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.