Intragenic regions (introns) are found in all classes of organism. Transcription of such genes must undergo a splicing reaction to produce the mature, functional form of RNAs. Introns can be divided into four categories by their splicing mechanisms, namely Group I, Group II, spliceosomal, and nuclear tRNA introns. The former two are self-splicing introns. Group I introns are ubiquitous, however, most metazoan mitochondrial genomes lack introns. A novel group I intron in the mitochondrial cytochrome oxidase I gene (cox1) of Cinachyrella auctraliensis, which belongs to the IB2 subgroup, encodes a putative homing endonuclease with two amino acid motifs of the LAGLIDADG family. The homing endonuclease may perform intron translocation. Splicing in the cox1 of the sponge was demonstrated by comparing the length of DNA and RNA sequences. The intron was spliced in vivo or in vitro as revealed by RT-PCR and sequencing. Group I introns are classified as ribozymes. The pre-mRNAs fold into specific configurations that facilitate attacks of free guanosine followed by two consecutive trans-esterification steps to remove the introns. The excised cox1 intron was found to form a circle with the 5¡¦-end linked to the 3¡¦-end. Two other forms of lariats were also found with the 5¡¦-end linked to the inside sequence of the intron. Mutagenesis of a key nucleotide, which participates base pairing of RNA secondary structure, in P7 region decreased the splicing activity of the intron.

In oviparous animals, maternal traits such as the investment of resources in eggs and oviposition site selection are often important determinants of offspring phenotypic quality, and may have an adaptive role in tailoring offspring phenotypes to local environmental conditions. This thesis examines the adaptive significance of two specific maternal traits in the green turtle (Chelonia mydas); namely the deposition of fat-soluble antioxidants in egg yolk, and the selection of nest sites via natal homing. (Please view 'front matter' file for full abstract)

Evolutionary relationships amongst strains of the fungal genus Leptographium and related taxa were inferred using the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat. To generate robust sequence alignments for phylogenetic analysis the relationship between DNA sequence variability and RNA structural conservation of ITS segments was examined. The results demonstrate that structural conservation of helical regions is facilitated by compensatory base changes, compensating insertions/deletions, and, possibly, RNA strand slippage. A high mol % G+C bias for ITS1 and ITS2 and structural constraints at the RNA level appear to limit the types of changes observed. Fifty strains of Leptographium were screened for the presence of introns within mitochondrial genes. Superimposing intron survey data onto the ITS-derived phylogenetic tree reveals that introns are absent from the small ribosomal RNA (rns) gene of all strains of L. procerum yet are found in all strains of L. lundbergii. Amongst members of L. wingfieldii, L. terebrantis, and L. truncatum intron distribution is stochastic and is not correlated to the evolutionary relationships amongst strains. A group II intron/LAGLIDADG homing endonuclease gene (HEG) composite element from the mt rns gene of L. truncatum strain CBS929.85 was characterized. Intron-catalyzed splicing was tested using ORF-less and ORF-containing precursor transcripts, and both versions of the intron readily self-splice under moderate temperature and ionic conditions (37 °C and 6 mM MgCl2). Cleavage activity of the intron-encoded protein (I-LtrII) was tested using an N-terminal His6-tagged and near native protein. The homing endonuclease cleaves double-stranded DNA 2 nucleotides upstream of the intron insertion site within the exon, generating 4 nucleotide 3’ OH overhangs. Intron splicing is not enhanced by the addition of I-LtrII and RNA-binding assays indicate that the His6-tagged protein does not bind to the intron. Phylogenetic relationships amongst the rns gene, intron, and amino acid sequences were inferred. An evolutionary model of the composite element is proposed in which the HEG invaded a group II intron and mobilized it. The mobile genetic element may be transmitted vertically amongst L. lundbergii strains and horizontally through lateral gene transfer amongst strains of L. wingfieldii, L. terebrantis, and L. truncatum.

In recent years, there has been a rapid evolution and deployment of wireless networks. In populated areas, high-rate data access is enabled anywhere and anytime with the pervasive wireless infrastructure such as the fourth-generation (4G) cellular systems, IEEE 802.11-based wireless local area networks (WLANs), and IEEE 802.16-based wireless metropolitan area networks (WMANs). In such a heterogeneous wireless access medium, multi-radio devices become a trend for users to conveniently explore various services offered by different wireless systems. This thesis presents radio resource management mechanisms, for bandwidth allocation, call admission control (CAC), and mobile terminal (MT) energy management, that can efficiently exploit the available resources in the heterogeneous wireless medium and enhance the user perceived quality-of-service (QoS). Almost all existing studies on heterogeneous networking are limited to the traditional centralized infrastructure, which is inflexible in dealing with practical scenarios, especially when different networks are operated by different service providers. In addition, in most current wireless networks, mobile users are simply viewed as service recipients in network operation, with passive transceivers completely or partially under the control of base stations or access points. In this thesis, we present efficient decentralized bandwidth allocation and CAC mechanisms that can support single-network and multi-homing calls. The decentralized architecture gives an active role to the MT in the resource management operation. Specifically, an MT with single-network call can select the best wireless network available at its location, while an MT with multi-homing call can determine a required bandwidth share from each network to satisfy its total required bandwidth. The proposed mechanisms rely on cooperative networking and offer a desirable flexibility between performance measures (in terms of the allocated bandwidth per call and the call blocking probability), and between the performance and the implementation complexity. With the increasing gap between the MT demand for energy and the offered battery capacity, service degradation is expected if the MT cannot efficiently manage its energy consumption. Specifically, for an uplink multi-homing video transmission, the existing studies do not guarantee that the MT available energy can support the entire call, given the battery energy limitation. In addition, the energy management mechanism should take account of video packet characteristics, in terms of packet distortion impact, delay deadline, and precedence constraint, and employ the available resources in the heterogeneous wireless medium. In this thesis, we present MT energy management mechanisms that can support a target call duration, with a video quality subject to the MT battery energy limitation. In addition, we present a statistical guarantee framework that can support a consistent video quality for the target call duration with minimum power consumption.

Evolutionary relationships amongst strains of the fungal genus Leptographium and related taxa were inferred using the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat. To generate robust sequence alignments for phylogenetic analysis the relationship between DNA sequence variability and RNA structural conservation of ITS segments was examined. The results demonstrate that structural conservation of helical regions is facilitated by compensatory base changes, compensating insertions/deletions, and, possibly, RNA strand slippage. A high mol % G+C bias for ITS1 and ITS2 and structural constraints at the RNA level appear to limit the types of changes observed. Fifty strains of Leptographium were screened for the presence of introns within mitochondrial genes. Superimposing intron survey data onto the ITS-derived phylogenetic tree reveals that introns are absent from the small ribosomal RNA (rns) gene of all strains of L. procerum yet are found in all strains of L. lundbergii. Amongst members of L. wingfieldii, L. terebrantis, and L. truncatum intron distribution is stochastic and is not correlated to the evolutionary relationships amongst strains. A group II intron/LAGLIDADG homing endonuclease gene (HEG) composite element from the mt rns gene of L. truncatum strain CBS929.85 was characterized. Intron-catalyzed splicing was tested using ORF-less and ORF-containing precursor transcripts, and both versions of the intron readily self-splice under moderate temperature and ionic conditions (37 °C and 6 mM MgCl2). Cleavage activity of the intron-encoded protein (I-LtrII) was tested using an N-terminal His6-tagged and near native protein. The homing endonuclease cleaves double-stranded DNA 2 nucleotides upstream of the intron insertion site within the exon, generating 4 nucleotide 3’ OH overhangs. Intron splicing is not enhanced by the addition of I-LtrII and RNA-binding assays indicate that the His6-tagged protein does not bind to the intron. Phylogenetic relationships amongst the rns gene, intron, and amino acid sequences were inferred. An evolutionary model of the composite element is proposed in which the HEG invaded a group II intron and mobilized it. The mobile genetic element may be transmitted vertically amongst L. lundbergii strains and horizontally through lateral gene transfer amongst strains of L. wingfieldii, L. terebrantis, and L. truncatum.

The marine birds comprising the order Procellariiformes are an ancient and diverse assemblage. A large proportion are both nocturnal and burrow-nesting at their breeding colonies, where in sharp contrast to their behaviour at sea, they are highly vociferous. Virtually nothing is known regarding the adaptive features of this process. Various aspects of vocal behaviour have therefore been investigated from 1981 to 1983 for seven species at breeding stations in both the boreal and sub-tropical North Atlantic Ocean. In addition, the problem of how these birds return to their correct burrows at night has been considered. A detailed study was conducted on the Manx Shearwater Puffinus puffinus. Various approaches showed that immatures contribute most to the calling heard. Males establish and defend burrows, but both sexes partake in aerial calling. Calling at ground level serves both sexual and territorial functions, whereas aerial calling is probably mainly concerned with sexual advertisement. Some males are more silent in flight than others. These probably represent birds as yet without burrows, perhaps the youngest age classes. Flighting activity probably expedites the acquisition of burrows and mates in these birds which are awkward on land, and aerial calling probably improves signalling efficiency in attracting mates. Six other species (Bulweria bulwerii, Calonectris diomedea, Puffinus assimilis, Hydrobates pelagicus, Oceanodroma castro, Pelagodroma marina) were studied. As with Puffinus puffinus, sexual differences in voice exist for all except Bulweria and Pelagodroma, which also lack aerial calls. Thus a functional link exists between flight calls and their sexual divergence. Selection probably favours such divergence in species where males leave burrows to display in flight; the sexual identity of those species whose males do not is unambiguous as they remain in burrows and call. The calls of Puffinus puffinus and Hydrobates pelagicus were compared at local and regional levels. Divergence exists between but not within islands. Vocal drift in Puffinus puffinus is also apparent after several years. The calls of the nocturnal Procellariiformes are reviewed and discussed in relation to their systematics. The potential use of calls in petrel systematics is also evaluated and shown to be useful. Observations on Puffinus puffinus showed that olfactory and auditory cues are not used for burrow homing. Experiments also confirmed this, and point to sufficient visual development in this species, although other senses may be emphasised in different ecological situations.

Pregnancy complications such as fetal growth restriction (FGR) are often attributed to poor uteroplacental blood flow, but the risk of systemic side-effects hinders therapeutic intervention. We have utilised novel placental-specific homing peptides to overcome this and have conjugated these to biocompatible liposomes. Peptide-conjugated liposomes were found to selectively bind to the outer syncytiotrophoblast layer of the human placenta and to the uteroplacental vasculature and labyrinth region of the mouse placenta. The novel vasodilator SE175 was selected as a nitric oxide donor with a favourable stability and release profile, to encapsulate in peptide-conjugated liposomes in an attempt to restore impaired uteroplacental blood flow in a mouse model of FGR, the endothelial nitric oxide synthase knockout mouse. Liposomes containing SE175 or PBS were prepared by lipid film hydration and targeting peptides coupled to the liposomal surface. Vehicle control, free SE175, PBS- or SE175-containing liposomes were intravenously injected on embryonic (E) days 11.5, 13.5, 15.5 and 17.5. Animals were sacrificed at E18.5 and fetal and placental weights recorded. Targeted delivery of SE175 significantly increased fetal weight compared to vehicle control but no other treatment groups, whilst significantly decreasing placental weight, indicating improved placental efficiency. Treatment was well tolerated, having no impact on litter size or resorptions. Targeted delivery of SE175, but no other treatment group, reduced a marker of lipid peroxidation in the placenta, indicating a reduction in oxidative stress. These data suggest that selective delivery of SE175 to the uteroplacental vasculature in peptide decorated liposomes may represent a novel treatment for FGR.

Many animals have ability to percieve the magnetic field of the Earth and use this clue for both orientation and navigation. Yet little is known about physiological mechanism that underlies this sensory ability. Although physiological mechanism still remains unclear, there are three major hypotheses how animals can detect the magnetic field. In this study I focused on the radical pair theory. I analyzed how manipulation of the ambient magnetic field influence the expression of CRY 1, CRY 2 and c-Fos in the pigeon´s retina. I observed in incerased numbers of CRY1, c-Fos and CRY1+c-Fos possitive cells in the ihned nuclear layer (INL) of the retina in animals sbjected to the periodical manipulation of the magnetic field inclination. These data demonstrate that the INL constains a population of neurons that are responsive to magnetic stimuli and strongly suggest that Cry 1 is involved in detection of the Earth magnetic field.

Aedes aegypti (Ae. aegypti) is one of the most important vectors of dengue, chikungunya and yellow fever viruses. The use of chemical control strategies such as insecticides is associated with problems including the development of insecticide resistance, side effects on animal and human health, and environmental concerns. Because current methods have not proven sufficient to control these diseases, developing novel, genetics-based, control strategies to limit the transmission of disease is urgently needed. Increased knowledge about mosquito-pathogen relationships and the molecular biology of mosquitoes now makes it possible to generate transgenic mosquito strains that are unable to transmit various parasites or viruses. Ae. aegypti genetic experiments are enabled, and limited by, the catalog of promoter elements available to drive transgene expression. To find a promoter able to drive robust expression of firefly (FF) luciferase in Ae. aegypti embryos, an experiment was designed to compare Ae. aegypti endogenous and exogenous promoters. The PUb promoter was found to be extremely robust in expression of FF luciferase in different stages of embryonic development from 2-72 hours after injection. In subsequent experiments, transformation frequency was calculated using four different promoters (IE1, UbL40, hsp82 and PUb) to express the Mos1 transposase open reading frame in Mos1-mediated transgenesis. Germline transformation efficiency and size of transgenic cluster were not significantly different when using endogenous Ae. aegypti PUb or the commonly used exogenous Drosophila hsp82 promoter to express Mos1 transposase. This study also describes the development of new tools for gene editing in the Ae. aegypti mosquito genome and the use of these tools to design an efficient gene drive system in this mosquito. Homing endonucleases (HEs) are selfish elements which catalyze double-stranded DNA (dsDNA) breaks in a sequence-specific manner. The activities of four HEs (Y2-I-AniI, I-CreI, I-PpoI, and I-SceI) were investigated for their ability to catalyze the excision of genomic segments from the Ae. aegypti genome. All four enzymes were found to be active in Ae. aegypti; however, the activity of Y2-I-AniI was higher compared to the other three enzymes. Single-strand annealing (SSA) and non-homologous end-joining (NHEJ) pathways were identified as mechanisms to repair HE-induced dsDNA breaks. TALE nucleases (TALENs) are a group of artificial enzymes capable of generating site-specific DNA lesions. To examine the ability of TALENs for gene editing in Ae. aegypti, a pair of TALENs targeted to the kmo gene were expressed from a plasmid following embryonic injection. Twenty to forty percent of fertile G0 produced white-eyed progeny which resulted from disruption of the kmo gene. Most of these individuals produced more than 20% white-eyed progeny, with some producing up to 75%. A small deletion of one to seven bp occurred at the TALEN recognition site. These results show that TALEN and HEs are highly active in the Ae. aegypti germline and can be used for gene editing and gene drive strategies in Ae. aegypti. / Ph. D.

No / There are several merits of mobile communication devices having multiple network interfaces as compared to traditional devices with just one interface. Smart phones these days are a true example of a mobile multi-homed communication device with heterogeneous network interfaces. Several solutions are available for unicast applications to provide seamless handover using the multiple interfaces of a multi-homed device in terrestrial networks. However, very little has been done on similar support for IP multicast mobility support for mobile satellite terminals in a ubiquitous multi-beam satellite network. Most of the schemes proposed for handovers in multi-homed devices place a lot of emphasis on maintaining the multi-homed device identity especially when the second interface joins the communication session. This increases complexity in the whole system. The issue of maintaining the multi-homed device identity plus the additional signalling messages involve are neither necessary nor desired in an IP multicast communication handover in a multi-beam satellite scenario. This paper seeks to exploit the group communication features of IP multicast (i.e., the fact that anyone can join or leave a multicast group at any time and from any location) and the multiple interfaces of a mobile Return Channel Satellite Terminal (RCST) to support IP multicast communication during handover when a mobile multi-homed RCST changes its point of attachment to the network from one satellite gateway to another.