2009 Research Symposium

2009 Research Symposium
 

COMPLETED RESEARCH
 


Following the oxidation of Zinctetraphenylporphyrin (ZnTPP) by Spectroelectrochemistry, Adam, Suhare
Professor: Dr. Eric Van Caemelbecke

Spectroelectrochemistry is an important technique in Chemistry which is used to determine the mechanisms and concentrations of species involved in oxidation-reduction processes. It is different from traditional Electrochemistry in that it allows for spectroscopic analyses while the oxidation-reduction reaction is taking place. Spectroelectrochemistry is not confined only to Chemistry as it is a powerful analysis tool in other disciplines such as Physics and Biology. This presentation describes an experiment we developed using Thin Layer Cyclic Voltammetry (TLCV), a technique which allows for spectroscopic analysis by using a specialized cell, to demonstrate the spectral changes that occurred when a sample of Zinctetraphenylporphyrin (ZnTPP) was oxidized. ZnTPP is a simple porphyrin complexed with zinc. Porphyrins have a characteristic soret band in addition to visible peaks in their spectra. ZnTPP, in addition to the soret band, has two visible bands. When oxidized, the soret band and one of the visible peaks are expected to collapse while the other visible peak increases. In our experiment, we successfully demonstrated these spectral changes that occurred in ZnTPP as it was converted to its oxidized form.
 


Determining Type of Fullerene Present in a Cosmetic Face Cream, Adam, Suhare
Professor: Dr. Taiya Fabre

Fullerenes are hollow, roughly spherical carbon based molecules that were discovered in 1985 by Robert Curl, Harold Kroto and Richard Smalley.  Carbon 60 (C60) is known as the third allotrope of carbon following graphite and diamond.  While some studies concluded that certain fullerenes are not toxic, other studies have shown some fullerenes to have “asbestos like pathogenicity” in mice.  Dr. Brandt’s lineless eye cream is an over the counter cream that is expected to prevent the depletion of collagen and delay the ageing process. One of the ingredients in this face cream is a fullerene which supposedly stops the actions of UVA and UVB by absorbing free radicals. The motivation behind this research is to determine if C60 is the fullerene that is present in the over the counter eye cream.  Mainly, high pressure liquid chromatography (HPLC) is used to analyze the face cream and compare it to commercially available C60.
 


Effects of Estradiol-17 Injections on Vitellogenin Production in Male Fundulis grandis, Anderson, Phillip T.; Brockman, Leah
Professor: Dr. Ann O. Cheek

Treated sewage effluents can introduce hormones and hormone-mimicking chemicals into the aquatic environment. Some sewage effluents contain enough estrogen or estrogen mimics to feminize male fish. Male fertility can be reduced with potentially negative consequences for fish populations. This experiment investigates the effects of increased estradiol in male Gulf killifish (Fundulis grandis). Males (n=6) were dosed with 2.5 microgram estradiol-17ß per gram body weight or with an equivalent volume of saline. To detect feminizing effects the amount of vitellogenin in the bloodstream was measured in the estrogen-treated and control groups. Vitellogenin is a protein typically produced in the female liver in response to circulating estrogen. The vitellogenin is released from the liver into the blood. The systemic vitellogenin travels in the blood stream to the female ovaries. When environmental estrogen or estrogen mimics are introduced to males the liver produces increased levels of vitellogenin. It is predicted that male killifish will show increased vitellogenin levels compared to control groups because these fish have sex-determining genes and the expression of sex is determined by outside influences. A major disruption in the fish population can have negative consequences on both the ecosystem of water systems near densely populated areas and on the human industries that rely on marine ecosystems for support.
 


The Analysis of MLC Through RT-PCR, Bonilla, Krissia; Gonzalez, Jenny
Professor: Dr. Rachel Hopp

The Myosin Light Chain gene, or MLC, is a gene that is crucial in the mechanism of contraction in muscles. The MLC in Caenorhabditis elegans was the focus of this experiment. C. elegans are microscopic nematodes that live in soil and eat bacteria. These worms were cultured in agar media and were maintained with a diet of Escherichia Coli. In this experiment cycles of polymerase chain reaction were performed. RNA from the C. elegans was extracted and used for the RT-PCR. The primers for this procedure were designed based on sequence information in www.wormbase.org. Worms were collected at the L3 stage. The RNA was extracted. After the extraction of RNA and amplification of cDNA by RT-PCR, the samples were analyzed by agarose gel electrophoresis. The amplicon size was expected to be less than 1823 base pairs (genomic fragment). The experiment was performed twice. The predicted band sizes were not observed. In future trials, factors such as the annealing temperature or the magnesium concentration could be altered to achieve the expected results. The success of this experiment can introduce new, important studies such as, the analysis of RNA at different developmental stages, measuring the expression of genes in different environments of the worm, and also the study of other muscle diseases. The study and experimentation on C. elegans have opened many doors to scientists to better understand the human body. For this reason, it is hoped that the study of C. elegans will be continued and improved.
 

 
The Developmental Study of the Unc-22 Gene, Abubakar, Natasha; Kim, Joyce
Professor: Dr. Rachel Hopp

In our experiment, our research was based on the study of muscle physiology. Unc-22 is used to study the protein twitchin, which regulates muscle contractions through the actin-myosin cycle and works to maintain normal muscle function.  When this gene is not present there is irregular muscle twitching that occurs in place of normal sinusoidal motion in C. elegans. We used primers of exons 6 and 10 to measure unc-22 in Caenorhabditis elegans (C.elegans), a nematode, at stage L3. These primers were designed to see if our results matched up with the fragment sizes predicted for our uniquely designed primers.  We had four experimental treatments containing a positive control, negative control, experimental RNA sample, and worm DNA, respectively. We used agarose gel electrophoresis to analyze our results. After staining our gel and putting it under the ultraviolet transilluminator, our results did not show a band at the expected amplified fragment sizes.  In fact, there was no band at all in the column containing the cDNA.  A possible error could have come from an incorrect annealing temperature or could have been from an inaccurate magnesium concentration. If we optimize this experiment, we will be able to conduct additional studies.  This research is vital to our future to increase our understanding of muscle physiology and associated diseases.
 

 
Finding the Protein Multidrug efflux system in Closely-Related Bacteria, Miron, Maria
Professor: Dr. Brenda Whaley

The purpose of my research was to study the divercity of Bacterica which carry  the Multidrug efflux system protein, GeneID 94821. The size and location of this gene are 391 AA and P31462[1-391] respectivably. It is the protein that confers, on bacteria, the ability to withstand antibiotics. The resistance is often due either to mutations that prevent antibiotic binding to the protein or to amplification of the gene encoding the protein. I used  Escherichia coli (strain K12), accession number  NC_000913, as the sample Bacteria carrying Multidrug efflux system protein. I searched  for in four different Bacterical groups (Shigella, Samonella, Yersinia, and Buchnera ) to see if they too carried this enzyme. Two bacteria where chosen from each group. The four closest matches were Shigella boydii and Shigella dysenteriae 1012 from the Shigells group and  Salmonella enterica subsp. arizonae serovar 62 and Salmone lla enterica subsp. enterica serovar Typhi str. CT18 for the Salmonella group. There were no good matches in Yersinia or Buchnera. The next step is to widen my search into other groups to see just how far spead this enzyme is found in bacteria.
 


“California’s Burning, Burning…” To burn or not to burn, Mithani, Farah
Professor: Dr. Betty Thompson

In this experiment, I have tested the effects of fire on soil. There is a difference of pH, nitrate, phosphate, and TDS. The soil used for testing was from one ecosystem. The three soil samples tested were of the natural soil, partially burned, and burned. Also, after the experimental burning process, there was a difference in plant growth of the Mungbeans. The pH for the partially burned and burned was higher than the natural soil. There was phosphate (4) present in both burned soils, but not in the natural. A higher nitrate was also present for both burned.  Overall, the three soil types had very different results in the testing experiments.
 


The Function and Amplification of the FKH-6 Gene, Hang, Kimberly; Ngo, Lynn
(2009 Symposium poster winners recognized at the annual Honors Convocation)
Professor: Dr. Rachel Hopp

FKH-6 is required for male differentiation so it has a larger affect on male than hermaphrodite nematodes. When FKH-6 is absent, feminization of the genitalia occurs. In studying the FKH-6 gene, polymerase chain reaction (PCR) was done in order to amplify the DNA. The interaction between Taq polymerase and dNTPs, aided by Mg2+, is required for the Taq enzyme to attach itself to the primer and synthesize new DNA.  Because Taq polymerase activity is initiated based on the primer and the interaction between Taq and dNTPs, different primers will require different amount of MgCl2. Therefore, multiple samples of the C. elegans DNA were amplified with various amounts of MgCl2 in order to determine which concentration of MgCl2 will yield new DNA. According to the recorded data, 3 mM of MgCl2 optimizes the amplification of the FKH-6 gene. Using 3 mM of MgCl2, the FKH-6 gene is again amplified at various cycles, but this time, thawed and fresh Taq polymerases were used for the purpose of comparison. Based on the results, there was no difference between the two polymerases.
 


Conservation of the purine-nucleoside phosphorylase encoding gene of E. Coli K-12 substr. MG1655 in other prokaryotes, Nguyen, John
Professor: Dr. Brenda Whaley

Escherichia Coli, more commonly known as E. coli, is a hardy common species of bacteria that is hosted in the intestines of many animals. When mentioned, E. coli often causes many to think of food poisoning and illness related to contamination and infection, but the reality of it is that most strains pose no threat to humans.  There are over 700 strains of E. coli that have been identified but the most widely recognized is O157:H7, which produces potent Shiga toxin that causes most of this bacterium’s trademark symptoms. The serotype focused in this project is the much more docile MG1655 substrain of the K-12 strain, with special attention on its purine-nucleoside phosphorylase protein and the gene that encodes it. The genome of this strain has been completely plotted. Purine-nucleoside phosphorylase is an important enzyme that participates in the purine salvage pathway, where nucleotides are created from intermediates (bases and nucleosides) that are created from the break down of other nucleotides such as RNA and DNA. The genome for the strain of E. coli in question can be located under the accession number NC_000913, and the gene that the purine-nucleoside phosphorylase enzyme is derived from is found under accession number NP_418801. The gene is 239 amino acids long. Due to its important activity of purine salvage in this strain of E. coli, one would expect the enzyme to be present in other species of bacteria as well. Through the use of bioinformatic references, one can observe that the gene sequence that codes for this enzyme is highly conserved in Shigella sonnei, Shigella dysenteriae, Salmonella enterica subsp. Enterica serovar, Yersinia mollaretii, and Yersinia pestis. With further research one can discover how widespread this enzyme is amongst prokarotes, and as the scope widens, how closely the gene is conserved.
 

 
Detecting unc-22 Gene Expression During Caenorhabditis elegans Development, Saquin, Claire; Baxley, Kenneth
Professor: Dr. Rachel Hopp

Caenorhabditis elegans is a nematode, about 1 mm in length, which is used extensively as a model organism due to its relative simplicity, high reproductive rate, ease of maintenance, short lifespan, and well studied biological processes and genome. C. elegans undergoes numerous developmental stages including egg, L1, L2, L3, L4, and adult. Throughout its stages, different genes are expressed in different stages. The unc-22 gene in C. elegans codes for Twitchin, which is a protein needed for muscle regulation of actomyosin contraction and relaxation and for muscle morphology. To detect the expression of the unc-22 gene during the larval L2 life stage, C. elegans were grown on petri plates up to L2 then collected for extraction of RNA. Two primers were developed for exons 1 and 3 found within that target gene’s genomic sequence. The primers were used to bind with the sample RNA from the L2 stage C. elegans and cDNA was developed from the RNA using reverse transcriptase. The cDNA was then amplified through PCR, then run through electrophoresis to find if the exons in the unc-22 gene between the two primers had been isolated, thereby verifying the presence of the gene during that life stage of C. elegans. To verify that the cDNA was compliment to the unc-22 DNA , the resulting sample was run through agarose gel electrophoresis and the lengths were compared. Study of unc-22 can be applied the understanding of human muscle disorders. The same process used to detect gene expression in C. elegans also can be used in detecting gene expression during development in humans in order to further advance genetic developmental understanding and treat developmental genetic disorders.
 


Acid Rain: Damaging Deposition or Passive Precipitate?, Sigireddi, Meenakshi; Razvi, Zain
Professor: Dr. Jacqueline Horn

The effects of moderate levels of acid deposition on microbial communities in soil were examined in three different regions after an artificial acid rain simulation.  Soil samples were taken from a suburban area, a state park, and a bayou. Acid depositions occurred in varying levels of pH, ranging from trials of pH level 2, 4, and 6.  The artificial acid rain consisted of de-ionized water containing dilute concentrations of Sulfuric Acid, a main component in acid rain. The acid application resulted in acidification of the soil and its microbial population, significantly altering the physiological characteristics of the colonies. The acid addition resulted in a decrease in total microbial biomass. Colony counts decreased by more than half, in some cases acid deposition resulted in a population a third of the size of expected colony growth. The relative amount of bacterial growth decreased with increased pH levels, for the bacterial community was not adapted to the more acidic conditions. The acid addition caused clear changes in the microbial community structure; however these results were less quantitative because the microbial species in each soil type already varied in size and composition. Overall, the acidification induced drastic changes in the microbial communities of each region.
 


Water Pollution: Adverse Effects on Eukaryotes, Sigireddi, Meenakshi
Professor: Dr. Betty Thompson

This bioassay provides for a quantitative analysis of pollution’s detrimental effects. This was accomplished by using yeast, Sacchraromyces Cerevisiae, as a test subject.  Different samples of water along the same waterway were tested, starting in rural areas with relatively little amounts of pollutants, to urban areas with increasing pollution. The yeast was then exposed to these various samples of water. The control tube of yeast fermented on pure glucose and de-ionized water. The control produced the most carbon dioxide, as did the yeast tested on unpolluted water sections. The yeast that fermented on samples of glucose and polluted water, however, produced the least amount of carbon dioxide. This shows that pollution has an adverse effect on the fermentation capabilities of eukaryotic yeast cells. By using yeast fermentation levels, water toxicity can be measured. The results showed that the rates of yeast fermentation were higher in water that came from the non- polluted regions of the waterway than water that came from more polluted areas.
 


The Effect of Secondhand Estrogen on Blood Proteins of Female Gulf killifish Fundulus grandis, Tanchico, Daren
Professor: Dr. Ann Cheek

Estradiol-17b, an estrogen, is the primary female hormone present in all vertebrates.  In female fish, estrogen triggers the production of specific proteins that are packaged into egg yolk. The major egg yolk protein is vitellogenin; it is produced in the liver, and then carried in the blood to eggs developing in the ovary.  What happens if estrogen levels are disturbed by external influences?  In this experiment, groups of female and male Gulf killifish (Fundulus grandis) were housed together in aquaria.  Females received no direct treatment, but were exposed to estrogen-dosed males or to saline-dosed males.  Since estrogen dosing results in estrogen excretion, females were exposed to secondhand estrogen in the environment and to potentially atypical behavior from their estrogen-treated companion males.  How will female physiology respond when exposed to estrogenized males?  Will female vitellogenin levels be affected after being exposed to secondhand estrogen?  Vitellogenin levels were measured in both groups of females.  Two outcomes are possible:  The females exposed to secondhand estrogen will produce more vitellogenin due to artificially elevated estrogen concentrations or they will produce the same amount of vitellogenin because they break down and excrete the excess estrogen.  If estrogen or estrogen-like chemicals are introduced into an ecosystem, this may disturb normal reproduction in the resident fish.
 


Genetic Analysis of the Human Homolog BBS5 Gene in the Nematode Model, Vander Wiele, Taylor; Adodo, Crystal
Professor: Dr. Rachel Hopp

BBS5 genes, observed in humans, produce a genetic disorder called the Bardet-Biedl syndrome. This syndrome in individuals is featured as obesity, mental retardation, and renal failure. A missense mutation was stated as the cause of BBS. Nematodes were employed as a model possessing the BBS5 genes; C. elegans expressed these genes in relation to ciliary functioning. In our further experiments, genetic analysis of the BBS5 genes was performed to bring further understanding of the expression of BBS5 genes. A PCR machine was used to observe the expression of the amplified DNA. Extraction of DNA was successful; however, results were inconclusive.
 


Determination of Stoichiometry and Equilibrium Constant in the Formation of a Porphyrin Metal and Imidazole Complex Using Spectrophotometric Titration, Villarreal, Ruben
Professor: Dr. Eric Van Caemelbecke

The purpose of this experiment was to determine the stoichiometry and equilibrium constant in the formation of tetraphenylporphyrin Zinc (Tpp)Zn and imidazole complex using spectrophotometric titration technique. A concentrated solution of Imidazole was added in 1 uL aliquots to a (Tpp)Zn solution. An absorbance versus mole to mole plot was generated and the stoichiometric coefficient was graphically determined (1.1). The equilibrium constant (105,190) was determined using the equilibrium equation of the reaction.

 

PROPOSED RESEARCH
 


The prevalence of Sulfate adenyltransferase, subunit 2 is various Prokaryotes., Joseph, Riya
Professor: Dr. Brenda Whaley

Theodore Escherich discovered the organism Escherichia coli, a model which is still used today in the study of bacterial genetics, physiology and biochemistry. It is the dominant facultative anaerobe present in the lower intestine of humans. If virulent traits are acquired by these organisms, diseases that introduce toxins to disrupt normal cellular functions such as urinary tract infections and neonatal meningitis can result. The particular strain studied in this experiment is similar to the wild type since it was maintained with very little genetic manipulation. This strain is rod shaped, not pathogenic and is optimal at 37ºC. 
 Sulfate adenylyltransferase subunit 2 is found in Escherichia coli strain K-12 (sub-strain MG1655). The circular DNA has 4639675 base-pairs. The accession number for the entire genome is NC_000913. The Genomic ID number is 947217 and the name of the gene is cysD. 85% of this gene consists of coding regions and it has a 50% GC content. The name of this particular gene is cysD - sulfate adenylyltransferase, subunit 2.
 The enzyme sulfate adenylyltransferase catalyzes the following chemical reaction:
 ATP + sulfate <=> diphosphate + adenylyl sulfate.
 This enzyme belongs to a family of nucleotidyltransferases. The three metabolic pathways this enzyme participates in are purine metabolism, selenoamino acid metabolism, and sulfur metabolism.
 A BLAST search shows that four bacterial species from the Enterobacteriales taxon also code for this enzyme 72 %, 100%, 97% and 90%, respectively.
1. Buchnera aphidicola str. 5A (Acyrthosiphon pisum),
2. Shigella sonnei Ss046,
3. Salmonella enterica subsp. enterica serovar Weltevreden str. HI_N05-537
4. Yersinia pestis Angola
 
 

16S rRNA m2G1207 Methylase in the World of Prokaryotes, Le, Janet
Professor: Dr. Brenda Whaley

The particular enzyme of interest is the 16S rRNA m2G1207 methylase, with a gene ID number of 948892, can be found in a variety of different bacteria. This enzyme is produced by the Escherichia coli strain K-12 substrate MG1655, with an accession number of NC_000913, a single, circular chromosome, 4,639,675 base pair sequence. Escherichia coli are pathogens that help maintain normal equilibrium in the intestinal tracts of animals. The E. coli strain K-12 substrate MG1655 is widely studied in the laboratories because it can be reproduced with minimal genetic mutations and it’s harmless. The gene length of the enzyme is 343 amino acids long, and it is located between 4,605,723 bp and 4,604,692 bp of the E. coli strain. This enzyme’s purpose is to methylate the guanosine, position 1207 of 16S rRNA in the 30S particle. The enzyme also catalyzes this reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N(2)-methylguanine. In the preliminary research the enzyme, 16S rRNA m2G1207 methylase in Escherichia coli strain K-12 substrate MG1655 was compared to other Enterobacteriales. In result, it was determined that it was similar to: the Shigella boydii Sb227, with a 98% identity, the Salmonella typhimurium LT2, with a 90% identity, and the Yersinia enterocolitica subsp. enterocolitica 8081, with a 68% identity. It was determined that 16S rRNA m2G1207 methylase had a 43% identity to Buchnera aphidicola str. 5A (Acyrthosiphon pisum), confirming it was not a true match. In conclusion, in the Enterobacteriales, the particular enzyme was expressed in other species like the Shigella, Salmonella and Yersenia, but not the Buchnera. Further research will be done using bioinformatics tools like Blast, Swiss-Prot and GenBank to determine this enzyme’s gene prevalence in other bacteria in the prokaryotic world.    
 


Effects of Various Inhibitors on the Decomposition of Hydrogen Peroxide with Catalase, Liang, Edison; Kuruvilla, Noble
Professor: Dr. John Ledford
Biological catalysts, enzymes, lower the activation energy of a reaction to increase its rate to a level that can allow for normal function of the system. Hydrogen peroxide is medically used as an antiseptic to sterilize wounds. The enzyme catalase is present in the blood stream to defend our body from exposure to hydrogen peroxide.
 
Catalase
2H2O2 (l)            -->       2H2O (l)    +   O2 (g)
 
We are in the process of developing new upper level chemistry laboratories to expand our offerings at HBU.   Catalase has been used widely in undergraduate labs as a means to study kinetics.  In our experiment, the reaction rate of the decomposition of hydrogen peroxide (H2O2) in the presence of catalase is examined by variation of the concentration of catalase solutions, the concentration of H2O2, the temperature of H2O2 solution, and the pH of H2O2 solution. Also, we investigated the effects of various inhibitors on the rate of this reaction. The inhibitors used were acetate, ethanol, methanol and nitrite. The best results were observed in 100% concentrated catalase, 100% concentrated hydrogen peroxide, hydrogen peroxide at 75-85°C, and hydrogen peroxide with a pH of 7. These conditions can be explained by the collision theory, the Arrhenius equation, and the degradation of proteins at uncharacteristic levels of pH.  We eventually hope to adapt this experiment for use in an upper level laboratory. 
 


Prevalence of L-fuculose-1-phosphate aldolase in the World of Prokaryotes, Nguyen, Jeannie
Professor: Dr. Brenda Whaley

Escherichia coli is an enterobacteria and the main facultative anaerobe commonly found among the microflora in the intestines of humans. The specific focus of this research is E. coli strain K-12 substrain MG1655. The accession number for the genome of the strain is NC_000913. This bacterium is rod shaped, non-pathogenic, and motile. It functions at an optimal temperature of 37°C (98°F) and is classified as a mesophile because of its affinity for moderate temperature environments such as the human body. The protein of focus within this strain of E. coli is the enzyme L-fuculose-1-phosphate aldolase. This protein is 215 amino acids in length and has a mass of 23,775 Da. It functions in carbohydrate degradation, specifically the metabolism of fructose and mannose. This enzyme is a part of the lyase family of enzymes, which catalyzes the addition or removal of a small molecule or group to either break or form a double bond. More specifically, the enzyme belongs to the aldolase class II family: AraD/fucA subfamily. The gene which codes for this protein is called fucA and has the ID number 947282. The purpose of this research project is to determine the prevalence of the enzyme L-fuculose-1-phosphate aldolase in organisms other than E. coli. Specifically, this research is focused on the protein sequence variation and conservation as well as the patterns of protein expression in the world of prokaryotes. Thus far, bacterial species Salmonella enterica subsp. enterica serovar Agona str. SL483 (YP_002147884), Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 (YP_151998), Shigella boydii CDC 3083-94 (YP_001881460), and Shigella flexneri 2a str. 301 (YP_708595) have been found to contain matches in protein sequences. The matches yield 92% range 1-215, 92% range 1-215, 99% range 69-215, and 100% range 1-215, respectively.
 


Occurence of RNA polymerase sigma S (sigma 38) factor in Prokaryotes, Ojelade, Jimi
Professor: Dr. Brenda Whaley

RNA polymerase sigma S (sigma 38) factor is an enzyme found in Escherichia coli strain K-12 substrate MG1655 bacteria. The accession number for this protein is NP_417221 with a gene ID of 947210. The pattern of this protein’s expression is thought to be found in other prokaryotes. This research is designed to discover the occurrence of this protein in the world of prokaryotes. It is 330 amino acids in length. The location of the gene for this protein is on nucleotide #2864581 through nucleotide #2865573 on the E. coli chromosome. This protein is involved in transcription through DNA binding as a sigma factor. The RNA polymerase belongs to the sigma 70 factor family and is a sigma transcription factor controlling a regulon of genes required for protection against external stresses. There is speculation that this RNA polymerase affects the expression of katE, to catalase HPII expression which converts harmful hydrogen peroxide molecules to water and oxygen, xthA, an endonuclease III concerned with repairing lethal DNA damage and the appABC operon as well as other genes by modifying the affinity of RNA polymerase for the promoters it binds to.  RNA polymerase sigma protein found in E. coli has shown similarity to RNA polymerase proteins found in the world of prokaryotes including a 98% identity similarity to Salmonella enterica subsp. arizonae serovar (YP_001569129), a 97% identity similarity to Yersinia pestis KIM (NP_668168), and a 92% identity similarity with Shigella boydii (YP_001881829). The prevalence of the DNA coding for this protein shows only slight differences between the gene sequences found in different prokaryotes, and perhaps the difference between these proteins shows that no two are exactly alike and their differences are specific between species.
 
 

Prevalence of L-idonate 5-dehydrogenase in Prokaryotes, Qasim, Saad
Professor: Dr. Brenda Whaley

Research will be conducted on the enzyme to determine the extent to which its sequence varies, to identify conserved regions, and to determine the enzyme’s general prevalence in the prokaryotic world. The enzyme of interest (accession number: NP_418688) is from the bacteria Escherichia coli and functions to catalyze the NADH/NADPH-dependent oxidation of L-idonate to 5-ketogluconate. This protein is predominately active in the carbohydrate acid metabolism and L-idonic acid degradation pathways. The source organism, Escherichia coli, is a Gram negative bacterium which is frequently found in the lower intestine of warm-blooded animals and is known to cause diarrhea, urinary tract infections, and pneumonia. The enzyme actually comes from the K-12 substrate MG1655 strain of E. Coli, with a genomic accession number of NC_000913, specifically located between the 4,491,398th and 4,492,429th base pairs [K-12 is a harmless strain which is commonly used in lab research due to its rapid growth rate and ability to flourish without complex chemicals]. More specifically, L-idonate 5-dehydrogenase is derived from the idnD gene (GeneID: 944769) and is composed of three-hundred and forty-three amino acids. To determine the prevalence of this enzyme and conduct proper research, the BLAST and Swiss-Prot program will be implemented. Blast will aid in using L-idonate 5-dehydrogenase as a reference sequence to which all other enterobacteriales organisms will be compared. At this point in research, L-idonate 5-dehydrogenase has a 97% and 83% identity match to Shigella sonnei Ss046 and Salmonella enterica subsp. Enterica serovar Dublin str. CT_02021853 respectively. No true matches were found in the genuses of Yersenia or Buchnera. Closest matches in these two genuses were of L-threonine 3-dehydrogenase and a multidrug resistance protein. Thus, with the aid of BLAST, the sequence of L-idonate 5-dehydrogenase will be compared to the sequence of other publically available prokaryotic entries.
 
 
 
Utilizing Internet Databases to Explore the Connection of NADH-dependent HCP oxidoreductase between Escherichia coli str. K-12 substr. MG1655 and Other Prokaryotes, Tanchico, Daren
Professor: Dr. Brenda Whaley

One of the most studied organisms in modern science is Escherichia coli (E. coli). E. coli str. K-12 substr. MG1655 is the specific bacterial species utilized in this research. This strain has been extensively used in biomedical research and is easy to work with. E. coli is a prokaryotic organism of the Enterobacteriaceae family of gamma-proteobacteria, it is most commonly found in the intestinal tract of humans and lives as a part of the digestive flora. Thanks to the development of modern technology, specific protein sequences may be studied and analyzed via the use of internet databases. The Basic Local Alignment Search Tool (BLAST) is a useful online tool which allows one to search data banks for a specific nucleotide or protein sequence. NADH-dependent HCP oxidoreductase is a putative enzyme which aids in the binding of iron and sulfur to certain cluster domains. This protein’s accession number is NP_415393 and it is comprised of 322 amino acids. E. coli str. K-12 substr. MG1655 has a 4,639,675 base pair circular genome with a chromosomal accession number of NC_000913. The gene that codes for NADH-dependent HCP oxidoreductase is referred to as hcr and its GeneID number is 947660; this gene lays between positions 910405 and 911373 of the E. coli genome thus, making it 968 base pairs in length. It is an important enzyme because; iron and sulfur proteins play an important role in the process of electron transport in certain enzymatic reactions. One of the most important processes involves the reaction in plant and algal ferredoxins; they act as the electron carriers in photosynthesis. BLAST will be used to search for other prokaryotic organisms that have protein sequences closely related to NADH-dependent HCP oxidoreductase in E. coli.
 


UNC-2 and The Studies of Migraine, Minh-Nguyen Do; Dang T Tran
Professor: Dr. Rachel Hopp

In the U.S, migraine is one of the most severe types of headache that may cause devastating problems for many Americans. In human, CACNA1A gene regulates the synthesis of serotonin. The mutation of this gene leads to the abnormal level of serotonin in the brain, which is one of the main triggering factors for migraine development. However, due to complication of human genome, unc-2 gene, the C. elegans homolog for CACNA1A, is often used in place of CACNA1A to research about migraine. The replication of unc-2 requires a specific concentration of MgCl2, good Taq polymerase, proper PCR technique and gel electrophoresis. Failure to comply with one of these requirements will hinder the whole replication process of unc-2.   
 


L-Asparaginase and Leukemia, Dang T Tran
Professor: Dr. Brenda Whaley

One of the most important methods to treat acute lymphoblastic leukemia is to introduce L-Asparaginase (EC 3.5.1.1) into the tumor cell. Since, unlike normal cell, leukemic cells are unable to synthesize the Asparagine for its survival, L-Asparaginase will deprive those cells from the source of asparagines by catalyzing the hydrolysis of  Asparaginase to aspartic acid and ammonia. I am studying the 321 amino acid protein L-Asparaginase of strain K-12 Escherichia Coli, a gram negative bacterium. The gene which produce  L-Asparaginase is iaaA. This gene is 966 base pairs long. It is located in the region from 865,791th to 866,756th base pair of the E. Coli chromosomes. However, the microbial genomic BLAST indicated that this enzyme may also be found in some but not all E. Coli related bacteria such as Shigella, Sonnei, or Salmonella Enterica with average of 80% structural identical. Recent data also indicated that this enzyme was widespread among other non-related bacteria based on the common regions of this protein shared among these microbes. This confirmation of the conserved regions in different bacteria can be used to aid the future studies about L-Asparaginase, which may improve the effective treatment against leukemia.
 


Conservation of Acetaldehyde-CoA dehydrogenase II, NAD-binding protein within Prokaryotes, Tran, Tammy
Professor: Dr. Brenda Whaley

Research will be conducted on the protein Acetaldehyde-CoA dehydrogenase II, NAD-binding (accession number: NP_4148885 and Gene ID: 945008) found in Escherichia coli strain K-12 substrate MG 1655 (accession number: NC_000913).  This protein is comprised of 316 amino acids.  The gene name is mhpF and is located between 372145 and 373096 in the E. coli genome.  This enzyme catalyzes the transformation of acetaldehyde into acetyl coenzyme A (Acetaldehyde + CoA + NAD=  Acetyl_CoA + NADH) and also acts as a chaperone protein for mhpE folding. Basic Local Alignment Search Tool (BLAST), which can be accessed on the National Center for Biotechnology Information (NCBI) website, will be utilized to find other prokaryotes that produce the same enzyme, determine the level of conservation, and identify the regions conserved.
 


BRC-1 and Its Relevance to Breast Cancer, Vu, Dung; Maharaj, Marla
Professor: Dr. Rachel Hopp

Today breast cancer has become the second leading cause of death in women. Extensive research is being done in hope of identifying particular genes responsible for the mutation of this life threatening disease. Studies in the past have shown evidence of a tumor suppressor gene brca-1 as one of the genes responsible for mutations in humans that develop breast cancer. Researchers have also discovered the ortholog of human’s brca-1 in the nematode, Caenorhabditis elegans (C. elegans), as being the brc-1 gene. Brc-1 has been proposed to be involved with DNA repair but the specific mechanism and function of brc-1 remains elusive. In this study, we selectively amplified the nematodes’s DNA with brc-1 primers using the technique of Polymerase Chain Reaction (PCR) and gel electrophoresis. By manipulating certain variables, such as MgCl2 concentration , the condition of Taq polymerase, and the PCR cycles, we were able not only to determine the size of our experimental amplicon, but were also able to identify the suitable conditions needed to better amplify this gene for future experimental research.
 


The expression pattern of 6-phosphogluconolactonase in bacteria, Vu, Ngoc - Dung
Professor: Dr. Brenda Whaley

Escherichia coli (E. coli) is a Gram negative bacterium that is frequently used as a model organism in microbiology studies today. The bacteria belong to a group of facultative anaerobic organism that makes ATP through either aerobic respiration or fermentation, depending on the availability of oxygen. 6-phosphogluconolactonase is an enzyme that catalyzes the hydrolysis reaction within the pentose phosphate pathway, one of the three essential pathways of E. coli’s central metabolism. The enzyme is composed of 331 amino acid residues and its NCBI accession number is NP_415288.  The gene encoding this enzyme is pgl and its NCBI ID number is 946398. pgl is 996 base pairs long and it extends from position 797809 to 798804 on the genome of E. coli. The E. coli genome is 4639675 base pairs long and its NCBI accession number is NC_000913. The analysis of protein alignment conducted in this study showed that this enzyme is also expressed by other members of Enterobacteriales including: Shigella dysenteriae Sd197, Yersinia frederiksenii ATCC 33641 YfreA_01_12, and Buchnera aphidicola str. Bp (Baizongia pistaciae). To explain the expression pattern of 6-phosphogluconolactonase, a hypothesis was generated from the result of this study.  It was thought that as the compositions making up our atmosphere changed through time, bacteria evolved to adapt to the new environment and utilize new source of energy for metabolism. Therefore, even though 6-phosphogluconolactonase enzyme is conserved among some families of bacteria, its function in metabolism might not be conserved as the organisms no longer carry out the pentose phosphate pathway. When the enzyme’s function is not maintained, its expression pattern will be altered.