Pseudomonas Aeruginosa Biofilm Formation in Different Environments

poster abstractVarious bacteria, such as the soil microbe Pseudomonas aeruginosa, form into strong structures to defend themselves from antibiotics and other harmful materials. These structures are called biofilms. The goal of this research is to isolate P. aeruginosa from several soil samples and determine whether they are able to form biofilms in those environments. Another goal of this research is to find out how different environmental factors affect the formation of Pseudomonas biofilms. We isolated P. aeruginosa from soil samples using Pseudomonas Isolation Agar plates. The colonies most similar to P. aeruginosa were picked, cultured, and tested by PCR in order to confirm that the strains were actually P. aeruginosa. Using these methods, so far we have collected 12 P. aeruginosa strains and we are collecting more strains from different soil samples. In future studies, we will determine whether these strains form biofilms in soil. We will also demonstrate the effect of magnesium on P. aeruginosa on biofilm formation. These studies will begin to investigate how altering environmental conditions can influence persistence of this bacterial pathogen in the soil. These studies can have broad implications for transmission of the bacterium from the environment to humans during disease

Cross-Layer Design in Dynamic Spectrum Sharing Systems

We consider a dynamic spectrum sharing system consisting of a primary user, whose licensed spectrum is allowed to be accessed by a secondary user as long as it does not violate the prescribed interference limit inflicted on the primary user. Assuming the Nakagami-m block-fading environment, we aim at maximizing the performance of secondary user's link in terms of average spectral efficiency (ASE) and error performance under the specified packet error rate (PER) and average interference limit constraints. To this end, we employ a cross-layer design policy which combines adaptive power and coded discrete M-QAM modulation scheme at the physical layer with a truncated automatic repeat request (ARQ) protocol at the data link layer, and simultaneously satisfies the aforementioned constraints. Numerical results affirm that the secondary link of spectrum sharing system combining ARQ with adaptive modulation and coding (AMC) achieves significant gain in ASE depending on the maximum number of retransmissions initiated by the ARQ protocol. The results further indicate that the ARQ protocol essentially improves the packet loss rate performance of the secondary link

Utilizing the C2Maps Platform for Characterizing Drug-Protein Relations, Generating Mobile Games, and Constructing Integrated Pathway Models

poster abstractThe C2Maps platform is a collection of genome-wide data that display the connections between drugs, diseases and genes. The C2Maps is used as a tool to compare and extrapolate known map data into unknown areas. By using C2Maps, researchers can compare genetic, sequential and physical information about disease specific proteins. Manual curation is important for the C2Maps platform in order to validate the literature mining approach and to overcome high levels of data noise generated from molecular networks. Currently we are examining specific drug-protein relationships in several diseases. In this research, the C-Maps website is being used to manually curate abstracts about disease specific drugprotein relations and then it is determined whether a drug “Up Regulates”, “Down Regulates”, or “Indirectly” affects a specific protein. Presently, more than 2000 specific protein-drug relations have been examined through the platform. We theorize that new drug-protein relations will be discovered through curation efforts. To broaden the scope of curation data generated, a C2Maps mobile game is in the process of being developed. This game takes advantage of novel technology in mobile development to create a game that will allow several researchers to contribute to the curation process. The data generated from the manual curation approach can be used to validate various protein-drug relationships in pharmacology and can determine the best possible drugs targeting specific proteins in cancer. Optimal drugs and their respective targets for a specific disease can then be incorporated into an integrative pathway model to analyze the mechanism of the drug. Specific properties of the drug, including chemical structure, can then be examined to determine how a specific drug acts on particular target proteins

Kif14 overexpression accelerates murine retinoblastoma development

The mitotic kinesin KIF14 has an essential role in the recruitment of proteins required for the final stages of cytokinesis. Genomic gain and/or overexpression of KIF14 has been documented in retinoblastoma and a number of other cancers, such as breast, lung and ovarian carcinomas, strongly suggesting its role as an oncogene. Despite evidence of oncogenic properties in vitro and in xenografts, Kif14's role in tumor progression has not previously been studied in a transgenic cancer model. Using a novel Kif14 overexpressing, simian virus 40 large T-antigen retinoblastoma (TAg-RB) double transgenic mouse model, we aimed to determine Kif14's role in promoting retinal tumor formation. Tumor initiation and development in double transgenics and control TAg-RB littermates were documented in vivo over a time course by optical coherence tomography, with subsequent ex vivo quantification of tumor burden. Kif14 overexpression led to an accelerated initiation of tumor formation in the TAg-RB model and a significantly decreased tumor doubling time (1.8 vs. 2.9 weeks). Moreover, overall percentage tumor burden was also increased by Kif14 overexpression. These data provide the first evidence that Kif14 can promote tumor formation in susceptible cells in vivo

Drug Discovery Through Drug Perturbation Pathway Modeling and Network Analysis

Due to intrinsic complex molecular interactions, the “one disease – one target – one drug” strategy for disease treatment is no longer the best option to treat cancers. To assess drug pharmacological effects, we assume that “ideal” drugs for a patient can treat or prevent the disease by modulating gene expression profiles of this patient to the similar level with those in healthy people. A new approach for drug-protein interactions curation, drug-drug similarity network comparison, and integrative pathway model construction and evaluation was introduced to determine optimal drugs for various cancers. Drug-protein interaction curation is conducted to discover novel drug-protein relationships and is categorized as: up regulated, down regulated, indirect up or down, ambiguous and unknown. The manual curation can be utilized for drug repurposing and examining drug mechanism on a pathway level. A drug-drug similarity network model is built by examining similar targets, therapeutic mechanisms, side effects, and chemical structures. Drug similarity analysis is useful for drug repositioning because similar drugs may have compatible therapeutic or toxic effects for a disease. Drug similarity networks are constructed and examined through a molecular network visualization platform. An integrative disease-specific pathway model is also built to gain a more holistic view of disease mechanisms by including every significant disease-specific protein. Including drugs on the pathway through target information can also offer a clear mechanism for the drug’s action. We also transform integrated pathways into network models and ranked drugs based on the network topological features of drug targets, drug-affecting genes/proteins, and curated disease-specific proteins. Combining our three approaches could potentially lead to advances in drug repurposing and repositioning

Optical coherence tomography enables imaging of tumor initiation in the TAg-RB mouse model of retinoblastoma

PURPOSE: Retinoblastoma is the most common primary intraocular malignancy in children. Although significant advances in treatment have decreased mortality in recent years, morbidity continues to be associated with these therapies, and therefore, there is a pressing need for new therapeutic options. Transgenic mouse models are popular for testing new therapeutics as well as studying the pathophysiology of retinoblastoma. The T-antigen retinoblastoma (TAg-RB) model has close molecular and histological resemblance to human retinoblastoma tumors; these mice inactivate pRB by retinal-specific expression of the Simian Virus 40 T-antigens. Here, we evaluated whether optical coherence tomography (OCT) imaging could be used to document tumor growth in the TAg-RB model from the earliest stages of tumor development. METHODS: The Micron III rodent imaging system was used to obtain fundus photographs and OCT images of both eyes of TAg-RB mice weekly from 2 to 12 weeks of age and at 16 and 20 weeks of age to document tumor development. Tumor morphology was confirmed with histological analysis. RESULTS: Before being visible on funduscopy, hyperreflective masses arising in the inner nuclear layer were evident at 2 weeks of age with OCT imaging. After most of these hyperreflective cell clusters disappeared around 4 weeks of age, the first tumors became visible on OCT and funduscopy by 6 weeks. The masses grew into discrete, discoid tumors, preferentially in the periphery, that developed more irregular morphology over time, eventually merging and displacing the inner retinal layers into the vitreous. CONCLUSIONS: OCT is a non-invasive imaging modality for tracking early TAg-RB tumor growth in vivo. Using OCT, we characterized TAg-positive cells as early as 2 weeks, corresponding to the earliest stages at which tumors are histologically evident, and well before they are evident with funduscopy. Tracking tumor growth from its earliest stages will allow better analysis of the efficacy of novel therapeutics and genetic factors tested in this powerful mouse model

Critical risk factors associated with investment in a renewable energy scheme (a life cycle risk analysis of an offshore wind farm in a net- zero community)

Following concerns about climate change, investment in renewables has become essential to achieve net-zero targets. However, there is a gap between essential and actual market share of renewable energy schemes due to associated risks. This research investigates Critical risk factors of investment in a Renewable energy scheme (The case of offshore wind in a net-zero community)”. The purpose of the research is to contribute mitigating risks of Renewable energy “in general” and “specific” to Offshore Wind farms to attract more investment. The study follows a combination of a literature review and structured interviews to identify and shortlist risks and then utilizes AHP method to evaluate major risks quantitatively. Based on the findings, Policy risks, Economic, Infrastructure and Technology, Financial and Environmental risks are respectively the most important risk categories for renewable energy investment. Moreover, the study highlights the importance of environmental risk especially for Offshore Wind farms due to nature of the infrastructure, location and severe weather conditions affecting operation and maintenance

Disruptive impacts of sustainability in project management and emerging sustainable practices in PMBOK 7th edition

Following concerns about climate change sustainable development has become an urgent need that requires institutional and governmental action. It is obvious that our unsustainable present has been built through projects by neglecting wider issues and Grand Challenges. Sustainability in project management has always been easy to understand but hard to implement in practice due to potential difficulties and lack of implicative solutions in PM standards. A structured review of 164 publications by (Silvius and Schipper 2014) indicates that the PM standards fail to seriously address the sustainability agenda. However, previous studies had a brief review on standards, and they were not updated as the PM standards are evolving during the time to adapt with new business needs. This research is the first study to investigate footprints of sustainability in PMBOK 7th edition with a more holistic and a purely theoretical perspective. The study considers sustainability as a crucial but disruptive aspect to be incorporated into the traditional project management functions. It proposes sustainability requires paradigm shifts which evolves current project management practices in a shift from process-based to a principle-based while creating value instead of focusing on deliverables and outputs

Critical risk factors associated with investment in a renewable energy scheme (a life cycle risk analysis of an offshore wind farm in a net- zero community)

Following concerns about climate change, investment in renewables has become essential to achieve net-zero targets. However, there is a gap between essential and actual market share of renewable energy schemes due to associated risks. This research investigates Critical risk factors of investment in a Renewable energy scheme (The case of offshore wind in a net-zero community)”. The purpose of the research is to contribute mitigating risks of Renewable energy “in general” and “specific” to Offshore Wind farms to attract more investment. The study follows a combination of a literature review and structured interviews to identify and shortlist risks and then utilizes AHP method to evaluate major risks quantitatively. Based on the findings, Policy risks, Economic, Infrastructure and Technology, Financial and Environmental risks are respectively the most important risk categories for renewable energy investment. Moreover, the study highlights the importance of environmental risk especially for Offshore Wind farms due to nature of the infrastructure, location and severe weather conditions affecting operation and maintenance

Disruptive impact of sustainability in project management and emerging sustainable practices in PMBOK 7th edition

Following concerns about exponential growth of world population, pollution, resource scarcity and its consequences sustainable development has become an urgent need that requires institutional and governmental action. It is obvious that our unsustainable present has been built through projects by neglecting wider issues and Grand Challenges. Sustainability in project management has always been easy to understand but hard to implement in practice due to potential difficulties and lack of implicative solutions in PM standards. This paper explores paradigmatic impacts of sustainability in project management practices and sustainability footprints in PMBOK 7th edition. In the first phase, the research follows an integrative literature review and thematically structure the review to synthesis the concepts to come up with a specific conclusion. In the second phase, researches will conduct interviews to strengthen the initial findings and generate new ideas about sustainable project practices. The study considers sustainability in project management as a crucial but disruptive aspect to be incorporated into the traditional management functions. It proposes sustainability as a key factor which evolves current project management practices in a shift from process-based to a principle-based while creating value instead of focusing on deliverables and outputs