2010 Research Symposium

Eighth Annual HBU Student Research Symposium — April 19, 2010
Abstracts of students who conducted their research with mentors in the College of Science and Mathematics.

 
COMPLETED RESEARCH

 
What Makes H5N1 Virulent? —  Al Hasan, Nabila XE "Alam, Jeremiah"
Professor:
Dr. Brenda Whaley

A 24 year old male, who served in the military based in Beijing, came down with H5NI infection in November of 2003. After 8 days of his hospitalization with pneumonia, he died of severe respiratory disease on 3rd December 2003.  The cause of death in this case remained undetermined for very long, however, after a series of tests and extensive research conducted, it was confirmed in 2006 that this was the earliest and the first case of human H5N1 infection in Beijing. The specimens from this man were stored and from them the virus has been successfully isolated. Research has shown that it is actually the hemagglutinin (HA) cleavage that activates the protein and contributes to virulence of the virus.
Based on the information obtained from GenBank database, the Influenza A virus segment 4 from the virus that killed a soldier in Beijing is a 1779 bp long gene which encodes hemagglutinin protein (Accession # ABQ58979). This contains a purine rich region that codes for the HA cleavage site. Duplication in this region leads to increase virulence and the ability of the virus to replicate in non target cells. Insertions of A’s and G’s in the gene sequence can lead to the insertion of basic amino acids in the protein sequence. In the 568 aa long HA protein (Accession # ABQ58979) the presence of basic amino acids such as Arginine and Lysine at the cleavage site can aid in infecting cells outside of respiratory tract. The protein sequence at the cleavage site for this virus is: QREGRRKKR/GLFG (/ represents the cleavage site).  Increased virulence due to insertion of these amino acids has been proved because of the 20 human H5N1confirmed cases in China, 13 have been fatal.
 


Copying and Pasting Without Degradation of ChromosomesCadis, Daniel
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

Most people have used the simple “Control-C” and “Control-V” copying and pasting short cuts on the computer. These controls are standard keyboard shortcuts. But what if every time you copied and pasted a document, you lost one or more words? This example is analogous to the importance of the telomere DNA in protecting chromosomes from degradation when they divide and replicate. The telomeres act as end caps on chromosomes by repeating a specific DNA sequence, basically tying up a loose end. Blackburn, Elizabeth and Szostak, Jack performed an experiment, which demonstrated that the telomere DNA sequence, when introduced to linear minichromosomes without telomeres, protected them from degradation. Greider, Carol discovered the enzyme responsible for the development of telomere DNA, naming it telomerase. For their work, the three shared the Nobel Prize in Physiology or Medicine in 2009. The implications of their research have been profound, extending to the study of aging and cancer cells. Furthermore, their work has allowed scientists to tie up the loose ends of the question of how chromosomes can be copied completely during cell division, much like a word document being copied and pasted without any degradation.
 


The Flu Shot: Should I Be Treated?Clark, Erica
Professor:
Dr. Barbara Benitez-Gucciardi

Infectious diseases and their spread have been a significant concern throughout history. Various diseases have taken a toll upon different populations. Mathematics has and continues to play a key role in modeling certain epidemic diseases and how they spread. Influenza is a common disease that has affected many human civilizations for generations. This study focuses on the transmission of this disease and the variations of how it spreads in order to predict the quantity of infected individuals and the duration of the infection. This is accomplished using an epidemic model developed by Kermack and McKendrick, known as the SIR model. Influenza is a dynamic disease primarily known for its frequent mutations and resistant strains. Due to this, how and when treatment is administered are major factors in attempting to control the spread of this infectious disease. Therefore, the model used in this study estimates the outcomes of treatment implemented in the population being modeled, such as how the treatment affects the number of infecteds. Different variations of treatment are researched, including predictions of when the optimal time is to introduce treatment, what proportion of the population should be treated to provide the optimal amount of the least number of infected individuals, and the development of resistant strains caused by the introduction of treatment.
 
 

Increased Virulence in Influenza A virus (A/HongKong/481/97(H5N1)) as a Result of Hemagglutinin MutationCook, Gary
Professor:
Dr. Brenda Whaley

In May 1997, a three-year-old boy in Hong Kong became infected with the H5N1 Avian Influenza virus, the first documented evidence of an avian virus breaking the species barrier to infect a person (Garwood).  The virus would continue to infect 18 people, leading to six deaths, and was only halted in the city by the widespread culling of its poultry.  Most patients presented with upper respiratory symptoms and pneumonia (as in a traditional case of influenza) (Taubenberger), but the lethality of this particular strain was atypical.  In the years to follow, study of other H5N1 strains that followed indicated a mutation that potentially explained its virulence.  A mutation in hemagglutinin (HA), a protein cleaved in normal influenza activation by a very specific mechanism, allowed it to be cleaved by more commonly produced proteases, such as proteases of the furin and subtilisin families (Taubenberger).  The insertion of additional basic amino acids in the HA cleavage site of the virus proved responsible for the mutation.  In studying the nucleotide sequence (GenBank Accession #: AF084279) and the protein sequence (GenBank Accession #: YP_308669.1) of the hemagglutinin from a 1997 Hong Kong H5N1 strain isolate, duplicated adenine and guanine purines led to the duplication of multiple basic arginine amino acids at the cleavage site.  Although this mutated H5N1 strain produced infection and necrosis of other organs, it failed to infect tissue outside the respiratory system in any documented human case in Hong Kong.  However, the insertion of basic amino acids, particularly the duplication of a purine-rich zone prior to the cleavage site (Perdue), suggests an explanation for the atypical and deadly nature of the 1997 Hong Kong H5N1 strain.
 


Insertion of Basic Amino Acids at Hemagglutinin Cleavage Sites Causes Increased Virulence in H5N1 in IndonesiaDao, Long
Professor:
Dr. Brenda Whaley

In Indonesia in 2005 there was an outbreak of H5N1 influenza virus which has lingered to the present.  The first confirmed case was a 38 year old male who died of related severe pneumonia compatible with the virus.  His two daughters also contracted the illness and died in a similar manner. Of the 163 confirmed cases of viral contraction, 135 have proven fatal.  Hospitalized patients have shown nonspecific symptoms in the first 48 hours of infection, but many thereafter displayed signs of severe pneumonia.  Many of the infected had come into contact with infected poultry.  The virus responsible for this is a variant of the single stranded RNA H5N1 influenza A virus. Perdue et al suggest that insertions at the purine rich region of a virus’ gene sequence for hemagglutinin results in increased virulence in influenza viruses.  In this virus, the insertions at segment 4 of the 1729 bp-long gene (accession number EF541394) have been identified.  Taubenberger suggests that the addition of basic amino acids, which insertions at a purine rich region would code for, would cause the cleavage necessary for protein activation and virulence.  An investigation of segment 4 of the 568 amino acid sequence of the hemagglutinin protein (accession number ABP51969) shows that there is indeed an addition of basic amino acids at the cleavage site (the amino acid sequence is QRESRRKKRGLFG), causing greater virulence. 
 


Michael Perdue’s article, “Virulence-associated sequence duplication at the hemagglutinin cleavage site of avian influenza viruses,” Virus Res.

Jeffery Taubenberger’s article, “Influenza virus cleavage into HA1, HA2: no laughing matter,” PNAS
 


RNA interference of the SGN-1 gene in C. elegansDao, Long; Ollre, Kimberley; Tejani, Faheen
Professor:
Dr. Rachel Hopp

The nematode Caenorhabditis elegans expresses the gene SGN-1, sarcoglycan.  SGN-1 has a single human homolog, ASCL-3, Achaete Scute Complex, which is a transcriptional repressor, inhibiting myogenesis.  Defects in the human gene have been found to be associated to autosomal recessive muscular dystrophy.  The expression of SGN-1 is essential in the negative control of locomotion.  A common method to observe the function of a specific gene is to use RNAi: the introduction of dsRNA which causes the deactivation of a specific gene through degradation of mRNA.  RNAi regulated knockdown of SGN-1 has been previously shown to cause phenotypes which include irregular head vibrations, abnormal head movements and hyperactivity.  A non-burrowing N2 C. elegans strain was used for this experiment.  Wormbase and OMIM were used to identify the specific gene sequence of SGN-1.  Primers were designed in silico using the E-RNAi web application.  PCR was used to amplify fragments of SGN-1 gene from an N2 worm DNA lysate.  PCR products were cloned into the pPR244(pDONRdT7), an established RNAi feeding vector.  The cloned vector was transformed into a DH5alpha strain of E. Coli, which is easily transformed, but contains RNAse 3, which degrades RNA.  HT115, conversely, is difficult to transform, but lacks RNAse 3.  The double stranded RNA constructs of the SGN-1 gene were transformed into an HT115 (DE3) E. Coli feeding strain and introduced to the nematodes.  Preliminary results suggest that after 48 hours, a small number of the observed nematodes exhibited a diminished level of locomotion.  Further experiments will be performed to confirm results.  Results will be reported at the symposium.
 


Mother of VinegarEscobar, Junior; Flores, Dulce
Professor:
Dr. Jackie Horn

Cellulose is an abundant polysaccharide that can be made by plants or in a more pure way by the assistance of bacteria. The characteristics of mother of vinegar were manipulated and expressed by altering the recipes, inoculating biochemical test, and testing the sensitivity of food pathogens.  After growing the mother of vinegar for five weeks in the seven glass jars, the substance from the bottom and the top of the jars were inoculated on a YGC medium.  All of the jars showed growth of Acetobacter bacteria, which were then tested in different biochemical tests as a biofilm, only BAP, EMP, and MRVP showed positive results, the other chemical tests showed a negative result.  Three food pathogens were inoculated into three different mediums, that were then tested for sensitivity to the biofilm.   In the nutrient agar, Bacillus subtilis and Salmonella showed greater sensitivity to the biofilm, but not on the other mediums. In vinegar, the Acetobacter species makes a biofilm composed of cellulose, this cellulose inhibits the growth of food pathogens. 
 


Acoustic Effects On Alpha Brain Waves: Differences in Electroencephalogram Recordings Between GendersBerrones, Lilly; Flores, Dulce; Floyd, Scott; Walne, Jennifer
Professor:
Dr. Rachel Hopp

The purpose of the experiment was to analyze the effect of various sounds and gender on alpha waves (brain activity). Participants were selected from the General Physiology class for the experiment and were briefed before being exposed to a variety of sounds (such as music and nature sounds). The independent variable was gender and the dependant variable in this experiment was different types of sounds. An electroencephalograph (EEG) furnished with BIOPAC software was used to analyze brain activity. It was hypothesized that calming sounds would result in increase alpha waves amplitude in both genders. The results did not support the hypothesis. Even though there was significant difference for one nature sound, the other nature sounds did not have a significant increase in the amplitude of alpha waves.
 


H5N1 Avian Flu in IndoesiaFolami, Woleola
Professor:
Dr. Brenda Whaley

On February 10th 2006, a 4 year old boy from Semerang, Central Java developed symptoms of the H5N1 avian flu virus. The little boy died on February 28th 2006. Investigation conducted by health and agricultural authorities discovered that chickens had died in the child’s neighborhood prior to him developing the symptoms. The virus that caused the boy’s disease is the influenza A virus, which was obtained from a throat swab of the patient. The HA gene sequence from this virus is 1659bp long and is assigned the accession number CY014204.
Nucleotide duplications in the purine rich region of the HA cleavage site in the HA gene can lead to insertions of nucleotides in that region. The duplications of As and Gs in the region of the gene sequence that codes for the HA cleavage site will lead to the insertion of arginines and lysines in the protein sequence at the cleavage site, since the codons for lysine are AAA and AAG and the codons of arginine are AGA and AGG. This will allow the HA protein to be more easily cleaved in host cells and allow the virus to replicate and spread throughout the body, causing infections in other organs rather than the virus being restricted to just the respiratory tract.
The boy’s protein sequence shows the presence of arginines and lysines at the cleavage site. This will suggest that the HA protein would have been easily cleaved and spread the virus outside the respiratory tract.
According to the NCBI website, the HA protein sequence from the virus isolated from this patient is 552 aa long with accession number ABI36048.
 


Taubenberger, Jeffery K. "Influenza virus hemagglutinin cleavage into HA1, HA2: No laughing matter."
 


Advancement in Medicine: Transplantation for TreatmentFonseca, Sharon
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

Transplantation of organs and tissues has revolutionized the field of medicine and science. American physicians Joseph E. Murray and E. Donnall Thomas won the 1990 Nobel Prize in Physiology or Medicine for being the key figures instrumental in making discoveries that made previously untreatable diseases now curable. Since the early 1900s, scientists, namely Alexis Carrel and Sir Peter Medawar, had believed that some "biological force" prevented successful transplantation of organs between individuals. Using prior knowledge gained during his army service years treating burnt patients with skin grafts and his research with kidney transplantation, Joseph E. Murray emerged as a pioneer with a fresh perspective that total body irradiation diminished the risk of rejection of the transplanted organ. Furthermore, thanks to his years of hands on clinical research with bone marrow transplants and cancer of the blood, Murray’s co-laureate, E. Donnall Thomas, was successful in diminishing the severe “graft-versus-host" reaction and developing bone marrow transplantation to treat leukemia. Additionally, Thomas remains an ardent supporter of stem cell research, viewing it as a way to treat diseases. Thus the pioneering contributions these two Nobel Prize laureates made to the field of medicine have been greatly significant in curing a number of people when other forms of treatment proved unsuccessful.


 
The Discovery of Gene Silencing by RNA InterferenceFouad, Marie
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

In 2006 The Nobel Prize for Physiology or Medicine went to Andrew Z. Fire and Craig C. Mello, scientists from the United States, for their discovery of ribonucleic acid (RNA) interference. Fire and Mello published their findings in the February 19, 1998 edition of the journal Nature. They had discovered that double-stranded RNA could inhibit the expression of genes, and therefore the production of specific proteins. They carried out their experiments by injecting messenger RNAs that code for specific proteins into the worm Caenorhabditis elegans and observing the effects.  Their discovery explained strange results observed by other scientists, particularly plant biologists, but the mechanism is also found to be present in animals, including humans. The mechanism of RNA interference is very important in protecting against viral infections and transposons. RNA interference has applications in scientific research, but its presence in humans gives it clinical implications in addition to these laboratory applications. Experiments are already being planned out to investigate how RNA interference can fit into the medical field. In fact some experiments on human cells and experimental animals are already under way. The discovery of RNA interference is Nobel Prize worthy because of its scientific research uses and its medicinal potential.
 


The Influence of HA Cleavage on Avian Influenza A VirulenceHadimohd, Anisha
Professor:
Dr. Brenda Whaley

On May 2, 2006 a 37 year old fruit street vendor was hospitalized for flu like symptoms in the village of Kubu Simbelang, Indonesia. In the following two weeks, six members of her extended family from four separate households were infected with the H5N1 avian influenza virus. Of these seven cases, six were fatal. This is the largest cluster of closely related cases of the avian influenza virus that has been reported in any country. The source of exposure for the initial case was the patient’s interaction with infected poultry feces but the spread of the infection to her family members however, is unknown. There is also no evidence of this infection spreading beyond the extended family cluster, possibly concluding that person to person transmission was inefficient and unsustainable.  The specific viral strain analyzed was isolated from a nasal swab of the 29 year old sister of the initial case. The gene segment, Influenza A virus (A/Indonesia/CDC595/2006(H5N1)) segment 4, is 1707 base pairs long. The protein associated with this gene segment is hemagglutinin, accession number ABI36155, and is 568 amino acids long. This virus, replicates in a defined subset of cells in the body: the lower and upper respiratory tract epithelial cells. For the virus to infect the host, hemagglutination must be cleaved by cellular proteases. In normal strains that infect humans, the cleavage site is an arginine between HA1 and HA2. However, some strains of avian influenza have an insertion mutation at the HA cleavage site, allowing the virus to become highly virulent, replicating throughout the entire body of birds. The human strain that is being analyzed have both arginine and lysine insertions immediately before the HA cleavage site which may contribute to the increased virulence of this particular virus strain.
 


Change of Science: String GalvanometerHassan, Nida
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

Development of technology used on the heart has made a positive impact in society. In 1903, Willem Einthoven discovered this powerful tool that changed the way science saw the functions of the heart. This study includes the way the string galvanometer shaped his life as well as influenced science in the future. Einthoven was successful in making a series of prototypes of a string galvanometer, which has been improved into what we know as an electrocardiogram. The electrocardiogram is a useful piece of equipment that helps interpret the activity of the heart recorded by skin electrodes. This standard galvanometer needed water-cooling and five people to operate, as these were some disadvantages. Advantages include the sensitivity of the string galvanometer because it allowed electric activity of the heart without causing damage to flesh and bones. Not only was Einthoven famous for this discovery, he also coined terms used to describe an EKG. The widely used term “Einthoven’s triangle” as well as letters used in describing this machine had originated by this Nobel Prize winner who won in Physiology or Medicine in 1924. Even though Einthoven had made a huge impact in the world, he continued to shine by using the EKG for cardiovascular disorders. Later in his life, he started to study specific heart sounds as different sounds gave clues for different disorders. These achievements gave a push in the right direction as new and improved versions of his discoveries are used in today’s world.
 


Microbial Champions of the SeaHassan, Nida; Ambrosy, Jay; Fields, Aisha
Professor:
Dr. Jackie Horn

Galveston Bay has been affected by contamination of the water in a negative manner. Typical contaminants, such as motor oil, fertilizer, and pesticides, pollute the saltwater bodies that affect marine life, beach goers, and fishermen. These affect ocean’s marine life and indirectly, it has affected humans. In this study, testing aerobes, anaerobes, and fungi will take place to see which one can clean the contaminants fastest and most efficiently in saltwater solution. After weeks of problem solving, research, and experimenting, an experiment has been developed to tackle the challenge of bioremediating the common contaminants mentioned. By using three different types of contaminants in separate test tubes as a nutrient broth in which the microbial organism (aerobic bacteria, anaerobic bacteria, and eukaryotic fungi) over a period of 3 weeks, it was possible to track the decreased volume of the broth and equate it to the amount of consumption of the microbe. It was concluded that the anaerobic bacteria had a significantly greater change than the other two types of microbes. Fungi most effectively decreased the contaminants. Other properties like the pH value and the physical appearance played an important role in determining the change. These tests were successful but more tests should occur to confirm results. Future experiments could consist of testing different types of fungi and prolonging the experiment to see more change.
 

 
Discovering Slime in the Ice MachineHolmes, Joseph; George, Amy
Professor:
Dr. Jackie Horn

Biofilms are a conglomerate of microorganisms (bacteria, archaea, protazoa, fungi and/or algae) that are stuck together or embedded in a self-produced matrix of polymeric compounds. Under the protective matrix, complex community interactions take place in which the cells interact via quorum sensing for the preservation and growth of the biofilm. The polymeric matrix of biofilms makes cleaning and sanitation of such equipment difficult, and as a result pathogenic microorganisms and other contaminants can be dispersed throughout a community.
The purpose of this experiment is to take samples of biofilms from the industrial ice machines and other industrial equipment used at HBU, to test for pathogenic and other harmful bacterium.
There are biofilms present in the ice machines both at HBU and at the different sources, and as a result of their presence the ice will be contaminated. However, with the knowledge of the biofilm’s composition we can employ a number of sanitation procedures to reduce biofilm growth and reduce the number of contaminants present in the ice.
In our experiments, we have seen biofilm growth, and we are currently attempting to see how different environmental factors affect growth.  We are also concerned by the diseases that can be caused by the bacteria in the biofilms, so we are attempting to manipulate the environmental factors to reduce the numbers of disease causing bacteria.
 
 

Influenza virus hemagglutinin cleavage of Human geneIyoob, Saba Arif
Professor:
Dr. Brenda Whaley

A nine year old boy, from South Jakarta suffered with H5N1 infection in September of 2006. At first he developed fever and a running nose on the 13th of September. After seven days, he was hospitalized and died on the 22nd. His history exhibited that the boy had contact with sick chickens which were kept as pets. The specimen was isolated from the boy and the virus was isolated. According to all the research hemagglutinin cleavage activates the protein and contributes to the virulence of the virus. From the GenBank database, Influenza A virus segment 4 (CYO17662) is 1779 base pair long gene which encodes for HA protein (ABL31744), and is 568 amino acids long. H5N1 is a subtype of Influenza A virus, which links to orthomyxoviridae viruses family. These viruses are ssRNA negative strand. In our research it was observed that the gene sequence which codes for the cleavage site for HA protein was a purine rich region. Duplication in a purine rich region increases the virulence of the virus. The insertion mutation of A’s and G’s at the cleavage site of HA, allows the virus to replicate throughout the bird’s body. The insertion responsible increases the number of basic amino acids (Arg-lys) at the HA cleavage site of the protein. The nucleotide sequence in our research that coded for the amino acids around the HA cleavage site consisted of guanine and adenine.Except amino acids leucine (l) and phenylalanine (f) codes as cytosine and thymine. Hence, in the nucleotide duplications in a “purine rich” region of the nucleotide sequence might increase the number of basic amino acids in the HA cleavage site of the protein.


“Influenza virus hemagglutinin cleavage into HA1, HA2: No laughing matter” by Taubenberger from Proceedings of National Academy of Sciences of the United States of America (PNAS)


"Virulence-associated sequence duplication at the hemagglutinin cleavage site of avian influenza viruses” by Perdue from Science Direct
 


The Discovery of the Intermediate Boson Vectors of the Weak Nuclear ForceLao, Patrick
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

In 1984, the Nobel Committee awarded its prize in Physics to Carlo Rubbia and Simon van der Meer for their substantial work in discovering the W and Z bosons as the communicative particles of the weak nuclear force. The unification of the electromagnetic force and the weak nuclear force into the electroweak force predicts the presence of the bosons as the necessary components of beta decay. However, scientists did not have the technological capabilities to experimentally observe these particles until Rubbia and van der Meer applied their extensive knowledge of particle physics to the task. Both Rubbia and van der Meer worked for CERN, the European organization for nuclear research, in Geneva, Switzerland where the most powerful Synchrocyclotron was available. Along with CERN’s top-notch technology, Rubbia’s ideas and van der Meer’s method of stochastic cooling lead to the first experimental observation of the super massive bosons. Since the bosons were found to be super massive (about 100 times the mass of a proton), it precluded their effect as short range force communicators. Therefore, the weak nuclear force operates under the scale of quarks and leptons, which are the elementary particles from which all matter is composed. Thus, beta decay occurs through the interaction of bosons. Van der Meer based his work off of Rubbia’s suggestion that a high energy accelerator can be used as a colliding beam device where a beam of protons and antiprotons are counter-rotating and colliding head-on. This process was to be repeated with new beams during months of operation. Thus, the W and Z bosons were successfully observed thanks to the ingenuity of Carlo Rubbia, the technological genius of Simon van der Meer, and the work of hundreds of other scientists.
 


Effects of Gender and Athletic Condition on Electrocardiogram Patterns and Blood Pressure MeasurementsMarachlian, Adriana; Gastineau, Tracy; Jones, William; Flores, Tyler; Luna, Paloma; Sparkman-Royo, Alex
Professor:
Dr. Rachel Hopp

An Electrocardiogram, or ECG, is a graphic measurement of the electrical activity of the heart through the analysis of recorded waves corresponding to atrial and ventricular depolarization and repolarization cycles. (BIOPAC, 2004) This method of heart analysis was performed in this experiment in order to compare differences in heart activity between males and females (MF subgroup) as well as athletes and non-athletes (AN subgroup).  The subjects were asked to execute a variety of tasks including deep breathing, light exercise, and the VALSALVA maneuver (blowing up a balloon) to record variations in their heart activity. Immediately following the required tasks, the subjects were connected to the electrocardiograph apparatus using electrodes and leads. The waves that were shown on the ECG were then used to analyze and compare the heart activity of the groups of subjects. Also, blood pressure was taken before and after exercise and before and after the VALSALVA maneuver to assess variations. 
 


Biofilm Growth Inhibition of Houston Baptist University Water Sources by Synthetic and Natural MeansMarachlian, Adriana; Luna, Paloma; Sparkman-Royo, Alex
Professor:
Dr. Jackie Horn

Biofilms occur when microorganisms irreversibly adhere to surfaces producing extracellular secretions that facilitate adhesion and provide a structural matrix. While the biofilm can be beneficial to the organisms that form it and, in some cases, to the surrounding environment, it can also be detrimental due of the inability to eliminate it. For this experiment synthetic means, ethylenediaminetetraacetic acid (EDTA) and N-acetyl-L-cysteine (NAC), as well as natural means, eucalyptus and peppermint oil, were used to inhibit biofilm formation. Both EDTA and NAC acted as chelating agents, which destabilized the negatively charged extracellular polysaccharides secreted by the bacteria, consequently reducing biofilm formation and stability. The natural oils worked by affecting biofilm formation on planktonic growth due to their hydrophobic nature, which interfered with the lipid bilayer of the cytoplasmic membranes. The effects of the inhibitory agents were observed in Winogradsky columns simulating the environments of three water sources found at Houston Baptist University: Hodo Residence College Lake, Friendship Pond, and Puddle. The experiment was conducted over the course of six weeks in which the mock ecosystems were subjected to regular dosages of the inhibiting agents for five weeks and no dosages for the last weeks. After performing the experiment, it was determined that peppermint oil and EDTA produced the best inhibitory response; this was followed by eucalyptus oil and NAC in that order of effectiveness. However, both EDTA and NAC had adverse side effects.
 


Integrated Circuit to an Integrated GlobeMendoza, Carlos
Professor:
Dr. Jackie Horn, Dr. Taiya Fabre, Dr. James Claycomb

By the integrated circuit, credited to Jack Kilby, the world at large has contracted to an integrated Globe known as the global village. The integrated circuit united separate components into a single, more efficient device. Through the discoveries of both Zhores Alferov and Herbert Kroemer, the incorporation of separate transistors was possible through the use of heterostructures. Separate functions are now united in a single structure. The accumulating effects resulted in an accelerating advancement in technology through the use of micro-chips which are applied to numerous modern, affordable appliances in communication. Global interconnection is made possible through the integrated circuit on which all high speed devices rely. With less detachment between societies and cultures, the effects upon the groups and its structures are now becoming relevant.
 


Gene Silencing Through RNAiMiron, Maria; Do, Kim; Bills, Brittney
Professor:
Dr. Rachel Hopp

RNA interference, otherwise known as RNAi, was first discovered in C. elegans, a microscopic worm commonly used to study cellular processes. When researchers injected dsRNA into the gonads of these worms and they noticed a gene-silencing effect. In order to examine this effect and capacities of RNAi, we introduced C. elegans, through the feeding method, with an RNAi knockdown of MRCK-1, myotonic dystrophy kinase-related Cdc42 binding kinase. This  gene is responsible for locomotion, the regulation of the growth rate, and body morphogenesis. Turning off this gene is shown to produce variant phenotypes of locomotion, slow growth, and organism morphology. PCR of the N2 worm DNA was done in order to amplify part of the MRCK-1 gene and gel electrophoresis was done to confirm the size of the PCR product. The PCR product was ligated to pPR244 RNAi feeding vector. Next we transformed the ligated vector into E. coli DH5alpha bacteria. Colonies were checked for gene presence by PCR and gel electrophoresis. A plasmid miniprep was utilized to extract and purify the DNA from DH5alpha in order to transform the vector into RNAi feeding E. coli strain HT115 bacteria. We spread bacteria over RNAi feeding plate and chunked N2 worms onto the plate. Phenotypes were observed, results will be presented.
 


The Function and Amplification of the FKH-6 Gene, Ngo, Lynn; Hang, Kimberly
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.
 


Insertion Mutation in Jiangsu H5N1 Hemagglutinin Gene Cleavage Site Increases VirulenceNguyen, Lily
Professor:
Dr. Brenda Whaley

The H5N1 avian influenza virus has come to the forefront of global concern in recent years. On November 24, 2007, a 24-year-old male from the Jiangsu Province of China exhibited symptoms of the virus and died in the hospital nine days later. The man had no evidence of being exposed to sick birds prior to becoming ill. On December 3 of 2007, one day after his death, the 52-year-old father of the young man was hospitalized for also developing symptoms of the H5N1 avian influenza virus. A vital surface glycoprotein, hemagglutinin (HA), is coded, translated as a single protein, and eventually cleaved  by an endoprotease at a site coded by a basic amino acid (usually arginine) in order to render mature forms of the protein subunits. These subunits allow for fusion and ultimately, virulence. However, it has been found that some avian influenza virus strains have an insertion mutation at the HA cleavage site comprised of additional basic amino acids. This consequently allows the HA to be cleaved by many other proteases other than the original specific endoprotease and thus cause the emergence of extremely virulent strains of avian influenza virus (Taubenberger).
Specifically, the influenza A virus HA gene isolated from Jiangsu province (China) in 2007 (accession: EU434686) is is 1704 base pairs long and codes for the 567 amino acids long hemagglutinin influenza A virus found in Jiangsu (accession: ABC8757).  The amino acid sequence of this specific avian influenza virus' HA gene had been found to have duplications of adenines an guanines at the cleavage site. This ultimately allowed for more arginines and lysines to be inserted at the cleavage site and allowed increased cleaving. Virulence would then be heightened due to a higher occurrence of fusion and would therefore increase the virus' ability to kill its hosts.
 


Electromagnetic Fields, Created by AC Current, on Bacterial GrowthPatel, Sarin; Slepicka, Bryan
Professor:
Dr. Jackie Horn

Some research has shown that electromagnetic fields cause abnormal growth and behavior amongst microorganisms. However, various studies have shown a large range of biological effects on bacteria, many of which are inconclusive. To study the effects of electromagnetic fields, various variables will be observed and measured under well defined conditions. The experimental models will be based on two different species of bacteria (Proteus mirabilis and Staphylococcus epidermidis); the first of which is gram negative and the other gram positive. The following variables will be applied to these microorganisms: Time (min), Frequency (Hz), and Wave forms.  Each microbe will be subjected to varying lengths of exposure in increments of 10, 20, and 30minutes. Electromagnetic field frequencies will be alternated between 13, 60, and 103 Hz. Also, wave forms will be modified as square and oscillating.  Application of these variables, suggest no alterations in cellular growth in Staphylococcus epidermidis when compared to the control. Additionally, experimental tests on Proteus mirabilis were inconclusive due to contamination, dilution errors, and swarming effects commonly seen with this bacterium.  Although the data for Staphylococcus epidermidis does not indicate a distinction in growth characteristics between the control and experimental plates, more studies with electromagnetic fields must be considered. Additionally, due to the differences in the cellular biology between prokaryotic cells and Eukaryotic cells, it is likely that electromagnetic fields may have a more pronounced effect on complex cells such as yeast and mammalian cells.
 


Increased virulence of the H5N1 virus due to nucleotide duplications near the HA cleavage siteSaquin, Claire
Professor:
Dr. Brenda Whaley

Increased H5N1 virulence from nucleotide duplications near the HA cleavage site
Influenza A virus subtype H5N1, also known as "bird flu", is a member of the Influenzavirus A genus in the Orthomyxoviridae viral family. The virus is known to cause illness in birds and other animal species, including humans. It has killed tens of thousands of birds and since 2003 has infected approximately 490 people and has killed about 290. The H5N1 viral gene sample AY555150 was isolated from a human in Thailand during an avian influenza outbreak which resulted in 17 confirmed cases with 12 deaths.
AY555150 is the hemagglutinin gene. It is a 1736 bp long linear RNA that codes for hemagglutinin, a 571 aa protein with accession number AY555150.2. A hemagglutinin cleavage site in the H5N1 virus has been found to contribute to the virulence of the virus in. Nucleotide duplications in a “purine-rich” region of the nucleotide sequence can cause insertion of arginines and lysines into the protein sequence and contribute to the ability of H5N1 viruses to infect cells outside of the respiratory tract. In the sample AY555150 there is indeed nucleotide duplications in the region just prior to the HA cleavage site. In the protein analyzed, the amino acids “agagga” are found at the HA cleavage site.  This mutation may account for the high mortality rate of those infected by the virus, particularly in the Thailand area where the sample was collected.
 


Pathogenicity of H5N1 influenza virus is linked to sequence of the hemagglutinin cleavage siteSlepicka, Bryan
Professor:
Dr. Brenda Whaley

In October of 2005, the Ministry of Health in Thailand confirmed a case of human infection with H5N1 avian influenza. The patient was a 48-year old male from Kanchanaburi Province. The patient developed symptoms on the 13th of October and later died on the 19th of October. Health Authorities were able to link the infection of this patient to close contact with diseased poultry. Thailand has had 25 confirmed cases of avian influenza, of which 17 have been fatal. Furthermore, the cleavage site of the hemagglutinin (HA) glycoprotein present in the gene sequence of the H5N1 influenza A virus (A/Thailand/676/2005(H5N1)) was found to be purine-rich (accession # DQ360835). Thus, these purine-rich sequences result in the insertion of basic amino acids, such as arginine and lysine, at the HA cleavage site of the protein (accession # ABC72655). The cleavage site for this protein contains the sequence KRRKKR↓G which has been associated with increased viral virulence. As in many viruses, the surface glycoprotein must be cleaved by cellular proteases in order to be activated and hence for viral infectivity to occur. The insertion of basic amino acids allows for the recognition and cleavage of HA by other cellular proteases that are not limited to the epithelial cells of the respiratory tract. Consequently, the H5N1 avian influenza virus can replicate throughout the body which may contribute to its lethality.
 


Cytotoxicity of Diruthenium(II) Complex Towards MCF-7 Cell Line Using MTT Assay in vitroSylvester, Tristin; Kim, Joyce
Professor:
Dr. Robert Towery

A diruthenium complex, Ru2(OCCH3)3(Fap)Cl, possessing two molecules of diruthenium, three actetates, and the intercalating ligand Fap, 2-fluoroanilinopyridine, was chosen for its solubility and possible anti-proliferative activity. This anti-proliferative activity was investigated by determining the dimetal’s cytotoxicity towards a human breast cancer cell line Michigan Cancer Foundation - 7, known as MCF-7. In this study, the activity of the dimetal complex at various micromolar concentrations, ranging from 10μM to 50 μM, was compared to the activity of 50 μM cisplatin, a positive control, using the MTT assay which is an assay that utilizes 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The encouraging results reported warrant further evaluation of the dimetal complex in vitro as a potential anti-proliferative cancer cell therapeutic agent.
 


H5N1 Influenza A Virus in ThailandTruong,Cindy
Professor:
Dr. Brenda Whaley

A 59 year old farmer from the Nong Bua Lam Phu Province in Thailand raised several fighting cocks on his farm. He developed a fever on the 14th of July and was admitted to the hospital 10 days later.  On August 10, it was reported that he died of severe pneumonia. The H5N1 Influenza A Virus (A/Thailand/NPLI/2006) was the virus that proved fatal to this victim.  The virus produces 11 proteins including hemagglutinin protein. The hemagglutinin gene sequence of the Thailand H5N1 Influenza A virus is 1718 bp long with the accession number of GQ466176.The protein associated with this gene sequence is 568 amino acids long and have an accession number of ACU46644. The Hemaglutinin protein is cleaved into HA1 and HA2 at the cleavage site. The amino acids inserted and surrounded by the cleavage site contribute to the virulence of the H5N1 Influenza A virus. The codons that surround the cleavage site of the (A/Thailand/NPLI/2006) Influenza A virus are AAA, AAG, AGA, and AGG. This indicates that there are duplications of A’s and G’s in this cleavage site area. The Duplications of A’s and G’s in the gene sequence at this cleavage site can cause insertion of arginines and lysines into the protein sequence at the HA cleavage site which increases the virulence of the virus. The amino acids inserted and surrounded by the cleavage site contribute to the virulence of the H5N1 Influenza A virus.
 


Vietnam H5N1Umer, Anum
Professor:
Dr. Brenda Whaley

WHO reported that 28 human cases of the H5N1 influenza virus were detected and 20 of these were fatal, including a 16 month old baby girl. H5N1 is very virulent and the only reason it did not spread so well was because a person has to be in very close contact with infected poultry to contract this virus. It is hard for the virus to jump from its animal host to infect the human, but if it did overcome this issue then it can cause a pandemic. H5N1 is a linear RNA virus that belongs to the Orthomyxoviridae family and its most natural reservoir is poultry. The Influenza virus that caused this chaos in Vietnam is specially known as A/Viet Nam/1203/2004(H5N1). It is 1707 bp long and its hemagglutinin protein with the accession number of AAW80717 is 568 amino acids longs. It is cleaved into HA1 and HA2 at the HA cleavage site. Basic Amino acids that surround or get inserted around the cleavage site have been discovered to be contributors to the virulence of the H5N1 influenza A virus. The cleavage site of the A/Vietnam/1203/2004(H5N1) virus is surrounded by a plethora of AAA, AAG, AGA, and AGG codons which implies duplications of A’s and G’s in this region. AAA and AAG code for lysine while AGA and AGG code for Arginine. These duplications cause the number of basic amino acids to increase around the cleavage site and this might be the reason behind the increased virulence.
 


Duplication of Arganine-lysine on the hemagluttinin protein favors cleavage and furthers the infectivity of Influenza A (A/HK/212/03 (H5N1) virusValverde Gabriella
Professor:
Dr. Brenda Whaley

The appearance of Influenza A virus (A/HK/212/03 (H5N1) caused great distress in Hong Kong, China, as sudden outbreaks occurred in small provinces in February 2003. Initially it was reported that members of a family that had been traveling to Fujian province had acquired the influenza A H5N1 strain. The department of Health in Hong Kong has reported that after 10 days of developing pneumonia like symptoms two members of the family, a 33 year old man his 8 year old daughter had died due to influenza A H5N1 strain. According to the World Health Organization (WHO) H5N1 is very fatal and has more than 60% mortality rate. Cleavage of the hemagglutinin (HA) is a very important step taken by the Influenza A virus (A/HK/212/03 (H5N1) to gain entry into the host cells. The highly pathogenic H5N1 strain contains nucleotide duplication in a purine-rich region found within the nucleotide sequence of the hemagglutinin (HA) gene (A/HK/212/03 (H5N1) of 1664 base pairs (accession number: AY575869), which codes for basic amino acids such as arginine-lysine in the hemagglutinin protein [Influenza A virus (A/HK/212/03 (H5N1)] of 551 aa (accession number: AAT39065). A purine- rich region in the nucleotide sequence was found in the Influenza A virus (A/HK/212/03 (H5N1) gene which produced repeated basic amino acids “RERRRKKR” within the hemagglutinin protein. This in turn triggered the cleavage of that specific HA glycoprotein into HA1 and HA2 which will initiate infection in the host cells.
 


Influenza A virus (A/Indonesia/CDC699/2006(H5N1))Varughese, Blessy
Professor:
Dr. Brenda Whaley

On July 6, 2006 a three year old girl located in the suburbs of Jakarta, Indonesia, died from the H5N1 avian influenza virus.  The girl was noted to come in contact with local chickens.  Soon after on June 23rd, she became ill.  Investigators later discovered the chickens tested positive for the H5N1 virus. The virus that caused her death is found in Influenza A virus (A/Indonesia/CDC699/2006(H5N1)).  It is a single stranded RNA negative-strand virus part of the Orthomyxoviridae family of viruses.  The gene sequence for hemagglutinin is 1707 base pairs with accession number CY014497.  The hemagglutinin protein has a length of 568 amino acids and the protein accession number is ABI36450.1. Hemagglutinin (HA) is activated by proteases.  In mammals, the tryptase Clara is a serine protease that cleaves HA in bronchial tissue, allowing for viral infection - only a localized effect.  Interestingly, nucleotide duplications in a “purine rich” region of the gene sequence of the HA cleavage site might increase the number of basic amino acids at the HA cleavage site of the protein.  This cleavage site sequence produces a virulent H5N1 avian virus strain that can be cleaved by other proteases and produce systemic infections in lung, liver, GI tract, etc.  The virus proved fatal for 57 out of 74 cases in Indonesia as of November 29, 2006, the most recent World Health Organization update of 2006.  An analysis of  ABI36450.1, shows the HA cleavage site has the sequence “…QRESRRKKR>GLFG…” (“>” shows cleavage location), containing a series of the basic amino acids arginine (R) and lysine (K).
 


UV-Vis Spectrophotometric Determination of Diruthenium Complex Properties with Nucleic AcidsIyoob, Saba; Brockman, Leah
Professor:
Dr. Robert B. Towery

This research project demonstrates DNA binding properties of a possible anticancer agent, dinuclear ruthenium compound Ru₂(CH₃CO₂)₃ (Fap)Cl.  This molecule contains two atoms of Ruthenium, three acetates and one 2-fluoroanilinopyridinate anion (Fap).  The UV-Visible spectra obtained from the Shimadzu 1501 Multiplex Diode Array Spectrophotometer provided evidence that Diruthenium complexes bind nucleotides containing the nitrogenous base guanine.  Previous research has shown no reaction between this dimetal complex and the nucleotides poly (A) and poly (U).  Dunbar, et al. have suggested that metal sites of a dinuclear complex are favorably poised to interact with purine bases such as guanine in an N-7, O-6 bridging ligand formation.  Diruthenium complexes can be utilized as potential antitumor agents in photochemotherapy.
 


PROPOSED RESEARCH
 

Fractal Dimension of Bacterial Chemotaxis and Eukaryotic Expansion in Nutrient-Starved Agar Ali, Noman; Do, Linh; Holmes, Joseph; Medi, Sai; Patel, Sarin
Professor:
Dr. Gardo Blado and Dr. James Claycomb

Fractalization is a geometric concept observed in an object that exhibits self-similarity over an extended finite scale range.  Examples of such objects include snowflakes, trees, broccoli, mountain ranges, and systems of blood vessels. To illustrate fractalization, physicists created a variety of softwares that utilize mathematical algorithms such as the box counting method to describe the nature of fractals in objects. In our research, we want to study the fractals of bacterial chemotaxis. By using chemical gradients, bacteria and other microorganism’s growth patterns, in certain media, resemble the fractals of branching of tree limbs and blood vessels. We plan to alter external parameters such as pH, nutrients, and temperature to determine changes in fractal dimension and see if it can shed light on chemotaxis. One way to measure those changes is by using a program called FracLac. This program calculates the different fractal dimensions base on bacteria’s responses to the changes in parameters by using box-counting method. By doing this, we hope to elucidate chemotaxis of bacteria. We also wish to popularize the idea of using fractal dimension as a quantitative measurement of fractalization in living systems.