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Query: UNIPROT:P06889 (Mol)
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When the oxygen atom in a peptide bond is replaced by a sulfur atom, the restriction in the available conformational space and the ability of thioamides to confer resistance to enzymatic degradation renders thioamides as potentially useful building blocks for drug design and protein engineering. The solvation free energy differences between conformers of the same dipeptide can be high. Yet, previous conformational studies, basing on the (phi, psi) conformational energy maps of thio-substituted dipeptides, neglected both explicit water interactions and free energy considerations. In this paper, the (phi, psi) conformational free energy maps are obtained by single umbrella sampling in an explicit water environment for both alanine dipeptide and the corresponding thioamide derivatives. The phi and psi angles for the minima in the relative energy maps calculated with dielectric of 80 are similar to the corresponding phi and psi angles in the relative free energy maps for both Ac-Ala-NHMe (Ac: acetyl; Ala: alanine) and Act-Alat-NHMe (Act: thio-acetyl; Alat: thio-alanine). However, some large differences between the relative energy and relative free energy of major minima indicate that the consideration of free energy is important in determination of the relative occupancy of particular minima. Free energy maps for both Ac-Ala-NHMe and Act-Alat-NHMe show that thio-substitution favors conformations where phi < 0 because of the deeper beta and alphaR minima. The changes in the position and relative stability of minima were explained in terms of the destabilization of the regions near phi = -120, 0 and 120, psi = 60, -60, 180, which correspond to the increased steric hindrance due to the bulkier sulfur atom.
J Mol Graph Model 2001
PMID:Conformational analysis of thiopeptides: free energy calculations on the effects of thio-substitutions on the conformational distributions of alanine dipeptides. 1176 49

Leucetta 'chagosensis' is a widespread calcareous sponge, occurring in shaded habitats of Indo-Pacific coral reefs. In this study we explore relationships among 19 ribosomal DNA sequence types (the ITS1-5.8S-ITS2 region plus flanking gene sequences) found among 54 individuals from 28 locations throughout the western Pacific, with focus on the Great Barrier Reef (GBR). Maximum parsimony analysis revealed phylogeographical structuring into four major clades (although not highly supported by bootstrap analysis) corresponding to the northern/central GBR with Guam and Taiwan, the southern GBR and subtropical regions south to Brisbane, Vanuatu and Indonesia. Subsequent nested clade analysis (NCA) confirmed this structure with a probability of > 95%. After NCA of geographical distances, a pattern of range expansion from the internal Indonesian clade was inferred at the total cladogram level, as the Indonesian clade was found to be the internal and therefore oldest clade. Two distinct clades were found on the GBR, which narrowly overlap geographically in a line approximately from the Whitsunday Islands to the northern Swain Reefs. At various clade levels, NCA inferred that the northern GBR clade was influenced by past fragmentation and contiguous range expansion events, presumably during/after sea level low stands in the Pleistocene, after which the northern GBR might have been recolonized from the Queensland Plateau in the Coral Sea. The southern GBR clade is most closely related to subtropical L. 'chagosensis', and we infer that the southern GBR probably was recolonized from there after sea level low stands, based on our NCA results and supported by oceanographic data. Our results have important implications for conservation and management of the GBR, as they highlight the importance of marginal transition zones in the generation and maintenance of species rich zones, such as the Great Barrier Reef World Heritage Area.
Mol Ecol 2002 Sep
PMID:Phylogeography of western Pacific Leucetta 'chagosensis' (Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia). 1220 25

We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and genealogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distribution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (FST = 0.161, PhiST = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. However, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo-Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km).
Mol Ecol 2003 Sep
PMID:Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani. 1291 76

The physiological responses of two species of coral trout (Plectropomus maculatus and Plectropomus leopardus) to capture, shallow water and low salinity stressors were investigated. The responses of P. maculatus and P. leopardus to capture stress were characterised by rapid and transient increases in glucose, haemoglobin, haematocrit and lactate, as well as an equally dramatic but delayed increase in cortisol levels that persisted for at least 72 h. The magnitude and duration of the response to capture stress was very similar in both species. In contrast, the levels of cortisol, glucose, lactate, haemoglobin and haematocrit were generally elevated sooner and to higher levels in P. maculatus than in P. leopardus after exposure to shallow water stress. Coral trout exposed to reduced salinity showed minimal changes in cortisol, glucose, lactate, haemoglobin and haematocrit, but such changes were not characteristic of a non-specific response to stress. Thus, the physiological stress responses of coral trouts are species-specific and dependent on the nature of the stressor. This observation probably reflects different cortical processes in the brains of P. maculatus and P. leopardus-a result that may be related to the differential variability of the respective environments in which the two species habit.
Comp Biochem Physiol A Mol Integr Physiol 2005 Mar
PMID:Physiological stress responses of two species of coral trout (Plectropomus leopardus and Plectropomus maculatus). 1579 97

Most broadcast spawning scleractinian corals synchronously release gametes during a brief annual spawning period. In southern Taiwan, the mass spawning of scleractinians occurs in lunar mid-March. The exact cues triggering this annual phenomenon remain unclear. A scleractinian coral, Euphyllia ancora has been selected as a model for the hormones and reproduction studies. Testosterone (T) and estradiol (E2) in free and glucuronided forms were identified and consistently detected in coral polyps throughout the year. Peak levels of free E2, glucuronided E2 and T were obtained in the coral tissue just prior to spawning. The presence of specific aromatase activity was demonstrated in coral tissue. Higher concentrations of free E2 than glucuronided E2 were detected in the coral tissue throughout the year. In contrast, higher levels of glucuronided E2 than free E2 and glucuronided T were found in seawater during mass coral spawning. Furthermore, immunoreactivity and biological activity of immunoreactive gonadotropin-releasing hormone (irGnRH) was detected and quantified in coral tissue. Coral extracts (irGnRH) and mammalian (m)GnRH agonist had a similar dose-dependent effect on luteinizing hormone (LH) release in black porgy fish pituitary cells (in vitro). Peak levels of irGnRH were detected during the spawning period. In in vivo experiments, mGnRH agonist time- and dose-dependently stimulated aromatase activity, as well as the levels of T and E2 in free and glucuronided forms in coral. In conclusion, our data suggest that irGnRH and glucuronided E2 may play important roles in the control of reproduction and mass spawning in corals.
Comp Biochem Physiol A Mol Integr Physiol 2006 Jul
PMID:Hormones and reproduction in scleractinian corals. 1648 37

Hybrids in coral reef fishes have traditionally been described based on external features using meristic characters and colouration to identify putative parental contributors. This study utilised molecular genetic techniques to verify hybrid status and identify putative parental species for five hybrid specimens (Labridae: Thalassoma) collected from Holmes Reef in the Coral Sea. Phylogenetic analyses support hybrid origins of the specimens. Mitochondrial COI gene, nuclear S7 (intron 1) and nuclear copy of mitochondrial (NUMT) D-loop region corroborate the identity of T. quinquevittatum as the maternal and T. jansenii as the paternal contributor. Backcrossing to parental species by hybrids and bi-directional gene exchange between the Holmes Reef populations of T. jansenii and T. quinquevittatum was detected, suggesting that hybrids are fertile and able to reproduce successfully. F(1) hybrids display a mixture of the colouration attributes of the two parental species, but subsequent backcrossed individuals were unrecognisable as hybrids and displayed colouration of either parental species. A large numerical imbalance exists between the putative parental species at Holmes Reef, with T. quinquevittatum outnumbering T. jansenii by approximately 25:1. In this case study, hybridization appears to be driven by ecological rather than evolutionary factors.
Mol Phylogenet Evol 2006 Jul
PMID:Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae). 1658 Dec 67

Coral reefs have suffered long-term decline due to a range of anthropogenic disturbances and are now also under threat from climate change. For appropriate management of these vulnerable and valuable ecosystems it is important to understand the factors and processes that determine their resilience and that of the organisms inhabiting them, as well as those that have led to existing patterns of coral reef biodiversity. The scleractinian (stony) corals deposit the structural framework that supports and promotes the maintenance of biological diversity and complexity of coral reefs, and as such, are major components of these ecosystems. The success of reef-building corals is related to their obligate symbiotic association with dinoflagellates of the genus Symbiodinium. These one-celled algal symbionts (zooxanthellae) live in the endodermal tissues of their coral host, provide most of the host's energy budget and promote rapid calcification. Furthermore, zooxanthellae are the main primary producers on coral reefs due to the oligotrophic nature of the surrounding waters. In this review paper, we summarize and critically evaluate studies that have employed genetics and/or molecular biology in examining questions relating to the evolution and ecology of reef-building corals and their algal endosymbionts, and that bear relevance to coral reef conservation. We discuss how these studies can focus future efforts, and examine how these approaches enhance our understanding of the resilience of reef-building corals.
Mol Ecol 2006 Nov
PMID:Conservation genetics and the resilience of reef-building corals. 1705 89

This study describes a chemometric analysis of 1H NMR spectra of canine plasma following oral single dose administrations of two food components (lycopene and oleuropein) and of two drug products, Fungoral (ketoconazole) and Adalat (nifedipine). Due to the high interday physiological variation, 1H NMR plasma data were first filtered (by applying orthogonal signal correction) and then subjected to principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). A distinct discrimination was achieved between samples obtained with and without administration of xenobiotics using both techniques. According to distance to model criterion and as shown by the Cooman's plots there was no overlap between the four models which proved to be specific for each xenobiotic. Moreover, it was shown that this approach has the potential to recognize subtle variations in the metabolic profile even if the administered xenobiotic itself could not be detected in the canine plasma by conventional HPLC methods.
Mol Pharm
PMID:1H NMR monitoring of the canine metabolic profile after oral administration of xenobiotics using multivariate statistics. 1726 55

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.
Mol Ecol 2007 Apr
PMID:Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. 1740 88

Lipids play a key role in thermal and photo-acclimation processes, yet they are often neglected in stress studies. We investigated the influence of different light intensities and an increase of temperature on the fatty acid composition of the coral Montipora digitata and its symbiotic algae (i.e., zooxanthellae). Coral branches were subjected to 3 different light intensities (7, 30 and 95% sea surface photosynthetic active radiation) in filtered seawater for 35 days. Fatty acids as methyl esters were determined using gas chromatography (GC) and verified by GC-mass spectrometry. Different light intensities, but only in combination with increased temperature, significantly affected the fatty acid composition of the coral host and zooxanthellae. Temperature and light intensity increases caused reductions in the proportion of polyunsaturated fatty acids in both the host and symbionts. Most changes occurred in the host coral, which suggests that the host is more susceptible to environmental change than the symbiont, or that the host shields the symbionts from environmental change.
Comp Biochem Physiol B Biochem Mol Biol 2007 Aug
PMID:Acclimation effect on fatty acids of the coral Montipora digitata and its symbiotic algae. 1755 17


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