Digital Commons Network^™

Assessment Of Virus-Induced Myocarditis In Human Heart Tissue Samples, Gabriel Galeotos

Honors Theses

The heart is a major organ whose function is to transport nutrients and waste throughout the body. This organ can become infected by pathogens, such as viruses, bacteria, or parasites. Infection of the middle heart layer, or myocardium, is often caused by a viral agent. This disease has three stages: viral infiltration, adaptive immune system activation, and finally either viral clearance or cardiac cell remodeling. During this process the immune system will begin to secrete cytokines, which are signaling molecules that alert other members of the immune pathways, and also participate in cardiac remodeling. Evaluating the correlation between the cytokine …

Studying The Behavioral Role Of The Kcnn2 Gene In Zebrafish Embryos, Gina Dragonette

Honors Theses

Introduction: Mutations in the KCNN2 gene have been linked to phenotypes of movement disorders and autism. The goal of this experiment was to use the CIUSPR-Cas9 system to create a deletion within the KCNN2 gene and to observe the effect on the expression of movement in zebra fish embryos.

Methods: Linearized Cas9 DNA and guide DNA underwent in vitm transcription (IVT) reactions to produce RNA to be injected into zebrafish embryos at the one cell stage. KCNN guide RNAs were produced for the KCNN2 and KCNN3 genes (to prevent KCNN3 protein function from compensating for loss ofKCNN2's protein function), and …

Evaluation Of The Effect Of The Humic Acid Inhibitor On Forensic Genetic Investigations Of Human Skeletal Remains, Madeline King

Honors Theses

Postmortem survival of DNA in human skeletal remains occurs due to the compact microstructure of the skeleton and its ability to provide a strong, protective physical barrier to environmental insults. On a molecular level, DNA preservation in bones/teeth involves electrostatic interactions between the negatively-charged DNA backbone and positively charged calcium residues in hydroxyapatite, the latter of which is one of the main components of bone microstructure. Despite these protections, over time endogenous DNA becomes damaged, limiting our ability to detect it and affecting its utility in making a positive identification. Hence, forensic genetic investigations of unidentified human remains (UHRs) are …

Phenotypic Analysis Of S. Aureus Strains From University Student Health Centers And Environmental Controls, Antonio Teixeira

Honors Theses

Methicillin-resistant Staphylococcus aureus (MRSA) is a group of pathogenic bacterial strains resistant to a class of antibiotics that is a major cause for concern in health care systems. There is a lack of study in whether health care centers are reservoirs for these bacteria, especially within developed countries. Five environmental swab samples were collected from five different university health care centers across the region, and 16 swab samples from a general university environment. Any isolated bacterial strains collected underwent five biochemical tests (mannitol fermentation, DNase activity, oxidase activity, catalase activity, and coagulase activity) to preliminarily identify S. aureus bacteria. 24% …

Investigating The Efficacy Of Dna Damage With Bleach In Forensic Laboratories And At Crime Scenes, Alyssa Tuccinardi

Honors Theses

Household/commercial bleach (6% NaOCl, sodium hypochlorite) degrades DNA through oxidative damage, production of chlorinated base products, and cleavage of DNA strands (breaking it into smaller and smaller fragments). The presence of these lesions significantly impacts the ability to generate a full genetic profile from an evidentiary sample. In fact, knowledge of the damaging effect of bleach on DNA is the basis for its use in forensic laboratories to clean workbenches and prevent cross-contamination of samples between cases. Additionally, bleach is used intentionally by criminals to clean up crime scenes and destroy DNA evidence. A previous study demonstrated that bleach has …

Persistent Borrelia Infection In Patients With Ongoing Symptoms Of Lyme Disease, Marianne J. Middelveen, Eva Sapi, Jennie Burke, Katherine Filush, Agustin Franco, Melissa Fesler, Raphael B. Stricker

Biology and Environmental Science Faculty Publications

Introduction: Lyme disease is a tickborne illness that generates controversy among medical providers and researchers. One of the key topics of debate is the existence of persistent infection with the Lyme spirochete, Borrelia burgdorferi, in patients who have been treated with recommended doses of antibiotics yet remain symptomatic. Persistent spirochetal infection despite antibiotic therapy has recently been demonstrated in non-human primates. We present evidence of persistent Borrelia infection despite antibiotic therapy in patients with ongoing Lyme disease symptoms. Methods: In this pilot study, culture of body fluids and tissues was performed in a randomly selected group of 12 patients with …

Antimicrobial Activity Of Bee Venom And Melittin Against Borrelia Burgdorferi, Kayla Socarras, Priyanka A. Theophilus, Jason Torres, Khusali Gupta, Eva Sapi

Biology and Environmental Science Faculty Publications

Lyme disease is a tick-borne, multi-systemic disease, caused by the bacterium Borrelia burgdorferi. Though antibiotics are used as a primary treatment, relapse often occurs after the discontinuation of antimicrobial agents. The reason for relapse remains unknown, however previous studies suggest the possible presence of antibiotic resistant Borrelia round bodies, persisters and attached biofilm forms. Thus, there is an urgent need to find antimicrobial agents suitable to eliminate all known forms of B. burgdorferi. In this study, natural antimicrobial agents such as Apis mellifera venom and a known component, melittin, were tested using SYBR Green I/PI, direct cell counting, biofilm …

Fishing As Therapy: Impacts On Job Satisfaction And Implications For Fishery Management, Tarsila Seara, Richard Pollnac, John J. Poggie, Carlos Garcia-Quejano, Iris Monnereau, Victor Ruiz

Biology and Environmental Science Faculty Publications

"This study presents unique comparisons, across space and time, regarding aspects of fishers’ perception of their job satisfaction and well-being between two geographic areas where fishing constitutes integral part of the local economy and culture: the Northeast Region US and the Caribbean. Examining differences in aspects of job satisfaction and well-being in such highly different environments (both human and natural) will provide information for developing models to understand how different stressors (e.g. changes in the natural, socio-cultural, economic and managerial environments) affect those whose livelihoods depend directly on fishery resources. Models elucidating relationships between environmental and anthropogenic changes and the …

Application Of Gis To Prioritize Brownfield Sites For Green Building Construction Based On Leed Criteria, Can B. Aktas, Paul Bartholomew, Sabrina Church

Civil Engineering Faculty Publications

Although there are many initiatives to create incentives for investors and developers to invest in and redevelop brownfield sites, efficient prioritization of brownfields by taking into account environmental, economic, and social constraints remains a challenge. This study introduces a method to screen numerous brownfields over large geographic areas by using geographic information systems (GIS) and to assess and prioritize such sites for green building suitability based on leadership in energy and environmental design (LEED) criteria. A case study was completed for the greater Bridgeport, Connecticut region. With 279 brownfield sites, the city has among the highest number of brownfields in …

Influence Of Tick And Mammalian Physiological Temperatures On Borrelia Burgdorferi Biofilms, Shafiq Shaikh, Venkata Arun Timmaraju, Jason Torres, Kayla Socarras, Priyanka A. Theophilus, Eva Sapi

Biology and Environmental Science Faculty Publications

The spirochaete bacterium Borrelia burgdorferi sensu lato is the aetiologic agent of Lyme disease. Borrelia is transmitted to mammals through tick bite and is adapted to survive at tick and mammalian physiological temperatures. We have previously shown that B. burgdorferi can exist in different morphological forms, including the antibiotic-resistant biofilm form, in vitro and in vivo. B. burgdorferi forms aggregates in ticks as well as in humans, indicating potential of biofilm formation at both 23 and 37 °C. However, the role of various environmental factors that influence Borrelia biofilm formation remains unknown. In this study, we investigated the effect …

Effect Of Rpon, Rpos And Luxs Pathways On The Biofilm Formation And Antibiotic Sensitivity Of Borrelia Burgdorferi, Eva Sapi, Priyanka A. Theophilus, Truc V. Pham, Divya Burugu, David Luecke

Biology and Environmental Science Faculty Publications

Borrelia burgdorferi, the causative agent of Lyme disease, is capable of forming biofilm in vivo and in vitro, a structure well known for its resistance to antimicrobial agents. For the formation of biofilm, signaling processes are required to communicate with the surrounding environment such as it was shown for the RpoN—RpoS alternative sigma factor and for the LuxS quorum-sensing pathways. Therefore, in this study, the wild-type B. burgdorferi and different mutant strains lacking RpoN, RpoS, and LuxS genes were studied for their growth characteristic and development of biofilm structures and markers as well as for their antibiotic sensitivity. …

Canine Filamentous Dermatitis Associated With Borrelia Infection, Marianne J. Middelveen, Gheorghe M. Rotaru, Jody L. Mcmurray, Katherine R. Filush, Eva Sapi, Jennie Burke, Agustin Franco, Lorenzo Malquori, Melissa C. Mcelroy, Raphael B. Stricker

Biology and Environmental Science Faculty Publications

Background: Although canine clinical manifestations of Lyme disease vary widely, cutaneous manifestations are not well documented in dogs. In contrast, a variety of cutaneous manifestations are reported in human Lyme disease caused by the spirochete Borrelia burgdorferi. A recently recognized dermopathy associated with tickborne illness known as Morgellons disease is characterized by brightly-colored filamentous inclusions and projections detected in ulcerative lesions and under unbroken skin. Recent studies have demonstrated that the dermal filaments are collagen and keratin biofibers produced by epithelial cells in response to spirochetal infection. We now describe a similar filamentous dermatitis in canine Lyme disease. Methods and …

Changes In Job Satisfaction Through Time In Two Major New England Fishing Ports, Tarsila Seara, Richard Pollnac, John J. Poggie

Biology and Environmental Science Faculty Publications

Fishing communities in the U.S. have been the subject of great transformation due to changes in availability of resources and the implementation of different rules and regulations to manage the fisheries and conserve fish stocks. Job satisfaction has been widely regarded as an important component of well-being especially among fishermen because the occupation of fishing includes attributes of ‘adventure,’ ‘challenge,’ and ‘being outdoors’ infrequently found in other employment. It has been previously demonstrated that management driven changes to fishing communities can directly and indirectly affect aspects of fishermen’s job satisfaction and, consequently, their wellbeing. This paper presents a unique through …

Perceived Adaptive Capacity And Natural Disasters: A Fisheries Case Study, Tarsila Seara, Patricia M. Clay, Lisa L. Colburn

Biology and Environmental Science Faculty Publications

Fishermen may be increasingly impacted by natural disasters, given sea level rise and the likely increased frequency and severity of storms associated with climate change. Planning for resiliency in the face of these disasters requires understanding the factors that influence fishermen’s capacity to adapt. The paper examines perceptions of adaptive capacity of New York and New Jersey commercial and for-hire fishermen one year after Hurricane Sandy. Subjective adaptive capacity to changes in the fishery in general and those caused by natural disasters was assessed. A comparison between commercial and for-hire fishermen revealed important differences and similarities with regard to attributes …

Social Bonds And Recovery: An Analysis Of Hurricane Sandy In The First Year After Landfall, Patricia M. Clay, Lisa L. Colburn, Tarsila Seara

Biology and Environmental Science Faculty Publications

Hurricane Sandy was one of the most devastating hurricanes to hit US shores. The brunt of the impact was felt in New York and New Jersey, especially among coastal towns such as fishing communities. A survey of these two states assessed social and economic impacts to 958 commercial and recreational fishermen and fishing-related business owners 12 months post-storm. Many businesses and communities were still struggling, due to heavy infrastructure damages and revenue losses with low insurance coverage, but also to disrupted fishing patterns for some species. Social bonds were credited by many as a key aid to recovery. Social bonds …

Evidence Of In Vivo Existence Of Borrelia Biofilm In Borrelial Lymphocytomas, Eva Sapi, Kunthavai Balasubramanian, Akhila Poruri, Jasmin S. Maghsoudlou, Kayla Socarras, Venkata Arun Timmaraju, Katherine Filush, Khusali Gupta, Shafiq Shaikh, Priyanka A.S. Theophilus, David F. Luecke, A. Macdonald, Bettina Zelger

Biology and Environmental Science Faculty Publications

Lyme borreliosis, caused by the spirochete Borrelia burgdorferi sensu lato, has grown into a major public health problem. We recently identified a novel morphological form of B. burgdorferi, called biofilm, a structure that is well known to be highly resistant to antibiotics. However, there is no evidence of the existence of Borrelia biofilm in vivo; therefore, the main goal of this study was to determine the presence of Borrelia biofilm in infected human skin tissues. Archived skin biopsy tissues from borrelial lymphocytomas (BL) were reexamined for the presence of B. burgdorferi sensu lato using Borrelia-specific immunohistochemical staining (IHC), fluorescent in …

Evaluating Human Cell Survival And Dna Damage After Exposure To Various Amounts Of Chlorine Dioxide And Exploring Its Use As A Potential Cancer Chemotherapy Agent, Niuska Mariana Alvarez Fuenmayor

SURF - Summer Undergraduate Research Fellowship Projects

Chlorine Dioxide (ClO₂) is a synthetic, green-yellowish gas with a chlorine-like, irritating odor that is used for the treatment of drinking water and food preservation. The aim of this study was to evaluate the genotoxic potential of the chlorine dioxide in mammalian cells and to determine what dose of ClO₂ is tolerable by normal cells and cells with aberrant DNA repair genes. Human and mouse embryonic cells were treated with various ClO₂ dilutions ranging from 2.5 mM to 25 mM. The cell viability and metabolic activity was determined via MTT, a colorimetric assay. Human HEK293 cells …

Indicators Of Climate Change And Social Vulnerability In Fishing Dependent Communities Along The Eastern And Gulf Coasts Of The U.S. Marine Policy, Lisa Colburn, Michael Jepson, Changhua Weng, Tarsila Seara, Jeremy Weiss

Biology and Environmental Science Faculty Publications

Changing climatic conditions are affecting the relationship between fishing communities and the marine resources they depend on. This shift will require an adaptive response on the part of policy makers and fishery managers. In the U.S., the National Oceanic and Atmospheric Administration (NOAA) established, in its fisheries agency (NOAA Fisheries), a set of social indicators of fishing community vulnerability and resilience to evaluate the impacts of changes in fishery management regimes. These indicators enhance the analytical capabilities within NOAA Fisheries for conducting fisheries social impact assessments and informing ecosystem-based fishery management. Building on the existing Community Social Vulnerability Indicators (CSVIs), …

Effectiveness Of Stevia Rebaudiana Whole Leaf Extract Against The Various Morphological Forms Of Borrelia Burgdorferi In Vitro, Priyanka Annabel Sugantham Theophilus, Maria J. Victoria, Kayla Socarras, Katherine R. Filush, Khusali Gupta, David F. Luecke, Eva Sapi

Biology and Environmental Science Faculty Publications

Lyme disease is a tick-borne multisystemic disease caused by Borrelia burgdorferi. Administering antibiotics is the primary treat-ment for this disease; however, relapse often occurs when antibiotic treatment is discontinued. The reason for relapse remains un-known, but recent studies suggested the possibilities of the presence of antibiotic resistant Borreliapersister cells and biofilms.In this study, we evaluated the effectiveness of whole leaf Stevia extract against B. burgdorferispirochetes, persisters, and bio-film forms in vitro. The susceptibility of the different forms was evaluated by various quantitative techniques in addition to differ-ent microscopy methods. The effectiveness of Stevia was compared to doxycycline, cefoperazone, daptomycin, and …

Taxonomy Of Usa East Coast Fishing Communities In Terms Of Social Vulnerability And Resilience, Richard Pollnac, Tarsila Seara, Lisa Colburn, Michael Jepson

Biology and Environmental Science Faculty Publications

Increased concern with the impacts that changing coastal environments can have on coastal fishing communities led to a recent effort by NOAA Fisheries social scientists to develop a set of indicators of social vulnerability and resilience for the U.S. Southeast and Northeast coastal communities. A goal of the NOAA Fisheries social vulnerability and resilience indicator program is to support time and cost effective use of readily available data in furtherance of both social impact assessments of proposed changes to fishery management regulations and climate change adaptation planning. The use of the indicators to predict the response to change in coastal …

Biofilm Formation By Borrelia Burgdorferi Sensu Lato, Venkata Arun Timmaraju, Priyanka A.S. Theophilus, Kunthavai Balasubramanian, Shafiq Shakih, David F. Luecke, Eva Sapi

Biology and Environmental Science Faculty Publications

Bacterial biofilms are microbial communities held together by an extracellular polymeric substance matrix predominantly composed of polysaccharides, proteins and nucleic acids. We had previously shown that Borrelia burgdorferi sensu stricto, the causative organism of Lyme disease in the United States is capable of forming biofilms in vitro. Here, we investigated biofilm formation by B. afzelii and B. garinii, which cause Lyme disease in Europe. Using various histochemistry and microscopy techniques, we show that B. afzelii and B. garinii form biofilms, which resemble biofilms formed by B. burgdorferisensu stricto. High-resolution atomic force microscopy revealed similarities in the …

Drift Algae In New Haven Harbor And Impacts On Benthic Communities, Roman Zajac, Andrea Mccarthy

Biology and Environmental Science Faculty Publications

In 2009 the University of New Haven initiated studies to develop a contemporary database and assessment of the benthic ecology of New Haven Harbor. Previous studies were last conducted in the 1970s and 1980s (e.g. McCusker, and Bosworth 1979, 1981, Rhoads and Germano 1982). Benthic populations and communities are excellent indicators of environmental conditions and are regularly used for environmental assessment in estuarine and coastal waters (e.g. Pearson and Rosenberg 1978, Rhoads et al. 1978, Zajac and Whitlatch 2001, Mangi 2003). Given the inherent ability of the benthos to integrate sediment and water quality, many environmental indicators and indices to …

Exploring The Association Between Morgellons Disease And Lyme Disease: Identification Of Borrelia Burgdorferi In Morgellons Disease Patients, Marianne J. Middelveen, Cheryl Bandoski, Jennie Burke, Eva Sapi, Katherine Filush, Yean Wang, Agustin Franco, Peter J. Mayne, Raphael B. Stricker

Biology and Environmental Science Faculty Publications

Morgellons disease (MD) is a complex skin disorder characterized by ulcerating lesions that have protruding or embedded filaments. Many clinicians refer to this condition as delusional parasitosis or delusional infestation and consider the filaments to be introduced textile fibers. In contrast, recent studies indicate that MD is a true somatic illness associated with tickborne infection, that the filaments are keratin and collagen in composition and that they result from proliferation and activation of keratinocytes and fibroblasts in the skin. Previously, spirochetes have been detected in the dermatological specimens from four MD patients, thus providing evidence of an infectious process. Methods …

Heterozygosity For A Hypomorphic Polβ Mutation Reduces The Expansion Frequency In A Mouse Model Of The Fragile X-Related Disorders, Rachel Adihe Lokanga, Ali Senejani, Joann B. Sweasy, Karen Usdin

Biology and Environmental Science Faculty Publications

The Fragile X-related disorders (FXDs) are members of the Repeat Expansion Diseases, a group of human genetic conditions resulting from expansion of a specific tandem repeat. The FXDs result from expansion of a CGG/CCG repeat tract in the 5’ UTR of the FMR1 gene. While expansion in a FXD mouse model is known to require some mismatch repair (MMR) proteins, our previous work and work in mouse models of another Repeat Expansion Disease show that early events in the base excision repair (BER) pathway play a role in the expansion process. One model for repeat expansion proposes that a non-canonical …

Pparγ Negatively Regulates T Cell Activation To Prevent Follicular Helper T Cells And Germinal Center Formation, Hong-Jai Park, Do-Hyun Kim, Jin-Young Choi, Won-Ju Kim, Ji Yun Kim, Ali Senejani, Soo Seok Hwang, Lark Kyun Kim, Zuzana Tobiasova, Gap Ryol Lee, Joseph Craft, Alfred L.M. Bothwell, Je-Min Choi

Biology and Environmental Science Faculty Publications

Peroxisome proliferator-activated receptor gamma (PPARγ) is a transcription factor that regulates lipid and glucose metabolism. Although studies of PPARγ ligands have demonstrated its regulatory functions in inflammation and adaptive immunity, its intrinsic role in T cells and autoimmunity has yet to be fully elucidated. Here we used CD4- PPARγ KO mice to investigate PPARγ -deficient T cells, which were hyper-reactive to produce higher levels of cytokines and exhibited greater proliferation than wild type T cells with increased ERK and AKT phosphorylation. Diminished expression of IκΒα, Sirt1, and Foxo1, which are inhibitors of NF-κΒ, was observed in PPARγ-deficient T cells that …

Mutation Of A Dna Repair Enzyme Causes Lupus In Mice, Ali Senejani, Yanfeng Liu, Dawit Kidane, Stephen E. Maher, Caroline J. Zeiss, Hong-Jae Park, Michael Kashgarian, Jennifer Madison Mcniff, Daniel Zelterman, Alfred L.M. Bothwell, Joann B. Sweasy

Biology and Environmental Science Faculty Publications

A replication study of a previous genome-wide association study (GWAS) suggested that a SNP linked to the POLβ gene is associated with systemic lupus erythematosus (SLE). This SNP is correlated with decreased expression of Pol β, a key enzyme in the base excision repair (BER) pathway. To determine whether decreased Pol β activity results in SLE, we constructed a mouse model of POLβ that encodes an enzyme with slow DNA polymerase activity. We show that mice expressing this hypomorphic POLβ allele develop an autoimmune pathology that strongly resembles SLE. Of note, the mutant mice have shorter immunoglobulin heavy-chain junctions and …

Filarial Nematode Infection In Ixodes Scapularis Ticks Collected From Southern Connecticut, Pabbati Namrata, Jamie M. Miller, Madari Shilpa, Patlolla Raghavender Reddy, Cheryl Bandoski,, Michael J. Rossi, Eva Sapi

Biology and Environmental Science Faculty Publications

It was recently demonstrated that the lone star tick Amblyomma americanum could harbor filarial nematodes within the genus Acanthocheilonema. In this study, Ixodes scapularis (deer) ticks collected from Southern Connecticut were evaluated for their potential to harbor filarial nematodes. Non-engorged nymphal and adult stage Ixodes scapularis ticks were collected in Southern Connecticut using the standard drag method. In situ hybridization with filarial nematode specific sequences demonstrated the presence of filarial nematodes in Ixodes ticks. Filarial nematode specific DNA sequences were amplified and confirmed by direct sequencing in Ixodes nymphal and adult ticks using either general filarial nematode or Onchocercidae family …

Cellular Roles Of Dna Polymerase Beta, Sreerupa Ray, Miriam-Rose Menezes, Ali Senejani, Joann Balazs Sweasy

Biology and Environmental Science Faculty Publications

Since its discovery and purification in 1971, DNA polymerase ß (Pol ߆) is one of the most well-studied DNA polymerases. Pol ß is a key enzyme in the base excision repair (BER) pathway that functions in gap filling DNA synthesis subsequent to the excision of damaged DNA bases. A major focus of our studies is on the cellular roles of Pol ß. We have shown that germline and tumor-associated variants of Pol ß catalyze aberrant BER that leads to genomic instability and cellular transformation. Our studies suggest that Pol ß is critical for the maintenance of genomic stability and that …

Spatial And Temporal Patterns In Macrofaunal Diversity Components Relative To Sea Floor Landscape, Roman Zajac, Brittney R. Gibbons, Joseph M. Vozarik

Biology and Environmental Science Faculty Publications

We examined temporal changes in macrofaunal α- and β-diversity over several spatial scales (within patches, among patches, across landscapes and across regions) in Long Island Sound on the northeast USA coast. Regional ε-diversity was estimated at 144 taxa, however γ-diversity fluctuated over time as did α- and β-diversity components. Based on additive partitioning, patch- and region-scale β-diversity components generally had the highest contributions to γ-diversity; lower percentages were found at within-patch and landscape scales. Multiplicative diversity partitioning indicated highest species turnover at within- and among patch scales. For all partition results, within-patch and patch-scale β-diversity increased sharply when hypoxia impacted …

Isolation Of Secreted Micrornas (Mirnas) From Cell-Conditioned Media, Claire L. Glynn, Sonja Khan, Michael J. Kerin, Roisin M. Dwyer

Forensic Science Publications

MicroRNAs (miRNAs) have been found to be stable in the circulation of cancer patients raising their potential as circulating biomarkers of disease. The specific source and role, however, of miRNAs in the circulation is unknown and requires elucidation to determine their true potential. In this study, along with primary tissue explants and primary stromal cells, three breast cancer cell lines were employed, including T47D, MDA-MB-231 and SK-BR-3. Tissue explants were harvested in theatre, with informed patient consent, and included tumour, tumour associated normal, and diseased lymph node samples. Cell-conditioned media containing all factors secreted by the cells were harvested. MiRNAs …