“Building connections with research microbiologists to improve undergraduate education”
Heike Bücking, South Dakota State University, Brookings, South Dakota
Michael Ibba, The Ohio State University, Columbus Ohio
Michael Polymenis, Texas A&M University, College Station, Texas
Joanne M. Willey, Hofstra University, Hempstead, New York
South Dakota State University, Brookings, South Dakota
An associate professor in the Biology and Microbiology Department at South Dakota State University, Heike Bücking received her master’s degree, doctorate, and postdoctoral lecturer qualification from the University of Bremen, Germany.
Her lab’s primary research focus is on nutrient transport, and resource exchange between the symbiotic partners in the arbuscular mycorrhizal and ectomycorrhizal symbiosis. Bücking notes that approximately 80% of all known land plants, including important crop species such as soybean, corn, wheat and rice, form this mutualistic symbiosis with ubiquitous soil fungi. “The fungus takes up nitrogen, phosphate and other nutrients from the soil, and transfers these nutrients to the host plant in exchange for carbohydrates,” she says. “In addition to the nutritional benefit, mycorrhizal fungi increase the resistance of plants against abiotic (drought, heavy metals, salinity, etc.) and biotic stresses.” The Bücking lab uses labeling approaches to track nutrient transport in the symbiosis, molecular and genomic techniques to understand how resource exchange across the mycorrhizal interface is triggered, and follow changes in the plant and fungal transcriptome before and after the symbiosis has been established. “The primary goal of these research projects is understanding how mycorrhizal benefits for the host plant can be maximized to improve the environmental sustainability of food and bioenergy crop production,” she says.
No stranger to working with beginning investigators, Bücking’s current research team includes several undergraduate and graduate students and a postdoctoral scientist. She also actively collaborates with scientists from national and international institutions.
Projects in the Bücking lab are funded by the National Science Foundation, the Department of Energy, the Sun Grant Initiative, and the South Dakota Wheat Commission. In addition to research activities, “I teach undergraduate and graduate courses in microbiology and in plant science and coordinate an REU (Research Experiences for Undergraduates) site on bioenergy that is funded by the National Science Foundation,” says Bücking. “The goal of this program is to provide motivated undergraduate students primarily from undergraduate institutions with low research activity and from underrepresented groups in the sciences with an opportunity to get actively involved in innovative research questions and to gain hands-on experiences in state of the art technologies.”
The Ohio State University, Columbus Ohio
Mike Ibba and colleagues are seeking to understand (i) the mechanisms that determine how cells ensure accurate translation of the genetic code and (ii) how changes in the underlying processes impact cellular health and contribute to microbial pathogenesis and disease. Because many of these processes are essential and unique to particular systems, they are ideal potential drug targets.
Here is how Ibba explains it: Ribosomes are the protein synthesis factories of the cell that translate the codons of mRNA into amino acids. Protein synthesis proceeds by delivery to the ribosome of aminoacyl-tRNAs, which pair with the corresponding mRNA sequences. Accurate aminoacyl-tRNA synthesis often requires an additional proofreading activity that significantly decreases error rates during translation of the genetic code. Our overall aim is to study the molecular mechanisms of proofreading and investigate how error rates impact microbial physiology and fitness and cellular responses to stress. In response to different environmental stresses, such as the presence of antibiotics, microbes direct resources away from translation to a variety of pathways that contribute to resistance. For example, some pathogens divert aminoacyl-tRNAs away from protein synthesis, using them instead to modify the cell wall and increase antibiotic resistance. We are studying the molecular mechanisms of several of these and other pathways, with the overall goal of understanding how microbes use control translation to establish antibiotic resistance.
With a team comprising a group leader and typically two or three postdocs, five or six doctoral students, and two to four undergraduates, the Ibba lab has been successful in developing a strong research-training environment for undergraduate and graduate students both from the Ohio State University and elsewhere. The lab also collaborates extensively and share resources with several neighboring labs, “making for a vibrant larger community that stimulates research and learning.
Through programs like ASMCUE and LINK, Ibba says he hopes to develop summer internship programs and partnerships more directly with faculty from predominantly undergraduate institutions. “In order to expand our training program in this direction, I would like to identify and connect with current and future faculty instrumental in student learning in undergraduate biology,” he says. Specifically, Ibba plans to address three goals that are key to successfully developing research training opportunities tailored to the needs of students and educators from predominantly undergraduate institutions:
1. Connecting with current and future faculty to identify potential research collaborations. (To help establish such collaborations, the team will co-sponsor faculty research sabbaticals in their lab.)
2. Meeting with undergraduates to discuss training and mentoring components they look for in an academic research internship.
3. Discussing with undergraduate educators how to better prepare our own trainees who wish to pursue a career in education.
Texas A&M University, College Station, Texas
In the lab of Michael Polymenis, research centers on understanding what exactly determines when cells begin a new round of cell division. “Knowing which (and how) cellular pathways affect the machinery of cell division will allow modulations of cell proliferation because such processes dictate how fast cells multiply,” says Polymenis. He and colleagues uses baker's yeast as a model organism as it has several properties that are useful for the lab’s research objectives. “Yeast is a genetically tractable eukaryote,” he says. “It has a machinery of cell division that is very similar to that of human cells. Furthermore, in yeast, the initiation of cell division is coupled to the formation of a bud. Hence, one can monitor the timing of initiation of division by phase microscopy.” These features enable relatively simple and inexpensive experimental strategies to decipher the genetic networks that control cell division.
Recently, with work performed mostly by a team of undergraduate students, the lab used comprehensive yeast deletion libraries to identify genes required for normal cell cycle progression ([Hoose et al, PLoS Genet, 2012; e1002590] and [Truong et al, G3(Bethesda), 2013; 10.1534/g3.113.007062]). Polymenis says the work has significantly expanded and reshaped the landscape of factors required for the timely initiation of division.
Polymenis and colleagues have begun large-scale functional interaction studies to determine how these factors are organized in distinct pathways and how they affect the cell division machinery. “To answer these questions, we construct all possible double mutant combinations of the factors we identified,” he says. “We then score these mutants for several phenotypes of interest that report on the timing of initiation of cell division.”
There a several opportunities for undergraduates to take part in these procedures. Students in the Polymenis lab perform genetic crosses of single mutants, selection steps to identify double mutant progeny, PCR-based genotype confirmation, scoring for phenotypes (growth rate, budding, and cell size, etc.), and computation of genetic interactions and graphical representation/clustering of the obtained data. “We expect that through this work students will be exposed to fundamental aspects of genetic analyses, from genotype to phenotypic manifestations,” says Polymenis. “The project is both divisible and scalable. Different portions of the project (sets of mutants, and/or steps in the analysis) can be performed in parallel at different sites. Students deposit the data in real time on wiki-based platforms. This is important because it allows accessibility to, and critical evaluation by all members of the various teams. ” For Polymenis, these aspects “greatly facilitate collaborations, without the need for close geographic proximity.”
Hofstra University, Hempstead, New York
Joanne Willey’s research centers on the filamentous soil bacterium Streptomyces coelicolor, which has a complex, fungal-like life cycle and produces most of the antibiotics currently used in human and veterinary medicine. In exploring the processes and molecules that govern this differentiation process, Willey and colleagues found a class of conserved biosurfactants needed for cellular differentiation. After her lab’s initial description of the biosurfactant SapB, more than 100 other so-called lanthipeptides have been found in a diverse collection of bacteria.
For Willey, the key to maintaining research relevance is the acquisition of extramural funding, as this provides not only equipment and supplies but also access to services such as genomic and proteomic analysis, and (more importantly) to the presence of a postdoc in the lab. However with respect to extramural funding, Willey says she is “keenly aware of the catch-22 many professors experience, particularly those at PUIs: getting the first grant depends on a strong publication record, but the data needed to publish can only be acquired if extramural funds are available.”
As a research-active member of the faculty at Hofstra University, a principally undergraduate institution (PUI), Willey is an ardent advocate for undergraduate research as well as sustained research productivity. “During my 20-year career at Hofstra, I have mentored more than 75 undergraduates, many of them members of underrepresented groups, as about a third of the student body at Hofstra are minority students,” she says. “At any given time, my research team includes three to five undergraduate students, a master’s-level student, and a postdoctoral fellow.”
Now that she is a “seasoned PI at a PUI,” Willey can offer valuable input to the undergraduate microbiology education community on the topic of grant proposal development. “I have served as a member of numerous NSF panels and have read many proposals submitted by undergraduate researchers (“RUI” proposals),” she says. “While some have been exceptional, it is not uncommon to find such proposals lacking for a want of guidance.” For this reason, Willey is happy to discuss research projects and assist in the development of RUI or AREA proposals (submitted to NSF or NIH, respectively).
ASMCUE and LINK Welcome Your Input
Looking for advice on ways to enhance undergraduate learning or just hoping to start a conversation about innovative ways to involve underrepresented minorities in research? The Annual ASM Conference for Undergraduate Educators (ASMCUE) and the ASM-NSF Leaders Inspiring Networks and Knowledge (LINK) programs welcome your interest. Contact the individual awardee for details.
LINK is sponsored by ASM with support from National Science Foundation grant no. 1241970.