2008 Research Symposium

Completed and Proposed Research Projects Presented at the 6th Annual Celebration of Scholarship Symposium, May 6-8, 2008

The Energy of Sound, Bishop, Chad
Professor: Dr. Betty Thompson and Dr. James Claycomb

There are sound waves being emitted from machines and nature every day. Yet, the energy from sound waves is ignored and allowed to dissipate into the surrounding environment.    This study is the first step towards using sound waves as an alternate form of energy. The experiment is designed to prove that a measurable amount of electricity is generated as sound waves pass through the diaphragm of a microphone. During the experiments it became clear that one could generate high voltage alternating current (about 2 volts), but low amounts of current from a single microphone receiving sound waves. When microphones were run in series and parallel the subsequent voltages and amperes readings grew in a somewhat linear fashion. Thus, the data supports the theory of a sound cell for electrical output. The practical applications for such a cell would be to capture motor noise from vehicles and appliances, and reintroduce the energy to the motor in such a way as to lower the external energy input. Another application could be to collect highway noise to defray the cost to run street and stop lights. This step was a positive one, but more research is needed before a final device can be constructed. 

RNAi: A Tool for Silencing the Troublemaker, Bishop, Chad
Professor: Dr. Rachel Hopp

Alzheimer’s disease (AD), the most common form of dementia in the United States, affects over 4.5 million and will continue to effect more as the population grows older. Promising new research using small interfering RNA (siRNA) has the potential of becoming a promising form of clinical therapy for patients. The premise is that RNAi can selectively alter gene expression of mutant alleles and thereby potentially allow clinicians to manipulate the creation of proteins that contribute to the neurodegenerative disease.   However, due to the use of T7 polymerase for in vitro synthesis of small interfering RNA (siRNA), it is difficult to make plasmids that are highly selective. Yet, new research seems to have found a method to circumvent the T7 polymerase restrictions. Such research proves only to be a building block to the future, but such building blocks are necessary to build a stairway to a cure. This review examines the methodology and conclusions of this promising research. There by lending weight to its conclusions and promise. 
Conservation of fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding protein within different bacterial organisms, Chandra, Aanchal
Professor: Dr. Brenda Whaley

There are several strains of Escherichia Coli. Most strains of the bacterium are harmless, although there are some strains that cause food poisoning in humans. The harmless strains of Escherichia Coli known to the human body can be very helpful. These strains can be found in the lower intestine of warm blooded animals, and in the normal flora of the gut. Harmless strains of Escherichia Coli can be particularly helpful to the body by occupying space within the intestine, and thereby preventing pathogenic bacteria from residing in the area. They also produce vitamin K for the body. The particular strain of bacteria responsible for producing fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding protein is named Escherichia Coli K-12, MG1655.
This particular protein is produced by three other bacterial organisms called Vibrio fischeri ES114, Escherichia coli strain K12 substrain W3110, Escherichia coli DH10B. The function of the protein is highly conserved within all of the organisms. Fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding protein consists of 406 amino acids. The gene coding for this protein is located between 3810754 and 3811974 nucleotides of the bacterial genome.
Fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding protein is involved in the catalysis of two steps in the biosynthesis pathway of coenzyme A. The first step involves the conjugation of cysteine to 4'-phosphopantothenate in order to synthesize 4-phosphopantothenoylcysteine. In the second step 4-phosphopantothenoylcysteine is decarboxylated, thereby forming 4'-phosphopantotheine. The NCBI accession number for this protein is NP_418096. This accession number can be found on www.ncbi.nih.gov. Blast is an excellent tool that allows the accession of proteins and genes found on various organisms. This tool allows the search of nucleic acid and protein sequences as the query. Once the nucleotide sequence or the protein sequence has been obtained through FASTA, blast can be used to obtain the different organisms that contain similar sequences. 
A Review of Quinolinate Synthase, L-aspartate Oxidase (B protein) Subunit Using Bioinformatic Programs, Copeland, Dillon
Professor: Dr. Brenda Whaley
The use of innovative bioinformatic programs such as Swiss-prot and GenBank facilitates an encompassing review of the protein known as quinolinate synthase, L-aspartate oxidase (B protein) subunit which is found in Escherichia coli strain K-12 substrate MG1655. The use of bioinformatics allows researchers to collaborate and catalog information relevant to the field of molecular biology. These programs allow researchers to construct a valuable and continually expanding database that is able to tolerate the incredible amount of information needed to study biology in the current age. In reference to quinolinate synthase, L-aspartate oxidase (B protein) subunit, the protein can be quickly accessed by using its unique accession number, NP_417069.1. Through this accession number it is further possible to investigate information pertaining to the protein such as pathways the enzyme is involved in, the gene that codes for it, and the ability to use a program called BLAST to find similar proteins in other organisms. This protein is involved in the synthesis of quinolinic acid from aspartate and dihydroxyacetone phosphate. The protein is 540 amino acids long and has a molecular weight of 60337 Da. The gene that codes for the protein is named nadB, it is 1,623 base pairs long and has its own unique number, 947049. 

Bioassay and Chemical Assay: Using Daphnia To Detect Toxic Water, Green, Fannie
Professor: Dr. Betty Thompson and Dr. Brenda Whaley

An experiment designed to test water quality by using Daphnia pollex and Daphnia magnum. This small group of crustaceans is very sensitive to toxin in the water. This group of experiments were started during the fall quarter of 2007 and concluded during the spring quarter 2008. The experiments proved that measurable amounts of copper toxicity existed in the HBU Retention Pond. The level of copper in this water varied from 1.5 parts per million (ppm) to 5 parts per million (ppm). This project proven that Houston’s tap water supported Daphnia growth and is safe for human consumption. The control water showed an explosion of daphnia growth, which can be explained by reproduction rates in the daphnia. The spring of 2008 experiment was conducted using dilute amounts of copper sulfate (20; 10; and 5 ppm). Each of the samples was done in triplicate and included 6 to 7 D. magnum. After 24 hours (day 1) the sample that included 20 ppm CuSO4 had a and a 100% death rate of the daphnia. Day 2, the D. magnum grown in10 ppm and the 5 ppm CuSO4 had a death rate of 100 %. By day three all copper sulfate water samples had a 100 % death rate. None of the three control waters included copper sulfate. The results proved that copper is toxic to the Daphnia. This study suggests that copper is toxic to small organism or life forms that protect our environment and cleanse our water from bacteria and disease. D. magnum should be made available for other students who may want to continue this project to determine if there is some specific factors that face our environment such as air and water pollution. Use of Daphnia in both chemical and bioassay could be used to find water pollution as described by the clean water act. 

Dihydrofolate synthase, Nematzadeh, Negarin
Professor: Dr. Brenda Whaley

Escherichia coli have been the bacteria of focus in many different research studies in the scientific field. The specific strand E. coli strand K-23 MG1655 has been extensively studied, particularly in the field of molecular biology and bioinformatics. The genetic research aims at sequencing the entire genome of the organism and thus obtaining a better understanding of gene translation, expressions, and relations. The goal basically is to identify the protein in both molecular and genetic levels in order to identify specific amino acids or nucleotides motifs and relate the protein functions. The similarity of the protein is also discussed to grasp an evolutionary perspective of the prokaryotic kingdom. The protein in this study, dihydrofolate synthase, is an enzyme which acts like a kinase, but is actually a ligase. The enzyme ATP reacts with 7,8-dihydropteroate and with the amino acid L-glutamate. The enzyme is 422 amino acids long and as the name implies, the enzyme catalyzes a step in the formation of folate. Folate is a vital molecule in the bacteria metabolism, for it aids in energy formation by interacting with biotin. This research in bioinformatics aims at identifying the protein occurrence in other bacteria, since it seems to be overtly vital for life. 

Phototropic Effect of Different Color Light on Plant Growth, Penrice, Christina
Professor: Dr. Betty Thompson

In this experiment mung bean plants were germinated and grown under different light conditions. Plants grow taller in green light than red and blue light. The mass of the shoot system was greater for red and blue light than green. Plants with insufficient light for photosynthesis will grow taller to compensate for the lack of light. Therefore the plants that were grown by green light were observed as being taller and efficient but they were not because the calculated mass for the plants grown in green light was less than the others. This was proven by measuring the mass and the height of the shoot system. Plants grown in yellow light were shorter but more massive. This experiment used an energy efficient white light (CFC) as a control. The height of the control plant was 12 centimeters and the mass was .250 grams. The plants grown in green light weighed .250 grams. The height was 17.5 centimeters. The plants grown in yellow light weighed .325 grams yet the height, 13 centimeters, was much shorter than plants grown in green light. The plants grown in red light grew to be 16.5 centimeters tall yet it weighed .300 grams. And plants grown in blue light was taller (19.5) than plants that were grown in green light and still had a higher mass of .310 grams. So a conclusion is drawn that plants do not grow efficiently in green light. The height of plants does not primarily indicate better growth. Plants that have insufficient light activate their shade avoidance mechanisms and grow taller without an increase in mass. My data supports this. Green light plants were 16.5 centimeter but only .250 g where as red and blue light plants had an average height of 18.0 cm and a mass of .310 g. Plants grew better in red and blue light. 

The Anti-bacterial Properties of Silver on E. coli and S. aureus, Philip, Karen
Professor: Dr. Jacqueline Horn

Silver has been used since ancient times in Egypt to slow the process of food spoilage. In modern technology, it is re emerging in importance. New technologies are taking advantage of silver nano-particles in everything from socks to Tupperware that advertise the antibacterial properties attributed to their products by the silver. The implication of this new technology is that the process of food spoilage can be slowed by inhibiting the growth of bacteria on food. In order to investigate the antibacterial properties of silver, we plated fine silver particles on nutrient agar which was then inoculated with E. coli and S. aureus. We then observed the bacterial growth on each plate at intervals of twenty-four and forty-eight hours. Our results indicate that silver does indeed inhibit bacterial growth for both bacterial species. In addition, the experiment suggests that the antibacterial effect was different for gram positive and gram negative bacteria. 

Detection of Casimir Force between Planar and Spherical Plates using Quartz Crystal Microbalance (QCM) Sensor, Tagore, Amitpal
Professor: Dr. Robert Towery

The Casimir force that emerges between two plates positioned in very close proximity to each other and with a great degree of parallelism. The nature of the force is quantum electromagnetic and emerges from the zero-point energy of a vacuum space. The total virtual electromagnetic fluctuations between the plates are limited by the fact that the wavefunctions of the photons must vanish at the plates, and thus, the Casimir force takes effect. Here, the force exerted between a flat plate and a spherical plate is determined using a Quartz Crystal Microbalance (QCM) sensor. The flat plate consists of the gold coating on the QCM crystal itself, and the spherical plate consists of a steel ball of radius 6 mm. The frequency of the piezoelectric crystal was measured from the point of closest separation and compared to the frequency at points of increasing separation. From a calibration curve previously established, the force exerted by the plates due to the Casimir effect is to be determined. No difference in frequency was observed. However, modifications to increase sensitivity are underway.

RQCM Determination of Polynucleotide Interaction with Diruthenium Complexes, Tat, Sara
Professor: Dr. Robert Towery

Nine MHz, AT-cut quartz crystals were used to examine the effects of diruthenium complexes on polynucleotide hybridization using a research quartz crystal microbalance (RQCM). When an electric field is applied to quartz, the resulting stress causes the crystal to resonate at a characteristic frequency, ultimately allowing detection of mass changes on the surface of the crystal. This is known as the converse piezoelectric effect.  In this project, polyethylene co-acrylic acid (PEAA) polymer was attached to the crystal surface to which a nucleic acid probe, polyadenylic acid (Poly A) was covalently bound. Hybridization through complementary binding between immobilized probe and a target, polyuridylic acid (Poly U), was performed in a water-saturated, temperature controlled reaction chamber. Successful hybridization of Poly A with Poly U was detected by significant decreases in crystal resonance frequency. Previous research with TMpyP porphyrin binding to polynucleotides has identified porphyrin’s ability to cleave nucleic acids. In fact, porphyrins are the basis of photodynamic therapy and other cancer drug strategies. Implementation of diruthenium complexes in this present investigation was executed in a similar manner to past porphyrin studies. Results indicate limited interaction between immobilized polynucleotides and diruthenium, possibly due to the absence of an electrostatic attraction.

Detection of Lead in Toys and Household Products, Todai, Veena; Tat, Sara; Garcia, Sam; Adeyekun, Moyosore; Cao, Christopher;
Professor: Dr. John Ledford

Due to the increasing discoveries of lead in numerous domestic products, anxiety has spiked in the general population. Lead, Pb+2, may be found in paint and some things you may least expect, including children’s toys. Recently, several Hannah Montana products were discovered to contain lead, including dolls and backpacks. The effects of lead are detrimental if ingestion occurs; lead poisoning results in health disorders that may end in fatality. There are numerous ways of detecting lead, one of which is qualitative analysis performed after the removal of organic substances through combustion. In this experiment, samples from three brands of garbage bags (Ruffies Pro, Glad, and Red Max) were incinerated in crucibles using a Bunsen burner to eliminate all the organic particles. The residual inorganic substances in each sample were then tested for lead by following the procedures in the Silver Group section in the Introduction to Semimicro Qualitative Analysis lab manual. Results were negative for the metal in all samples. According to solubility rules, the chlorides of Lead (Pb+2), silver (Ag+1), and mercury (II) (Hg+2) are insoluble in 6M HCl, while the chlorides of all other metals are soluble. Furthermore, since lead (II) chloride dissolves in hot water while silver chloride and mercury (II) chloride do not, this served as the basis of the separation of lead from the silver and mercury ions.

Genomes to Genomes vs. functional consistency of glutamate--cysteine ligase enzyme, Villarreal, Ruben
Dr. Brenda Whaley

Research will be conducted on the enzyme glutamate--cysteine ligase found in Escherichia coli. This enzyme will be compared between different genomes at a sequence to sequence resolution. It is the goal of this research to find the similarities in the protein sequence that can be found among variations of this enzyme in multiple organisms. Escherichia coli’s glutamate—cysteine ligase will be used as the reference sequence to which all other organisms will be compared to. Escherichia coli is an important gram-negative prokaryotic bacterium that is commonly found in the intestines of most animals. This facultative anaerobe has the ability to transfer DNA to its neighboring growth through conjugation and transformation. This usually non-pathogenic bacteria, can serve several purposes in the gut but certain strains can be infectious in the gut. Among its better uses is the production of Vitamin K, which helps in blood coagulation. The enzyme of interest, glutamate—cysteine ligase (Protein Accession = YP_001464000), catalyses the formation of gamma-L-glutamyl-L-cysteine in coupling with dephosphorylation of ATP into ADP. This protein in Escherichia coli contains 518 amino acids and is encoded by 1557 base pairs within the genome (Gene Accession = NC_009801.1). E. coli’s genome spans a length of 4979619 bps (Genome Accession = NC_009801) and glutamate—cysteine ligase is found at the position between 2977068..2975512 bps. The BLAST program will be used to perform statistical and comparitive analysis of protein and nucleotide sequences. BLAST can be found in the following at http://www.ncbi.nlm.nih.gov/blast/Blast.cgi . Many search filters can be applied while using BLAST such as a protein query, which compares your amino acid sequence with those of publicly available entries, or nucleotide Blast, which is a similar base pair comparison. The technology encompasses many public databases and brings a powerful tool to independent researchers looking for patterns that link gene to function. 

Semiclassical Carnot Cycle, Zachary, Christopher
Professor: Dr. Gardo Blado

The classical Carnot cycle is a theoretical process through which the optimum efficiency of heat engines may be obtained. The process involves isothermal and adiabatic processes using high temperature and low temperature heat baths as its energy source. Using classical thermodynamics, the Carnot cycle gives a simply quantifiable result of the optimum efficiency. The following work applies the quantum mechanics of high temperature systems to the cycle in order to generate a high temperature semi-classical Carnot cycle. This is done by treating the system as a three dimensional particle in a box. A major result of the analysis is that contrary to classical thermodynamics, the internal energy of a system does not only depend on the temperature but also on the volume of the chamber. Similar works have been done in which the Carnot cycle is analyzed using quantum mechanics but these works use isoenergetic reactions instead of isothermal processes. Further investigations on the efficiency of Carnot engine is in progress. 

8-amino-7-oxononanoate synthase, Abubakar, Natasha
Professor: Dr. Brenda Whaley

In recent years biological studies and technology have been greatly advanced by genetics research. Our understanding of human genetics has benefited from studies of bacterial genetics. Most bacteria have a quick generation life and changes to their genome are rapidly induced. These factors allow for observations in genes and their functions. Escherichia coli, commonly known as E. coli, has numerous proteins which allow it to perform metabolic functions. The 8-amino-7-oxononanoate synthase enzyme is important in producing energy through glycolysis and aerobic respiration. This enzyme actually produces CoA (coenzyme A) as a byproduct when reacting 6-carboxyhexanoyl-CoA with the amino acid L-alanine. The protein is 384 amino acids (accession number NP_415297) and the gene for this protein is 1154 bp long. It is found on the positive strand of the 4,639,675 bp genome of E. coli strain K-12 substrate MG1655 at positions 809604 - 810758. My study will use bioinformatics to better understand the relationship of this E. coli protein with similar enzymes in other prokaryotic organisms. 
BLAST is a software tool that can be used to search sequence databases such as GenBank accessed online at www.ncbi.nih.gov. My research uses BLAST to identify other prokaryotes that produce 8-amino-7-oxononanoate synthase and compare the sequence to that of E. coli. Conserved regions will be identified.

Isoleucyl-tRNA synthetase in E. coli, Aggarwal, Charu
Professor: Dr. Brenda Whaley

Escherichia coli E24377A is an enterotoxigenic E. coli (ETEC) isolate. ETEC is responsible for traveler’s diarrhea, which characterizes a large volume of watery diarrhea. Isoleucyl-tRNA synthetase can catalyze the synthesis of Ile-tRNA. This enzyme (accession number YP_001461194) has been isolated as a protein product of E. coli E24377A. Isoleucyl-tRNA synthetase is 938 amino acids long. The size of the gene is 2816 base pairs and is located from 25606 – 28422 base pairs within the E. coli genome which is 4979619 bp in length. The gene id number is 5587280 and the accession number of the genome is NC_009801.
The research used Basic Local Alignment Search Tool, called BLAST which can be accessed via National Center for Biotechnology Information (NCBI) database. This search program compares predicted query protein sequences with the sequence of known bacterial proteins contained in the GenBank sequence database accessible on-line at www.ncbi.nlm.nih.gov. BLAST will be used to identify isoleucyl-tRNA synthetase – in other prokaryotes and produce sequence alignments for the proteins, allowing comparison of conserved regions.

Gamma-Glu-putrescine synthase, Amaechi, Chinyere
Professor: Dr. Brenda Whaley

Escherichia coli (E. coli) is one of the main organisms used to study bacterial genetics and physiology. E. coli is mainly found in the human lower intestine and it can cause disease in the host organism especially when they acquire virulence traits. E. coli is widely used in the laboratory today because it is cost effective, well-researched, and it is very easy to use and manage. The non-pathogenic strain MG1655 is the wild-type E. coli that has been maintained with very little genetic manipulation. Gamma-Glu-putrescine synthase is an enzyme that is produced by Escherichia coli Strain K-12 Substrain MG1655. The accession number of the protein is NP_415813.4 and it is comprised of 472 amino acids. The name of the gene is puuA and it has a gene ID of 946202 with a molecular weight of 53177.16. The size of the gene is 1419 base pair and the gene is located between positions 1357514…1358932 in the genome. Accession number of the genome is NC_000913.2. The function of this enzyme is to breakdown putrescine using the biosynthesis of gamma-L-glutamylputrescine. The reaction catalyzed by this enzyme involves: ATP + L-glutamate + Putrescine = ADP + Phosphate + Gamma-L-glutamylputrescine. The enzyme’s pathway consists of polyamine metabolism, putrescine degradation, from putrescine and L-glutamate to gamma-glutamylputrescine. This enzyme belongs to the gluatamine synthase family.
BLAST is an acronym for Basic Local Alignment Search Tool. It is available on the National Center for Biotechnology Information (NCBI) homepage. The types of data derived with the use of BLAST are a protein data and a DNA data. BLAST compares the sequence of a protein with a protein database and will be used to find the evolutionary and functional relationships between E. coli puuA and its gene products with those of other prokaryotic organisms.

Glutamine Synthetase, Chaudhuri, Parul
Professor: Dr. Brenda Whaley

Escherichia coli can be found in human body and most warm blooded animals. In most animals, it is found in the lower intestine. Some strains of E. Coli can be harmful and cause certain diseases, but most are harmless. It is a gram-negative straight rod, it uses flagella to move, or it is non-motile. My protein is glutamate synthetase or Escherichia coli strain K-12 substrain MG1655 (found through NCBI accession number NP_418306). This protein is 469 amino acids long. The enzyme activity of glutamate sythetase is controlled by abundant glutamine through adenylation. The gene name for this protein is glnA. The location of the gene is between 4054648 and 4056057 in the genome. The gene is 1410 bp within a genome that is 4639675 bp nucleotides long. I have been able to obtain all this information through the GenBank sequence database available on-line at www.ncbi.nlm.nih.gov/. Blast is a software search engine that can also be accessed through National Center for Biotchnology Information (NCBI) database.
Basic Local Alignment Search Tool (Blast) is a search program that one can use to compare the predicted protein sequences with known bacterial proteins. I will use BLAST to find other prokaryotes that produce glutamate synthetase and compare the sequences of these proteins to determine conserved regions. 

Colorectal Cancer & RNAi, Le, Theresa
Professor: Dr. Rachel Hopp

Colorectal cancer is ranked as one of the most prevalent kinds of cancer in the world, second in cancer deaths behind lung cancer in the United States (Kleinsmith, 2006). RNA interference (RNAi) is a mechanism that silences the expression of genes in a sequence-specific manner at the post-transcriptional level. In recent research studies regarding viruses and cancer, RNAi has been utilized to prevent virus replication and the production of tumors, including those associated with colorectal cancer (Wei et al., 2006). Two of the many genes that have been the focus of colorectal cancer research are p53 and Bcl-2. P53 is a tumor suppressor gene with pro-apoptotic functions. Mutations within the gene render it to become inactivated and lose its ability to stimulate cell death. On the other hand, Bcl-2 is an oncogene that inhibits apoptosis. Watson and colleagues observed and evaluated the expression of p53 and Bcl-2 independently of each other in colorectal tumors. Resulting data suggested that p53 negative coupled with Bcl-2 positive phenotype was an indicator of good prognosis for colorectal cancer (Watson et al., 2005). In a different research, Jiang and Milner examined the relationship between p53 and Bcl-2 and discovered that Bcl-2 suppresses the pro-apoptotic activity of p53 (Jiang and Milner, 2007). RNAi was utilized to silence Bcl-2, which resulted in significant induction of p53-dependent apoptosis (Jiang and Milner, 2007). Although the use of RNAi in colorectal cancer treatment and prevention is still under study, it has been noted for its efficiency and accurate specificity (Wei et al., 2006). Because of this accuracy, RNAi can be utilized to target mutant genes involved in the apoptotic pathway in cancer cells. Thus, continuing research by using RNAi to target specific genes can help determine the exact genes responsible for colorectal cancer and their roles in inhibiting or stimulating the apoptosis of cancer cells. 

The Influence and Effects of Dietary Vitamins vital for Humans towards the bacterium Escherichia coli, Nguyen, Diem
Professor: Dr. Jackie Horn

The relationship between E. coli and Human beings is both positive and negative. On the positive side, it is a necessity that humans have the harmless strains of the E. coli as part of the normal flora of the gut. However, strains of E. coli can cause gastroenteritis, urinary tract infections, and neonatal meningitis. Dietary vitamins such as C, B12, and E are known to benefit mammals by assisting in regular metabolism. Vitamin C is an essential nutrient for humans. Abscorbate is an antioxidant, which will protect against the oxidative stress of free radicals in the body. Vitamin E is also known as an antioxidant and has been shown to modulate immune system functions in various species. In a case study of vitamin E and the phagocytic functions of macrophages in chickens, it was concluded that supplemental vitamin E consumption mediated phagolytic activity against E. coli. B12, manufactured by the bacterium, is used for energy production. The effects of vitamin C, B12, and E will be tested to how they affect the growth of the bacterium. With the use of nutrient agar plates, different concentrations of the vitamins will be mixed with the nutrient agar. These plates of different vitamin concentration were used to grow E. coli from the lab and a mixture of bacteria found in tap water. The results indicated that each vitamin affected the bacteria differently. For the E. coli, vitamins C, B12, and E all increased growth at some concentration. At high concentrations of vitamin C prevented growth of the E. coli while there were bacterial growth on all ranged of concentrations of vitamin B12, and E.

Role of livin Gene in Caner Treatment using siRNA, Rajan, Celin
Professor: Dr. Rachel Hopp

Apoptosis is sometimes called the programmed cell death in a multicellular organism. The lack of sufficient apoptosis contributes to the uncontrolled growth of cells, which may become cancerous. Livin is also called melanoma inhibitor of apoptosis protein (IAP). Livin is involved in tumor cell resistance to apoptosis by the inhibition of caspase-3. High levels of expression of livin have been correlated with tumor progression. In order to knock down the gene expression of the livin gene, RNA interference (RNAi) can be used to silence it. Small interfering RNA (siRNA) can trigger RNAi which can affect apoptosis, cell cycle, and proliferation of the cells. Intracellular interference of livin gene expression resensitizes human tumor cells to apoptosis. This process may be very essential in stopping cancer cells from spreading and in helping to destroy these cells effectively.

Inhibition of Viral Replication and Protein Expression of Hepatitis C using RNAi, Riahi, Ryan
Professor: Dr. Rachel Hopp

RNA interference (RNAi) allows for a specific means of silencing gene expression by leading to degradation of target RNA molecules. There is potential of using RNAi for disease prevention which has led to research concerning clinical RNAi application. RNAi has been demonstrated to combat RNA viral infections, most notably Hepatitis C (HCV). Use of RNAi against HCV would allow for both the degradation of the virus’ RNA genome as well as the prevention of viral gene expression. Studies have shown that RNAi therapy can be used to target specific portions of the RNA produced by the HCV (Wilson and Richardson, 2005). The results indicate that the small inhibitory RNA (siRNA) NS5B was able to specifically inhibit HCV RNA replication and protein expression by ninety percent (Trejo-Avila et al., 2007). RNAi therapy against HCV has promising research that might lead to new ways to control once incurable viral diseases.

The Effects of Antibacterial Body Wash on Normal Human Skin Flora, Richardson, Adam and White, Brittany
Professor: Dr. Jackie Horn

Triclosan is an antibiotic found in numerous common household items ranging from cutting boards to cosmetic products to toilet seats. It is suggested by many microbiologists that the overabundance of this antibacterial agent is to blame for the rising occurrence of infectious diseases. This is attributed to the fact that bacteria have begun developing resistance to triclosan and many other antibiotics. One product commonly containing triclosan is body wash. This study was conducted to investigate whether or not the use of a body wash containing triclosan is beneficial to humans.
The effects of an antibacterial liquid body wash containing Triclosan (Soap A) were compared to those of a normal, non-antibacterial liquid body wash (Soap B). Swabs were collected and cultured from both male and female subjects after using both forms of soap. While initially, both soaps cleansed the skin of any significant bacteria, Soap “A” showed prolonged resilience against bacterial growth while Soap “B” showed increasing growth of bacteria throughout the progression of a day. Thus, it was concluded that while Triclosan containing soaps do eradicate bacteria responsible for odor, disease and other negative components for an extended period, it also kills and prevents the growth of beneficial microbes responsible for protecting against pathogenic infections, maintaining skin health, and cleansing skin of impurities. Because of this, the removal of these beneficial microbes can actually have more detrimental effects over time than beneficial. Consequently, it was determined that body wash minus an antibacterial agent is more beneficial to human skin than that of an antibacterial body wash.

The Utilization of Web-Based Genomic Comparison Tools To Investigate the Relationships Between Adenylosuccinate synthetase of Eschericia coli str. K-12 substr. MG1655 and Other Prokaryotic Cells, Richardson, Adam
Professor: Dr. Brenda Whaley

Eschericia coli (E. coli) str. K-12 substr. MG1655 is a bacterial species containing a 4,639,675 nucleotide, circular DNA genome . Specifically within this genome, the gene PurA is found in the region of base pairs 4402710 – 4404008 and is 432 amino acids long . It is located directly downstream from the yjeT gene and is located directly upstream from the nsrR gene. The PurA gene codes for the protein responsible for generating the enzyme adenylosuccinate synthetase. Adenylosuccinate synthetase is responsible for initially catalyzing the de novo synthesis of AMP . It acts by conjugating IMP and L-aspartate while hydrolyzing GTP into GDP accompanied by Mg2+ . The NCBI online sequence databases and BLAST software will be used for an in-depth analysis of the specific nucleotide sequences of the adenylosuccinate synthetase protein. In addition the E. coli sequences will be compared to the sequences of the PurA gene and gene product with that of other prokaryotic organisms.

Familial Alzheimer’s Disease – RNAi Mediated Silencing of the Presenilin 1 (PS1) Process Alters Cellular Reaction to Caspase Activation and Apoptosis, Roberts, Landria N
Professor: Dr. Rachel Hopp

Presenilin 1(PS1), one of the four proteins that compose the gamma-secretase complex, is encoded for by the presenilin 1 gene (PSEN1). Pathogenic mutations of the presenilin 1 gene (PS1) have been determined to be one the major causes of Familial Alzheimer’s disease (FAD). Evidence shows that these mutations increase the effectiveness of caspase activation and apoptotic cell death, however, the manner in which the mutations in this gene lead to neurodegeneration has not yet been clearly determined. Caspase activation and excessive apoptotic cell death have been suggested to play instrumental roles in neurodegenerative diseases. This review will focus on recent experimental research based on the use of RNA interference (RNAi) to silence the expression of the genes encoded by the γ-secretase complex and determine whether cellular sensitivity to caspase activation will be affected. 

pGLO Bacterial Transformation Lab, James, Michael
Professor: Dr. Jacqueline Horn

Genetic transformation often involves taking genetic material from one organism and inserting it into another organism causing the host to express the traits of the donor organism. The genetic transformation of a pGLO plasmid from Aequoea victoria into E. coli is achieved by a Calcium Chloride/Heat Shock. Upon successful uptake, the pGLO plasmid is expressed in the form of Ampicillin resistance and Green Fluorescent Protein (GFP), a protein that causes the bacteria to glow in the presence of ultraviolet light. Using a hydrophobic interaction chromatography (HIC) column GFP is able to be extracted from the bacteria cultures as a pure protein. Introducing this type of lab in a biology class introduces students to the field of biotechnology. Exploring bacterial resistance and gene expression are foundational in understanding basic biological concepts. The laboratory techniques used in this lab, pouring agar plates, CaCl2 heat shock, and using chromatography columns are also foundational to launching successful careers in biology.

The use of BLAST and the comparison of prokaryotic Fused Diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino)uracil reductase, between E. coli and other prokaryotes, Wease, Erica
Professor: Dr. Brenda Whaley

E. Coli K-12 is the one of the most studied bacteria. E. Coli K-12 is non-pathogenic, has had it’s entire genome mapped, and is used for many commercial purposes including the production of insulin for human use. Escherichia coli, but more specifically E. coli strain K-12, substrain MG 1655 (accession # NC_000913) is the organism that produces the enzyme fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase. The enzyme Fused Diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino)uracil reductase is coded in the E. coli genome by the Rib-D gene and is 367 aa long. According to one source: “ The ribD gene encodes a bifunctional enzyme that catalyzes the second (deamination) and third (reduction) steps in the riboflavin biosynthesis pathway. The N-terminal domain encodes the deaminase activity, and the C-terminal domain encodes the reductase activity (Richter97).” The gene for Rib-D is positioned on the NC_000913.2 chromosome at 432,679-433,782. The DNA for NC_000913.2 is circular in nature and is 4,639,675 bp long. BLAST can be found at the NCBI website www.ncbi.nlm.nih.gov. BLAST (Basic Local Alignment Search Tool), is used to search databases using an amino acid or nucleic acid sequence. BLAST compares the sequence you give to similar sequences it finds and reports the similarities in percentages. BLAST helps you find proteins or nucleic acid sequences that are similar and therefore allows you to compare sequences within one species or maybe many different species. Therefore, BLAST is a unique tool that helps scientists find common links among many organisms and within organisms. I will use BLAST to identify other prokaryotes that produce the enzyme fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino)uracil reductase and compare the sequence of these proteins to that of E. coli.

RNAi as a Treatment for HPV-positive Cervical Cancer, and as an Adjuvant Therapy to Cisplatin, Yee, Nicholas
Professor: Dr. Rachel Hopp

RNA interference is a mechanism in which eukaryotes regulate gene expression by using double stranded RNA (dsRNA). Also used as a defense mechanism against infections by viruses, RNAi inhibits the expression of their genes and antigens by using small interfering RNA (siRNA) to degrade specific viral messenger RNA (mRNA). This can be used to silence genes and prevent the manufacture of harmful proteins.
Cancer caused by HPV presents a very good model for RNAi therapy research as the oncogenes that cause cancer, E6 and E7, are exhibited only in the cancerous cells. RNAi therapy can be designed to specifically inhibit the action of such oncogenes.
In a study, a single dose of siRNA silenced genes for a period of four days. The silencing of E6 yielded an increase in the amount of cellular p53 tumor suppressor protein, and reduced cell growth. The silencing of E7 resulted in apoptosis of the cells. These findings can be used to enhance cancer therapies. One such therapy involves the use of cisplatin, a chemotherapeutic agent used to treat advanced cervical cancer. siRNAs that attack the E6 and E7 oncogenes can increase the effect of cisplatin on cancerous cells in the cervix.   

RNAi Interference to Inhibit Expression of Human Papillomavirus Genes E6 and E7 as Treatment for Cervical Cancer, Gleason, Jacob
Professor: Dr. Rachel Hopp

Cervical cancer is the second most common disease affecting women. The leading cause of this cancer is human papillomavirus (HPV). There are more than sixty types of HPV, but the most common to cause cervical cancer are strains 16 and 18. HPV causes human cells to express the oncogenes E6 and E7 which leads to cancer. Small interfering RNAs (siRNA) can be used as therapeutic nucleic acids to control or inhibit the production of tumors.  E6 and E7 are genes that are only expressed in HPV positive cells. They transcribe an mRNA transcript that can be translated into E6 and E7 viral proteins. E6 viral protein is known to degrade the cellular protein p53 (a tumor suppressor) which governs the cell cycle, and also causes an anti-apoptotic effect which makes the infected cells immortal. E7 viral protein targets retinoblastoma protein (pRb) which will interfere with cellular senescence and cellular differentiation. These Viral proteins are necessary to cause normal cells to become cancer cells, and the introduction of siRNAs into these cancer cells may lead to the inhibition of viral protein translation and the reintroduction of the p53 and pRb pathways. Tests, both in vitro and in vivo, have been done and the data shows promising results that may lead to a cure for cervical cancer. These tests have also shown that siRNA can be successfully made to target E6 and E7 mRNA transcripts and that specific siRNAs are more effective than others.

Symbiosis and Insect Diversification: an Ancient Symbiont of Sap-Feeding Insects from the Bacterial Phylum Bacteroidetes, Harris, Kantrell 
Professor: Dr. Curtis Henderson

Many phylum of insects have inherited obligate, vertically transmitted bacterial symbionts that provision hosts with vital nutrients that are not found in their restrictive diet. It has been scientifically proven that some of these bacteria have been shown to descend from ancient infections. The large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts, belonging to the phylum Bacteroidetes. Analyses of the 16S rRNA genes confirm that the symbiont phylogeny is congruent with the phylogeny of insect hosts as currently known. These results verify the ancient acquisition of a symbiont by a shared ancestor of these insects, dating the original infection to at least 260 million years ago. As visualized in a species consisting of spittlebug (Cercopoidea) and in a species of sharpshooter (Cicadellinae), the symbionts have particularly large cells with an elongate shape averaging more than 30m in length. In situ hybridizations support the fact the these symbionts are congruent to the phylum Bacteroidetes. “Candidatus Sulcia muelleri” is proposed as the name of the new symbiont. 

Linezoid versus Vancomycin in Treatment of Complicated Skin and Soft Tissue Infections, Martinez, Jesse Edward Sr.
Professor: Dr. Curtis Henderson

Skin and soft tissue infections are becoming a common site in clinics and hospitals throughout the world. The morbidity rate of skin and soft tissue infections (SSTIs) continue to increase in communities and hospitals. The deeper an infection penetrates soft tissue, the more likely surgical intervention is necessary. Certain medical conditions make treatment even more difficult. Conditions like diabetes mellitus or the human Immunodeficiency virus increase morbidity by hindering an already difficult to treat condition. This research was conducted to determine the effectiveness, safety and tolerance between Linezoid and Vancomycin in treating complicated skin and soft tissue infections to include methicillin-resistant staphylococcus aureas (MRSA). Patients considered in this research were either suspected or proven to have MRSA complicated SSTIs or having co-morbid SSTIs (diabetes mellitus or HIV). The study was randomized, controlled and involved the cooperation of nations from around the world. This research took place over a six month period, from October 2002 to March 2003. Randomized patients received either 600mg Linezoid every twelve hours orally or 1 gram of Vancomycin every 12 hours intravenously. Patients were monitored at different intervals throughout this study, the data was collected and a comparison conducted. Final results demonstrated that Linezoid was far superior in the treatment of SSTIs, co-morbid SSTIs and infections that were MRSA, than that of Vancomycin. Treatment with Linezoid was well tolerated, while adverse reactions were similar in both medications. While Linezoid proved superior to Vancomycin in the treatment of SSTIs and MRSA, Vancomycin resistant staphylococcus aureas (VRSA) cases are also surfacing among other multi-drug resistant (MDR) infections and making treatment even more difficult. Vancomycin a glycopeptide, has established itself as the first line of defense against methicillin-resistant Staphylococcus aureas infections. Cases involving vancomycin-resistant Staphylococcus aureus are increasing at a dangerous rate as noted in a research study submitted to the American Society for Microbiology in October for consideration. “High-Level Vancomycin-Resistant Staphylococcus aureas Isolates Associated with Polymicrobial Biofilm” this study demonstrates that vancomycin, however effective, against MRSA, is presented with an up hill battle in providing a defense toward super-bugs. The VRSA was found in a nephrostomy tube of a hospitalized patient in New York. The tube was sent to the Centers for Disease Control and Prevention (CDC) where it was cut and tested using an array of techniques, which included plasmids, PCR and DNA sequencing analysis. Results proved positive for resistance to but not limited toward vancomycin and included aminoglycosides, fluoroquinolones, macrolides, penicillin, and tetracycline. Isolates showed susceptible to chloramphenicol, rifampin, trimethoprim-sulfamethoxazole and linezoid. Linezoid once again demonstrated its superiority in the treatment of both MRSA and VRSA infections respectively. 

Wind Powered Gliders, Abbasi, Madiha
Professor: Dr. James Claycomb

In an age of oil and gas crisis I will pursue to develop a new way of air transportation that will not require the use of fuel. Compared to a powered aircraft, a glider has only three main forces acting on it: lift, drag, and weight. In order for a glider to fly, it must generate lift to oppose its weight. To generate lift, a glider must move through the air. But the motion of a glider through the air also generates drag. In a powered aircraft, the thrust from the engine opposes the drag. But a glider has no engine to generate thrust. With the drag unopposed, a glider quickly slows down until it can no longer generate enough lift to oppose the weight. I propose that the power of the wind and the friction it causes as it collides with the surface of the glider can be harnessed by windmill type structures attached at efficient positions on the body of the glider. Though these structures will cost the glider efficiency in the form of weight and drag, these windmill structures will also produce thrust by harnessing an outside force other than fuel: wind. I also propose to attach thrust producing fans at the back or bottom of the glider that will be powered by a motor that converts mechanical energy (wind turning the fans of the windmill type structures) into electrical energy. The thrust produced by the by such motion will out produce the costs of such structures on a glider thereby allowing the glider to stay aloft by producing enough lift to oppose the weight.

Untitled, James, Michael
Professor: Dr. Brenda Whaley

Eschericia coli strain K-12 is one of the most common strains used by biologists to identify gene types in other bacteria. The first sequence of E. coli K-12 was completed in 1922 and has since become the foundation for understanding bacterial structures. One sub-strain of E. coli K-12, MG1655, produces UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ( GenBank: NP_414630) also know as MurD. This protein is 438 amino acids in length and catalyzes a reaction that produces peptidoglycan, a polymer that gives structural strength to the cell wall of the bacteria. Coming from a genome (GenBank: NC_000913) of 4,639,675 bp in length, the 1317 bp gene that produces MurD is located between position 97,087 and position 98,403. By obtaining the FASTA sequence for this protein you can use the Basic Local Alignment Search Tool (BLAST), located on the PubMed home page, to search for common protein sequences in other organisms. BLAST works by comparing nucleotides or amino acids in the query sequence to those in its databases to determine what may be possible matches. The information obtained from a BLAST can help you to better understand what protein or gene you are working with based on the characteristics or information from the other organisms. I will use BLAST to study UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase in prokaryotes and compare sequence conservation in different organisms. 

For the Insect Pathogen Photorhabdus luminescence, Which End of a Nematode Is Out?, Murillo, Alma
Professor: Dr. Curtis Henderson

 The entomopathogenic bacterium Photorhabdus luminescens is transmitted between insect larvae via the nematode Heterorhabditis bacteriophora. Within the nematodes there is the dauer juvenile (DJ) stage in which it retains P. luminescens in its intestine and releases its bacteria into the hemocoel of the insect host. The transmission of the bacterium via its nematode vector is studied in this report using a green fluorescent protein. The protein was placed in the intestine and extended toward the anus. Incubation of DJ nematodes in vitro in insect hemolymph induced regurgitation of the bacteria. After a 30 minute lag, the bacteria exits the mouth. In this case, the regurgitation reaction was induced by a low molecular weight, heat and protease-stable, anionic component present in arthropod and hemolymph and in supernatants from insect cultures. Being able to visualize P. luminescens in the DJ nematode intestine provides information on the mechanism of release of the bacteria during infection of insect larvae. 

The Elusion of HIV-1 from RNA Interference by Modifications in Sequence-Specificity and RNA Structure, Tat, Sara
Professor: Dr. Rachel Hopp

Since the discovery of RNA interference (RNAi), abundant research has been conducted using this natural mechanism for gene flow control. This phenomenon involves double-stranded RNA utilized to silence certain genes and is highly significant in furthering the understanding of gene regulation and function. Present research uses RNA in attempts to treat various disorders such as viral infections, cancers, and sexually transmitted diseases. 
While RNA silencing appears to have therapeutic potential, it faces many challenges regarding viral resistance before it can be medicinally efficient and effective. The human immuno-deficiency virus type 1 (HIV-1) has been recently shown to display a mutation that allows it to rapidly escape from short interfering RNAs (siRNA) that have previously caused antagonistic effects on this retrovirus. After the introduction of either a single-nucleotide substitution or a deletion of the targeted sequence in the RNA virus, several mutants exhibited better replication than their wild-type counterparts in the presence of siRNA.
Laboratory experiments executed on HIV-1 with RNAi have shown conflicting results. Substantial conclusions were drawn concerning the degree of sequence homology and the tolerance levels of particular target sequences. Though some of the scientific findings were contrasting, it is not at all doubtful that HIV-1 possesses certain adaptation features that allow it to evade the effects of RNAi.