Graduate research in the School of Plant Sciences •

Currently undergoing updates! (Spring 2018)

Lourena Arone, Plant Pathology, PhD

Aflatoxins are potent mycotoxins that contaminate foods and feeds worldwide, causing developmental and immune system suppression, cancer, and death for humans and animals.  Aflatoxins are genotoxins and they could be carried over along the food chain, having crucial impacts in agriculture, trade, food safety and health.My research explores impacts of farming practices on fates of aflatoxins and aflatoxin-producing fungi in the environment. I seek to understand intraspecific genetic variability, gene flow and test the possibility that certain aflatoxin-producers are differentially adapted to agroecosystems. 

Liz Bowman, Plant Pathology, PhD

Global climate change affects ecosystems by altering seasonal patterns, which have a strong effect on numerous biotic and abiotic processes. Plant-fungal symbioses – which influence plant physiology, nutrient and water uptake, growth rates, and decomposition – are crucial for continued ecosystem function. An understanding of how plant-fungal interactions respond to these climatic alterations is integral to future conservation. My research focuses on ectomycorrhizal fungi and fungal endophytes associated with Ponderosa pine in the Santa Catalina mountains. Using a combination of field studies, greenhouse experiments, and molecular techniques to assess how these plant-fungal communities will respond to future climate change.

Andrea Carter, Plant Sciences, PhD

Water scarcity is a growing global issue that particularly affects arid regions, where annual precipitation and natural water resources are especially low. Agriculture productivity in dryland regions faces a multitude of challenges including persistent water scarcity, frequent droughts, and high climatic variability. If droughts become more common, widespread, and persistent -- as projected by climate change forecasts -- arid and semi-arid regions will have difficulty sustaining viable agricultural systems. My research focuses on the physiological mechanisms of drought tolerance in grains, specifically barley.  I am particularly interested in rooting characteristics.  My work has involved field trials comparing the performance of low-input barley varieties to high yielding, high input varieties under high and low irrigation conditions.  Overall, I am interested in cultural methods and breeding efforts for low input (minimal water and fertilizer) production.  

Wen Chen, Plant Sciences, PhD

Small RNAs are widespread in eukaryotes and involved in many cellular processes. In plants, Pol IV siRNAs, as produced by the plant specific RNA polymerase Pol IV, mediate de novo DNA methylation, a pathway called RNA directed DNA methylation (RdDM). RdDM is involved in the genome stability and resistance against foreign DNA. Although RdDM functions in the nucleus, Pol IV siRNAs and their effector AGO4 unexpectedly accumulate in both the cytoplasm and the nucleus. My focus is to unravel the regulatory mechanism for the sub-cellular localization of AGO4, with projects from three aspects undergoing: 1. How the RdDM components affect the localization of AGO4; 2. What the sub-cellular localization pattern of other important RdDM components is; 3. How post-translational modification contributes to the sub-cellular localization of AGO4, and what proteins are associated with AGO4. The projects are mainly carried out within the model plant Arabidopsis, using both molecular and biochemical techniques . 

Connel Ching’anda, Plant Pathology, PhD

Crop contamination by Aflatoxin is one of the major food safety problems in Sub-Saharan Africa. Aflatoxin producing fungi vary widely by regions. Such variations also suggest their differences to colonise and produce aflatoxins in crops. Understanding the genetic make-up of such fungi is an important step for designing appropriate intervention strategies. I study aflatoxin producing fungi in Malawi by using molecular biology and microbiology tools.

Kelly Dew-Budd, Plant Sciences, PhD

I am currently in the process of choosing a primary focus. I have two areas of interest at present. First, heat stress can affect the fertility of important crops. In certain tomato varieties, a brief encounter with heat during pollination can prevent fertilization of the female gametophyte. To try to elucidate the mechanism behind the sensitivity of some varieties and the tolerance of others, I am exploring heat induced gene expression changes in tolerant and sensitive varieties. In parallel with this activity, I am exploring telomere elongation. The ends of chromosomes are protected by a repeated DNA sequence that requires special replication machinery. One required part of the replication mechanism is an RNA template. In Arabidopsis, the gene TER1 is hypothesized to be the template for telomere elongation. I am disrupting the function TER1 using CRISPR/CAS9 to delete the telomere base-pairing region important for telomere elongation in an effort to confirm or bring to question the function of TER1.

William Gurley, Plant Sciences, PhD

The function of cereal endosperm is of critical importance to society as the source for a significant portion of the human diet, either through direct consumption or indirectly through animal feed. Additionally, endosperm acts as a source of embryonic nutrition, thus supporting the propagation of these plants. In light of its biological and technological importance, it is critical that we understand the processes and mechanisms which control the production and storage of protein and carbohydrate in cereal endosperm. A greater understanding of these systems will contribute to increased yields and nutrition, ultimately serving to produce an agriculture that is more profitable and sustainable. I am working on the gene regulatory networks that control storage protein expression in the endosperm. Currently, I am investigating interactors of Prolamin-box Binding Factor that contribute to its role in the activation of storage protein expression.

Aasiya Hamzazai, Plant Sciences, PhD

Plants face diverse challenges when cultivated or occurring naturally in stressful environments. I am particularly interested in the importance of drought and pathogens in shaping plant survival and crop plant yields. My aim is to contribute to human well-being by enhancing plant productivity and survival under environmental stress, with the additional aim of training junior researchers and stakeholders.

Jen Noble, Plant Sciences, PhD

Pollen tube reception is essential for successful double fertilization, which precedes seed formation in flowering plants. This process involves direct cell-to-cell contact between the pollen tube (which delivers the male gametes) and the female gametophyte (which houses the female gametes). During pollen tube reception, the pollen tube enters the female gametophyte and releases the sperm to complete fertilization.  I am interested in understanding the roles of female  gametophyte-expressed genes in pollen tube reception and how their expression is regulated. In  addition to studying regulation of genes involved in pollen tube reception, I am also interested in understanding the evolution of these genes and how they may be involved in reinforcing species barriers.

Shuzo Oita, Plant Pathology, PhD

Endophytic fungi play important roles not only in biodiversity but also in biocontrol for agriculture. It is known that plant species influence the composition of endophyte communities, but the species turnover of endophytic fungi under local/global climate change is largely unknown. My research focuses on the relationships between endophytic fungal community and climate change in boreal forests. In my first year of research I am linking endophyte communities of boreal forest trees to tree-ring analyses, and using next-generation amplicon sequencing methods to evaluate geographic distributions of endophytes in wild plants.

Pummi Singh, Plant Pathology, PhD

Aflatoxins are carcinogenic metabolites produced by the fungus Aspergillus flavus and certain other Aspergilli. These fungi colonize a wide range of crops such as maize, groundnuts, cotton, spices and tree nuts. Aflatoxin contamination of crops can cause huge economic losses. Consumption of toxin contaminated crops can have detrimental health effects including stunted growth, immunosuppression, liver cancer, and fatality in certain situations. I am interested in understanding the population structure and diversity of aflatoxin producing fungi to design effective management practices using microbiological and molecular techniques along with field work based approaches.

Brian Smith, Plant Pathology, PhD

Horizontal gene transfer (HGT) is frequent and important in biology, especially in bacteria that influence human health and sustainability. HGT often is associated with advantageous traits in hosts (e.g., acquisition of antibiotic resistance).  However, the costs of large-scale HGT are not well studied.  Such costs could render pathogenic bacteria ineffective, renew antibiotic sensitivities in multi drug resistant strains, or increase susceptibility to other organisms.  Understanding the genetics of these costs could translate to crop protection or medical treatments.  I investigate current gaps in understanding the relationship of HGT and microbial pathogenesis. I study horizontal gene transfer and microbial pathogenesis through various Pseudomonas sp. and a 1Mb megaplasmid.  I use tools from microbiology, genetics, genomics, and molecular biology. 

Seth Steichen, Plant Sciences, PhD

The cultivation of photosynthetic microalgae has proven to be an effective method for the production of a number of valuable products.  In light of growing concerns over global energy sources, the production of renewable biofuels has gained a great deal of attention.  Many species of microalgae accumulate high concentrations of storage lipids which can be readily converted to biodiesel.  While this practice demonstrates a number of advantages, including the utilization of marginal lands and the capture of atmospheric carbon, efficiency must still be increased to match current energy technologies.  My research focuses on the ability of a particular species of algae, Auxenochlorella protothecoides, to adapt its biology to grow efficiently in very low phosphate media. Correlation between gene expression, metabolomics, and epigenetic data collected from cultures of adapting algae will aid in understanding and exploiting the molecular mechanisms underlying this phenomenon, leading to more efficient cultivation.

Josh Weaver, Plant Sciences, PhD

The replacement of fossil fuels with sustainable alternatives is important for our growing global population. Identification and characterization of previously unidentified plant variants is important to understand gene function. My work focuses on enhancing the biofuel-relevant genetics of switchgrass, a bioenergy crop. I use biotechnology techniques to propagate uniquely identified genotypes and cutting-edge tools of molecular biological and genomics for screening variant phenotypes and trait mapping.