Plant Path. & Plant-Microbe Biology Projects

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These are the Plant Pathology and Plant-Microbe Biology projects that our Summer Research Scholars will be tackling in 2018.  Faculty members associated with each project are also listed. You can read more about their programs by clicking on their names.

1. Flying fungi

FungiInvestigate the remarkable processes that fungi have evolved for dispersal and survival in an introduction to the sciences of aerobiology and plant epidemiology. As part of a research team, you'll learn how fungal plant pathogens move anywhere from microns to thousands of kilometers to cause disease. Plant systems involved include wine grapes, fruit and vegetable crops.
Lab 50%, Field 50% Faculty: Gadoury

2. Don't let their size fool you...

Despite their small genomes and lack of cellular machinery, viruses still pack a big punch: plants infected with viruses show a number of symptoms ranging from leaf discoloration to fruit deformities to death of the plant.  In this project, you will learn how to design, construct, and use genetically engineered viruses to study how plant viruses cause symptoms in their host.  You will also use proteomics techniques to probe the protein-protein interaction underpinnings of symptom development.  You will gain skills in molecular biology, plant virus biology, and diagnosing virus infection, as well as protein extraction, detection, and proteomic analysis.
Lab 70%, Greenhouse 30% Faculty: Fuchs

3. The orchard is on fire!

fire blight on leavesFire blight, caused by the bacterium Erwinia amylovora is one of the most devastating diseases of modern apple orchards and destroys 100s of acres of high-value apples each year. While antibiotics are the most effective way to manage the disease early in the season, they are ineffective at later stages of the disease. Moreover, organic apple producers are unable to use antibiotics and are left with few viable options. Each year numerous biological control options are developed for managing fire blight, but they often provide poor control and are not optimized for temperate production regions. Scholars will examine the use of plant growth regulators and biological controls for managing fire blight. Scholars will have opportunities to visit actual fire blight outbreaks and learn about modern apple production.
Lab 50%, Field 50% Faculty: Cox

4. Smile!

fungiThis project requires familiarity with software for creation of Computer-Generated Animation (CGA) and digital imagery.  The student will be embedded within the research program of a major national research project on strawberry diseases involving Cornell University, The University of Florida and the US Department of Agriculture, with the goal of producing the CGA and digital image content required for educational videos depicting various aspects of pathogen growth and infection.
Lab 80%, Greenhouse/Field 20% Faculty: Gadoury

5. Endangered apples!

apple scabApple Scab caused by the fungus Venturia inaequalis has limited the sustainable production of apples in temperate climates. The pathogen has become resistant to many of the safest and most environmentally responses fungicides. Multi-drug resistant V. inaequalis has caused disastrous production failures in apple production operations throughout the eastern US apple industry. Scholars will determine how farm management practices impact the evolution of resistant populations of V. inaequalis in an effort to help growers produce disease free apples safely and sustainably. They will look at population changes in fungicide target site genes and microscopic growth. In addition, scholars will have opportunities to visit orchards with disease outbreaks and learn about modern apple production.
Lab 50%, Field 50% Faculty: Cox

6. Fun with Fungi!

Fungi are relentless opponents in crop production systems worldwide. How do fungal pathogens get in the field in the first place? Once they are there, how do they spread? Knowledge of a pathogen’s biology and epidemiology can answer these questions and is critical to successful management of disease in the field. In this project, scholars will investigate the biology and epidemiology of Phoma betae, a seedborne pathogen of table beet. Investigations will utilize molecular and morphological methods to understand the reproductive strategy and dispersal of this pathogen.
Lab 60%, Field 40% Faculty: Pethybridge

7. Lights Out!

pathogenic fungiLight has a poorly understood regulatory role in the production and release of inoculum by several plant pathogenic fungi. Be part of a team that is exploring how light intensity, quality, and timing can be used to moderate or inhibit sporulation, and thereby affect the incidence and severity of disease.
Lab 90%, Field 10% Faculty: Cadle-Davidson, Gadoury

8. From whence they came: Using wild tomatoes from the Andean Mountains to study vascular colonization of the bacterial canker pathogen

wild tomatorBacterial canker of tomato, caused by the Gram-positive pathogen Clavibacter michiganensis subsp. michiganensis (Cmm), continues to be one of the most economically devastating bacterial diseases of tomatoes worldwide. The bacterium systemically colonizes the plant, often resulting in plant death. The disease lowers yield and reduces marketability of the fruit by forming “bird’s-eye lesions” during infection. During this summer project, you will gain hands-on plant pathology experience by using wild tomato species to observe vascular spread of the bacterium using Cmm isolates expressing an enhanced green fluorescent protein. Under a Laser Scanning Confocal Microscope, you will observe plant morphological characteristics that hinder or benefit the spread of the pathogen, track patterns of colonization, and quantify disease in the greenhouse.
Greenhouse: 30%     Lab: 30%       Microscopy: 40%      Faculty: C. Smart

9. Chillin' in the Hopyard!

Hop yardThose cool early summer nights may be great for sleeping, but they aren't so good for some plant diseases! Investigate how cold temperatures can kill the fungus that causes hop powdery mildew, and how those same cold temperatures can also make hop plants more resistant to infection. This work will involve both hop yard investigations into how leaf temperatures supercool at night and how the disease spreads in the early season, as well as laboratory studies where the Scholar will learn various microscopy skills, including scanning electron microscopy! If you like working outside, but also want to improve your microscopy skills, Chillin' in the Hopyard is just for you!
Lab 50%, Field 50% Faculty: Cadle-Davidson, Gadoury

10. Magical rusts and where to find them

RustNew York State is one of the leading producers of shrub willow as a bioenergy feedstock.  However, a fungal rust pathogen aims to thwart our progress.  In this project, you will help decipher the genetic structure of Melampsora spp. isolates using a genome-wide-strategy to gain a clearer picture of these organisms’ populations.  You can expect to be smitten with the bright orange spores, while expanding your knowledge of microbiology and molecular techniques. 
Lab 70%, Field 30% Faculty: C. Smart

11. Modern weapons for an old battle: can we win the fight against fire blight with next-gen genomics?

plant injectionFire blight, caused by the gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases of apple trees. In recent years, research has been revolutionized due to increased throughput technologies and a reduction in genome sequencing costs. You will be involved in a project that takes advantage of next-gen genomics, including genome and transcriptome sequencing, to better understand host-pathogen interactions, characterize natural resistance sources in apples, and identify genomic regions (QTLs), molecular markers, and underlying genes using the genetic diversity available at the US apple germplasm repository in Geneva, NY. You will inoculate apple trees in the greenhouse to determine susceptibility to fire blight and then map out the genetic resistance source. Results of this research will ultimately be used for genetic enhancement of fire blight resistance in apples by deploying resistance alleles in commercially favored backgrounds.
Lab 50%, Greenhouse/field 50% Faculty: Khan

12. Protecting peppers, pumpkins, and zucchini from a devastating pathogen

phytophthoraPhytophthora capsici is a devastating pathogen of many vegetable crops, including peppers, tomatoes, pumpkins, and zucchini. Currently, there are no resistant zucchini or pumpkin varieties commercially available for growers. As part of our project to develop disease-tolerant varieties, you will inoculate and evaluate breeding lines in replicated trials in the greenhouse and field. We are also currently investigating how tolerant plants are able to avoid succumbing to disease. You will contribute to our understanding of this pathosystem as you use confocal microscopy with a green fluorescent protein-tagged isolate and quantitative PCR to see how well the pathogen colonizes different plant tissues in genotypes with varying levels of susceptibility.
Lab 60%, Field 40% Faculty: C. Smart

13. Early detection of disease symptoms and multi-dimensional visualization of disease progress in real time for gene identification

imagingPlants develop symptoms in response to pathogen attacks that can be visualized and quantified. Fire blight, caused by the gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases to apples. So far, there are no reliable, precise and high-throughput methods to detect early symptoms in response to pathogen attack and to quantify disease susceptibility/resistance. You will be involved in testing chlorophyll fluorescence and infrared thermal imaging for early disease detection. You will also work on developing real-time imaging of fire blight infection to monitor disease progress with concurrent sampling and characterization of transcripts to identify specific spatiotemporal molecular mechanisms. This research will provide new insights into physiological changes in response to disease development and lead to more fire blight resistant apples through the identification of novel molecular markers. 
Computer/lab 60%, Greenhouse/field 40%, Faculty: Khan

14. Telling the stories behind the science

interviewHow do we tell the stories of science? There is so much interesting research going on (just look at all the other projects listed here!), but most people will never hear about them. Come assist us to develop episodes of Food + Science, a podcast that aims to tell the stories of the science behind how food gets to your table. You will help with ongoing interviews and audio editing, and pitch, interview, and put together one full new episode. 
Lab: 80%, Field 20% Faculty: C. Smart

15. Spread of the red

red blotched blotch is a recently recognized viral disease of grapevines that is caused by a DNA virus named grapevine red blotch virus.  Contribute to research efforts addressing virus spread by testing the transmission potential of its treehopper vector and searching for alternative hosts.  Research will involve designing, optimizing, and implementing experiments utilizing techniques such as nucleic acid extraction, polymerase chain reaction, dissection, agroinoculation, sequencing, and fluorescence microscopy.
Lab 70%, Greenhouse 30% Faculty: Fuchs