- Slides: 38
NASA-PAIR/ Proteomics Projects Crystal Austin Gerardo Lopez Elham Sarabi
Interesting Info about Sea Urchin • About 10 cm across and the spines are about 2 cm • The spines are used for protection, movement and for trapping drifting algae • They move surprisingly fast on their tube feet and spines • They can also re-grow broken spines • Used in public aquariums as an indicator for water quality
Habitat and Distribution: • Live only in the ocean & can not survive in fresh water. They are found from the intertidal to the deep ocean. • Besides the S. California Coast,
Location on the Food Chain • Primary Food- Diet consists of algae, plankton, periwinkles, and mussels • Predators- they are eaten by crabs, sunflower stars, snails, sea otters, some birds, fish and even people.
Reasons Why We Study the Vitelline Envelope… • Location on egg? • What is the vitelline envelope? • Significance in fertilization • Significance in research
Outline: I. Question Being Asked II. Data Collection III. Choosing the Best Model IV. Predicting the molecular weights of the unknown data sets V. Results Obtained
Questions Being Asked? *Does the Vitelline Envelopes polypeptides from two species of sea urchins have the same molecular weight? * Using the mechanically isolated Vitelline Envelope in one species of sea urchin, are the two chemical methods giving the same results with respect to the number and size of polypeptides?
Purpose: TO DETERMINE THE MOLECULAR WEIGHTS OF UNKNOWN PROTEIN BANDS IN A GEL BY USING STATISTICAL MODELS.
Comparing Strongylocentrotus Purpuratus to Lytechinus Pictus • File Studied: -S. purp, L. pictus, DTT treatment, 15% gel • How DTT treatment works. OH OH | | HS-CH 2 -CH-CH-CH 2 -SH • Goal: -Analyze file for comparisons.
Comparing Chemical Treatments w/ a Manual Method • File Studied: -“Sea urchin VE removal” • Methods of isolating the polypeptides: -DTT -Alpha-amylase
Comparing Chemical w/ a Manual Cont. . . -Manual (standard) • Goal: -Analyze file for comparison. -Find the relationship between the two chemical treatments and the manual method.
Methods Used: • Using the 15% gel sample and the 12% gel sample, we approximated the dye front for each based on the end of the gel readings. • We then isolated each lane on a new sheet and read the cm migrated for each band. (In order to get the best result, we adjusted the brightness and contrast in adobe photoshop) • For each lane we ran three trials, then averaged for best results. • We recorded all data on excel for future calculations.
Methods Continued: • Using the recorded dye front and measured values, we calculated the relative mobility by dividing the cm migrated by the centimeters to the dye front. • Using the standard, we calculated the best fit model with linear, quadratic, cubic, 4 th, and some nonstandard functions
Modeling: • Looking for the best fitting model: y = a+bx+cx^2 y =a+bx+cx^2+dx^3 y = a+bx+cx^2+dx^3+ex^4 Nonlinear: y = a+bx+c. LNx • Choosing the best model
In Concluson. . . The 12% gel sample contain less errors in fitting a model, than the 15% gel sample. After choosing a nonlinear standard model, it was found that the natural log yeilded the smallest standard deviation. It also maximized the degrees of freedom overall, allowing us to have a more normal distribution.
References • http: //www. yorvic. york. ac. uk/projects/2/2. 2. 3. 1. htm • http: //www. sidwell. edu/sidwell. resources/bio/ Virtual. LB/sea. html • http: //stanford. edu/group/Urchin/nathistory. h tml • http: //www. wcaslab. com/tech/Dithiothreitol. h tm • Proteomics: Dr. Edward J. Carroll, JR. • Data Analysis: Dr. Larry Clevenson
THANK YOU!!!!!!! We Thank Dr. Carroll, Dr. Clevenson, Dr. Shubin, Vred, and our fellow students for a great CSUN/JPL- PAIR Program!