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From fundamental insights to better plants, sustainably grown, serving the world

SIPS students awarded NSF Graduate Research Fellowships

-Magdalen Lindeberg

Congratulations to SIPS graduate students Kate Harline, Adriana Hernandez, and Nathan Scinto-Madonich, Liz Mahood, Arielle Johnson and undergraduates Patrick O’Briant, Jeffrey Yen, George Stack, and Allison Coomber who have received NSF-GRFP awards or honorable mentions for 2019! The National Science Foundation Graduate Research Fellowship Program is the country’s oldest fellowship program that directly supports graduate students in various science, technology, engineering and mathematics fields and who are pursuing research-based master’s and doctoral degrees at accredited United States institutions.

Molecular Meter-sticks: miRNA Zones of Action Define Growth Rates To Calibrate Organ Size

Kate Harline, graduate student in the Roeder Program (awardee)

Strict regulation of organ size is crucial to successful multicellular development across the tree of life. Yet, the complex mechanisms that monitor organ size are enigmatically resistant to perturbation. MicroRNAs (miRNAs) are promising standards for calibrating organ size. miRNAs could maintain stable measures in growing organs because they selectively silence mRNAs in zones of action near where they are expressed. Activity zones have been shown to be important in organ patterning. For example the boundary made by miR166 and tasiARF (a small RNA) acting as morphogens is sufficient to establish leaf polarity. Additionally, disruption of the activity zone of miR319a  (miR319aOE) results in overgrown leaf margins. I hypothesize the mir319a activity zone at the base of leaves provides a standard to calibrate organ size. Taking inspiration from yeast cell studies, I think organ size is calibrated by comparing a cellular component that is constant with size to one that scales with size. In leaves size would be calibrated with the fixed amount of diffusible miR319a providing a standard against which the changing concentration of a protein expressed in each cell is compared. A readout of this activity zone is likely growth rate. miR319a targets and silences the TCP family of growth suppressing transcription factors. I hypothesize the region of fast growth at the base of leaves represents the activity zone of mir319a calibrating organ size. I propose a unique combination of (1) confocal live imaging, (2) computational modeling and (3) synthetic biology to investigate mir319a as an organ size calibrator in the model plant A. thaliana. This study will investigate a novel conceptual framework that can inspire studies across the tree of life and inform applied agricultural innovations.


The Genetic Regulatory Networks Underlying the Evolutionary History of a Highly Polymorphic Lily, Calochortus venustus (Liliaceae)

Adriana Hernandez, graduate student in the Specht program (awardee)

Evolutionary research as applied to biodiversity studies relies on understanding the genetic basis of polymorphic, ecologically significant traits. It is imperative to conservation efforts to study these themes in flower pigmentation and petal spots, as these traits are both highly variable and they serve clear ecological roles in signaling the presence of rewarding nectar in exchange for pollen transfer. Despite their importance, the genetic and evolutionary mechanisms underlying petal pigmentation are not well understood across broad evolutionary scales. Once understood, we can leverage these data to predict how shifts in global climate may alter floral genetic networks, downstream pigmentation patterns, and resulting ecological interactions. For my dissertation research, I am developing a model lineage in which to elucidate the evolution of floral color — the genus Calochortus (Liliaceae). I will model gene regulatory networks (GRNs) of contrasting floral phenotypes across Calochortus and will identify single nucleotide polymorphisms (SNPs) responsible for variation in petal pigmentation. This will reveal how floral pigmentation patterns evolved, are regulated, and are maintained in polymorphic species. Moreover, I will identify abiotic stresses that correlate with geographic distribution and pigment variation and incorporate these variables into ecological niche modeling.


Probing the genetic and molecular factors that control rice root system architecture under low phosphate conditions: does ART1 play a role?

Nathan Scinto-Madonich, graduate student to be joining the Pineros program (awardee)

Acid soils (pH < 5) comprise 50% of arable land and limit crop production due to their low phosphate (Pi) and toxic aluminum (Al3+) soil concentrations. Roots interact directly with these adverse conditions and can mediate effective responses to individual stresses through changes in root system architecture (RSA), but the dual presence of low Pi and toxic Al3+ highlights the need to understand their simultaneous effects on RSA. Al RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) regulates Al3+ toxicity responses in rice and is homologous to Arabidopsis thaliana SENSITIVITY TO PROTON RHIZOTOXICITY 1 (STOP1), which has been shown to mediate RSA changes to low Pi  and toxic Al3+. A rice line with a truncated ART1 transcript (art1), and near-isogenic lines (NILs) with reciprocal ART1 alleles have shown markedly different Al3+ tolerance responses and root growth inhibition by Al3+, and represent an opportunity to investigate the intersection of molecular pathways controlling abiotic stress tolerance between Al3+ toxicity and low Pi. Root system physiology, gene expression analysis, and modern genomics approaches will be combined to investigate the molecular mechanisms that shape root system architecture in the context of a complex environmental stress: acid soils.


Effects of urban greenspace percentage and local-scale plant biodiversity on pollinator assemblages of Fragaria ananassa

Patrick O’Briant, Plant Sciences ’19 (awardee)

Patrick O’Briant is in the process of deciding the best program at Cornell in which to conduct his research


Unraveling the Epigenomic Landscape of the Apomixis-Controlling Region in Paspalum notatum

Jeffrey Yen, Plant Sciences ’19 (awardee)

Jeffrey Yen will be attending UC Davis for a PhD in Integrated Genetics and Genomics. He will most likely be working in the Dubcovsky program on wheat breeding and genetics.


Mapping Toxicity: Charting the Diversity, Biosynthesis and Evolutionary Significance of Latex Metabolites in Euphorbia using Multi-Disciplinary Approaches

Liz Mahood, graduate student in the Moghe program (honorable mention)

Little is known about the metabolic composition of latex in Euphorbia, partially due to the shortcomings of current approaches for metabolite identification. Studying the metabolic pathways involved in Euphorbia latex composition will increase our understanding of the diversification in Euphorbia and may provide an explanation for the genus’ unusually large size. Specifically, this may be done through two objectives: (1) characterizing the latex metabolome of species across Euphorbia to correlate latex metabolic diversity with lineage diversification rates, and (2) identifying enzymes involved in latex metabolic pathways and constructing the evolutionary history of these enzymes across Euphorbia and Euphorbiaceae.


A Sticky Situation: The Function of Rubber in Common Milkweed (Asclepias syriaca)

Arielle Johnson, graduate student in the Jander program (honorable mention)


The Genetic Underpinning of Context-Dependent Association between Salix spp. and Arbuscular Mycorrhizae

George Stack, Plant Sciences ’19 (honorable mention)

George Stack is starting graduate research in Larry Smart’s program, working on industrial hemp.


Characterization and Neutralization of Deleterious Alleles in Cassava

Allison Coomber, Plant Sciences ’19 (honorable mention)

Alison Coomber is currently living in New Orleans and working as a lab technician. She will begin a PhD in Functional Genomics at North Carolina State University in the fall of 2019.

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