Recent research has identified dung beetles as bioindicator species found in a wide range of environments. Bioindicators function as monitors for the health of an ecosystem, which can be determined by analyzing the function, population, or status of the species in said environment. The purpose of our project was to determine if dung beetle diversity and abundance differed between primary and secondary rainforests. We conducted a study in the transition zone between tropical wet forest and premontane rainforest at the El Jamaical Field Station in Costa Rica. We acquired feces from both cows and horses near the field station. For trial 1, we made four bait traps using cow feces and one control for each of the forest types. Within each forest type, we placed the bait traps 25 meters apart. We then repeated the experiment using horse feces for trial 2. Traps sat for a period of 24 hours to allow dung beetles time to burrow into the traps. We then collected and processed the samples. Processing consisted of sifting and breaking down the feces in a meticulous manner to find, collect and identify all dung beetles present. We identified a total of 303 beetles in trial one and 0 in trial 2.

Mercury (Hg) is a hazardous contaminant that can be transferred from aquatic to terrestrial environments by emerging aquatic insects. Terrestrial predators, such as spiders, that live along shorelines of water bodies may consume emerging aquatic insects and become contaminated with Hg. Mercury-contaminated spiders may pose a risk to arachnivorous songbirds. The degree to which most families of spiders are contaminated with Hg and the risk they pose to songbirds is not well understood. The objectives of this study were to determine 1) Hg concentrations in two families of shoreline spiders (long-jawed orbweavers, [Tetragnathidae] and crab spiders [Thomisidae]) and 2) determine the risk these spiders pose to arachnivorous birds. We collected representatives from two families of spiders from the shorelines of 10 ponds located at the LBJ National Grassland in north Texas, USA. Both spider taxa in the present study were contaminated with Hg, however long-jawed orb weavers had significantly higher concentrations of Hg in their tissues than crab spiders (p < 0.001; average Hg concentration = 346 ng/g and 35.7 ng/g respectively). We calculated wildlife values for various songbirds to determine health risks that these Hg-contaminated spiders may pose to songbirds. Spider-based wildlife values revealed that one of the families of shoreline spiders, Tetragnathidae, had concentrations of MeHg high enough that they may pose a risk to arachnivorous songbirds that consume spiders along the shorelines of ponds.

Mercury (Hg) is a toxic environmental contaminant formed in aquatic systems by bacterial methylation of inorganic mercury deposited from the atmosphere. Historically Hg contamination of food webs was thought to be restricted to aquatic systems. However recent research has shown that emergent aquatic insects such as dragonflies are contaminated with Hg as aquatic larvae, and then transport it to terrestrial ecosystems when they emerge from the water as adults. Terrestrial predators such as birds can be contaminated with Hg when the consume Hg-contaminated dragonflies. Because dragonfly larvae are top predators in aquatic systems, they contain high concentrations of Hg when they emerge from aquatic systems and can potentially pose a threat to the health of birds that feed on them. The objective of this study was to estimate the Total Hg (THg) concentrations in dragonflies across ecoregions in the South Central U.S. and the hazard Hg-contaminated dragonflies pose to dragonfly-consuming birds. I estimated THg concentrations in dragonflies by using published data on THg concentrations in predatory fish (pF) in 14 ecoregions and converting it to THg concentrations in gomphid dragonflies (gD) assuming a linear relationship (gD) = 0.0856(pF) + 25.92 constructed using data from Haro et al. 2013. The variation of predicted dragonfly THg was mapped by ecoregion using GIS software. GIS analysis tools were used to assess the risk the predicted THg in dragonflies that would pose a health hazard to dragonfly-consuming red winged blackbirds (Agelaius phoeniceus) in each ecoregion.

Mercury (Hg) is a highly toxic environmental contaminant found in all waterbodies on earth. Emergent aquatic insects (like mosquitoes) transfer Hg from the aquatic systems to terrestrial consumers such as spiders. The objective of this study was to examine Hg concentrations in larval mud daubers (Sceliphron caementarium) and their spider prey in mud dauber nests. Adult mud daubers capture spiders with a paralyzing sting to use as the food source for the larvae in their nest. I collected 350 mud dauber nests from three bridges on the Trinity River and one building 40 m inland from the Trinity River in Fort Worth, TX. The nests contained 74 mud dauber larvae and over 2,000 spiders of five different families. I used a Direct Mercury Analyzer to determine the total Hg concentration of mud dauber larvae and five spider taxa. All mud dauber larva and spiders were contaminated with Hg. The inland site had the lowest concentration of Hg in the spiders, suggesting that the spiders at this site were more reliant on low Hg terrestrial prey than high Hg aquatic prey. This is the first study to demonstrate that mud daubers nesting along river systems are part of the mercury cycle because of their use of shoreline spiders as prey for their larvae.

Leaf cutter ants are the rainforest’s most prolific herbivore, eating more vegetation than any other type of creature. The ants have a profound effect on the Neotropical ecosystem, for they improve the richness of the soil, and, by removing leaves from the trees, allow sunlight to reach the lower levels of the forest, facilitating plant growth and diversity. Leaf cutter ants are selective in the plant materials they harvest. The goal of this study is to determine whether leaf cutter ants have a preference for fragile versus tough leaves by examining the relationship between level of leaf damage by leaf cutter ants and leaf toughness among a number of plant species. Leaves damaged by leaf cutter ants of several plant species were identified and collected from the trails of two ant nests in El Jamaical Field Station in Costa Rica. Area of leaf cutter herbivory were traced and recorded as the measurements for level of leaf herbivory. Leaf toughness was quantified as the force required for tearing the leaf apart by using a gravity-based tearing device. From the obtained data, we will examine the level of leaf herbivory of each leaf of the same species against its toughness to see whether leaf cutter ants prefer cutting fragile leaves over tough leaves in order to minimize energy cost. We will also compare this foraging pattern between species to see whether there is a variation in the ants’ preference among different plant species.

Over the last few decades, there has been increasing concern regarding the environmental presence and biological effects of endocrine disrupting compounds. Studies aimed at determining the adverse impacts associated with exposures to thyroid disrupting compounds have focused primarily on the ability of such compounds to alter patterns of growth and development; however, the actions of thyroid hormones extend well beyond these basic functions. As such, there is a need to investigate the potential for thyroid disrupting compounds to alter other physiological processes. Recent studies have suggested a role for thyroid hormones in the regulation of immune function. As such, it is reasonable to suspect that exposure to endocrine disrupting chemicals that impair thyroid activity will lead to alterations in immune function and subsequent changes in pathogen and disease resistance. Using the fathead minnow (Pimephales promelas) as a model organism, this study sought to determine the impact of propylthiouracil (PTU, a known thyroid inhibitor) on various aspects of immune function including immune gene expression, spleen index and pathogen resistance. To achieve this, male fathead minnows were divided into two groups – a control and a PTU-exposed group. Following a 21day exposure period, both groups were challenged with the pathogen Yersinia ruckeri, and mortality was monitored for 14 days to assess pathogen resistance. In addition, tissues (i.e., liver, spleen and kidney) were sampled at 8 hours and 72 hours post infection for the assessment of immune gene expression and spleen index. PTU exposed males were less able to survive pathogen infection relative to the controls. In addition, PTU-exposed males had significantly lower spleen index than the controls following injections, suggesting that they had a reduced ability to elicit an immune response. Gene expression of certain immune genes also showed a change in pattern of expression, signifying potential pathways and proteins that are particularly affected by thyroid hormone presence. These results show that chemically-induced decreases in thyroid hormone levels can suppress immune function and demonstrate that the immune system is a target for thyroid disrupting chemicals.

Neotropical rain frogs serve as an indicator of habitat and ecological disruption in tropical rainforests through species-specific response to environmental stimuli. These responses are reflected in preference of habitat, such as primary or secondary forest, which may provide insights into the health and stability of not only Neotropical rain frogs and amphibians, but also of the surrounding ecosystem. We studied the diversity and abundance of rain frogs at the El Jamaical Field Station in Costa Rica, located in a transition zone between tropical rainforest and premontane rainforest, by overturning leaf litter along previously established trails that passed through both forest types, photographing found individuals, and recording discovery locations on a map. Focusing our study on the primary and secondary forests, we predicted that the diversity and abundance of rain frogs would be greater in the primary forest than in the secondary due to differences in diversity of trees and flora, humidity, temperature, and light levels. Data analysis will include species identification, proximity to dry streams, and comparison between primary and secondary forest.

The Syr Darya, one of the largest rivers in southern Kazakhstan, is a major source of freshwater feeding the Aral Sea. In the 1950s, water was diverted from the Syr Darya to support agricultural production leading to the drying of the Aral Sea, which has been characterized as one of the worst environmental catastrophes in modern day history. Mismanagement of these diverted waters has paved the way for potential surface water contamination in the Aral Sea Basin. While efforts to revive the Aral Sea are underway, few investigations have sought to assess the impacts of potential heavy metal contamination in the Syr Darya Watershed. As such, the goal of this study was to assess the presence and biological effects of heavy metal contaminants in the Syr Darya. This was accomplished by collecting water and sediment samples from five sites and roach (Rutilus rutilus) samples from three sites along the Syr Darya. Water, sediment, and roach muscle tissue samples were analyzed for a suite of contaminants, while roach liver, brain, gonad, and gill tissues were analyzed for the expression of genes considered to be biomarkers of heavy metal exposures (e.g., metallothionein and superoxide dismutase). Water and fish muscle tissue analysis revealed the presence of multiple heavy metals above local regulatory limits. Roach fish from two of the three sites experienced alterations in the expression of genes considered biomarkers of contaminant exposure suggesting that chemical loads at some of the sites in the Syr Darya were sufficient to induce biological effects. Data collected as part of this study will be utilized to complete an ecological risk assessment of the Syr Darya River basin.

Alzheimer’s disease is a neurodegenerative disorder characterized by the presence of amyloid beta (Aβ) plaques. This pathology results in neuronal dysfunction and eventual cell death. Aβ plaques come from the buildup of beta-amyloid protein which clump together and block cell-to-cell signaling at synapses. To stimulate Aβ production, our lab uses an inflammation model utilizing lipopolysaccharide (LPS) injections. When mice are given intraperitoneal LPS injections over the course of one week they show a significant increase of Aβ in the brain. When a second course of LPS is administered following a two-week recovery period, Aβ levels return to baseline levels. The initial exposure to LPS protects the mouse from a second exposure, preventing further increase in the Aβ. One likely explanation is that the initial exposure primes the immune system, enabling the mouse to quickly initiate an antibody response upon subsequent exposure to LPS. The objective of the present study was to investigate the antibodies produced after the second course of LPS in 5xFAD mice. Plasma antibody levels were measured, and co-localization of antibodies around hippocampal Aβ plaques was investigated. We found that mice who received a second course of LPS injections had a significantly higher amount of IgG co-localized around plaques compared to non-treated control animals. This correlated with higher levels of IgG in the plasma. This data suggests that LPS exacerbates the antibody response in 5xFAD mice, and that these antibodies may specifically target Aβ.

Changes in early physiological development due to chemical effluent exposure can be determined by measuring the levels of gene expression. Genes involved in cardiovascular and neurological development, as well as growth, serve as sensitive endpoints in toxicity tests involving the use of larvae. The purpose of this research was to determine when during development the level of gene expression was high enough for contaminant-induced decreases in expression to be detected. A suite of genes involved in growth, cardiovascular and neurological development was examined in embryos and larvae from 0 to 11 days post hatch. This information was used to determine time points at which selected genes were most highly expressed. For the growth-related genes, expression levels of growth hormone (gH) were highest at Days 4-7 and 11, levels of growth hormone receptor (gHR) at Days 1-7 and 11, and levels of insulin-like growth factor (igf1) at Days 4-11. For the thyroid hormone receptors, thyroid hormone receptor-α (TRα) showed highest expression levels at Days 3-11 and thyroid hormone receptor-β (TRβ) showed highest levels at Days 2-5 and 9. For the deiodinase enzymes, deiodinase-1 (Dio1) expression levels were highest at Days 2-3 and 7-11, levels of deiodinase-2 (Dio2) were highest at Days 7-11, and levels of deiodinase-3 (Dio3) were highest at Days 1-5. Vegfa, a gene involved in cardiovascular development, had levels of gene expression that were highest at days 7-11. HuC, a gene involved in neurological development, had the highest level of gene expression at days 7-11. When the level of expression of these genes is highest is when they have the greatest potential to be used in toxicity tests to measure alterations in expression.

Cancer is the second-leading cause of death in the US. Cancer cells are characterized by loss of regulation of the cell cycle that results in uncontrolled proliferation. To drive this high rate of cellular division, cancer cells have mutated to increase uptake of important nutrients including glucose and vitamins by increasing the number of glucose receptors and vitamin transporters, including biotin receptor, on their surface. Due to this difference in expression of biotin receptor between cancer and normal cells, research focusing on the use of biotin-conjugated molecules has gained attention as a method for anticancer drug delivery.
Another characteristic unique to certain cancer cells is that they exhibit dysregulation in normal cellular redox balance, such that the cellular environment becomes more reducing. A more reducing environment favors the generation of reactive oxygen species (ROS). Many metal-based anticancer drugs have taken advantage of this feature of cancer cells in an attempt to increase the levels of ROS to the point that harmful oxidation reactions occur that lead to cell death. Specifically, the iron atom of ferrocene has been shown to lead to the generation of damaging ROS upon oxidation from Fe2+ to Fe3+.
A problem with current cancer treatment is that the chemotherapeutics often are not specific to cancer cells and can lead to negative side effects. As a result, anticancer drugs with high specificity and cytotoxicity are needed to improve treatments. This research project focuses on testing the cytotoxicity of a variety of biotin-ferrocene derivatives on cancer (HeLa) and non-cancer (293HEK) cell lines. HeLa cells are known to express high levels of biotin receptor and are predicted to have more reducing cellular environments; additionally, 293HEK cells express low levels of biotin receptor and are predicted to have less reducing environments. The tested compounds have three main features: a biotin moiety, a ferrocene core, and a variable linker covalently bound to the ferrocene moiety. We hypothesize that the biotin-containing compounds will enter HeLa cells more efficiently than 293HEK cells, allowing for the ferrocene moiety to reduce oxygen, leading to increased ROS generation and cell death.
Here, we demonstrate that ferrocene shows dose-dependent cytotoxicity specific to HeLa cells, while one of the compounds shows dose-dependent cytotoxicity specific to 293HEK cells. Interestingly, two of the compounds show dose-dependent cytotoxicity to both cell lines. These findings are particularly intriguing in that there appears to be a difference in specificity between some of the compounds. However, future studies are required to reveal how these differences in cytotoxicity are related to the differences in chemical moieties and by what mechanisms these compounds are acting to cause specific cytotoxicity.

Most plants acquire mineral nutrients from the soil. However, in nutrient-poor environments, some plants have evolved carnivorous traits that allow them to obtain nutrients by capturing and digesting insects. For example, the carnivorous pitcher plant Sarracenia alata uses passive pitfall traps to capture their insect prey. Although studies have examined prey composition for S. alata, few have included a comparison to the insects available in the environment. The purpose of this study was to compare prey capture of S. alata pitchers with the available insects to determine whether this species is selective in prey capture. The available insects were sampled using artificial sticky traps in the vicinity of the pitchers. The insects in the study were identified first to the level of order and then further identified to “morphospecies” as a means of examining preference on a finer scale. The results show that the pitchers captured only a subset of the available insects. The average number of orders captured by each pitcher (1.8 ± 1.0 SD) was lower than that captured by artificial traps (2.8 ± 0.5). Likewise, the average number of morphospecies captured by the pitchers (4.5 ± 4.8) was lower than that captured by the artificial traps (6.8 ± 3.5). These results support the hypothesis that S. alata is selective in its prey capture, but further studies are needed with different methods of measuring the available insects in order to avoid potential bias.

Rainbow trout, Oncorhynchus mykiss, exhibit two life-history strategies: resident rainbow trout and migratory steelhead trout. Previous research has shown that the migratory decision is highly heritable. Recently, interest has focused on the GREB1L gene as studies in several populations of rainbow trout have found alleles associated with migration. This project aimed to measure allelic associations between GREB1L and migratory life-history in rainbow trout from Sashin Creek, Alaska. Sequence data suggests that all individuals, regardless of migratory trajectory, had alleles associated with migration. These results confirm that there are population specific genetic effects that determine the migratory life-history of rainbow trout.

A distinctive feature in many tropical trees is the presence of red young leaves which turn green with maturity. Some theories as to why the young leaves are red is because it could signal to herbivores that the young leaf is full of toxins, or that it is low in nutrients. During a spring break trip to the TCU Field Station in Costa Rica we tested the hypothesis that green leaves have more herbivory damage than red ones. Fifteen trees were randomly sampled in the secondary forest. All the leaves were counted on the selected trees and we recorded the total number of both red and green leaves and then how many leaves of each color had herbivore damage. We then analyzed the ratio of damaged red and green leaves to determine if red leaves are predated on less than green leaves. This will help us understand if this means that red leaves have a natural defense against herbivory.

The Texas horned lizard (Phrynosoma cornutum) is a threatened species in the state of Texas whose main dietary staple is believed to be the harvester ant (Pogonomyrmex spp.). In two South Texas towns horned lizards are consuming many ants and termites other than harvester ants and so we developed DNA barcoding methodology to help identify these taxa in the DNA extracted from horned lizard feces. We used a small portion of the mitochondrial cytochrome oxidase I gene to confirm morphological identifications and to identify ants and termites to the species level from horned lizard scat.

Euglossine, or Orchid bees, belong to a monophyletic clade of neotropical bees and are specialized pollinators for orchids in the neotropics. Orchid bees are used to study the effects of deforestation and pollination patterns because the males collect fragrances, and therefore by using scents, can be tracked and counted throughout a habitat. Because previous research has shown that scent preference and orchid bee diversity varies across different habitats, we wanted to compare the abundance and diversity of euglossine bees in a forest edge, a secondary forest, and a primary forest near San Ramón, Costa Rica. By placing different scents on filter papers, we counted and identified the number of bees attracted to each scent. We found a variation in scent preference and species diversity across the different forest types. At a forest edge, more bees were attracted to eugenol, while in the secondary forest, most bees preferred cineole. Methyl salicylate was the scent preferred in the primary forest. Scent preference also varied between different species and species diversity was different between the habitat types. While Eulaema meriana was common in both habitats, E. meriana was observed more frequently in the forest edge, while Euglossa imperialis was not seen in the forest edge and was more abundant in the secondary forest and the primary forest. These findings indicate that changes in habitat type and forest structure can impact orchid bee diversity, thus affecting the tropical ecosystem.

Hepatitis C Virus (HCV) is a bloodborne pathogen that infects approximately 3 million people in the United States and 140 million people worldwide. Once infected, only 15-25% of patients are able to clear the virus from their systems without treatment, leaving 75-85% of affected individuals with a chronic, life-long infection. Chronic HCV is often asymptomatic until decades after infection, so many patients are unaware of the need for treatment until damage has already reached advanced stages. Long-term HCV infection can lead to several serious diseases, including chronic hepatitis, liver cirrhosis, and liver cancer. In the United States, chronic HCV infection is the leading cause for liver transplants. As a RNA virus, mutations in the HCV genome are relatively common. Currently, there are 6 genotypes and at least 50 subtypes of the virus, which can affect response both to pharmaceutical treatment and to the host innate immune response.
When HCV infects a cell, the cell fights the infection by turning on the expression of antiviral genes, such as interferon-beta (IFNb). Once IFNb is produced, it is secreted from the cell and in turn activates expression of interferon-stimulated genes (ISGs) in the same cell and surrounding cells, thereby triggering the host innate immune response. HCV produces proteins that are capable of blocking IFNb. Without IFNb, the host is unable to fight off the HCV infection, which allows the infection to become chronic. Our lab has shown that the HCV non-structural protein NS5A inhibits Sendai Virus (SV)-induced IFNb gene expression, and is also vital to viral replication.
This study focuses on two mutant forms of HCV NS5A. NS5A 10A is the K2040 mutant with a lysine deletion, and has been shown to result in increased levels of viral replication. NS5A H27 is the L2198S mutant with a lysine to serine substitution, and has been shown to result in decreased levels of viral replication. We hypothesize that the differences in levels of replication between the two mutants is due to differential inhibition of SV-induced IFNb gene expression. Cells expressing NS5A 10A should have lower levels of antiviral gene expression, while expression of NS5A H27 should lead to higher levels of antiviral gene expression. RT-PCR and q-RT-PCR was performed on HEK 293 cells in order to measure differences in gene expression of IFNb and ISGs MX1, OAS1, and TRIM14 in the presence or absence of Sendai Virus and NS5A. GAPDH was used as an endogenous control, as GAPDH levels are unaffected by viral infection. Cells were infected using Sendai Virus in order to trigger the IFNb antiviral pathway, and were transfected with the different mutant forms of NS5A.

Oxidative stress in the brain is a known contributor to the development of neurodegenerative diseases, including Alzheimer’s. The focus of this project is to target the amyloid-β plaque formations and reactive oxygen species (ROS) derived from misregulated metal-ions that lead to disease-causing oxidative stress. The present investigation is measuring the antioxidant reactivity of the new molecule L4. L4 contains two radical scavenging pyridol groups along with a metal-binding nitrogen rich ligand system. It was hypothesized that increasing the number of pyridol groups in our small molecule library would increase the radical scavenging activity, which in turn may provide cells protection from oxidative stress. The radical scavenging ability of L4 was quantified using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical assay and this was compared to other radical scavenging small molecules to evaluate the effect of the additional radical scavenging group on the antioxidant activity. The interaction of L4 with redox active metal-ions such as copper(II) was also evaluated to show the molecule’s ability to target misregulated metal-ions in diseased tissues.

Monika Hailey
SRS 2017
Neilson Group
Synthesis of Silicon-Nitrogen Polymer Precursors
The Neilson research group focuses on developing synthetic routes to new organic-inorganic hybrid polymers. Specifically, one class of potential polymers contain silicon-nitrogen bonds, alternating with organic spacer groups along the polymer backbone. These two elements were chosen in order to obtain a system whose stability is similar to that of organic (carbon-based) polymers. Organic polymers are very stable and can be found in everyday life. In addition, silicon-oxygen polymers are used in several commercial applications. Silicon-nitrogen polymers could possibly serve as precursors to other new polymeric and/or solid state materials.
Experiments were conducted to produce a variety of small molecule precursors to the new silicon-nitrogen polymer system. Seven silicon-nitrogen small molecules were synthesized, in fairly good yield, and characterized using 1H NMR spectroscopy. When attempting to purify some of these small molecules, there was some thermal decomposition, possibly leading to the desired polymer. Future experiments will investigate the synthetic potential of these new compounds.

Molecularly imprinted polymers (MIPs) are advantageous to chemists both in their ability to drive the equilibrium of a reaction toward a desired product and in chromatography. In this project we focused on the use of MIPs in a chromatographic sense to selectively isolate menthyl-(hydroxymethyl)-phenyl phosphinate in the SP form from a mixture of both diastereoisomers. Both R and S configurations are made in equal proportions but the yield from isolation and crystallization of each pure diastereoisomer is low. Production of a polymer containing pockets specific to the configuration of one diastereoisomer enables an easier method to isolate one diastereoisomer through absorption by the polymer and subsequent release. The potential for MIPs for these P-stereogenic compounds lies in the increase yield of pure crystals and therefor decreased cost of production.

This project was aimed to prepare stable isosteric analogs of S-adenosylmethione (SAM) whose sulfur atom is replaced by a nitrogen atom and to evaluate these analogs for the SAM riboswitch-binding activities and antibacterial activities. In bacteria, SAM binds to the SAM riboswitch, which regulates the biosynthesis of methionine and cysteine, two amino acids essential for survival. Therefore, synthetic molecules that bind to SAM riboswitches have the potential to kill bacterial cells.
Three different classes of SAM riboswitches exist in bacteria (SAM I, II, and III). Each class of SAM riboswitch gene under control of T7 promoter was prepared by the overlapping extension polymerase chain reaction of synthetic oligonucleotides. Each SAM riboswitch gene was successfully cloned into the pUC19 plasmid and verified by DNA sequencing. A high concentration of each SAM riboswitch DNA was prepared by PCR and further converted to the corresponding SAM riboswitch RNA molecules by in vitro transcription using T7 RNA polymerase. All three classes of SAM riboswitches will be tested for binding to the synthesized SAM analogs.

Traditionally the genetic code has utilized the canonical twenty amino acids in order to construct proteins and facilitate life. The process of translation involves an RNA template and codons that will be read and matched to corresponding tRNA molecules carrying charged amino acids. An aminoacyl tRNA synthetase specific to each amino acid is responsible for loading and charging the amino acid to the tRNA. In recent years, a few orthogonal pairs of the tRNA and aminoacyl tRNA synthetase have been utilized to expand the genetic code past the traditional 20 amino acids. Expanding the genetic code allows for new insight into protein function, structure, and interactions within the cell. The introduction of new amino acids could lead to proteins with new chemical or biological activity and even advantageously alter function leading to evolutionary events. In our research we attempt to incorporate unnatural amino acids using a leucyl-tRNA synthetase from Methanobacterium thermoautotrophicum and a tRNA which will suppress the amber stop codon (TAG). A mutant LeuRS lacking an editing domain (MLRS CP1) was generated. The best mutant was isolated and sequenced. The leucine binding site, determined from sequence homology, was randomized at five amino acids to create a library of mutants. The best mutant is selected through a positive selection process where only MLRS CP1 that add an amino acid to the tRNA will survive in the presence of chloramphenicol. Finally, in a negative selection step, those mutants which add natural amino acids to the tRNA will die in the presence of 5-fluorouracil. The library can then be used for further experiments to determine how effectively unnatural amino acids are incorporated.

In U.S., about 63% of households include pets. However, certain pets (such as dogs) have the instinct to run away from the house. Yet, it is impossible for the pet owners to watch their pets all the time. Therefore, a portable and inexpensive handheld tracking system can be a useful tool for helping the owners to watch their pets.
This project intend to employ iBeacon, which is a technology released by Apple Inc., to build a tracking system. The iBeacon technique can achieve distance measurements based on the Received Signal Strength (RSS). The RSS value will change as the distance between Beacon and the signal receiving device change. Moreover, the iBeacon tag device for pets (called iBeacon tags) is small (in the size of a quarter) enough to put on the collar of a pet. The application will store the information of beacons (including UUID, which is used to distinguish different beacons) that provide by users, and continually detect the signal from the beacons. When the signal is not strong enough, which means the Beacon is out of the controllable range, then the application will alert the user.

Hearing aids aim to process and modify sounds into the most desirable forms for hearing impaired people to receive. However, due to multiple reasons including inconvenience and limited quality, only 20 percent of the people in the US who could benefit from a hearing aid wear one. This figure is likely to be much lower in other less developed countries.

Recently, smartphones with powerful computation capability and great mobility have emerged as a possible alternative for this problem. We have developed a preliminary iOS application with certain sound processing functionalities. It is able to collect all the sounds in the vicinity and amplify custom frequencies depending on the prescriptions of a specific user. In addition, the application can also produce different output on either the left or the right headphone piece. We have taken initial steps to make the system operate wirelessly with a Bluetooth earpiece; however, due to time and resources constraints, the application has not yet able to divide two distinct output like what it does on the normal iPhone earpiece. Also, a method for shifting sounds to lower frequency has not yet been implemented. We also have not yet tested the program to its fullest potential due to the sole access to only built-in iPhone’s microphone. A special microphone with many features such as noises canceling, separate streaming, and high sampling rate will enables us fully customize and prepare the application for future technologies. Our future system is expected to address these challenges.

In this experiment, we examine the non-linear dynamics of a mechanical system consisting of an inverted pendulum with one free-turning rotational degree-of-freedom attached to a computer-controlled cart with one linear degree-of-freedom. Using a Quanser Linear Servo Base Unit with Inverted Pendulum and paired software package, we used first principles to develop the non-linear control system needed to move the pendulum from stable equilibrium to unstable equilibrium and maintain unstable equilibrium. This combines the self-erecting inverted pendulum experiment and the classic pendulum experiment. Through the paired software package, we were able to derive the dynamic equations to develop the transfer function and proportional-velocity feedback system that describe the linear motion of the cart, successfully creating the non-linear control system for both phases of the experiment.