Dissertations / Theses on the topic 'Applied biological science'

Navigation is at the heart of today’s mobile robotic systems. The use of landmarks for the guidance of autonomous systems is an essential part of the process. Shape, size, and colour are some of the properties of the landmarks. In this work biological and other methods have been developed for navigating a simulated mobile robot back to its home. Optical flow which is not a property of the landmarks but a property of the camera motion, has been used for building topological maps which are used to localise a robot. The advantage of this approach is that there is no need for storing or retrieving images. Any computation is performed on the basis of vectors. Metric maps are generated using a parsimonious localisation and mapping algorithm using a laser range finder. The purpose of this research is to effectively navigate a robot to its home position using computationally efficient biological and other techniques for navigation. Biology is seen as an alternative solution to the problems robots’ encounter which include algorithmic complexity, performance, and power consumption among others. Biological inspiration provides simple, yet effective methods for the solutions of such problems. The careful examination of such methods has twofold gain. The study of the principles of biological organisms entails making better autonomous systems that will, in turn help us perceive and understand better the underlying mechanisms of biological organisms. It is therefore essential to have an understanding of how biological and robotic systems work. This work discusses the techniques and strategies found both in animals and robots. It then goes on to describe the implementation of a series of simulation algorithms inspired by biology and other fields that assist in the navigation process, and in particular, homing. Their results are discussed and analysed. The novelty of this research lies in its methods for robot homing that make use of optical flow information to recognise a location as well as methods based on a laser range finder to avoid obstacles, perform path planning, localise a robot, and map the environment.

This thesis focuses on algorithms related to ancestral genome reconstruction and phylogenetics analyses. Specially, it studies insertion and deletion (indel) in genomic sequences, their utilities for (1) evolutionary studies of species families, (2) multiple alignment and phylogenetic trees reconstruction assessment, and (3) functional DNA sequence annotation. Here, the indel scenarios reconstruction problem is presented, in a likelihood framework, and it can be stated as follows: given a multiple alignment of orthologous sequences and a phylogenetic tree for these sequences, reconstruct the most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomic sequences, and is important for studying evolutionary processes, genome function, adaptation and convergence. In this thesis, first, we showed that we can solve the IMLP using a new type of tree hidden Markov model whose states correspond to single-base evolutionary scenarios and where transitions model dependencies between neighboring columns. The standard Viterbi and Forward-backward algorithms are optimized to produce the most likely ancestral reconstruction and to compute the level of confidence associated to specific regions of the reconstruction. A heuristic is presented to make the method practical for large data sets, while retaining an extremely high degree of accuracy. The developed methods have been made available for the community through a web interface. Second we showed the utilities of the defined indel score for assessing the accuracy of multiple sequence alignment and phylogenetic tree reconstruction. Third, the provided method is included into the framework of the ancestral protein reconstruction of phages under a reticulate evolution and the evolutionary studies of the carcinogencity of the Human Papilloma Vir
Cette thèse traite d'algorithmes pour la reconstruction de génomes ancestraux et l'analyse phylogénétique. Elle étudie particulièrement les scénarios d'insertion et délétion (indels) dans les séquences génomiques, leur utilité (1) pour l'étude des familles d'espèces, (2) pour l'évaluation des alignements multiples de séquences et la reconstruction phylogénétique, (3) et pour l'annotation de séquences génomiques fonctionnelles. Dans cette thèse, le problème de la reconstruction du scénario d'indels est étudié en utilisant le critère de maximum de vraisemblance. Ce problème peut être défini de la manière suivante: étant donné un alignement multiple de séquences orthologues et un arbre phylogénétique traduisant l'histoire évolutive de ces séquences, reconstruire le scénario d'indels le plus vraisemblable capable d'expliquer les brèches présentes dans l'alignement. Ce problème, dénommé ''Indel Maximum Likelihood Problem (IMLP)'', est une importante étape de la reconstruction de séquences ancestrales. Il est également important pour l'étude des processus évolutifs, des fonctions des gènes, de l'adaptation et de la convergence.Dans une première étape de cette thèse, nous montrons que l'IMLP peut être résolu en utilisant un nouveau type de données combinant un arbre phylogénétique et un modèle de Markov caché. Les états de ce modèle de Markov caché correspondent à un scénario évolutif d'une colonne de l'alignement. Ses transitions modélisent la dépendance entre les colonnes voisines de l'alignement.Les algorithmes standard de Viterbi et de Forward-Backward ont été optimisés pour produire le scénario ancestral le plus vraisemblable et pour calculer le niveau de confiance associé aux prédictions. Dans cette thèse, Nous présentons également une heuristique qui permet d'adapter la méthode à des données de grandes tailles. En second, nous montrons l'utilité du score d'indel dans l'évaluatio

The central issued explored by this research is whether forensic anthropology can be characterized as being fundamentally different from academically-oriented biological anthropology. My view--and thesis statement--is that they are not two fundamentally-differing pursuits. While I recognize that important differences do exist between these fields, I argue that the differences are not sufficient to draw a stark line between academically-oriented biological anthropology and its medico-legal application. The principal source of data marshaled in support of this view is my dozen-plus years experience as a student. then practitioner, of forensic anthropology. One hundred forensic anthropology case reports of mine are utilized to illustrate an example of the product that forensic anthropologists routinely supply to medico-legal and governmental agencies. However, more important than this product are the processes behind the issuance of such reports. I argue that while the product may be different--a necessity because the intended audience certainly is--the conscientious forensic anthropologist employs the same analytical processes as when engaged in academic pursuits. Thus, it is my position that forensic anthropologists remain biological anthropologists while performing medico-legal services.

Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 122- 131). Also available for download via the World Wide Web; free to University of Oregon users.

Every year hundreds of cetaceans strand on New Zealand beaches. Options for dealing with disposal of their carcasses are few, creating significant problems for the Department of Conservation (DOC). More often than not their carcasses are buried in beaches at or just above high water mark, near where the animals have stranded. The primary objective of this thesis is to determine the effects of cetacean burial on beach sediments, and evaluate potential health and safety risks associated with this practice. A secondary objective of this thesis is to appraise the appropriateness of one location DOC has repeatedly transported cetacean carcasses to and buried within beach sediments, Motutapu Island in Waitemata Harbour. The chemical effects of cetacean burial over a six-month period are reported for two sites at which animals were buried in 2008, Muriwai and Pakiri beaches; the biological effects of this burial are reported for one of these sites, Muriwai Beach, 12 months post burial. Intertidal faunal and floral inventories are provided for six sites around Motutapu Island, and these then compared and contrasted with inventories compiled from an additional 290 intertidal sites between Whangarei Heads and Tauranga Harbour, North Island East Coast, to appraise the relative uniqueness of intertidal species diversity around Motutapu Island. At both Muriwai and Pakiri beaches, nitrogen and phosphate concentrations in surface sands changed considerably following cetacean burial, although over six months the effect was localized and elevated concentrations of these two chemicals that could be attributed to a buried carcass did not extend more than 40 m from the site of whale burial. Deep-core profiles revealed nitrogen and phosphate concentrations at and in the immediate vicinity of cetacean burial approximately six months after burial to be markedly elevated to the level of the water table, but elevated concentrations attributable to the buried carcass were not observed greater than 25 m from the site of burial. Elevated concentrations of nitrogen and phosphates in beaches persist in surface sediments for at least six months post burial. Twelve months post cetacean burial no significant difference in species richness or abundance were apparent in intertidal communities extending along transects proximal to and some distance from the Muriwai Beach carcass; there is no evidence for any significant short-term (to 12 months) biological effects of cetacean burial in beaches. Of those shores on Motutapu Island accessible by earth-moving equipment and large vessels capable of dealing with and transporting large cetacean carcasses, Station Bay appeared to be the most appropriate site for whale burial. However its small size and relatively high biological value (fairly high species richness for comparable shores between Whangarei Heads and Tauranga) renders it an inappropriate long-term option for whale burial. Other shores on Motutapu Island host some of the highest species richness of all shores surveyed between Whangarei Heads and Tauranga Harbour, rendering them entirely inappropriate locations for burying cetaceans, over and above other variables that may influence disposal location identification (such as archaeological sites, dwellings and accessibility). Motutapu Island is not considered an appropriate location for cetacean burial within beaches. Alternative disposal strategies need to be explored for dealing with cetaceans that strand on Auckland east coast beaches. Although burial is the most convenient and most economical strategy to dispose of cetacean carcass, especially in mass stranding events or when cetaceans are of large size, and the biological effects of this practice are not considered significant (for the one whale that could be studied), persistent enrichment of beach sediments with organic matter could result in prolonged persistence of pathogens in beaches, causing unforeseen risks to human health and safety. Recommendations are made to minimize possible threats to public following burial of cetaceans in beaches, until the potential health risks of burial are more fully understood.

This dissertation presents the applications of state-of-the-art computation techniques and data analysis algorithms in three physical and biological problems: assembling DNA pieces, optimizing self-assembly yield, and identifying correlations from large multivariate datasets. In the first topic, in-depth analysis of using Sequencing by Hybridization (SBH) to reconstruct target DNA sequences shows that a modified reconstruction algorithm can overcome the theoretical boundary without the need for different types of biochemical assays and is robust to error. In the second topic, consistent with theoretical predictions, simulations using Graphics Processing Unit (GPU) demonstrate how controlling the short-ranged interactions between particles and controlling the concentrations optimize the self-assembly yield of a desired structure, and nonequilibrium behavior when optimizing concentrations is also unveiled by leveraging the computation capacity of GPUs. In the last topic, a methodology to incorporate existing categorization information into the search process to efficiently reconstruct the optimal true correlation matrix for multivariate datasets is introduced. Simulations on both synthetic and real financial datasets show that the algorithm is able to detect signals below the Random Matrix Theory (RMT) threshold. These three problems are representatives of using massive computation techniques and data analysis algorithms to tackle optimization problems, and outperform theoretical boundary when incorporating prior information into the computation.
Engineering and Applied Sciences

xi, 119 p. : ill. (some col.)
The evolutionary history of protein families can be difficult to study because necessary ancestral molecules are often unavailable for direct observation. As an alternative, the field of computational phylogenetics has developed statistical methods to infer the evolutionary relationships among extant molecular sequences and their ancestral sequences. Typically, the methods of computational phylogenetic inference and ancestral sequence reconstruction are combined with other non-computational techniques in a larger analysis pipeline to study the inferred forms and functions of ancient molecules. Two big problems surrounding this analysis pipeline are computational error and statistical uncertainty. In this dissertation, I use simulations and analysis of empirical systems to show that phylogenetic error can be reduced by using an alternative search heuristic. I then use similar methods to reveal the relationship between phylogenetic uncertainty and the accuracy of ancestral sequence reconstruction. Finally, I provide a case-study of a molecular machine in yeast, to demonstrate all stages of the analysis pipeline. This dissertation includes previously published co-authored material.
Committee in charge: John Conery， Chair； Daniel Lowd， Member； Sara Douglas， Member； Joseph W. Thornton， Outside Member

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 185-213).
In this thesis, I use coastal measurements of dissolved O₂ and inert gases to provide insight into the chemical, biological, and physical processes that impact the oceanic cycles of carbon and dissolved gases. Dissolved O₂ concentration and triple isotopic composition trace net and gross biological productivity. The saturation states of inert gases trace physical processes, such as air-water gas exchange, temperature change, and mixing, that affect all gases. First, I developed a field-deployable system that measures Ne, Ar, Kr, and Xe gas ratios in water. It has precision and accuracy of 1 % or better, enables near-continuous measurements, and has much lower cost compared to existing laboratory-based methods. The system will increase the scientific community's access to use dissolved noble gases as environmental tracers. Second, I measured O₂ and five noble gases during a cruise in Monterey Bay, California. I developed a vertical model and found that accurately parameterizing bubble-mediated gas exchange was necessary to accurately simulate the He and Ne measurements. I present the first comparison of multiple gas tracer, incubation, and sediment trap-based productivity estimates in the coastal ocean. Net community production estimated from ¹⁵NO₃⁻ uptake and 02 /Ar gave equivalent results at steady state. Underway O₂/Ar measurements revealed submesoscale variability that was not apparent from daily incubations. Third, I quantified productivity by O₂ mass balance and air-water gas exchange by dual tracer (³He/SF₆ ) release during ice melt in the Bras d'Or Lakes, a Canadian estuary. The gas transfer velocity at >90 % ice cover was 6 % of the rate for nearly ice-free conditions. Rates of volumetric gross primary production were similar when the estuary was completely ice-covered and ice-free, and the ecosystem was on average net autotrophic during ice melt and net heterotrophic following ice melt. I present a method for incorporating the isotopic composition of H₂O into the O₂ isotope-based productivity calculations, which increases the estimated gross primary production in this study by 46-97 %. In summary, I describe a new noble gas analysis system and apply O₂ and inert gas observations in new ways to study chemical, biological, and physical processes in coastal waters.
by Cara Charlotte Marie Manning.
Ph. D.

Spider silk displays a unique balance of high tensile strength and extensibility, making it one of the toughest materials on the planet. Dragline silk, also known as the lifeline of the spider, represents one of the best studied fiber types and many labs are attempting to produce synthetic dragline silk fibers for commercial applications. In these studies, we develop a minifibroin for expression studies in bacteria. Using recombinant DNA methodology and protein expression studies, we develop a natural minifibroin that contains the highly conserved N- and C-terminal domains, along with several internal block repeats of MaSp1. We also characterize a family of small cysteine-rich proteins (CRPs) and demonstrate that these factors are present within the spinning dope of the major ampullate gland using MS analysis. Biochemical studies and characterization of one of the family members, CRP1, demonstrate that this factor can self-polymerize into higher molecular weight complexes under oxidizing conditions, but can be converted into a monomeric species under reducing conditions. Self-polymerization of CRP1 is also shown to be independent of pH and salt concentration, two important chemical cues that help fibroin aggregation. Overall, our data demonstrate that the polymerization state of CRP1 is dependent upon redox state, suggesting that the redox environment during fiber extrusion may help regulate the oligomerization of CRP molecules during dragline silk production.

xii, 127 p. ： ill. (some col.)
I developed software to incorporate the FlamMap fire model into an agent-based model, Envision, to enable the exploration of relationships between wildfire, land use, climate change, and vegetation dynamics in the Willamette Valley. A dynamic-link library plug-in utilizing row-ordered compressed array lookup tables converts parameters between polygon-based Envision data and grid-based FlamMap data. Modeled fires are determined through Monte-Carlo draws against a set of possible fires by linking historic fire data to future climate projections. I used classification and regression tree (CART) and logistic regression to relate ignitions to human and land use factors in the Willamette Valley above the valley floor from 2000-2009. Both methods showed decreasing distance to major and minor roads as key factors that increase ignition probability for human ignitions but not for lightning ignitions. The resulting statistical model is implemented in the FlamMap plug-in to provide a dynamic ignition probability map over time.
Committee in charge: Dr. Bart Johnson， Co-Chair； Dr. Scott Bridgham ，Co-Chair； Dr. John Bolte； Member

Much of what we know about temperature-dependent sex determination (TSD) in reptiles stems from constant temperature incubation studies in the laboratory. In recent years, as TSD studies moved into the field it became evident that TSD was much more complex than previously thought. The present study attempted to reveal the complexity of TSD, as it relates to other features of the species' biology and physical characteristics tractable only in the field, such as fluctuations in incubation temperature and reproductive life history. To this end I studied the ecology of the turtle Carettochelys insculpta, a TSD species inhabiting the wet-dry tropics of northern Australia from 1996 to 1998. I tested hypotheses associated with movements, activity, behaviour, reproduction, nest site choice, nest temperatures, embryonic survival, embryonic aestivation, hatch-ling sex ratios, and emergence in the species. Each of these was also considered in the context of the influence of the wet-dry tropics. Compared to other turtles inhabiting lotic habitats, C. insculpta occupied considerably larger home ranges, covering up to 10 km of river. Of previously published factors influencing home range size, low productivity of the (micro) habitat may best explain the extensive home ranges in C. insculpta. Patchiness and low nutrient value of the chief food (aquatic vegetation) of C. insculpta may force turtles to cover large expanses of river to acquire sufficient energy for growth and reproduction. Females were more active, moved farther, and occupied larger home ranges than males. Home ranges of females comprised 1-4 activity centres, many of which were associated with thermal springs. I suggest that females may exhibit increased activity and movements relative to males because of sexual inequality in parental investment, where food is particularly limiting (e.g., in species with biennial reproduction). Biennial reproduction in the population allowed the examination of the influence of reproductive condition on home range size, movements, and activity. Reproductive condition did not influence home range or activity, but gravid turtles moved father between successive sightings than non-gravid females. Individual data corroborate these findings, with females moving farther between successive sightings while gravid compared to while spent. Contrary to previous reports, turtles did not appear to move into estuarine areas or lowland flood plains during the wet season, but moved into the riparian forest and possibly into wetlands adjacent to the main channel in the vicinity of their dry season home ranges. During the study I documented the turtles' use of small, localized thermal springs discharging from the river bottom. Dataloggers attached to the carapace to monitor ambient water temperatures recorded the frequency and duration of thermal spring use by individuals. Turtles used the thermal springs frequently during the winter (4-6 months) when river temperatures were lower than that of the thermal springs (8 = 29 � 0.52� C). Turtles often utilized thermal springs for several consecutive hours, leaving the springs only to surface for air. Thermal springs may be derived from ground water (which maintains a temperature equivalent to the annual mean air temperature), rather than from a specific geothermal heat source. Nine of 19 radio-telemetered adult females were seen to use thermal springs, of which seven were gravid and two non-gravid. Thus, gravid turtles may seek thermal springs more than non-gravid turtles. Frequency, duration, and timing of usage collectively suggest active thermoregulation as the primary function of thermal spring use. Utilization of thermal springs probably permits turtles to be more active in cooler months, which may enhance growth rates and accumulation of energy for reproduction. Onset of nesting along river stretches with thermal springs preceded nesting in a stretch not known to have thermal springs by 24 days. Thus, I speculate that by warming themselves on thermal springs in the months prior to nesting, turtles may have accelerated follicular development and nested earlier. Female C. insculpta matured at ca. 6 kg body mass (38.0 cm carapace length, 30.5 cm plastron length). Turtles produced egg sizes and clutch sizes similar to that of other turtle species of similar size. Turtles reproduced every second year, but produced two clutches in each breeding year, ca. 40 days apart. Thus, it appeared that females were energy limited, possibly due to the low available energy content of the dry season diet (aquatic vegetation). Life history theory predicts that if some costly behaviour is associated with reproduction, skipping years could reduce that cost and allow savings to be directed into future reproduction. The present study revealed no obvious accessory behaviour in the population. Within years, clutch mass did not differ between early (first) and late (second) clutches. However, earlier clutches tended to have more and smaller eggs per clutch but than later clutches, a new finding for turtles that has been demonstrated in lizards and other animals. Because the study spanned both years with 'big' and 'small' wet seasons, I was able to examine how the magnitude of the wet season influenced reproductive characteristics. Following big wet seasons turtles produced larger, heavier, and more eggs per clutch than they did after small wet seasons. Relationships among body size, egg size, and clutch size were evident after two big wet seasons but not apparent after two small wet seasons. Collectively, annual variation in reproductive characteristics and current life history theory suggest that a big wet season is a plentiful time for the turtles. I investigated beach selection of nesting pig-nosed turtles (Carettochelys insculpta) along a 63 km stretch of river in 1997 and 1998. I used three classes of beaches to examine beach choice: beaches with nests, beaches with only crawls, andbeaches without nests or crawls. Across these beach types I compared aspect, solar exposure, temperature, substrate moisture, height, water depth at approach, and the height of cohesive sand. I located 82 nesting beaches with 221 nests, and identified 171 potential nesting beaches based on previously published criteria. Beaches with nests had a greater substrate moisture content and corresponding higher cohesive sand line (hereafter CSL) than beaches without nests. Beaches with nests also had a higher CSL than beaches with only crawls. Apparently, turtles could not excavate a nest chamber above the CSL due to loose substrate consistency causing sand to fall in on itself. Turtles could only nest at low elevations below the CSL on beaches with lower substrate moisture. Turtles apparently avoided nesting on these beaches due to the higher probability of nest flooding, as corroborated by a concurrent study. Beach temperatures increased with a seasonal increase in air temperatures, and were influenced by aspect and total angle of solar exposure. Temperatures did not differ among beaches with nests, beaches with only crawls, and beaches without crawls or nests. Therefore, there was no indication that turtles were manipulating offspring sex through choice of nesting beach. However, turtles may be manipulating sex by nesting in areas with particular thermal characteristics within beaches. Two related aspects of hatchling emergence were studied. Using emergence phenology data, nest temperatures, historical weather data, and a developmental model, I tested the hypothesis that delayed hatching occurred in C. insculpta, and that such a delay would allow hatchlings to time their emergence to match the onset of the wet season. Hatchling C. insculpta emerged, on average, 17 days later than dates predicted from a developmental model. Combined with observations of hatchlings remaining in eggs until emergence, these results confirmed delayed hatching in nature. This delay was synchronized with initial river rises associated with the onsetof wet season rains, and is consistent with published criteria for embryonic aestivation. On a diel scale, I generated predictions of two potentially competing models for nocturnal emergence in hatchling turtles, based on the knowledge that air temperatures decrease with season during the emergence period. A test of those predictions for C. insculpta produced ambiguous results. However, further analysis indicated that C. insculpta, and probably other nocturnally emerging turtle species, respond to a decline in diel temperature rather than an absolute temperature. The former would ensure nocturnal emergence, while the latter is experienced during the day as well as at night. Nocturnal emergence may be associated with nesting in open microhabitats. The 'decision' of when and where to nest can influence both offspring survival and hatchling sex ratios in animals with temperature-dependent sex determination (TSD). Knowledge of how these maternal attributes influence the incubation environment is an important first step in hypothesizing why TSD evolved in a particular species. 1 studied the influence of nest site choice and timing of nesting on embryonic survival and hatchling sex ratios. Predation and flooding were the major sources of embryonic mortality. Embryonic survival was influenced by both lay date and nest site choice: In one year when nesting began later, nests laid later and at lower elevations were destroyed by early wet season river rises. In other years early nesting precluded flood mortality. However, turtles did not nest at the highest available elevations. I hypothesized that turtles were unable to nest at higher elevations because the sand was dry and not cohesive. A field experiment demonstrated that turtles were constrained to nest at lower elevations where they could construct a nest chamber. A mathematical model predicting hatchling sex from fluctuating temperatures was applied to temperature data from 102 natural nests. Resultsconfirmed a type la pattern of TSD, whereby males are produced from cooler temperatures and females from warmer temperatures. The principal determinant of hatchling sex was lay date. Clutches laid earlier in the season produced mainly males, while later clutches yielded mostly females, due to seasonal ramping of air and sand temperatures. However, nest site choice also exerted an influence on hatchling sex. Female-producing clutches were deposited at higher elevations than male-producing clutches. The onset of nesting was not influenced by water temperatures, but may have been related to the magnitude of the previous wet season(s). Turtles nested earlier after two 'big' wet seasons and later following two 'small' wet seasons. This pattern indicates that the wet season is a plentiful time for the turtles. Adaptive 'differential fitness' models for the evolution of TSD have recently been reviewed and clarified. The differential fitness model that best fits C. insculpta is the 'timematching' model, whereby one sex benefits more than the other from early hatching. Male C. insculpta hatched 2-3 weeks earlier then females, on average. Benefit to early hatching males and, therefore, the ultimate selective mechanism (e.g., growth, time to mature) is unknown. Obtaining such data will likely prove difficult in such a long-lived species. A recent adaptive explanation for the evolution and maintenance of temperaturedependent sex determination (TSD) in reptiles rests upon the assumption that mothers can predict or manipulate offspring sex. I postulated that four physiological and behavioural criteria must be met in order for this assumption to be valid: (1) a strong correlation must exist between substrate temperatures during nest site choice and nest temperatures during the period of development when sex is determined in the egg (thermosensitive period = TSP). (2) Assuming that (1) is possible, mothers would need to be capable of correcting for temporal factors obscuring the predictable thermalcharacteristics of nest sites. This could be accomplished in two ways. By contracting nesting times mothers could assess the relative temperatures of alternate nest sites with some accuracy. A protracted distribution of nesting times could greatly reduce a mother's ability to distinguish between, for example, a cooler nest site at a warmer time and a warmer nest site at a cooler time. Alternatively, mothers would need to be able to incorporate temporal changes in nest site temperatures. (3) Sufficient variation in thermal profiles among nest sites, relative to the breadth of temperatures producing both sexes (pivotal temperatures), would be necessary. For example, if most nests produced both sexes, then depth of the eggs would be the deciding factor determining sex, leaving little opportunity for nest site choice to produce one sex or the other. (4) Mothers would need access to nest sites spanning a range of thermal profiles in order to produce either offspring sex. To this end, home range size relative to the number and location of nesting beaches should be important. I tested these four predictions in Carettochelys insculpta, a beach nesting turtle with TSD, using three years of field data on nest site choice, nesting times, thermal characteristics of nests, hatchling sex ratios, and movements of nesting turtles. A strong positive correlation existed between assessable substrate temperatures at nest site choice and mean daily TSP temperatures in all three years. However, the proportion of explained variation was highly variable among years, and low in 1998. Accordingly, the proportion of nests in which substrate temperatures at nest site choice predicted offspring sex correctly was low in 1998 (48- 62 %, depending on treatment of the data). Nesting times were normally distributed, and combined with diel changes in nest site temperatures greatly reduce a turtle's ability to distinguish between sites that would produce different sexes. Considerable among-clutch variation in thermal profiles to produce variable sex ratios existed, agreeing with other studies on turtles. Radiotelemetry indicated that home rangesencompassed several nesting beaches with differing thermal profiles, indicating scope for producing the desired sex. However, the seasonal increase in air temperatures resulted in an overriding effect of mostly males being produced in early (first) clutches and mainly females being produced in late (second) clutches. Collectively, the results suggest that C. insculpta mothers would find it difficult to predict, and therefore, manipulate hatchling sex, supporting the conventional notion that TSD mothers have little or no control over offspring sex.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Applied Biological Sciences, 1988.
Title as it appeared in M.I.T. Graduate List September 1988: Heparin degrading enzymes from Flavobacterium heparinum.
Includes bibliographical references.
by Joseph James Francis Zimmerman.
Ph.D.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Applied Biological Sciences, 1986.
Title as it appeared in M.I.T. Graduate List June 1987: Control of the structure-function properties of yeast glucans.
Bibliography: leaves 166-171.
by Spiros Jamas.
Sc.D.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Applied Biological Sciences, 1986.
MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE.
Bibliography: leaves 157-166.
by Sew-Wah Tay.
Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Applied Biological Sciences, 1986.
MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE
Bibliography: leaves 217-231.
by Jonathan Seth Dordick.
Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Applied Biological Sciences, 1985.
MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE.
Vita.
Includes bibliographical references.
by Stanley David Rose.
Ph.D.

Bibliography: p. 297-320.
In this thesis we thus wish to consider the concept of self-organization as an overall paradigm within which various theoretical approaches to the study of development may be described and evaluated. In the process, an attempt is made to give a fair and reasonably comprehensive overview of leading modelling approaches in developmental biology, with particular reference to self-organization. The work proceeds from a physical or mathematical perspective, but not unduly so - the major mathematical derivations and results are relegated to appendices - and attempts to fill a perceived gap in the extant review literature, in its breadth and attempted impartiality of scope. A characteristic of the present account is its markedly interdisciplinary approach: it seeks to place self-organization models that have been proposed for biological pattern formation and morphogenesis both within the necessary experimentally-derived biological framework, and in the wider physical context of self-organization and the mathematical techniques that may be employed in its study. Hence the thesis begins with appropriate introductory chapters to provide the necessary background, before proceeding to a discussion of the models themselves. It should be noted that the work is structured so as to be read sequentially, from beginning to end; and that the chapters in the main text were designed to be understood essentially independently of the appendices, although frequent references to the latter are given. In view of the vastness of the available information and literature on developmental biology, a working knowledge of embryological principles must be assumed. Consequently, rather than attempting a comprehensive introduction to experimental embryology, chapter 2 presents just a few biological preliminaries, to 'set the scene', outlining some of the major issues that we are dealing with, and sketching an indication of the current status of knowledge and research on development. The chapter is aimed at furnishing the necessary biological, experimental background, in the light of which the rest of the thesis should be read, and which should indeed underpin and motivate any theoretical discussions. We encounter the different hierarchical levels of description in this chapter, as well as some of the model systems whose experimental study has proved most fruitful, some of the concepts of experimental embryology, and a brief reference to some questions that will not be addressed in this work. With chapter 3, we temporarily move away from developmental biology, and consider the wider physical and mathematical concepts related to the study of self-organization. Here we encounter physical and chemical examples of spontaneous structure formation, thermodynamic considerations, and different approaches to the description of complexity. Mathematical approaches to the dynamical study of self-organization are also introduced, with specific reference to reaction-diffusion equations, and we consider some possible chemical and biochemical realizations of self-organizing kinetics. The chapter may be read in conjunction with appendix A, which gives a somewhat more in-depth study of reaction-diffusion equations, their analysis and properties, as an example of the approach to the analysis of self-organizing dynamical systems and mathematically-formulated models. Appendix B contains a more detailed discussion of the Belousov-Zhabotinskii reaction, which provides a vivid chemical paradigm for the concepts of symmetry-breaking and self-organization. Chapter 3 concludes with a brief discussion of a model biological system, the cellular slime mould, which displays rudimentary development and has thus proved amenable to detailed study and modelling. The following two chapters form the core of the thesis, as they contain discussions of the detailed application of theoretical concepts and models, largely based on self-organization, to various developmental situations. We encounter a diversity of models which has arisen largely in the last quarter century, each of which attempts to account for some aspect of biological pattern formation and morphogenesis; an aim of the discussion is to assess the extent of the underlying unity of these models in terms of the self-organization paradigm. In chapter 4 chemical pre-patterns and positional information are considered, without the overt involvement of cells in the patterning. In chapter 5, on the other hand, cellular interactions and activities are explicitly taken into account; this chapter should be read together with appendix C, which contains a brief introduction to the mathematical formulation and analysis of some of the models discussed. The penultimate chapter, 6, considers two other approaches to the study of development; one of these has faded away, while the other is still apparently in the ascendant. The assumptions underlying catastrophe theory, the value of its applications to developmental biology and the reasons for its decline in popularity, are considered. Lastly, discrete approaches, including the recently fashionable cellular automata, are dealt with, and the possible roles of rule-based interactions, such as of the so-called L-systems, and of fractals and chaos are evaluated. Chapter 7 then concludes the thesis with a brief assessment of the value of the self-organization concept to the study of biological development.

The subject area for this thesis is detection of chromosomal regions or QTL causing complex variation at the phenotypic level. In particular, the differentiation of sources of additive and non additive variation. Unlike QTL mapping using divergent or inbred lines, this study aims to explore methods within populations, facilitating direct application of techniques such as marker assisted selection. Specifically, objectives were to evaluate a linear model or variance components (VC) approach to explore the existence and magnitude of variation caused by additive, dominant and imprinted QTL segregating in general pedigrees. This has been achieved by combining extensive simulation and analysis of real commercial poultry data. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared by hierarchical extension to incorporate more variance components, and likelihood ratio test statistics derived from the comparison of full with reduced or null models. A range of additive, dominant and imprinted QTL effects were simulated within two-generation poultry, pig and human type pedigrees. Effects of family size and structure on power, accuracy of variance component estimation, and distribution of the test statistic, were evaluated. Empirical thresholds were derived by simulating populations under the null hypotheses for each type of simulated pedigree and permutation analysis in real data. In the commercial poultry data, dominant and imprinted QTL effects were found for bodyweight and conformation score. Under simulation, although power to detect QTL effects was high in two-generation livestock pedigrees, considerable variation was found in power and behaviour of test statistics. Power to detect dominance was greater in pig and poultry than human type pedigrees with theoretical thresholds increasingly conservative as the number of dams per sire decreased, highlighting the need for empirical derivation of the critical test statistic. The detection of variance caused by imprinted genes and in particular estimates of variance components were also heavily dependent upon the number of sire and dam families used to estimate them. Results showed that VC analysis can be used to routinely detect genetic effects including imprinting and dominance in complex pedigrees. The work presented is the most extensive evaluation of the detection of non additive QTL using VC methods to date. Results challenge standard assumptions made about power and null distributions and show that optimal use of methodology is dependent on pedigree structure.

Biorilms are structured communities of bacterial cells enclosed in a self-produced polymeric matrix that are adherent to an inert or living surface. Their growth on the surface of catheter lines, artificial joints and other surgical implants is of major medical concern. As many laboratory strains have become accustomed to standardised conditions, they are not necessarily representative of clinical strains. This study investigated the effect of horse blood, human blood and human blood components on biofilm. formation by clinical and laboratory isolates of Escherichia coli and Campylobacter jejuni using a 96-well microtitre plate method, crystal violet staining and confocal laser scanning microscopy. The results for the E. coli laboratory isolatesi ndicated a decreasein biofilm fonnation in Luria-Bertani (LB) broth supplemented with lysed horse blood, whole and lysed human blood, human plasma, human serum and whole and lysed human red blood cells. Conversely, the results for the E. coli clinical isolates showed an increase in biofilm formation in LB broth supplemented with either lysed horse blood or lysed human blood. Supplementation with human serum decreased biofilm formation by these clinical strains, whilst the addition of human plasma appeared to be inhibitory to biofilm formation. Of the clinical E. coli, only the urine derived strains showed a significant increase in biofilm formation in LB broth with added whole human red blood cells or whole human blood and produced haemolysin. The results for the C. jejuni isolates used in this study indicated a large increase in biofilm formation when grown in Bolton Broth (BB) supplemented with lysed horse blood, lysed human blood or lysed human red blood cells. This increased biofilm formation was not observed for cultures grown in BB supplemented with human serum, human plasma, whole human blood, iron or whole human red blood cells.

This thesis is a continuation of experimental work conducted by Pickup el al. (1997) analysing nickel resistant bacteria isolated from effluent discharged from a sewage outfall in the Lake District, Cumbria. Its aim is to further characterise the nickel resistance determinant ftom Enterobacter cloacae FBA30. FBA30 was found to harbour a 55-60 kb plasmid designated pFBA30 which confers nickel resistance on its host and in laboratory strains of E. coh. pFBA30 is transferable to enteric relatives, but not to non-enteric species and is considered to have a narrow host range. A 10.2kb Sad restriction fi7agment was cloned fi7om pFBA30, which exhibited constitutive nickel resistance both in its original host and in laboratory strains of Eschericia coli. Further work on the 10.2 kb Sacl fragment localised the nickel resistance locus to an internal 2.3 kb PvuII restriction fragment exhibiting extensive homology to the nre determinant of plasmid pTOM9 (Schmidt and Schlegel, 1994). This fragment and a further 1.75 kb Smal fragment derived from it, were used as DNA probes to examine other bacterial strains isolated from the same site. Six strains showing extensive homology were retained for further study (Pickup et al., 1997). The nickel resistance of the six strains appears to be chromosomally encoded. The strains were sorted into groups based upon their sampling date and size of restriction fragment homologous to the probe developed from pFBA30. Group A isolates carry a homologous Null fragment approximately 6.5 kb in size whereas group B isolates carry a 2.5 kb Null fragment. All strains display constitutive nickel resistance and are capable of expressing resistance under both anaerobic and aerobic growth conditions. Furthermore, each strain was discovered to be resistant to a spectrum of heavy metals and antimicrobial agents. Each group consists of a range of enteric bacterial species including Klebsiella, Citrobacter and Enterobacter species.

Multiple sclerosis (MS) is the most common autoimmune inflammatory demyelinating disorder of the human nervous system affecting nearly 1 million people worldwide every year. Current treatments for first-line nontoxic therapy of the relapsing-remitting form of the disease are two forms of recombinant IFN(3, Ia and 1(3 andglatiramèr acetate. The pathogenesis of MS is highlighted by an inflammatory response and myelin destruction. Several recent studies have reported alterations in immune variables such as cytokine concentrations, immune-related molecules such as MHC and adhesion molecules and chemokines; which may contribute to an imbalance between Thi and Th2 T cellmediated immune response. The aims of the present study were to characterize the cytokinetic profile of MS patients through investigating the secretion of the main pro and anti-inflammatory cytokines from peripheral blood mononuclear cells of MS patients compared to controls, and to investigate cytokine receptor expression levels in T and NK cells. In addition, the induction of apoptosis and the involvement of adhesion molecules and metalloproteinases in oligodendrocyte destruction are examined. Finally, the effect of IFN(3 treatment on cytokine secretion levels as well as on the aforementioned immunoregulatory molecules was evaluated. The study population consisted of 60 MS patients (20 untreated, 20 treated with IFNf3-lcz and 20 treated with IFN(3-1(3) in parallel with 25 controls. Serumlplasma samples and peripheral blood mononuclear cells (PBMCs) were isolated from each participant. Using the enzyme linked immunospot (ELISPOT) assay the numbers of cytokine-secreting PBMCs were measured for the following cytokines: IFN-y, TNF-a, IL- 12, IL- 10 and IL-4. The expression levels of the cytokine receptors IL- 1 2R(3 1, IFN-y, IL- 1 OR, TNFaR were estimated in the surface of lymphocytes using flow cytometry and serum levels of soluble CD95, ICAM- 1, VCAM-1, metalloproteinase-9 (MMP-9) and the tissue inhibitor, metalloproteinase-1 (TIMP-1) were evaluated in all samples. The ELISPOT assay proved a very sensitive and valuable tool for characterisation of the cytokine profile of MS patients. Decreased numbers of PBMCs secreting IL-b 0 and IL-4, and increased numbers of PBMCs secreting TNF-a, IL-12 and IFN-y were observed in MS patients compared to healthy controls. Treatment with IFN(3 elevated IL-IO and IL-4 levels, and decreased TNF-a, IL-12 and IFN-y levels in these patients. IFN(3/lci was more efficient in decreasing IL-12 secreting cells and IFN(3/1(3 in decreasing IFN-y, and TNF-a secreting cells and elevating IL-4 and IL- 10 secreting cells Increased expression of IL-12Rj31 and TNF-aR was observed in NK cells and decreased expression of WN-7R and IL-I OR was shown in T cells of MS patients compared to controls. IFNf3 therapy reduced IL-12R(3l levels in I and NK cells (IFNf3-la was more effective), and TNF-uR levels in I cells (IFNj3- 1(3 was more effective), but it increased IFN-1R and IL-1OR in T and NK cells of MS patients. Increased levels of the soluble CD95 apoptosis marker were observed in serum of MS patients compared to controls, which further increased after IFN(3 treatment (IFN(3-10 was more efficient). Increased levels of soluble ICAM-1 and VCAM-1 were observed in serum of MS patients compared to controls, which were further increased after treatment with IFN(3 (IFN-1a was more efficient in increasing sICAM-1 and IFNI3-113 in increasing sVCAM- 1 levels) Increased levels of MMP-9, decreased levels of TIMP- 1, and increased MMP-9ITIMP- I ratio was found in serum of MS patients compared to controls, and treatment with IFN decreased MMP-9 levels, increased TIMP-1 levels and decreased MMP-9/TIMP-1 levels ITCXTII 1.. 4'P + tss i,p s a ,lvaS it"j*.. These results indicate an over expression of Thi type cytokines in MS accompanied by a concomitant suppression of Th2 type immune response as well as by alterations in the expression of cytokine receptors. A consequent activation of other immunoregulatory elements (sCD95, adhesion molecules, metalloproteinases) was also observed which was partly modified by IFNI3 treatment. This study provides important evidence on the role of cytokines and of other inflammatory molecules in MS pathogenesis and highlights possible mechanisms of action of IFNI3 treatment, offering new perspectives for novel, more efficient, diagnostic, and therapeutical approaches for the disease.

Nucleic acid amplification methods (PCR) were investigated for the detection of Campylobacter species in foods and environmental waters. A novel species-specific PCR was adapted into a high-throughput, colorimetric end-stage detection format (PCR ELISA). The sensitivity of detection of the PCR ELISA assay was equivalent to one genome copy and was demonstrated to be 100-fold more sensitive than a conventional gel electrophoresis-based PCR method. The novel species-specific PCR assay was adapted into a quantitative real-time format (TaqMan) for accurate quantification of the numbers of C. jejuni cells present in food samples. Quantification was demonstrated over six orders of magnitude between 1.2 x 101 to 1.2 x 107 genome equivalents per reaction, with a limit of detection of 10 genome equivalents. The PCR ELISA and real-time PCR assays were validated for the specific and sensitive detection of C. jejuni and C. coil in naturally contaminated food and environmental water samples. Methods for the extraction of DNA from foods and enrichment cultures were investigated and an optimised method (PrepMan) determined. The PCR ELISA and real-time PCR assays significantly reduced the time taken for the detection of C. jejuni and C. co/i in foods and waters to seven hours and two and a half hours respectively. Previous studies have indicated that detection of mENA by reverse transcriptase PCR (RT-PCR) may reflect viability in the detected organism. RT-PCR assays were m developed for the detection of thee C. jejuni mRNA targets, DNase treatment of extracted RNA was optimised and appropriate controls for RT-PCR in bacteria established. The assays were applied to the detection of heat-killed and chlorine-killed cell suspensions with diflèrentiation between viable and heat-killed cells being demonstrated. However, problems with target-dependent variations in the halilives of the mRNA targets were identified which have major implications for the use of RT-PCR to establish the viability of contaminating pathogens in processed food samples. The PCR ELISA and real-time PCR assays are high-throughput methods for the sensitive and specific detection of C. jejuni and C. coli in foods, and are an important model for other foodborne pathogens.

Broodiness in the domestic hen is characterized by incubation of eggs and subsequent care of the young. Incubation behaviour is initiated by increased plasma progesterone and oestrogen from maturing ovarian follicles that induce nesting behaviour. This is subsequently transformed into incubation behaviour by increased plasma prolactin in association with decreased gonadotrophin and ovarian steroid secretion. Gonadotrophin secretion is under the stimulatory and inhibitory control, respectively, of gonadotrophin releasing hormone-I (GnRFI-I) and gonadotrophin inhibitory hormone (GnIH). Prolactin secretion is controlled by the stimulatory action of the hypothalamic neuropeptide, vasoactive intestinal polypeptide (VIP). The aim of this study was to increase understanding and knowledge of the interactions between these hormones and neuropeptide in the neuroendocrine control of incubation behaviour in the domestic hen. Observations were made using fluorescence immunocytochemistry with additional data on progesterone receptor mRNAs, using PCR to localize the receptor. Hypothalamic progesterone receptor immunoreactivity (PR-ir) was seen in several hypothalamic nuclei and areas including the organum vasculoswn terminalis (OVLT) and basal hypothalamic tuberal region (TU). The density of cells containing PR-ir in the OVLT and TU, but not at other hypothalamic loci, was lower in incubating than in laying hens. In the anterior pituitary gland, PR-ir was localised in luteinizing hormone (LH) but not prolactin cells, and the density of cells containing LH and PR-ir was lower in incubating than in laying hens. The density of prolactin cells was higher in incubating than in laying hens. Progesterone receptor B mRNA was found in It the TU and pituitary gland in both laying and incubating hens. Prolactin receptor, but not progesterone receptor, was co-localised in VIP neurones in the TU. The number of visible VIP-ir cell bodies containing prolactin receptor was greater in incubating than in laying hens. Nerve fibres containing VIP did not contact GnRH-I-ir cell bodies, but potential contact between those VIP and GnRJ-I-I fibres was seen in the median eminence. GnIH was localized in cells in the paraventricular nucleus (PVN) in incubating and laying hens did not contain PR-ir and had terminals in the median eminence. The density of GnIH neurones did not differ between laying and incubating hens, but their size of the cell bodies was significantly larger in incubating hens. Although GnRFI-Iir and GnIH-ir fibres were abundant in the PVN, they were not observed to come into close contact. It is concluded that incubation behaviour and associated changes in either prolactin or gonadotrophin secretion could be mediated through progesterone receptor B in the OVLT and TU. Progesterone is likely to exert feed-back control of LH secretion at the level of the pituitary gland in laying, but not in incubating hens through progesterone receptor B. Prolactin may act directly on basal hypothalamic VIP neurones to regulate it own secretion. Increased GnIH release in incubating hens may contribute to depressed gonadotrophin secretion.

Momordica charantia fruit is traditionally used as a vegetable in the Indian subcontinent and is claimed to have hypoglycaemic effects in human and experimental diabetes. The oral administration of M. charantia fruit juice was investigated for its effects in streptozotocin (STZ)-induced diabetes in rats. The results of this study have revealed that the fruit juice administration reduced the blood glucose levels, improved glucose tolerance and increased blood insulin levels and body weights in STZ-induced diabetes in rats. However, the treatment of fruit juice did not completely normalize these parameters as the values were still significantly different from those of age-matched controls. The systolic blood pressure was significantly increased in diabetic animals when compared to untreated diabetic rats. The treatment of Lvi. charantia to diabetic animals completely prevented such an increase as the values were not significantly different from that of age-matched controls. The administration of M charantia to STZ-induced diabetic rats also reduced the absorption of glucose by the brush border of small intestine. A similar reduction in glucose uptake by muscle cells in vitro was also observed. In an immunohistochemical study of the pancreas on number and distribution of endocrine cells, a significant increase in the number of insulin positive cells was observed in Lvi charantia treated-diabetic animals as compared with untreated diabetic rats. However, their number was still significantly less than that obtained for control animals. The effect of M charantia treatment on myelinated fibre abnormalities in the tibial nerve of STZ- induced diabetic and control rats was also investigated. The mean cross-sectional myelinated fibres area (p C 0.03), axonal area (p C 0.02) and myelin area (p < 0.04) including the mean maximum myelinated fibres area (p C 0.03) were significantly reduced in untreated diabetic animals when compared with age-matched controls. In the M. charatia treated diabetic animals, myelinated fibre area and myelin area were significantly greater than untreated diabetics (p C 0.05) and not significantly different from age-matched controls. The mean value for the maximum fibre area was also significantly greater than that of untreated diabetics (p< 0.05) and was not significantly different from that of age-matched controls. In summary, the administration of M. charantia normalised the structural abnormalities of peripheral nerves in experimental diabetes. The changes in STZ-induced diabetes related to oxidative stress and expression of P450 and GST isoenzymes was studied. The results indicated an increase in CYP4Adependent laurie acid hydroxylation in liver, kidney and the brain of STZ-diabetic rats. An increase in CYP2B-dependent aniline hydroxylation and CYP lA-dependent ethoxycoumarin-O-deethylase activities was also observed. A significant increase in aminopyrene-N-demethylase activity was observed only in rat kidney while there was a decrease in the liver and brain of diabetic rats. A significant increase in NADPHdependent lipid peroxidation (LPO) in kidney of diabetic rats was also observed. On the other hand, a decrease in hepatic LPO was seen during chronic diabetes. During diabetes an increased expression of CYP1AI, CYP2E1 and CYP4A2 proteins was also seen by western blot analysis. Mi charantia fruit juice feeding modulated the protein expression and catalytic activities in a tissue and isoenzyme specific manners. A marked decrease in hepatic glutathione (GSH)) content and glutathione Stransferase (GST) activity and an increase in brain OSH and GST activity was observed in diabetic rats. On the other hand, renal GST was markedly reduced while GSH content was moderately higher than that of control rats. Western blot and immunohistochemical analysis using specific antibodies have confirmed the tissue specific alterations in the expression of OST isoenzymes. M. charantia juice feeding, in general, reversed the effect of long tenn STZ-diabetes on the modulation of both P450-dependent monooxygenase activities and GSH-dependent oxidative stress related LPO and GST activities. These effects were found to be tissue specific and related to the modulation of various specific isoenzymes during diabetes. These results have suggested that the modulation of xenobiotic metabolism and oxidative stress in various tissues may be related to altered metabolism of endogenous substrates and hormonal status during diabetes. These findings reported in this thesis may have implications in elucidating the therapeutic use of M charantia in the management of diabetes mellitus.

The ring dove (Streptopelia risoria) is a usefUl animal model for the identification of neural and hormonal determinants of reproductive behaviours. Studies were undertaken to investigate the role of dopamine and progesterone in the expression of sexually differentiated patterns of behaviours during the breeding cycle, and provide the first mapping of tyrosine hydroxylase immunoreactive (Til-ir) structures in the ring dove brain. Quantitative analysis revealed increased TFJ-ir cells, in male and female brooding doves, in the nuclei periventricularis magnocellularis, dorsomedialis anterior thalami, pretectalis medialis; and in the nucleus dorsomedialis posterior thalami in female brooding birds. This confirms that increases in dopamine activity during the brooding period are exhibited in regions integrating neuroendocrine and sensory information to mediate the expression of parental defence behaviours. Immunofluorescence studies revealed no co-localisation of progesterone receptor (PR-fr) in TM-fr cells, but demonstrated the presence of TH-fr terminals in axosomatic contact with PR-fr-containing cells in the preoptic region, which may enable dopamine activation of the progesterone receptor, via the Dl receptor. A collaborative study with the University of Hiroshima, demonstrated increased progesterone concentrations in the diencephalon of male brooding doves compared with non-breeding male doves. Measurement of 3[3-HSD enzymatic activity confirmed the synthesis of progesterone in the ring dove diencephalon. This may be sexually differentiated and mediated by proliferating glial cells, under the influence of VIP and prolactin. Primary glial cell culture techniques established the presence of PR-fr in cultured ring dove brain cells. These studies suggest that nest defence behaviour in male and female ring doves may be mediated by differentially elevated levels of centrally acting progesterone, arising as a consequence of increasing dopante activity in the preoptic area. The possibility of progesterone inhibition of y-aminobutyric acid (GABA) activity, to disliThibit dopamine neuronal activity during incubation and brooding, and enable the expression of defensive behaviours is discussed.

The newborn screening for congenital hypothyroidism (CR) started in the West in the sixties. The guidelines for screening were introduced in the majority of western countries some 30 years ago and were adapted in 1997 by the World Health Organization. The United Arab Emirates (UAE) started newborn screening for CH in 1998 and was considered one of the leading countries in the Middle East to apply this programme nationwide. Before newborn screening for CH in the UAE, little was known about the epidemiology of the disease in this part of the world which shares the same epidemiological pattern of the Gulf region and the Middle East This nationwide study investigated the epidemiological pattern of CH in the UAE in terms of assessment of biological and environmental components and their significance in the relatively increased incidence of the disease in this community compared to the worldwide incidence (1:30004000). This study employed radioimmunoassay technique used by the newborn screening programme to measure the capillary Thyroid Stimulating Hormone (TSR) for all newborns at the week of age. In addition, chemical and radiological techniques were employed to screen for positive cases. Firstly, cases detected have been studied in terms of prevalence of the disease in the UAE in relation to other parts of the world and the definition of the epidemiological components and its association to the prevalence of the disease. The study included the investigation of the genotypic pattern of congenital hypothyroidism in the UAE among certain cases with familial dyshormonogesis phenotype. The results show high incidence of the disease compared to the worldwide incidence and also it showed a specific epidemiological pattern. Secondly, the study employed the data obtained in newborn screening for CH in a longitudinal study of TSR pattern of the population and its use to monitor the iodine uptake of this population. This part of study also studied other important implications of the TSR pattern which included the TSR surge and the prevalence of sub clinical cases in which TSH is the main monitor. Thirdly, the study evaluated the controversial issues in the newborn screening programme in the preanalytic and post-analytic phases of the programme. The role of incorporation of the pre and post analytical quality control of the programme in reduction of the morbidity of the disease. Nevertheless, this study provides an overview for the epidemiological pattern of congenital hypothyroidism in the UAE and forms a basic epidemiologic background for further detailed studies that would focus on the clinical aspect and prognostic outcome of the disease. It may be concluded that the clinical picture of congenital hypothyroidism has changed dramatically since newborn screening was instituted in the UAE. Population-based registers and linked-databases can provide very useful information for evaluating screening programmes, and extending current knowledge of the epidemiology of congenital hypothyroidism. This is the first epidemiological study of CH in the UAE in which data from population-based registries were linked, the epidemiologic patterns and associated factors are more representative. The study delineates the significantly increased incidence of congenital hypothyroidism compared to the universal incidence and the clear correlation of this incidence with certain risk factors. Some of these are local which pertain to this area of the world and end in constituting this specific epidemiological pattern.

The susceptibility of human lungs to carcinogens depends on the metabolic balance between activation and detoxification pathways, though for the tumour to develop depcnds on activation of cell immortalisation pathway. The correlation of these pathways has not been reported. The present study described the correlation in transcription of genes of two phases of drug metabolism pathways and immortalisation pathway in four lung cell lines namely; a normal lung cell line (CDD32Lu), alveolar adenocarcinoma (A549), pleural adenocarcinoma (1-1460), and a drug resistance large cell carcinoma (COR-L23/5010). The levels of transcripts of Phase I (CYPL4I, CYPIA2 and CYP2EI), phase II (GSTMJ) and immortalisation (hTERT) genes were investigated. There was evidence suggesting that the transcription of CYPJAI, and CYP/A2 is of cell specific since CYPIAJ transcribed in the A549 eell line only, while CYPIA2 was transcribed in the H460 cell line. The present study validates the ability of CYPIA2 to be expressed in cell line. Moreover, the present study showed abundant expression of CYP2E/ and GSTMJ mRNA in normal and lung cancer cell lines suggesting that these genes may play no active role in lung carcinogenesis. In addition, the transcription level of immortalisation gene (hTERT) and telomerase activity was determined and observed in the A549 cell line only. The novel finding of this research is the cb-transcription of CYPJAJ and JITERT in the A549 cell line. The co-transcription was further analysed by induction of CYPJAJ in all cell lines with the AhR ligands TCDD and 3-MC. The finding reveals the existence of CYPIAI and hTERT co-transcription. Despite the fact that transcription of CYPJAI was observed CYP1A1 activity was not detected even after cell treatment with CYP1A1 inducers. This was possibly due to scarcity of CYP1A! and limited level of haem in the extrahepatic tissue. This study demonstrated a novel basal and induced co-transcription of CYP1AJ and hTERT. The regulation of co transcription was analysed by silencing CYPIAJ using siRNA technology and observing hTERT knockdown. Silencing of CYP1AI was subsequently downregulate hTERT transcription and reduces cells viability. The mechanism of co-transcription was investigated to rule out the involvement of suggested AhR signalling pathway. This was carried out by determining the level of mRNA expression of those genes, which their proteins were involved in the AhR signalling pathway. The results obtained suggest the role of the AhR signalling pathway in the co-transcription of CYPJAJ and hTERT. The data obtained from gene knockdown experiments revealed silencing of CYPJAJ alters hTERT expression and cell proliferation. The present study suggests that siRNA technology can be used as a reliable tool for the validation of co-transcription. Moreover, the concomitant silencing of CYPJAJ and hTERT and inhibition of cells proliferation not only validate the co-transcription but also a valuable finding to be considered as a novel therapeutic target, which may contribute to management of lung cancer. The transcription of CYPIAJ and hTERT has been identified as a cancer risk marker in a diverse range of cancers, the data of the present study suggests the use of CYPJA] 5iRNA as optional gene therapy in cancer management, where CYPJAJ plays a major risk.

The action of AcrAB-ToIC, a multidrug efflux system of Escherichia co/i, is largely responsible for the increased intrinsic resistance of this organism to many antimicrobial agents. The level of mRNA specific to the acrAB efflux genes is elevated by six-fold during exponential phase of growth in LB broth. In MOPS minimal medium supplemented with 0.4 % (w/v) glucose, levels of acrA mRNA remain higher for a prolonged period of time concurrent with the delayed onset of stationary phase, suggesting that transcription of this gene is linked with active growth. A case for transcriptional activation of this gene by RNA polymerase associated with the "housekeeping" sigma factor, a 7o, is presented. Investigation of acrAB transcription in E. co/i SD1648 using the acrAB::lacZ reporter system encoded on a plasmid (pNN602) appears to contradict these fmdings, suggesting that acrAB transcription is induced upon entry into stationary phase. This paradox is attributed to fundamental differences between the two methods of investigating transcription, and suggests that acrAB expression is subject to post-transcriptional regulation or that the plasmid based reporter system fails to convey an important aspect of control. Notably acrA niRNA levels suggest transient induction of acrA transcription upon transition into stationary phase of growth; however this is secondary to the observed exponential phase peak in transcript levels. In addition to the general stress conditions already found to induce acrAB transcription including 0.4 % (v/v) ethanol and 0.5 M sodium chloride, bile salts (cholate and deoxycholate), ampicillin, and growth on certain carbon sources, were found to induce acrAB transcription. A family of isogenic mutant strains based on the lacZ derivative of E. co/i MG1655 (SD 1648) harbouring specific gene disruptions was constructed in order to investigate the effect of key regulatory factors on transcription of the acrAB genes. CRP-cAMP, FIS, H-NS, Rob, AcrR, OmpRJEnvZ, CsrAB, and SdiA were all found to have significant effects on acrAB transcription. A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay, using the Roche LightCyclerTM Instrument, was developed for the purpose of this investigation of acrA gene transcription. The assay was used specifically to quantify acrA mRNA levels; however the method can readily be applied to the study of other E. coli genes. The method was uniquely applied to the investigation of acrAB transcription throughout the growth cycle of E. co/i during batch culture in LB broth, in order to ascertain the patterns of expression for this gene. Following this, the RT-PCR assay was used as a novel approach to determining the start of transcription for the acrAB genes. Where transcription is initiated from more than one promoter, this method could be applied further to determine the relative strengths of each promoter, in vivo, under different conditions. In the case of the acrAB genes a promoter was located between 224 and 383 bases upstream from the acrA start of translation. This suggests that at least two promoters exist upstream of the acrAB genes, the implications of which are discussed.

The United Arab Emirates (UAE), like many other developing countries, has witnessed a rapid development in many aspects of life during the last three decades. The discovery of oil in the middle of the last century has contributed to significant social change and UAE, along with other Gull Arab States, have experienced a rapid transition in its socio-economic status. Rapid economic growth in IJAE has brought about marked changes both in lifestyles and in patterns of health and disease. With the greater availability of housemaids, cars, televisions and other sophisticated household appliances, the lifestyles of UAE nationals have become more sedentary, and watching television and eating snacks are some of the main4eisure-time activities. The consumption of traditional food items have also decreased with urbanization and life-style changes in the UAE community, and hypertension have become a major public health problem. To date, there are no systematic studies of the relationship between hypertension and socioeconomic factors such as income and demographic factors including education and occupation in the UAE population have been undertaken. Since each community has its own common and unique socioeconomic determinants for cardiovascular diseases, particularly hypertension, it is important to study these variables in individual communities. In the UAE, it is believed that the effect of income, education and occupation are much weaker than in the developed countries due to the differences in the educational levels and the differences in the economy of the country. This study investigated the association between the incidence of hypertension and socioeconomic factors including income. The study included 500 hypertensive adults aged 20-65 years from the Primary Health Care (PHC) Clinics along with a randomly selected sample of 500 normotensive control subjects. Face-to-face interviews were done and data were gathered on socio-economic status (SES). age, gender, nationality, educational level, occupation, place of living (urban and semiurban), parity, income level, cigarette smoking habit, physical activity, lifestyle habits, body mass index, social support, chronic life difficulties, perceived stress and iritability. Hypertension was defined according to World Health Organization (WHO) criteria as Systolic Blood Pressure (51W) > 140 mm Hg and/or Diastolic Blood Pressure (DBP) > 90 mm Hg and/or on antihypertensive treatnent. The data were analyzed using the Statistical Packages for Social Sciences (SPSS). Student's t-test, Mann-Whitney test, chi-square test and ANOVA test were used to assess the relationship between these factors and the incidence hypertension. SBP and DBP. For the Arab expatriates, the present study found a statistically significant association between socioeconomic factors (particularly income and education) and the incidence of hypertension and elevated blood pressure. In contrast, the study has also found no significant relationship between the incidence of hypertension and socioeconomic factors among UAE nationals. The results of this study showed a significant relationship between most of the studied psychosocial risk factors and hypertension. There was a significant relationship between hypertension and social support, perceived stress and chronic life difficulties. The results provided clear evidence that the effect of psychosocial risk factors in the development of hypertension is more pronounced among Arab expatriates compared to UAE nationals. Not surprisingly, the study has also found a significant relationship between the incidence of hypertension and some of the known hypertension-related risk factors. A significant association was found between the incidence of hypertension and body mass index, cholesterol abnornmlity. smoking, saturated fat consumption, excessive salt constiiiiption. physical exercise, cardiovascular disease, diabetes, renal problems and family history of hypertension. In addition, psychosocial stressors and other personal health habits such as diet (saturated fat consumption), physical activity, smoking and body weight are significantly related to blood lipid profiles. There was also a significant association between many of the above-mentioned risk factors and the socioeconomic factors, particularly, income and education. However, the pattern and the strength of these associations were not similar for UAE nationals and expatriates. The study observed relatively lower levels of the above-mentioned risk factors among UAE nationals with low socioeconomic status as compared to the expatriate group. Differences between the two groups with regard to the relationship between socioeconomic factors and the incidence hypertension is interesting and deserves further exploration. In conclusion, it would seem that the differences in SES and the prevalence ofhypertension morbidity are mediated at least in part, by some hypertension-related risk factors observed in this study. Despite the limitations and difficulties in measuring SES (particularly income), the evidence observed in this study that SES is a major determinant of hypertension especially among expatriates living in the UAE is of significant clinical importance.

Xerostomia (dryness of the mouth) is a prevalent condition amongst elderly and diabetic populations which leads to marked alterations in oral health. The parotid glands play major roles in maintaining salivary secretions to assist in the lubrication and protection of the oral cavity and in digestion. This study investigated the effects of ageing and streptozotocin (STZ)-induced diabetes on the structure and function of the rat parotid gland. Rats (2-6, 12, 16-18 and 22-24 months old) were obtained from a recommended Home Office supplier and diabetic rat models were achieved by employing STZ. The results showed that aged glands were disorganised and infiltrated with connective tissues, lipid droplets and mast cells compared to younger control glands. A significant (P < 0.05) reduction in the mean acinar cell number was also observed in aged glands. Parotid glands taken from STZ-induced diabetic rats showed extensive infiltration of lipid droplets when compared to glands of agematched control rats. Acetylcholine (ACh), noradrenaline (NA) or isoprenaline (ISOP) elicited marked increases in amylase release from parotid acini of 2-6 month old (control) rats. However, this amylase release was significantly (Pc0.05) reduced in parotid acini of 12, 16-18 and 22-24 month old rats. In parotid segments of STZinduced diabetic rats, both ACh and NA (1xl0 5 M for both) evoked a significant (P < 0.05) reduction in amylase secretion when compared to responses obtained from age-matched control rats. Similarly, in parotid acini from STZ-induced diabetic rats, both ACh and NA induced the dose-dependent release of aniylase, but this response was significantly (Pc0.05) reduced compared to the results from age-matched control rats. In Fura-2-loaded parotid acinar cells, significant (Pc0.001) reductions in the peak and plateau phases of ACh-evoked Ca 2 signals (17340/17380) from parotid acinar cells isolated from animals aged 16-18 months were observed, compared to parotid acinar cells of 2-6 month old rats. In parotid acinar cells of STZ-induced diabetic rats a significant (PcO.00l) reduction in only the plateau phases of the Ca 2 signals was observed, in 2.5 mM [Ca2 ]0. However, in 0 mM [Ca2 ]3 the plateau phase remained inhibited, but basal Ca2 signals were also reduced in parotid acinar cells of STZinduced diabetic rats, but not in parotid acinar cells of age-matched control rats. An elevation in the total Ca 2 concentration in whole gland segments from STZ-induced diabetic rats was also observed compared to age-matched control rats. Treatment of glands from 2-6 and 12 month old rats with .t-butyl hydroperoxide (tH202) resulted in marked time-dependent (2 and 4 Lu) increases in cytochrome c fluorescence, compared to untreated glands. In contrast, treatment of glands from 22-24 month old rats for the same time periods showed no apparent increases in cytochrome c compared to the other two age groups. Incubation of acini with either 0.5, 1 or 2 mM H202 resulted in significant (Pc0.05) increases in amylase release compared to basal levels in the absence of H202. In addition, stimulation of acini suspensions with either ACh, NA or ISOP (1x10 7 M-lxlO4 M for all) resulted in the dose-dependent release of amylase above basal level. However, pretreatment of acini with 1 mM H202 followed by the addition of either ACh, NA or ISOP resulted in significant (Pc0.05) decreases in amylase release compared to responses with secretagogues alone. Analysis of acyl lipids showed that the TAGIPL ratio was significantly (PC0.01) higher in glands from aged animals compared to younger animals. Glands from STZinduced diabetic animals showed significant (P < 0.05) alterations in total acyl lipid profiles, 16:1/16:0 and 18:1/18:0 fatty acid ratios, relative proportions ofPL and TAG aèyl lipids and [ 14C] labelled TAG/PL ratios. The results of this study showed that both ageing and STZ-induced diabetes was associated with marked morphological and physiological changes in the rat parotid gland.

Understanding the biophysical processes underlying biological and biotechnological processes is a prerequisite for therapeutic treatments and technological innovation. With the exponential growth of computational processing speed, experimental findings in these fields have been complemented by dynamic simulations of developmental signaling and genetic interactions. Models provide means to evaluate "emergent" properties of systems sometimes inaccessible by reductionist approaches, making them test beds for biological inference and technological refinement.

The complexity and interconnectedness of biological processes pose special challenges to modelers; biological models typically possess a large number of unknown parameters relative to their counterparts in other physical sciences. Estimating these parameter values requires iterative testing of parameter values to find values that produce low error between model and data. This is a task whose length grows exponentially with the number of unknown parameters. Many biological systems require spatial representation (i.e., they are not well-mixed systems and change over space and time). Adding spatial dimensions complicates parameter estimation by increasing computational time for each model evaluation. Defining error for model-data comparison is also complicated on spatial domains. Different metrics compare different features of data and simulation, and the desired features are dependent on the underlying research question.

This dissertation documents the modeling, parameter estimation, and simulation of two spatiotemporal modeling studies. Each study addresses an unanswered research question in the respective experimental system. The former is a 3D model of a nanoscale amperometric glucose biosensor; the model was used to optimize the sensor's design for improved sensitivity to glucose. The latter is a 3D model of the developmental gap gene system that helps establish the bodyplan of Drosophila melanogaster; I wished to determine if the embryo's geometry alone was capable of accounting for observed spatial distributions of gap gene products and to infer feasible genetic regulatory networks (GRNs) via parameter estimation of the GRN interaction terms. Simulation of the biosensor successfully predicted an optimal electrode density on the biosensor surface, allowing us to fabricate improved biosensors. Simulation of the gap gene system on 1D and 3D embryonic demonstrated that geometric effects were insufficient to produce observed distributions when simulated with previously reported GRNs. Noting the effects of the error definition on the outcome of parameter estimation, I conclude with a characterization of assorted error definitions (objective functions), describe data characteristics to which they are sensitive, and end with a suggested procedure for objective function selection. Choice of objective function is important in parameter estimation of spatiotemporal system models in varied biological and biotechnological disciplines.

Thesis (Ph. D.)--Harvard University--Massachusetts Institute of Technology Division of Health Sciences and Technology, Program in Medical Engineering and Medical Physics, 1989.
Includes bibliographical references (leaves 372-393).
by Mehmet Toner.
Ph.D.