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Meet the Students of the AFRI Program

Graduate Students

William Holdsworth

William Holdsworth joined the Mazourek lab after rotations with the Mazourek, Nelson and Sorrells groups. Bill's PhD research projects include breeding for oomycete resistance, genotype by sequencing in vegetables, and developing SNP markers for gene pyramiding in the Mazourek group breeding program.


Anna Levina

Anna Levina joined the De Jong lab after three rotations, including the De Jong, Sorrells, and Mazourek groups. Anna's PhD research projects leverage resources developed by the SolCAP project. She has genotyped a tetraploid potato population with over 8,000 SNP markers and is now working to map loci that confer resistance to common scab.


Both graduate students are engaged in applied breeding programs that release cultivars utilizing modern genomics.

Undergraduate Students

2013

Min Sun Song was involved with several programming and bioinformatics projects related to the Rice Diversity project in the McCouch Lab. Her main focus was the creation of a web-based visualization tool for rice genotyping data using php and javascript.


Daniel Waizman

Daniel Waizman interned with the MetaMaize project of Rebecca Nelson's laboratory, which is focused on identifying the endophytic microbiome of above ground maize tissues. Daniel was involved in all aspects of the MetaMaize project. He harvested and processed maize tissues from the field and in storage in preparation for microbe culturing and DNA isolation, cultured diverse fungi and bacteria from internal maize tissues on selective microbiological media, purified microbial cultures to homogeneity in preparation for their identification by gene sequencing, prepared media for the project, was involved in troubleshooting technical challenges associated with the research, and prepared field plants for crossing.


Alexander Chin

Alexander Chin assisted with an insect resistance project with the Mutschler group. His work focused on determining the genetic regulation of both acylsugar level and chemotype of the type IV glandular trichomes of the Solanum pennellii wild tomatoes, with the goal of uncovering which chemotype (glucose or sucrose) would be most effective against silverleaf whiteflies. His involvement in this experiment entailed evaluating whitefly oviposition rates and trichome densities on different leaf positions. Alex also aided in inducing plants with jasmonic acid to assess the distinct odors they produce on different leaf positions and ages.


John Owens

John Owens returned to the Mazourek group in 2013 to phenotype peppers and cucurbits for virus symptoms.


Nick Beibel worked on genotyping in pepper using PCR markers and participated in all aspects of the breeding program as part of the Mazourek group.


Jie Yung worked on improving the Sol Genomics Network database. She wrote new software to aid researchers in easily converting identifiers for genes to other sets of identifiers that were widely used before the genome was sequenced.


Samuel Moijueh returned to the Sol Genomics Network to analyze mRNA expression in different tomato tissues and create tracks on the genome browser that reflect the gene expression in each tissue. He used tools such as TopHat, samtools, and other next-generation sequencing analysis programs.


2012

Jessica Johnston

Jessica Johnston, an undergrad from University of Texas – Pan American, worked in the Mutschler group assisting with lab, greenhouse, and field work in the tomato breeding program. In addition to helping with disease resistance projects, Jessica contributed to the insect resistance effort by assessing insect oviposition rates. She also worked on a special project investigating the relationship between acylsugar production in type IV glandular trichomes, leaf position, and plant age.


Manuel Romo

Manuel Romo, an undergraduate from Texas A&M International University, worked in the Nelson group and focused on identifying genes with quantitative effects on resistance to Northern Corn Leaf Blight (NLB) in maize. Manuel contributed to all aspects of the program, including sample collection, DNA extraction, inoculation, and disease scoring. He also participated in a special project investigating the tasselseed1 mutant associated with greater NLB susceptibility.


John Owens

John Owens worked in the Mazourek group to evaluate and troubleshoot barcode data collection systems for use in vegetable field plots.


Samuel Moijueh worked at the Sol Genomics Network (SGN) to improve their website software. He implemented an interface to enable the web-start of a Java application called GenomeView, which allows users to view structural genome data in more detail. Certain users can also edit the annotations and store the data back to the database, resulting in a distributed annotation system for genome features integrated with the SGN database.


Kathyrn Blackley

Kathyrn Blackley worked at Gramene developing a tool that allows inference of gene networks based on normalized gene expression data gathered from many different experiments. She wrote R scripts that allow improved processing of input data, permutation testing on the data for significance, and graphical display of the results, which depicts only the genes of interest and genes to which they are likely to be connected.


2011

Paulo Garcia Jr.

Paulo Garcia Jr., an undergraduate intern from Texas A&M, worked with the Nelson group where he was involved in daily activities related to managing a maize disease resistance nursery. He also individually spearheaded a new project aimed at identifying maize endophytes using abundant data from the Buckler lab on campus.


Omar Vasquez

Omar Vasquez , an undergraduate intern from Texas A&M, worked with the Mutschler group where he participated in the field program planting and maintaining fields and collecting phenotypic data. Omar was individually responsible for the genotyping of tomato breeding lines to confirm the presence of introgressions.


Benjamin Gordon worked at the Sol Genomics Network curating Solanaceae data for loading into the database, including Solanaceae pathogens. He also wrote Perl scripts to organize the data.


Zach Hempstead and Cindy Chen assisted with bioinformatics and programming projects, using Perl and PHP to complete a variety of objectives related to the Gramene project. Programs developed functionality for interacting with relational databases, parsing biological data, and creating user interfaces for biologists.


Samantha Klasfeld

Samantha Klasfeld was a Cornell undergraduate summer intern in the Mazourek group. In addition to helping in the field, she assembled a panel of pepper germplasm with contrasting disease resistance and quality traits and co-developed and tested SNP markers linked to those traits. Markers that perform well in diverse backgrounds are highly useful for pyramiding simply inherited traits with Phytophthora capsici resistance in pepper.


Elena Olsen served as a student TA for Plant Genetics PLBR2250 where she worked on the development of a lab exercise exploring insect resistance in Arabidopsis.


Katherine Scheibel worked as a student TA for Plant Genetics PLBR2250; she designed and led a lab activity focused on virus resistance in squash.


2010

Chris Mancuso

Chris Mancuso worked for the Nelson lab contributing to a large research study of disease resistance in maize, focusing mainly on Northern Corn Leaf Blight (NLB). He was involved in a wide range of field and lab activities, including field nursery management, disease inoculations and phenotyping, and large scale maize pollinations, which were complimented with lab diagnostics, including high throughput DNA extraction and genotyping. He worked towards fine mapping and characterizing quantitative disease resistance loci of NLB in maize.