There is no single methodology toward freshwater conservation planning, and few analytical tools exist for summarizing ecological risks at a landscape scale. I constructed a relative risk model, the Ecological Risk Index (ERI), to combine the frequency and severity of human-induced stressors with mappable land and water use data to evaluate impacts to five major biotic drivers: energy sources, physical habitat, flow regime, water quality, and biotic interactions. It assigns 3 final risk rankings based on a user-specified spatial grain. In a case study of the 5 major drainages within the upper Tennessee River basin (UTRB), U.S.A, differences in risk patterns among drainages reflected dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among watersheds. Also, the relative importance of threats is sensitive to the spatial grain of the analysis. An evaluation of the ERI procedures showed that the protocol is sensitive to how extent and severity of risk are defined, and threat frequency-class criteria strongly influenced final risk rankings. Multivariate analysis tested for model robustness and assessed the influence of expert judgment by comparing my original approach to a quantile-based approach. Results suggest that experts were less likely to assign catchments to high-risk categories than was the quantile approach, and that 3 final risk rankings were appropriate. I evaluated the influence of land use on freshwater ecosystems by studying the relationship between land cover changes and the persistence of freshwater mussels. First, historical species data were collected and the Upper Tennessee River Mussel Database (UTRMD) was constructed. The UTRMD contains >47,400 species records from 1963-2008 distributed across nearly 2,100 sampling sites. My study suggests that 30 years of land cover change does not explain observed freshwater mussel declines. Quantitative surveys are recommended basin-wide to provide more accurate information about mussel distribution and abundance. Lastly, results suggest that streams with repeated mussel surveys have increasing populations, including active recruitment in several beds. Additional quantitative surveys since 2004 have probably provided more accurate species and population counts, although actual population sizes are still uncertain. / Ph. D.

The aim of this diploma thesis is to compare natural and human-influenced malacocenoses in the vicinity of the villages Krasíkov and Domaslav in the district of Tachov, Czech Republic. Inventory research was conducted between 2012 and 2013. A total of 36 gastropod species were found, and a total of 1088 snail shells were collected. On some of the surveyed sites (the farm Krasíkov, Domaslav, the pond near Ovčí vrch) the influence of anthropic stress is evident. Four species found during this study are also listed in the Red List of Threatened Species of the Czech Republic (Aegopinella nitidula, Balea perversa, Ena montana, Vertigo pusilla). Based on the results of the research, two variants of the didactic use of a such malacological research were created in the teaching of natural science and biology. Keywords: Mollusca, Gastropoda, malacocenosis, species diversity, ecology of mollusk assemblages, Krasíkov.

Le processus de biominéralisation confère aux organismes qui le développent une valeur adaptative. La coquille carbonatée des mollusques intègre les fonctions de protection biomécanique à différentes échelles. La coquille résulte de l'association de composés inorganiques et d'une matrice organique protéique, médiatrice du contrôle biologique de la minéralisation. L'analyse du protéome de la coquille chez 4 espèces de bivalves met en évidence deux patrons fonctionnels et leur degré de conservation phylogénétique : l'un lié au contrôle de la minéralisation stricto sensu ; l'autre à la protection immune. L'étude de populations vivant à l'état naturel en mer Baltique, dont les eaux présentent localement de fortes variations ioniques montre que le protéome intègre également l'impact de conditions environnementales limitantes. L'anthropocène impose un rythme adaptatif pressant aux organismes et la modification acido-basique des eaux océaniques est susceptible d'impacter sensiblement les organismes calcifiants. La signature de mécanismes adaptatifs du contrôle biologique de la biominéralisation se traduit dans le protéome de la coquille. Les implications sont particulièrement signifiantes dans un contexte d'intérêt de développement aquacole grandissant. / In this study, the SMPs from four commercially important and divergent bivalve species crassostrea gigas (pacific oyster), Mya truncata (soft shell clam), Mytilus edulis (blue mussel) and Pecten maximus (king scallop) were extracted and analysed using standardized extraction protocol and proteomic pipeline. This enables us to identify critical elements of basic biomineralization tool kit for calcification process irrespective of their shell morphology, mineralogy and microstructure. In addition, it enables the identification of SMPs that are specific to calcite and aragonite mineralogies. The signifiant numbers of SMPs found species-specific were hypothesized as adaptation to their modus vivendi. In fact, the latter proteins possess immunity-related functions and fit into specific pathway, phenoloxidase, suggesting their role in defense against pathogen. The comparative study of shell proteome of mussels living in full marine condition, North Sea and the Iow saline Baltic Sea showed the modulation of the SMPs that constitute the basic biomineralization tool kit. Higher modulation of chitin related proteins and non-modulated protein such as carbonic anhydrase, EGF and fibronectin domain containing proteins points out the impaired scaffold and mineral nucleation process in Baltic mussel. The modulation of immunity related proteins denote the influence of biotic components. These investigations show the functional diversity of SMPs and their roles beyond shell formation in the bivalvesand put forth the idea that shell is dynamic, endowed with both biochemical and mechanical protection.

Cento e vinte caracóis da espécie Achatina fulica, divididos em quatro grupos segundo situação, primeiro grupo originário de criação em cativeiro (LAB) no Heliciário Experimental Professora Doutora Lor Cury - FMVZ/USP, os três grupos restantes de animais asselvajados provenientes da área urbana de Pirassununga: quintal com horta(DPE), terreno baldio com pomar(MBA) e terreno baldio murado contendo entulho(CJA). Os animais foram abatidos por resfriamento e submetidos a 2 tipos de avaliação, externa e interna. A primeira tratou da pesagem corporal e mensuração do comprimento e largura da concha. Na avaliação interna fracionou-se da carcaça, em concha, carne, glândula prostática/útero, glândula de albumina/ovotestis, massa de ovos e número de ovos. Além do peso absoluto das partes, foram considerados, o percentual de peso das frações em relação ao peso corporal dos animais. O delineamento experimental foi inteiramente casualisado, cada grupo de animais oriundo de cada local foi considerado um tratamento, que passou a denominar-se situação, cada animal foi considerado uma unidade amostral. Realizou-se a análise da variância e teste de Tukey para comparação de médias, verificação de possíveis correlações entre as variáveis. O resultados da avaliação externa se mostraram significativos, destacando-se as médias para a situação LAB (52,63 g de peso médio, 76,28mm de comprimento de concha e 43,96mm de largura de concha) sendo o limite inferior o tratamento CJA (31,48g de peso médio, 68,71mm de comprimento de concha e 37,17mm de largura de concha). Os resultados quanto ao peso médio de concha foram iguais entre os tratamentos LAB(12,88g) e CJA(11,64g), no que diferiram de DPE(5,87g) e MAB(0,57g). Quanto ao percentual houveram diferenças, apresentando valor superior na proporção concha/carcaça para o tratamento CJA, logo seguido dos demais tratamentos. No peso médio de carne, o tratamento LAB(10,04 g) foi superior aos demais DPE(6,26g) MAB(5,92g) e CJA(6,49g). Entretanto quanto as médias da proporção de carne na carcaça não houveram diferença significativas. O peso médio de glândula prostática foi superior em LAB(1,29 g) e teve como limite inferior CJA(0,45g), quanto a glândula de albumina estes resultados foram similares, entretanto para a média da somatória entre as glândulas e massa de ovos os valores para LAB foram elevados (11,89g) se comparados ao limite inferior CJA(2,04g).As correlações na avaliação externa foram lineares e significativas. A glândula prostática apresentou correlação positiva com peso corporal, comprimento, largura, concha e glândula de albumina, que apresentou correlação somente com as variáveis ligadas ao aparelho reprodutor / 120 land snails of the species Achatina fulica were arranged into four groups according to situation in which the first group was collected from the heliciculture site (LAB) at the Heliciário Experimental Professora Doutora Lor Cury – FMVZ/USP and the other three groups, made up of wild individuals, were collected from a vegetable garden (DPE), a land lot with fruit crop (MBA) and an empty walled lot containing waste material (CJA), in a urban area in Pirassununga, São Paulo state, Brazil. The animals were slaughtered through freezing and assessed externally and internally. The external assessment included body weight and shell length and width measurements. For the internal evaluation, the carcass was fragmented into shell, meat, prostate/uterus gland, albumen/ovotestis gland, egg clutches and number of eggs. Besides total weight of fragments, the percentages of fragment weight in relation to body weight were considered. The experiment drawing used was totally at random where each group of animals from each site was considered what we named of situation, and each animal was taken as a sample unit. For mean comparisons and possible correlations among variables it was used the analysis of variance and the Test-t (Tukey). The obtained results were significant for external assessment where the higher mean values were found in the situation LAB (52,63g mean weight, 76,28mm shell length and 43,96mm shell width), and the situation CJA (31,48g mean weight, 68,71mm shell length and 37,17mm shell width) corresponding to the lower limit. The results for mean shell weight were the same between the situations LAB (12,88g) and CJA (11,64g), but different in DPE (5,87g) and MAB (0,57g). There were differences in the percentage assessment where results of a higher value for the rate shell/carcass in CJA were found, followed by the other situations results. The obtained result in LAB (10,04g) was higher than in DPE (6,26g), MAB (5,92g) and CJA (6,49g) situations for mean meat weight. However, there was no significant difference found for mean carcass meat rate. The prostate gland mean weight was higher in LAB (1,29g) and a lower limit was shown in CJA (0,45g); these results were similar for the albumen gland. However, higher values were found for mean total amount between glands and egg clutches in LAB situation (11,89g) when compared to the lower limit in CJA (2,04g). The rates for external assessment were linear and significant. The prostate gland showed a positive correlation to body weight, shell length and width, and albumen gland, which in turn showed only a correlation to the variables related to the reproductive system

Cento e vinte caracóis da espécie Achatina fulica, divididos em quatro grupos segundo situação, primeiro grupo originário de criação em cativeiro (LAB) no Heliciário Experimental Professora Doutora Lor Cury - FMVZ/USP, os três grupos restantes de animais asselvajados provenientes da área urbana de Pirassununga: quintal com horta(DPE), terreno baldio com pomar(MBA) e terreno baldio murado contendo entulho(CJA). Os animais foram abatidos por resfriamento e submetidos a 2 tipos de avaliação, externa e interna. A primeira tratou da pesagem corporal e mensuração do comprimento e largura da concha. Na avaliação interna fracionou-se da carcaça, em concha, carne, glândula prostática/útero, glândula de albumina/ovotestis, massa de ovos e número de ovos. Além do peso absoluto das partes, foram considerados, o percentual de peso das frações em relação ao peso corporal dos animais. O delineamento experimental foi inteiramente casualisado, cada grupo de animais oriundo de cada local foi considerado um tratamento, que passou a denominar-se situação, cada animal foi considerado uma unidade amostral. Realizou-se a análise da variância e teste de Tukey para comparação de médias, verificação de possíveis correlações entre as variáveis. O resultados da avaliação externa se mostraram significativos, destacando-se as médias para a situação LAB (52,63 g de peso médio, 76,28mm de comprimento de concha e 43,96mm de largura de concha) sendo o limite inferior o tratamento CJA (31,48g de peso médio, 68,71mm de comprimento de concha e 37,17mm de largura de concha). Os resultados quanto ao peso médio de concha foram iguais entre os tratamentos LAB(12,88g) e CJA(11,64g), no que diferiram de DPE(5,87g) e MAB(0,57g). Quanto ao percentual houveram diferenças, apresentando valor superior na proporção concha/carcaça para o tratamento CJA, logo seguido dos demais tratamentos. No peso médio de carne, o tratamento LAB(10,04 g) foi superior aos demais DPE(6,26g) MAB(5,92g) e CJA(6,49g). Entretanto quanto as médias da proporção de carne na carcaça não houveram diferença significativas. O peso médio de glândula prostática foi superior em LAB(1,29 g) e teve como limite inferior CJA(0,45g), quanto a glândula de albumina estes resultados foram similares, entretanto para a média da somatória entre as glândulas e massa de ovos os valores para LAB foram elevados (11,89g) se comparados ao limite inferior CJA(2,04g).As correlações na avaliação externa foram lineares e significativas. A glândula prostática apresentou correlação positiva com peso corporal, comprimento, largura, concha e glândula de albumina, que apresentou correlação somente com as variáveis ligadas ao aparelho reprodutor / 120 land snails of the species Achatina fulica were arranged into four groups according to situation in which the first group was collected from the heliciculture site (LAB) at the Heliciário Experimental Professora Doutora Lor Cury – FMVZ/USP and the other three groups, made up of wild individuals, were collected from a vegetable garden (DPE), a land lot with fruit crop (MBA) and an empty walled lot containing waste material (CJA), in a urban area in Pirassununga, São Paulo state, Brazil. The animals were slaughtered through freezing and assessed externally and internally. The external assessment included body weight and shell length and width measurements. For the internal evaluation, the carcass was fragmented into shell, meat, prostate/uterus gland, albumen/ovotestis gland, egg clutches and number of eggs. Besides total weight of fragments, the percentages of fragment weight in relation to body weight were considered. The experiment drawing used was totally at random where each group of animals from each site was considered what we named of situation, and each animal was taken as a sample unit. For mean comparisons and possible correlations among variables it was used the analysis of variance and the Test-t (Tukey). The obtained results were significant for external assessment where the higher mean values were found in the situation LAB (52,63g mean weight, 76,28mm shell length and 43,96mm shell width), and the situation CJA (31,48g mean weight, 68,71mm shell length and 37,17mm shell width) corresponding to the lower limit. The results for mean shell weight were the same between the situations LAB (12,88g) and CJA (11,64g), but different in DPE (5,87g) and MAB (0,57g). There were differences in the percentage assessment where results of a higher value for the rate shell/carcass in CJA were found, followed by the other situations results. The obtained result in LAB (10,04g) was higher than in DPE (6,26g), MAB (5,92g) and CJA (6,49g) situations for mean meat weight. However, there was no significant difference found for mean carcass meat rate. The prostate gland mean weight was higher in LAB (1,29g) and a lower limit was shown in CJA (0,45g); these results were similar for the albumen gland. However, higher values were found for mean total amount between glands and egg clutches in LAB situation (11,89g) when compared to the lower limit in CJA (2,04g). The rates for external assessment were linear and significant. The prostate gland showed a positive correlation to body weight, shell length and width, and albumen gland, which in turn showed only a correlation to the variables related to the reproductive system

L’huître du pacifique Crassostrea gigas est l'espèce marine la plus cultivée avec une production supérieure à 4 millions de tonnes pour l'année 2010. En France, C. gigas est cultivée depuis la fin des années 1970. Cependant, cette espèce souffre d’un syndrome de mortalité estivale depuis les années 1980, avec une amplification depuis 2008 qui touche jusqu'à 100 % des naissains. Ce syndrome de mortalité est un phénomène multifactoriel, basé sur l’interaction de nombreux facteurs: stress environnementaux, caractéristiques physiologiques et génétiques de l’huître, présence et virulence de pathogènes. L’huître du pacifique C. gigas est une espèce estuarienne qui est soumise aux pressions anthropiques comme la pollution du milieu côtier. Ces événements représentent des sources potentielles de stress en zones ostréicoles. Cependant, les connaissances sur les effets des polluants comme les pesticides sur C. gigas restent fragmentaires. Les périodes d’épandage d’herbicides coïncident parfois avec la période de reproduction des huîtres, raison pour laquelle nous considérons que ces produits chimiques pourraient affecter la génération suivante d'huîtres. Parmi les pesticides, le diuron est le plus fréquemment détecté sur les côtes françaises, avec une concentration maximale rapportée de 0,78 µgL-1. L'exposition directe aux herbicides affecte le transcriptome des huîtres qui est le premier niveau de réponse face à l'exposition du polluant. Il a été démontré que l'exposition parentale au diuron a des effets génotoxiques chez C. gigas au stade de naissain. Une variabilité phénotypique de trait d’ histoire de vie a été observée aussi pour ces naissains. Un autre effet possible des pesticides serait la modification de marques épigénétiques. Il est connu que les facteurs environnementaux telle que la pollution par des composés chimiques peuvent modifier l'épigénome et par conséquent le phénotype des individus et de leurs descendance en agissant au niveau trans-générationnel. Ces dernières observations nous permettent d’émettre l’hypothèse de l’implication de mécanismes épigénétiques suite à l’interaction avec des produits phytosanitaires. Ces mécanismes modifieraient le phénotype des huîtres au stade de naissains par l'exposition parental. Pour tester cette hypothèse nous avons étudié la méthylation globale de l'ADN (méthylome), qui est un de principal marques épigénétiques, et le transcriptome des naissains issus de géniteurs exposé au Diuron. Nous avons identifié des modifications du méthylome et du transcriptome qui ont un lien avec le phénotype de trait d'histoire de vie de ces naissains. Ces résultats démontreraient qu’une exposition indirecte ou parentale du diuron modifie la méthylation et l'expression de fonctions de gènes spécifiques, expliquant en partie la variabilité phénotypique observée. / The Pacific Oyster Crassostrea gigas is the most cultivated marine species in the world with a production superior to 4 millions of tons in 2010. In France, C. gigas is cultivated since the end of 1970s. However, this specie suffers from a syndrome of summer mortalities since the 1980s, with an amplification since 2008 affecting up to 100% of spats. This syndrome of mortality is a multifactorial phenomenon, based on the interaction of many factors: Environmental factors, genetic and physiologic features of the oysters, and the presence and virulence of pathogens. The Pacific Oyster C. gigas is an estuarine specie which is subjected to anthropogenic pressures such as pollution of the coastal environment. These events represent a potencial source of stress in oyster farm areas. However, the knowledge about the effects of pollutants such as pesticides on C. gigas remain fragmented. The herbicide application periods may coincide with the oyster breeding period, reason for which we consider that these chemicals could affect the next generation of oysters. Among pesticides, diuron is the most frequently detected on the French coast, with a maximum reported concentration of 0.78 µgL-1.The direct exposure to herbicides affects the transcriptome of oysters which is the first level of response to the exposure of pollutants. It was shown that parental exposure to diuron has genotoxic effects on C. gigas at the spat stage. A phenotypic variability of life history traits has also been observed for these spats. Another possible effect of pesticides would be the modification of epigenetic marks. It is known that environmental factors such as pollution by chemical compounds can alter the epigenome and consequently the phenotype of individuals and of their offspring acting at a transgenerational level. These last observations allow us to hypothesize the involvement of epigenetic mechanisms in response to interactions with herbicide products. These mechanisms could modify the phenotype of oysters spat state by parental exposure. To test this hypothesis we studied the genome-wide DNA methylation (methylome), which is a main epigenetic mark, and the transcriptome of the spat from diuron-exposed genitors. We identified methylome and transcriptome changes that are related to the phenotype of life history trait of these spats. These results show that an indirect or parental exposure to the diuron is able to modify the methylation and the expression of specific gene functions, partially explaining the phenotypic variability observed.

Shell organic matrix proteins in fossils are valuable geochemical archives for studying ancient environments and food webs. Compound-specific studies of stable carbon isotope ratios offer particularly good resolution of trophic level of consumers and the identities of primary producers and can be used to detect diagenetic alteration of isotopic ratios. To interpret compound specific isotope data, however, controlled diet studies in the laboratory are needed to reveal trophic enrichment patterns of 13C in tissues and shell organic matter. This study examines the relationship between d 13C of 11 amino acids in diet, soft tissues, and shell organic matter in laboratory-cultured Strombus alatus, an herbivorous marine gastropod. The d 13C values of amino acids in this animal's foot and mantle tissues are consistently enriched in 13C relative to the diet. Phenylalanine (+1.8 ppm) and alanine (+3.8 ppm) showed the least fractionation between diet and tissues, while aspartic acid (+10.7 ppm) and glutamic acid (+14.6 ppm) showed the greatest enrichment. On average, nonessential amino acids exhibited greater enrichment than did essential amino acids (+7.1 ppm vs. + 4.1 ppm). Shell organic matter amino acids showed a very similar pattern, with aspartic and glutamic acids again showing the greatest enrichment (+7.2 ppm and +11.1 ppm respectively). Nonessential amino acids in shell (+4.9 ppm) were also more enriched than the essential amino acids (+3.5 ppm). Overall, the carbon isotopic compositions of amino acids in shell organic matrix appear to parallel those in animal tissue, validating the utility of employing this material as a surrogate for animal tissue in fossil samples. Interpreting trophic position information in consumers is difficult, however, as the variation in the magnitude of trophic enrichments for glutamic and aspartic acids between species, tissue types and diet is still poorly understood. As phenylalanine has the most consistent diet-consumer enrichments, the most suitable application for d 13C isotope analysis at this time is the reconstruction of base food sources.

Florida's Plio-Pleistocene strata record episodes of sea-level highstands. The age of the strata is often ambiguous as there are no consistently reliable dating techniques that can be unequivocally applied to many of the units. The lack of preservation of continuous Plio-Pleistocene sedimentary sequences is a consequence of Pleistocene mean sea-levels not flooding peninsular Florida, the low volume of sedimentary supply, and the lack of new accommodation space. This study investigates a 6 m cyclothem-type set of six shallow-marine shell beds separated by five subaerially exposed packstone beds. These strata are part of the biostratigraphically-defined early Pleistocene (1.1 -- 1.6 Ma) Bermont formation and were likely deposited during a 160 kyr interval between 1.3 and 1.1 Ma. The shell beds are mollusk-rich and contain moderately well-sorted fine sands. The packstones contain sparry calcite cements and show evidence of subaerial weathering, such as an irregular upper solution surface, root molds, and sparry freshwater calcite cements. The upper surfaces of the packstones are unconformities that separate five episodes of highstand deposition. A grain-size analysis shows an upward-coarsening trend between depositional episodes, which most likely indicates a progressively decreasing water depth. The bivalve assemblages suggest a mean paleodepth during the deposition of the shell beds of approximately 7.5 m; alternatively, in situ Anodontia alba, which colonized these units after deposition, point to a depth of 1 m. A subsidence rate of 6 m/Ma is inferred from the thickness of deposits near the locality. Based on a comparison of the height of the strata with ex isting eustatic curves, the early Pleistocene age of the formation, and the 6 m/Ma subsidence rate, the most parsimonious duration for the interval between the cyclothems is 41 kyr, dominantly forced by obliquity orbital variability. Combining the data indicates that the early Pleistocene sea level was between 11.2 and 14.4 m above sea level (asl); previous estimates of early Pleistocene highstands have shown an elevation approximately 15 m asl. If the 1 m depth of Anodontia alba is used, the depth was likely 6.3 m asl.

This Ph.D. dissertation integrates stable isotope and trace element geochemistry in modern and fossil gastropod shells to study low-latitude marine paleoenvironments. First, stable isotopes (delta18O and delta13C) and Sr/Ca ratios are used to examine low-latitude temperature and salinity variations recorded in Plio-Pleistocene (3.5-1.6 Ma) fossils from western Florida during periods of high-latitude warming and "global" cooling. The middle Pliocene Pinecrest Beds (Units 7 and 4) and the overlaying Plio-Pleistocene Caloosahatchee Formation generate significantly different delta18O-derived paleotemperatures but identical Sr/Ca ratios. High delta18O values, together with low delta13C values and brackish fauna, indicate that Unit 4 was deposited in a lagoonal environment similar to modern Florida Bay. In contrast, relatively low delta18O and high delta13C values in Unit 7 and Caloosahatchee Formation represent deposition in an open-marine environment. The observed Unit 7 and Caloosahatchee paleotemperatures are inconsistent with middle Pliocene warming event, but consistent with the Plio-Pleistocene cooling trend. To quantify modern upwelling and freshening signals and contrast these signals between the tropical eastern Pacific (TEP) and southwestern Caribbean (SWC), methodologies are developed for reconstructing seasonal upwelling and freshening patterns from modern tropical gastropod shells from Panama using: 1) paired oxygen and carbon isotopic profiles and delta18O-delta13C (delta-delta) correlations, and 2) deviation from baseline delta18O values that represent conditions free of seasonal upwelling or freshening influences. Shell delta18O values normalized to the baseline faithfully record modern conditions of little or no upwelling in SWC and Gulf of Chiriqui, and strong upwelling in the Gulf of Panama, as well as strong freshwater input in most areas. The baseline and delta-delta methods are applied to identify and quantify changes in upwelling and freshening in the Neogene TEP and SWC seawaters associated with the final closure of Central American Isthmus. The records reveal significant upwelling in late Miocene SWC and mid Pliocene TEP waters, strong freshening in SWC waters from 5.7-2.2 Ma, and minimal seasonal upwelling and/or freshening variations in Plio-Pleistocene SWC waters. The reconstructed paleotemperatures agree with the global cooling trend through the late Miocene, but lack evidence for middle Pliocene warming or late Neogene global cooling.

Biomineralization is a process encompassing all mineral containing tissues produced within an organism. The most dynamic example of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this remarkable architecture. Subsequently, for the past decade considerable research have been undertaken to identify and characterize the protein components involved in biomineralization. Despite these efforts the general understanding of the process remains ambiguous. This study employs a novel molecular approach to further the elucidation of the shell biomineralization. A microarray platform has been custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from the mantle, an organ involved in shell formation. This microarray has been used as the primary tool for three separate investigations in an effort to associate transcriptional gene expression from P. maxima to the process of shell biomineralization. The first investigation analyzes the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and each analyzed for gene expression with PmaxArray 1.0. Over 2000 ESTs were differentially expressed among the tissue sections, identifying five major expression regions. Three of these regions have been proposed to have shell formation functions belonging to nacre, prismatic calcite and periostracum. The spatial gene expression map was confirmed by in situ hybridization, localizing a subset of ESTs from each expression region to the same mantle area. Comparative sequence analysis of ESTs expressed in the proposed shell formation regions with the BLAST tool, revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell formation genes. The second investigation correlates temporal EST expression during P. maxima larval ontogeny with transitions in shell mineralization during the same period. A timeline documenting the morphologicat microstructural and mineralogical shell characteristics of P. maxima throughout larval ontogeny has been established. Three different shell types were noted based on the physical characters and termed, prodissoconch I, prodissoconch 11 and dissoconch. PmaxArray 1.0 analyzed ESTs expression of animals throughout the larval development of P. maxima, noting up-regulation of 359 ESTs in association with the shell transitions from prodissoconch 1 to prodissoconch 11 to dissoconch. Comparative sequence analysis of these ESTs indicates a number of the transcripts are novel as well as showing significant sequence similarities between ESTs and known shell matrix associated genes and proteins. These ESTs are discussed in relation to the shell characters associated with their temporal expression. The third investigation uses PmaxArray 1.0 to analyze gene expression in the mantle tissue of P. maxima specimens exposed to sub-lethal concentrations of a shell-deforming toxin, tributyltin (TBT). The shell specific effects of TBT are used in this investigation to interpret differential expression of ESTs with respect to shell formation functions. A lethal and sublethal TBT concentration range was established for P. maxima, noting a concentration of 50 ng L- 1 TBT as sub-lethal over a 21 day period. Mantle tissue from P. maxima animals treated with 50 ng L- 1 TBT was assessed for differential EST expression with untreated control animals. A total of 102 ESTs were identified as differentially expressed in association with TBT exposure, comparative sequence identities included an up-regulation of immunity and detoxification related genes and down-regulation of several shell matrix genes. A number of transcripts encoding novel peptides were additionally identified. The potential actions of these genes are discussed with reference to TBT toxicity and shell biomineralization. This thesis has used a microarray platform to analyze gene expression in spatial, temporal and toxicity investigations, revealing the involvement of numerous gene transcripts in specific shell formation functions. Investigation of thousands of transcripts simultaneously has provided a holistic interpretation of the organic components regulating shell biomineralization.