Natural Sciences

The Quantification of Transgene Copy Number in Immune T-Cell Mouse Model

The two transgenic mouse models developed in the Sarafova Lab enable the investigation of the role of a novel cis-regulatory element (NCE) in CD4 expression during T-cell differentiation. To produce the transgenic mice, two bacterial artificial chromosomes (BACs) were inserted into respective mouse genomes; one BAC includes the NCE, and the other BAC has no NCE. The BACs contain a reporter gene called enhanced green fluorescent protein (EGFP) in the place of the CD4 gene, so the expressed level of CD4 can be measured, and the effect of the NCE on CD4 expression can be elucidated. To accurately analyze the EGFP fluorescence and determine the effect of the NCE, we needed to determine how many copies of the BAC integrated into each transgenic mouse genome. Using quantitative real time PCR (qPCR) and Southern blot, we show that the two mouse models contain different copy numbers of EGFP. We also show that variable cycle PCR and qPCR are effective ways to investigate relative gene copy numbers.

Predicting Key Drug Properties From Chemical Structure

Volume of distribution and clearance are both pharmacokinetic properties that determine the half-life of molecules. Currently, these properties cannot be accurately predicted without collecting experimental data. New methods for predicting these properties could facilitate the development of promising molecules for advancement into clinical trials. Therefore, we have preformed correlations between known structural features of molecules (e.g. charge, polarity, surface area) and experimental values for volume of distribution and clearance. These correlations have allowed us to develop a model for predicting the half-life of a molecule based solely on its chemical structure.

Confining Particles with the Motion of Shepherd Moons

I will write a program in Python involving the orbit of two moons around a planet. Many planets in our solar system have moons. Sometimes, when there is excess dust and icy or rocky debris orbiting the planet as well, the moons can help herd this dust into defined rings. For example, two of Saturn’s moons, Prometheus and Pandora, define Saturn’s F ring. They do so by orbiting on either side of the dust ring. Any dust that tries to escape is either absorbed by the moons’ gravitational pulls, or is pushed back into the ring by the different speeds of the moons. The outer moon travels at a relatively fast speed, thus speeding up any stray particles of dust that try to escape the ring, swirling them back towards the ring. Similarly, the inner moon travels slower, slowing down any dust that tries to escape the ring by traveling in towards the planet.

For my project, I will model the shepherd moons Prometheus and Pandora orbiting Saturn and herding dust particles between them into a ring. I will use vpython to create a 3D simulation of the planet and moon system. The moons orbit at slightly different speeds and different distances from the planet. In my model the orbits will be circular, since that is a sufficient approximation of a realistic elliptical orbit for this exercise. I will then model small particles between the moons’ orbits to show the dust ring they help contain. The dust will look like a cloud or ring-shaped plane made up of dots. I will animate them so that they move in or out towards the moons and stick to the moons if they collide due to the moons’ gravitational pulls. I will also attempt to animate the particles so that they can be pushed back into the ring by the moons velocities and motion trajectories. I will include a graph of the moons’ and a dust particle’s motion to show more clearly how they interact with each other.

This simulation and accompanying graphs will illustrate how the motion of shepherd moons help create rings around planets.

Launch Simulation of a Saturn V Rocket

The first step of almost any space mission is to place a satellite or capsule into high Earth orbit, a task that can only reasonably be accomplished with a multi-stage rocket. The mathematical concepts necessary for achieving a circular orbit of the desired altitude at the desired time are quite complex, so the goal of this simulation is to reduce such complexities down to a visual representation of the launch and orbital insertion of the rocket. Specifically, the motion of a Saturn V rocket, of the type that sent astronauts to the moon, will be examined. This visualization should allow viewers to grasp the nature of some of the maneuvers necessary to reach the moon, while additionally giving a sense of the altitudes and speeds that these rockets reached.

A Novel Role for Notch in Neuronal Connectivity in C. Elegans

Simulation of A Pendulum

This project stimulates the movement of a simple gravity pendulum and allows the user to explore the factors that influence the frequency of the pendulum. The program allows the users to input several factors that may or may not influence the frequency of the pendulum: the length of the string, the initial angle of the mass, the planets (with different gravitational constants) and mass of the object. The program will then generate an animation of the pendulum and the trace of the mass under the chosen conditions.
To make the animations more educational, the program will also offer comparisons between the default pendulum and the user-selected pendulum to show whether the user- selected variable contributes to the (proportional, anti-proportional) change of frequency. What’s more, the program will provide graphic analysis of the trajectory of the mass and calculations of the angular frequency, the frequency and the period of the pendulum.
If possible, this program will also incorporate the possibilities of air resistance to make the simulation more realistic. This addition involves another user input variable to generate one more force that influences the movement.
The program will be created using Python programming. The 3D animations will be designed by using VPython module, the graphic analysis and plotting will be generated by pylab module and the other sample calculations by built-in functions in Python.

Red Maple Seedling Survival Rate in a
Davidson College Ecological Preserve Forest

Investigations of many large forest ecosystems have documented that white tailed deer (Odocoilus virginianus) populations have reached densities that threaten the regeneration of forest canopy trees throughout much of North America. The Davidson College Ecological Preserve (DCEP) represents a set of small, fragmented forest habitats, and many of these fragments have high edge to area ratios that may foster extremely high deer densities.  We conducted an experiment to determine if white tailed deer adversely affected seedling survival of a hardwood canopy species, red maple (Acer rubrum), in one DCEP mixed pine hardwood forest.  We randomly selected 3 spatial blocks within a 0.5 ha area and established 3 plots in each block.  One plot used metal caging to exclude all potential mammalian herbivores, another excluded large herbivores, but allowed entrance by small mammals, and the third was a completely exposed control.  We transplanted 50 first year red maple seedling into each plot and then monitored them for survival from June to November, 2016.  Red maple seedlings in the exposed plots in all three blocks showed approximately 50% less survival than either of the two caged treatments.  The two caged treatments showed similar survival in all blocks.  These results suggest that mammalian herbivory has the potential to reduce red maple regeneration in the forest studied.  However, the similar survival rates in the two caged treatments could result from a cage effect that discouraged small mammals from entering the exclosures or reflect low levels of small mammal herbivory on red maple seedlings.  Results of a follow up experiment suggest that small mammals visit control plots and plots with cages that exclude deer but provide entrances large enough for small mammals at similar rates.  Our results indicate that deer may be the main animal source of red maple seedling mortality in the forest studied.