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.
Globally, there is demand for increased meat production. Texas, a leader in cattle production in the United States, has met this demand utilizing confined animal feeding operations (CAFOs) containing hundreds to thousands of cattle. To increase production efficiency, cattle receive growth-promoting hormone treatments to enhance growth and increase cattle mass. These hormonally-active compounds (HACs) have been found in cattle waste, feedlot runoff, and surface waters. The ultimate goal of this project was to identify watershed characteristics that promote the transport of cattle-associated HACs to surface waters. Therefore, the objectives of this pilot study were to: 1) identify and define a study area for evaluating HACs in Texas watersheds and 2) begin preliminary assessments of HAC activity in watersheds downstream of cattle feedlots. A suitable study site was identified using satellite imagery, elevation data and the ArcGIS hydrology tool pack. Sample sites were selected within this area based on geographical features and position to CAFOs. Caged fish studies, followed by analysis of estrogen-responsive gene expression, were utilized to assess the presence and activity of HACs. Though no statistically significant alterations in estrogen-responsive gene expression metrics were observed, females from three of the four sites downstream of CAFOs experienced 2.9 to 3.7-fold and 1.9 to 5.3-fold decreases in the expression of estrogen receptor alpha and vitellogenin, respectively. This could have larger implications as previous research by Miller et al. 2007 forecasted that a 50% reduction in vitellogenin plasma concentration could result in a 41.8% decrease in average population size after one year.
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.
(Presentation is private)
The combination of inorganic porous silicon (pSi) and flexible biocompatible polymers has been shown to yield more beneficial hybrid scaffolds for tissue engineering (i.e. use of synthetic materials to facilitate healing). PSi has a variety of tunable properties, including pore size, pore volume and non-toxic degradation; the addition of a flexible polymer component provides the benefit that such a construct can easily conform to any shape of the actual site of an injury/disease, suggesting that pSi/polymer composites can be suitable candidates for localized drug delivery.
In this work, composite materials consisting of oxidized porous silicon (ox-pSi) with particle size of ~ 30 μm and pore size of 40-100 nm and thin polycaprolactone (PCL) films. PCL solid films were fabricated from an initial fibrous structure that was exposed to a temperature of 65-80 oC causing fusion of these fibers into a solid film. Ox-pSi particles were then physically embedded into PCL films, resulting in ~30-40% loading of ox-pSi (ox-pSi/PCL film). Ox-pSi particles of the composite were loaded with a model cytotoxic (anticancer) drug-camptothecin (CPT). Drug release from the ox-pSi particles alone and ox-pSi/PCL film composites was monitored fluorometrically, showing distinct release profiles for each material.
Ox-pSi/PCL film composites release a CPT payload in accordance with the Higuchi release model and showed a significant decrease in burst effect compared to ox-pSi particles only. In addition, composite evolution after 5 weeks in a given solution was examined by determining weight loss and surface morphology/composition (FESEM). Overall weight loss of the composites was less then 10% mainly attributed to pSi particles detachment and dissolution.
Iron plays a pivotal role in metabolism and transport processes in nature but can also be used to accomplish important chemical transformations on the bench top; recently, iron(II) salts have been shown to catalyze direct Suzuki – Miyaura coupling of N-heterocyclic compounds and arylboronic acid derivatives in the presence of oxygen. Presented herein are three tetra-aza macrocyclic iron(III) complexes [L1Fe(III)(Cl)2]+ (L1Fe), [L2Fe(III)(Cl)2]+ (L2Fe), and [L3Fe(III)(Cl)2]+ (L3Fe) [L1 (Pyclen)=1,4,7,10-tetra-aza-2,6-pyridinophane; L2 =3,6,9,15-tetraazabicyclo[9.3.1]penta-deca-1(15),11,13-trien-13-ol; L3 =3,6,9,15-tetra-azabicyclo[9.3.1]penta-deca-1(15),11,13-trien-12-ol] that catalyze the coupling of pyrrole and phenylboronic acid. Following the synthesis and reactivity studies, investigation into the oxidation state of the iron center throughout the catalytic cycle was explored. The results of this work to date will be presented and will facilitate the understanding of challenging chemical reactions catalyzed using inexpensive earth abundant metals such as iron.
Nanomaterials based on cerium (IV) oxide, CeO2, have been extensively investigated due to interesting chemistry from a readily available transition between Ce3+ and Ce4+. Oxygen vacancies present in the oxide lattice combined with the available redox transition gives CeO2 materials antioxidant and enzyme mimetic behavior. The addition of tri-valent, fluorescent ions such as Eu3+ further increase the oxygen vacancy concentration, may allow control over the Ce3+/Ce4+ ratio, and may add fluorescence to the doped material. These properties give europium doped cerium oxide (EuCeO¬2) potential applications within biological systems.
Eumelanin is a complex dark brown pigment originating from the oxidation and oligomerization of tyrosine. The pigment can also be synthesized through the auto-oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA). While its structure has not been fully determined, eumelanin has shown antioxidant and free-radical scavenging behavior, strong UV-VIS absorption, and conductive properties. The pigment has been researched for its radiation damage protection, and for activity against amyloids associated with Parkinson’s and Alzheimer’s disease.
Our research thus far has focused on the controlled synthesis of various EuCeO2 nanomaterials, and their interaction with the auto-oxidation of L-DOPA to eumelanin as measured through the observation of eumelanin fluorescence at 471 nm. Nanorods, nanowires, and nanocubes of EuCeO2 were each synthesized with a range of dimensions and europium content. EuCeO2 nanorods and nanocubes were synthesized through precipitation of EuCe(OH)3 and a subsequent hydrothermal reaction between 100°C and 180°C. Nanowires were synthesized using electrospinning and annealing techniques. All materials were analyzed using transmission electron microscopy (TEM), energy dispersive x-ray analysis (EDX), and powder x-ray diffraction (XRD).
The presence of CeO2 or EuCeO2 materials in L-DOPA containing solutions consistently suppressed the eumelanin-associated fluorescence intensity. Various parameters, including temperature, pH, nanomaterial concentration and morphology, and europium doping concentration have been evaluated for their potential impact on the evolution of eumelanin from L-DOPA in the presence of these EuCeO2 nanomaterials.
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.
Author(s): Jhansi Kalluri Chemistry & Biochemistry Giridhar Akkaraju Biology Jeffery Coffer Chemistry & Biochemistry Julianna West Biology
Advisor(s): Jeffery Coffer Chemistry & Biochemistry
Plant based nanotechnology for drug delivery and anti-inflammatory therapy
Jhansi Kalluri, Julianna West, Giridhar Akkaraju, Leigh Canhm and Jeffery L. Coffer*
Chronic inflammation is one of the characteristics of Alzheimer’s, cancer, and selected auto inflammatory diseases. Medicinal plant extracts rich in polyphenols have shown the ability to aid in the prevention of degenerative diseases such as Alzheimer’s due to their anti-inflammatory and anti-oxidant properties. One of the problems of using polyphenols to treat these diseases is their potentially low bioavailability and short half-life in vivo. An alternative to using free compound is to use plant polyphenol-loaded nano/micro particles to increase their bioavailability and half-life.
Equisetum arvense is a silicon accumulator plant serving as a source for a viable eco-friendly route for fabricating nanostructured porous silicon (pSi) drug delivery carriers; at the same time, if selected plant components contain medicinally-active species as well, then the single substance can provide not only the nanoscale high surface area drug delivery carrier (pSi), but the drug itself. With this idea in mind, porous silicon was fabricated from stems/fronds of the silicon accumulator plant Equisetum arvense and the anti-inflammatory activity of the leaf components (aqueous ethanol extract) of Equisetum arvense was tested using a luciferase assay. We evaluated the dose dependent activity of the extract to inhibit TNF-induced NF- kB activation. Our long-term goal is to measure the anti-inflammatory activity of extract-loaded porous silicon particles in a sustained manner.
Semiconducting silicon (Si) is a promising element that has been extensively studied in various fields ranging from microelectronics to bio-relevant applications.1 In fact, nanostructured porous silicon has received widespread attention due to its unique chemical and physical characteristics.1 Another relatively more well-defined example of nanostructured silicon is Si nanotubes (SiNTs) with well-characterized sidewalls, inner void space and lengths, allowing opportunities to study its potential properties in diverse fields, such as Li ion batteries, solar cells.2,3 In particular, SiNTs are potential vectors in drug delivery systems. The available interior free space of the NTs offer the material the ability of confining a desired amount of payload of therapeutic agents. Moreover, the available silanol groups on the surface of the NTs also enable attachment to a linker, whose other end is subsequently attached to a drug molecule of interests. Within a biological environment, therapeutic molecules of interest can be released in a sustained manner into targeted sites through either dissolution of the SiNT carriers or their detachment from the linkers.
In terms of therapeutic candidates, cisplatin has been renowned for its ability to treat a variety of cancers including lymphomas, carcinomas, etc. Due to low chloride ions concentrations (4-12mM) in the intracellular environment of cancer cells, chloride ligands on cisplatin are readily displaced by water, producing either cis-[PtCl(NH3)2(H2O)]+ or cis-[Pt(NH3)2(H2O)2]2+ aquo complexes, which actively target DNA and trigger apoptosis.4 However, since drug resistance is developed in cancer cells and undesirable interactions between cisplatin and other biological molecules occur, the therapeutic effects become diminished and negative side effects are also observed.5,6 In order to enhance the therapeutic efficiency of cisplatin, in this project, SiNTs are employed as carriers that can be loaded with cisplatin and potentially deliver the drugs to the desired sites. For the purpose of controlling the release of cisplatin from SiNTs, 3-aminopropyltriethoxysilane (APTES) is employed as the linker, which can covalently bind to the nanotubes through the available silanol groups on the surface, and the amino group on the other end of APTES can subsequently coordinate cisplatin.
In this study, SiNTs with lengths less than 1 µm are used (for optimal cellular uptake), and a sidewall thickness ~ 10 nm for desirable dissolution within a biological environment. Moreover, the distinct porous morphology of the nanotubes permits infiltration of the molecules of interest. By varying solvents (acetone and toluene) of APTES solution and functionalization time, the amount of cisplatin loaded into SiNTs can be modulated ranging from 20-40 weight %, thereby suggesting the ability of SiNTs to carry therapeutic agents.
1. Canham, L.T. Hanbook of Porous Silicon. Switzerland: Springer International Publishing AG, 2014.
2. Tesfaye A, Gonzalez R., Coffer J., Djenizian T. Porous Silicon Nanotube Arrays as Anode Material for Li-Ion Batteries, ACS Appl Mater. Inter. 2015, 7, 20495−20498.
3. Gonzalez-Rodriguez R., Arad-Vosk N., Rozenfeld N, Sa’ar A, Coffer JL (2016) Control of CH3NH3 PbI3 Perovskite Nanostructure Formation through the Use of Silicon Nanotube Templates, Small 2016, 12, 4477–4480.
4. Ma P., Xiao H., Li C., Dai Y., Cheng Z., Hou Z., Lin J. Inorganic nanocarriers for platinum drug delivery, Materials Today 2015, 18(10), 554-564.
5. Martin L.P., Hamilton T.C., Schilder R.J. Platinum Resistance: The Role of DNA Repair Pathways, Clin Cancer Res. 2008, 14(5):1291-1295.
6. Xue X., You S., Zhang Q., Wu Y., Zou G., Wang P. C., Zhao Y., Xu Y., Jia L., Zhang X., Liang X. Mitaplatin Increases Sensitivity of Tumor Cells to Cisplatin by Inducing Mitochondrial Dysfunction, Mol. Pharmaceutics, 2012, 9 (3), 634–644.
Various total syntheses of the Lycorine-type pharmacologically active alkaloids hippadine and pratosine have been developed. However, most of these synthetic routes require prohibitively expensive materials and/or achieve yields that are subpar, making these schemes unlikely to be used in an industrial setting. Current research involves developing better synthetic methods for these two alkaloids starting with a 6,7-disubstituted isoquinoline. These syntheses are appealing since they utilize readily available starting materials and avoid expensive catalysts. The key step in the synthetic scheme centers around an intramolecular de Mayo photocyclization which involves a reaction between an alkene moiety in the isocarbostyril system and a 1,3-diketone (a functionalized tether on nitrogen), which forms a third ring in the structure of the molecule. Research on a model system (an isocarbostyril without the substituents at positions 6 and 7) for these natural products has been done in order to elucidate the optimal conditions for each step on the synthetic strategy. Initial attempts were made in order to synthesize the 6,7-disubstituted isocarbostyril with the 1,3-diketone tether so that the deMayo photocyclization could be performed. However, the established synthetic strategy led to compounds along the synthetic route that had very undesirable solubility properties. To resolve this issue, the substituents were replaced with bulkier, more non-polar moieties in order to increase the solubility of the compound in ethyl ether.
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.