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1
Raharjo, Joko Purnomo. "The performance analysis of real estate construction firms (RECF) in Indonesia." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/228029/1/Joko%20Purnomo_Raharjo_Thesis.pdf.
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This thesis examines the efficiency, productivity, and survival of real estate construction firms in Indonesia. By applying a meta-frontier approach, the results show that efficiency and productivity of the firms are relatively low. The gap between the industry and the small, medium, and large is high. This suggest that the overall industry could obtain remarkable efficiency and productivity improvement if firms could access technologies used by more efficient firms. Designing policy and managerial interventions for each group would have greater impacts. The survival analysis demonstrates that profit margin, income diversification, experience and structure are strongly related to firm survival.
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Taylor, L. "The recB and recC gene products of Escherichia coli." Thesis, University of Newcastle Upon Tyne, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355080.
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Wilson, R. E. "The recB-recC region of the Escherichia coli chromosome." Thesis, University of Newcastle Upon Tyne, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.375598.
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Vickridge, Elise. "Management of E. coli sister chromatid cohesion in response to genotoxic stress." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS172/document.
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La réplication fidèle de l’ADN au cours du cycle cellulaire est essentielle au maintien de l’intégrité du génome à travers les générations. Toutefois, de nombreux éléments peuvent perturber et compromettre la réplication et donc cette intégrité. La mitomycine C (MMC) est une molécule génotoxique utilisée en chimiothérapie. Elle forme des liaisons covalentes entre les deux brins d’ADN, ce qui est un obstacle à la bonne réplication de l’ADN. La rencontre de la fourche de réplication avec une liaison covalente entre les deux brins d’ADN va aboutir à une cassure double brin. Escherichia coli (E.coli) est un modèle d’étude très étendu car facile d’utilisation, permettant d’aborder des notions complexes. E coli possède divers mécanismes pour réparer ces lésions dont le régulon SOS. Le régulon SOS est un ensemble de gènes sous contrôle d’un promoteur réprimé par la protéine LexA. En réponse à des dommages à l’ADN, LexA est dégradé et les gènes du régulon sont activés.En utilisant une technique de biologie moléculaire qui permet de quantifier l’interaction entre deux chromatides sœurs restées cohésives derrière la fourche de réplication (étape appelée cohésion des chromatides sœurs), nous avons montré qu’en réponse à des cassures double brin générées par la MMC, la cohésion entre les chromatides sœurs nouvellement répliquées est maintenue. Ce phénomène est dépendant de RecN, une protéine induite de façon précoce dans le régulon SOS. RecN est une protéine de type SMC (structural maintenance of chromosomes), un groupe de protéines impliqué dans la dynamique et la structure du chromosome. En parallèle, des techniques de microscopie confocale et de marquage du chromosome par des protéines fluorescentes ont permis de montrer que la protéine RecN est impliquée dans une condensation globale du nucléoide suite à un traitement par la MMC. Cette condensation du nucléoide s’accompagne d’un rapprochement des chromatides sœurs ségrégées. Ces deux phénomènes, médiés par RecN pourraient permettre une stabilisation globale des nucléoides et favoriser l’appariement des chromatides sœurs pour permettre la recombinaison homologue.De façon intéressante, l’inhibition de Topoisomérases de type II (Topoisomerase IV et Gyrase) permettent de restaurer le phénotype d’un mutant recN en viabilité et en cohésion des chromatides sœurs. Les Topoisomérases sont des protéines qui prennent en charge les liens topologiques générés par la réplication et la transcription). Les liens topologiques non éliminés par les Topoisomerases permettraient de garder les chromatides sœurs cohésives et favoriser la réparation, même en l’absence de RecN.De plus, une expérience de RNA seq (séquençage de tout le transcriptome de la bactérie) a révélé que dans un mutant recN, le régulon SOS est moins induit que dans les cellules sauvages. Ceci va de pair avec une déstructuration des foci de réparation RecA. Il est possible que le rapprochement des chromatides sœurs médié par RecN permettrait de stabiliser le filament RecA et donc l’induction du SOS.L’ensemble de ces résultats suggère que RecN, une protéine de type SMC, permet de maintenir la cohésion entre les chromatides sœurs nouvellement répliquées, favorisant la réparation de cassures double brins par recombinaison homologueMaintaining genome integrity through replication is an essential process for the cell cycle. However, many factors can compromise this replication and thus the genome integrity. Mitomycin C is a genotoxic agent that creates a covalent link between the two DNA strands. When the replication fork encounters the DNA crosslink, it breaks and creates a DNA double strand break (DSB). Escherichia coli (E.coli) is a widely used model for studying complex DNA mechanisms. When facing a DNA DSB, E. coli activates the SOS response pathway. The SOS response comprises over 50 genes that are under the control of a LexA-repressed promoter. Upon a DSB induction, RecA, a central protein of the SOS response will trigger the degradation of LexA and all the SOS genes will be expressed.We have developed a novel molecular biology tool that reveals contacts between sister chromatids that are cohesive. It has been shown in the lab (Lesterlin et al. 2012) that during a regular cell cycle, the two newly replicated sister chromatids stay in close contact for 10 to 20 min before segregating to separate cell halves thanks to the action of Topoisomerase IV. This step is called sister chromatid cohesion. We have used this molecular biology tool to study sister chromatid cohesion upon a genotoxic stress induced by mitomycin C (MMC). We have shown that sister chromatid cohesion is maintained and prolonged when the cell is facing a DSB. Moreover, this sister chromatid cohesion is dependent on RecN, an SOS induced structural maintenance of chromosome-like (SMC-like) protein. In the absence of RecN, the proximity between both sister chromatids is lost and this has a deleterious effect on cell viability. By tagging the chromosome with fluorescent proteins, we have revealed that RecN can also mediated a progressive regression of two previously segregated sister chromatids and this is coordinated with a whole nucleoid compaction. Further studies showed that this genome compaction is orderly and is not the result of a random compaction in response to DNA damage.Interestingly, inhibiting TopoIV in a recN mutant fully restores viability and sister chromatid cohesion suggesting that RecN’s action is mainly structural. Preserving cohesion through precatenanes is sufficient to favor repair and cell viability even in the absence of RecN.An RNA-seq experiment in a WT strain and a recN mutant revealed that the whole SOS response is downregulated in a recN mutant. This suggests that RecN may have an effect on the induction of the SOS response and thus RecA filament formation. This is in good agreement with the change in RecA-mcherry foci formation we observed. In the WT strain, the RecA-mcherry foci are defined as described in previous work. However, in the recN, the RecA-mcherry foci seemed to form bundle like structures. These RecA bundles were previsously described by Lesterlin et al. in the particular case of a DSB occurring on a chromatid that has already been segregated from its homolog. This could mean that in the absence of recN, the sister chromatids segregate and RecA forms bundle like structures in order to perform a search for the intact homologous sister chromatid.Altogether, these results reveal that RecN is an essential protein for sister chromatid cohesion upon a genotoxic stress. RecN favors sister chromatid cohesion by preventing their segregation. Through a whole nucleoid rearrangement, RecN mediates sister chromatid regression, favoring DNA repair and cell viability
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Dulermo, Rémi. "Etude des mécanismes de l'extrême tolérance aux radiations de la bactérie Deinococcus deserti par une approche de génomique fonctionnelle." Aix-Marseille 2, 2009. http://theses.univ-amu.fr.lama.univ-amu.fr/2009AIX22100.pdf.
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Le génome de Deinococcus deserti, une bactérie très radiotolérante, a été analysé et comparé à ceux de D. Radiodurans et D. Geothermalis. Environ 230 protéines sont spécifiquement conservées chez ces 3 espèces, dont IrrE, un régulateur essentiel pour la radiotolérance. D. Deserti possède plusieurs gènes supplémentaires liés à la réparation de l’ADN, dont imuY et dnaE2 (ADN polymérases translesionnelles). En plus, D. Deserti a 3 recA qui codent pour 2 protéines RecA différentes (RecAC et RecAP). Pour étudier ces gènes, des outils génétiques ont été mis au point. Différents résultats suggèrent qu’IrrE, nécessaire pour l’induction de plusieurs gènes après irradiation, a une activité peptidase. Les 2 RecA sont fonctionnelles pour la réparation de l’ADN. D. Deserti est mutable par UV, ce qui nécessite ImuY, DnaE2 et RecAC, mais pas RecAPThe genome of Deinococcus deserti, a highly radiation-tolerant bacterium, was analyzed and compared to those of D. Radiodurans and D. Geothermalis. About 230 proteins are specifically conserved in these 3 species, including IrrE, a regulator protein essential for radiotolerance. D. Deserti has several supplementary DNA repair genes, like imuY and dnaE2 (translesion DNA polymerases). Moreover, D. Deserti has 3 recA that code for 2 different RecA proteins (RecAC et RecAP). To study these genes, genetic tools were developed for D. Deserti. Different results suggest that IrrE, required for the induction of several genes after irradiation, has peptidase activity. The 2 RecA proteins are functional for DNA repair. D. Deserti is mutable by UV, which requires ImuY, DnaE2 and RecAC, but not RecAP
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Ames, Cory. "Reef Fish Assemblage Biogeography Along the Florida Reef Tract." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/459.
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Understanding the biogeography of reef fish assemblages is paramount to reef conservation, management, and conducting appropriate population survey designs. Reef fish assemblages are a multispecies complex of reef-associated fish and are shaped by multiple environmental and biological factors (e.g. temperature, depth, benthic habitat, and topographic relief), which determine the species constituents residing in an area. Assemblages typically change with latitude where the number of families, genera, and/or densities of species specific to warmer climates decrease poleward into colder climate regimes. The Florida Reef Tract (FRT) extends for 595 km from the Dry Tortugas in the south-west to Martin County in the north, crossing a sub-tropical to temperate climate transition. This study investigates the biogeography of reef fish assemblages throughout the FRT to determine if they correspond to previous regional delineations that were primarily based on coastal geomorphology. Multivariate density analyses show that depth, habitat, relief, and region are major factors in determining the assemblages. Four main ecoregions were evident based on depth, benthic habitat, relief and latitudinal region: Dry Tortugas (DT), Florida Keys (FK), Southeast mainland (SE), and Bahamas Fracture Zone (BF). DT split into four biogeographic assemblage regions primarily based on depth, and relief. FK split into five biogeographic assemblage regions with a sixth extending through Broward County primarily based on depth, habitat type, and relief. SE split into four biogeographic assemblage regions primarily based on depth, and region. BF split into three biogeographic assemblage regions primarily based on depth, and region. These sixteen assemblages represent the current composition of reef fish based on four factors. Numerous other factors also affect reef fish assemblages (e.g. past and present fishing pressure, mangrove nursery habitat, and coral death) that were not part of the analysis but are discussed. The final reef fish assemblage regions were associated with previous benthic habitat maps in order to view their spatial extent. Having a map of current biogeographic reef fish assemblages serves as a baseline and allows more accurate management and monitoring of future reef fish populations.
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Rech, Alexander [Verfasser]. "Werkwohnungen / Alexander Rech." Frankfurt : Peter Lang GmbH, Internationaler Verlag der Wissenschaften, 2016. http://d-nb.info/1102805289/34.
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Geange, Shane Wallace. "An evaluation of prior residency and habitat effects on the persistence of settling reef fishes : a thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Biology /." ResearchArchive@Victoria e-Thesis, 2010. http://hdl.handle.net/10063/1169.
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Scales, Helen Joanna. "Exploitation of coral reef fishes for the Live Reef Fish Trade." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615075.
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Nothdurft, Luke David. "Microstructure and early diagenesis of recent reef building scleractinian corals, Heron reef, Great Barrier Reef : implications for paleoclimate analysis." Thesis, Queensland University of Technology, 2008. https://eprints.qut.edu.au/16690/1/Luke_D._Nothdurft_Thesis.pdf.
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Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales.
The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was
documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations.
This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.
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Nothdurft, Luke David. "Microstructure and early diagenesis of recent reef building scleractinian corals, Heron reef, Great Barrier Reef : implications for paleoclimate analysis." Queensland University of Technology, 2008. http://eprints.qut.edu.au/16690/.
Full textAbstract:
Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales. The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations. This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.
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Stephenson, Christy Michelle. "Foraminiferal Assemblages on Sediment and Reef Rubble at Conch Reef, Florida USA." Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3367.
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ABSTRACT
Foraminiferal Assemblages on Sediments and Reef Rubble
at Conch Reef, Florida USA
Christy Stephenson
Benthic foraminiferal assemblages are widely used to interpret responses of the benthic communities to environmental stresses. This study compares epibiotic foraminiferal assemblages, collected from reef rubble, with those from reef sediments. The study site, Conch Reef, is the site of the Aquarius Underwater Habitat research facility and includes protected areas used only for scientific studies. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract, no projects have focused on the assemblages that occur at Conch Reef.
Sediment and reef rubbles samples were collected via SCUBA from a depth range of 13 to 26 m during October 2008. Foraminiferal assemblages were assessed and compared between the two sample types. A total of 117 foraminiferal species, representing 72 genera, 37 families, and 8 orders were identified in 13 sediment samples and 21 rubble samples.
In the rubble samples, 70 genera were identified, including 12 symbiont-bearing genera representing 20% of the total assemblage, 12 stress-tolerant genera representing 6%, planktic foraminifers representing 1%, and 46 other smaller foraminiferal genera representing 73% of the total foraminiferal assemblage. The rubble samples were quite homogenous. The mean (+SD) Fisher alpha α diversity of genera in these samples was 12.9 + 1.4.
Sediment samples included 60 of the same genera. The 12 symbiont-bearing genera represented 41% of the total assemblage, 10 stress-tolerant genera represented 3%, planktic taxa represented 2%, and 40 other smaller foraminiferal genera represented 54% of the total assemblage. Overall, the taxonomic assemblages were very similar between the sample types, with sediment assemblages clearly representing the local and regional reef foraminiferal assemblage. The mean (+SD) Fisher alpha α for sediment samples was 11.4 + 2.3, which is not significantly different from that found for the rubble samples.
A concentration ratio comparing relative abundances in sediment vs. rubble samples revealed that shells of larger, symbiont-bearing taxa were about 2.5-5.5 times more concentrated in the sediment, indicating winnowing of smaller taxa. Shells of Siphonatera, an agglutinated miliolid, and Textularia, an agglutinated textularid, were more abundant in sediments than in rubble, indicating high preservation potential. The concentration ratio provides a new taphonomic index that reflects the size and durability of foraminiferal taxa.
The mean FORAM Index (FI) for the sediment samples (5.57 + 0.83) indicates that water quality at Conch Reef is suitable for calcifying symbioses. The most abundant symbiont-bearing genera were Amphistegina, Laevipeneroplis, Asterigerina, and Archaias.
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Kleinwächter, Lutz. "Reif für die Weltpolitik?" Universität Potsdam, 2010. http://opus.kobv.de/ubp/volltexte/2010/4162/.
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Bereits vor zehn Jahren diskutierten wir über die außenpolitische Reife deutscher Eliten. Das Ergebnis war widersprüchlich, kritisch ernüchternd. Gegenwärtig, 20 Jahre nach der deutschen Einheit, ist es an der Zeit, erneut nachzufragen. Die Welt- und Europapolitik sind im Fieber. Die neokonservative Marktwirtschaft – bis vor Kurzem noch siegessicher – erodiert. Die westliche Welt steckt am Beginn des 21. Jahrhunderts in einer Systemkrise. Hektische Gipfel jagen einander, von Kopenhagen über London und Davos bis nach München. Da ist die Frage erlaubt: Wie steht es in solch turbulenten Zeiten eigentlich um die deutsche Außenpolitik?
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Fuchs, Eran 1963. "Fluorescence in reef corals." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/8966.
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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Ocean Engineering, 1999.Includes bibliographical references (p. 248-251).
Fluorescence can be a powerful tool for probing biological systems. Prior measurements from Caribbean corals identified five fluorescing pigments in reef corals. In this thesis I study coral fluorescence spectra. I wanted to learn if fluorescence could be useful for large scale mapping and monitoring of the reef as a part of an effort to stop the recently reported global decline in coral reefs condition. 3D excitation I emission spectra, average wavelength locations and shape variability studies of each of the pigments is presented. I also present an in situ corrununity study of the species Montastraea cavernosa and investigate the variability of fluorescence emission among colonies of one species at one location. Coral's fluorescence emission spectrum can result from the excitation of one or more fluorescing pigments. A mathematical algorithm was developed to separate coral fluorescence spectra into individual components. The un-mixing algorithm was combined with a prediction model whose purpose was to predict the response that will be produced by any excitation light source given knowledge of the response produced by a different light source. Energy coupling between two of the pigments was discovered. An empirical coupling efficiency factor was defined and calculated to account for this energy transfer. The energy coupling between these pigments may have important consequences in future investigation of coral's evolution. A new experimental method to separate the reflectance and fluorescence spectral components of fluorescing corals was developed for in vivo and in situ data. Two experimental methods are proposed to measure and calculate a newly defined quantity, "practical fluorescence efficiency". This efficiency factor is essential for correct prediction of coral spectra under different illumination conditions. This part of my work will benefit optical models that calculate light interaction with the bottom of the ocean in shallow waters. Lastly I present a prototype Fluorescence Imaging Laser Line Scanner system and discuss its potential use as a remote sensing system for reef mapping and monitoring. Recommendations are made to better tune the system to the fluorescence characteristics of reef corals.
by Eran Fuchs.
Ph.D.
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Wormald, Clare Louise. "Effects of density and habitat structure on growth and survival of harvested coral reef fishes /." View online ; access limited to URI, 2007. http://0-digitalcommons.uri.edu.helin.uri.edu/dissertations/AAI3277014.
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Ceh, Janja. "Coral-associated microbial communities in reef-building corals of Ningaloo Reef Western Australia." Thesis, Ceh, Janja (2011) Coral-associated microbial communities in reef-building corals of Ningaloo Reef Western Australia. PhD thesis, Murdoch University, 2011. https://researchrepository.murdoch.edu.au/id/eprint/8480/.
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Coral reefs are at risk and human-induced environmental stressors in synergism with microorganisms have been shown to be the key players for their deterioration. Little is known about the dynamics of coral-microbial associations through different life stages of the coral holobiont and virtually nothing is known about coral-microbial partners in Western Australian coral reef systems. This project intended to investigate the presence, diversity, community structure and role of coral-associated microbes in Ningaloo Reef spawning and brooding corals. Different coral life stages were assessed.
To determine ‘normal ranges’ of coral-associated microbes, three coral species (Acropora tenuis, Pocillopora damicornis and Favites abdita) were tagged and examined over a period of one year, with sampling deployed every three months. One coral species was additionally sampled on Rottnest Island, 1200km south of Ningaloo Reef, to provide comparisons between coral-associated microbes in different geographical areas. The community structure of the coral-associated microorganisms was analysed by phylogenetic analysis of 16S rRNA gene clone libraries. Principal component analysis (PCA) revealed that samples grouped according to time and not species, indicating that coral-microbial associations may be a result of environmental drivers such as oceanographic characteristics, benthic community structure and temperature. Tissue samples from Rottnest Island corals revealed similarities in bacteria to the samples at Ningaloo Reef. This study highlights that coral-associated microbial communities are highly diverse; however, the complex interactions that determine the stability of these associations are not necessarily dependant on coral host specificity.
Reproduction plays a crucial role in the survival of species, therefore, data was acquired from three adult coral colonies, Acropora tenuis (broadcast spawner), Pocillopora damicornis (brooder) and Tubastrea faulkneri (ahermatypic), before and after coral mass spawning to determine if and through which drivers coral microbial communities changed through this event. A contemporary 454 sequencing approach was implemented and results revealed distinct bacterial shifts through coral mass spawning for all corals, independently of reproductive activity. Clear changes in bacterial assemblages were also detected for brooders after planulation. This infers that coral-associated microbial communities change through a coral mass spawning event and are likely driven by environmental factors and the respective bacterial community in the seawater, as well as by actual coral reproduction. Differences in coral-microbial communities reflected different life styles between brooding and spawning corals. Most α-Proteobacteria increased in abundance after spawning as well as after planulation, suggesting that specific bacteria are involved in coral reproduction irrespective of reproductive strategies; particularly bacteria affiliated with the Roseobacter clade followed this pattern.
The assessment of seawater collected from the broadcast spawning coral A. tenuis and P. damicornis after spawning and planulation, respectively revealed that adult corals, irrespective of their reproductive strategy release bacteria with their offspring which likely increases the fitness in the following processes involved in settlement and survival. Species affiliated with the genera Roseobacter and Alteromonas appear to play important roles in coral reproduction and early life history in corals.
Isolates from P. damicornis planulae were mainly affiliated with the genera Vibrio and Alteromonas and were found to be similar to bacteria released by the mother colony during planulation.
Finally the establishment of coral-microbial partnerships in coral larval stages and the potential role of these symbiotic relationships were studied. The early onset of bacterial associations in brooding and broadcast spawning corals was visualized, exploring bacterial presence and their location in the coral organism, determining when and how bacteria enter coral tissues and their cycling of nutrients towards the coral-symbiotic algal partners. Nano-scale Second Ion Mass Spectrometry (SIMS) was applied to detect, image and map the uptake and translocation of 15N from bacteria into coral larvae on a sub-cellular level. The study also combined Fluorescent In Situ Hybridisation (FISH) to co-localize the labelled substrate with bacteria and Transmission Electron Microscopy (TEM) to allow for ultra-structural resolution images to provide high resolution images. This study for the first time demonstrated the beneficial role of specific bacteria in translocating nitrogen into the coral holobiont, which is particularly important in the nutrient-poor environments corals live in.
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Aaby, Alyssa Anne. "Testing the ArcGIS Marine Data Model : using spatial information to examine habitat utilization patterns of reef fish along the west coast of Hawaii /." Connect to this title online, 2004. http://hdl.handle.net/1957/4061.
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Fisco, Dana. "Reef Fish Spatial Distribution and Benthic Habitat Associations on the Southeast Florida Reef Tract." NSUWorks, 2016. http://nsuworks.nova.edu/occ_stuetd/408.
Full textAbstract:
The Florida Reef Tract (FRT) extends from the tropical Caribbean up the southeast coast of Florida into a temperate environment where tropical reef assemblages diminish with increasing latitude. This study used data from a three-year comprehensive fishery-independent survey to quantify reef fish spatial distribution along the Southeast FRT and define where the assemblage shifts from tropical to temperate. A total of 1,676 reef fish visual census samples were conducted to assess the populations on a stratified-random selection of sites of marine hardbottom habitats between the Miami River and St. Lucie inlet. Multivariate analyses were used to investigate differences in assemblages among sites. Depth (m), general habitat (reef or hardbottom), and slope (high or low) strata were examined to explain the dissimilarities between assemblages. A general trend of cold-tolerant temperate fish dominated the northern assemblages and more tropical species dominated further south. Seven reef fish assemblage biogeographic regions were determined. In shallow habitats the data clustered in three spatial regions: One south of Hillsboro inlet, one in Northern Palm Beach south of Lake Worth inlet, and one north of Lake Worth inlet. The assemblage in deep habitats mainly split in close proximity to the Bahamas Fracture Zone south of Lake Worth Inlet. The presence of reef habitat aided in splitting the southern assemblage regions from the northern all-hardbottom assemblage regions in both the shallow and deep habitats. Substrate relief was significantly correlated with the differences in the northernmost deep assemblages but did not appear to affect the remainder of the shallow and deep assemblages. This bioregional study creates a baseline assessment of reef fish assemblages of the Southeast FRT for future analyses.
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Hobbs, Michael David. "On the regulation of RecA nucleoprotein filament formation by the RecF, RecO, RecR, RecX and SSB proteins : a biochemical analysis /." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Chien, Ya-Li, and 簡雅莉. "Helix-unwinding and single-strand DNA binding activities of escherichia coli RecF, RecO and RecR." Thesis, 1996. http://ndltd.ncl.edu.tw/handle/63655641800884202892.
Full textAbstract:
碩士國立陽明大學
遺傳學研究所
84
recF，recO和recR基因是原先被發現參與RecF途徑之基因，目前有許多證據顯示此三個基因產物作用於DNA重組的同一步驟。現今有關RecF，RecO和RecR蛋白的在DNA重組途徑中所扮演的角色仍不清楚。 在本論文中，我們針對已純化的RecF，RecO和RecR蛋白的生化功能作進一步之探討，以期瞭解這些蛋白在DNA重組和修復上扮演的角色。主要的工作包括：(1)探討RecF，RecO和RecR與DNA結合之能力；(2)探討RecF，RecO和RecR的helix-unwinding活性。 首先，在RecF，RecO和RecR與DNA結合能力方面，我們證實單獨的RecF或RecO可以與ssDNA結合，而RecR不能。但在有RecO存在下，則RecR可與ssDNA結合。當RecF，RecO和RecR同時與ssDNA作用時，發現這三個蛋白皆可與ssDNA結合。 而在DNA unwinding活性方面，我們發現RecO有明確的活性，RecO的helix-unwinding活性需要有ATP及鎂離子，ATP之需求可以dATP取代，但無法以ATPγS或其它NTP替代，鎂離子之需求可以錳離子取代，但無法以鈣離子或鋅離子取代，RecOunwind helix的能力與RecO蛋白質之濃度成正比，當RecO之量可飽和結合至ssDNA時，其unwilnd DNA之活性最高，最後此活性會受到高濃度之鎂離子或鹽的抑制。根據我們發現RecO具有helix-unwinding活性，認為RecFOR在DNA重組作用中扮演新的角色。在本文中有將有詳細討論。 The recF, recO and recR genes were originally identified as those affecting the RecF pathways of recombination in Escherichia coli. Several lines of genetic evidence suggest that the recF, recO and recR gene products function at the same step of recombination, possibly at an early presynaptic step. The exact role of RecFOR in DNA recombination are not known. In this work, the interactions of RecF, RecO and RecR with ssDNA and the helix-unwinding activities of RecF, RecO and RecR were examined. We observed that single RecF or RecO can bind to ssDNA while single RecR cannot. In the presence of RecO, but not RecF, the RecR was found to associate with ssDNA. When the RecF, RecO and RecR were reacted with ssDNA, all three proteins were found to associate with DNA. With regards to helix-unwinding activity, we observed that RecO possesses such an activity. The helix-unwinding activity of RecO requires the presence of MgCl2 and ATP in the reaction mixture. The requirement of ATP can be substituted by dATP, but cannot be substituted by ATPγS or other NTPs. The requirement of magnesium can be substituted by manganese, but not by calcium or zinc. The unwinding activity is proportional to the concentration of RecO protein and is sensitive to high concentration of MgCl2 or NaCl. Maximal unwinding was observed when the RecO protein to DNA nucleotides was greater than 0.05. Our finding that RecO possesses helix-unwinding activity suggests a new role of ReeFOR in DNA recombination. A model for the possible involvement of RecFOR in DNA recombination is presented.
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候武勳. "Cloning of recF gene and construction of recF mutant of streptomyces lividans." Thesis, 1993. http://ndltd.ncl.edu.tw/handle/06664026112073713600.
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Webb, Brian Lynn. "Characterization of the Escherichia coli RecF and RecR proteins and their role in recombinational DNA repair." 1997. http://catalog.hathitrust.org/api/volumes/oclc/39475544.html.
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曾玉琴. "Grouping of RecF pathway recombination genes in escherichia coli." Thesis, 1993. http://ndltd.ncl.edu.tw/handle/80502672342493549135.
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Lee, Chuan-Chan, and 李權展. "Construction and characterization of recF mutants of streptomyces lividans 66 ZX7." Thesis, 1997. http://ndltd.ncl.edu.tw/handle/86231224343043581087.
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Wen, Chen-Yu, and 溫振宇. "Regulation and Biological Functions of R-loop: Roles of RecF Pathway and DNA Topoisomerases." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/23217513442238525029.
Full textAbstract:
碩士國立臺灣大學
微生物學研究所
97
The R-loop structure, an RNA-DNA hybrid with a single-stranded DNA region, has been observed during transcription elongation. However, the regulation and biological functions of R-loop still remain largely unknown. In this study, we took advantage of the bacterial genetic model system to solve these problems. We have found that several cellular factors, such as RecF, RNase H and DNA topoisomerases, are involved in the regulation of R-loop formation and thereby modulating its associated cellular functions. Forced expression of human activation-induced deaminase (hAID) in bacteria was utilized to stimulate mutagenesis and the stimulated folds were then used to represent the different levels of R-loop in various strains and conditions. Specifically, the involvement of RecF pathway is supported by the following observations: (i) The fold of AID-stimulated mutagenesis (ASM) in RecF-activated strain JC7623 (recBC sbcBC) was much higher than those measured in other related mutants; furthermore, additional expression of RNase H or TopA suppressed the ASM fold. (ii) Plasmid-mediated lethality, run-away plasmid replication and cellular filamentation phenotype were also exclusively observed in JC7623 cells. (iii) Most importantly, all these phenotypes could be suppressed by ectopic expression of functional RNase H and TopA. (iv) Over-expression of TopA and gyrase reduced and enhanced the filamentation phenotype in RecF-activated bacteria, respectively. In sum, our results suggested that formation of excess R-loops contributes to all the phenotypes observed in RecF-activated JC7623 cells. Furthermore, we have also revealed many novel functions of R-loop in recombination, DNA replication, cellular filamentation and lethality.
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Drees, Julia C. "The novel RecA regulator proteins RecC DinI, RdgC and PsiB." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Robu, Mara-Eliza. "Roles of RecA and RecG proteins in replication fork regression." 2003. http://www.library.wisc.edu/databases/connect/dissertations.html.
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"RECL 4 (=RECL 96) - 15-Aug-92." 1992. http://biblio-dev.laurentian.ca:8180/jspui/handle/10219/1130.
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"RECL 191 -." 2011. http://biblio-dev.laurentian.ca:8180/jspui/handle/10219/543.
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"RECL 263 -." 2011. http://biblio-dev.laurentian.ca:8180/jspui/handle/10219/849.
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"RECL 50A -." 2011. http://biblio-dev.laurentian.ca:8180/jspui/handle/10219/1160.
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"RECL 59 -." 2011. http://biblio-dev.laurentian.ca:8180/jspui/handle/10219/1194.
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Hempson, Tessa N. "Coral reef mesopredator trophodynamics in response to reef condition." Thesis, 2017. https://researchonline.jcu.edu.au/53079/19/53079-hempson-2017-thesis.pdf.
Full textAbstract:
Habitat degradation in coral reef ecosystems is occurring at an unprecedented rate and scale around the world. This habitat decline is driven by both intensifying local stressors and the escalating effects of global climate change. Concurrently, the ubiquitous loss of large consumers from ecosystems, known as trophic downgrading, has important ramifications for the function and resilience of both terrestrial and marine ecosystems. Mesopredators represent an important component of coral reef ecosystems, both economically, supporting large reef fisheries, and ecologically, as potentially important drivers of reef trophodynamics. While there has been substantial focus on the effects of habitat degradation on the small-bodied reef fish community, which is closely associated with the reef benthos, relatively little is known about the implications for piscivorous reef mesopredators. These large-bodied, mobile species are less directly reliant on the reef benthos, and likely to experience the strongest effects of habitat degradation mediated via the fish community on which they prey. This thesis addresses this important research gap by focusing on four key implications of habitat degradation for mesopredators and their role in coral reef trophodynamics.
Dietary adaptability is likely to be an important factor in determining the vulnerability of piscivorous mesopredators to changing prey availability associated with habitat degradation. In chapter 2, I use stable isotope analyses of carbon (δ¹³C) and nitrogen (δ¹⁵N) to investigate whether coral trout (Plectropomus maculatus), in the Keppel Island group on the southern Great Barrier Reef (GBR), can switch their diet to exploit the altered prey base on degraded reefs. Coral bleaching and sediment-laden flood plumes have driven extensive live coral loss on these reefs. The resulting shift in dominant prey species from pelagic plankton-feeding damselfishes to benthic algal-feeding species, represents a shift in the principal carbon pathways in the food web. The δ¹³C signature in coral trout shifted from a more pelagic to a more benthic signal, reflecting the prey community shift, and demonstrating that trout appear to alter their diets as reefs degrade. Nitrogen signatures also indicated that trout with a more benthic carbon signature were feeding at a lower trophic level, indicating a shorter food chain on degraded reefs. Despite this apparent adaptability, mesopredator populations at this location are in steep decline, driven primarily by reduced total available prey biomass.
Thus, despite dietary flexibility conferring a degree of trophic resilience in the short term, mesopredators are nonetheless vulnerable to the effects of habitat degradation. Due the relative longevity of many mesopredator species, sublethal effects of changing prey resources may be difficult to detect. Chapter 3 investigates whether a common mesopredator species (Cephalopholis argus) in the Seychelles inner island group shows evidence of a loss of condition due to habitat degradation. Following extensive live coral loss during the 1998 mass bleaching event, some reefs have regained high coral cover, while others have experienced a regime shift to an algae-dominated state. Stable isotope analyses demonstrated that C. argus on regime-shifted reefs fed lower down the food chain, on a narrower range of carbon sources, than those on recovering reefs, suggesting a simplification of the food web. Histology of liver tissue showed reduced hepatocyte vacuolation in fish from regime-shifted reefs, and reduced lipid stores in spawning females. Reduced energy reserves can lead to decreased growth rates, fecundity and survivorship, ultimately resulting in long-term population declines.
Long-term effects of regime-shift in coral reef ecosystems can substantially alter the trophic structure of fish communities, yet understanding of how these changes manifest through time is limited. In chapter 4, I use a 20-year dataset documenting changes in the benthic and reef fish communities on the Seychelles inner island reefs, to examine how trophic structure has changed on recovering and regime-shifted reefs following the 1998 mass bleaching event. I demonstrate how reef fish communities become increasingly dissimilar, as the benthic states diverge with time since disturbance. Trophic pyramids of relative biomass on regime-shifted reefs developed a concave structure, with increased herbivore biomass supported by increased algal resources, a loss of mid trophic level specialist species, including corallivores, and biomass in the upper trophic levels maintained by large-bodied generalist species. In contrast, on recovering reefs, after an initial loss of mid trophic level biomass, pyramids developed a bottom-heavy structure, which is commonly predicted in stable ecosystems by the theory of energy transfer efficiency in food webs.
Benthic habitat and associated fish communities can also be altered via climate-driven shifts in coral assemblages. One of the predicted characteristics of novel future coral ecosystems is a loss of thermally sensitive coral taxa and an increasing dominance of taxa with higher thermal tolerance, many of which have low structural complexity. In chapter 5, I used a patch reef experiment at Lizard Island on the northern GBR to investigate the effects of thermally 'vulnerable' and 'tolerant' coral assemblages on the trophodynamics of reef mesopredators and their prey fish communities. Fish communities which established naturally on the low structure 'tolerant' patch reefs had lower diversity, abundance and biomass than 'vulnerable' reefs with higher structural complexity. The introduction of a mesopredator (Cephalopholis boenak) had a greater impact on the prey fish community composition of 'tolerant' reefs than 'vulnerable' reefs, and total lipid content of C. boenak indicated that those introduced to 'tolerant' reefs had lower energy reserves than those on 'vulnerable' reefs, indicating a sub-lethal cost to condition.
My research provides novel insight into the effects of habitat degradation on the trophodynamics of coral reef mesopredators, mediated via the fish community on which they prey. I demonstrate that while certain mesopredator species may be able to adapt their diets to changing prey availability, their trophic niche becomes altered as they feed further down the food chain, and they may experience sub-lethal costs due to reduced energy reserves. This work highlights the importance of improving our understanding of how mesopredators are affected by habitat degradation, particularly with respect to the long-term implications of sub-lethal effects for their populations. Sustainable management of these species into the future will require the explicit recognition of the potential for such costs to mesopredator condition as reefs degrade.
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Bierwagen, Stacy L. "Functional roles of reef sharks on the Great Barrier Reef." Thesis, 2019. https://researchonline.jcu.edu.au/64966/1/JCU_64966_bierwagen_stacy_2019_thesis.pdf.
Full textAbstract:
Stacy Bierwagen studied how reef sharks utilise and influence coral reef ecosystems. She found that reef shark populations are stable and have distinct food web links and prey compared to other predatory fishes on the Great Barrier Reef. This information benefits the understanding of reef shark roles on coral reefs.
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Drew, Christina Ashton. "Spatial ecology of reef fish in backreef and coral reef habitats." 2006. http://www.lib.ncsu.edu/theses/available/etd-04172006-133049/unrestricted/etd.pdf.
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Hou, Shang-Ju, and 侯尚儒. "Coral Reef Patch Mapping." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/78553194759526420403.
Full textAbstract:
碩士國立交通大學
土木工程系所
102
Coral reef is formed by the corals’ growth and accumulation. According to the geography, it can be divided into two parts: the flat and the slope. By its construction, coral reef can be divided into three types: the fringing reef, the barrier reef and the atoll reef. The atoll reef areas on Dongsha Island are what being researched in this study, and this research aims at detecting and drawing the location of reefs around the Dongsha atoll area. The data used in this research includes digital elevation model (DEM) and satellite images. Three 1/5000 drawings had been chosen as the researched area depending on the characteristics of terrain, and their locations are: the middle of the lagoon area, the junction of the lagoon and the reef plat, and the reef plat. Trend surface analysis and object based segmentation are the two reef location-detecting ways that this research uses. The first one can only detect the location of reefs in DEM, while the second can detect both in DEM and the satellite images. The detected results will be compared with the real situation basing on the human observation of DEM and the sketched map of the reefs distribution. According to the different ways and combinations, it proves that object based segmentation in combination of the image of DEM, serves best. Among the five different analyses, the best one is DEM weight of 4 and image weight of 1. The average accuracy of the three areas is above 0.97, and the Kappa coefficient is higher than 0.84.
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Hubble, Marc. "The ecological significance of body size in tropical wrasses(Pisces : Labridae)." Thesis, 2003. https://researchonline.jcu.edu.au/81/1/01front.pdf.
Full textAbstract:
Among terrestrial organisms, body size exhibits predictable relationships with many characteristics including growth rate, mortality rate, longevity, reproductive traits, abundance, species richness and habitat use. However, the majority of studies
identifying such relationships have looked at a limited range of terrestrial taxa, in particular mammals, birds and beetles. These patterns have received much less attention among marine organisms and consequently their generality is questionable. Factors influencing growth of organisms in terrestrial and marine environments may be
fundamentally different. This variation could result in considerable differences in growth processes among marine and terrestrial organisms and influence constraints on
body size among species in these environments. The principal aim of this study was to identify whether numerous body size-related patterns observed in terrestrial taxa were repeated in a group of coral reef fishes, and assess reasons for differences when
predicted relationships were not detected.
This study employed a multispecific comparative approach to examine life history and ecological correlates of body size in coral reef fishes of the wrasse family (Pisces:
Labridae), a group in which species range in length from 4cm to over 2m. To account for the influence of evolutionary history of species on the patterns observed, a working hypothesis for a wrasse phylogeny was derived for the sampled species. This phylogeny was integrated into the analyses for Chapters 2 and 3 of this thesis.
The study comprised four main data chapters examining relationships between body size and a range of life history traits and other ecological characteristics. In
Chapter 2, the relationships between maximum body size of species and growth rate, mortality rate and longevity were examined among ten species of wrasses which
encompassed a ten-fold size range. Based on current theory it was predicted that there should be a positive relationship between maximum size of species and maximum age and a corresponding negative relationship between maximum species size and mortality rate. Both of these relationships were detected for the wrasses studied here. Conceptual models indicating ways in which differences among body sizes of fish species can arise
were developed and tested. It was found that in some species larger size was simply attained by growing at the same rate as smaller species but for a longer period of time. In other species faster growth enabled the attainment of larger body size but at the cost iiof
shortened life-span. There was limited evidence that by growing faster individuals became larger and less susceptible to predation sooner, resulting in larger body sizes and longer life spans. A further idea was that smaller species are smaller because they have determinate growth and stop growing sooner than larger species. Wrasse species studied here exhibited the range from indeterminate to determinate growth but there was
no apparent relationship between maximum body size of species and growth strategy.
In Chapter 3 covariation between maximum size of species and reproductive characteristics was explored. It was predicted that smaller species should mature and
change sex at a smaller proportion of maximum size and proportionally earlier in life than larger species. They were also expected to have greater reproductive effort than
larger species. Despite this, none of these relationships between maximum species size and reproductive traits were evident. Relationships between maximum size and size at
maturity and sex change were in fact opposite to those expected as smaller species matured and changed sex at a greater proportion of maximum size than larger species.
Similarly, short-lived species matured and changed sex proportionally later in life than long-lived species. In general, body size appeared more important than age in
determining when maturation and sex change occurred both among and within species. Energy invested per reproductive episode was not significantly related to species body size.
In Chapter 4, covariation among body size, growth rate, longevity, reproductive effort and size/age at maturity and size/age at sex change was examined in the wrasse
Halichoeres melanurus. Individuals were sampled at four locations along a latitudinal cline. Consistent with patterns identified to date it was predicted that with an increase in latitude there should be a decrease in growth rate, and an increase in body size and longevity. Initial growth rate was slightly slower at the two higher latitude locations and the maximum body size and maximum age of individuals within populations did tend to increase with an increase in latitude. It was also considered that an increase in latitude should be associated with an increase in the proportion of adult size and age attained
before maturation and sex change, and an increase in reproductive effort. However, there was no consistent relationship between the latitude at which individuals were
sampled and the proportion of maximum size/age attained at maturity or sex change. In addition reproductive effort of individuals did not vary predictably as latitude increased.
Individuals collected at the Palm Islands matured relatively earlier, exhibited greater iiireproductive
effort and changed sex proportionally earlier in life than those collected at Kimbe Bay, Lizard Island and Heron Island.
In Chapter 5, relationships between body size and ecological characteristics including local abundance, species richness, habitat use and depth range, were
investigated among all wrasse species present at a range of locations. Based on patterns identified within both marine and terrestrial taxa it was predicted that the smallest species would not be the most abundant with abundances peaking in species of small to intermediate size. Very large species were expected to have low abundances. This relationship was expressed for the wrasse species examined here. In addition, the body size-species richness distribution of wrasses at a number of locations was log normal, with many species of small to intermediate size and low numbers of very small or very large species. Smaller reef fish species were expected to be associated with a smaller range of microhabitats than larger species, be more habitat specific and have smaller depth ranges than larger species. The small wrasse species examined here were found to use a small, intermediate or large diversity of available microhabitats, whereas the
larger species consistently used a wide diversity of microhabitats. Depth ranges of small species lay on a continuum from very small to very large, whereas larger species consistently had large depth ranges.
Variation between some of the patterns observed in this study and those described in previous studies, demonstrates the need to replicate similar studies in a wide range of organisms inhabiting a wide range of habitats before their generality can be assessed.
Repeating similar studies among species within a large range of reef fish families is crucial to determine the utility of species body size as a predictor of life history
characteristics and other ecological variables in reef fishes.
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Hubble, Marc. "The ecological significance of body size in tropical wrasses (Pisces: Labridae) /." 2003. http://eprints.jcu.edu.au/81.
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Bay, Line K. "The population genetic structure of coral reef fishes on the Great Barrier Reef /." 2005. http://eprints.jcu.edu.au/14.
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Bay, Line Kolind. "The population genetic structure of coral reef fishes on the Great Barrier Reef." Thesis, 2005. https://researchonline.jcu.edu.au/14/1/01front.pdf.
Full textAbstract:
The population genetic structure of species may be determined by complex interactions
among many ecological, evolutionary and genetic processes. I investigated the
population genetic structure of coral reef fishes on the Great Barrier Reef (GBR),
Australia to better understand how these various processes may interact in a natural
system. I firstly examined the spatial genetic structure of a low dispersal species to
determine if its genetic structure varied among spatial scales and among regions located
in the centre and on the periphery of its distributional range. I then examined the
population genetic structure of species with different dispersal potentials and among
species sampled at central and peripheral locations in their species range.
Using mtDNA control region sequences and three microsatellite loci, I examined
the spatial genetic structure of a direct developing coral reef fish, Acanthochromis
polyacanthus, with comparatively low dispersal rates. The spatial genetic structure of
this species was scale-dependent with evidence of isolation-by-distance among regions,
but not within regions. Very strong genetic structure was detected among reefs within
regions consistent with a metapopulation model. Pairwise genetic distances increased
from offshore and older populations, to inshore and younger ones, supporting a
metapopulation propagule-pool model of colonisation. Genetic diversities, mismatch,
and coalescence analyses all identified large variation in the demographic history of this
species among populations and regions. Evidence of genetic bottlenecks was detected
by mismatch analysis in the majority of populations sampled, but in most populations
these bottlenecks appeared to be older since genetic diversities and coalescence based
population growth estimates did not indicate recent genetic bottlenecks. In contrast,
three populations displayed low genetic diversities and large population growth rates
indicating a more recent genetic bottleneck. Reductions in genetic diversities of local
populations resulted in overall lower genetic diversity and a higher regional expansion
rate in the southern region located towards the distributional margin of this species. In
all, these results suggest that A. polyacanthus exists as a metapopulation within regions
on the GBR and that metapopulation dynamics may differ among regions located in the
centre and on the periphery of this species.
The pelagic larval duration (PLD) can both affect and record the ecology and
evolution of coral reef fishes and emerging evidence suggests that this trait displays
considerable intraspecific variation. Here I present new estimates of PLD for ten species
of Pomacentridae and two species of Gobiidae, and coupled with previously published
estimates, examine spatial and temporal variation of PLDs within and among these
species. In eight of the twelve species examined here, within-population mean PLDs
differed between sampling times, locations within regions, and among regions. In
contrast, the range of these same PLD estimates overlapped at all spatial and temporal
scales examined in eleven of the twelve species, but not between regions in one species
(Amphiprion melanopus). Therefore, despite tight error estimates typically associated
with estimates of PLD taken from a particular population at a particular time in some
taxa, the overlapping ranges in PLD reported here indicate that the length of the pelagic
larval phase is a much more plastic trait than previously appreciated.
Pelagic larval duration (PLD) is a commonly used proxy for dispersal potential
in coral reef fishes. Here I examine the relationship between PLD, genetic structure and
genetic variability in coral reef fishes from one family (Pomacentridae) that differ in
mean larval duration by more than a month. Genetic structure was estimated in eight
species using a mitochondrial molecular marker (control region) and in a sub-set of five
species using nuclear molecular markers (ISSRs). Estimates of genetic differentiation
were similar among species with pelagic larvae, but differed between molecular
markers. The mtDNA indicated no structure while the ISSR indicated some structure
between the sampling locations. I detected a relationship between PLD and genetic
structure using both markers. These relationships, however, were caused by a single
species, Acanthochromis polyacanthus, which differs from all the other species
examined here in lacking a larval phase. With this species excluded, there was no
relationship between PLD and genetic structure using either marker. Genetic diversities
were generally high in all species and did not differ significantly among species and
locations. Nucleotide diversity and total heterozygosity were negatively related to
maximum PLD, but again, these relationships were caused by A. polyacanthus and
disappeared when this species was excluded from these analyses. These genetic patterns
are consistent with moderate gene flow among well-connected locations and indicate
that at this phylogenetic level (i.e., within family) the duration of the pelagic larval
phase is not the primary factor affecting patterns of genetic differentiation.
Using mtDNA (control region) and nuclear (ISSR) markers, I investigated the
population genetic structure of three congeneric species pairs of pomacentrid coral reef
fishes (Pomacentridae) in the context of species’ borders theory. This theory predicts that population located on the periphery of the species’ range should be smaller and
more fragmented and hence, display stronger genetic structure and lower genetic
diversities compared to more centrally located populations. Each species pair consisted
of one species sampled at two central locations within its geographic range, and another
species sampled at the same locations but which constituted one location toward the
centre of its range and another close to its edge. Contrary to expectations from theory, I
did not find the predicted border effects in the population genetic structure of the
species examined. Gene flow estimates did not differ among central and peripheral
species. Genetic diversities were not lower in peripheral populations compared to
central populations or in species sampled towards the periphery compared to those
sampled in the centre of their ranges. Indeed, genetic diversities were much greater in
the peripheral species compared to their central counterparts. The distribution of genetic
variation indicated that secondary contact among differentiated lineages may, in part, be
responsible for the high genetic diversity in these peripheral species. Elevated mutation
rates mediated by environmental stress on the species’ margin may have contributed
further genetic variability in these species.
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Hill, Jocelyn K. "Reef Check benthic survey error: a case study on the Great Barrier Reef." Thesis, 2002. https://researchonline.jcu.edu.au/47504/1/47504-hill-2002-thesis.pdf.
Full textAbstract:
Minimization of observer-related error is important for coral reef monitoring programs because highly variable data will decrease the resolution by which environmental change can be detected. Thirty-eight Reef Check volunteers were tested on their benthic identification skills on the Great Barrier Reef and their performance improved after practice and feedback sessions. Participants who had prior experience with environmental volunteer programs initially scored consistently higher than those without this experience. A similar but less consistent trend was found for more experienced divers. This information can be used to assess how much training volunteers require to remove the effects of different experience attributes. All participants' scores moderated towards the end of the study. The misidentifications still made involved similar benthos for all participants. This may reflect a lack of previous familiarity with these benthos types. The Reef Check categories that participants found most difficult to identify included hard coral, soft coral, recently killed coral, sponge and other benthic organisms. The effectiveness of future training sessions could be increased if focus is placed on these problem areas of identification within these categories.
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Hall, Vicki R. "Injury and regeneration of common reef-crest corals at Lizard Island, Great Barrier Reef /." 1998. http://eprints.jcu.edu.au/8.
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Hall, Vicki R. "Injury and regeneration of reef-crest corals at Lizard Island, Great Barrier Reef, Australia." Thesis, 1998. https://researchonline.jcu.edu.au/8/1/01front.pdf.
Full textAbstract:
Corals are frequently injured by natural processes and human activities. The response of scleractinian corals to damage is dependent on the nature and extent of damage, the characteristics of the injury, the life-histories of the coral, and the prevailing abiotic and biotic conditions. In this thesis I have examined several aspects of injury including (1) the nature and extent of natural injury, (2) the response of corals to injuries with different characteristics and (3) the influence of morphology and life-history in response to damage.
The spatial and temporal patterns of coral injury were recorded to determine the nature and extent of damage in common reef-crest corals at Lizard Island. The total amount of partial mortality on reef-crest corals was low (<2%) although there was a three-fold difference among sites. Sites with low partial mortality had reef-crest assemblages dominated (both numerically and in cover) by tabular and bushy corals. These corals have low levels of partial mortality, and on average, fewer small colonies with injuries. Conversely, the site where the partial mortality was three times higher had a lower abundance and cover of tabular corals, and an increase in the number and cover of massive and digitate corals. Massive and digitate corals, on average, have a higher amount of partial mortality and more small colonies with injuries.
The amount of injury present on a colony at a particular time is a balance between vulnerability (i.e. frequency of injury and resilience to damage) and recovery rate. An investigation into the patterns of injury over time showed that vulnerability to damage and recovery of injuries was species specific. In general Goniastrea retiformis had a high number of old injuries, a slow regeneration rate, and was injured infrequently, suggesting that injuries tended to accumulate on colonies over time. The addition of new injuries was also low for Acropora gemmifera, however colonies had few pre-existing injuries and faster recovery rates, reducing the accumulation of injuries on colonies. The injury dynamics for A. hyacinthus differed between censuses because of a change in injury regimes from routine to catastrophic, the latter regime caused by an outbreak of Acanthaster planci. Under routine conditions, there were few pre-existing injuries on colonies, a moderate addition of new injuries, and rapid regeneration, suggesting a fast turn-over of injuries. Under catastrophic conditions, there were many more pre-existing injuries, a high number of new injuries, and more injuries increasing in size than recovering, resulting in an accumulation of injuries.
The regeneration of injuries was influenced by the characteristics of the injury including initial size, type, and position within the colony The complete regeneration of an injury was more probable for small injuries (0 - 4 cm2) than larger injuries. However, recovery rates were also dependent on the type of injury as scraping injuries had a much faster regeneration rate than tissue mortality or breakage. Additionally, recovery was influenced by the position of injuries within colonies for one species Porites mayeri where the rate of regeneration of central injuries was greater than edge injuries. Conversely, the recovery of central and edge injuries was similar for A. robusta, A. hyacinthus, A. palifera, Pocillopora damicornis, and Porites lichen. Variations in levels of partial mortality, zones of tissue from which regeneration can take place, degrees of settlement by other organisms, intensities of damage, and amounts of resources available for regeneration all contributed to the differences in recovery rates found between injuries with varying characteristics.
The regeneration of injuries requires resources that are in limited supply. In this study, there was a marked effect of injury on reproduction for A. hyacinthus, A. gemmifera and G. retiformis, inferring a trade-off between reproduction and regeneration. Presumably the resources usually available for gamete production are being reallocated towards polyp regrowth and defence against fouling organisms. In contrast, injury had no effect on the survival or growth of colonies over nine months for the three species. This result suggests that future reproduction is being preserved through the iteration of new polyps but at the expense of current reproduction. It also suggests that these species are resistant to damage since their survival was unaltered by damage in the short-term.
Species resistant to damage have evolved two alternative, but not mutually exclusive, strategies in response to injury. Corals can invest resources in defensive mechanisms to avoid damage (avoidance strategies) or regrow lost parts after injury has occurred (tolerance strategies). Both strategies were utilised by corals in this study, although the amount of investment in either strategy varied. Generally, the longer-lived species, G. retiformis and A. gemmifera, seemed to invest more resources towards defence than the shorter-lived A. hyacinthus since the number of new injuries present on colonies was higher for the latter species. Conversely, the shorter-lived coral invested more in tolerance strategies by responding to infrequent damage events or minimal tissue losses with rapid regrowth. The cost of such a strategy is that shorter-lived species are more vulnerable to repetitive injury.
Experimental studies showed that branching species had more regrowth potential than massive and semi-massive species supporting the hypothesis by Jackson (1979) that morphology plays a role in the pattern of investment in regeneration and defence. The morphology of a coral influences its longevity, reproductive output, growth rate, and other life-history processes including regeneration. Consequently, the morphological strategy of an organism has evolved over time in response to a large number of biotic and abiotic processes including partial mortality.
In conclusion, this study on injury and regeneration of scleractinian corals has increased our knowledge of the underlying mechanisms that affect the recovery of corals from damage, and has provided a basis for understanding the consequences of different injury regimes on coral reefs. This is important because injury can adversely affect corals at the individual, population and community level and thus impact on the general ecology of coral reefs.
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