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.

This report examines the function, accuracy, and ease of use of an XBOX Kinect™ as a 3D surface scanner. The purpose of this experiment is to demonstrate the utility of a Kinect™ for XBOX 360 (Microsoft®) paired with Skanect (Occipital) and MeshLab software packages as a low cost solution to surface scanning and processing. My conclusion is that the Kinect™ is able to accurately model the recorded point cloud as a continuous 3D surface that matches the contour and scale of the test subject surface. Both Skanect and MeshLab effectively interpolated the smoothing of the 3D surfaces and provided higher resolution imaging than an unaltered image. The resultant resolution of the contoured surface is higher than the resolution of the 3D printers used in this experiment, demonstrating an effective digital duplication of a physical surface.

For this project, a digital grip gauge was designed for Lockheed Martin to measure the grip length of the aircraft skin of the F-35. The objective of the electrical group is to ensure that the gauge will be capable of recognizing when the measurement has stabilized. When stabilized, a light will turn on, which allows the operator to know the measurement is ready for reading. We developed three prototypes that each complete this objective. The first prototype uses two force sensitive resistors (FSR) powered by Arduino. The Arduino code is programmed to turn on a light when the forces on the sensors are equal for a certain range within different zones. The second prototype consists of a comparator circuit with two FSRs connected to a NAND gate. When both FSRs measure the same force, within a range, a light will turn on. The third prototype utilizes two small push buttons that complete a circuit. When both buttons are pressed, the circuit is completed and a light will turn on, indicating to the operator that the part is flush with the aircraft skin and the measurement is stabilized. While each of these prototypes satisfies the objective, the third prototype was ultimately selected due to size constraints of the gauge design.

Compressive line sensing is a process of acquiring data and reconstructing images. The objective of this study is to explore the impact of the two parameters that are used in the image reconstruction algorithm on the quality of the reconstructed image. These two parameters are the compression ratio and the line group. The compression ratio is the ratio of the number of measurements taken at each line vs. the resolution of each line. The line group is the number of lines that are grouped together and solved jointly when reconstructing the image. A higher compression ratio results in degraded image quality because less measurement data is used to reconstruct the image. The larger the line group, the better the quality of the image at a cost of longer computation time. The key is to find a balance between the compression ratio and line group choices so that the image is reconstructed with as little data as possible while still maintaining a high image quality. We will present images reconstructed with different compression ratio and line group based on the data obtained in air and in water.

The objective of our work is to design and build a depth gauge that efficiently and accurately measures the depth of a narrow hole, and give feedback via an electronic screen on the device. This design is being made for Lockheed Martin and will allow their employees to measure a large amount of rivet holes both quicker and more accurately than their current solution. Speeding up the measuring process while retaining accuracy will cut down on production time significantly. Our design was founded on the idea of a small hole gage, we modified the gage to be set up as a probe and anchor onto the back side of the hole. The probe has been coined as a “split-ball” due to its inner shaft splitting the outer shaft that contains a ball type end effecter. Our prototype has been through many iterations utilizing the on campus Fab Lab to 3D print most of our parts. Our mechanical team has been in close work with our electrical team to ensure that the mechanics and electronics function together seamlessly.

The objective of our work is to design and build a depth gauge that efficiently and accurately measures the depth of a narrow hole, and give feedback via an electronic screen on the device. This design is being made for Lockheed and Martin and will allow their employees to measure a large amount of rivet holes both quicker and more accurately than their current solution. Speeding up the measuring process while retaining accuracy will cut down on production time significantly. Our design is small enough to be held in one hand and contains a wire probe that is plunged into the hole and latches onto the other side. The probe is “Tweezer-like” in design, with two wires that collapse and expand with the use of a button. Many parts of our design are made using a 3D printer for convenience and repeatability. Our design is able to communicate with electronics stored within the gauge that measures the depth and displays to an LCD screen.

Klein Tools is a major hand tools manufacturer in US focused on electrical and utility applications for professionals. One of Klein Tools products is called a fish rod that is used by professional electricians to pull wiring through walls, conduit, and plenums to route wire from one place to another. The current fish rod assembly process at Klein Tools involves manual dispensing of glue into the metal connectors before affixing them to fiberglass rods. The objective of this Klein Tools-sponsored project is to improve the throughput of assembly system and increase the accuracy and the consistency of the amount of glue dispensed to reduce product failures and adhesive waste.

The overall system in development consists of an automated metal connector orientation system, conveyor belt assembly, a glue dispensing system and a control system. Through the application of vibratory hopper feeders, pneumatic rotary tables and grippers, sensing cameras, break line sensors, and a conveyor belt, the system will orient the metal connectors glue side up, and present the connectors with adhesive to the operator for final assembly of the fish rods.

In this research project, the aim was to create a small, self-operated robot car to transport items. In addition, the robot-car can generate a distance when traveling through unknown places, and self-locate them in the next travels. The student authors hope that this robot car can be used to physically communicate and send medical supplies between severe patients and doctors in hospitals.

This study involved the examination of core samples from the Lower Cretaceous aged Kiamichi Formation of the East Texas Basin in order to interpret its organic and elemental geochemistry using various techniques. The Kiamichi Formation may have the potential to be a source rock for hydrocarbons, and may be a plausible target for oil and gas companies to produce using unconventional techniques. Since this formation has yet to be thoroughly analyzed, this project has lead to further understanding of its potential by using techniques such as handheld x-ray fluorescence tool to estimate for the abundance of rare earth elements and trace metals, as well as a CHNS analyzer to determine the amount of organic carbon of the formation. Upon completion of the sample analysis, this geochemical information about the Kiamichi Formation provides beneficial information for further research on the overall Kiamichi Seaway.

Influence of Isolation Stress on Aβ Production and Cognitive Function in 5xFAD mice Baroni, N. J.,1 Peterman, J. L.1, White, J. D.1, Eimerbrink, M. J.1, Paulhus, K. C.2, Thompson, M. A.2, Chumley, M. J.2 & Boehm G. W.1,
1Department of Psychology, Texas Christian University
2Department of Biology, Texas Christian University
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects nearly 44 million people worldwide, and is increasing exponentially in prevalence. Thus, research into its causes and prevention is crucial. Transgenic mouse models of Alzheimer's disease are often used to better study AD pathology. These mice have genetic mutations that result in heightened production of amyloid beta (Aβ), a pathological hallmark of AD. It has been well established that stress can influence AD pathology. This study investigates how isolation stress influences the production of amyloid beta in 5xFAD transgenic mice. In addition, we investigated whether isolation stress impacts cognition in the contextual fear conditioning (CFC) paradigm. The mice were group-housed or isolated for both 2 and 3 months, followed by cognitive testing and tissue collection. Specifically, we utilized histochemistry to examine Aβ plaque counts and an ELISA to examine soluble Aβ production. We found that isolated 5xFAD+ mice had significantly more amyloid beta plaques than group-housed animals. 5xFAD+ mice isolated for 3 months also displayed a cognitive deficit in contextual fear conditioning. All together, our results support the research that isolation stress influences Aβ production and cognitive function, and extends that to the 5xFAD transgenic mice.

Alzheimer’s Disease (AD) is a neurodegenerative disease currently affecting about 5.5 million Americans, and the number of people affected may rise as high as 16 million by 2050. Characteristic AD pathology of deteriorating cognitive function is correlated with neurofibrillary tangles of tau protein and Amyloid-beta (Aβ) plaques. Aβ is a peptide resulting from cleavage of the Amyloid Precursor Protein (APP) primarily present within neuronal cell membranes. The Aβ peptide can be cleaved at different lengths, but Aβ1-42 is the most neurotoxic. Aβ1-42 primarily aggregates in the hippocampus, where it further stimulates the release of cytokine proteins initiating an inflammatory response. Previous studies in our lab have shown that short-term inflammation induced by injection of lipopolysaccharide (LPS) leads to an inflammatory response that stimulates production of Aβ1-42 peptides. The goal of this project was to determine whether this effect could be exacerbated through a second injection series of LPS after a fourteen-day recovery interval, thus modeling multiple, independent, bacterial infections, like that seen in humans. The animals were given 7 days of 250 mg/kg LPS or saline injections, a two-week break, and another 7 days of LPS or saline. Contrary to what was predicted, Aβ levels were not potentiated. This effect was found to be related to decreased inflammatory response upon secondary administration of LPS, as IL-1β mRNA was significantly lower in the group that got two rounds of LPS. Current studies of our lab are evaluating whether these results are related to the presence of antibodies to LPS or a specific tolerance mechanism.

The challenge of taking care of aged patients who lost control of their bladders and bowel movements is to respond to the patients’ needs in a timely manner, which often requires a caretaker (e.g. a family member or a hired assistant) to stay on watch 24/7. In light of advance in cloud computing, we present a real-time low-cost monitoring and notification system that can continuously monitor the patients bedding condition, detect the conditions that help is needed and notify the care-takers. The system consists of TI SensorTags, Raspberry Pis, and IBM Bluemix. The TI SensorTag is a sensing device, while Raspberry Pi acts as a messenger receiving data collected by TI SensorTags via Bluetooth technology and transmitting the data to Bluemix, a cloud-based platform developed by IBM, via WiFi.

The system frequently senses bedding conditions of patients. Data is uploaded to a server residing on IBM Cloud, which processes data and sends appropriate notifications. The availability of cloud technology and small signal processing units, as well as advance in sensor technologies, allow us to build a low-cost system that can help caregivers address the patients’ needs effectively. As a result, the quality of care for patients is improved.

Personality psychologists often apply clustering techniques on questionnaire data to model personality structure. Inspired by this work, we apply techniques from topological data analysis (TDA) to understand the structure of this data. The data comes from Cattell’s Sixteen Personality Factor Questionnaire (collected by Bell, Rose, & Damon in 1972). Subjects were 969 adult male volunteers divided into three age groups: 25 to 34, 35 to 54, and 55 to 82. We use persistent homology (a TDA tool) to cluster the data and identify that personality structure is slightly different between the age groups. It is also curious to note that data from the youngest age group appears to have a topological “hole”, which raises questions of the psychological significance. This work suggests that additional research, including applying TDA tools to other questionnaire data sets can provide insights to the study of personality.