A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that beta-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus(+) ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram(+) bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus(+) fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded beta-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.

Design and analysis of group key exchange protocols

A group key exchange (GKE) protocol allows a set of parties to agree upon a common secret session key over a public network. In this thesis, we focus on designing efficient GKE protocols using public key techniques and appropriately revising security models for GKE protocols. For the purpose of modelling and analysing the security of GKE protocols we apply the widely accepted computational complexity approach. The contributions of the thesis to the area of GKE protocols are manifold. We propose the first GKE protocol that requires only one round of communication and is proven secure in the standard model. Our protocol is generically constructed from a key encapsulation mechanism (KEM). We also suggest an efficient KEM from the literature, which satisfies the underlying security notion, to instantiate the generic protocol. We then concentrate on enhancing the security of one-round GKE protocols. A new model of security for forward secure GKE protocols is introduced and a generic one-round GKE protocol with forward security is then presented. The security of this protocol is also proven in the standard model. We also propose an efficient forward secure encryption scheme that can be used to instantiate the generic GKE protocol. Our next contributions are to the security models of GKE protocols. We observe that the analysis of GKE protocols has not been as extensive as that of two-party key exchange protocols. Particularly, the security attribute of key compromise impersonation (KCI) resilience has so far been ignored for GKE protocols. We model the security of GKE protocols addressing KCI attacks by both outsider and insider adversaries. We then show that a few existing protocols are not secure against KCI attacks. A new proof of security for an existing GKE protocol is given under the revised model assuming random oracles. Subsequently, we treat the security of GKE protocols in the universal composability (UC) framework. We present a new UC ideal functionality for GKE protocols capturing the security attribute of contributiveness. An existing protocol with minor revisions is then shown to realize our functionality in the random oracle model. Finally, we explore the possibility of constructing GKE protocols in the attribute-based setting. We introduce the concept of attribute-based group key exchange (AB-GKE). A security model for AB-GKE and a one-round AB-GKE protocol satisfying our security notion are presented. The protocol is generically constructed from a new cryptographic primitive called encapsulation policy attribute-based KEM (EP-AB-KEM), which we introduce in this thesis. We also present a new EP-AB-KEM with a proof of security assuming generic groups and random oracles. The EP-AB-KEM can be used to instantiate our generic AB-GKE protocol.

An improved modal strain energy method for damage assessment

The modal strain energy method, which depends on the vibration characteristics of the structure, has been reasonably successful in identifying and localising damage in the structure. However, existing strain energy methods require the first few modes to be measured to provide meaningful damage detection. Use of individual modes with existing strain energy methods may indicate false alarms or may not detect the damage at or near the nodal points. This paper proposes a new modal strain energy based damage index which can detect and localize the damage using any one of the modes measured and illustrates its application for beam structures. It becomes evident that the proposed strain energy based damage index also has potential for damage quantification.

On the feasibility of using servo-mechanisms in wireless multimedia sensor network deployments

This paper considers the use of servo-mechanisms as part of a tightly integrated homogeneous Wireless Multi- media Sensor Network (WMSN). We describe the design of our second generation WMSN node platform, which has increased image resolution, in-built audio sensors, PIR sensors, and servo- mechanisms. These devices have a wide disparity in their energy consumption and in the information quality they return. As a result, we propose a framework that establishes a hierarchy of devices (sensors and actuators) within the node and uses frequent sampling of cheaper devices to trigger the activation of more energy-hungry devices. Within this framework, we consider the suitability of servos for WMSNs by examining the functional characteristics and by measuring the energy consumption of 2 analog and 2 digital servos, in order to determine their impact on overall node energy cost. We also implement a simple version of our hierarchical sampling framework to evaluate the energy consumption of servos relative to other node components. The evaluation results show that: (1) the energy consumption of servos is small relative to audio/image signal processing energy cost in WMSN nodes; (2) digital servos do not necessarily consume as much energy as is currently believed; and (3) the energy cost per degree panning is lower for larger panning angles.

An alginate-based hybrid system for growth factor delivery in the functional repair of large bone defects

The treatment of challenging fractures and large osseous defects presents a formidable problem for orthopaedic surgeons. Tissue engineering/regenerative medicine approaches seek to solve this problem by delivering osteogenic signals within scaffolding biomaterials. In this study, we introduce a hybrid growth factor delivery system that consists of an electrospun nanofiber mesh tube for guiding bone regeneration combined with peptide-modified alginate hydrogel injected inside the tube for sustained growth factor release. We tested the ability of this system to deliver recombinant bone morphogenetic protein-2 (rhBMP-2) for the repair of critically-sized segmental bone defects in a rat model. Longitudinal [mu]-CT analysis and torsional testing provided quantitative assessment of bone regeneration. Our results indicate that the hybrid delivery system resulted in consistent bony bridging of the challenging bone defects. However, in the absence of rhBMP-2, the use of nanofiber mesh tube and alginate did not result in substantial bone formation. Perforations in the nanofiber mesh accelerated the rhBMP-2 mediated bone repair, and resulted in functional restoration of the regenerated bone. [mu]-CT based angiography indicated that perforations did not significantly affect the revascularization of defects, suggesting that some other interaction with the tissue surrounding the defect such as improved infiltration of osteoprogenitor cells contributed to the observed differences in repair. Overall, our results indicate that the hybrid alginate/nanofiber mesh system is a promising growth factor delivery strategy for the repair of challenging bone injuries.

A new generation of high voltage pulsed power converters

Improving efficiency and flexibility in pulsed power supply technologies are the most substantial concerns of pulsed power systems specifically for plasma generation. Recently, the improvement of pulsed power supply becomes of greater concern due to extension of pulsed power applications to environmental and industrial areas. A current source based topology is proposed in this paper which gives the possibility of power flow control. The main contribution in this configuration is utilization of low-medium voltage semiconductor switches for high voltage generation. A number of switch-diode-capacitor units are designated at the output of topology to exchange the current source energy into voltage form and generate a pulsed power with sufficient voltage magnitude and stress. Simulations have been carried out in Matlab/SIMULINK platform to verify the capability of this topology in performing desired duties. Being efficient and flexible are the main advantages of this topology.

A new pulsed power supply topology based on positive buck-boost converters concept

Improving efficiency and flexibility in pulsed power supply technologies is the most substantial concern of pulsed power systems specifically with regard to plasma generation. Recently, the improvement of pulsed power supply has become of greater concern due to the extension of pulsed power applications to environmental and industrial areas. With this respect, a current source based topology is proposed in this paper as a pulsed power supply which gives the possibility of power flow control during load supplying mode. The main contribution in this configuration is utilization of low-medium voltage semiconductor switches for high voltage generation. A number of switch-diode-capacitor units are designated at the output of topology to exchange the current source energy into voltage form and generate a pulsed power with sufficient voltage magnitude and stress. Simulations carried out in Matlab/SIMULINK platform as well as experimental tests on a prototype setup have verified the capability of this topology in performing desired duties. Being efficient and flexible are the main advantages of this topology.

Renewable energy sources and frequency regulation : survey and new perspectives

As the use of renewable energy sources (RESs) increases worldwide, there is a rising interest on their impacts on power system operation and control. An overview of the key issues and new challenges on frequency regulation concerning the integration of renewable energy units into the power systems is presented. Following a brief survey on the existing challenges and recent developments, the impact of power fluctuation produced by variable renewable sources (such as wind and solar units) on sysstem frequency performance is also presented. An updated LFC model is introduced, and power system frequency response in the presence of RESs and associated issues is analysed. The need for the revising of frequency performance standards is emphasised. Finally, non-linear time-domain simulations on the standard 39-bus and 24-bus test systems show that the simulated results agree with those predicted analytically.