesses and seeks to understand how these organisms take advantage of Earths minerals to produce energy as well as influence carbon, nitrogen, iron, and uranium cycling in aquatic, soil, and sedimentary environments.

Dr. Mark Wilkins Department of Biological Systems Engineering

Production of ethanol from Nebraska waste wood sources

Nebraska and other Central Plains states have experienced a massive spread of eastern redcedar trees that are disrupting traditional prairie ecosystems and degrading pasture land. Also, the emerald ash borer was recently found in Nebraska and will inevitably destroy Nebraska’s ash trees. Unfortunately, most of Nebraska’s eastern redcedar and ash trees have no lumber value; therefore, their current value is limited to providing heat through combustion. This project will look at using modified sulfite-based pretreatments to remove lignin from ash and redcedar wood.  Then, the wood will be hydrolyzed enzymatically to produce fermentable sugars, which will be fermented to produce ethanol.

Dr. Bin Yu School of Biological Sciences & Center for Plant Science Innovation

RNA Silencing in Plants

RNA silencing is a process triggered by 21-24 nucleotide RNAs to repress gene expression. The Yu lab is interested in understanding the mechanisms governing RNA silencing and development of RNA silencing based technologies that can be used to improve crop traits.