Thinking Outside the Box: Using Computer Science Skills to Make Sense of the Biology of Life

While I liked coding and the logical aspects of computer programming, my gut was telling me I hadn\u27t quite found my niche yet. In what field could my computer science skills make a difference while also providing me with challenging problems to solve? As these questions percolated through my subconscious, I came across a brief article about a field called “bioinformatics.

Functional analysis of a missense mutation in the serine protease inhibitor SPINT2 associated with congenital sodium diarrhea.

Membrane-bound serine proteases play important roles in different biological processes. Their regulation by endogenous inhibitors is poorly understood. A Y163C mutation in the SPINT2 gene encoding the serine protease inhibitor Hepatocyte Growth Factor Inhibitor HAI-2 is associated with a congenital sodium diarrhea. The functional consequences of this mutation on HAI-2 activity and its physiological targets are unknown. We established a cellular assay in Xenopus laevis oocytes to study functional interactions between HAI-2 and candidate membrane-bound serine proteases expressed in the gastro-intestinal tract. We found that the wild-type form of HAI-2 is a potent inhibitor of nine gastro-intestinal serine proteases. The Y163C mutation in the second Kunitz domain of HAI-2 resulted in a complete loss of inhibitory activity on two intestinal proteases, prostasin and tmprss13. The effect of the mutation of the homologous Y68C in the first Kunitz domain of HAI-2 is consistent with a differential contribution of the two Kunitz domains of HAI-2 in the inhibition of serine proteases. By contrast to the Tyr to Cys, the Tyr to Ser substitution did not change the inhibitory potency of HAI-2, indicating that the thiol-group of the cysteine rather than the Tyr deletion is responsible for the HAI-2 loss of function. Our functional assay allowed us to identify membrane-bound serine proteases as cellular target for inhibition by HAI-2 wild type and mutants, and to better define the role of the Tyr in the second Kunitz domain in the inhibitory activity of HAI-2

COMPLIANCE TESTING OF IOWA’S SKID-MOUNTED SIGN DEVICE

A wide variety of traffic control devices are used in work zones, some of which are nont ormally found on the roadside or in the traveled way outsideofthe work zones. These devices are used to enhance the safety of the work zones by controlling the traffic through these areas. Due to the placement of the traffic control devices, the devices themselves may be potentially hazardous to both workers and errant vehicles. The impact performance of many work zone traffic control devices is mainly unknown and to date limited crash testing has been conducted under the criteria of National Cooperative Highway Research Program (NCHRP) Report No. 350, Recommended Procedures for the Safety Performance Evaluation of Highway Features. The objective of the study was to evaluatethe safety performance of existing skid-mounted sign supports through full- scale crash testing. Two full-scale crash tests were conducted on skid-mounted sign supports to determine their safety performance according to the Test Level 3 (TL-3) criteria set forth in the NCHRP Report No. 350. The safety performancevaluations indicate that these skid-mounted sign supports did not perform satisfactorily in the full-scale crash tests. The results of the crash tests were documented, and conclusions and recommendations pertaining tothe safety performance of the existing work zone traffic control devices were made

Optical interferometer in space

The present design concepts for a Laser Gravitational Wave Observatory in Space are described. Laser heterodyne distance measurements are made between test masses located in three spacecraft separated by roughly 10(exp 6) km. The major technology issues are: the reduction of spurious acceleration noise for the test masses to below 2 x 10(exp -15) cm/sq sec/Hz(0.5) from 10(exp -5) to 10(exp -3) Hz; and the measurement of changes in the difference of the antenna arm lengths to 5 x 10(exp -11) cm/Hz(0.5) from 10(exp -3) to 1 Hz with high reliability. The science objectives are: to measure discrete sinusoidal gravitational wave signals from individual sources with periods of 1 second to 1 day; to measure the stochastic background due to unresolved binaries; and to search for gravitational wave pulses with periods longer than 1 sec from possible exotic sources such as gravitational collapse of very massive objects

Lamb and Wool Production as Influenced by Breed of Ewe and Management System (Progress Report)

This study was designed to evaluate lifetime productivity of the FDT ewe compared to the straightbred Targhee ewe under range and farm flock conditions found in South Dakota

A model of interacting Navier-Stokes singularities

We introduce a model of interacting singularities of Navier-Stokes, named pin\,cons. They follow a Hamiltonian dynamics, obtained by the condition that the velocity field around these singularities obeys locally Navier-Stokes equations. This model can be seen of a generalization of the vorton model of Novikov, that was derived for the Euler equations. When immersed in a regular field, the pin\,cons are further transported and sheared by the regular field, while applying a stress onto the regular field, that becomes dominant at a scale that is smaller than the Kolmogorov length. We apply this model to compute the motion of a dipole of pin\,cons. When the initial relative orientation of the dipole is inside the interval (0, pi/2), a dipole made of pin\,con of same intensity exhibits a transient collapse stage, following a scaling with dipole radius tending to 0 like (tc - t) power 0.63. For long time, the dynamics of the dipole is however repulsive, with both components running away from each other to infinity.Comment: 24 pages 13 figure

On two intrinsic length scales in polymer physics: topological constraints vs. entanglement length

The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo simulations of a three dimensional lattice model. In unknotted and unconcatenated rings, topological constraints manifest themselves in the static properties above a typical length scale $dt \sim 1/\sqrt{l\phi}$ ($\phi$ being the volume fraction, $l$ the mean bond length). Although one might expect that the same topological length will play a role in the dynamics of entangled polymers, we show that this is not the case. Instead, a different intrinsic length de, which scales like excluded volume blob size $\xi$, governs the scaling of the dynamical properties of both linear chains and rings.Comment: 7 pages. 4 figure