Organisms Commons^™

Assessing Arthropod Responses To Volatile Organic Compounds From The Algal Microbiome Of A Sloth Using Drosophila Melanogaster, Lilli Gordon

Honors Theses

Sloths contain an unexplored ecosystem of microbial diversity in their fur, including algae, fungi, bacteria, and arthropods. These symbionts are able to communicate through the chemicals they release, including volatile organic compounds (VOCs), which can lead to unique ecological interactions. The VOCs released from the algal polycultures of sloth hairs merit further investigation in their ability to cause a response from other organisms in this microbial community and within a broader ecological context. This research team aimed to assess the response of Drosophila melanogaster as test subjects when exposed to VOCs of the algal microbiome of a sloth. Exploratory research …

Effects Of Strong Oxidants Present In Acer Spp. On Hemolysis Methemoglobin Production In Equine Erythrocytes, Gabrielle Mcgeorge, Jeffrey Lehman

Undergraduate Honors Thesis Projects

Maple toxicosis is a deadly condition affecting equines after they have ingested wilted leaves of the genus Acer (i.e., maple species). It is characterized by hemolytic anemia and methemoglobinemia. Although the toxins responsible for causing toxicosis have not been identified, they are thought to be strong oxidants. The objective of this study is to determine the effect of eight compounds (galloyl derivatives) found in Acer spp. on hemolysis and methemoglobin production in bioassays with equine erythrocytes. Seven of the compounds are known constituents of Acer spp. that are commercially available. One of the compounds--acertannin--was isolated and characterized from leaf extracts …

Restoration Agriculture In Louisiana: On The Prospects And Ethics Of Creating A Permanent, Dynamic Agricultural System Suited For Louisiana's Environment, Noah Willsea

Honors Capstones

No abstract provided.

Purification And Functional Characterization Of The Iron-Responsive Transcription Factor Aft1 From C. Glabrata, Jade Ikahihifo-Bender

Senior Theses

Due to its unique ability to serve as both an electron donor and acceptor, iron is utilized as a co-factor for many biological processes, including electron transfer, oxygen binding, and vitamin synthesis. Iron is also a key factor during fungal infections as the human host and invading pathogens battle over limited iron pools. The primary iron-responsive transcription factor Aft1 in the opportunistic pathogenic yeast Candida glabrata responds to iron deficiency by activating expression of iron acquisition genes. However, the mechanisms for sensing intracellular iron levels and regulating Aft1 activity in response to iron are unknown. The C. glabrata iron regulation …

Microbiological Study In A Gneissic Cave From Sri Lanka, With Special Focus On Potential Antimicrobial Activities, Ethige Isuru P. Silva, Pathmakumara Jayasingha, Saman Senanayake, Anura Dandeniya, Dona Helani Munasinghe

International Journal of Speleology

The emergence of antibiotic resistance is a global health crisis, thus the search for novel antimicrobial compounds has become a continuous necessity. Underexplored and extreme environments, such as cave ecosystems, have been identified as a promising potential source for the discovery of novel microorganisms with novel antimicrobial compounds (AMC). This study presents the first cave microbiological investigation in Sri Lanka, with a special preference for bioprospecting of novel AMC. The cave sediment characterization demonstrated the presence of close to strong acidic conditions (pH 3.1 – 3.3) and thus indicates the possibility of isolating acidophilic microorganisms. Eight cave wall/ceiling fungal strains …

3d Printing Of Human Microbiome Constituents To Understand Spatial Relationships And Shape Parameters In Bacteriology, Jacques Izard, Teklu Kuru Gerbaba, Shara R. P. Yumul

Department of Food Science and Technology: Faculty Publications

Effective laboratory and classroom demonstration of microbiome size and shape, diversity, and ecological relationships is hampered by a lack of high-resolution, easy-to-use, readily accessible physical or digital models for use in teaching. Three-dimensional (3D) representations are, overall, more effective in communicating visuospatial information, allowing for a better understanding of concepts not directly observable with the unaided eye. Published morphology descriptions and microscopy images were used as the basis for designing 3D digital models, scaled at 20,000×, using computer-aided design software (CAD) and generating printed models of bacteria on mass-market 3D printers. Sixteen models are presented, including rod-shaped, spiral, flask-like, vibroid, …

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …

Epidemiology And Outcomes Of Hospitalized Adults With Sars-Cov-2 Community-Acquired Pneumonia In Louisville, Kentucky, Julio A. Ramirez, T'Shura Ali, Thomas Chandler, Stephen P. Furmanek, Daniya Sheikh, Vidyulata Salunkhe, Steven Gootee, Mohammad Tahboub, William A. Mattingly, Demetra Antimisiaris, Jiapeng Huang, Jose Bordon, Rodrigo Cavallazzi, Paul Schulz, William P. Mckinney, Dawn Balcom, Mark Burns, Ruth Carrico, Forest W. Arnold, Cerid Covid-19 Study Group

The University of Louisville Journal of Respiratory Infections

Background: During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 community-acquired pneumonia (CAP) has been the primary cause of hospitalization. The objective of this study was to evaluate the clinical characteristics and outcomes of 1,013 patients hospitalized with SARS-CoV-2 CAP from September 2020 through March 2021 in Louisville, Kentucky.

Methods: This was a retrospective observational study of 1,013 patients hospitalized with SARS-CoV-2 CAP at eight of the adult hospitals in the city of Louisville from September 2020 through March 2021. Patients with 1) a positive reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2, 2) fever, cough, or …

Sociodemographic, Clinical Characteristics, And Outcomes Of Influenza Pneumonia Patients Admitted In A Tertiary Care Hospital In Karachi, Pakistan: Findings From A Cross-Sectional Study, Fazal Ur Rehman, Muhammad Arslan Ahmed, Kashif Aziz, Mahmooda Jabeen Ashraf, Tazein Amber, Sumera Aziz Ali

Section of Internal Medicine

Objective: To determine the sociodemographic, clinical characteristics, and outcomes of influenza pneumonia patients in tertiary care hospital, Karachi Pakistan.
Study design: A cross-sectional study.
Place and duration of study: The Aga Khan University Hospital Karachi Pakistan from January 2013 to December 2018. Methodology: All adult patients who were older than 18 years and suspected to have viral pneumonia were included in the study. Data were abstracted on 105 patients and were entered on preformed proforma after reviewing the files of patients.
Results: Ninety-four (89.5%) patients were influenza positive and 15.2% (n=16) had been vaccinated. Around 92.4% (n=97), 81.9% (n=86) and …

Streptococcus Cristatus – An Oral Bacterium Causing A Case Of Mild Bacteremia And “Possible Endocarditis”, Camilo Guzman, Adi Zaclli, John Molinari

Medical Student Research Symposium

Streptococcus cristatus is a member of the Mitis streptococcus group. Like other members of this group, it resides in mucosal surfaces of the oral cavity but rarely causes disease. We present a case of S. cristatus bacteremia and “possible endocarditis” (per the modified Duke criteria) in a 59-year-old male suffering from end- stage cryptogenic cirrhosis. To date, it is the fifth reported case of disease caused by the microbe, and the first adult case in which S. cristatus was the sole microbe identified. Our patient had a history of dental caries and poor dentition, which were likely the source of …

Functional Influence Of 14-3-3 (Ywha) Proteins In Mammals, Elizabeth Barley, Santanu De

Mako: NSU Undergraduate Student Journal

The 14-3-3 (YWHA) proteins are homologous, ubiquitous, and conserved in most organisms ranging from plants to animals and play important roles in regulating key cellular events such as cell signaling, development, apoptosis, etc. These proteins consist of seven isoforms in mammals, termed under Greek alphabetization: beta (β), gamma (γ), epsilon (ε), eta (η), tau/theta (τ), sigma (σ), and zeta (ζ). Each of these isoforms can interact with a plethora of binding partners and has been shown to serve a distinct role in molecular crosstalk, biological processes, and disease susceptibility. Protein 14-3-3 isoforms are scaffolding proteins capable of forming homodimers and …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Covid-19 Presenting With Spontaneous Pneumothorax, Intisar Ahmed, Hunaina Shahab, Muhammad Arslan Ahmed, Muhammad Sohaib

Section of Cardiology

The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease mainly affects respiratory system. Its common clinical findings include fever, cough and shortness of breath. Characteristic radiological features of the disease include peripherally distributed, bilateral ground-glass opacities, predominantly involving the lower lung zones. In this report, we present a case of COVID-19 disease presenting with spontaneous pneumothorax. A 26-year male patient was admitted to the Emergency Department with fever, dry cough, shortness of breath and right-sided chest pain. Radiographic imaging of the patient revealed pneumothorax on the right and peripherally distributed non-homogenous opacification. …

Evolution, Ecology, And Zoonotic Transmission Of Betacoronaviruses: A Review, Herbert F. Jelinek, Mira Mousa, Eman Alefishat, Wael Osman, Ian Spence, Dengpan Bu, Samuel F. Feng, Jason Byrd, Paola A. Magni, Shafi Sahibzada, Guan K. Tay, Habiba S. Alsafar

Research outputs 2014 to 2021

Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other …

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R_rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …

Characterizing The Physiology And Genetics Of Contact Dependent Growth Inhibiton Systems In Burkholderia Species, Alice Elizabeth Oates

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Contact-dependent growth inhibition (CDI) systems mediate interbacterial competition. The genes encoding these systems are widespread among Gram-negative bacteria, including Burkholderia pathogens. CDI systems of Burkholderia species are composed of two-partner secretion pathway proteins and function to deliver the toxic C-terminus of a polymorphic surface-exposed exoprotein BcpA (Burkholderia CDI protein A) to the cytoplasm of neighboring recipient bacteria upon cell-cell contact. Specific outer and inner membrane proteins facilitate BcpA translocation both out of the donor bacterium and into the recipient cell cytoplasm. Most Burkholderia species-specific CDI translocation factors in recipient cells are unknown. BcpA intoxication functions as a mechanism by …

Novel Mammalian Models For Understanding And Treating Spinal Cord Injury, Michael B. Orr

Theses and Dissertations--Physiology

Spinal cord injury (SCI) is devastating and often leaves the injured individual with persistent dysfunction. The injury persists because humans have poor wound repair and there are no pharmacologic treatments to induce wound repair after SCI. The continued efforts to discover therapeutic targets and develop treatments heavily relies on animal models. The purpose of this project is to develop and study novel mammalian models of SCI to provide insights for the development and effective implementation of SCI therapies.

Lab mice (Mus musculus) are a powerful tool for recapitulating the progression and persistent damage evident in human SCI, but …

Bacterial Association Networks From Healthy And Cancer-Associated Gut Microbiomes, Mark Loftus

Electronic Theses and Dissertations, 2020-2023

The human gastrointestinal tract is colonized by a diverse community of symbiotic microorganisms, mainly bacteria, that are known to play essential roles in maintaining the health of their human host. Disruption of this bacterial community has been associated with numerous diseases, including Colorectal Cancer (CRC). CRC is one of the leading causes of cancer-related deaths worldwide. As such, focus has been placed on the modulation of the bacterial community within the cancer-associated gut microbiome as the next step in possible CRC treatment and prevention strategies. To use the bacterial community for these purposes, a better understanding of the associations that …

Cellular Bioenergetics Regulates Cell Proliferation During Mammalian Regeneration, Sandeep Saxena

Theses and Dissertations--Biology

Mammalian system consists of stress-sensing molecules that regulates their cellular response against damage, injury and oncogenic stress. During vertebrate regeneration, cells responding to injury re-enter the cell cycle and proliferate to form new tissue. Cell cycle re-entry or arrest is at least partly regulated by cellular senescence which negatively impacts the proliferative pool of cells during regeneration. What remains unclear is whether cells in regenerating systems possess an increased propensity to proliferate and are refractory to signals that induce senescence. My thesis work has focused on how fibroblasts from the ear pinna differentially regulate healing in highly regenerative mammals (e.g., …

Comparisons Of Oral, Intestinal, And Pancreatic Bacterial Microbiomes In Patients With Pancreatic Cancer And Other Gastrointestinal Diseases, Mei Chung, Naisi Zhao, Richard Meier, Devin C. Koestler, Guojun Wu, Erika De Castillo, Bruce J. Paster, Kevin Charpentier, Jacques Izard, Karl T. Kelsey, Dominique S. Michaud

Department of Food Science and Technology: Faculty Publications

Background: Oral microbiota is believed to play important roles in systemic diseases, including cancer. Methods: We collected oral samples (tongue, buccal, supragingival, and saliva) and pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S rRNA genes using high-throughput DNA sequencing.

Results: Bray–Curtis plot showed clear separations between bacterial communities in the oral cavity and those in intestinal and pancreatic tissue samples. PERMANOVA tests indicated that bacterial communities from buccal samples were similar to supragingival and saliva samples, and pancreatic duct samples were similar to pancreatic tumor samples, but all other samples were significantly different from each …