Research Projects
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Arabidopsis plasma membrane signaling
Plants respond to environmental changes such as drought by a complex
network of signaling proteins whose levels of protein phosphorylation are modulated throughout
the cell. Our lab is using a mass spectrometric-based quantitative phosphoproteomic pipeline to
identify the key components of these signaling networks initiated by hormones and osmosensing
receptor proteins at the plant plasma membrane. Arabidopsis thaliana is the model organism
under study since it provides facile genetic tests for hypotheses derived from the chemical
analyses to ensure that the measured changes play important roles in
planta.
MS/MS spectrum from Arabidopsis 14N/15N labeling
In Arabidopsis and other plants, protein kinases represent the largest
of all gene families present in the genome, pointing to a complexity in the phosphoproteome that
remains poorly understood. The main goal of this project is to increase our understanding of
receptor-like kinase mediated signaling. Untargeted ‘discovery’ measurements are performed through a pipeline of
metabolic labeling of intact plants with 15N/14N and a high resolution Orbitrap-based tandem mass
spectrometer followed by targeted measurements using chemically synthesized heavy isotope
phosphopeptide standards and a triple quadrupole tandem mass spectrometer. Finally, reverse
genetic experiments using Arabidopsis plants containing mutations in the phosphorylated amino
acids provide final tests of the in planta functions for these posttranslational modifications. These
experiments have the potential to reveal important new information on key members of hormone and drought
signaling pathways in plants as well as provide a general technological platform and paradigm for
similar studies by other researchers.
Molecular basis for the electrocyte
The electric eel (Electrophorous electricus) is a fresh water fish from
South America, the only species within the genus Electrophorous. Reaching up
to 6 feet in length, E. electricus is capable of generating both weak
(millivolt, from Sach’s organ) and strong (in excess of 600 volts, from strong and
Hunter’s organs) electric discharges generated within electrocytes, which
encompass the majority of the tail of the fish.
Electrophorus electricus
Over 700 species of electric fish have been identified. The vast majority
of these fish are capable of producing only weak electric discharges that are
used for navigation and communication. Interestingly, electric organs have
evolved at least seven times in independent lineages. The morphology of the
electric organ varies from fish to fish, but they are all composed of
electrocytes which share certain molecular characteristics between
species.
E. electricus is unique among electric fish as it has one weak and two
strong-voltage electric organs. As in other electric fish, E. electricus uses
it's weak electric organ to navigate and communicate; additionally, it uses
it's strong voltage electric organs in predation and defense.
Our lab is involved in a collaboration to investigate the genetic basis for
electrocyte differentiation and function using genomic, transcriptomic and
proteomic technologies, with the electric eel as
our primary model. Identification of the genes and regulatory networks that
guide electrocyte development has the potential to open up new avenues of
applied research in medical and energy fields as well as to provide basic
insight on this fascinating evolutionary development.
Blood-borne biomarkers for colorectal cancer
Colorectal cancer accounts for 10% of annual cancer diagnoses in the US and is the second leading cause of cancer deaths. Early detection of colorectal cancer is crucial to increase survival, but current detection methods are highly invasive or not sensitive enough to achieve early diagnosis. Consequently, the rate of people undergoing recommended colon cancer screening is low. The work done in this laboratory, in collaboration with William F. Dove’s oncology laboratory and colleagues at UW Hospital, uses quantitative proteomics to discover and validate serum protein markers of colorectal cancer for the eventual purpose of developing a minimally invasive biomarker screen.
Apc(Min/+) mouse with Spirulina
There are three aims to this study:
- Discovery of blood protein biomarkers in the serum of the Apc(Min/+) mouse model of intestinal cancer compared to wild-type. For this study, mice are metabolically labeled in vivo with stable isotopes of 14N and 15N Spirulina algae and combined to form four pairs of mutant and wild-type. Following multiple methods of chromatography separation, the blood peptides are analyzed using shotgun proteomics on an LTQ-Orbitrap XL mass spectrometer. Differences in protein amount between wild-type and mutant provide evidence of potential biomarkers.
- Validation of blood protein biomarkers in the serum of the Apc(Pirc/+) rat using SRM mass spectrometry. This rat model, which mimics colorectal cancer in humans, is being used for a large-scale validation of protein biomarkers from the mouse discovery study (aim 1) and the proteins of highly upregulated mRNAs from tumor compared to normal epithelial tissues.
- Validation of blood protein biomarkers in the serum of humans using SRM mass spectrometry. This study is a validation that the biomarkers changing in the prior two aims are changing in humans. With this information, we can plan larger-scale human studies for the eventual development of a blood protein biomarker screen in humans.
Maskless Array Synthesizer development and application
This section is under construcion
Medicago truncatula signaling and symbiosis
This section is under construcion