Posted June 1, 2018 by Ashley Washburn
Plant Transformation Core Research Facility | Morrison Microscopy Core Research Facility |
Proteomics and Metabolomics Facility | Bioinformatics Core Research Facility | Flow Cytometry Service Center |
The Office of Research and Economic Development’s “Strong to the Core” series highlights some of the University of Nebraska-Lincoln’s more than 35 core research facilities, which house shared instruments, equipment and technology, and provide training, expert consultation and collaboration opportunities to the university community and beyond. The series provides researchers and industry partners with information about the cores’ capabilities and accessibility.
The second edition features the five core facilities in Nebraska’s Center for Biotechnology, which in addition to infrastructure, offers the university research community a weekly seminar series, workshops and short courses, plus student fellowships and scholarships. The center is funded by the Nebraska Research Initiative, the National Science Foundation, the National Institutes of Health and a loyal group of university researchers who use the center’s core facilities.
Center director Daniel Schachtman talked to ORED about the center’s five cores, which include the Bioinformatics Core, the Flow Cytometry Core, the Morrison Microscopy Core, the Plant Transformation Core and the Proteomics and Metabolomics Core.
ORED: Who can use the facilities?
Schachtman: There are three groups of users: internal, including faculty, staff and students from all University of Nebraska campuses; external researchers from other academic institutions; and private companies, ranging from doctors’ organizations to electronics companies to biotech startups.
ORED: What kind of training and support is available to help researchers use the facilities that the cores offer?
Schachtman: It ranges from fee for service, or full-service, to self-service. In most cases, directors and technicians run the experiments and instruments and analyze the results, with or without faculty involvement. For some equipment and projects, researchers can use the instruments independently after receiving proper training.
Center staff teach a course for graduate students every spring, which introduces them to the technology and services. We also hold workshops once or twice per year on different topics to familiarize researchers with the cores.
ORED: How do researchers sign up to use the cores?
Schachtman: For the microscopy core, self-service users can sign up online. For the other four, researchers should contact the core’s manager or director to schedule usage (contact information included below).
ORED: How do you envision the cores’ user base growing?
Schachtman: It would be ideal to increase external customer usage, especially from industry, from places like Boston and San Francisco, where there are many biotech startups. The external customers help subsidize fees for internal users because they pay higher rates. External customers also help build our capabilities and infrastructure.
ORED: Are there plans for equipment acquisition in the cores?
Schachtman: We have three new microscopes in the microscopy core, which range from $100,000 to $500,000. In that core, we’d like to get involved in initial preparation and quality assessment of samples for cryo-electron microscopy. The cryo-electron microscopes cost $4 million to $8 million, which is why our users would send samples away for analysis.
We’re also working to acquire a new mass spectrometer to analyze samples for untargeted metabolomics, which will allow users to look at a very wide range of small molecules from a wide range of sample types. The flow cytometers are aging, so we need a new instrument in that core. For the plant transformation facility, we have a new laboratory space to enable expansion and will add additional laminar flow hoods and more staff.
With these facilities, it’s crucial to stay at the forefront of technology. If the equipment gets old, we fall behind in research, which is very competitive. Our main goal is to help faculty and their research, because we wouldn’t exist without them. We want them to walk out happy, so we are very customer-service focused. To that end, we’re always looking for faculty input. If there is enough demand for certain instruments, we will pursue their purchase.
This is one of the best publicly funded cores for crop plant transformation in the world. The facility can conduct transformation of the major commodities, including maize, soybeans, sorghum, wheat and more. Using genetic engineering, researchers can test hypotheses in various crops and create products that can actually be used in the field. The best example is the herbicide-resistant trait that was developed in the core. In 2018, 40 million acres of soybeans and 10 million acres of cotton will be planted with this trait.
The core also facilitates basic research, such as investigating the nutritional quality of a soybean variety or testing hypotheses related to increasing plants’ stress or salinity tolerance.
Director: Tom Clemente, Eugene W. Price Distinguished Professor of Biotechnology, 402-472-1428
Location: N308 Beadle Center
This core has the most users on campus of the five. It offers a range of different microscopes and expertise that are unique on campus. With confocal microscopes, researchers can study live cells. High-resolution microscopes known as TEM, or transmission electron microscopes, enable determination of whether a virus is present in samples or examination of subcellular organelles for ultrastructural analysis of biological samples. The SEM, or scanning electron microscope, enables users to look at sample topographic or surface structures at 30 times to 500,000 times magnification, in samples such as bacteria, nanoparticles and carbon nanotubes.
Examples of some of the core’s current projects:
- Studies on biofilms to shed light on how food-contaminating bacteria grow in refrigerated conditions.
- Studies on viruses, such as Zika and HIV, to build the foundation for more effective vaccines, as well as basic research on infection mechanisms and their pathological effects.
- Plant studies that reveal how proteins enhance drought and heat tolerance.
- Since 2013, the core has assisted many undergraduate students from different Nebraska universities with evaluating their laboratory work on bacteriophage analysis. This is part of the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, jointly administered by the University of Pittsburgh and the Howard Hughes Medical Institute’s science education division.
Director: You (Joe) Zhou, research professor, 402-472-5935
Location: E119.5 Beadle Center
In this core, researchers can delve into organisms’ inner workings and learn how the abundance of proteins and small molecules from plants, animals and humans are modified. They can study, for example, regulation of signaling and metabolic pathways by looking at the changes in abundance of proteins and/or metabolites in cases where the organism is being stressed by the environment, treated with drugs or when a gene is modified.
Some of the large projects the facility is working on include:
- Studies on the changes in the metabolite profiles that corn roots exude.
- Identification of new Bacillus plant growth-promoting rhizobacteria for management of crop disease.
- Investigation of the impact of drugs on the non-mevalonate pathway in Plasmodium, which is responsible for malaria, and Staphylococcus, or staph infection.
- Study of the regulation of alpha phenol-soluble modulins produced by methicillin- resistant Staphylococcus aureus, or MRSA, which are responsible for its virulence.
Director: Sophie Alvarez, research associate professor, 402-472-4575
Location: E154 Beadle Center
This core offers education, analysis and computational services in bioinformatics and computational biology. Often, researchers’ datasets are extremely large, and they need help analyzing and managing them. The core’s experts can help them make sense of the information and find biologically important patterns. They also can provide support for bioinformatics software and analyses at the Holland Computing Center, which is free for up to three hours per year, per faculty member.
Director: Jean-Jack Riethoven, research assistant professor, 402-472-7949
Location: E204 Beadle Center
This facility provides methods for users to look at cells and particles submerged in liquid to study cellular functions, or to study small organisms, such as microbes, in the environment. The flow sorter can pull certain cells from a mixture using specific cellular labels and instruct the instrument to pull out the labeled cells and manipulate them downstream. This core is often used by immunologists to study infected cells.
Manager: Dirk Anderson, 402-472-3129
Location: Ken Morrison Life Sciences Research Center, Room 160