Platform Presentation Abstracts –
ECSC 2021
Erum Ajmal, Chemistry, Adelphi University. 1 South Avenue, Garden City, NY, 11530
Synthesis of phenyl pyridines, pyridazines and pyrimidines to test for their inhibition on the enzyme Uridine Nucleoside Ribohydrolase (UNH)
Trichomoniasis, a common sexually transmitted disease is caused by a parasite Trichomonas vaginalis. In order for this parasitic protozoan to reproduce, it has to obtain specific nucleobases from its host. For this reason, a potential inhibition for this parasite would be the inhibition of enzymes that produce such nucleobases, such as uridine nucleoside ribohydrolase (UNH). A preliminary result had shown that a compound, 3-(3-methylpyridin-2-yl) benzonitrile, showed significant inhibition of UNH, with an IC50 value of 14 μM. Derivatives similar to this molecule were made using Suzuki cross-coupling reaction. A phenylboronic acid was reacted with an aryl bromide and palladium as catalyst to synthesize phenyl pyridines, pyridazines, pyrazines and pyrimidines. Synthetic results using Suzuki reactions and biological data of the derived compounds obtained against UNH will be discussed.
Christopher Annabi, Biology Department,
Iona College, 715 North Avenue, New Rochelle, NY 10801
BacM ISOFORMS ARE GENERATED THROUGH ALTERNATIVE START SITE SELECTION
BacM is a bactofilin expressed by Myxococcus xanthus that contributes to the bacteria’s rod-shaped morphology. BacM has been observed as a large (BacM-L) and small isoform (BacM-S) that differ at their N-termini by ~27 amino acids. Two hypotheses regarding the generation of these isoforms were considered. One hypothesis suggests BacM-L is synthesized as a precursor protein that is cleaved by a protease at the sites of cytoskeleton elongation. An alternative hypothesis suggests that BacM-L and BacM-S are generated through alternative start site selection by the ribosome. These hypotheses were tested by engineering a plasmid containing bacM with its 5′ untranslated sequence; point mutations were introduced using PCR-directed mutagenesis. Mutants were made to abolish the first start codon (M1L), abolish the putative second start codon (V24L), and introduce a frameshift between the first and second start codons (K8 frameshift). When observed by immunoblot, mutants M1L and K8 frameshift expressed only BacM-S, whereas mutant V24L expressed only BacM-L. Additional mutants were made to abolish a putative internal ribosome binding sequence using silent mutations (ΔRBS2), introduce a silent mutation to the internal start valine (V24V), mutate the valine start codon to a methionine (V24M), and mutate the valine start codon to a leucine start codon (V24L-UUG). When observed by immunoblot, mutants ΔRBS2 and V24V expressed only BacM-L, while mutants V24M and V24L-UUG expressed both isoforms. These results are consistent with the hypothesis that BacM-L and BacM-S are generated through alternative start site selection.
Kate Arildsen, Faculty Mentor: Dr. Vijaykumar Veerappan Department of Biology,
Eastern Connecticut State University, 83 Windham St, Willimantic, CT 06226
CHARACTERIZATION OF DEREGULATED ANTHOCYANIN PIGMENTATION (DAP) MUTANT IN THE MODEL LEGUME PLANT MEDICAGO TRUNCATULA
Anthocyanins and proanthocyanins (PAs) are flavonoid compounds produced in various plant organs, such as leaves, fruit, and seeds. These compounds are involved in a number of important plant physiological functions. The pigments attract pollinators and lead to seed dispersal, as well as providing UV protection and acting as a feeding deterrent from herbivores. In addition to the benefits conferred to plants, anthocyanins and PAs have agricultural and pharmaceutical applications. To discover novel genes that regulate and control anthocyanin and PA accumulation in plants, we are using a forward genetics approach in the model legume plant Medicago truncatula. A large mutant population was created by inserting the tobacco retrotransposon Tnt1 into the R108 ecotype of M. truncatula by the Noble Research Institute. By screening approximately 4,000 mutants, several mutants were identified that were defective in anthocyanin and PA pigment production. One of the mutants deregulated anthocyanin pigmentation (dap) shows increased numbers of reddish anthocyanin spots on both adaxial and abaxial sides of the leaves compared to the wild-type, indicating the misexpression of anthocyanin pigmentation. dap is a novel mutant because mutants with similar phenotypes have not been reported. I will present data on the detailed phenotypic characterization, quantification of anthocyanin pigments,Tnt1 insertion analysis and mRNA expression of selected flavonoid biosynthetic and known transcriptional factor genes.
Noah Bach, Sydney Scheck, & Jessica Wang. Psychology Department,
Ithaca College, 953 Danby Rd, Ithaca, NY, 14850
BAD EDUCATION: A CONTENT ANALYSIS OF PORTRAYALS OF TEACHERS AND SCHOOL PERSONNEL ON TEEN SHOWS, SITCOMS, AND TV DRAMAS
Media messages are powerful influences on how we perceive and interact with the world around us. Schools often serve as the backdrop for popular teen shows, sitcoms, and TV dramas - but what do children learn about teachers and schools from watching television? Qualitative studies (Dalton & Linder, 2008; Mitchell & Weber, 1995; Swetnam, 1992) of the portrayal of teachers in TV shows and films have identified common stereotypes about teachers (e.g., nerdy, funny but ineffective, popular and perfect, grumpy burnout). However, there have been few quantitative content analyses of the portrayals of teachers and other school personnel (e.g., principals, counselors, coaches). This descriptive content analysis examined portrayals in nine different programs (teen shows, sitcoms, and TV dramas) covering three decades of television. Three episodes of each program were analyzed by trained pairs of coders to assess the characters’ demographics, archetypes, relationships and interactions with students, and types of activities shown on-screen. Findings showed that teachers were seldom portrayed actually teaching content, grading, or preparing for class. Instead, they were often shown involved in their personal life and relationships, bantering with students, engaging in rivalries and conversations with other teachers, and dealing with students’ problems. Students, teachers, and principals were often engaged in unprofessional dialogues and behaviors with each other. The demographic analysis showed that the majority of teachers portrayed were white males (although principals and students reflected more diversity), and except for school administrators, other personnel (e.g., librarians, nurses, custodians) were rarely shown.
Sean P. Carrigan, Virginia E. Glazier PhD, Niagara University
REPURPOSED DRUGS WITH ANTIFUNGAL ACTIVITY AGAINST Cryptococcus neoformans HAVE ADDITIONAL EFFECTS ON CAPSULE FORMATION
The fungus Cryptococcus neoformans has the capability to be pathogenic with life threatening effects to individuals with a compromised immune system. In resource limited countries, there is a greater need for affordable yet effective drugs that treat C. neoformans infections because of the high rates of HIV/AIDS infections. Repurposing a drug that has already been approved by the FDA not only saves money as these drugs are off-patent, it also saves time trying to discover a new drug that would have to go through FDA regulations before it is safe for human use. Drugs such as thioridazine and trifluoperazine have been identified to have antifungal effects in previous studies, however their mechanisms of action are still unclear. We hypothesize that in addition to having an antifungal effect, these drugs may also influence the capsule formation of Cryptococcus neoformans as well as it’s cell wall structure. We have found that both thioridazine and trifluoperazine appear to influence capsule formation, a key component in Cryptococcus neoformans pathogenesis. Additional tests on cell wall integrity and cell wall integrity signaling pathways suggest that these drugs may impact capsule formation in a manner that is independent of the cell wall structure.
Maya Carvalho-Evans, Biology, Manhattan College
4513 Manhattan College Pkwy, The Bronx, NY 10471
REGENERATION OF CHAPARRAL SPECIES AFTER FIRES
Fires are a frequent occurrence for chaparral plants of coastal California. Historically, fires occurred before human interference, but they have become more frequent with human presence. Several chaparral species require fire for seed germination. Additionally, many chaparral species regenerate foliage from axillary and adventitious buds near ground level after fires. These two strategies allow chaparral species to be dominant in fire-dominated coastal California regions. Chaparral species are also very resistant to summer drought, making them well adapted to coastal California. The above characteristics allow chaparral species to compete effectively in coastal regions. Chaparral species have strong regeneration capacities after fires. The anatomical characteristics of adventitious buds of four chaparral species were studied. Plants of Ceanothus leucodermis and Adenostoma fasciulatum many visible adventitious buds while Quercus dumosa and manzanita (Arctostaphylos sp.) did not have visible buds near ground level on stems. Anatomically, the buds of the four species had very distinctive buds. Buds of C. leucodermis and A. fasciulatum were well developed with apical meristems with extensive vascular tissues. Buds of Q. dumosa were less developed and while buds of manzanita were deeply embedded within stems. Buds of manzanita had the least developed vascular tissues of the four species. Buds of the four species had very different characteristics. However, the buds are well suited for emergence after fires.
Olivia Daddio, Noy Kremer, and Alex Smith, Dept. of Psychology,
Ithaca College, Ithaca, NY, 14850
SNAKE HABITATS VS. GLAMOUR TIPS: A CONTENT ANALYSIS OF GENDERED MESSAGES IN CHILDREN’S ACTIVITY BOOKS
Previous studies have analyzed gender messages in children’s television programs, commercials, and literature, noting that girls and women are often underrepresented and portrayed in stereotypical ways (Berry et al., 2017; Hamilton et al., 2006; Matthes et al., 2016). However, there has been little research on gendered messages in activity books aimed at children and young teens, despite their popularity. Using the activity as the unit of analysis, a total of 843 activities were coded from five books (e.g., crosswords, word searches, sudoku, image matching, tips). Each activity was examined by a pair of trained coders analyzing target audience (boy, girl, neutral), text and visual content (e.g., activity instructions, themes, colors, animals), and characters (including their gender, race, age and body type). Findings showed that books geared towards girls were far more likely to include messages regarding physical appearance and relationships, with a lighter color scheme (especially pink). Books geared towards boys were much more likely to include content related to sports, cars, and creatures like bugs, snakes, and spiders. Content in the one gender-neutral book aligned more with that of the books geared towards boys. Additionally, the vast majority of characters portrayed in all books were white and primarily featured characters of the gender that matched the target audience.
Gaia Fakhoury, Dr. Fan Jianwei, Dr. Wacker Sarah, Ryan Torres,
Manhattan College Department of Chemistry and Biochemistry, Riverdale, New York, 10471
CHARACTERIZATION OF BACILLUS SUBTILIS BIOFILMS USING FLUORESCENCE SPECTROSCOPY
Many bacteria form complex multicellular communities known as biofilms. Biofilms are a common source of human infections and are specifically associated with chronic infections and with infections resulting from biomedical implants. Biofilm-derived infections are particularly difficult to treat since the structure of biofilms provides bacteria with resistance to diverse environmental stresses, antimicrobial agents, and host immune systems. Despite the importance and ubiquity of biofilms, most microbial investigations focus on cultures of free-living bacterial cells. Thus, the precise mechanisms that regulate biofilm assembly remain largely unknown. This research uses the bacterial model organism Bacillus subtilis to characterize the molecular basis of biofilm formation. One potential strategy for characterizing these biofilms relies on fluorescence spectroscopy of the molecules within biofilms. As bacterial biofilms are complex and dynamic ecosystems, we hypothesize that the biofilms generated by different strains of B. subtilis, or by a single strain of B. subtilis under varying media conditions, will have different fluorescence profiles due to their makeup of fluorescent molecules. To test this hypothesis we conduct fluorescence spectroscopy to measure profiles of B. subtilis biofilms and compare them with the fluorescence profiles of known biological molecules.
Khaitlyn Figueroa, Dr. Sarah Wacker, Chemistry and Biochemistry Dept.,
Manhattan College 4513 Manhattan College Pkwy 10471
THE MECHANISM OF ACTIVATION OF BIOFILM FORMATION
Bacillus subtilis is a non-virulent, soil-dwelling bacterium that can form biofilms through a symbiotic relationship with plant roots. B. subtilis biofilms grow over roots, providing a barrier to protect the plant from exogenous factors such as pathogens, as well as triggering plant defense systems. While some plant molecules, including polysaccharides, are known to stimulate formation of biofilms, the complete mechanism by which biofilms are activated is unclear. We predict that there are common chemical signals from the metabolism of plants that stimulate B. subtilis biofilm formation. We tested a variety of plant samples to see if they stimulate biofilm formation and fractionated the samples to characterize the stimulating molecules. Pyruvate is a pivotal metabolite in all living cells. B. subtilis is able to excrete pyruvate as well as to use it as the sole carbon source and one of the signaling proteins of B. subtilis biofilms can bind pyruvate. Thus, we also tested whether pyruvate is involved in biofilm formation. Our observations indicate that a variety of plant parts promote biofilm formation. This finding suggests that the symbiotic relationship between plants and B. subtilis is a result of the recognition of general molecules, such as those involved in metabolism, by B. subtilis. Our attempt to categorize the stimulatory molecules shows that large hydrophilic molecules stimulate the biofilm pathway best. Future work includes further characterization of these molecules.
Deirdre Franks Department of Biology, Manhattan College;
4513 Manhattan College Parkway Riverdale, New York 10471
BENDING STRESSES OF PRIMARY AND SECONDARY BRANCHES OF TREES
The purpose of tree branches is to produce leaves for photosynthesis. Primary tree branches attached to main stems produce secondary branches in turn to spread laterally to accept as much sunlight as possible. The overall purpose of this study was to determine if the mechanical properties of secondary branches were similar to those of primary branches. The main stress for tree branches is bending stress which results from the weight of the branch by gravity. The hypothesis of this study was that bending stresses of are similar to primary and secondary branches. Branches of twenty tree species were collected around Manhattan College campus. The lengths of primary branches varied from 0.58 to 3.4 m with a mean of 1.8 m. The lengths of secondary branches varied from 0.29 to 1.36 m with a mean of 0.80 m. For the twenty species, primary branch stress ranged from 2.2 to 7.7 with an average of 4.26 MPa. For example, for Acer saccharum, Cercis canadensis, Plantanus occidentalis, Prunus serrulata, and Quercus mongolica with primary bending stresses were 6.8, 3.1, 2.2, 3.1, and 3.7 MPa, respectively. The bending stresses of the twenty primary branches and seventy-seven secondary branches were 4.26 and 4.20 MPa, respectively. A t-test shows probability for these data were between 0.20 and 0.40 indicating that the bending stresses of primary and secondary branches were similar. Overall, these data indicate that bending stresses were similar for the trees of our study.
Letícia Guibunda, Biology Department,
Ithaca College - 953 Danby Road Ithaca, New York 14850
TARDIGRADE TOUGH TIMES: A GLOBAL COLLECTION ANALYSIS
The Tardigrade Tough (TT) global collection project began in the summer of 2020 as an option for continued student research in the midst of the pandemic. Participants were able to conduct research from various locations, allowing this project to reach a global scale. Tardigrades which are also known as water bears or moss piglets are microscopic extremotolerant organisms. Their ability to withstand diverse conditions/environments all over the world made them an ideal organism to collect and study in a remote home laboratory setting. During the summer the project began with 12 participants collecting moss and lichen samples, and as the project continued more collectors joined the effort, gathering samples from Brasil, Canada, Germany, and the United States. Over 600 samples were collected, labeled, photographed, and then stored in a cool and dry place until they could be brought back to Ithaca College for further study. 320 (51%) of these samples were rehydrated to be screened for tardigrades and other organisms. We used 18s PCR followed by Sanger Sequencing on 31 tardigrade samples and a Hypsibius exemplaris control. The sequencing results allowed for phylogenies to be constructed that revealed some unexpected results, such as various tardigrades that originated from the same sample belonging to relatively far-related species. As more samples are screened and sequenced we hope to learn more about the global distribution of tardigrade species and identify a new lab appropriate species.
Kimberly Heller, Stephanie Roberts, Dr. Bryan Wilkins PhD., Department of Biochemistry
Manhattan College, 4513 Manhattan College Parkway, Bronx, NY 10471
UNDERSTANDING INTERACTIONS BETWEEN HISTONE DNA AND RPLS IN S. CEREVISIAE
Mass spectrometry (MS) is an analytical technique that can be used for the identification of unknown proteins, based on peptide mass predications. Our lab utilizes a protein-protein crosslinking system, in vivo, that allows us to covalently trap interacting prey proteins with a selective bait target. Isolation of these bait-prey complexes are then subjected to MS analysis for identification of prey proteins that efficiently crosslink to the target. We use histone proteins as our bait because we are interested in understanding the nucleosomal interactome and identifying proteins that influence chromatin dynamics. Using the unnatural amino acid p-benzoylphenylalanine, which captures protein-protein interactions upon UV-irradiation, we encode the crosslinking probe, site-specifically into our bait. This provides high spatial resolution of identified binding partners. Interestingly, this technique identifies ribosomal proteins crosslinking to histone proteins at the nucleosomal surface. This is unusual, considering that ribosomes and chromosomes are separated by the nuclear membrane. We find convincing levels of ribosomal large proteins, RL1A, RPL3, RL5A, RL8A, RPL10, and RL15B bound to the histone H2A acidic patch. Here, we genetically tag the identified ribosomal proteins in an attempt to biochemically prove their presence in the nucleus and characterize their histone binding functionality.
Sharifa Kelly; Carl Hoegler Ph.D, Natural Sciences (Biology),
Mount Saint Mary College (330 Powell Ave, Newburgh, NY 12550)
THE EFFECTS OF ORTHO GROUND CLEAR (AMMONIUM NONOATE) AND SPECTRACIDE (DIQUAT DIBROMIDE) ON BROWN PLANARIA (GIRARDIA TIGRINA)
Little is known about the ecological toxicity of many herbicides used to control household weeds. This project focused on two such herbicides- Ortho Ground Clear (Ammonium Nonoate) [GC] and Spectracide (Diquat Dibromide) [Spect]. The purpose of the study was to determine the toxicity of these herbicides on the light escape behavior and head regeneration in brown planaria . In Phase l of the study, the lethal concentration for each herbicide was determined for whole intact flatworms. Spect (10-3) caused 100% lethality after one day (n=3). GC (10-3) and GC (10-5) did not cause death; however, escape behavior of intact worms was slower than the controls. In Phase ll, six decapitated planaria were exposed to GC or Spect to determine the effects on the progress of head regeneration. In controls (Poland spring water), regeneration of the head and eyes was complete in about 1 week. A sub-lethal dose of Spect (10-4) slowed down head regeneration, but GC concentrations of 10-4 and 2.5 X 10-4 had little effect on regeneration. There appeared to be a direct relationship between Spect concentration and prevalence of delays during the head regeneration process. In Phase III, six decapitated planaria were exposed to Spect to determine their effect on light escape behavior. In control (Poland spring water), the flatworms escape a beam of light in about 15-20 seconds. Flatworms exposed to Spect (10-4) took a significantly longer period of time (about 3 X longer) (p<0.001) than controls or those in 10-5 or 10-6 Spect.
Aimen Khurram, Miriam Duncan, Sarah Wacker PHD. Biochemistry Department
Manhattan College, 4513 Manhattan College Pkwy, Riverdale, New York, 10471
THE ROLES OF TYROSINE KINASES IN BACTERIAL BIOFILMS
Bacterial cells often organize themselves into complex multicellular communities that carry out specialized tasks. These communities, which involve the collective behavior of different cell types, are frequently referred to as biofilms. Cells in a biofilm are encapsulated in a matrix of material that holds them together. Biofilms are of immense importance to public health because of their role in certain infectious diseases and their ability to share nutrients and stay sheltered from harmful factors in the environment, such as antibiotics, and a host body's immune system. This research study will closely look at a bacteria known as Bacillus subtilis, which will be used to understand the role of tyrosine kinases in the regulation of bacterial biofilms. Prior research has concluded that the proteins EpsA and EpsB are both integral in biofilm formation as EpsA modulates EpsB while EpsB phosphorylates other proteins. These two proteins are required for robust production of EPS, a polysaccharide in the biofilm matrix. This research study will explore the roles of a second tyrosine kinase in B. subtilis, PtkA, and its cognate modulator TkmA. We hypothesize that PtkA has a role in biofilm formation, similar to the role of EpsB. We tested the role of PtkA by creating deletion and phosphomimetic mutants of PtkA and testing their biofilm phenotypes. An understanding of tyrosine kinases and the regulatory pathways that assist in biofilm formation can inform how bacteria come together to cause disease, potentially curtailing the infection cycle of various bacterial pathogens.
Ryan P. Kreiser, 2. Aidan K. Wright, under the supervision of Dr. Ryan Limbocker Department of Chemistry and Life Science,
United States Military Academy, West Point, NY 10996
QUANTIFYING THE CYTOTOXICITY OF TOXINS AND PROTEIN MISFOLDED OLIGOMERS AS A FUNCTION OF CELL MEMBRANE COMPOSITION
Alzheimer’s disease (AD), a progressive, currently incurable neurodegenerative disorder that affects nearly 50 million people around the world, is hallmarked by the aggregation of the 42-residue form of the amyloid-β protein (Aβ42). Transient oligomeric species are formed during the Aβ42 deposition process, and these aggregates are highly cytotoxic and thought to play an important role in the onset and development of AD. Previous research suggests that these oligomers cause cell death by interacting with the cellular membrane, therein disrupting membrane integrity and ion homeostasis. We therefore surmised that altering the composition of the cellular membrane would affect the extent of the interactions between protein misfolded oligomers and the cell. Through a variety of tissue culture experiments using SH-SY5Y cultured neuroblastoma cells, we altered the membrane composition of the neurons by incubating them with varying concentrations of key membrane lipid components, such as gangliosides, ceramide, sphingomyelin, docosahexaenoic acid and eicosapentaneoic acid, and measured the resilience of these altered cells to Aβ42 oligomers and melittin, the latter of which is a model of acute cellular toxicity which we chose for its similarity in mechanism to Aβ42 oligomers. We found that these membrane lipids affected the resilience of the cells to these toxins in differing ways, either by increasing, decreasing, or non-linearly changing their health as a function of lipidic enrichment. These findings demonstrate the importance of membrane composition in mediating the resistivity of cells to toxic biomolecules.
Velu Krishnan, Institute of NeuroImmuno Pharmacology and Department of Biological Sciences,
Seton Hall University (South Orange, NJ, 07079)
NETWORK META-ANALYSIS ON NICOTINE'S MODULATION ON HIV-ASSOCIATED DEMENTIA
HIV-Associated Dementia (HAD) is a significant comorbidity that many HIV-patients face. Our study utilized the Ingenuity Pathway Analysis license from QIAGEN to identify/analyze the pathways underlying nicotine’s neuroprotection on HAD pathology. The Qiagen Knowledge Base (QKB) defines HAD as “Dementia associated with acquired immunodeficiency syndrome (disorder).” Although much remains unknown about HAD pathology, previous research from the QKB shows that upregulated molecules associated with exacerbating HAD include CCL2, L-glutamic acid, GLS, POLG, and POLB. The initial findings focused on molecules associated with HAD. So the Pathway Explorer tool was used to connect nicotine with GLS, POLG, and POLB by intermediary molecules since they previously lacked direct connections to nicotine. The Molecule-Activity-Predictor (MAP) tool showed limited evidence for nicotine’s neuroprotective effects since only the GLS and L-glutamic acid pathways were downregulated. Thus, to view the network more holistically and simulate how molecules in the human body interact with each other, the 35 molecules in the pathway were all connected to each other using the Connect tool. It was then found that each of these 35 molecules (includes transcription regulators, cytokines, kinases, and other enzymes/proteins) in the pathway could be individually inhibited using the MAP tool while simultaneously activating nicotine in order to realize nicotine’s neuroprotective effects at varying degrees according to the downregulation of the 5 specific HAD pathology pathways. These findings confirm nicotine’s therapeutic properties for HAD when given alongside specific inhibitory drugs for one or many of these 35 molecules. Research partially supported by R01DA0462582.
Rachel Mojica, Department of Chemistry and Biochemistry,
Manhattan College, 4513 Manhattan College Pkwy, The Bronx, NY 10471
PURIFICATION AND CHARACTERIZATION OF THE PROTEIN KIND THAT IS INVOLVED IN BACILLUS SUBTILIS BIOFILM FORMATION
Purification and Characterization of the Protein KinD that is involved in Bacillus subtilis Biofilm Formation Rachel Mojica Other authors: Upasana Chowdhury, Juan Lara-Garcia, Sarah Wacker Department of Chemistry and Biochemistry Manhattan College Abstract. Biofilms are important structures in agriculture, bacterial infections, and environmental settings. They are communities of bacteria that grow attached to a surface and encapsulated in a self-made matrix. The bacteria Bacillus subtilis form biofilms that are regulated through a biochemical pathway that begins with four kinases: KinA, KinB, KinC, and KinD, and results in the increased transcription of two main operons: epsA-O and tapA-sipW-tasA, that produce the components of the biofilm matrix. It has been demonstrated that KinA and KinB regulate entry into sporulation while KinC and KinD contribute to biofilm formation itself. Understanding the biofilm pathway in detail could have a huge, positive impact on Agronomy. To better understand the biofilm pathway of B. subtilis, a biochemical characterization of the kinase, KinD, was conducted. KinD is an integral membrane protein with an extracellular sensor domain and an intracellular histidine kinase domain. We hypothesize that KinD is an important protein for binding small molecules and interacting with other proteins in the biofilm pathway. To purify KinD, separate His-tagged constructs of the extracellular and intracellular domains were created. After purification with Nickel resin, the protein constructs were characterized using a gel filtration column. The protein yield has been found to be low and the protein appears to have multiple oligomeric states. The purification protocols will be revised and improved to generate higher yields of KinD protein that can be used in binding studies with other biofilm proteins.
Kevin Nelson, Carlos Ventura, Edina Saljanin, Brian Stockman, Melissa VanAlstine-Parris
Department of Chemistry, Adelphi University, 1 South Ave, Garden City, NY 11530
SYNTHESIS OF PHENYL PYRAZOLES FOR THE INHIBITION OF UNH IN TRICHOMONAS VAGINALIS
Trichomoniasis, one of the most common sexually transmitted diseases in the world, is caused by the parasitic protozoan Trichomonas vaginalis. Current treatments use 5-nitroimidazoles to damage DNA residues, but due to increasing resistance over time, there has been a need to find new methods. Another potential is by inhibiting the function of the parasite’s nucleoside ribohydrolases, specifically the UNH, which is important for metabolizing uridine from host cells. Compounds from a fragment collection were tested for inhibition of UNH. Out of the many fragments, a phenyl pyrazole, 4-(1-methylpyrazol-4-yl)benzamide, was seen to have caused moderate inhibition. To increase inhibition at lower concentrations, compounds were synthesized with a change to the position and/or type of functional group on the phenyl ring of the aforementioned fragment by way of a Suzuki reaction. This reaction was done by combining
Franchesca Pepaj, Chemistry and Biochemistry Department,
anhattan College, 4513 Manhattan College Pkwy, The Bronx, NY 10471
INVESTIGATING THE DEPENDENCE OF BIOFILM PHENOTYPES ON SPECIFIC GENES
Biofilms are complex communities of microorganisms that attach to surfaces and produce an extracellular matrix that cannot be penetrated by many antibiotics. The bacterial strain Bacillus subtilis is a model organism for studying biofilm formation. Our goal is to find genetic variations in the genes responsible for biofilm formation to see whether this is the cause of the variation in phenotypes seen among various wild isolates of B.subtilis. We focused on two strains in particular, Bs12 and Bs20, because of a genetic variation found in their SinI gene. As SinI is an important biofilm formation protein, we hypothesize that these genetic variations are responsible for the altered phenotype seen in the wild isolates. First a deletion mutation of the sinI gene was generated to determine whether a biofilm can form without SinI; as expected, a SinI mutant was unable to form a biofilm. To test the genetic variations found in SinI we cloned a plasmid containing the Bs12 and Bs20 genes for SinI. This plasmid was transformed into the lab strain, 3610, to see if there is any variation among biofilm phenotypes. This project provides insight into how natural variation arises among wild isolates to create differing biofilm phenotypes.
Liam Sasser, Ryan Limbocker, Department of Chemistry and Life Science,
United States Military Academy, West Point, NY 10996
ATTENUATION OF CYTOTOXITY CAUSED BY PROTIEIN MISFOLDED OLIGOMERS USING SMALL MOLECULE COUNTERMEASURES
Alzheimer’s disease (AD) is a presently incurable neurodegenerative disorder characterized by progressive memory loss and cognitive impairment. Highly transient and heterogenous oligomeric aggregates of the 42-residue form of the amyloid-β protein (Aβ42) play a central role in the onset and progression of AD. We postulated that the cytotoxic effects of Aβ42 oligomers to neuronal cells could be mitigated using small molecule countermeasures by targeting either their rate of formation or their ability to bind cell membranes. We leveraged a variety of tissue culture measurements to test the health of SH-SY5Y neuroblastoma cells after their exposure to oligomers of Aβ42 and varying concentrations of potential small molecule countermeasures, including vitamins and natural products. We found that Vitamins A and E and epigallocatechin gallate (EGCG) alleviated the toxicity of Aβ42 oligomers to cells through unique mechanisms, where the vitamins improved cell health through the aspecific enhancement of cell viability and EGCG specifically targeted Aβ42 oligomers. Chemical kinetics measurements demonstrated that EGCG disaggregates insoluble Aβ42 species, therein reducing the concentration of toxic oligomers in solution. These findings demonstrate a paradigm to investigate potential countermeasures against oligomeric species in AD.
Brandon Thrope, Dept. of Chemistry,
Manhattan College, 4513 Manhattan College Parkway, Riverdale, NY 10471
IDENTIFICATION OF RIBOSOMAL PROTEINS INTERACTING WITH CHROMATIN IN GENETICALLY MODIFIED YEAST CELLS
Ribosomal proteins (RPs) are synthesized in the nucleolus of eukaryotic cells. Prior studies have shown that these small proteins interact with nucleosomes as a regulator of chromatin function. Utilizing a mass spectral (MS) in vivo crosslinking approach, we have identified several RPs from the large (60S) subunit, which make direct contacts with the nucleosome. The RP interactions occur at the histone H2A acidic patch, a well known docking site for numerous chromatin related proteins. Here, we aim to verify the histone-RP contacts we observed via MS using in vivo unnatural amino acid crosslinking and immunoprecipitation. Using an expanded genetic code in yeast we selectively encode a UV-inducible crosslinker, p-benzoylphenylalanine, into the histone H2A acidic patch, allowing the probe to distribute itself across the native chromatin landscape. The amino acid performs a cross-linking reaction via formation of a diradical, under UV light irradiation, forming covalently trapped protein-protein interactions. The histone has an HA-tag, a common peptide sequence used for detection, and the RPs have genetically encoded myc tags. We use immunoprecipitation to isolate the RP and then use western blotting to visualize the HA tag on the histone. We have identified several RPs that may bind to the nucleosome ,including RPL1A, RPL3, RPL8A, RPL10, and RPL15A. This research has already shown promising results that RPL3 forms a unique bond to the histone H2A acidic patch.
Will Torres and Dr. Carl Giuffre; Department of Mathematics and Computer Science
Adelphi University, Garden City, New York, 11542
A SIMPLE AGENT-BASED MODEL OF THE EUROPEAN HONEY BEE OVERWINTERING PROCESS
Temperature and environment directly impact the overwintering behavior of the European honey bee, Apis mellifera. Since A. mellifera species often live in temperate climate areas, they undergo physiological adaptive changes, forming a thermoregulating cluster around the queen bee. This cluster, known as the superorganism, changes its size based on air temperatures in the surrounding environment. The cluster moves around the frame structure, consuming stored resources, providing food and shelter for the reproductive member of the colony. We demonstrate this clustering phenomenon as a simple game, written in Python, that incorporates temperature data from the National Oceanic and Atmospheric Administration (NOAA). The game, an agent-based model, simulates the overwintering process of the A. mellifera superorganism, and the expected survivorship of a simulated honey bee cluster.
Ryan J. Torres, Chemistry & Biochemistry,
Manhattan College, 4513 Manhattan College Parkway, Riverdale, NY 10471
GENOTYPE-PHENOTYPE CHARACTERIZATION OF BIOFILMS PRODUCED BY BACILLUS SUBTILIS WILD ISOLATES
Biofilms are communities of microbes that live within a self-produced extracellular matrix and are important in various ecological and medical settings. Bacillus subtilis is a bacteria known to produce biofilms that protect some plants from pathogens. All strains of B. subtilis, however, are not equally able to protect plants or form biofilms. This research aims to understand the genetic basis for why some strains of B. subtilis form more robust biofilms than others. We examined the differences in biofilm structure of twenty wild isolates. This was done by characterizing each of their biofilms on several types of media. In concert, genomic DNA was sequenced from all twenty wild isolates. Also, the abundance of a particular protein was analyzed by dye-staining and fluorescence spectroscopy. Our findings indicate that most wild isolates produced a more robust biofilm than our laboratory strain. The intensity of biofilm produced was found to be media dependent. When analyzing the sequences of the strain of bacteria that are B.subtilis, several coding genetic variations were found in genes affiliated with the regulation of biofilm formation as well as structural genes. These variations lead to possible sites for further testing in relation to the biofilm structure produced.
Davi Vanegas, Chemistry,
Adelphi University, 1 South Ave, Garden City, NY, 11530
SYNTHESIS OF 2-(2-METHYLPYRIDIN-3-YL)PHENOL DERIVATIVES AS URIDINE NUCLEOSIDE RIBOHYDROLASE INHIBITORS
Trichomoniasis is a sexually transmitted disease that is caused by a parasite called Trichomonas vaginalis. The parasite does not create nucleobases and will obtain them from the host to reproduce. Uridine nucleoside ribohydrolase (UNH) is one of the salvage pathway enzymes used by the parasite to obtain nitrogenous bases. There are treatments for trichomoniasis but some strains of the parasite are growing resistant and new treatments are needed. Using a different pathway, potential inhibitors can be used as treatment against the parasitic infection. 2-(2-Methylpyridin-3-yl)phenol (Figure 1) was found to inhibit UNH with an IC50 value of 1.9 µM. Using this scaffold, derivatives were made using the Suzuki reaction. Suzuki reaction is a cross-coupling reaction that combines a boronic acid and an aryl halide with a palladium catalyst, to create biaryl compounds. After the compound was made, they were tested against the parasite to obtain an IC50. The goal is to create a compound that can inhibit UNH at a sub micromolar IC50 value.
Anil Venkatesh, Department of Mathematics and Computer Science,
Adelphi University, 1 South Ave, Garden City, NY 11530
Viren Sachdev, Department of Mathematics and Computer Science,
Adelphi University, 1 South Ave, Garden City, NY 11530
INTERNAL SYMMETRIES IN MUSICAL 12-TONE ROWS
The twelve-tone technique is a method of music composition from the Serialist school of Western music. This technique ensures that all twelve notes of the Western chromatic scale are given equal precedence by establishing a fixed permutation or “row” of notes that determines the structure of the composition. This technique has helped Serialist composers to produce novel atonal pieces and has also generated interest among mathematicians for the rigid and repetitive structures it engenders. In 2003, Hunter and von Hippel used group theory to enumerate equivalence classes of 12-tone rows under a group of music-theoretic symmetries. They found that highly symmetric rows constitute just 0.13% of row classes, yet these rows arise in 10% of actual compositions. Focusing on the twelve-tone compositions of Schoenberg, Webern, and Berg, we show that well half of these compositions contain unusually high levels of symmetry. We first introduce a flexible standard for quantifying the incidence of short repetitions and symmetries in tone rows. This standard generalizes the notion of symmetry in the literature, uncovering many themes and motifs that were undetected in the analysis of Hunter and von Hippel. Using the theory of lattices and partially ordered sets, we then study the set of symmetry classes under several standard gradings. We find that the portion of highly symmetric compositions in each composer’s corpus is stable under choice of grading, and that this portion ranges from 48% (Berg) to 95% (Webern). Lastly, we use statistical methods to confirm that the Serialist composers Schoenberg, Webern, and Berg displayed a significant preference for symmetry in their work.
Sarah Weynand, Department of English, Tony Kapolka, Department of Mathematics and Computer Science,
Wilkes University, Wilkes-Barre, PA 18766
PREPARATION AND EXPLORATION OF A JESUS NOVEL DATA SET
Beginning with 75 pericopes of Jesus’ baptism narrative, we scored each based on more than twenty-five dimensions to determine both their narrative form and the function. Form dimensions measured include basic readability metrics such as grade level, word length, and passage emotion/sentiment analysis. Narrative-specific forms calculated included Haswell’s ‘tactics’ of understanding, knowing, and language and audience sense and Stanzel’s narrative hextant. A pericope’s function is assigned to one of four categories: mythologizing, traditional, demythologizing, and deconstructing. Data set prepared, machine learning techniques (decision trees, SVM, kNN, and a Naive-bayes classifier) are then used to investigate whether the narrative form follows narrative function.