Coccosphere geometry measurements from culture experiments on the coccolithophore species Calcidiscus leptoporus, Calcidiscus quadriperforatus and Helicosphaera carteri

Coccolithophores are a key phytoplankton group that exhibit remarkable diversity in their biology, ecology, and calcitic exoskeletons (coccospheres). An understanding of the physiological processes that underpin coccosphere architecture is essential for maximizing the information that can be retrieved from their extensive fossil record. Using culturing experiments on four modern species from three long-lived families, we investigate how coccosphere architecture responds to population shifts from rapid (exponential) to slowed (stationary) growth phases as nutrients become depleted. These experiments reveal statistical differences in cell size and the number of coccoliths per cell between these two growth phases, specifically that cells in exponential-phase growth are typically smaller with fewer coccoliths, whereas cells experiencing growth-limiting nutrient depletion have larger coccosphere sizes and greater numbers of coccoliths per cell. Although the exact numbers are species-specific, these growth-phase shifts in coccosphere geometry are common to four different coccolithophore families (Calcidiscaceae, Coccolithaceae, Isochrysidaceae, Helicosphaeraceae), demonstrating that this is a core physiological response to nutrient depletion across a representative diversity of this phytoplankton group. Polarised light microscopy was used for all coccosphere geometry measurements.

Mesocosm experiment on warming and acidification effects in 2012: Microzooplankton data

Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.

Seawater carbonate chemistry and biological processes of coccolithophore (Gephyrocapsa oceanica and Coccolithus pelagicus ssp. braarudii) during experiments, 2011

All species of coccolithophore appear to respond to perturbations of carbonate chemistry in a different way. Here, we show that the degree of malformation, growth rate and stable isotopic composition of organic matter and carbonate produced by two contrasting species of coccolithophore (Gephyrocapsa oceanica and Coccolithus pelagicus ssp. braarudii) are indicative of differences between their photosynthetic and calcification response to changing DIC levels (ranging from ~1100 to ~7800 µmol/kg) at constant pH (8.13 ± 0.02). Gephyrocapsa oceanica thrived under all conditions of DIC, showing evidence of increased growth rates at higher DIC, but C. braarudii was detrimentally affected at high DIC showing signs of malformation, and decreased growth rates. The carbon isotopic fractionation into organic matter and the coccoliths suggests that C. braarudii utilises a common internal pool of carbon for calcification and photosynthesis but G. oceanica relies on independent supplies for each process. All coccolithophores appear to utilize bicarbonate as their ultimate source of carbon for calcification resulting in the release of a proton. But, we suggest that this proton can be harnessed to enhance the supply of CO2(aq) for photosynthesis either from a large internal HCO3- pool which acts as a pH buffer (C. braarudii), or pumped externally to aid the diffusive supply of CO2 across the membrane from the abundant HCO3- (G. oceanica), likely mediated by an internal and external carbonic anhydrase respectively. Our simplified hypothetical spectrum of physiologies may provide a context to understand different species response to changing pH and DIC, the species-specific delta p and calcite "vital effects", as well as accounting for geological trends in coccolithophore cell size.

Asymmetric hydrogen flame in a heated micro-channel: role of Darrieus-Landau and thermal-diffusive instabilities

Present work examines numerically the asymmetric behavior of hydrogen/air flame in a micro-channel subjected to a non-uniform wall temperature distribution. A high resolution (with cell size of 25 μm × 25 μm) of two-dimensional transient Navier–Stokes simulation is conducted in the low-Mach number formulation using detailed chemistry evolving 9 chemical species and 21 elementary reactions. Firstly, effects of hydrodynamic and diffusive-thermal instabilities are studied by performing the computations for different Lewis numbers. Then, the effects of preferential diffusion of heat and mass transfer on the asymmetric behavior of the hydrogen flame are analyzed for different inlet velocities and equivalence ratios. Results show that for the flames in micro-channels, interactions between thermal diffusion and molecular diffusion play major role in evolution of a symmetric flame into an asymmetric one. Furthermore, the role of Darrieus–Landau instability found to be minor. It is also found that in symmetric flames, the Lewis number decreases behind the flame front. This is related to the curvature of flame which leads to the inclination of thermal and mass fluxes. The mass diffusion vectors point toward the walls and the thermal diffusion vectors point toward the centerline. Asymmetric flame is observed when the length of flame front is about 1.1–1.15 times of the channel width.

Structure et biogéographie des communautés de pico- et de nanoeurcaryotes pélagiques autour de l'archipel du Svalbard

L’Arctique s’est réchauffé rapidement et il y a urgence d’anticiper les effets que cela pourrait avoir sur les protistes à la base de la chaîne alimentaire. Le phytoplancton de l’Océan Arctique inclut les pico- et nano-eucaryotes (0.45-10 μm diamètre de la cellule) et plusieurs de ceux-ci sont des écotypes retrouvés seulement dans l’Arctique alors que d’autres sont introduits des océans plus méridionaux. Alors que les océans tempérés pénètrent dans l’Arctique, il devient pertinent de savoir si ces communautés microbiennes pourraient être modifiées. L’archipel du Svalbard est une région idéale pour observer la biogéographie des communautés microbiennes sous l’influence de processus polaires et tempérés. Bien qu’ils soient géographiquement proches, les régions côtières entourant le Svalbard sont sujettes à des intrusions alternantes de masses d’eau de l’Arctique et de l’Atlantique en plus des conditions locales. Huit sites ont été échantillonnés en juillet 2013 pour identifier les protistes selon un gradient de profondeur et de masses d’eau autour de l’archipel. En plus des variables océanographiques standards, l’eau a été échantillonnée pour synthétiser des banques d’amplicons ciblant le 18S SSU ARNr et son gène pour ensuite être séquencées à haut débit. Cinq des sites d’étude avaient de faibles concentrations de chlorophylle avec des compositions de communauté post-efflorescence dominée par les dinoflagellés, ciliés, des alvéolés parasites putatifs, chlorophycées et prymnesiophytées. L’intrusion des masses d’eau et les conditions environnementales locales étaient corrélées avec la structure des communautés ; l’origine de la masse d’eau contribuant le plus à la distance phylogénétique des communautés microbiennes. Au sein de trois fjords, de fortes concentrations de chlorophylle sous-entendaient des activités d’efflorescence. Un fjord était dominé par Phaeocystis, un deuxième par un clade arctique identifié comme un Pelagophyceae et un troisième par un assemblage mixte. En général, un signal fort d’écotypes liés à l’Arctique prédominait autour du Svalbard.

Dinoflagelados (Peridiniales, Prorocentrales) do microplâncton na plataforma continental e talude do extremo sul do Brasil (inverno 2005, verão 2007)

This study aimed at identifying morpho-species of microplankton dinoflagellates (> 20 μm) of the order Peridiniales and Prorocentrales off Santa Marta Grande Cape, CSMG (SC, 28º 40’ S) and Albardão-Chui, AC ( r S, 34º 40’ S) during oceanographic cruises conducted in winter 2005 and summer 2007. Plankton samples were obtained by vertical net (mesh size 20 μm) hauls preserved with formaldehyde 4% and analyzed using the inverted microscope equipped with a digital camera. The identification of Peridiniales species was based on the number and morphology of thecal plates enhanced with Calco Fluor White M r 2 whenever necessary and the identification of Prorocentrales was based on cell size, shape, presence of apical processes, pore pattern and marks at the intercalary band. We identified 25 species, including Protoperidinium (11), Prorocentrum (6), Corythodinium (3), Podolampas (2), Oxytoxum (2) and Heterocapsa (1). Prorocentrum species were widely distributed on the continental shelf of southern Brazil, while Peridiniales species were mainly found off Albardão-Chui during winter, especially under the influence of the plume of La Plata River. Oxytoxum milneri was the first time recorded in southern Brazil, while Protoperidinium cassum var. cassum , P. curtipes and Heterocapsa triquetra , were first registered in Brazil.

Bioremediation of piggery effluents using Scenedesmus Obliquus microalga [Resumo]

Effluents from intensive pig farms present high nutrient concentration, mainly ammonium, contributing to water eutrophication and pollution. Microalgae ability to deplete inorganic nutrients makes them an efficient effluent bioremediation tool. Scenedesmus obliquus was grown in piggery effluent (without any pretreatment) diluted with tap water at 5%v/v (187±25mg/L N-NH4+) and compared with growth in synthetic Bristol media. A 21-days trial was performed in 1L bubble-column reactors illuminated by fluorescent and LED lamps(3klux). Microalgae growth was monitored through OD540nm, dry weight and Chlorophyll content and also by flow cytometry in terms of autofluorescence read in FL3 channel (>670 nm), cell size (FSC), internal complexity (SSC) and cell membrane integrity (PI). S. obliquus cells have grown slower in pig effluent (mmax=0.13-19d-1) than in Bristol media (mmax=0.46-0.50d-1) although after 15 days the biomass productivity observed for the pig waste cultivation, operated under LED (0.127gL-1d-1) was similar to those attained for the Bristol media after 8 and 12 days (0.130 and 0.129 gL-1d-1 using Fluorescent and LED lights, respectively). The Chlorophyll content was correlated to FL3 autofluorescence, with R2>0.97 for Bristol and R2>0.92 for pig waste cultures. Regarding cell size and complexity, Bristol cultures did not show significant differences along time, while cells grown on pig waste increased, attaining FSC and SSC values similar to those observed for Bristol cultures. However, pig waste led to higher percentage of cells with permeabilised membrane (up to 18%) than Bristol cultures (7%). For pig waste experiments, ammonium removal rates were 95% with final values within legal limits. S. obliquus cultivations proved to be an efficient system for direct piggery effluent bioremediation, attaining biomass productivities similar to those obtained in synthetic media. Using LED lighting enables to reduce the energy consumption while maintaining microalgae growth and bioremediation performance. Scale-up to an outdoor 150L photobioreactor is underway.

Some parameters that affect CDMA capacity analysis. Results using GIS based simulation

In previous papers we describe a model for capacity analysis in CDMA systems using DC-Cell, a GIS based planning tool developed at Universidad Politecnica de Valencia, and MATLAB. We show some initial results of that model, and now, we are exploring different parameters like cell size, proximity between cells, number of cells in the system and “clustering” CDMA in order to improve the planning process for third generation systems. In this paper we show the results for variations of some of these parameters, specifically the cell size and number of cells. In CDMA systems is quite common to suppose only one carrier frequency for capacity estimation, and it is intuitive to think that for more base stations, mean more users. However the multiple access interference problem in CDMA systems could establish a limit for that supposition in a similar way that occurs in FDMA and TDMA systems.

Development of novel therapeutics and in vitro models for spinal cord injury

Spinal cord injury (SCI) is a devastating condition, which results from trauma to the cord, resulting in a primary injury response which leads to a secondary injury cascade, causing damage to both glial and neuronal cells. Following trauma, the central nervous system (CNS) fails to regenerate due to a plethora of both intrinsic and extrinsic factors. Unfortunately, these events lead to loss of both motor and sensory function and lifelong disability and care for sufferers of SCI. There have been tremendous advancements made in our understanding of the mechanisms behind axonal regeneration and remyelination of the damaged cord. These have provided many promising therapeutic targets. However, very few have made it to clinical application, which could potentially be due to inadequate understanding of compound mechanism of action and reliance on poor SCI models. This thesis describes the use of an established neural cell co-culture model of SCI as a medium throughput screen for compounds with potential therapeutic properties. A number of compounds were screened which resulted in a family of compounds, modified heparins, being taken forward for more intense investigation. Modified heparins (mHeps) are made up of the core heparin disaccharide unit with variable sulphation groups on the iduronic acid and glucosamine residues; 2-O-sulphate (C2), 6-O-sulphate (C6) and N-sulphate (N). 2-O-sulphated (mHep6) and N-sulphated (mHep7) heparin isomers were shown to promote both neurite outgrowth and myelination in the SCI model. It was found that both mHeps decreased oligodendrocyte precursor cell (OPC) proliferation and increased oligodendrocyte (OL) number adjacent to the lesion. However, there is a difference in the direct effects on the OL from each of the mHeps; mHep6 increased myelin internode length and mHep7 increased the overall cell size. It was further elucidated that these isoforms interact with and mediate both Wnt and FGF signalling. In OPC monoculture experiments FGF2 treated OPCs displayed increased proliferation but this effect was removed when co-treated with the mHeps. Therefore, suggesting that the mHeps interact with the ligand and inhibit FGF2 signalling. Additionally, it was shown that both mHeps could be partially mediating their effects through the Wnt pathway. mHep effects on both myelination and neurite outgrowth were removed when co-treated with a Wnt signalling inhibitor, suggesting cell signalling mediation by ligand immobilisation and signalling activation as a mechanistic action for the mHeps. However, the initial methods employed in this thesis were not sufficient to provide a more detailed study into the effects the mHeps have on neurite outgrowth. This led to the design and development of a novel microfluidic device (MFD), which provides a platform to study of axonal injury. This novel device is a three chamber device with two chambers converging onto a central open access chamber. This design allows axons from two points of origin to enter a chamber which can be subjected to injury, thus providing a platform in which targeted axonal injury and the regenerative capacity of a compound study can be performed. In conclusion, this thesis contributes to and advances the study of SCI in two ways; 1) identification and investigation of a novel set of compounds with potential therapeutic potential i.e. desulphated modified heparins. These compounds have multiple therapeutic properties and could revolutionise both the understanding of the basic pathological mechanisms underlying SCI but also be a powered therapeutic option. 2) Development of a novel microfluidic device to study in greater detail axonal biology, specifically, targeted axonal injury and treatment, providing a more representative model of SCI than standard in vitro models. Therefore, the MFD could lead to advancements and the identification of factors and compounds relating to axonal regeneration.

Effects of nitrogen limitation on Dunaliella sp.–Alteromonas sp. interactions: from mutualistic to competitive relationships.

Interactions between photosynthetic and non-photosynthetic microorganisms play an essential role in natural aquatic environments and the contribution of bacteria and microalgae to the nitrogen cycle can lead to both competitive and mutualistic relationships. Nitrogen is considered to be, with phosphorus and iron, one of the main limiting nutrients for primary production in the oceans and its availability experiences large temporal and geographical variations. For these reasons, it is important to understand how competitive and mutualistic interactions between photosynthetic and heterotrophic microorganisms are impacted by nitrogen limitation. In a previous study performed in batch cultures, the addition of a selected bacterial strain of Alteromonas sp. resulted in a final biomass increase in the green alga Dunaliella sp. as a result of higher nitrogen incorporation into the algal cells. The present work focuses on testing the potential of the same microalgae–bacteria association and nitrogen interactions in chemostats limited by nitrogen. Axenic and mixed cultures were compared at two dilution rates to evaluate the impact of nitrogen limitation on interactions. The addition of bacteria resulted in increased cell size in the microalgae, as well as decreased carbon incorporation, which was exacerbated by high nitrogen limitation. Biochemical analyses for the different components including microalgae, bacteria, non-living particulate matter, and dissolved organic matter, suggested that bacteria uptake carbon from carbon-rich particulate matter released by microalgae. Dissolved organic nitrogen released by microalgae was apparently not taken up by bacteria, which casts doubt on the remineralization of dissolved organic nitrogen by Alteromonas sp. in chemostats. Dunaliella sp. obtained ammonium-nitrogen more efficiently under lower nitrogen limitation. Overall, we revealed competition between microalgae and bacteria for ammonium when this was in continuous but limited supply. Competition for mineral nitrogen increased with nitrogen limitation. From our study we suggest that competitive or mutualistic relationships between microalgae and bacteria largely depend on the ecophysiological status of the two microorganisms. The outcome of microalgae–bacteria interactions in natural and artificial ecosystems largely depends on environmental factors. Our results indicate the need to improve understanding of the interaction/s between these microbial players

Morphogenesis of the Arabidopsis Shoot Apical Meristem

Phyllotaxis patterns in plants, or the arrangement of leaves and flowers radially around the shoot, have fascinated both biologists and mathematicians for centuries. The current model of this process involves the lateral transport of the hormone auxin through the first layer of cells in the shoot apical meristem via the auxin efflux carrier protein PIN1. Locations around the meristem with high auxin concentration are sites of organ formation and differentiation. Many of the molecular players in this process are well known and characterized. Computer models composed of all these components are able to produce many of the observed phyllotaxis patterns. To understand which parts of this model have a large effect on the phenotype I automated parameter testing and tried many different parameter combinations. Results of this showed that cell size and meristem size should have the largest effect on phyllotaxis. This lead to three questions: (1) How is cell geometry regulated? (2) Does cell size affect auxin distribution? (3) Does meristem size affect phyllotaxis? To answer the first question I tracked cell divisions in live meristems and quantified the geometry of the cells and the division planes using advanced image processing techniques. The results show that cell shape is maintained by minimizing the length of the new wall and by minimizing the difference in area of the daughter cells. To answer the second question I observed auxin patterning in the meristem, shoot, leaves, and roots of Arabidopsis mutants with larger and smaller cell sizes. In the meristem and shoot, cell size plays an important role in determining the distribution of auxin. Observations of auxin in the root and leaves are less definitive. To answer the third question I measured meristem sizes and phyllotaxis patterns in mutants with altered meristem sizes. These results show that there is no correlation between meristem size and average divergence angle. But in an extreme case, making the meristem very small does lead to a switch on observed phyllotaxis in accordance with the model.

Assessment of the spatial variability in Tall wheatgrass forage using LANDSAT 8 satellite imagery to delineate potential management zones

Little information is available on the degree of within-field variability of potential production of Tall wheatgrass (Thinopyrum ponticum) forage under unirrigated conditions. The aim of this study was to characterize the spatial variability of the accumulated biomass (AB) without nutritional limitations through vegetation indexes, and then use this information to determine potential management zones. A 27-×-27-m grid cell size was chosen and 84 biomass sampling areas (BSA), each 2 m(2) in size, were georeferenced. Nitrogen and phosphorus fertilizers were applied after an initial cut at 3 cm height. At 500 °C day, the AB from each sampling area, was collected and evaluated. The spatial variability of AB was estimated more accurately using the Normalized Difference Vegetation Index (NDVI), calculated from LANDSAT 8 images obtained on 24 November 2014 (NDVInov) and 10 December 2014 (NDVIdec) because the potential AB was highly associated with NDVInov and NDVIdec (r (2) = 0.85 and 0.83, respectively). These models between the potential AB data and NDVI were evaluated by root mean squared error (RMSE) and relative root mean squared error (RRMSE). This last coefficient was 12 and 15 % for NDVInov and NDVIdec, respectively. Potential AB and NDVI spatial correlation were quantified with semivariograms. The spatial dependence of AB was low. Six classes of NDVI were analyzed for comparison, and two management zones (MZ) were established with them. In order to evaluate if the NDVI method allows us to delimit MZ with different attainable yields, the AB estimated for these MZ were compared through an ANOVA test. The potential AB had significant differences among MZ. Based on these findings, it can be concluded that NDVI obtained from LANDSAT 8 images can be reliably used for creating MZ in soils under permanent pastures dominated by Tall wheatgrass.

Performance comparison of C-V2X and WAVE protocols for vehicular to infrastructure communications: simulation of the highway use case

The objective of this thesis is the analysis and the study of the various access techniques for vehicular communications, in particular of the C-V2X and WAVE protocols. The simulator used to study the performance of the two protocols is called LTEV2Vsim and was developed by the CNI IEIIT for the study of V2V (Vehicle-to-Vehicle) communications. The changes I made allowed me to study the I2V (Infrastructure-to-Vehicle) scenario in highway areas and, with the results obtained, I made a comparison between the two protocols in the case of high vehicular density and low vehicular density, putting in relation to the PRR (packet reception ratio) and the cell size (RAW, awareness range). The final comparison allows to fully understand the possible performances of the two protocols and highlights the need for a protocol that allows to reach the minimum necessary requirements.

Designing a 161-element Ku-band microstrip reflectarray of variable size patches using an equivalent unit cell waveguide approach

An equivalent unit cell waveguide approach (WGA) to designing 4 multilayer microstrip reflectarray of variable size patches is presented. In this approach, a normal incidence of a plane wave on an infinite periodic array of radiating elements is considered to obtain reflection coefficient phase curves for the reflectarray's elements. It is shown that this problem is equivalent to the problem of reflection of the dominant TEM mode in a waveguide with patches interleaved by layers of dielectric. This waveguide problem is solved using a field matching technique and a method of moments (MoM). Based on this solution, a fast computer algorithm is developed to generate reflection coefficient phase curves for a multilayer microstrip patch reflectarray. The validity of the developed algorithm is tested against alternative approaches and Agilent High Frequency Structure Simulator (HFSS). Having confirmed the validity of the WGA approach, a small offset feed two-layer microstrip patch array is designed and developed. This reflectarray is tested experimentally and shows good performance.

Cell-free reconstitution of vacuole membrane fragmentation reveals regulation of vacuole size and number by TORC1.

Size and copy number of organelles are influenced by an equilibrium of membrane fusion and fission. We studied this equilibrium on vacuoles-the lysosomes of yeast. Vacuole fusion can readily be reconstituted and quantified in vitro, but it had not been possible to study fission of the organelle in a similar way. Here we present a cell-free system that reconstitutes fragmentation of purified yeast vacuoles (lysosomes) into smaller vesicles. Fragmentation in vitro reproduces physiological aspects. It requires the dynamin-like GTPase Vps1p, V-ATPase pump activity, cytosolic proteins, and ATP and GTP hydrolysis. We used the in vitro system to show that the vacuole-associated TOR complex 1 (TORC1) stimulates vacuole fragmentation but not the opposing reaction of vacuole fusion. Under nutrient restriction, TORC1 is inactivated, and the continuing fusion activity then dominates the fusion/fission equilibrium, decreasing the copy number and increasing the volume of the vacuolar compartment. This result can explain why nutrient restriction not only induces autophagy and a massive buildup of vacuolar/lysosomal hydrolases, but also leads to a concomitant increase in volume of the vacuolar compartment by coalescence of the organelles into a single large compartment.