Identification of functional domains and evolution of Tc1-like transposable elements.

Tc1-like transposable elements from teleost fish have been phylogenetically examined to determine the mechanisms involved in their evolution and conserved domains of function. We identified two new functional domains in these elements. The first is a bipartite nuclear localization signal, indicating that transposons can take advantage of the transport machinery of host cells for nuclear uptake of their transposases. The second is a novel combination of a paired domain-related protein motif juxtaposed to a leucine zipper-like domain located in the putative DNA-binding regions of the transposases. This domain coexists with a special inverted repeat structure in certain transposons in such phylogenetically distant hosts as fish and insects. Our data indicate that reassortment of functional domains and horizontal transmission between species are involved in the formation and spread of new types of transposable elements.

Geochemistry of crustal formation and evolution

Terrestrial planets produce crusts as they differentiate. The Earth’s bi-modal crust, with a high-standing granitic continental crust and a low-standing basaltic oceanic crust, is unique in our solar system and links the evolution of the interior and exterior of this planet. Here I present geochemical observations to constrain processes accompanying crustal formation and evolution. My approach includes geochemical analyses, quantitative modeling, and experimental studies. The Archean crustal evolution project represents my perspective on when Earth’s continental crust began forming. In this project, I utilized critical element ratios in sedimentary records to track the evolution of the MgO content in the upper continental crust as a function time. The early Archean subaerial crust had >11 wt. % MgO, whereas by the end of Archean its composition had evolved to about 4 wt. % MgO, suggesting a transition of the upper crust from a basalt-like to a more granite-like bulk composition. Driving this fundamental change of the upper crustal composition is the widespread operation of subduction processes, suggesting the onset of global plate tectonics at ~ 3 Ga (Abstract figure). Three of the chapters in this dissertation leverage the use of Eu anomalies to track the recycling of crustal materials back into the mantle, where Eu anomaly is a sensitive measure of the element’s behavior relative to neighboring lanthanoids (Sm and Gd) during crustal differentiation. My compilation of Sm-Eu-Gd data for the continental crust shows that the average crust has a net negative Eu anomaly. This result requires recycling of Eu-enriched lower continental crust to the mantle. Mass balance calculations require that about three times the mass of the modern continental crust was returned into the mantle over Earth history, possibly via density-driven recycling. High precision measurements of Eu/Eu* in selected primitive glasses of mid-ocean ridge basalt (MORB) from global MORs, combined with numerical modeling, suggests that the recycled lower crustal materials are not found within the MORB source and may have at least partially sank into the lower mantle where they can be sampled by hot spot volcanoes. The Lesser Antilles Li isotope project provides insights into the Li systematics of this young island arc, a representative section of proto-continental crust. Martinique Island lavas, to my knowledge, represent the only clear case in which crustal Li is recycled back into their mantle source, as documented by the isotopically light Li isotopes in Lesser Antilles sediments that feed into the fore arc subduction trench. By corollary, the mantle-like Li signal in global arc lavas is likely the result of broadly similar Li isotopic compositions between the upper mantle and bulk subducting sediments in most arcs. My PhD project on Li diffusion mechanism in zircon is being carried out in extensive collaboration with multiple institutes and employs analytical, experimental and modeling studies. This ongoing project, finds that REE and Y play an important role in controlling Li diffusion in natural zircons, with Li partially coupling to REE and Y to maintain charge balance. Access to state-of-art instrumentation presented critical opportunities to identify the mechanisms that cause elemental fractionation during laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis. My work here elucidates the elemental fractionation associated with plasma plume condensation during laser ablation and particle-ion conversion in the ICP.

Prevalence of upper-body symptoms following breast cancer and its relationship with upper-body function and lymphoedema

This investigation describes the prevalence of upper-body symptoms in a population-based sample of women with breast cancer (BC) and examines their relationships with upper-body function (UBF) and lymphoedema, as two clinically important sequelae. Australian women (n=287) with unilateral BC were assessed at three-monthly intervals, from six to 18 months post-surgery (PS). Participants reported the presence and intensity of upper-body symptoms on the treated side. Objective and self-reported UBF and lymphoedema (bioimpedance spectroscopy) were also assessed. Approximately 50% of women reported at least one moderate-to-extreme symptom at 6- and at 18-months PS. There was a significant relationship between symptoms and function (p<0.01), whereby perceived and objective function declined with increasing number of symptoms present. Those with lymphoedema were more likely to report multiple symptoms and presence of symptoms at baseline increased risk of lymphoedema (ORs>1.3, p=0.02). Although, presence of symptoms explained only 5.5% of the variation in the odds of lymphoedema. Upper-body symptoms are common and persistent following breast cancer and are associated with clinical ramifications, including reduced UBF and increased risk of developing lymphoedema. However, using the presence of symptoms as a diagnostic indicator of lymphoedema is limited.

Physical function and health-related quality of life of older adults undergoing hospital rehabilitation : how strong is the association?

The purpose of this research is to report preliminary empirical evidence regarding the association between common physical performance measures and health-related quality of life (HRQoL) of hospitalized older adults recovering from illness and injury. Frequently, these patients do not return to premorbid levels of independence and physical ability. Rehabilitation for this population often focuses on improving physical functioning and mobility with the intention of maximizing their HRQoL for discharge and thereafter. For this reason, longitudinal use of physical performance measures as an indicator of improvement in physical functioning (and thus HRQoL) is common. Although this is a logical approach, there have been mixed results from previous investigations into the association between common measures of physical function and HRQoL amongst other adult patient populations.1,2 There has been no previous investigation reporting the association between HRQoL and a variety of common physical performance measures in hospitalized older adults.

Chlamydial infection of immune cells : altered function and implications for disease

Chlamydia trachomatis is an obligate intracellular bacterial pathogen that infects the genital and ocular mucosa of humans, causing infections that can lead to pelvic inflammatory disease, infertility, and blinding trachoma. C. pneumoniae is a respiratory pathogen that is the cause of 12–15% of community-acquired pneumonia. Both chlamydial species were believed to be restricted to the epithelia of the genital, ocular, and respiratory mucosa; however, increasing evidence suggests that both these pathogens can be isolated from peripheral blood of both healthy individuals and patients with inflammatory conditions such as coronary artery disease and asthma. Chlamydia can also be isolated from brain tissues of patients with degenerative neurological disorders such as Alzheimer’s disease and multiple sclerosis, and also from certain lymphomas. An increasing number of in vitro studies suggest that some chlamydial species can infect immune cells, at least at low levels. These infections may alter immune cell function in a way that promotes chlamydial persistence in the host and contributes to the progression of several chronic inflammatory diseases. In this paper, we review the evidence for the growth of Chlamydia in immune cells, particularly monocytes/macrophages and dendritic cells, and describe how infection may affect the function of these cells.

Empirical analysis of freeway traffic oscillation : its safety impact and evolution

Traffic oscillations are typical features of congested traffic flow that are characterized by recurring decelerations followed by accelerations. However, people have limited knowledge on this complex topic. In this research, 1) the impact of traffic oscillations on freeway crash occurrences has been measured using the matched case-control design. The results consistently reveal that oscillations have a more significant impact on freeway safety than the average traffic states. 2) Wavelet Transform has been adopted to locate oscillations' origins and measure their characteristics along their propagation paths using vehicle trajectory data. 3) Lane changing maneuver's impact on the immediate follower is measured and modeled. The knowledge and the new models generated from this study could provide better understanding on fundamentals of congested traffic; enable improvements to existing traffic control strategies and freeway crash countermeasures; and instigate people to develop new operational strategies with the objective of reducing the negative effects of oscillatory driving.

Assessment of function and clinical utility of alcohol and other drug web sites : an observational, qualitative study

Background The increasing popularity and use of the internet makes it an attractive option for providing health information and treatment, including alcohol/other drug use. There is limited research examining how people identify and access information about alcohol or other drug (AOD) use online, or how they assess the usefulness of the information presented. This study examined the strategies that individuals used to identify and navigate a range of AOD websites, along with the attitudes concerning presentation and content. Methods Members of the general community in Brisbane and Roma (Queensland, Australia) were invited to participate in a 30-minute search of the internet for sites related to AOD use, followed by a focus group discussion. Fifty one subjects participated in the study across nine focus groups. Results Participants spent a maximum of 6.5 minutes on any one website, and less if the user was under 25 years of age. Time spent was as little as 2 minutes if the website was not the first accessed. Participants recommended that AOD-related websites should have an engaging home or index page, which quickly and accurately portrayed the site’s objectives, and provided clear site navigation options. Website content should clearly match the title and description of the site that is used by internet search engines. Participants supported the development of a portal for AOD websites, suggesting that it would greatly facilitate access and navigation. Treatment programs delivered online were initially viewed with caution. This appeared to be due to limited understanding of what constituted online treatment, including its potential efficacy. Conclusions A range of recommendations arise from this study regarding the design and development of websites, particularly those related to AOD use. These include prudent use of text and information on any one webpage, the use of graphics and colours, and clear, uncluttered navigation options. Implications for future website development are discussed.