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Search Results: 1 - 10 of 191569 matches for " Gates D "
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Clade D Symbiodinium in Scleractinian Corals: A “Nugget” of Hope, a Selfish Opportunist, an Ominous Sign, or All of the Above?
Michael Stat,Ruth D. Gates
Journal of Marine Biology , 2011, DOI: 10.1155/2011/730715
Abstract: Clade D Symbiodinium are thermally tolerant coral endosymbionts that confer resistance to elevated sea surface temperature and bleaching to the host. The union between corals and clade D is thus important to management and coral conservation. Here, we review the diversity and biogeography of clade D Symbiodinium, factors linked to increasing abundances of clade D, and the benefits and drawbacks of associating with clade D for corals. We identify clade D Symbiodinium as uncommon pandemically distributed generalists found in higher abundances on reefs exposed to challenging sea surface temperatures and local stressors or with a history of bleaching. This distribution suggests that clade D Symbiodinium are mostly opportunistic endosymbionts, whereby they outcompete and replace optimal symbionts in health-compromised corals. We conclude by identifying research gaps that limit our understanding of the adaptive role clade D Symbiodinium play in corals and discuss the utility of monitoring clade D Symbiodinium as indicators of habitat degradation in coral reef ecosystems. 1. Introduction Scleractinian corals form obligate endosymbioses with uni-cellular photosynthetic dinoflagellates in the genus Symbiodinium [1, 2]. The Symbiodinium translocates newly fixed organic carbon to the host coral and, in return, receive inorganic waste metabolites from host respiration and an environment free from predators [3].This mutually beneficial symbiosis contributes to the productivity of coral reef ecosystems, promotes deposition of calcium carbonate skeletons, and creates the structural framework that protects coastlines and serves as habitat for the extraordinary biodiversity found in coral reef ecosystems [4]. A consortium of bacteria, archaea, viruses, and fungi also forms close associations with corals and contributes collectively to the overall function and environmental thresholds of corals (e.g., [5–8]). These coral-microorganism communities are collectively described as the coral holobiont. Climate change and other anthropogenic impacts have already damaged an estimated 30% of the world’s coral reefs, and further declines in the integrity of coral reef ecosystems are projected for the near future [9]. A suite of often synergistic factors are contributing to the declining health of corals including global stressors such as elevated sea water temperatures and ocean acidification and local stressors like increased nutrient loading, sedimentation, and pollution [9]. The best documented and arguably most acutely damaging environmental conditions for corals are
Vegetable and Fruit Intakes of On-Reserve First Nations Schoolchildren Compared to Canadian Averages and Current Recommendations
Allison Gates,Rhona M. Hanning,Michelle Gates,Kelly Skinner,Ian D. Martin,Leonard J. S. Tsuji
International Journal of Environmental Research and Public Health , 2012, DOI: 10.3390/ijerph9041379
Abstract: This study investigated, in on-reserve First Nations (FN) youth in Ontario, Canada, the following: (a) the intakes of vegetable and fruit, “other” foods and relevant nutrients as compared to current recommendations and national averages, (b) current prevalence rates of overweight and obesity and (c) the relationship between latitude and dietary intakes. Twenty-four-hour diet recalls were collected via the Waterloo Web-Based Eating Behaviour Questionnaire (WEB-Q) (n = 443). Heights and weights of participants were self reported using measured values and Body Mass Index was categorized using the International Obesity Task Force cutoffs. Food group and nutrient intakes were compared to current standards, Southern Ontario Food Behaviour data and the Canadian Community Health Survey, Cycle 2.2, using descriptive statistics. Mean vegetable and fruit, fibre and folate intakes were less than current recommendations. Girls aged 14–18 years had mean intakes of vitamin A below current recommendations for this sub-group; for all sub-groups, mean intakes of vegetables and fruit were below Canadian averages. All sub-groups also had intakes of all nutrients and food groups investigated that were less than those observed in non-FN youth from Southern Ontario, with the exception of “other” foods in boys 12–18 years. Prevalence rates of overweight and obesity were 31.8% and 19.6%, respectively, exceeding rates in the general population. Dietary intakes did not vary consistently by latitude (n = 248), as revealed by ANOVA. This study provided a unique investigation of the dietary intakes of on-reserve FN youth in Ontario and revealed poor intakes of vegetables and fruit and related nutrients and high intakes of “other” foods. Prevalence rates of overweight and obesity exceed those of the general population.
Understanding Mammalian Genetic Systems: The Challenge of Phenotyping in the Mouse
Steve D. M Brown ,John M Hancock,Hilary Gates
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020118
Abstract: Understanding mammalian genetic systems is predicated on the determination of the relationship between genetic variation and phenotype. Several international programmes are under way to deliver mutations in every gene in the mouse genome. The challenge for mouse geneticists is to develop approaches that will provide comprehensive phenotype datasets for these mouse mutant libraries. Several factors are critical to success in this endeavour. It will be important to catalogue assay and environment and where possible to adopt standardised procedures for phenotyping tests along with common environmental conditions to ensure comparable datasets of phenotypes. Moreover, the scale of the task underlines the need to invest in technological development improving both the speed and cost of phenotyping platforms. In addition, it will be necessary to develop new informatics standards that capture the phenotype assay as well as other factors, genetic and environmental, that impinge upon phenotype outcome.
Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium
Xavier Pochon, Hollie M. Putnam, Fabien Burki, Ruth D. Gates
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029816
Abstract: Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.
The effect of fracture aperture and flow rate ratios on two-phase flow in smooth-walled single fracture
A. A. Alturki,B. B. Maini,I. D. Gates
Journal of Petroleum Exploration and Production Technologies , 2013, DOI: 10.1007/s13202-012-0047-5
Abstract: This work experimentally examines the co-current flow of oil and water in moderately oil-wet smooth-walled single fractures. The focus of our investigation is on studying the effects of varying fracture aperture and flow rate ratios on relative permeability to oil and water. The phase distribution and flow regimes within the fracture were closely monitored and found to vary with the flow rate ratio and total flow rate, and appeared to have a direct impact on the relative permeability. Experimental relative permeability data exhibited variations in shape indicating the effects of fracture aperture and flow ratios. Also, the data show the effects of oil–water phase interference, and phase saturation changes on the relative permeabilities for each fracture configuration. A couple of two-phase relative permeability models, namely, viscous coupling model, and homogenous single-phase approach, were tested against the experimental relative permeability data. This work provides insight into the nature of two-phase flow in a single fracture and could help in better modeling of more complex fracture networks.
Fish Food in the Deep Sea: Revisiting the Role of Large Food-Falls
Nicholas D. Higgs, Andrew R. Gates, Daniel O. B. Jones
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0096016
Abstract: The carcasses of large pelagic vertebrates that sink to the seafloor represent a bounty of food to the deep-sea benthos, but natural food-falls have been rarely observed. Here were report on the first observations of three large ‘fish-falls’ on the deep-sea floor: a whale shark (Rhincodon typus) and three mobulid rays (genus Mobula). These observations come from industrial remotely operated vehicle video surveys of the seafloor on the Angola continental margin. The carcasses supported moderate communities of scavenging fish (up to 50 individuals per carcass), mostly from the family Zoarcidae, which appeared to be resident on or around the remains. Based on a global dataset of scavenging rates, we estimate that the elasmobranch carcasses provided food for mobile scavengers over extended time periods from weeks to months. No evidence of whale-fall type communities was observed on or around the carcasses, with the exception of putative sulphide-oxidising bacterial mats that outlined one of the mobulid carcasses. Using best estimates of carcass mass, we calculate that the carcasses reported here represent an average supply of carbon to the local seafloor of 0.4 mg m?2d?1, equivalent to ~4% of the normal particulate organic carbon flux. Rapid flux of high-quality labile organic carbon in fish carcasses increases the transfer efficiency of the biological pump of carbon from the surface oceans to the deep sea. We postulate that these food-falls are the result of a local concentration of large marine vertebrates, linked to the high surface primary productivity in the study area.
Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution
Xavier Pochon,Hollie M. Putnam,Ruth D. Gates
PeerJ , 2015, DOI: 10.7717/peerj.394
Abstract: Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.
Multi-gene analysis of the symbiotic and free-living dinoflagellate genus Symbiodinium
Xavier Pochon,Hollie M Putnam,Ruth D Gates
PeerJ , 2015, DOI: 10.7287/peerj.preprints.267v1
Abstract: Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.
When Superspace Is Not Enough
S. James Gates Jr,W. D. Linch,J. Phillips
Physics , 2002,
Abstract: We give an expanded discussion of the proposal that spacetime supersymmetry representations may be viewed as having their origins in 1D theories that involve a special class of real Clifford algebras. These 1D theories reproduce the supersymmetric structures of spacetime supersymmetric theories after the latter are reduced on a 0-brane.
New Approximations for the Area of the Mandelbrot Set
Daniel Bittner,Long Cheong,Dante Gates,Hieu D. Nguyen
Mathematics , 2014,
Abstract: Due to its fractal nature, much about the area of the Mandelbrot set $M$ remains to be understood. While a series formula has been derived by Ewing and Schober to calculate the area of $M$ by considering its complement inside the Riemann sphere, to date the exact value of this area remains unknown. This paper presents new improved upper bounds for the area based on a parallel computing algorithm and for the 2-adic valuation of the series coefficients in terms of the sum-of-digits function.
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