Our experiments aimed to investigate responses of the marine cyanobacteria Prochlorococcus and Synechococcus to toxic arsenic species, such as arsenate, and to understand cellular mechanisms that contribute to arsenic tolerance. We used two strains of Prochlorococcus, a high-light adapted MED4 and low-light adapted MIT9313, both axenic, for cultivation experiments. For...
Streptococcus pneumoniae and Influenza A Virus both primarily infect the upper respiratory tract, with more severe disease occurring during coinfection than would be caused by either pathogen independently. Until recently, characterization of the interactions between these two pathogens has occurred exclusively in the context of a host or using host-derived...
Freshwater systems cycle carbon along a spatial and temporal biogeochemical continuum, across which ecosystem processes contribute to transformations of organic matter (OM). Various ecological constraints impact rates OM transformation and production and consumption of the energetic end of respiration, methane. Microbiological processing and complete reduction of carbon substrates to methane...
Toxin production by cyanobacterial harmful algal blooms (cyanoHABs) in freshwater systems has lasting ecological and human impacts. Nutrients, light availability, hydrology, and microbial community composition impact the frequency and intensity of toxic cyanoHABs. Climate change will exacerbate toxic cyanoHABs, making real time and predictive monitoring a vital tool for managing...
The phylum Cnidaria contains three main branches: Anthozoa (corals, sea anemones) Medusozoa (jellyfish, hydra), and Endocnidozoa. This latter branch is characterized by parasitism and contains the microscopic fish-parasites Myxozoa. Myxozoa are highly simplified, consisting of only a few cell types, however they have retained the nematocyst stinging cells and complex...
Pseudomonas aeruginosa is a ubiquitous environmental microbe, opportunistic pathogen, and a highly social organism. P. aeruginosa utilizes a wide array of cooperative behaviors to adapt to the environmental conditions around it. These behaviors include quorum sensing (QS), a form a cell-to-cell signaling that coordinates the expression of secreted products in...
In recent decades the habitat of North American beaver (Castor canadensis) has expanded from boreal forests into pan-Arctic tundra ecosystems. It is unknown how the advance of beavers into Arctic watersheds will impact microbial communities responsible for the mineralization of organic matter (OM), which has implications for carbon cycling. To...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Pre-spawning mortality (PSM) presents a major problem for population recovery of spring Chinook salmon (Oncorhynchus tshawytscha) in the Willamette River basin. In certain reaches and years, PSM has exceeded 90%. Histology has been used as the primary diagnostic method to investigate PSM in the Chinook Salmon, and a collection of...
To examine the macrophage response to M. avium, I compared inflammasome and cytosolic sensor expression and activation. My result demonstrated that virulent strains of M. avium (A5 and 104) suppress IL-1β production and induce IFN-β production in macrophages. M. avium mutants deficient at DNA export in the biofilm exhibited reduced...
Background: Mycobacterium abscessus (MAB) is a rapidly growing opportunistic pathogen that causes infections in immunocompromised patients. The highly impermeable cell wall and surface transport systems are major contributing factors to MAB intrinsic resistance, influencing the efficacy of bactericidal antibiotics. Phages are promising alternatives to antibiotics and have been used in...
Pseudoloma neurophilia is the most common pathogen reported in zebrafish (Danio rerio) research facilities and is an important threat to the zebrafish model. This microsporidian parasite can cause clinical disease, but more importantly is a causative agent of non-protocol induced variation in research. Studies utilizing infected zebrafish, could potentially confound...
Phytoplankton initiate the marine carbon cycle by fixing carbon dioxide into biologically available compounds. These abundant single celled organisms mediate carbon flux from the atmosphere to the deep ocean and are the base of the marine food web, supplying new carbon to higher trophic levels. Phytoplankton are highly diverse and...
Coral reef ecosystems continue to be significantly altered by disease epizootics, but why some host populations remain resistant while others succumb to outbreaks remains unknown. Research across diverse animal and plant host systems has revealed that disease severity is strongly influenced by host genetics and by environmental influences on both...
Corals provide a diversity of ecosystem services, are among the most biologically diverse ecosystems on Earth, and directly support ~500 million people globally; however, corals are increasingly experiencing significant threats and are undergoing severe bleaching events as the result of the warming climate. Using a two-year data set surrounding a...
On coral reefs, disturbances rarely occur in isolation. Global stressors such as increasing seawater temperature often coincide with local stressors like nutrient pollution. In the face of increasing anthropogenic stress, corals can function as environmental sentinels, although little is known about how multiple stressors interact to disrupt their associated bacterial...
Gut-brain communication consists of bidirectional routes between cognitive centers of the brain and peripheral intestines. This bidirectional communication is the result of the interplay between enteroendocrine cells (EECs), enteric nervous system, central nervous system, the vagus nerve, and our microbiota. Multiple studies have associated gut microbial dysbiosis with neurological disorders...
Vibrio bacteria are commonly found in freshwater, marine, and estuarine environments. Members of this genus can exist in commensal relationships with marine animals or as planktonic bacteria, however, they are well known for their roles as pathogens towards humans and animals. In this dissertation, I investigated aspects of host-bacteria relationships...
The myxozoan Ceratonova shasta is an intestinal parasite of salmon and trout that causes ceratomyxosis, a disease characterized by severe inflammation of the intestine that can lead to hemorrhaging, necrosis, and death of the fish host. The parasite is endemic to the Pacific Northwest of the United States and Canada,...
Ceratonova shasta is an obligate endoparasite of salmonid fish that is endemic to the Pacific Northwest of North America. The parasite has a complicated lifecycle with two distinct spore stages and two obligate hosts, a salmonid and a freshwater annelid. Myxospores released from infected salmonid hosts, infect Manayunkia occidentalis (freshwater...
Agricultural and companion animals are integral to our way of life as they provide us with nourishment, financial resources, transportation, and companionship. However, pets, managed animals in the agricultural industry, as well as wild populations of food animals are all subject to health and mortality risks. The gut microbiome is...
Seagrasses and coral reefs play important roles in nutrient cycling, coastal protection, and maintaining marine biodiversity. However, these coastal marine organisms are declining globally due to anthropogenic stressors, such as rising ocean temperatures, ocean acidification, and eutrophication. These organisms live in close association with their microbiomes, which can be beneficial...
Utilization of zebrafish, Danio rerio, has steadily increased and its applications have expanded into numerous fields of science. Applying elevated temperatures (32°C to 37°C) to this organism has allowed researchers to conduct climate change, human cancer and infectious disease studies. Though zebrafish can be acclimated from the standard 28°C to...
A critical barrier to effective management of deep-sea resources is a lack of understanding by society of the benefits received from the oceans. To address this knowledge gap, we applied an iterative design-based research methodology to evaluate (1) how to effectively use an exhibit to increase public literacy of the...
In biomedical applications, it is often of interest to test the alternative hypothesis that the means of three or more groups follow a strictly monotonic trend such as u1 > u2 > u3 against the null hypothesis that the group means are either equal or unequal but are not monotonic....
The bioavailability of chemical compounds in the marine environment fundamentally influences the growth and physiology of microorganisms. Organic and inorganic chemicals that are produced by some marine plankton can be consumed by other plankton for energy production, growth, or to initiate essential physiological processes. Cultures of the diatom Thalassiosira pseudonana,...
The lagoons spanning Alaska’s Beaufort Sea coast provide a unique habitat for arctic wildlife. These lagoons and the food webs they support face extreme seasonality with nine months of ice cover followed by a spring thaw that pulses a large amount of freshwater and nutrients into the lagoons. Bacteria link...
Myxozoans are an enigmatic group of obligately parasitic, microscopic cnidarians. They diverged from their free-living relatives over 600 million years ago and have highly reduced genomes. However, they have retained nematocyst stinging cells which characterize the phylum Cnidaria. Free-living cnidarians utilize this cellular weaponry for defense and predation whereas the...
Investigations of 16S rRNA gene sequences hallmark modern microbiology. These sequences provide culture-independent insight into the abundance and distribution of microbiota and serve as a principle resource through which microbial community diversity is measured. Consequently, researchers rely on 16S gene sequences to test hypotheses rooted in ecology, evolution, and disease....
Diatoms play a major role in ocean biogeochemical cycles and are important tools in bioengineering for natural products and nanotechnology. Diatoms and other algae growing at varying resource-limited growth rates allocate carbon to different metabolic pathways to optimize growth; however, the molecular mechanisms controlling these pathway gating strategies are not...
Biotic and abiotic processes at continent-ocean interfaces cycle a disproportionate mass of carbon and nutrients relative to their global surface area, and microbial activity is a principal determinant of organic and inorganic matter flux in these transition zones. Most studies using modern high-throughput ‘omics techniques to link microorganisms with costal...
The waterborne, myxozoan parasite Ceratonova shasta is endemic to the Pacific Northwest and can be lethal to its secondary salmonid host, including the culturally, economically, and recreationally important spring Chinook salmon (Oncorhynchus tshawytscha) of the Deschutes River, OR. Previously described genotypes of C. shasta exhibit specificity with their salmonid hosts....
Marine sediments are vast sources and reservoirs of methane, a potent greenhouse gas. Most of this methane is anaerobically oxidized by archaea before it can reach the overlying ocean, though the efficiency of this process often depends on methane fluxes and mechanisms of fluid transport. Anaerobic methanotrophic archaea, or ANME,...
This is the 4th edition of a book that was initiated with the annotation of the function of all the genes in the most commonly studied baculovirus, AcMNPV. It has been almost six years since I reviewed this literature. As a measure of the research that has occurred over this...
At a time of rapid global change, a socio-ecological system (SES) approach can provide a framework through which to quantify and communicate the risks and uncertainties of coupled human-natural systems. Islands, and tropical coral reef islands in particular, can be excellent models for SES research since they may be considered...
The modern world has presented many threats to the health and stability of ecosystems worldwide. One of the most biodiverse ecosystems, coral reefs, faces particularly strong pressures, and is already declining rapidly in complexity and area. Although the stressors that affect reefs are diverse, ranging from nutrient pollution to overfishing,...
Bacterial aggregation is a strategy employed by many pathogens to establish infection. Mycobacterium avium subsp. hominissuis (MAH) undergoes a phenotypic change, microaggregation, when exposed to the respiratory epithelium. This aggregation is an important step in the pathogenesis of the infection, laying the foundation for biofilm formation. We therefore compared how...
The myxozoan parasite Ceratonova shasta threatens both juvenile and adult salmonid populations in the Pacific Northwest region of the United States, causing intestine necrosis and hemorrhaging, along with high mortality in some fish strains. It induces an inflammatory tissue response in susceptible strains of fish; understanding the interactions between C....
In a process called quorum sensing (QS), the bacterial pathogen Pseudomonas aeruginosa uses small diffusible signals to coordinate cooperative behaviors via secreted “public goods”. Under QS-dependent growth conditions, social cheaters arise with mutations in lasR, the gene for the primary QS signal receptor. These cheaters do not produce public goods....
Agrobacterium species transform plant cells by targeting a portion of plasmid-encoded bacterial DNA to the host nucleus. Genetic transformation by A. tumefaciens and A. rhizogenes requires secreted effector proteins. The tumor-inducing (Ti) plasmid from virulent A. tumefaciens encodes VirE2, a secreted single-stranded DNA-binding protein required for efficient transformation of hosts....
Microbial-induced calcite (CaCO₃) precipitation (MICP) is a well-known natural phenomenon where microbes precipitate calcite in their environment as a result of metabolic activity. It has recently been of interest as a bioengineered technique to stabilize soils for construction applications. A known metabolic pathway to induce MICP is ureolysis, where introduced...
Gadusol is a UV-B-absorbent compound found in fish and other marine organisms where it is presumed to play a role as a sunscreen and antioxidant. In light of commercial potential as a replacement for problematic synthetic sunscreens, a process to produce recombinant gadusol in the yeast Saccharomcyces cerevisiae was investigated....
Parasites are ubiquitous members of ecological communities, capable of contributing to the decline of vulnerable populations. Therefore, monitoring parasite level is a critical component for host management. Molecular tools, such as quantitative polymerase chain reaction (qPCR), can be valuable additions to monitoring protocols that assess parasitic disease risk to hosts....
Zebrafish (Danio rerio) are one of the most commonly used animal models in biomedical research. Zebrafish resource facilities, like the Zebrafish International Resource Center (ZIRC) in Eugene, Oregon, are the main providers and keepers of numerous zebrafish wild-type, mutant, and transgenic lines. Although ZIRC maintains live zebrafish at various life...
Mycobacterium avium subspecies hominissuis (MAH) is an opportunistic pathogen that is ubiquitous in the environment and often isolated from faucets and showerheads. MAH mostly infects humans with an underlying disease, such as chronic pulmonary disorder (COPD), cystic fibrosis (CF), or are immunocompromised, though infections in patients without concurrent disease are...
Koi herpesvirus (KHV) is a highly pathogenic virus of common carp and koi. KHV becomes latent in recovered koi or exposed koi without symptoms, and the latent infection can reactivate under stress conditions. KHV reactivation from latency often occurs when water temperature rapidly rises above 17 °C. Dissolved O2 is...
The combined activities of diverse heterotrophic marine microorganisms significantly shape global biogeochemical cycles, but models of these activities are currently limited to aggregate microbial community processes, and it remains unclear how community structure and the functional roles of specific microbial taxa should be integrated into these models. Therefore, understanding the...
Cell-cell communication in bacteria is understood to facilitate the coordination of population-wide cooperative behavior in the form of concerted gene expression. The opportunistic pathogen Pseudomonas aeruginosa uses such a communication mechanism to regulate a large group of genes important to virulence strategies in this bacterium. This general mechanism of communication...
A method for large quantity dsRNA production was developed since a small amount of dsRNA synthesized in vitro with commercial kits are used for small scale bioassay evaluations. Developing a large-scale production system for dsRNA is critical for practical RNAi application, especially for non-transgenic RNAi-based control. However, large-scale analysis or...
Cooperative behaviors in bacteria are increasingly appreciated for their relevance to microbial ecology and utility as model systems for social evolution. One example is the secretion of siderophores, a structurally diverse group of compounds that chelate extracellular iron. Siderophore production is considered cooperative because the benefits can be shared with...
Oceanic carbon cycling plays a major role in determining global atmospheric CO₂. A better understanding of dissolved organic matter and its constituents in the water column and how it affects marine carbon cycling is sought after. This study successfully measured osmolytes, low molecular zwitterionic compounds derived from amino acids, in...
Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that can produce as many as 17 different toxins and are responsible to cause a wide array of gastrointestinal (GI) and histotoxic diseases in humans and animals. As individual strains produce a subset of these toxins, C. perfringens strains can be classified...
Cyprinid herpesvirus 1 (CyHV1) infects all scaled and color varieties of common carp Cyprinus carpio, including koi. While it is most often associated with unsightly growths known as ‘carp pox,’ the underlying lesion (epidermal hyperplasia) can arise from a variety of disease processes. CyHV1-induced epidermal hyperplasia may occur transiently in...
Phytoplankton and microzooplankton comprise the base and the first link of the marine food web, respectively. These microbes are key drivers of marine carbon and nutrient cycles. Phytoplankton convert atmospheric CO₂ into organic carbon, and microzooplankton consume phytoplankton, packaging phytoplankton carbon into particulate forms that have a variety of fates:...
Marine mammals are top predators that are essential for the health and function of our oceans. These top predators are often affected by various factors that can be detrimental to their populations. Therefore, there is a need to evaluate undetermined causes of deaths and to better understand known diseases in...
Koi herpesvirus (KHV) is highly pathogenic to Cyprinus carpio. KHV can also become latent in recovered fish and reactivate from latency under stressful conditions. Understanding KHV latency is important for development of strategies against herpesvirus latent infection. Our previous studies found KHV ORF6 mRNA is detectable during latent infection. In...
High counts of fecal indicators, used to signal the potential presence of pathogens associated with untreated waste, result in the classification of water bodies throughout the United States as impaired. Nonpoint sources of unknown origin that contribute to fecal contamination make management of impaired waters challenging, as they are difficult...
The advent of improved DNA sequencing technologies has allowed the analysis of various microbial communities. Bloom-forming freshwater cyanobacteria can produce toxins and taste-and-odor compounds that can negatively affect drinking water supplies. Here, I have employed second- and third-generation sequencing technologies to characterize bloom-forming freshwater cyanobacterial genomes and their associated heterotrophic...
Historically, the difficulty of obtaining pure cultures of abundant marine
microbial plankton has an obstacle to reconstructing the underlying
mechanisms of biogeochemistry in the ocean. While a number of dominant
marine species from the ocean surface have been cultured, the dominant
microbial plankton of the dark ocean proved far more...
Pseudomonas aeruginosa is an environmental bacterium which
opportunistically infects humans. Commonly residing in irondepleted
environments, P. aeruginosa uses iron-chelating
molecules called siderophores to scavenge iron from its
environment. The most prevalent siderophore used by P.
aeruginosa is known as pyoverdine. After the cell synthesizes and
secretes pyoverdine, the molecule binds...
The acquired ability of Salmonella to express varying morphotypes when placed in nutrient-limited conditions is hypothesized to predict increased resistance to food processing interventions. Two of the morphotypes expressed by Salmonella are Red, Dry and Rough (RDAR) and Smooth and White (SAW). Increased resistance is predicted for the RDAR morphotype...
C. perfringens is a spore-forming, gram-positive, anaerobic pathogenic bacterium capable of causing a wide variety of diseases in both humans and animals. However, the two most common illnesses in humans are C. perfringens type A food poisoning (FP) and non-food-borne (NFB) gastrointestinal (GI) illnesses. Interestingly, these two major diseases are...
Nitrification is the process within the global Nitrogen Cycle where ammonia (NH3) is oxidized to nitrate (NO₃⁻) and can be carried out by two distinct groups of bacteria. The ammonia-oxidizing bacteria (AOB) first oxidize NH₃ to nitrite (NO₂⁻), and second, the nitrite-oxidizing bacteria (NOB) oxidize NO₂⁻ to NO₃⁻. In aerobic...
Respiratory infections caused by nontuberculous mycobacteria (NTM), especially Mycobacterium avium, can lead to progressive, recurrent disease that is refractory to therapy. Bacterial biofilms are intrinsically resistant to a variety of stressors and pressures, including host killing mechanisms and antibiotic therapy. Though it is becoming increasingly evident that NTM biofilms are...
Limnology is undergoing a transition to high-throughput -omic analysis of freshwater
bacterial communities. An important first step in making the transition is to
characterize several genomes that can be used as references to guide metagenome
assembly and analysis. Here I characterize four new freshwater cyanobacterial
genomes, a pair of lake...
Cyclic nitramines are a class of compounds that include most of the commonly used explosives today. These are among the most common toxicants released into the environment as a result of human activity, generated on military ranges, battlefields, and production sites. Of these, hexahydro-1,3,5-trinitro-1,3,5- triazine (RDX) is of particular interest,...
In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of microbial communities shift as the system moves away from a healthy state is critical to assessing disease progression and to formulate any potential mitigation strategy....
29 Dec 2015: Rosales SM, Vega Thurber R (2015) Correction: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLOS ONE 10(12): e0146208. https://doi.org/10.1371/journal.pone.0146208
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is...
Humans and viral disease are inextricably intertwined. Viral disease plays an immeasurable role in human life, from the disease and economic burden associated with every facet of contending with human viral disease, to managing the consequences of viral disease in organisms important to our food supply, economy, and entertainment. The...
Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic...
While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass...
Hepatocellular carcinoma (HCC) is one of the most lethal human cancers. The search for targeted treatments has been hampered by the lack of relevant animal models for the genetically diverse subsets of HCC, including the 20-40% of HCCs that are defined by activating mutations in the gene encoding β-catenin. To...
Cases of pulmonary diseases caused by Mycobacterium avium complex (MAC) have increased over the years and have become a major health concern in Europe, Asia, and the United States. MAC, comprised of M. avium species and M. intracellulare, are found everywhere in the environment: in water sources and the soil....
Photosynthetic energy allocation strategies were investigated in the marine diatom, Thalassiosira pseudonana, grown under a wide range of light limitation. Steady-state, continuous cultures were established at three light-limited growth rates. Simultaneous measurements of photosynthetic activity were made that targeted different points in photosynthetic energy flow from gross to net photosynthesis....
Phospholipase C enzymes hydrolyze the rare membrane lipids phosphatidylinositol-4-phosphate (PIP) and phosphatidylinositol-4,5-bisphosphate (PIP2) PIP into inositol triphosphate (IP3) and diacylglycerol (DAG). Phospholipase C enzymes of the β subtype (PLC-β) function specifically in the signal transduction pathways regulated by Gαq-coupled seven transmembrane receptors. These signaling pathways link plasma membrane receptor activation...
Mycobacterium avium subsp hominissuis (MAH) is an opportunistic environmental pathogen that causes respiratory and gastrointestinal illness in immunocompromised persons such as those with chronic respiratory diseases or AIDs, respectively. In recent years, there has been a significant increase in the incidence of nontuberculous mycobacterial (NTM) lung infections, including in cystic...
Over 100 monthly bacterioplankton DNA samples, from each of the surface and 200 m depths at the Bermuda Atlantic Time-series Study (BATS) site, were analyzed for community assembly processes. Correlation networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the two depths were remarkably similar...
The recent identification of multiple genotypes of the salmonid parasite Ceratonova shasta with different virulence levels in Chinook salmon (Oncorhynchus tshawytscha) suggests that it may be possible to immunize fish against subsequent infection and disease. We hypothesized that exposure of Chinook salmon to the less virulent parasite genotype (II) prior...
Cyprinid herpesvirus 3 (CyHV-3), commonly known as koi herpesvirus (KHV), is a member of the Alloherpesviridae and is a deadly pathogen for koi and common carp, Cyprinus carpio. It causes severe gill necrosis and nephritis, dermal ulceration and hemorrhage, and mass mortality of up to 100% of affected fish. Fish...
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic inflammatory bowel disease that affects ruminant populations worldwide. The characteristic stages of the disease make diagnosis difficult, resulting in silent transmission among animals in a herd for years before proper detection of the infection. The extensive...
Wild fish populations are typically infected with a variety of micro- and macroparasites that may affect fitness and survival, however, there is little published information on parasite distribution in wild juvenile salmonids in three upper tributaries of the Willamette River, OR. The objectives of this survey were to document (1)...
Bacteria found in clarified ovine rumen fluid are capable of degradation of high-energy explosives such as RDX (Hexahydro-1,3,-trinitro‐1,3,5‐triazine) and HMX (Octahydro‐1,3,5,7‐tetranitro‐1,3,5,7-tetrazocine).
Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into hatcheries through untreated water sources. Many pathogens exist naturally within the environment (with the exception of introduced pathogens) and the presence of a...
Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Herewe examined spatial and short-term temporal variability in marine viral abundance...
The within-host interactions that can occur as a result of mixed infections in wildlife likely influence the outcome of an infection. We investigated the infection frequency and outcome as well as the potential mechanisms regulating mixed infections with two Ceratonova shasta genotypes within the Chinook salmon host. Previous research in...
Correction
25 Aug 2014: The PLOS ONE Staff (2014) Correction: Histopathologic Alterations Associated with Global Gene Expression Due to Chronic Dietary TCDD Exposure in Juvenile Zebrafish. PLOS ONE 9(8): e106605. https://doi.org/10.1371/journal.pone.0106605
Lactic Acid Bacteria (LAB), an important group of organisms in modern food production, are known to secrete a unique compound called exopolysaccharide (EPS). EPS is economically important because it enhances functional properties in food and may confer beneficial health effects to consumers. Novel strains of Lactococcus lactis, Streptococcus thermophilus, and...
Peptide-phosphorodiamidate morpholino oligomers (PPMOs) are synthetic DNA mimics that bind and silence gene targets. Through designing PPMOs that silence essential or resistance genes in pathogens, these antisense oligomers could be utilized as novel antimicrobials. Towards this end, my thesis employed minimum inhibitory concentration assays (MICs) to identify PPMOs capable of...
In most environments, ammonia (NH₃) is oxidized to nitrate (NO₃⁻) via the intermediate nitrite (NO₂⁻). This is a microbe-driven process involving phylogenetically distinct types of microorganisms, namely, ammonia-oxidizing bacteria (AOB) and Thaumarchaea (AOA), and nitrite-oxidizing bacteria (NOB). Nitrosomonas europaea and Nitrobacter winogradskyi are the best studied AOB and NOB, respectively,...
Surface disinfection of fertilized fish eggs is widely used in aquaculture to reduce
extraovum pathogens that may be released from brood fish during spawning, and this is routinely
used in zebrafish (Danio rerio) research laboratories. Most laboratories use approximately 25-50 ppm unbuffered chlorine solution for 5-10 min. Treatment of embryos...
The Autographa californica M nucleopolyhedrovirus (AcMNPV) sulfhydryl oxidase Ac92 is essential for production of infectious virions. Ac92 also interacts with human p53 and enhances human p53-induced apoptosis in insect cells, but it is not known whether any relationship exists between Ac92 and native p53 homologs from insect hosts of AcMNPV....
Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host...
Background: Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) are synthetic DNA/RNA analogs that silence expression of specific genes. We studied whether PPMOs targeted to essential genes in Acinetobacter lwoffii and A. baumannii are active in vitro and in vivo. Methods: PPMOs were evaluated in vitro using MIC and viability assays, and in...
The genome sequence of a baculovirus from Hemileuca sp. was determined. The genome is 140,633 kb, has a G+C content of 38.1%, and encodes 137 putative open reading frames over 50 amino acids. 126 of these ORFs showed similarity to other baculovirus genes in the database including all 37 core...
The microsporidian parasite, Pseudoloma neurophilia, is the most commonly diagnosed infectious disease in laboratory populations of the zebrafish, Danio rerio. Infections by P. neurophilia are generally subclinical, however, they can become acute either incidentally or due to experimental immune suppression. Non-protocol induced variation can confound results in laboratory experiments using...