Development of Gene Expression Markers of Acute Heat-Light Stress in Reef-Building Corals of the Genus Porites

Coral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide.

Characterizations of the Major Coral Diseases of the Philippines: Ulcerative White Spot Disease and Novel Growth Anomalies of Porites

Coral reefs are in decline worldwide and coral disease is a significant contributing factor. However, etiologies of coral diseases are still not well understood. In contrast with the Caribbean, extremely little is known about coral diseases in the Philippines. In 2005, off Southeast Negros Island, Philippines, I investigated relationships between environmental parameters and prevalence of the two most common coral diseases, ulcerative white spot (UWS) and massive Porites growth anomalies (MPGAs). Samples were collected along a disease prevalence gradient 40.5 km long. Principal component analyses showed prevalence of MPGAs was positively correlated with water column nitrogen, organic carbon of surface sediments, and colony density. UWS was positively correlated with water column phosphorus. This is the first quantitative evidence linking anthropogenically-impacted water and sediment to a higher prevalence of these diseases. Histological and cytological alterations were investigated by comparing tissues from two distinct types of MPGA lesions (types 1 and 2) and healthy coral using light and electron microscopy. Skeletal abnormalities and sloughing, swelling, thinning, and loss of tissues in MPGAs resembled tissues exposed to bacterial or fungal toxins. Both lesion types had decreases in symbiotic zooxanthellae, which supply nutrients to corals. Notable alterations included migrations of chromophore cells (amoebocytes) (1) nocturnally to outer epithelia to perform wound-healing, including plugging gaps and secreting melanin in degraded tissues, and (2) diurnally to the interior of the tissue possibly to prevent shading zooxanthellae in order to maximize photosynthate production. Depletion of melanin (active in wound healing) in type 2 lesions suggested type 2 tissues were overtaxed and less stable. MPGAs contained an abundance of endolithic fungi and virus-like particles, which may result from higher nutrient levels and play roles in disease development. Swollen cells and mucus frequently blocked gastrovascular canals (GVCs) in MPGAs. Type 1 lesions appeared to compensate for impeded flow of wastes and nutrients through these canals with proliferation of new GVCs, which were responsible for the observed thickened tissues. In contrast, type 2 tissues were thin and more degraded. Dysplasia and putative neoplasia were also observed in MPGAs which may result from the tissue regeneration capacity being overwhelmed.

Aspects of the transplantation, storage and maintenance of corals (Montastraea Faveolata, Acropora Cervicornis and A. Palmata)

The purpose of this study is to explore aspects of coral transplantation for restoration. Montastraea faveolata cores of 2.54 and 5.0 cm were stored in aquaria, on an array and on the substrate. Survival on the array and substrate were 100% for 12 and 11 months respectively. Branches of Acropora cervicornis had 75.0 % survival on the substrate and 91.7% on the array. Disease caused mortality for the A. cervicornis and the 2.54 cm cores in the aquaria but not for the 5.0 cm cores. Growth was significantly higher for A. cervicornis and A. palmata branches stored on an array than in an open seawater system. The storage type affected growth patterns of both species. M. faveolata fed three times/week increased in surface area significantly more than those fed once and twice/week. Corals fed once per week significantly increased their polyp density. Corals had intermittent respiration while under sub-aerial conditions.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Seawater carbonate chemistry and weight of two Atlantic corals Favia fragum and Porites astreoides during experiments, 2011

Rising concentrations of atmospheric CO2 are changing the carbonate chemistry of the oceans, a process known as ocean acidification (OA). Absorption of this CO2 by the surface oceans is increasing the amount of total dissolved inorganic carbon (DIC) and bicarbonate ion (HCO3) available for marine calcification yet is simultaneously lowering the seawater pH and carbonate ion concentration ([CO3]), and thus the saturation state of seawater with respect to aragonite. We investigated the relative importance of [HCO3] versus [CO3] for early calcification by new recruits (primary polyps settled from zooxanthellate larvae) of two tropical coral species, Favia fragum and Porites astreoides. The polyps were reared over a range of ?ar values, which were manipulated by both acid-addition at constant pCO2 (decreased total [HCO3] and [CO3]) and by pCO2 elevation at constant alkalinity (increased [HCO3], decreased [CO3]). Calcification after 2 weeks was quantified by weighing the complete skeleton (corallite) accreted by each polyp over the course of the experiment. Both species exhibited the same negative response to decreasing [CO3] whether ?ar was lowered by acid-addition or by pCO2 elevation-calcification did not follow total DIC or [HCO3]. Nevertheless, the calcification response to decreasing [CO3] was nonlinear. A statistically significant decrease in calcification was only detected between Omega aragonite = <2.5 and Omega aragonite = 1.1-1.5, where calcification of new recruits was reduced by 22-37% per 1.0 decrease in Omega aragonite. Our results differ from many previous studies that report a linear coral calcification response to OA, and from those showing that calcification increases with increasing [HCO3]. Clearly, the coral calcification response to OA is variable and complex. A deeper understanding of the biomineralization mechanisms and environmental conditions underlying these variable responses is needed to support informed predictions about future OA impacts on corals and coral reefs.

Mineralogy, mineral chemistry, and genesis of precious metal-bearing volcanogenic massive sulfide deposits in the Newfoundland Appalachians, Canada: the Ming deposit as example

The Ming deposit, Newfoundland Appalachians, is a metamorphosed (upper greenschist to lower amphibolite facies), Cambro-Ordovician, bimodalmafic volcanogenic massive sulfide (VMS) deposit that consists of several, spatially-associated, elongated orebodies composed of stratabound semimassive to massive sulfides and/or discordant sulfide stringers in a rhyodacitic footwall. Copper is the main commodity; however, the deposit contains precious metal-bearing zones with elevated Au grades. In this study, field observations, microscopy, and micro-analytical tools including electron microprobe, laser ablation inductively coupled plasma mass spectrometry, and secondary ion mass spectrometry were used to constrain the relative timing of precious metal emplacement, the physico-chemical conditions of hydrothermal fluid precipitation, and the sources of sulfur, precious metals, semi-metals and metals. The ore mineral assemblage is complex and indicates an intermediate sulfidation state. Pyrite and chalcopyrite are the dominant ore minerals with minor sphalerite and pyrrhotite, and trace galena, arsenopyrite and cubanite. Additional trace phases include tellurides, NiSb phases, sulfosalts, electrum, AgHg±Au alloys, and oxides. Silver phases and precious metals occur predominantly in semi-massive and massive sulfides as free grains, and as grains spatially associated with arsenopyrite and/or sulfosalts. Precious metal phases occurring between recrystallized pyrite and within cataclastic pyrite are rare. Hence, the complex ore assemblage and textures strongly suggest syngenetic precious metal emplacement, whereas metamorphism and deformation only internally and locally remobilized precious metal phases. The ore assemblage formed from reduced, acidic hydrothermal fluids over a range of temperatures (≈350 to below 260ºC). The abundance of telluride and Ag-bearing tetrahedrite, however, varies strongly between the different orebodies indicating variable ƒTe₂, ƒSe₂, mBi, and mSb within the hydrothermal fluids. The variations in the concentrations of semi-metals and metals (As, Bi, Hg, Sb, Se, Te), as well as Au and Ag, were due to variations in temperature but also to a likely contribution of magmatic fluids into the VMS hydrothermal system from presumably different geothermal reservoirs. Sulfur isotope studies indicate at least two sulfur sources: sulfur from thermochemically-reduced seawater sulfate and igneous sulfur. The source of igneous sulfur is the igneous footwall, direct magmatic fluid/volatiles, or both. Upper greenschist to lower amphibolite metamorphic conditions and deformation had no significant effect on the sulfur isotope composition of the sulfides at the Ming deposit.

(Table 2) Radiocarbon dating on cold-water corals collected in the Mediterranean Sea

This study presents newly obtained coral ages of the cold-water corals Lophelia pertusa and Madrepora oculata collected in the Alboran Sea and the Strait of Sicily (Urania Bank). These data were combined with all available Mediterranean Lophelia and Madrepora ages compiled from literature to conduct a basin-wide assessment of the spatial and temporal occurrence of these prominent framework-forming scleractinian species in the Mediterranean realm and to unravel the palaeo-environmental conditions that controlled their proliferation or decline. For the first time special focus was placed on a closer examination of potential differences occurring between the eastern and western Mediterranean sub-basins. Our results clearly demonstrate that cold-water corals occurred sparsely in the entire Mediterranean during the last glacial before becoming abundant during the Bølling-Allerød warm interval, pointing to a basin-wide, almost concurrent onset in (re-)colonisation after ~13.5 ka. This time coincides with a peak in meltwater discharge originating from the northern Mediterranean borderlands which caused a major reorganisation of the Mediterranean thermohaline circulation. During the Younger Dryas and Holocene, some striking differences in coral proliferation were identified between the sub-basins such as periods of highly prolific coral growth in the eastern Mediterranean Sea during the Younger Dryas and in the western basin during the Early Holocene, whereas a temporary pronounced coral decline during the Younger Dryas was exclusively affecting coral sites in the Alboran Sea. Comparison with environmental and oceanographic data revealed that the proliferation of the Mediterranean corals is linked with enhanced productivity conditions. Moreover, corals thrived in intermediate depths and showed a close relationship with intermediate water mass circulation in the Mediterranean sub-basins. For instance, reduced Levantine Intermediate Water formation hampered coral growth in the eastern Mediterranean Sea during sapropel S1 event as reduced Winter Intermediate Water formation did in the westernmost part of the Mediterranean (Alboran Sea) during the Mid-Holocene. Overall, this study clearly demonstrates the importance to consider region-specific environmental changes as well as species-specific environmental preferences in interpreting coral chronologies. Moreover, it highlights that the occurrence or decline of cold-water corals is not controlled by one key parameter but rather by a complex interplay of various environmental variables.

Guia didático-metodológico para aprendizagem e memorização dos conhecimentos disseminados nos moocs – Massive Open Online Courses

The present research has character exploratory, bibliographic and qualitative. It is based in consolidated scientific arguments in cognitive theories inspired in constructivist method and, under this perspective proposes to develop a didactic guide oriented to students of courses MOOCs - Massive Open Online Courses that will make it possible to maximize the utilization and the assimilation of the knowledge available in these courses. Intends also prepare these students in practice of a methodology of storage that enables the knowledge acquired are not lost nor be forgotten over the course of time. The theoretical framework, based on the theories of Meaningful Learning (Ausubel), the Genetic Epistemology (Piaget), Socioconstructivist (Vigotsky) and the Multimedia Learning (Mayer), subsidizes the understanding of important concepts such as meaningful learning, previous knowledge, and conceptual maps. Supported by fundamental contribution of the Theory of Categories, which are inter-related to concepts applicable to teaching methodology supported by use of structured knowledge maps in the establishment of the binomial teaching-learning; and with valuable study performed by teachers Luciano Lima (UFU) and Rubens Barbosa Filho (UEMS) that culminated with the development of Exponential Effective Memorization Method in Binary Base (Double MEB).

Satellites around massive galaxies since z∼ 2

The accretion of minor satellites has been postulated as the most likely mechanism to explain the significant size evolution of massive galaxies over cosmic time. Using a sample of 629 massive (M_star~ 10^11 M_⊙) galaxies from the near-infrared Palomar/DEEP-2 survey, we explore what fraction of these objects have satellites with 0.01 < M_sat/M_central < 1 (1:100) up to z= 1 and what fraction have satellites with 0.1 < M_sat/M_central < 1 (1:10) up to z= 2 within a projected radial distance of 100 kpc. We find that the fraction of massive galaxies with satellites, after background correction, remains basically constant and close to 30 per cent for satellites with a mass ratio down to 1:100 up to z= 1, and close to 15 per cent for satellites with a 1:10 mass ratio up to z= 2. The family of spheroid-like massive galaxies presents a 2–3 times larger fraction of objects with satellites than the group of disc-like massive galaxies. A crude estimation of the number of 1:3 mergers a massive spheroid-like galaxy has experienced since z~2 is around 2. For a disc-like galaxy this number decreases to ~1.

Measuring star formation in high-z massive galaxies: a mid-infrared to submillimetre study of the GOODS NICMOS Survey sample

We present measurements of the mean mid-infrared to submillimetre flux densities of massive (M_*≳ 10^11 M_⊙) galaxies at redshifts 1.7 < z < 2.9, obtained by stacking positions of known objects taken from the GOODS NICMOS Survey (GNS) catalogue on maps at 24 μm (Spitzer/MIPS); 70, 100 and 160 μm (Herschel/PACS); 250, 350 and 500 μm (BLAST); and 870 μm (LABOCA). A modified blackbody spectrum fit to the stacked flux densities indicates a median [interquartile] star formation rate (SFR) of SFR = 63[48, 81] M_⊙ yr^−1. We note that not properly accounting for correlations between bands when fitting stacked data can significantly bias the result. The galaxies are divided into two groups, disc-like and spheroid-like, according to their Sérsic indices, n. We find evidence that most of the star formation is occurring in n≤ 2 (disc-like) galaxies, with median [interquartile] SFR = 122[100, 150] M_⊙ yr^−1, while there are indications that the n > 2 (spheroid-like) population may be forming stars at a median [interquartile] SFR = 14[9, 20] M_⊙ yr^−1, if at all. Finally, we show that star formation is a plausible mechanism for size evolution in this population as a whole, but find only marginal evidence that it is what drives the expansion of the spheroid-like galaxies.

System to predict bipolar disorder crises analysing massive data

Durante el desarrollo del proyecto he aprendido sobre Big Data, Android y MongoDB mientras que ayudaba a desarrollar un sistema para la predicción de las crisis del trastorno bipolar mediante el análisis masivo de información de diversas fuentes. En concreto hice una parte teórica sobre bases de datos NoSQL, Streaming Spark y Redes Neuronales y después diseñé y configuré una base de datos MongoDB para el proyecto del trastorno bipolar. También aprendí sobre Android y diseñé y desarrollé una aplicación de móvil en Android para recoger datos para usarlos como entrada en el sistema de predicción de crisis. Una vez terminado el desarrollo de la aplicación también llevé a cabo una evaluación con usuarios.

Robust Uncertainty Quantification and Scalable Computation for Computer Models with Massive Output

Uncertainty quantification (UQ) is both an old and new concept. The current novelty lies in the interactions and synthesis of mathematical models, computer experiments, statistics, field/real experiments, and probability theory, with a particular emphasize on the large-scale simulations by computer models. The challenges not only come from the complication of scientific questions, but also from the size of the information. It is the focus in this thesis to provide statistical models that are scalable to massive data produced in computer experiments and real experiments, through fast and robust statistical inference.

Chapter 2 provides a practical approach for simultaneously emulating/approximating massive number of functions, with the application on hazard quantification of Soufri\`{e}re Hills volcano in Montserrate island. Chapter 3 discusses another problem with massive data, in which the number of observations of a function is large. An exact algorithm that is linear in time is developed for the problem of interpolation of Methylation levels. Chapter 4 and Chapter 5 are both about the robust inference of the models. Chapter 4 provides a new criteria robustness parameter estimation criteria and several ways of inference have been shown to satisfy such criteria. Chapter 5 develops a new prior that satisfies some more criteria and is thus proposed to use in practice.