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Ten diverse graduate student projects funded by Schmittau-Novak

-Magdalen Lindeberg

What do squash beetles, cold hardiness genes, and plastoglobule kinases have in common? All three are addressed by graduate student projects recently funded through the Schmittau-Novak Small Grants Program.

Supported by a bequest from the estate of Jean Schmittau in honor of Joseph Novak, Plant Biology Professor Emeritus, the Schmittau-Novak Small Grants Program is designed to provide graduate students in the School of Integrative Plant Science with the opportunity to experience the process of writing and reviewing proposals, and implementing a research plan of their own design.

Proposals were due on August 1 and reviewed in early September by a panel of senior SIPS graduate students.  One of the anonymous reviewers reflected how much she appreciated the opportunity to think about research topics beyond the focus of her own lab and projects. “It was also very inspiring to see the creativity of the applicants in their proposals.”

Ten proposals were selected for funding with awards ranging from $4,385 to $9000.  The funded projects span diverse topics including the chemical-ecology of plant-microbe interactions, the molecular basis of plant-insect interactions, the genetic control of plant stem cell development, the molecular biology of cold tolerance in grapevines, and the development of decision making tools to improve farm-to-market sales. Mia Howard, whose project focuses on the influence of soil microbes on plant competition and defense, spoke to how empowering it is to obtain one’s own funding and the important role that small grants programs have played in her research career.

A goal of the program was to foster collaborations, exemplified by the project proposed by Dustin Wilkerson, Laura Dougherty, and Chris Hernandez. Dustin commented that he had the initial idea of grafting different willows and looking at gene expression levels but that he needed help to make the idea a reality. “So I reached out to Chris because he had experience interpreting 3′ RNA seq data and Laura because she is more familiar with grafting and RNA extractions/ library prep and together we developed the experimental design”.  Laura and Chris additionally emphasized the value of working on crop plants outside the scope of their thesis work and the opportunity to develop and test new data analysis pipelines.

Faculty program director Dan Buckley commented, “Another exciting aspect of this program is the ability to support projects that pair graduate and undergraduate students. These projects provide our undergrads with a world-class research experience while our grads get valuable mentoring experience. This is a fantastic program and I’m excited to see where our students will take it in the future.” The program is co-directed by Teresa Pawlowska.

Response and counter response: understanding genetic drivers of plant defenses in squash to herbivory by a beetle pest

Lauren Brzozowski is a PhD candidate in Plant Breeding and Genetics with Michael Mazourek, interested in using plant genomics and chemical ecology to develop insect resistant plant varieties to reduce on-farm chemical inputs. Lina Hernandez is a PhD candidate in Ecology and Evolutionary Biology with Anurag Agrawal, working on regional variation of oviposition traits in the weevil Rhyssomatus sp., a milkweed specialist.  They will be investigating gene expression in Cucurbita pepo and its specialist pest, Acalymma vittatum, to identify the molecular mechanisms underlying host preference. Award amount: $4,976

The role of Xanthomonas vasicola pv. musacearum type III effectors in pathogenicity and virulence on banana

Zoe Dubrow is a PhD candidate in Plant Pathology and Plant-Microbe Biology with Adam Bogdanove, studying the role of type III effector proteins in bacterial virulence and pathogenicity.  She will be investigating how differences in the effector repertoires of bacterial pathogens Xanthomonas vasicola pv. musacearum and Xanthomonas vasicola pv. vasculorum contribute to differences in their host ranges. If individual effectors are found to play important roles in virulence, further work can focus on plant interaction targets. Award amount: $4,631

Plastoglobules: a chloroplast lipoprotein micro-component with specialized functions in isoprenoid metabolism

Elena Michel is a PhD candidate in Plant Biology with Klaas van Wijk, whose program is focused on the role of plastoglobules in plastid development and stress response. She will be investigating the roles of kinase proteins in plastoglobules by phenotyping kinase mutants, using cross-linking to find interacting proteins, and identifying proteins co-expressed with the kinases. Award amount: $4,480

Examining the importance of soil microbial community shifts in mediating plant competitive and defensive phenotypes during oldfield succession

Mia Howard is a Plant Biology student studying the chemical ecology of plant-microbe-insect interactions in Dr. André Kessler’s lab. She is examining how plant competitive and defensive phenotypes change over 1-15 years following agricultural use. She will be conducting both field surveys and manipulative experiments, and using a combination of microbial community and plant metabolic profiling. The award will also fund a summer internship for an undergraduate research mentee. Award amount: $9,000

Developing innovative sensory strategies to aid NY farm-to-market growers

Hannah Swegarden works in Dr. Phillip Griffiths’ vegetable improvement program at Cornell’s NYSAES, where she investigates nutrition and consumer perception of quality traits in leafy brassica vegetables.  Zoe Friedberg is an undergraduate in International Agriculture and Rural Development.  Under the advisement of Hannah, Zoe will explore the influence of different “modes of interaction” between farmer-vendors and consumers sampling fresh produce at three NYC farmers markets. Through fresh produce sampling, they will evaluate means of eliciting sensory feedback from consumers for their efficiency and potential to guide farmers in making cultivar decisions. Award amount: $8,913

Proteomics to provide mechanistic insight into virus-host interactions for symptom development

Larissa Osterbaan is pursuing a Ph.D. in plant pathology in the Fuchs program, using molecular biology and proteomics techniques to reveal mechanisms of symptom development for grapevine fanleaf virus.  Preliminary work from this project has narrowed down the symptom determinant to a single amino acid in the viral encoded polymerase.  This award will support co-immunoprecipitation and mass spectrometry studies to identify proteins interacting with the polymerase. Award amount: $5,000

Transcriptional profiling of the shot apex in Zea mays using single-nuclei RNA-Seq

Jack Satterlee is doing graduate studies in the Scanlon lab, using a combination of single-cell gene expression analysis and CRISPR/Cas9-enabled molecular lineage tracing to better understand development in maize. This award will support his efforts to develop and optimize a low-cost method for single-nuclei RNA-Seq in maize. This approach will allow for characterization of novel cell types and developmental states within the maize shoot apex as well as serve as a platform for use by others within the SIPS community and beyond. Award amount: $4,997

Partitioning transcriptome-wide variation and rootstock by scion interactions in reciprocal polyploid grafts

Dustin Wilkerson is a PhD student working with Larry Smart on mapping genetic resistance to willow leaf rust in the biomass energy crop shrub willow. Laura Dougherty is a PhD student working in Kenong Xu’s lab, focused on uncovering genes that control tree architecture and fruit quality in apple. Christopher Hernandez is a PhD student working with Michael Mazourek and is interested in improving plants more efficiently using genomic data in tandem with conventional breeding methodology. The three co-PIs will explore the interactions between gene expression and phenotypes using 3’ RNA-seq to examine expression levels in the root and shoot tip of reciprocally grafted willow with diploid, tetraploid, and a triploid progeny in all possible graft combinations.  Expression levels will be related to phenotypic measurements. This will aid in the understanding of heterosis in shrub willow and generally elucidate rootstock by scion interactions in woody perennials. Award amount: $6,000

The Old exonuclease and its potential role in biofilm regulation and DNA repair during infection of crucifers by Xanthomonas campestris pv. campestris

Chris Peritore-Galve is a Ph.D. student in the program of Chris Smart, studying two bacterial pathogens of vegetables with a focus on the role of the Old nuclease of Xanthomonas campestris pv. campestris in regulation of biofilms.  In collaboration with the Chappie lab in the Dept. of Molecular Medicine, Chris will be characterizing the function of the Old nuclease during disease, and elucidating the roles of the domains that give the protein its nuclease activity. Award amount: $5,000

When cold isn’t enough: the effects of thermal amplitude on acclimation of grapevine buds

Al Kovaleski is a Ph.D. candidate in Horticulture, examining aspects of cold hardiness in grapevines.  The objective of this project is to measure how temperature and temperature cycling affect acclimation in grapevines, with a goal of adapting existing prediction models for cold hardiness. Changes in gene expression in grapevine buds will also be evaluated to identify specific genes and enriched pathways related to cold hardiness.  Award amount: $4,385

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