The blood-brain barrier is a very selective membrane that works to protect the brain from most pathogens; however, this means that it is a difficult therapeutic target for drug targeting. Cutting-edge nanotechnology research is being performed by Dr. Elizabeth Nance on targeted drug delivery mechanisms to combat brain tumors such as glioblastomas, neuromas etc. Nance’s group has found and supported good drug release results with poly-ethylene glycol coating (PEG) for which they hope to perform controlled and targeted release. Currently, there is a lack of molecular level understanding of the drug-polymer interactions that dictate controlled release. Better computational models are needed to understand release kinetics and facilitate rational design of biomaterials to control the release or retention of a particular drug or enzyme. In the present work, molecular dynamics (MD) simulations were used with GROMACS software to study glutamate diffusion in water to validate our method and set a baseline for more advanced systems. Diffusion constants calculated with the Einstein equation based on glutamate diffusion in MD were consistent with experimental values of ∼0.75 μm2/msec. We are currently extending this approach to probe glutamate diffusion in the presence of biocompatible polymers such as PLGA (poly(lactic-co-glycolic acid)) and PEG. Then, we compared and contrasted the diffusion constants to make sure they were on the same order of magnitude as glutamate. We also studied the system kinetics to discover the polymeric matrix that allows the system to get closest to a diffusion-limited rate. We will relay this to Dr. Nance to modify her experiments to lead to improved drug delivery systems that help fight off brain cancers.

Peptoids are a novel polymer with a molecular structure similar to proteins. They can be used for numerous applications such as drug delivery agents, scaffold material, and nucleation agents. Certain peptoids can also self-assemble into functional and tunable structures such as nanosheets and nanofibers. Recent experimental research uncovered that chains of N-ethylcarboxylate – N-ethylphenylchloryl (Nce-Npe) peptoids can aggregate to form clusters in a calcium chloride solution and form nanofibers in the presence of a mica surface. It was also found that calcium ions facilitate the aggregation of these peptoids. In order to characterize the solution-state behavior of these peptoids on the atomic scale, we used molecular dynamics simulations. Molecular dynamics simulations utilize Newton’s laws and fitted empirical equations to produce the trajectory of the peptoids over time. We setup several systems of varying size and ion concentration and ran these simulations using a three-site water model and an AMBER99sb-ildn forcefield with parameters optimized to describe peptoid systems more accurately. We ran these simulations on Hyak, a high-performance computing cluster at UW, using the GROMACS software package. Through analysis of the peptoid trajectory, we found that aromatic pi-stacking drives clustering and ion-carboxylate interactions dictate the structure and stability of the peptoid clusters. We also observed an increase in both the rate of aggregation and number of ion interactions as the concentration of calcium ions increased. These simulations are essential to understanding the self-assembly of peptoids and similar polymers in complex environments.

Targeted therapies designed to inhibit hyperactive oncogenic signaling have demonstrated some encouraging clinical responses. However, many of these responses are not durable as tumors may develop new mutations to “work around” pathway inhibition leading to drug resistance. Technologies that enable more efficient discovery of “suites” of drugs that inhibit multiple pathway nodes are needed. The SABRE (Splice Acceptor Brilliant Reporter) platform was developed to provide an unbiased method to screen large compound libraries and dramatically improve the speed and efficiency for which novel targeted therapeutics can be identified. SABRE is built on the premise that oncogenic changes in gene transcription can be harnessed as powerful reporters of pathway activation status. SABRE utilizes gene trap technology coupled with a drug selection process to isolate cells that generate a robust “off to on” luciferase signal in response to pathway inhibition. Via massively parallel comparative analysis, multiple traps let nature provide the best reporter for further analysis and drug discovery. We employed the SABRE technology to identify insertion sites specific to the MAPK (mitogen-activated protein kinase) pathway, an oncogenic pathway that is implicated in a plethora of cancers. Experiments were performed using the human melanoma cell line A375, containing BRAFV600E mutation. SABRE lentiviral transduced A375 cells were treated with trametinib, an inhibitor of MAPK pathway, and clones were isolated that emitted a positive luciferase signal upon drug treatment. To determine if these reporters were MAPK pathway specific, the platform was used to screen a 6000+ compound library. Results from the screen found that 70% (28/40) of the top drug hits were known to directly modulate the MAPK pathway revealing the power of the SABRE gene trap technology to generate a panel of reporters specific to an unlimited number of cancer signaling pathways. SABRE holds the promise for discovering untapped drug therapies for cancer.

Lake Kapowsin in Pierce County, formed approximately 500 years ago when the Electron Mudflow from Mount Rainer dammed a valley creek, was recently designated Washington’s first freshwater aquatic reserve. In light of this new designation, the Washington Department of Natural Resources contracted University of Washington Tacoma staff to collect summertime water quality data to be used in future watershed management decisions. Field sampling was carried out once a month from June to October 2016 at three stations along a lake transect from inlet to outlet. Water samples were collected at surface and near-sediment depths to monitor chlorophyll a, total suspended solids, turbidity, and alkalinity, and in situ vertical profiles of temperature, pH, specific conductivity, and dissolved oxygen were measured. Secchi depth was also recorded and phytoplankton samples were collected by vertical net (20 µm mesh) tows. Elevated chlorophyll concentrations in the water column, coupled with a shallow Secchi depth, give indication of high algal productivity leading to poor light penetration. Consequently, Lake Kapowsin, despite its shallow depth, experiences thermal stratification between June and September due to the inhibited light penetration. This thermal stratification, in concert with the high algal productivity and bacterial aerobic respiration at the bottom of the lake, results in anoxic conditions and reduced pH in the bottom waters. These resultant conditions lead to a release of phosphorus and, to a lesser degree, nitrogen from the sediment. Ultimately, the persistent anoxic bottom waters capped with warmer waters makes the lake more suitable for warm water fish than cold water fish. The elevated productivity and anoxia in Lake Kapowsin is likely due primarily to naturally occurring eutrophication owing to the flooded forest inundated during the creation of the lake.