Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution

SGER: Detection of Bioterrorism-Linked Microbial Pathogens Using Surface Acoustic Wave Liquid Sensors

Bioterrorism threats and attacks in civilian environments require sensors that can rapidly and accurately detect minute quantities of pathological bioagents. Selective and inexpensive sensors are urgently needed to detect pathogens in liquid environments, including food and water supplies. Conventional laboratory analyses are time-consuming, labor-intensive and inconsistent with the expedient response required in the wake or possibility of a bioterrorist act.The activities proposed in this Small Grant for Exploratory Research (SGER) are multidisciplinary and involve two faculty members from the University of Maine. Dr. Mauricio Pereira da Cunha, from the Department of Electrical and Computer Engineering, will provide expertise in the area of sensor platform development in general, and acoustic wave sensors in particular. Pereira DaCunha is a 2002 NSF CAREER award recipient, who has worked for more than 16 years in the acoustics microwave area. Dr. Paul Millard, from the Department of Chemical and Biological Engineering, is a microbiologist with more than 15 years of experience in microbial detection and analysis. Both Pereira da Cunha and Millard are affiliated with the University of Maine\u27s Laboratory for Surface Science and Technology, a multidisciplinary laboratory with appropriate facilities for the realization of the proposed tasks. This project determined the validity of integrating biomolecular technology with a novel SH-SAW sensor platform. This NSF SGER initiative permitted proof-of-concept verification of the LGS SH-SAW biosensor device and the results gave rise to a full proposal. It is expected that research and development of this particular sensor will permit the further creation of sensors for use in a wide range of environmental, medical, industrial, homeland security, and military applications. By providing a rapid, reliable and ultimately, inexpensive sensor, the development of this technology will contribute to general well-being of the population at large, and serve as a starting point for the development of an important new class of biosensors

SENSORS: Detecting Microbial Pathogens with Novel Surface Acoustic Wave Devices in Liquid Environments

This SENSORS proposal integrates research and education to exploit the sensitivity of a new family of LGX crystal devices operated in novel Shear Horizontal Surface Acoustic Wave (SH-SAW) propagation directions by combining them with highly selective molecular padlock probes to detect specific nucleic acid sequences associated with bacteria such as Escherichia coli O157:H7, Salmonella typhi, and Vibrio cholerae in aqueous solutions. The anticipated fundamental advances in sensor science and engineering will be relevant to numerous applications, including rapid response to bioterrorism, healthcare, epidemiology, agriculture, food safety, and pollution avoidance and mitigation. This SENSORS program builds upon the initial proof-of-concept results provided by an NSF SGER project funded by the divisions of Electrical and Communication Systems, and Bioengineering and Environmental Systems. The intellectual merit of this proposal rests in the creative, integrated research and education activities related to combining the recently identified LGX SH-SAW devices with molecular padlock probe technology to permit the design, fabrication, testing, and optimization of prototype biosensors. The specific research objectives of this SENSORS program are to: (i) Identify the surface density chemistry for increased sensitivity; (ii) Investigate and identify the optimal LGX SH-SAW orientation and device design for operation with the padlock technology; (iii) Study and develop the molecular padlock probe system to operate effectively in conjunction with the LGX SH-SAW device; (iv) Fabricate and test the prototype SH-SAW liquid biosensors; (v) Identify and optimize a procedure for sensor regeneration; and (vi) Characterize and optimize the sensor\u27s dynamic range and cross-effects due to temperature and other physical and chemical factors. The educational objective of this SENSORS program is to provide a multidisciplinary learning experience to students ranging from high school to graduate student level in the area of sensors in general, and biosensors in particular. Broader impacts will be achieved through the following programs and activities to: (i) Train and interact with high school audiences through two major ongoing programs at University of Maine (UMaine), NSF Research Experiences for Teachers (RET) and the GK-12 Sensors; (ii) Involve undergraduates from Maine and other institutions directly into the research project under the umbrella of the ongoing NSF Research Experience for Undergraduates (REU) program at the UMaine; (iii) Expand existing undergraduate Sensor Technology and Instrumentation and Biochemical Engineering Engineering courses at the UMaine by adding modules relating to biosensors devices and systems; (iv) Identify appropriate Capstone projects for undergraduates involving cross-disciplinary research and design projects; (v) Enhance existing graduate level courses Microscale Bioengineering and Design and Fabrication of Acoustic Wave Devices by incorporating research results into the course; (vi) Contribute to the new interdisciplinary multi-institutional NSF Integrative Graduate Education and Research Traineeship (IGERT) program in functional genomics, which involves UMaine, the Jackson Laboratory, and the Maine Medical Center Research Institute; (vi) Provide a experimental and/or theoretical thesis topics for Masters and Ph.D. students; (vii) Disseminate the research and educational material on a project website, and through conferences and printed literature. The SENSORS project proposed here is designed to result in tangible research and educational benefits. It will provide a knowledge base critical to creation of the next generation of biosensors for single unit production and future integration into arrays. It also seeks to establish a model program whereby cross-disciplinary education is integrated with a state-of-the-art research program, providing a rich learning experience for students ranging from high school to graduate student level. Finally, the project will help to strengthen U.S. research and educational capabilities in an area of high technology that currently is in need of highly trained industry and academic professionals

Using Protege for automatic ontology instantiation

This paper gives an overview on the use of Protégé in the Artequakt system, which integrated Protégé with a set of natural language tools to automatically extract knowledge about artists from web documents and instantiate a given ontology. Protégé was also linked to structured templates that generate documents from the knowledge fragments it maintains

Web based knowledge extraction and consolidation for automatic ontology instantiation

The Web is probably the largest and richest information repository available today. Search engines are the common access routes to this valuable source. However, the role of these search engines is often limited to the retrieval of lists of potentially relevant documents. The burden of analysing the returned documents and identifying the knowledge of interest is therefore left to the user. The Artequakt system aims to deploy natural language tools to automatically ex-tract and consolidate knowledge from web documents and instantiate a given ontology, which dictates the type and form of knowledge to extract. Artequakt focuses on the domain of artists, and uses the harvested knowledge to gen-erate tailored biographies. This paper describes the latest developments of the system and discusses the problem of knowledge consolidation

Automatic extraction of knowledge from web documents

A large amount of digital information available is written as text documents in the form of web pages, reports, papers, emails, etc. Extracting the knowledge of interest from such documents from multiple sources in a timely fashion is therefore crucial. This paper provides an update on the Artequakt system which uses natural language tools to automatically extract knowledge about artists from multiple documents based on a predefined ontology. The ontology represents the type and form of knowledge to extract. This knowledge is then used to generate tailored biographies. The information extraction process of Artequakt is detailed and evaluated in this paper

SENSORS: A Novel Lateral Field Excited Acoustic Wave Sensor for Chemical and Biological Agents

Sensors for the sensitive and selective detection of chemical agents and a biological agent are being developed. The sensor structure consists of a piezoelectric platform that is coated with a film that selectively sorbs a chemical or biological agent of interest. The sensitivity of the sensor is embodied in the sensor platform, which consists of a quartz crystal that is excited by a lateral electric field. The exciting electrodes are placed opposite to the sensing surface, and the sensing film is attached directly to the sensor platform. This arrangement is in contrast to the standard quartz microbalance (QCM), where the sensing surface is normally coated with a gold film, and it offers increased sensitivity along with selectivity. The high sensitivity exhibited by this novel lateral-field-excited (LFE) QCM is attributed to the fact that the sensor can measure both electrical and mechanical property changes in the sensing film caused by the sorbed chemical or biological agent. The selectivity of the LFE-QCM sensor is obtained by performing molecular filtering directly in the sensing film. In this specific project the LFE-QCM sensor is being designed to detect two specific chemicals and one biological agent. The target chemicals are dimethyl phosponate (DMMP), which simulates VX and G nerve agents, and an organophosphate pesticide that is chemically similar to many other chemical-warfare agents. The biological agent is E. coli O157:H7, which could appear in food or water supplies. In order to realize the desired chemical and biological sensors, the research team is exploring several issues relating to the LFE-QCM platform and the sensing film. These issues include the optimum electrode geometry in the LFE-QCM platform, the development of novel polymer and silica films for the detection of organophosphates in water, and the coupling of E. coli antibodies to the sensing surface. Homeland security as well as environmental and industrial health concerns dictate that improved chemical and biological sensors must be developed and deployed. After various sorbate-selective films have been attached to the LFE-QCM surface, they will be exposed to the chemical simulants and the biological agent in order to determine the sensing properties. It is anticipated that the proposed work on these organo-phosphorus chemicals and E. coli can be extended to development of selective sensors for other significant chemical and biological agents. In addition, by coupling with existing GK-12 and REU programs, this project will contribute to the education of a number of students and teachers who will participate in the research program

EXP-SA: Explosives Tracking: A Microsystem for Detection of Bacterial Endospores as Self-Replicating Nucleic Acid Taggants

This proposal presents an integrated research and educational plan directed toward the production, detection, and identification of bacterial endospore taggants for explosive tracking. While the most immediate application of the research is related to stemming the activities of bioterrorists, the anticipated fundamental advances in bioengineering and sensor science and engineering will have significant societal relevance to other applications, including first-responder activities, healthcare, food safety, and pollution avoidance and mitigation. Intellectual Merit The investigators propose to combine bioengineering of Bacillus stearothermophilus endospores with microdevices for sample processing and taggant identification. A surface acoustic wave (SAW) microdroplet mixing/transport/incubator system will be coupled with molecular padlock probe technology for sensitive identification of bioengineered endospores. The specific research tasks are to: (i) Generate a number of different Bacillus spores, each with a unique DNA sequence or sequences spliced into its genome; (ii) Investigate and identify the optimal SAW device designs needed to germinate spores, lyse vegetative bacteria, transport, mix, and heat microdroplet samples; (iii) Design subsystems for DNA isolation; (iv) Develop a fluorescence-based molecular padlock probe system for DNA identification that can operate effectively in conjunction with the SAW fabrication microsystem platform; (v) Fabricate and test the proposed prototype identification system. Broader Impacts Broader impacts will be achieved through the following programs and activities to: (i) Train and interact with high school audiences through two major ongoing programs at University of Maine (UMaine), NSF Research Experiences for Teachers (RET) and the GK-12 Sensors; (ii) Involve undergraduates from Maine and other institutions directly into the research project under the umbrella of the ongoing NSF Research Experience for Undergraduates (REU) program at the UMaine; (iii) Identify appropriate Capstone projects for undergraduates involving cross-disciplinary research and design projects; (iv) Enhance existing graduate level courses (1) Microscale Bioengineering and (2) Design and Fabrication of Acoustic Wave Devices by incorporating research results into each course; (v) Contribute to the interdisciplinary multi-institutional NSF Integrative Graduate Education and Research Traineeship (IGERT) program in functional genomics, which involves UMaine, the Jackson Laboratory, and the Maine Medical Center Research Institute; (vi) Provide thesis topics for M.S. and Ph.D. students; (vii) Disseminate the research and educational material on a project website, and through conferences and printed literature. Project Outcomes ReportNew investigative tools are desperately needed to determine the origin and transit routes of contraband explosive materials, and the individuals who transport them. A powerful strategy for tracking and identifying specific lots of explosives is the incorporation or labeling with pre-and post-detonation identification tags, or taggants. This project involves the production, detection, and identification of bacterial endospore taggants for explosive tracking. It combines bioengineering of environmentally resistant Geobacillus thermoglucosidasius endospores with development of microdevices for sample processing and taggant identification. A surface acoustic wave (SAW) bacterial lysis system is coupled with on-chip fluorescence-based quantitative polymerase chain reaction (PCR) for identification of bioengineered endospores.Geobacillus spores with a unique DNA sequence encoded in well-retained plasmids have been generated. Optimal SAW device structures have been designed, fabricated and tested for lysis of the vegetative bacteria. A number of on-chip structures for multiplex PCR analysis have been created and tested. DNA release and fluorescence-based PCR analysis for identification of specific genomic DNA sequences can now be interfaced to the SAW microsystem platform to comprise an important part of the overall detection system. We anticipate that aspects of this technology will be useful for tracking contraband materials such as explosives, environmental monitoring, and potentially medical diagnostic applications. This project has fostered the multidisciplinary training of numerous undergraduate and graduate students in molecular biology, microbiology, biochemistry, and bioengineering

Generating adaptive hypertext content from the semantic web

Accessing and extracting knowledge from online documents is crucial for therealisation of the Semantic Web and the provision of advanced knowledge services. The Artequakt project is an ongoing investigation tackling these issues to facilitate the creation of tailored biographies from information harvested from the web. In this paper we will present the methods we currently use to model, consolidate and store knowledge extracted from the web so that it can be re-purposed as adaptive content. We look at how Semantic Web technology could be used within this process and also how such techniques might be used to provide content to be published via the Semantic Web