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Loyola University Chicago

LUROP

Center for Experiential Learning

Biology Summer Research Fellows, Summer 2013

 

Julia Coppi

Year: Senior

Major(s): Biology

Mentor: Castignetti, Domenic

Department: Biology

Project Title:  Streptococcus mutans Metabolism in Saliva

Project Abstract:  Dental caries, tooth decay, is a chronic disease affecting children and adults worldwide. Streptococcus mutans (s. mutans) is bacteria commonly found in human mouths and is largely the cause of dental caries. The high rate of acid production depends on the bacteria's metabolism. Diets high in sucrose give the bacteria more nutrients, and therefore a more acidic mouth environment. The s. mutans depend on sugar in their metabolism to grow and reproduce and can create extensive oral biofilms that house s.mutans other bacteria, and therefore more acid. Without treatment, that network of bacteria can produce acid that attacks tooth enamel. Dental care companies have used fluoride compounds in toothpastes, mouthwash, and foams to inhibit bacterial-caused decay. The fluoride molecules found in these products are traditionally either sodium fluoride (NaF) or monofluorophosphate (MFP). Each chemical works to decrease acid production of s. mutans.  

The research being done aims to grow streptococcus mutans in nutrient-rich systems with NaF or MFP and observe the growth and pH changes in the manipulated environments. Once either NaF or MFP comes in contact with the S. mutans, decreased acid production and limited biofilm formation is shown. By characterizing growth of S. mutans alone and with fluoride, we will be able to better understand the streptococcus mutans strain ATCC and how common fluoride agents can affect their debilitating nature to oral structure.

 

Melaney Dunne

Year: Junior

Major: Biology (Ecology emphasis)

Mentor: Hoellein, Timothy

Department: Biology

Project Title:  The effect of predation and competition on behavior of the invasive Asian clam, Corbicula fluminea

Project Abstract: The Asian Clam, Corbicula fluminea, is invasive in the Chicago River. Since 2012, we have studied effects of clam behavior such as nitrogen cycling, sediment carbon abundance, and interactions with a predator. Results suggest clams affect nitrogen cycling through ammonium excretion and denitrification enhancement. Clam burrowing was inhibited due to direct perturbation via a predator or changes to sediment composition. 

Follow up experiments will test 1) size dependence of clam predator choice and 2) competitive clam interactions. Crayfish predators will be exposed to a range of clam sizes, testing how predators select clam prey, and if clams reach a size refuge. Varying crayfish size will determine if size affects clam prey selection. Interactions will be recorded for 1 hour. After 24 hours, clams will be checked for burial, movement, and siphon usage. We predict burial, movement, and siphon usage to decrease as predator interactions increase. Crayfish behavior will be analyzed by intensity and duration according to methods developed in year 1 of our project. We will test effects of density on clam behavior in the stream facility. Density will vary from 2-30 per tray. Trays will be marked to track long-term movement. Siphon usage, burrowing, movement, and mortality will be recorded. We will use strong replication, statistical analyses, and design follow up experiments according to results. Data will be combined with 2012 data for publication in a peer-reviewed journal. 

 

Safiya Elahi

Year: Senior

Major: Biology

Mentor: Mierisch, Jennifer

Department: Biology

Project Title:  Cell Morphology and Its Role in Shaping the Gonad

Project Abstract: During embryonic development, cells migrate from different locations and interact with each other in order to form functional organs. To do this, cells must send out extensions along which to move. They change their usual shapes to form these protrusions, which attach to a target location and guide the cell's migration. Without these morphological changes, the cell cannot correctly move. Cell morphology is also important for the structure and function of organs. In humans, certain somatic and germ cells must find each other and interact in order to form a functional gonad. Similarly, in Drosophila melanogaster fruit flies, somatic cells and germ cells must move and interact to form a functional gonad. These cells must regulate germline development through cell-cell interactions with the developing germ cells at multiple stages in order to form a functional organ. Previous studies have identified a number of mutants that affect gonad formation through a variety of genetic screens. We are specifically interested in genes that seem to affect the ability of the somatic cells of the gonad to migrate and interact with each other and with germ cells. We will use live imaging to observe the cell morphology and interaction in fruit fly embryos and to determine the role of protrusions in gonad formation. We hope to gain insight into different types of defects and the genes from which they arise, and eventually to find how these genes may affect development in other tissues and organs.


Sana Iqbal

Year: Junior

Major: Biology

Mentor: Kelly, John

Department: Biology

Project Title:  Impacts of Wastewater Effluent on Bacterial Communities in Freshwater Ecosystems

Project Abstract: As cities in the United States grow, wastewater treatment is becoming a prominent issue. Municipal wastewater treatment plants are effective at removing pathogens from wastewater, but are not designed for the removal of pharmaceuticals and personal care products, resulting in discharge of wastewater effluent containing an ever changing mixture of biologically active compounds into river ecosystems. This widespread addition of effluent can have significant impacts on organisms in the receiving streams. This project will assess the effects of effluent on stream bacterial communities using an urbanization gradient. Bacterial communities within sediments from three streams in Baltimore that vary in the intensity of wastewater inputs will be examined via molecular methods. DNA will be extracted from the stream sediments and sent for pyrosequencing, so that the bacterial composition of these communities can be studied. Statistical tests will be applied to determine correlations between the intensity of wastewater discharge and stream bacterial community composition. DNA extracted from the sediment samples will also be studied using qPCR, a technique that amplifies a target sequence and provides quantitative data. We will use qPCR to quantify genes involved in antibiotic resistance, as an indicator of the ecological effects of effluent. In summary, this research will result in transformative concepts of riverine bacterial biodiversity and its response to anthropogenic influences.


Monica Janeczek

Year: Junior

Major: Biology

Mentor: Putonti, Catherine

Department: Biology

Project Title:  Viral Adaptation to Multiple Host Species

Project Abstract: In virology, pathogens differ in the number of host species they can infect. Specialists are specific to a single host species while generalists are able to target multiple host species. Currently, in many viral systems it is unknown which type is more advantageous for proliferation when exposed to ideal conditions. The results can help explain viral host shifting in terms of disease transmittance. This concept can also be applied to the development of vaccines: A virus is introduced to a novel host, acquires adaptations, and then is reintroduced as an attenuated virus back into the human host species. In the proposed work, one will deliberately manipulate the conditions of the viral strain, phiX174, in order to evolve both a generalist and specialist. In doing so, the genotypic and phenotypic effects will be compared. One will use DNA sequencing to analyze the mutational differences between the two viral populations, determining the specific genes and gene products that are beneficial to each condition. Likewise, progeny will be assessed by quantitatively analyzing viral plaques.


Neil Kuehnle

Year: Senior

Major: Biology (Molecular emphasis)

Mentor: Doering, Jeffrey

Department: Biology

Project Title:  Characterization of Satellite III Histone Modifications in Human Cancer Cells

Project Abstract: The Human Genome project left out the heterochromatic regions. Our lab is constructing a detailed map of the short arm of chromosome 21 (HC21p) as a model for understanding the structure and function of heterochromatic regions in general. Heterochromatic genomic regions are rich in normally unexpressed tandemly repetitive satellite sequences. Recent work has revealed that satellite expression is highly elevated in cancer cells compared to normal tissue. Satellite III (SatIII) repeats showed the greatest increase in expression, but it is not known if all SatIII subfamilies show equal changes in expression. We have designed PCR primers for four of ten SatIII regions on HC21p and optimized them for total genomic DNA so that they can be used in quantitative PCR (qPCR) assays. We performed chromatin immunoprecipitation (ChIP) using antibodies specific for various histone modifications on a line of transformed cells, HEK 293T. We have assayed ChIP samples of 293T cells using qPCR on the promoter region of GAPDH, a constitutively-active gene, as a control. We will produce primers for the additional regions and assay their histone modifications in 293T cells vs. normal samples. We hypothesize that SatIII subfamilies will display histone modifications consistent with expressional activation, and will display different levels depending on region. If different levels of activation are found, this could leads to the development of biomarkers for cancer detection and prognosis.


Chelsey Leffel

Year: Senior

Major: Biology

Mentor: Pickett, F. Bryan

Department: Biology

Project Title:  Humanizing Cardiac Troponins In Zebrafish

Project Abstract: Length Dependent Activation of cardiac myofibril contraction force and the Frank-Starling principle describe the important relationship between cardiac myofibril length and strength of contraction in the vertebrate heart, yet the actual biochemistry behind this process has yet to be completely elucidated. In our project, the zebrafish contractile proteins, the troponins, will be altered to determine if Length Dependent Activation is altered. The cardiac contractile proteins, including the troponins, appear to be involved in detecting the increased stretch of the heart muscle, that occurs from the bolus of blood returning to the heart. Single myofibrils that are stretched activate a regulatory response called Length Dependent Activation (LDA). This elicits a stronger contraction force. If LDA is changed by introducing mutant troponins, this result will provide strong supporting evidence that troponin is one site of LDA regulation, and will provide more insight into the regulation of this important aspect of heart physiology. My project in the Pickett lab will use the zebrafish as a model system to explore the role of TnnI1B with a change in the 112th amino acid in the polypeptide chain. We will attempt to partially humanize the contractile apparatus of the heart by introducing the human TnnI1B with the amino acid change protein under the regulation of a zebrafish heart specific promoter.  


Emily Lenczowski

Year: Senior

Major: Biology

Mentor: Ye, Hui

Department: Biology

Project Title:  Synaptic leakage in Alzheimer's Disease - Does the AD brain have more "brain noise"?

Project Abstract: Alzheimer's disease(AD), a neurodegenerative disorder that is characterized by loss of memory, severe motor deficits,and eventual death,is the most prevalent form of dementia. Recent studies show that nerve cells are more excitable in the AD brain and the chemical that is responsible for excitatory cell communication, glutamate,has been found accumulated in the memory center of the brain-the hippocampus.This increase in glutamate triggers vast cell death,or apoptosis, which is a major AD pathology. However, when cell communication was evaluated in the AD hippocampus it was found to be reduced. What, then,causes the accumulation of excessive glutamate in the AD brain? We hypothesize that this is largely due to glutamate leaking out of the cell which is a spontaneous event termed "brain noise." This study will test whether the excessive glutamate observed in AD could be largely due to the enhanced synchronized glutamate release. This release will be recorded using whole-cell patch clamp techniques on the CA1 pyramidal neurons in the hippocampus.We will challenge the cells with B-Amyloid, the protein whose accumulation serves as one of the hallmarks of AD.The frequency and amplitude of spontaneous releases will be analyzed in the control and challenged groups. The anticipated outcomes of this research will pin-point the cellular mechanism underlying dysfunctional cell communication in AD and identify a potential functional role of the underrepresented brain noise in the AD brain.


Christopher Lenkeit

Year: Junior

Major: Biology

Mentor: Mierisch, Jennifer

Department: Biology

Project Title:  Understanding the Relationship between Ribbon and Lola in the Developing Gonad

Project Abstract: In order to form functional tissues multiple cell types must be specified and migrate to the appropriate location to allow proper interaction. One of the best ways to study this process is by studying the formation of the gonads. In humans we see interactions between somatic and germ cells, which are required for germ cell development and fertility. In Drosophila we are able to study a similar process during gonad development. Genetic screens have identified some of the specific genes involved in gonad formation. My research will focus on the genes Lola and Ribbon, which encode BTB transcription factors. Mutations in these genes result in somatic cells that do not migrate and interact properly causing incorrect gonad formation. Due to information from other studies we will investigate if these two genes cooperate during the formation of the gonads in embryos, using genetics, cell labeling and microscopy. Another reason we are interested in these two genes in particular is because we know that BTB transcription factors interact with one another, and we would like to know if these two factors physically interact. We will do so by generating a tagged version of the Ribbon protein. If there is an interaction we will investigate what their transcriptional targets are. Our hope for this project is that we will increase our understanding of how the gonad forms, allowing us to eventually see how these genes may cooperate in other tissues during development.


Samer Martini

Year: Senior

Major: Biology

Mentor: Laten, Howard

Department: Biology

Project Title:  Is Transposon mobilization responsible for major evolutionary change? Detecting, isolating, and sequencing retrotransposons found in the DNA of Trifolium Nigrescens, an ancestor of the white clover plant.

Project Abstract: Retrotransposons are repeating DNA sequences that have the unique ability to replicate and insert themselves on the genome of their host organism. In particular, I will be testing the theory that transposon mobilization after plant interspecies hybridization is responsible for major evolutionary change by analyzing particular transposable element families that are found in T. nigrescens. T. nigrescens is a close relative and ancestor of T. repens, a plant (white clover) that has many of the same transposable elements that are found in T. nigrescens. By detecting, isolating, and sequencing these retrotransposons via a technique known as sequence specific amplification polymorphism (SSAP), one can take a closer look at the evolutionary significance of these specific elements by analyzing their insertion frequencies in T. nigrescens. Once this is done, many conclusions can be drawn. If, for example, it is discovered that the DNA sequence of a retrotransposon almost exactly matches one found in T. repens, and that this particular element is repeated much more often in T. repens DNA than in T. nigrescens, then one can conclude that transposition mobilization was indeed responsible for some of the major evolutionary change that occurred when T. repens evolved from T. nigrescens. If my project succeeds, then one would be able to use SSAP to compare transposable elements found in other plants and animal species, and be able to draw conclusions about their evolutionary histories.


Nathan Pecoraro

Year: Junior

Major: Biology

Mentor: Pickett, F. Bryan

Department: Biology

Project Title:  Analyzing the Function of Zebrafish Heart Contractile Proteins

Project Abstract: The troponins are important regulators in heart contractions and thus we can use them to our advantage. We are studying a zebrafish form of TnI called Tnni1B. This protein expresses in both developing and adult hearts, thus it provides strong evidence that the cardiac TnI are formed in this organism. I hypothesize that mutated strains will change the contraction of the heart due to the key relationship between the troponins and the heart contractions. The mutated form of the protein will consist of replacing a Threonine (T) amino acid located at position 112 along the polypeptide chain with either a Proline or Alanine. The reason behind this is because these mutations will cause an important post-translational event to fail to occur, which may subsequently prevent Tnni1B from causing a normal heartbeat. The goal behind making these transgenics with the mutated version of the protein is that I expect to see a change in the contractile force and, with the assistance of Dr. Alexey Vornikov, we can take our fish to Dr. de Tombe's experiment force measuring set up to assess the contraction force exerted by normal and mutant heart muscle. This will allow us to determine whether or not the mutation is preventing the Tnni1B from causing a normal heartbeat or not.


Sylwia Rychtarczyk

Year: Senior

Major: Biology

Mentor: Castignetti, Domenic

Department: Biology

Project Title:  Analysis of Coordinated System Response of M. loti

Project Abstract: Microbes adapted to thrive in iron deficient environments produce siderophores for iron chelation. Siderophores are small, high-affinity iron chelating agents secreted by bacteria and fungi when grown under low iron stress. Quorum sensing is a way bacteria use to control certain responses, possibly the production of siderophores and one class of quorum sensors (QS), N-acyl homoserine lactones (AHLs), have been suggested to play roles as chemical signals for intraspecies communication. AHLs act as transcription autoinducers which then activate gene expression. The goal of this study is to understand if there is a correlation between AHLs and siderophores in response to scarcity of iron in the environment. My hypothesis is that both QS and siderophores are produced in an iron starved environment by our bacterium (Mesorhizobium loti ). Using a Chrome-Azurol S (CAS) assay and o-nitrophenyl-ß-D- galactoside(ONPG) assay that tests for siderophore and QS concentration, the current results show siderophore concentration increasing steadily with time but no correlation with the production of QSs. If this study confirms that bacteria in an iron deficient environment communicate with each other via the release of QSs to produce iron-chelating siderophores, then this will allow for a possible way to control bacteria without directly killing them. By inhibiting or destroying QSs, it may be possible to prevent the emergence of virulence in a bacterium.

 

Randall Treffy

Year: Sophomore

Major: Biology (Molecular emphasis)

Mentor: Rochlin, William

Department: Biology

Project Title:  EphB/ephrin-B1 axon guidance and localization

Project Abstract: Axons in the developing nervous system follow precise and complex routes to find their targets. They respond to both repulsive and attractive cues in order to navigate to and select their targets. Ephrin-B1 is a guidance cue that works through EphB receptor tyrosine kinases, and has already been linked to innervation of the lingual epithelium in rats by Rochlin lab. The goal of my study will be to determine if ephrin-B1 plays a role in earlier axon navigation and later nervous system development by examining the response of geniculate and trigeminal ganglion (which both innervate the tongue) to ephrin-B1 ligand in vitro. I will also attempt to localize ephrin-B1 ligand in both these earlier and later stages, using antibody staining for the earlier stage and mutant beta-galactosidase mice for later stage ephrin-B1 localization. Lastly, I will examine the effects of removing ephrin-B1 from various tissues using mutant mice. This will help us to further determine the role ephrin-B1 plays in axon navigation, both earlier and later in development than our previous work.


Sandy Vien

Year: Junior

Major: Biology

Mentor: Williamson, Kim

Department: Biology

Project Title:  Assessing the role of long non-coding RNAs in malaria transmission by episomal expression of grl2 and grl3 in Plasmodium falciparum

Project Abstract:  The malarial parasite Plasmodium falciparum is responsible for the infection of over one hundred million people and for the deaths of 660,000 lives each year. Present drugs target the disease-causing asexual parasites, reducing symptoms; however, they are not effective against the malarial transmission form, the gametocyte. Little is known about the mechanism of differentiation into gametocytes. A locus on chromosome 9 holding the gene Pfgdv1 and three long non-coding RNAs (lncRNAs), grl1, grl2, and grl3 are found to be vital to gametocytogenesis although how they interact with each other has not been assessed. Grl2, downstream of Pfgdv1, is thought to enhance Pfgdv1 expression while grl1 and grl3 are antisense transcripts believed to downregulate expression of Pfgdv1 and grl 2 respectively. Addition of grl2/grl3 expression constructs in wild type (wt) and gametocyte-deficient parasites (Gdef) will help explain their roles in expression of Pfgdv1. Expression constructs will be made by PCR amplification and purification of grl2/grl3 encoding DNA from genomic DNA and their insertion into the pCBM BSD plasmid. We hypothesize that grl2/grl3 expression constructs will increase gametocytemia when paired with the wt strain. In the Gdef strain, gametocyte production will be enhanced less dramatically due to incomplete complementation. Our study of the mechanism in gametocytogenesis will illuminate how lncRNAs affect P.falciparum genes and how its genes are expressed as a whole.

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