Microbiology Commons^™

Cave Cyanobacteria Showing Antibacterial Activity, Vasiliki Lamprinou, Kyriaki Tryfinopoulou, Emmanuel N. Velonakis, Alkiviadis Vatopoulos, Smaragdi Antonopoulou, Elizabeth Fragopoulou, Adriani Pantazidou, Athena Economou-Amilli

International Journal of Speleology

Cave Cyanobacteria - thriving in an ‘extreme’ environment with interesting species biodiversity - are supposed to be a potential source of bioactive compounds. Lipid extracts from pure cultures of two recently established Cyanobacteria from Greek caves, Toxopsis calypsus and Phormidium melanochroun, were used for antibacterial screening against human pathogenic bacteria (reference and clinical isolates). Antimicrobial Susceptibility testing for both taxa was carried out using the disc-diffusion (Kirby Bauer) method, while preliminary data applying the standard broth microdilution method for the determination of the Minimal Inhibitory Concentration (MIC) are given only for T. calypsus. Antibacterial activity was demonstrated against the …

Characterization And Fluorescence Of Yellow Biofilms In Karst Caves, Southwest Slovenia, Janez Mulec, Andreea Oarga-Mulec, Rok Tomazin, Tadeja Matos

International Journal of Speleology

Biofilms of different colours that colonize surfaces within karst caves represent a source of nutrients. They occur commonly and abundantly at sites with sediments, and close to seepages or underground rivers. Golden-yellow subaerial biofilms are particularly well observed because of their contrast with their surroundings, the characteristics of the pigment and recently, even more, due to the characteristics of light-emitting diode (LED) illumination. Yellow microbial biofilms were sampled from three caves in southwestern Slovenia, Dimnice, Križna jama and Sveta jama. The highest concentration of cultivable microbes (2.33×10⁸ CFU/g) and the biggest number of identified bacteria (66.0%) were retrieved from …

Promoting Genome Stability Via Multiple Dna Repair Pathways, Scott Cukras

USF Tampa Graduate Theses and Dissertations

Maintaining genome integrity is indispensible for cells to prevent and limit accruement of deleterious mutations and to promote viable cell growth and proliferation. Cells possess a myriad of mechanisms to detect, prevent and repair incurred cellular damage. Here we discuss various proteins and their accompanying cellular pathways that promote genome stability. We first investigate the NEDD8 protein and its role in promoting homologous recombination repair via multiple Cullin E3 ubiquitin ligases. We provide specific mechanisms through which, UBE2M, an E2 conjugating enzyme, neddylates various Cullin ligases to render them catalytically active to degrade their substrates by the proteasome. We show …

Cyanobacteria, Algae And Microfungi Present In Biofilm From Božana Cave (Serbia), Slađana Popović, Gordana Subakov Simić, Miloš Stupar, Nikola Unković, Dragana Predojević, Jelena Jovanović, Milica Ljaljević Grbić

International Journal of Speleology

Phototrophic microorganisms (cyanobacteria and algae) and microfungi, were identified from biofilm on the walls of the entrance of BožanaCavein west Serbia. Temperature, relative humidity and light intensity were measured, and chlorophyll a content determined. Light intensity differed from the entrance inwards. However, Chl a content was not proportional to light intensity, instead it was positively correlated to biofilm weight. Biofilm samples from two sites were also observed using a scanning electron microscope. Coccoid forms of cyanobacteria were abundant at the sampling site with the lowest light intensity, while members of the order Nostocales were predominant at the sampling site with …

Inhibition Of Shp2 Suppresses Mutant Egfr-Induced Lung Tumors In Transgenic Mouse Model Of Lung Adenocarcinoma, Valentina E. Schneeberger, Yuan Ren, Noreen Luetteke, Qingling Huang, Liwei Chen, Harshani R. Lawrence, Nicholas J. Lawrence, Eric B. Haura, John M. Koomen, Domenico Coppola, Jie Wu

Molecular Biosciences Faculty Publications

Epidermal growth factor receptor (EGFR) mutants drive lung tumorigenesis and are targeted for therapy. However, resistance to EGFR inhibitors has been observed, in which the mutant EGFR remains active. Thus, it is important to uncover mediators of EGFR mutant-driven lung tumors to develop new treatment strategies. The protein tyrosine phosphatase (PTP) Shp2 mediates EGF signaling. Nevertheless, it is unclear if Shp2 is activated by oncogenic EGFR mutants in lung carcinoma or if inhibiting the Shp2 PTP activity can suppress EGFR mutant-induced lung adenocarcinoma. Here, we generated transgenic mice containing a doxycycline (Dox)-inducible PTP-defective Shp2 mutant (tetO-Shp2CSDA). Using the rat Clara …

The Νsaα Specific Lipoprotein Like Cluster (Lpl) Of S. Aureus Usa300 Contributes To Immune Stimulation And Invasion In Human Cells, Minh Thu Nguyen, Beatrice Kraft, Wenqi Yu, Dogan Doruk Demicrioglu, Tobias Hertlein, Marc Burian, Mathias Schmaler, Klaus Boller, Isabelle Bekeredjian-Ding, Knut Ohlsen, Birgit Schittek, Friedrich Götz

Molecular Biosciences Faculty Publications

All Staphylococcus aureus genomes contain a genomic island, which is termed νSaα and characterized by two clusters of tandem repeat sequences, i.e. the exotoxin (set) and 'lipoprotein-like' genes (lpl). Based on their structural similarities the νSaα islands have been classified as type I to IV. The genomes of highly pathogenic and particularly epidemic S. aureus strains (USA300, N315, Mu50, NCTC8325, Newman, COL, JH1 or JH9) belonging to the clonal complexes CC5 and CC8 bear a type I νSaα island. Since the contribution of the lpl gene cluster encoded in the νSaα island to virulence is unclear to date, we deleted …

Exploring The Pathogenic And Drug Resistance Mechanisms Of Staphylococcus Aureus, Whittney Burda

USF Tampa Graduate Theses and Dissertations

We have previously identified σS, an ECF sigma factor that is important in the virulence and stress response of S. aureus. Transcriptional profiling of sigS revealed that it is differentially regulated in a variety of laboratory and clinical strains of S. aureus, suggesting that there exists a regulatory network that modulates its expression. In order to identify direct regulators of sigS expression, we performed a biotin pull down assay in tandem with mass spectrometry. We identified CymR as a direct regulator and observed that sigS expression is increased in cells lacking cymR. In addition, transposon mutagenesis was performed to identify …

Investigation Of Post-Translational Modifications In Staphylococcus Aureus, Christina Nadia Krute

USF Tampa Graduate Theses and Dissertations

The work presented herein details post-translational modifications (PTMs) in Staphylococcus aureus that are involved in mediating the stress response and normal cellular processes. The first PTM that was investigated is regulated intramembrane proteolysis (RIP) for the activation of the ECF sigma factor σS. We achieved this by analyzing the role of the site-1 protease, which we termed “putative regulator of sigmaS” (PrsS), as it is predicted to be the first enzyme in the RIP cascade, leading to the activation of σS. It was determined that the putative site-1 protease, prsS, mimics transcriptional profiles of sigS; with expression low in all …

Exploring The Role Of Intracellular Aminopeptidases In Staphylococcus Aureus Pathogenesis, Devon Nicole Marking

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a remarkably pathogenic bacterium that is widely prevalent among the human population. It is the leading agent of skin and soft tissue infections, and is also responsible for causing an array of severe and life threatening diseases. The invasiveness of the pathogen, coupled with increasing antibiotic resistance seen for S. aureus infections, makes this bacterium a prominent public health concern. The extended pathogenicity of S. aureus is largely due to its repertoire of virulence factors, which are typically characterized by being bound to the cell wall, or secreted into the extracellular environment. Previously, our lab identified a …

A Functional Approach To Resolving The Biogeocomplexity Of Two Extreme Environments, Haydn Rubelmann Iii

USF Tampa Graduate Theses and Dissertations

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal …

Mechanisms And Molecular Biology Of Major Tumor Suppressors, Brienne E. Engel

USF Tampa Graduate Theses and Dissertations

This dissertation is devoted to the study of the molecular biology of major tumor suppressors, defined as those that prevent the cellular processes identified as the hallmarks of cancer. Specifically, the major tumor suppressors pRb and STK11 are explored in the context of osteosarcoma and lung cancer, respectively.

RB1 was the first tumor suppressor gene discovered. Over four decades of work have revealed that the Rb protein (pRb) is a master regulator of biological pathways influencing virtually every aspect of intrinsic cell fate including cell growth, cell-cycle checkpoints, differentiation, senescence, self-renewal, replication, genomic stability and apoptosis. While these many processes …

Role And Regulation Of Snon/Skil And Plscr1 Located At 3q26.2 And 3q23, Respectively, In Ovarian Cancer Pathophysiology, Madhav Karthik Kodigepalli

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is one of the most common causes of gynecological cancer related deaths in women. In 2014, the estimated number of deaths due to ovarian cancer is 14,270 with occurrence of over 22, 240 new cases (National Cancer Institute, http://seer.cancer.gov/statfacts/html/ovary.html). Despite improvement in treatment strategies, the 5-year survival rate is still below 50% mainly due to chemoresistance and relapse. Amplification of chromosomal region 3q26 is a common characteristic in various epithelial cancers including ovarian cancer. This region harbors various oncogenes including the TGFβ signaling mediators EVI1 and SnoN/SkiL, PKCι and PIK3CA amplified at 3q26.2 and 3q26.3, respectively, in ovarian …

Karst Estuaries: A Newly Described Ecosystem Governed By Aquifer Hydrology, Damian M. Menning

USF Tampa Graduate Theses and Dissertations

The overall goal of this dissertation is to define the hydrological, geochemical, and biological characteristics of a Karst Estuary. These types of estuaries represent a unique ecosystem created by freshwater inputs from direct flow through karst conduits and/or diffuse flow through a karst matrix. In order to determine the characteristics of a Karst Estuary we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, multiple geochemical parameters, microbial communities in the water column and sediment, and macrofaunal communities in the sediment along a transect from a submarine spring through the Gulf of Mexico. Four sites were selected along …

Ice Caves On Extraterrestrial Bodies: What Are The Prospects For Speleogenesis And Detection?, Penelope J. Boston

The International Workshop on Ice Caves

Potential mechanisms for creating cavities in icy extraterrestrial bodies have been tentatively explored by several authors. On one hand we have examples of mechanisms that create caves in water ice here on Earth. In addition, there may be unique mechanisms on other Solar System objects that do not occur on Earth but might produce cavities, e.g. sublimation of comets upon perihelion passage. The methods of detecting such cavities depend upon the nature of the icy body in question, the potential for orbital or landed missions to visit those bodies in the future, and remote or landed methods for detecting the …

The Show Cave Of Diros Vs. Wild Caves Of Peloponnese, Greece - Distribution Patterns Of Cyanobacteria, Vasiliki Lamprinou, Daniel B. Danielidis, Adriani Pantazidou, Alexandra Oikonomou, Athena Economou-Amilli

International Journal of Speleology

The karst cave ‘Vlychada’of Diros, one of the oldest show caves in Peloponnese, sustains extended phototrophic biofilms on various substrata – on rocks inside the cave including speleothems, and especially near the artificial lighting installation (‘Lampenflora’). After a survey of the main abiotic parameters (Photosynthetically Active Radiation -PAR, Temperature -T, Relative Humidity -RH, Carbon Dioxide -CO₂) three clusters of sampling sites were revealed according to Principal Component Analysis (PCA): i) the water gallery section predominately influenced by CO₂, ii) the dry passages influenced by RH and PAR, and iii) the area by the cave exit at …

Bartonella Henselae Infection And Host Response In The Zebrafish Embryo Model, Amorce Lima

USF Tampa Graduate Theses and Dissertations

The Gram-negative bacterium Bartonella henselae (Bh) is an emerging zoonotic pathogen that has been associated with a variety of human diseases including bacillary angiomatosis which is characterized by vasoproliferative tumor-like lesions on the skin and internal organs of some immunosuppressed individuals. Several virulence factors associated with Bartonella-induced pathogenesis have been characterized. However, the study of those virulence factors has been limited to in vitro cell culture systems due to the lack of a practical animal model. Therefore, we wanted to investigate whether the zebrafish embryo (Danio rerio) could be used to model human infection with Bh. We investigated …

Airborne Microorganisms In Lascaux Cave (France), Pedro M Martin-Sanchez, Valme Jurado, Estefania Porca, Fabiola Bastian, Delphine Lacanette, Claude Alabouvette, Cesareo Saiz-Jimenez

International Journal of Speleology

Lascaux Cave in France contains valuable Palaeolithic paintings. The importance of the paintings, one of the finest examples of European rock art paintings, was recognized shortly after their discovery in 1940. In the 60’s of the past century the cave received a huge number of visitors and suffered a microbial crisis due to the impact of massive tourism and the previous adaptation works carried out to facilitate visits. In 1963, the cave was closed due to the damage produced by visitors’ breath, lighting and algal growth on the paintings. In 2001, an outbreak of the fungus Fusarium solani covered the …

Cancer And Infection, Kathleen Hope Plummer

USF Tampa Graduate Theses and Dissertations

E. coli is the most frequently isolated Gram negative pathogen from bacteremia in cancer patients and is repeatedly recovered from many other extraintestinal illnesses. These infections are commonly endogenous in nature and interfere with the treatment of cancer resulting in increased healthcare costs, morbidity, and mortality rates. Cancer and the treatments related to cancer cause alterations in the microbiome of the gut and other organs. Despite this point, there is a serious lack of knowledge about the genetic types of E. coli infecting cancer patients. This gap results in vague prevention strategies and limited treatment options for cancer patients. Multi …

Topological Data Analysis Of Properties Of Four-Regular Rigid Vertex Graphs, Grant Mcneil Conine

USF Tampa Graduate Theses and Dissertations

Homologous DNA recombination and rearrangement has been modeled with a class of four-regular rigid vertex graphs called assembly graphs which can also be represented by double occurrence words. Various invariants have been suggested for these graphs, some based on the structure of the graphs, and some biologically motivated.

In this thesis we use a novel method of data analysis based on a technique known as partial-clustering analysis and an algorithm known as Mapper to examine the relationships between these invariants. We introduce some of the basic machinery of topological data analysis, including the construction of simplicial complexes on a data …

From Co2 To Cell: Energetic Expense Of Creating Biomass Using The Calvin-Benson-Bassham And Reductive Citric Acid Cycles Based On Genomic Data, Mary Ann Mangiapia

USF Tampa Graduate Theses and Dissertations

Abstract

The ubiquity of the Calvin-Benson-Bassham cycle (CBB) amongst autotrophic organisms suggests that it provides an advantage over a wide range of environmental conditions. However, in some habitats, such as hydrothermal vents, the reductive citric acid cycle (rCAC) is an equally predominant carbon fixation pathway. It has been suggested that the CBB cycle poses a disadvantage under certain circumstances due to being more energetically demanding compared to other carbon fixation pathways. The purpose of this study was to compare the relative metabolic cost of cell biosynthesis by an autotrophic cell using either the CBB cycle or the rCAC. For both …

Investigating The Diversity Of Single-Stranded Dna Bacteriophages In Marine Environments, Max Stephen Hopkins

USF Tampa Graduate Theses and Dissertations

There are estimated to be 1030 virus-like particles in the world's oceans. Most are viruses that infect bacteria, called `bacteriophages' or simply `phages'. Phages exert tremendous influence on marine biogeochemical cycling because they are responsible for about half of all bacterial death in the oceans, causing nutrient release into the dissolved and particulate organic matter pools. Traditional paradigms of phage biology held that most of these ocean phages belonged to the Caudovirales group: phages that contain a double-stranded DNA genome within a geometric capsid `head' to which a `tail' is joined, in one of several morphological variants, that is the …

Marine Viral Diversity And Spatiotemporal Variability, Dawn Goldsmith

USF Tampa Graduate Theses and Dissertations

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 10³⁰. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. …

Genetic Basis For The Virulence Of Enterohemorrhagic Escherichia Coli Strain Tw14359, Jason Kyle Morgan

USF Tampa Graduate Theses and Dissertations

Enterohemorrhagic Escherichia coli (EHEC) is a virulent pathotype of E. coli that is associated with major outbreaks of hemorrhagic colitis and the life-threatening kidney disease hemolytic uremic syndrome. For successful host colonization and attachment to the intestinal mucosa, EHEC requires the locus of enterocyte effacement (LEE) pathogenicity island, which encodes a type III secretion system (TTSS) responsible for secreting and translocating effector proteins into host colonocytes. Regulation of the LEE is primarily directed through the first operon, LEE1, encoding the locus encoded regulator (Ler), and occurs through the direct and indirect action of several regulators. The 2006 U.S. spinach outbreak …

Microbial Communities In A Coastal Cave: Cova Des Pas De Vallgornera (Mallorca, Western Mediterranean), Antoni Busquets, Joan J. Fornós, Freddy Zafra, Jorge Lalucat, Antoni Merino

International Journal of Speleology

As a part of an ongoing project on the role of microbes in the biogeochemistry of Majorcan caves, the species diversity of microbial communities present in cave pools of anchialine waters in the Cova des Pas de Vallgornera (Mallorca, western Mediterranean) is investigated by a culture-dependent method. Two-hundred and forty-eight strains isolated from this characteristic cave environment of the littoral karst are identified by whole-cell-MALDI-TOF mass spectrometry and phylogeneticaly by 16S rRNA gene sequences. Total cell counts and species diversity of the bacterial communities decreas with the distance to the entrance of the cave and to the sea. Strains are …

Structure-Based Design Of Novel Inhibitors And Ultra High Resolution Analysis Of Ctx-M Beta-Lactamase, Derek Allen Nichols

USF Tampa Graduate Theses and Dissertations

The emergence of CTX-M class-A extended-spectrum β-lactamases, which confer resistance to second and third-generation cephalosporins, poses a serious health threat to the public. CTX-M β-lactamases use a catalytic serine to hydrolyze the β-lactam ring. Specifically, the hydrolysis reaction catalyzed by CTX-M β-lactamase proceeds through a pre-covalent complex, a high-energy tetrahedral acylation intermediate, a low-energy acyl-enzyme complex, a high-energy tetrahedral deacylation intermediate after attack via a catalytic water, and lastly, the hydrolyzed β-lactam ring product which is released from the enzyme complex. The crystallographic structure of CTX-M at sub-angstrom resolution has enabled us to study enzyme catalysis as well as perform …

Identification And Ss-Lactam Resistance In Aquatic Isolates Of Enterobacter Cloacae And Their Status In Microbiota Of Domica Cave In Slovak Karst (Slovakia), Barbora Gaalova, Alena Donauerova, Milan Seman, Helena Bujdakova

International Journal of Speleology

Domica Cave is located in the Slovak Karst National Park in southern Slovakia. Heterotrophic cultivable psychrophilic and mesophilic microbiota were confirmed to be prevalent in this cave. Escherichia coli was the most abundant bacterium, followed by Enterobacter species and Serrratia species. Enterobacter cloacae isolates belong to the group of faecal contaminants (coliforms) of concern in water. Their status in cave ecosystem is questionable, but we observed E. cloacae in water samples all years round suggesting an autochthonous origin. We were concerned with possible contamination of the cave water with resistant E. cloacae from animal farms located 2-3 km from the …

National Park Service Cave Ecology Inventory And Monitoring Framework, Gretchen M. Baker, Steven J. Taylor, Shawn Thomas, Rick Olson, Kathy Lavoie, Marie Denn, Steven Thomas, Hazel Barton, Kurt Helf, Rene Ohms, Joel Despain, Jim Kennedy, David Larson

National Cave and Karst Management Symposium 2013

A team developed the Cave Ecology Inventory and Monitoring Framework for National Park Service (NPS) units. It contains information for NPS cave managers across the United States to determine how to inventory and monitor cave ecology. Due to the wide geographical scope of NPS caves and their many different types, the document does not prescribe exact protocols. Instead, it provides guidance for what types of inventory and monitoring are possible, a framework for deciding how to prioritize inventory and monitoring activities, and references to specific protocols that are already in place at NPS cave parks.

Keywords: cave ecology, cave microbiology, …

Mycological Study For A Management Plan Of A Neotropical Show Cave (Brazil), Erika Linzi Silva Taylor, Maria Aparecida De Resende Stoianoff, Rodrigo Lopes Ferreira

International Journal of Speleology

Caves are stable environments with characteristics favoring the development of microorganisms. The allocthonous input of organic matter and microbes into the warm Neotropical caves may favor the development of filamentous fungi, including pathogenic species. Histoplasma capsulatum is a pathogenic species commonly found in caves and associated with bat and bird guano. Many Brazilian caves have been historically visited due to scenic and religious tourism. The objective of this study was to perform a microbiology study for a management plan of a show cave in Brazil, focusing on the presence and distribution of pathogenic and opportunistic fungi in the cave. Statistics …

Epilithic And Aerophilic Diatoms In The Artificial Environment Of Kungsträdgården Metro Station, Stockholm, Sweden, Lena Norbäck Ivarsson, Magnus Ivarsson, Johannes Lundberg, Therese Sallstedt, Catarina Rydin

International Journal of Speleology

The Kungsträdgården metro station is an artificial and urban subsurface environment illuminated with artificial light. Its ecosystem is almost completely unknown and as a first step to better understand the biology and rock wall habitats the diatom flora was investigated. A total of 12 species were found growing on the rock walls of Kungsträdgården metro station. The results show the diatom flora in Kungsträdgården to be dominated by e.g. Diadesmis contenta, Diadesmis perpusilla, Pinnularia appendiculata, Nitzschia amphibia, Nitzschia sinuata and Diploneis ovalis. One species, Caloneis cf. aerophila, has never been reported from Sweden before. …

Comparative Microbial Community Composition From Secondary Carbonate (Moonmilk) Deposits: Implications For The Cansiliella Servadeii Cave Hygropetric Food Web, Annette Summers Engel, Maurizio G. Paoletti, Mattia Beggio, Luca Dorigo, Alberto Pamio, Tiziano Gomiero, Claudio Furlan, Mauro Brilli, Angelo Leandro Dreon, Roberto Bertoni, Andrea Squartini

International Journal of Speleology

The microbial diversity of moonmilk, a hydrated calcium carbonate speleothem, was evaluated from two Italian caves to provide context for the food web of highly-specialized troglobitic beetles, Cansiliella spp. (Leptodirinae), with distinctive carbon and nitrogen isotope values indicative of a novel food source. The moonmilk and associated percolating waters had low to no extractable chlorophyll, with an average organic C:N ratio of 9, indicating limited allochthonous input and a significant contribution from microbial biomass. The biomass from moonmilk was estimated to be ~10⁴ micro- and meiofaunal individuals per m² and ~10⁷ microbial cells/ml. Betaproteobacteria dominated the …