Visual-Motor processing provides a mechanism for animals to translate visual cues into useful information for locomotion. My research aims to investigate this mechanism by analyzing the responses made by fruit flies to certain visual stimuli. I accomplish this by first tracking and quantifying fruit fly locomotion when two flies are present. By quantifying this behavior I can create a behavioral map of fly responses in relation to other fruit flies. I can then replace one of the flies with a cylindrical, fly-sized magnet that is readily controlled by me. This step is important because by controlling the magnet it is possible to reproduce large amounts of a specific behavior, instead of watching two flies interacting randomly and waiting for relevant interactions. It also will allow me to investigate the affects of object speed and angle of approach and create a behavioral map of the fly's locomotor response. Once this is accomplished it will then be possible to test fruit fly responses to visual stimuli presented on an LED screen surrounding the fly and to measure brain activity in the flies while these stimuli are displayed. Ultimately we hope to identify the neurons that are responsible for visual-motor processing and how they accomplish the transition from visual input to locomotor response.

Colloidal zinc oxide nanocrystals (NCs) become charged with electrons upon reduction with decamethylcobaltocene. Understanding this redox chemistry can further develop research on quantum dot sensitized solar cells and other various applications of NCs. The goal of my project is to determine whether this electron transfer can be characterized by an equilibrium constant K_eq, and if so, to see which variables in the reaction affect the K_eq. Two models were tested: (1) in which the concentration of NCs would affect the K_eq, and another (2) in which it would not. Using data from optical titrations, I found that the K_eq is affected by NC concentration and is therefore better described by model (1). Similarly, other variables are currently being tested in order to refine a working model that can accurately describe the reaction of NCs with reductants. The contribution of a simple model for these charge transfer processes can be applied to various areas.

Two strains of Botryococcus braunii algae were grown in three different sets of conditions to compare growth characteristics and lipid production. One species, UTEX LB 572, was a Race A Botryococcus braunii from the culture collection of the University of Texas in Austin. The second species, AC 762, was a Race B Botryococcus braunii from the culture collection of the University of Caen, France. UTEX 572 was found to produce two hydrocarbon chain lengths of C:16 and C:18 in a 2:3 ratio respectively. The AC 762 was found to produce hydrocarbons called botryococcenes of chain lengths between C:30 and C:36. The lipid chain lengths of both strains were evaluated by mass spectrometry. The UTEX 572 lipid content was quantified by analytical spectrometry after direct transesterification of the lipid content to biodiesel. The AC 762 lipid content was quantified by a photospectrometry technique developed by UC Berkeley researchers Eroglu and Melis (1985). Cells of both species were harvested during exponential growth phase from 400 mL of growth media and then freeze dried and analyzed gravimetrically. Nine flasks of each species were grown with 3000 lux average light intensity on a 12h:12h light:dark cycle at room temperature averaging 22° C. Three flasks of each species were grown with 1.5% CO2 in BG-11 media, three flasks of each species were grown in BG-11 media with air only and three control flasks were grown in respective carrier medias as those used in the algae collection of origin. Knowledge of the rates at which AC 762 and UTEX 572 produce hydrocarbons as well as the specific lengths and proportions of those hydrocarbons contributes to data needed for comparison of economic considerations in industrial applications.

Until recently, little research has been done on C-S bond formation in transition-metal catalyzed transformations compared to other carbon-heteroatom bonds such as C-N, C-O, and C-P. As sulfur-based coupling partners (thiol and disulfide for example) tend to poison transition-metal catalysts, development of C-S bond formation has been slow. However, a recent nickel-catalyzed system shed new light on this difficult transformation. In this context, C-H functionalization is a sustainable and straightforward approach to sulfur-containing heteroaromatic production. C-H activation is a process whereby a carbon-hydrogen bond is cleaved, thereby allowing the exposed carbon atom to form new bonds. Thus, in order to expand the above research of C-S bond formation toward development of short synthesis for fused thiophene systems, focus was placed on a palladium catalyzed cascade-type reaction system. C-H activation reactions can and have been manipulated to work in a cascade-type fashion. By combining cascade-type methodology with the reduced environmental impact of C-H activation, these fused thiophenes can be synthesized cleanly and efficiently. The test substrates in this work are O,O-diethyl S-phenyl phosphorothioate and 4,4,5,5-tetramethyl-2-(thiophen-2-yl)-1,3,2-dioxaborolane. Both substrates were chosen because they contain sulfur, thereby aiding the C-H activation process. By effecting a C-H activation with a palladium catalyst at one of the ortho carbons of the phenyl ring with the boronic ester of the thiophene, the first C-C bond will be formed. In the time immediately after this first transformation, the now-changed palladium complex is able to insert into the S-P bond of the phenyl-based compound. This step sets up the second reaction, whereby the phosphorothioate directing group is cleaved along the S-P bond and the resulting thiol is coupled to a carbon atom to close the ring. This molecule is known as benzo[b]thieno[2,3-d]thiophene.

Everyday, people's lives are affected by the weather; whether sunshine or rain, weather is a part of daily life. Extreme weather events can bring normal activities to a halt. Weather events known as "blocking" involve a pause in the of the typical passage of storms in the jet stream, causing weather systems to stay in place for lengthened periods of time. Wintertime blocking events often cause extreme cold winter temperatures over land, and data show that blocking frequency is increasing. A potential cause for this is due to sea ice loss and the warming of the Atlantic Ocean. Our investigation is of the extraordinary January 2012 blocking event over Europe. The nature of this extreme event was tested using the Weather and Research Model applied to the domain including the Western Arctic Ocean, the North Atlantic Ocean, and Europe, with a resolution of 40 kilometers. The event was simulated over the period from January 15, 2012 to February 6, 2012, with horizontal boundaries and initial conditions constrained by atmospheric observations. In a series of model integrations, we manipulated the thickness of sea ice and sea surface temperature in high altitudes and found that there is a link between thinner sea ice and warmer ocean temperatures and an increased intensity of the blocking event over Europe. This discovery allows for a better understanding of the potential impacts of melting sea ice as the climate changes. 

Alternative energy sources have been becoming a greater necessity as fossil fuels become higher in demand and pollution endangers the world. Dye-sensitized solar cells have been of increasing interest in the last twenty years as a possible low-cost and efficient alternative to conventional fuel sources. Porphyrins are synthetic analogs of chlorophyll, the molecule responsible for molecular oxygen. Our group has synthesized a number of porphyrins and constructed solar cells using these compounds as the light harvesting pigments necessary to produce energy. Our goal is to determine the change in energy gathering potential and binding capability of the porphyrins to the cells based on the substituent groups bound to the parent molecule. These results will be presented as well as our progress toward optimizing a working dye-sensitized solar cell.

Hybrid organic/inorganic composites of conjugated polymers with quantum dots are of interest due to their potential for low-cost, solution processable solar cells and photodetectors. We use photoinduced absorption (PIA) spectroscopy to study charge generation in hybrid bulk heterojunction blends of the conjugated polymers with PbS quantum dots. We have previously shown that selective excitation of the quantum dots leads to formation of positively charged polarons on the conjugated polymer. By computing the relative yields of long-lived holes following photoexcitation of both the polymer and quantum dot phases, we estimate that more long-lived polarons are produced per absorbed photon by the polymer phase than the quantum dot phase. In this study, we aim to determine whether the formation of long-lived charge carriers due to quantum dot photoexciation is wavelength-dependent by investigating the polaron yield resulting from selective PbS excitation at varying energies in the near infrared. These results will give insight into the process of hole transfer from photoexcited quantum dots to the organic host polymer.

Chemical modifications to histones, such as acetylation, phosphorylation, methylation and SUMOlyation, play a major role in dictating gene expression by changing the structure of chromatin. In particular, the modification of histone H4 by SUMO (called SUMOylation) was reported to be associated with gene repression. However, preliminary results from our lab show that the structure of SUMOylated chromatin resembles transcriptionally active, rather than silent chromatin. In order to comprehend how SUMO achieves gene silencing, biochemical studies with nucleosomes containing uniformly and site-specifically SUMOylated histones are necessary. Here we present a synthetic strategy to produce histone H4 modified by SUMO at Lysine 12. This strategy requires two native chemical ligation reactions. The first is between two fragments of H4- one synthetic and one recombinant. The second is a ligation between the SUMO-3 isoform and H4. In order to achieve the ligation of SUMO-3 to the side-chain of Lys in H4, we have developed a new ligation auxiliary. The synthesis of this auxiliary will be presented along with its application toward the total synthesis of SUMOylated histone H4. By understanding how SUMO-H4 controls gene function we hope to identify novel means to change cellular processes that result in diseases such as cancer.

Quantum dots (QDs) are the precursor for numerous burgeoning technologies, including more efficient solar panels and high definition LED displays. QDs are small, soluble crystallites of a semiconductor material that have unique qualities since their electrons are confined in all three dimensions in a region of space smaller than the de Broglie wavelength of their electrons. This allows the electrons to occupy spectrally sharp energy levels like an element or a molecule. Their electronic properties can be tuned as a function of their size. In our lab, indium phosphide QDs are prepared under an inert atmosphere of dinitrogen by hot injection of a phosphine precursor into an indium salt and fatty acid solution. Taking aliquots of the reaction mixture at different time intervals during QD growth allows us to chart the rate of particle evolution and provides information about particle size and uniformity. Indium phosphide is a member of the III-V semiconductor class, meaning they are made from elements from column three and column five of the periodic table, and have desirable properties like direct band gaps which allow these materials to efficiently absorb and emit light as well as faster carrier mobility than II-VI quantum dots. The synthesis of III-V QDs has not allowed for size- uniformity or tunability to be achieved because of the uncontrolled reactivity of the precursors, in particular the group V precursors. Our group has recently uncovered an important acid-catalyzed pathway leading to phosphine speciation during indium phosphide QD growth. My project focuses on addressing this issue by incorporating new, more stable precursors and chelating capping agents to better stabilize the reaction products and intermediates, which would be crucial in controlling the formation and therefore the properties of the resulting quantum dots.

Electrospray ionization (ESI) is a powerful tool for transferring intact protein complexes from solution to the gas phase. ESI creates multiply charged ions with a net positive (cation) or negative (anion) charge. Although the structures of gas-phase protein cations have been investigated extensively, relatively little research addressing the structures of negatively charged protein ions exists in the literature. In my research, I use ion mobility (IM) to measure drift times, or the time an ion takes to traverse a gas-filled drift tube in the presence of a weak electric field. The drift times for ions depend on their charge and collision cross section (CCS), which to a first approximation, is the orientationally averaged projected cross section of its structure. Therefore, the drift times of ions depend on their structure. Preliminary CCS values that I have measured for protein complex anions are slightly smaller than values in the literature for the analogous protein complex cations, which suggests that the anions are more compact than the cations. One challenge in interpreting those results is the anions had a lower absolute number of charges than the analogous cations, so the results may not be directly comparable. The focus of my research is to make more direct comparisons between the structures of protein complex cations and anions. To this end, I am developing methods to reduce the number of charges on protein complex cations to values equal to those observed previously for the anions. CCS values determined for these charge-reduced cations will be directly comparable to those measured for the anions, and should reveal any structural differences between protein complex cations and anions. These results will also be useful for calibrating other IM experiments and determining how best to use IM to characterize the native structures of protein complexes.

Cysteine and homocysteine are two important amino acid biomarkers related to human health. The presence of homocysteine at high concentrations in the bloodstream is correlated with various disorders such as cardiovascular and Alzheimer's diseases. Healthy cysteine levels are important in preventing lethargy, edema, and liver damage. Because of their critical roles in human health, we report the development of fluorescent and chromogenic indicators to monitor homocysteine and cysteine concentrations rapidly and inexpensively using absorption and fluorescence spectroscopy. Several aldehyde-modified probes have been developed for thiol detection, with their function based on spectral changes associated with their respective heterocyclic products formed upon reaction with cysteine and homocysteine. These reaction products exhibit specific excitation, emission, and absorbance wavelengths related to the concentration of target analytes. In the case of fluorescein dialdehyde, our previously reported results indicated a UV-vis absorbance change and fluorescence quenching in response to both analytes. We hypothesize that judicious selection of experimental conditions will allow improved sensitivity and selectivity for specific analytes. The current study focuses on optimizing experimental conditions by evaluating several pH values and excitation wavelengths. The data shows that the response of fluorescein dialdehyde to thiols is pH-, wavelength-, and time-dependent, with difference in the responses toward cysteine and homocysteine. Further investigation of these and related compounds will elucidate the mechanism responsible for the selectivity and allow for increased utility of this class of aldehyde-modified probes

Author: Amanda Tanadinata, Karol Bomsztyk, Daniel Mar. Background: Apart from DNA mutations, alterations in chromatin structure, also referred to as epigenetic changes, have been shown to be among principal causes of tumor genesis that leads to cancer. However, unlike mutations, the usage of these chromatin alterations in gene expression is reversible. This feature, in fact, is what has nurtured the idea of creating an epigenetic-based treatment for cancer. One such treatment uses the compound 5-aza-2’-deoxycytidine (5-aza-dC), a DNA methyltrasferase inhibitor. DNA methylation can be crucial for transcriptional repression and activation, by altering recruitment of enzymes and transcription factors to chromatin . The goal of this study was to profile a set of pathways through the analysis of 5-aza-dC -mediated changes in DNA methylation, mRNA expression , RNA Polymerase II, histone marks, and enzymes. Method: Colorectal cancer cell line (HCT116) cells treated with or without 5-aza-dC were probed with different antibodies to see chromatin density differences at specific sites of the genome by Matrix Chromatin Immunoprecipitation (Matrix ChIP). Methylated DNA Immunoprecipitation (MeDIP), was used to assay DNA methylation sites at selective gene sites. The results were then quantified with real time PCR. In this study, SPARC promoter, H19, and UBE2b were examined specifically. Results: Treatment with 5-aza-dC increased SPARC mRNA levels, and reduced DNA methylation This was associated with changes in RNA polymerase II levels ,histone acetylation and methylation, and chromatin modifying enzymes at the SPARC but not the control H19 and UBE2b genes. Conclusion: These results imply that 5-aza-dC induced de-methylation of selective genomic sites alters enzyme binding and chromatin structure which then causes changes in rates of transcription.

Two 5-membered rings with a nitrogen at one of the fusion sites is the core structure for a variety of natural products known as pyrrolizidine alkaloids. Many of these compounds are produced by plants as a defense mechanism due to their hepatotoxicity. Other varieties of these compounds, however, have been shown to possess antiviral, anticancer, antidiabetic, and antiobesity drugs. Because of their inherent biological activity and the relative costliness of extracting these compounds from natural sources, they have become an important synthetic target. Previously in the Michael group, a palladium catalyst was developed to facilitate the addition of an N-H bond across a C=C bond. This transformation is known as hydroamination. When the protected amine and alkene are present in the same molecule, cyclization occurs, forming 5- and 6-membered nitrogen containing heterocycles. This most recent work sought to extend the capabilities of this reaction by replacing the amine protecting group with a highly electron deficient aldehyde. Thus after the initial addition of the N-H bond across the C=C bond occurs, the C=C bond will then perform a nucleophilic attack on the aldehyde forming a second ring fused to the first. This reaction sets 3 new stereocenters, forms 2 new rings, and generates a C-N and C-C bond in a single, diastereoselective step. The substrate synthesized in order to test this reaction was a 7 carbon terminal diene amine coupled with dimethyltartrate and subsequently oxidized to generate the desired diene-amide-aldehyde functionality. This substrate when submitted to the hydroamination conditions resulted in the diastereoselective formation of the tri-substituted pyrollizidine in 35% yield. Further work in this project will include application of these methods to the synthesis of several natural pyrrolizidine alkaloids. It is hoped that further manipulation of the substrate will allow expansion of the range of attainable targets to that of indolizidines and quinolizidines.

 Transition-metal ions promote a wide range of vital enzymatic biological and chemical processes involving dioxygen (O₂), including photosynthetic H₂O splitting, biosynthesis of neurotransmitters, and DNA replication and repair. These are some of the most fundamental processes of life, and yet they are also some of the most poorly understood. A complete grasp of how these processes function at the chemical level is therefore of critical importance to our development of technology that improves our lives and the world around us. For example, understanding how to efficiently oxidize H₂O to O₂ is essential to the development of renewable solar fuels and fuel cells. The challenge for research lies in that these transition-metal containing enzymes are inherently difficult to probe by traditional spectroscopy methods because of their structural complexity. The difficulty in characterizing these species and their reactions, coupled with their importance in the natural world, has made them a subject of intense research across all scientific disciplines. The Kovacs research group studies the structure and reactivity of these transition-metal containing enzymes, or metalloenzymes. Our research method involves modeling a metal ion’s local environment with a ligand scaffold and implementing changes to these so-called biomimetic models that may elucidate how reactivity corresponds with various structural and electronic modifications. Spectroscopy is more diagnostic in these simpler models because the complex proteins that obscure the active site in the actual enzyme are not incorporated into the model. By comparing similarities in reactivity between the biomimetic model and the actual enzyme, we may help elucidate properties and chemistry of the enzyme itself. Preliminary work has been undertaken with a novel series of thiolate ligated, coordinatively unsaturated Co(II) complexes; the reactivity of these complexes with O₂ and O₂^- is currently being probed.

In the Puget Sound marine ecosystem, a large estuary complex located in the Pacific Northwest, plankton species are impacted by both seasonal variations and water chemistry. Salinity and pH data are collected monthly by Ocean Research College Academy (ORCA) students during State of Possession Sound (SOPS) trips, near the urban center of Everett and the Snohomish River delta. We studied salinity and pH data in parallel to plankton samples collected in a vertical tow by a 20µ plankton net. By collecting these data at different stations within the Possession Sound subsystem, we are able to compare varied salinity and pH data to account for spatial differences, in tangent with the collected plankton samples. We focused on Coscinodiscus spp.,  Pseudo-nitzschia spp.,  and adult Copepoda spp., for our plankton species, as they were typically the largest populations in every cruise. The data we collected showed that plankton were most numerous within water of a pH between 6.3-6.7 and a salinity of 28ppt-31ppt. Samples collected that strayed from the 6.3-6.7 pH range or went above or below 26-31ppt had either no, or significantly fewer amounts of plankton.