Diving Behaviour of Red-Eared Sliders (Trachemys Scripta Elegans) Under the Risk of Predation

Predation risk influences a variety of behavioral decisions of many organisms and results in animals having to trade-offs safety with other behaviors. The effects of predation, however, have been largely ignored in the study of vertebrates that forage underwater (divers). I tested the predictions of an on optimal diving model that incorporates the risk of predation, using red eared slider turtles (Trachemys scripta elegans). Specifically, I tested the hypothesis that divers will increase their surface time when instantaneous risk decreases with time at the surface. By using a model aerial predator and exposing turtles to both risk and no risk treatments, I tested how turtles perceive risk at the surface and whether they increase or decrease their surface time depending on how they assess risk. The model's predictions for situations in which risk at the surface is decreasing with time spent there-likely to be the case for aerial predation-were supported by the results. I found that surface time and time spent submerged per dive were significantly greater when turtles were at risk and that turtles also spent more time resting at the bottom when exposed to this treatment. Interestingly, turtles under risk engaged in vigilance behaviors while on the bottom just prior to surfacing. This behavior could have implications for model predictions and future experiments are needed to test whether subsurface vigilance may alter diving decisions made under risk.

Design and development of an enzyme-linked biosensor for detection and quantification of phosphate species

The objective of this study is to design and development of an enzyme-linked biosensor for detection and quantification of phosphate species. Various concentrations of phosphate species were tested and completed for this study. Phosphate is one of the vital nutrients for all living organisms. Phosphate compounds can be found in nature (e.g., water sediments), and they often exist in aninorganic form. The amount of phosphates in the environment strongly influences the operations of living organisms. Excess amount of phosphate in the environment causes eutrophication which in turn causes oxygen deficit for the other living organisms. Fish die and degradation of habitat in the water occurs as a result of eutrophication. In contrast, low phosphate concentration causes death of vegetation since plants utilize the inorganic phosphate for photosynthesis, respiration, and regulation of enzymes. Therefore, the phosphate quantity in lakes and rivers must be monitored. Result demonstrated that phosphate species could be detected in various organisms via enzyme-linked biosensor in this research.

Is Rapid Adaptation to New Environments Fueled by Old Mutations? A Case Study of Copper Tolerance on Mimulus guttatus

Rapid adaptation and tolerance is a phenomenon experienced by a variety of organisms typically because of new and harsh environments. Mimulus guttatus, a plant commonly seen on the west coast of the United States, is a prime example as it has rapidly evolved to soil contamination by copper due to mining in California in the last 150 years. There have been two hypotheses posed by researchers as to the genetic basis of how organisms have evolved so quickly which I set out to study: 1) There is a low frequency of tolerant genotypes in the ancestral population otherwise known as standing variation or 2) new mutations occurred once exposed to a new environment. In the past, researchers found it difficult to distinguish between the two because they lacked the technology we have today for DNA analysis. I used four different populations of M. guttatus from varying locations in order to address which hypothesis was valid. I conducted both survival assays of these populations and DNA analysis of known tolerant and non-tolerant lines using a copper oxidase gene. I found that there was at least some degree of tolerance in all populations in the survival assays, supporting the hypothesis of standing variation. I also found patterns within DNA analysis suggesting the copper oxidase gene would be useful for further study to verify the standing variation hypothesis. The results from this experiment helps in understanding rapid evolution not just in the context of soil contamination by metals but also ties back to why an alarming number of species are not able to adapt to our constantly changing world.

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

GDGT and n-alkane data of sediment core GeoB4901-8

The tight coupling between the atmospheric and oceanic circulation in the equatorial Atlantic region makes this area an important region for paleoclimatic research. Previous studies report the occurrence of large amounts of terrigenous material and soil organic carbon (SOC) within the marine sediments of the eastern Gulf of Guinea. We use the accumulation rates (AR) of branched glycerol dialkyl glycerol tetraethers (GDGTs) to identify variations in SOC delivery to the Niger Fan over the last 35 ka, and compare these records to long-chain n-alkanes as a proxy for higher plant material, to an inorganic proxy for terrigenous input (aluminum AR) and to indicators for the marine productivity (AR of carbonate and crenarchaeol). In addition, sea surface temperatures (SSTs) are calculated based on the TEX86H index and environmental factors affecting the SST-reconstructions are discussed. Our results indicate that Al AR are closely connected to the rate of mean sea level change after 15 ka BP, with an additional influence of the increased monsoonal precipitation and extended vegetation cover corresponding to the African Humid Period (14.8-5.5 ka BP). Branched GDGT AR appears to be determined by shelf erosion in addition to the interplay of monsoonal precipitation and vegetation cover controlling soil erosion. Long-chain n-alkane concentrations clearly show a different trend than the other proxies, which might be due to their predominant eolian transport. Paleo-SSTs show a clear shift from colder temperatures during the last glacial period (20-22 °C) to warmer temperatures during the Holocene (24-26 °C). However, TEX86H-based SSTs are cold-biased compared to recent SSTs and Mg/Ca-based SST reconstructions, which is probably caused by a high seasonality of the Thaumarchaeota, with a maximum productivity of these organisms during the cold summer months. However, a sub-surface production of GDGTs and/or a potential bias of SST reconstruction by terrestrial input could not be completely excluded.

Seawater carbonate chemistry and biological processes during experiments with postlarvae of barnacle of Semibalanus balanoides and Elminius modestus, 2010

Ocean acidification and global warming are occurring concomitantly, yet few studies have investigated how organisms will respond to increases in both temperature and CO2. Intertidal microcosms were used to examine growth, shell mineralogy and survival of two intertidal barnacle post-larvae, Semibalanus balanoides and Elminius modestus, at two temperatures (14 and 19°C) and two CO2 concentrations (380 and 1,000 ppm), fed with a mixed diatom-flagellate diet at 15,000 cells ml-1 with flow rate of 10 ml-1 min-1. Control growth rates, using operculum diameter, were 14 ± 8 µm day-1 and 6 ± 2 µm day-1 for S. balanoides and E. modestus, respectively. Subtle, but significant decreases in E. modestus growth rate were observed in high CO2 but there were no impacts on shell calcium content and survival by either elevated temperature or CO2. S. balanoides exhibited no clear alterations in growth rate but did show a large reduction in shell calcium content and survival under elevated temperature and CO2. These results suggest that a decrease by 0.4 pH(NBS) units alone would not be sufficient to directly impact the survival of barnacles during the first month post-settlement. However, in conjunction with a 4-5°C increase in temperature, it appears that significant changes to the biology of these organisms will ensue.

(Table T2) Relative signal intensity of intact polar lipids in sediments from ODP Sites 207-1257 and 207-1258

We report results from the analysis of intact polar lipids (IPLs) in sediments from Ocean Drilling Program Sites 1257 and 1258. IPLs, constituting the cell membranes of living organisms, were detected in organic-lean sediments but not in underlying organic-rich black shales. Microbial activity in organic-lean sediments is likely due to sulfate-dependent oxidation of methane whereas difficulties detecting IPLs in black shales are interpreted to result from unfavorable signal-to-noise ratios due to low cell concentrations in combination with extremely high analytical noise created by uncharacterized organic matrix. IPLs found are consistent with a low-diversity community of archaea and bacteria. The concentrations of IPLs are more than one order of magnitude lower than those in Neogene deep subsurface sediments at the Peruvian margin, suggestive of significantly lower cell concentrations in Demerara Rise. This finding is consistent with inferred low rates of subsurface microbial activity.

Seawater carbonate chemistry and hydrogen ions and carbonate chemistry in calcifying fluid of coral Astrangia poculata during experiments, 2011

A generalized physicochemical model of the response of marine organisms' calcifying fluids to CO2-induced ocean acidification is proposed. The model is based upon the hypothesis that some marine calcifiers induce calcification by elevating pH, and thus Omega aragonite, of their calcifying fluid by removing protons (H+). The model is explored through two end-member scenarios: one in which a fixed number of H+ is removed from their calcifying fluid, regardless of atmospheric pCO2, and another in which a fixed external-internal proton ratio ([H+]E/[H+]I) is maintained. The model is able to generate the full range of calcification response patterns observed in prior ocean acidification experiments and is consistent with the assertion that organisms' calcification response to ocean acidification is more negative for marine calcifiers that exert weaker control over their calcifying fluid pH. The model is empirically evaluated for the temperate scleractinian coral Astrangia poculata with in situ pH microelectrode measurements of the coral's calcifying fluid under control and acidified conditions. These measurements reveal that (1) the pH of the coral's calcifying fluid is substantially elevated relative to its external seawater under both control and acidified conditions, (2) the coral's [H+]E/[H+]I remains constant under control and acidified conditions, and (3) the coral removes fewer H+ from its calcifying fluid under acidified conditions than under control conditions. Thus, the carbonate system dynamics of A. poculata's calcifying fluid appear to be most consistent with the fixed [H+]E/[H+]I end-member scenario. Similar microelectrode experiments performed on additional taxa are required to assess the model's general applicability.

Carbon isotope composition of lipids from bones and host sediments of the Atlantic and Pacific Oceans

Carbon in lipids separated from organic matter of fish and marine mammal bones from bottom of the Pacific and Atlantic oceans has d13C values ranging from -21.6 to -25.8 per mil and is isotopically lighter than that in lipids and total organic matter of host sediments. During fossilization of organic phosphate carbon isotope composition of bound lipids of fish bone becomes lighter and that of bones of mammals becomes heavier, possibly as a result of metabolisms of these organisms and composition of phospholipids in them.

Seawater carbonate chemistry and biological processes of sand dollars Dendraster excentricus during experiments, 2011

Reduction in global ocean pH due to the uptake of increased atmospheric CO2 is expected to negatively affect calcifying organisms, including the planktonic larval stages of many marine invertebrates. Planktonic larvae play crucial roles in the benthic-pelagic life cycle of marine organisms by connecting and sustaining existing populations and colonizing new habitats. Calcified larvae are typically denser than seawater and rely on swimming to navigate vertically structured water columns. Larval sand dollars Dendraster excentricus have calcified skeletal rods supporting their bodies, and propel themselves with ciliated bands looped around projections called arms. Ciliated bands are also used in food capture, and filtration rate is correlated with band length. As a result, swimming and feeding performance are highly sensitive to morphological changes. When reared at an elevated PCO2 level (1000 ppm), larval sand dollars developed significantly narrower bodies at four and six-arm stages. Morphological changes also varied between four observed maternal lineages, suggesting within-population variation in sensitivity to changes in PCO2 level. Despite these morphological changes, PCO2 concentration alone had no significant effect on swimming speeds. However, acidified larvae had significantly smaller larval stomachs and bodies, suggesting reduced feeding performance. Adjustments to larval morphologies in response to ocean acidification may prioritize swimming over feeding, implying that negative consequences of ocean acidification are carried over to later developmental stages.

(Table 3, Page 417) Table 3. The concentrations of Zn, Cu, Pb, Cd, Ni, Co, Ag, Mn and Fe in a soluble in 1M HCl fraction of ferromanganese nodules of Slupsk Furrow in the southern Baltic sea

The concentration of Zn, Cu, Pb, Cd, Ni, Co, Ag, Mn, Fe, Ca, Mg, K and Na in molluscs Macoma balthica, Mya arenaria, Cardium glaucum, Mytilus edulis and Astarte borealis from the southern Baltic was determined. The surface sediments and ferromanganese concretions associated with the molluscs were also analysed for concentration of these metals. Species- and region-dependent differences in the metal levels of the organisms were observed. The properties of molluscs analysed which have a tendency toward elevated biological tolerance of selected trace metals were specified. The interelement relationship between metal concentrations in the soft tissue and the shell was estimated and was discussed.

Colonialism, political unconscious and cognitive mapping in the space of the film "Captain Phillips"

The purpose of this article has been made through a Marxist analysis of the US film "Captain Phillips" (PaulGreengrass, 2013), based on a true story. I have found how the evolution of capitalism in the West continuesto consolidate the belief reified in a historical and geographical superiority of the political and socioeconomicwestern models regarding Africa and Asia lowers models. At the same time, through categories like dialecticalmaterialism, criticism of diffusionist theory and application of cognitive mapping to large geopoliticalspaces located in most poor areas of the world, I have realized a remark about currently being articulatingthe political unconscious of working class in rich countries and the poor in poor countries, establishing arelationship between the ideological representation that takes an individual from his historical reality (ona scale that moves from local to global), and how he has developed a mental ability to escape of the responsibilityto make a critical review of what's happening around him in all areas. Finally, through physicalspace captured in the film, I have realized a materialist critique of globalized business process that takesplace through the carriage of goods, outlining spatial and cognitively limits of the mentality of our time, bothamong "winners"as among the "losers", based on the spatial movement of capital.

Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

Individual-based modelling of the development and transport of a Karenia mikimotoi bloom on the North-West European continental shelf

In 2006, a large and prolonged bloom of the dinoflagellate Karenia mikimotoi occurred in Scottish coastal waters, causing extensive mortalities of benthic organisms including annelids and molluscs and some species of fish ( Davidson et al., 2009). A coupled hydrodynamic-algal transport model was developed to track the progression of the bloom around the Scottish coast during June–September 2006 and hence investigate the processes controlling the bloom dynamics. Within this individual-based model, cells were capable of growth, mortality and phototaxis and were transported by physical processes of advection and turbulent diffusion, using current velocities extracted from operational simulations of the MRCS ocean circulation model of the North-west European continental shelf. Vertical and horizontal turbulent diffusion of cells are treated using a random walk approach. Comparison of model output with remotely sensed chlorophyll concentrations and cell counts from coastal monitoring stations indicated that it was necessary to include multiple spatially distinct seed populations of K. mikimotoi at separate locations on the shelf edge to capture the qualitative pattern of bloom transport and development. We interpret this as indicating that the source population was being transported northwards by the Hebridean slope current from where colonies of K. mikimotoi were injected onto the continental shelf by eddies or other transient exchange processes. The model was used to investigate the effects on simulated K. mikimotoi transport and dispersal of: (1) the distribution of the initial seed population; (2) algal growth and mortality; (3) water temperature; (4) the vertical movement of particles by diurnal migration and eddy diffusion; (5) the relative role of the shelf edge and coastal currents; (6) the role of wind forcing. The numerical experiments emphasized the requirement for a physiologically based biological model and indicated that improved modelling of future blooms will potentially benefit from better parameterisation of temperature dependence of both growth and mortality and finer spatial and temporal hydrodynamic resolution.

The role of coccolithophore calcification in bioengineering their environment.

Coccolithophorids are enigmatic plankton that produce calcium carbonate coccoliths, which over geological time have buried atmospheric CO2 into limestone, changing both the atmosphere and geology of the Earth. However, the role of coccoliths for the proliferation of these organisms remains unclear; suggestions include roles in anti-predation, enhanced photosynthesis and sun-screening. Here we test the hypothesis that calcification stabilizes the pH of the seawater proximate to the organisms, providing a level of acidification countering the detrimental basification that occurs during net photosynthesis. Such bioengineering provides a more stable pH environment for growth and fits the empirical evidence for changes in rates of calcification under different environmental conditions. Under this scenario, simulations suggest that the optimal production ratio of inorganic to organic particulate C (PIC : POCprod) will be lower (by approx. 20%) with ocean acidification and that overproduction of coccoliths in a future acidified ocean, where pH buffering is weaker, presents a risk to calcifying cells.