College of Science and Mathematics 2021-2022 Projects

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  • 2021-2022 First-Year Scholars: Zayaan Azfar, Chemistry; Hannah Sowell, Chemistry; Alexander Cope, Chemistry

    • Microplastics are everywhere.  We find them in the ocean, in our lakes and our food. Identifying microplastics versus naturally present items in our environmental samples is the struggle.  You will be trained on the identification of microplastics.  First samples need to be oxidized to remove the organic matter. Once the organic matter is gone, the samples are filtered and microplastics in the environmental samples are identified using a microscope. Further analysis may take the form of a micro-FTIR analysis. 

      1. Effectively utilize proper laboratory techniques.
      2. Ability to separate microplastics from environmental samples.
      3. Evaluate and analyze experimental data.
      4. Reflect on undergraduate research.
      1. Review of the literature.
      2. Oxidize samples to remove organic material.
      3. Tabulate the quantity of microplastics using a microscope.
      4. Participate in research meetings.
      5. Photograph microscopy data for journal articles.
      6. Manage sample sources and data bases.
    • Dr. Marina Koether,

  • 2021-2022 First-Year Scholars: Grace Kurniawan, Biochemistry; Noam Lewit, Chemistry; Indus Wasti, Biology; Breauna Strawder, Biology; Taylor Moore, Biochemistry 

    • Coronavirus was first detected in December 2019 at Wuhan city, China and currently this virus infected 209 million and killed 4.4 million people worldwide. Some vaccines have been approved for emergency use; however, still there are no effective antiviral drugs and peptides available for treatment. While many researchers are focusing their research on small-molecule antiviral drugs, fewer studies are dedicated for antiviral peptides. Covid-19 drug design can be directed toward three major ways: i) targeting the virus, ii) targeting viral proteins, and iii) targeting the host-cell proteins. Designing drug and peptides to target the viral proteins has several benefits since they could be highly specific against the virus while maintaining minimal detrimental effects on humans. Our long-term goal is to design, synthesize and evaluate the efficacy of highly potent and selective antiviral peptides targeting the spike protein of SARS-CoV-2.

      The SARS-CoV-2 is a positive-sense single-stranded RNA (ssRNA) virus. This virus translates four structural and many non-structural proteins. One of the most important structural protein is spike (S) protein which allows the virus to be attached into the host surface by interacting with human angiotensin-converting enzyme-2 (hACE2) receptors present in the upper and lower respiratory system. Recent studies show that the SARS-CoV-2 has 10-20 times greater affinity to the hACE2 receptors, resulting in greater transmissibility.

      The S protein comprises of S1 and S2 domains. The S1 domain is responsible for binding to ACE2 receptors via its receptor-binding domain (RBD). The interaction between the receptor-binding domain (RBD) and the ACE2 receptor is the critical route of entry for the virus. Therefore, the S protein is a potential target for drug or vaccine development. Small molecules or peptides can be designed as therapeutics that will disrupt the interaction between the S protein and the ACE receptor; however, small molecules are not ideal for targeting the large protein-protein interactions (PPIs). Peptides, on the other hand, can disrupt the PPIs effectively as they possess larger surface compared to small molecules and thus specifically bind the interface binding region. 

      Our central hypothesis is that antiviral peptides which were known to inhibits SARS and other viruses can be repurposed and improved for effective covid treatment. Our group recently computationally screened antiviral peptides that were known to work against SARS-CoV-1 and other viruses, targeting the receptor-binding domain (RBD). Our results demonstrated that some peptides including S2P25, S2P26, and AVP1795 were the most promising candidates which could potentially block the entry of SARS-CoV-2. 

      Aim 1:  Based on the screening results, the inhibition efficiency of the best peptides against RBD will be performed by protein binding assay. 

      Aim 2: To elucidate the structural determinants of potency, native mass spectrometry (MS) will be employed to validate the lead peptides binding and interaction with RBD. 

      The expected outcome of this project to identify potent antiviral peptide and advance our knowledge of how these peptides can be further improved. The expected results will have a very positive impact on the public heath imposed by covid-19 pandemic.

    • This research training will help students to gain experiences on performing interdisciplinary research, collecting, and analyzing computational and experimental data, interpreting, and presenting results, presenting in conference, writing, and publishing manuscripts. These diverse research experiences in computational chemistry, peptide characterization, protein binding assay, and native MS will help students to pursue their graduate study in biomedical science or secure a position in the pharmaceutical/biochemical industry.

    • Student will do various tasks in the different phase of the projects including:

      1. reading and reviewing scientific articles
      2. performing computer aided peptide design
      3. characterizing peptides
      4. conducting protein binding assay experiment and analyzing data
      5. acquiring and interpreting mass spectrometry data
      6. drafting a poster, a presentation, and a manuscript.
    • Dr. Mohammad A. Halim, and Glen Meades, 


  • 2021-2022 First-Year Scholars: Alaina Westee, Biochemistry; Arianna Parrish, Biology

    • DNA is the genetic material responsible for life. The coordination of four base pairs that make up DNA, commonly referred to as A, T, G, and C, define how a cell survives, grows, and functions. A major mechanism in which DNA achieves this is through the production of proteins. Proteins are cellular machines that are encoded within DNA, and a stretch of DNA that produces a protein is called a gene. Notably, humans have roughly 20,000 protein-coding genes, and each human genome consists of over 3 billion base pairs. These extreme numbers underscore the importance of regulating which genes are on and which are off. Indeed, uncontrolled gene expression often leads to cellular dysfunction and disease, most notably cancer. To prevent this, organisms rely on a set of proteins called transcription factors to regulate their gene expression. These proteins bind specific DNA sequences to either promote or repress the first step in protein production.

      In our laboratory (Dr. Michael Van Dyke), we discover the preferred DNA-binding sequence and biological significance of unknown transcription factors using the model organism Thermus thermophilus. The work specific to this project will revolve around the ferric-uptake regulator (FUR) protein family. These proteins are evolutionarily conserved and regulate gene expression based on cellular levels of the essential metal, iron. Thermus thermophilus has three FUR homologs; however, these proteins are dramatically understudied. Currently, only one relevant scientific publication exists for the FUR family in Thermus thermophilus. Thus, we are uniquely poised to discover novel biochemical insights regarding the function of these unknown transcription factors. Importantly, the incoming student will learn many biochemical and bioinformatic techniques widely used throughout scientific laboratories and develop critical thinking and experimental design skills that will help them succeed in future scientific endeavors. 

    • Students will be trained and received practice in the following areas:

      1. E. coli protein expression and purification
      2. DNA-protein binding assays: electrophoresis mobility shift assay (EMSA), restriction endonuclease protection assay (REPA), bio-layer interferometry, restriction endonuclease protection selection and amplification (REPSA)
      3. Bioinformatics: DNA sequencing, DNA alignments, genome browser, motif occurrence, gene ontology
      4. DNA biology: PCR, DNA cloning
      5. RNA biology: in vitro transcription assays, quantitative PCR
    • Each week the student will learn, prepare and perform experiments under the guidance of their mentor. Before each experiment, the mentor and student will go over, in-depth, how the experiment works, the predicted outcome (hypothesis), and how this experiment will help evolve the current scientific literature. Additionally, the student will keep a detailed laboratory notebook that will be updated each day the student comes into the lab. 

    • Dr. John Barrows,


  • 2021-2022 First-Year Scholar: Andersen Kelsey, Biochemistry

    • Excess nutrients from human activities, such as fertilizer application and wastewater treatment, can enter freshwater systems and have negative impacts on both environmental and human health. The objective of this project is to collate and analyze existing nutrient data to improve utility for research on nutrient impacts on freshwater environment health in Georgia. As population growth and land use changes occur, more effective nutrient management is needed, which depends on accessible and meaningful data. Through this work, we aim to identify gaps in our knowledge of local threats to freshwater system health, evaluate ecosystem services in support of community sustainability, and inform adaptive management of our freshwater resources. In time, we hope to develop a web platform as part of increasing accessibility for these data; as such, students with a background in statistics or web development are highly encouraged to apply, but all are welcome.

    • Students will learn to:

      1. find and read scientific literature
      2. access, download, and organize information from large water quality databases
      3. apply methods of temporal and spatial analysis
      4. develop scientific communication skills through discussions and presentations.

      If interested, opportunities to begin learning and using R, a free and open-source statistical analysis and data visualization software, may be available as the project progresses. Students will have the opportunity to earn co-authorship on published papers resulting from this work.

    • Students will be trained in data collection and organization, conducting scientific literature searches, and engaging with assigned readings. We will meet weekly to check in and discuss progress and/or challenges, and students will keep an informal journal to help guide self-reflection throughout the research experience. Work on this project will require access to a computer and internet connection and can be done remotely. This project will rely heavily on the use of Excel spreadsheets; Excel is available free to students through the university's Microsoft Office 365 subscription.

    • Dr. Daniel Hoffman,

  • 2021-2022 First-Year Scholar: Ruben Muniz, Physics

    • In this project, the student will first do online research about Benford's phenomenon, and then about human height growth. Any other natural processes can be chosen for research as well. Then the data will be compared to those of basic algebraic functions, and the closest one will be chosen for a further comparison. All the data related to the previously mentioned functions can be found in the article First Digit Probability and Benford's Law. As the result, a conclusion about the nature of a particular process will be made in terms of the probability of its first digits.

    • Upon completing this project, students will be able to:

      1. Use online resources for collecting data.
      2. Organize collected data using an Excel file.
      3. Perform data analysis using graphing software.
      1. The student will do online research and prepare a report to the advisor every week.
      2. The student will meet with the advisor every week to discuss what was done and future plans.
    • Dr. Irina Pashchenko,

  • 2021-2022 First-Year Scholars: Tatum Havard, Environmental Engineering; Faith Arends, Environmental Science

    • All living organisms talk by a process called cell signaling. Understanding how cells communicate is a fundamental challenge in biology, with applications in the fields of medicine, industry, and ecology. In this project, we will use predatory myxobacteria as the model system to study cell signaling and gene regulation mechanisms.

      Myxobacteria are single-celled social bacteria that are present in soil. They move in groups like wolves on the prowl and prey on other soil microbes, digesting them by secreting a cocktail of lytic enzymes. When starved, they aggregate to form fruiting bodies, where rod-shaped bacteria undergo complex remodeling to become spherical dormant spores so they can survive the harsh conditions.

      Myxobacteria influence the behavior of other organisms. For example, they secrete chemicals that attract unsuspecting prey bacteria towards them. Some soil bacteria respond to their threat by constructing a firewall that prevents myxobacteria from advancing towards them. Myxobacteria produce bioactive metabolites including antimicrobials such as myxovirescin, and epothilones: a class of microtubule-targeting agents used in the treatment of breast cancer. They exhibit a broad range of predatory activity against disease-causing bacteria and yeast such as Salmonella, Methicillin-resistant Staphylococcus aureus, and Candida albicans. Investigating how myxobacteria successfully prey on harmful pathogens could lead to novel therapies to combat infections caused by these organisms.

      In this project, we will use molecular cloning to create gene knockouts in myxobacteria to study the importance of these genes in myxobacterial signaling responses during predation and starvation.

    • The project aims to provide students with sufficient information to understand fundamental concepts in bacterial genetics and cell signaling. The program will provide hands-on experience in the investigation and manipulation of microorganisms. I will work closely with students to design and execute a project(s) that will help them develop critical thinking, increase their understanding of science and the scientific process, and push them towards becoming independent thinkers. At the end of this project, students should be able to:

      1. Understand their research project through literature review.
      2. Design experiments and analyze data using scientific methods.
      3. Maintain proper documentation of experimental techniques, observations, and data.
      4. Demonstrate understanding of the research project through written and/or oral presentations.
      1. Students will plan, execute, and analyze experiments for their assigned project.
      2. Students will document their experimental procedures, observations, and results in the provided laboratory notebooks and the laboratory computer.
      3. They will present their data in lab meetings and in an internal or external symposium as opportunity arises.
      4. Play an active role in lab maintenance of the Rajagopalan research lab.
    • Dr. Ramya Rajagopalan,

  • 2021-2022 First-Year Scholar: Temidayo Solaru, Biology

    • The process of muscle formation requires the careful coordinated expression of a number of genes both unknown and unknown during embryonic development. We use the fruit fly, Drosophila melanogaster, as a model organism to study the formation and patterning of muscle in the developing embryo.   Key to this process is akirin, a nuclear protein that is essential for expression of a variety of muscle patterning genes.  We have a small number (i.e., 35) known or predicted gene loci that are likely candidate interactions with Akirin during Drosophila muscle development.  This project will involve creating novel genetic lines and collection of embryos from these genetic lines for analysis of their muscles. This project will use both classical and molecular genetic techniques to uncover new genes that interact with akirin during muscle patterning.  This project will also involve high-resolution confocal microscopy to describe the phenotypes of uncovered genes.

    • Students will use a wide variety of classical insect breeding and genetic techniques, techniques in labeling and imaging the muscles of insect embryos, and microscopic techniques for data analysis.

    • The student will be responsible for insect care and breeding maintenance, assisting with general lab duties, and planning experiments.  Weekly meetings with the PI will be essential to student success.

    • Dr. Scott Nowak,

  • 2021-2022 First-Year Scholars: Arianna Cox, Biology; Kailen Parks, Biochemistry

    • The Hudson lab at Kennesaw State University is broadly interested in: (1) understanding how cells in the body become neurons; and (2) how neurons connect to one another to make neural circuits and how those circuits control an animal's behavior. To do this, we primarily use a nematode model (Caenorhabditis elegans) help us answer these questions. Nematode worms have many advantages for studying the nervous system. First, they have an invariant cell lineage, which means that whenever a cell divides, we know exactly what its daughter cells are going to be. Second, they're see-through, which means that we can actually see neuronal cell bodies and axon bundles without having to dissect the animals. Third, we can use fluorescent reporter genes to label individual cells in the worm's brain. Finally, we can use genetics to change the underlying genes required for nervous system development and function. By creating mutations that change the fate of a neuron or the shape of an axon, we can figure out which genes are required for making the nervous system and how that affects behavior. Is this relevant to humans and human neurological disorders? Oh yes! The genes required for shaping the worm's nervous system are the same genes required to shape the human nervous system. As such, we can look at the worm version of a human disease gene and understand what the consequences are for mutating that particular gene and how it affects nervous system development and function. We have two main projects on-going in the lab. The first one is to examine a class of proteins called transcription factors to figure out how they affect whether a cell becomes a neuron or something else. Second, we are examining how sensory neural circuits connect together, and whether defects in nervous system connectivity lead to behavioral defects.

    • A first-year student joining the lab would work with a master's student and contribute to one or more of the projects described above. Having learned how to handle worms, they'd use those worm-picking skills and basic genetics to build worm strains, examining those strains using a fluorescence microscope, then imaging those strains and looking for nervous system defects. As an adjunct to this, they would learn additional transferrable skills including polymerase chain reaction assays, automated image analysis coding and strain freezing. Students will maintain a lab notebook and be trained in how to archive data on cloud-based servers and other back-up devices. They will present their data in weekly lab meetings, and also at the end of the academic year at the KSU Student Research Symposium. If schedules permit, they will also be invited to attend weekly research seminars in the College of Science and Mathematics, and monthly Worm Club (12 noon, third Monday of the month at Emory University), where they can see research presentations from other worm-based labs in the Atlanta metro area including labs at Emory University, Georgia Tech, and Georgia State. Students making exceptional progress will be encouraged to present their data at the regional Society for Developmental Biology meeting.

    • In addition to the research approach described above, a first-year student would be expected to contribute to lab maintenance by making growth media, cleaning lab glassware and maintaining instruments.

    • Dr. Martin Hudson,


  • 2021-2022 First Year Scholar: Amal Samih, Undeclared

    • Our lab studies regulation of genes and molecular mechanisms that control muscle tissue development. Recently, we have stumbled over an interesting fact that we are trying to better understand. It turns out that a well-known nuclear protein called Mef2 can completely flip sides as it transforms from an activator to a repressor. It means that the very same genes that once have been turned on by Mef2 later become turned off by Mef2. Additional experiments revealed that a certain area in the Mef2 molecule is to blame for this conversion. We have designed an experiment where this area of Mef2 will be swapped for a piece from another nuclear protein. Our hope is that the resulting chimeric protein will always act as an activator, unlike the original Mef2. We seek an enthusiastic and capable person to create such construct and test it in vivo (we work on fruit flies). The ideal candidate should have a major in Biology (or Chemistry) and the ability to spend 5-8 hr/week in the lab. Prior lab experience is not important.

    • The student will learn the following techniques:

      1. Various basic lab techniques
      2. Molecular cloning
      3. DNA isolation and purification
      4. DNA electrophoresis
      5. Restriction analysis
      6. Fly husbandry and genetics
      7. Working with binoculars and microscopes
      8. Cryosectioning
      9. Immunostaining and fluorescence imaging
      10. Beta-galactosidase assay
    • Visit the lab at least 3 days a week, follow individual research plan, prepare buffers and consumables as necessary, meet weekly with the mentor.

    • Dr. Anton Bryantsev,