Ecological modelling of the phytoplankton dynamics in the northern Gulf of Aqaba (Red Sea)

The Gulf of Aqaba represents a small scale, easy to access, regional analogue of larger oceanic oligotrophic systems. In this Gulf, the seasonal cycles of stratification and mixing drives the seasonal phytoplankton dynamics. In summer and fall, when nutrient concentrations are very low, Prochlorococcus and Synechococcus are more abundant in the surface water. This two populations are exposed to phosphate limitation. During winter mixing, when nutrient concentrations are high, Chlorophyceae and Cryptophyceae are dominant but scarce or absent during summer. In this study it was tried to develop a simulation model based on historical data to predict the phytoplankton dynamics in the northern Gulf of Aqaba. The purpose is to understand what forces operate, and how, to determine the phytoplankton dynamics in this Gulf. To make the models data sampled in two different sampling station (Fish Farm Station and Station A) were used. The data of chemical, biological and physical factors, are available from 14th January 2007 to 28th December 2009. The Fish Farm Station point was near a Fish Farm that was operational until 17th June 2008, complete closure date of the Fish Farm, about halfway through the total sampling time. The Station A sampling point is about 13 Km away from the Fish Farm Station. To build the model, the MATLAB software was used (version 7.6.0.324 R2008a), in particular a tool named Simulink. The Fish Farm Station models shows that the Fish Farm activity has altered the nutrient concentrations and as a consequence the normal phytoplankton dynamics. Despite the distance between the two sampling stations, there might be an influence from the Fish Farm activities also in the Station A ecosystem. The models about this sampling station shows that the Fish Farm impact appears to be much lower than the impact in the Fish Farm Station, because the phytoplankton dynamics appears to be driven mainly by the seasonal mixing cycle.

N-Heterocyclic carbene complexes of silver, rhodium and iron: structures, dynamics and catalysis

The research performed in the framework of this Master Thesis has been directly inspired by the recent work of an organometallic research group led by Professor Maria Cristina Cassani on a topic related to the structures, dynamics and catalytic activity of N-heterocyclic carbene-amide rhodium(I) complexes1. A series of [BocNHCH2CH2ImR]X (R = Me, X = I, 1a’; R = Bz, X = Br, 1b’; R = trityl, X = Cl, 1c’) amide-functionalized imidazolium salts bearing increasingly bulky N-alkyl substituents were synthetized and characterized. Subsequently, these organic precursors were employed in the synthesis of silver(I) complexes as intermediate compounds on a way to rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl, R = Me (3a’), R = Bz (3b’), R = trityl (3c’); X = I, R = Me (4a’)). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. However, while the rotation barriers calculated for the complexes in which R = Me, Bz (3a’,b’ and 4a) matched the experimental values, this was not true in the trityl case 3c’, where the experimental value was very similar to that obtained for compound 3b’ and much smaller with respect to the calculated one. In addition, the energy barrier derived for 3c’ from line shape simulation showed a strong dependence on the temperature, while the barriers measured for 3a’,b’ did not show this effect. In view of these results and in order to establish the reasons for the previously found inconsistency between calculated and experimental thermodynamic data, the first objective of this master thesis was the preparation of a series of rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-benzyl-3-R-imidazolin-2-ylidene; X = Cl, R = Me, Bz, trityl, tBu), containing the benzyl substituent as a chiral probe, followed by full characterization. The second objective of this work was to investigate the catalytic activity of the new rhodium compounds in the hydrosilylation of terminal alkynes for comparison purposes with the reported complexes. Another purpose of this work was to employ the prepared N-heterocyclic ligands in the synthesis of iron(II)-NHC complexes.

The coupling between electron transfer and Protein/Solvent Dynamics in Photosynthetic Reaction Centers: Spectroscopic Studies in Amorphous Matrices

We investigated at the molecular level protein/solvent interactions and their relevance in protein function through the use of amorphous matrices at room temperature. As a model protein, we used the bacterial photosynthetic reaction center (RC) of Rhodobacter sphaeroides, a pigment protein complex which catalyzes the light-induced charge separation initiating the conversion of solar into chemical energy. The thermal fluctuations of the RC and its dielectric conformational relaxation following photoexcitation have been probed by analyzing the recombination kinetics of the primary charge-separated (P+QA-) state, using time resolved optical and EPR spectroscopies. We have shown that the RC dynamics coupled to this electron transfer process can be progressively inhibited at room temperature by decreasing the water content of RC films or of RC-trehalose glassy matrices. Extensive dehydration of the amorphous matrices inhibits RC relaxation and interconversion among conformational substates to an extent comparable to that attained at cryogenic temperatures in water-glycerol samples. An isopiestic method has been developed to finely tune the hydration level of the system. We have combined FTIR spectral analysis of the combination and association bands of residual water with differential light-minus-dark FTIR and high-field EPR spectroscopy to gain information on thermodynamics of water sorption, and on structure/dynamics of the residual water molecules, of protein residues and of RC cofactors. The following main conclusions were reached: (i) the RC dynamics is slaved to that of the hydration shell; (ii) in dehydrated trehalose glasses inhibition of protein dynamics is most likely mediated by residual water molecules simultaneously bound to protein residues and sugar molecules at the protein-matrix interface; (iii) the local environment of cofactors is not involved in the conformational dynamics which stabilizes the P+QA-; (iv) this conformational relaxation appears to be rather delocalized over several aminoacidic residues as well as water molecules weakly hydrogen-bonded to the RC.

The Influence of Baseline Metabolic Rate and Exercise Training on Cardio-Respiratory Dynamics

Speeding the VO2 kinetics results in a reduction of the O2 deficit. Two factors might determine VO2 kinetics: oxygen delivery to muscle (Tschakovsky and Hughson 1999) and a muscle 'metabolic inertia' (Grassi et al. 1996). Therefore, in study 1 we investigated VO2 kinetics and cardiovascular system adaptations during step exercise transitions in different regions of the moderate domain. In study 2 we investigated muscle oxygenation and cardio-pulmonary adaptations during step exercise tests before, after and over a period of training. Study 1 methods: Seven subjects (26 ± 8 yr; 176 ± 5 cm; 69 ± 6 kg) performed 4 types of step transition from rest (0-50W; 0-100W) or elevate baseline (25-75W; 25-125W). GET and VO2max were assessed before testing. O2 uptake and were measured during testing. Study 2 methods: 10 subjects (25 ± 4 yr; 175 ± 9 cm; 71 ± 12 kg) performed a step transition test (0 to 100 W) before, after and during 4 weeks of endurance training (ET). VO2max and GET were assessed before and after of ET (40 minutes, 3 times a week, 60% O2max). VO2 uptake, Q and deoxyheamoglobin were measured during testing. Study 1 results: VO2 τ and the functional gain were slower in the upper regions of the moderate domain. Q increased more abruptly during rest to work condition. Q τ was faster than VO2 τ for each exercise step. Study 2 results: VO2 τ became faster after ET (25%) and particularly after 1 training session (4%). Q kinetics changed after 4 training sessions nevertheless it was always faster than VO2 τ. An attenuation in ∆[HHb] /∆VO2 was detectible. Conclusion: these investigations suggest that muscle fibres recruitment exerts a influence on the VO2 response within the moderate domain either during different forms of step transition or following ET.

Identity dynamics and the emergence of new organizational arrangements: A multi-level study

Organizational and institutional scholars have advocated the need to examine how processes originating at an individual level can change organizations or even create new organizational arrangements able to affect institutional dynamics (Chreim et al., 2007; Powell & Colyvas, 2008; Smets et al., 2012). Conversely, research on identity work has mainly investigated the different ways individuals can modify the boundaries of their work in actual occupations, thus paying particular attention to ‘internal’ self-crafting (e.g. Wrzesniewski & Dutton, 2001). Drawing from literatures on possible and alternative self and on positive organizational scholarship (e.g., Obodaru, 2012; Roberts & Dutton, 2009), my argument is that individuals’ identity work can go well beyond the boundaries of internal self-crafting to the creation of new organizational arrangements. In this contribution I analyze, through multiple case studies, healthcare professionals who spontaneously participated in the creation of new organizational arrangements, namely health structures called Community Hospitals. The contribution develops this form of identity work by building a grounded model. My findings disclose the process that leads from the search for the enactment of different self-concepts to positive identities, through the creation of a new organizational arrangement. I contend that this is a particularly complex form of collective identity work because it requires, to be successful, concerted actions of several internal, external and institutional actors, and it also requires balanced tensions that – at the same time - enable individuals’ aspirations and organizational equilibrium. I name this process organizational collective crafting. Moreover I inquire the role of context in supporting the triggering power of those unrealized selves. I contribute to the comprehension of the consequences of self-comparisons, organizational identity variance, and positive identity. The study bears important insights on how identity work originating from individuals can influence organizational outcomes and larger social systems.

Dynamics of small interfering RNA - FRET based integrity measurements of siRNA in the cuvette & inside cells

RNAi ist ein bedeutendes Werkzeug zur Funktionsanalyse von Genen und hat großes Potential für den Einsatz in der Therapie. Obwohl effiziente Knockdowns in der Zellkultur erzielt werden, erweist sich eine in vivo Anwendung als schwierig. Die großen Hürden sind dabei der Transport der siRNA ins Zielgewebe und deren voranschreitende Degradierung.rnMarkierte siRNA kann sowohl zur eigenen Integritätsmessung als auch zur Lokalisierung verwendet werden. Zwei Farbstoffe an den jeweiligen 3’- bzw. -5’-Enden des Sense- bzw. Antisense-Stranges erzeugen ein robustes FRET-System (Hirsch et al. 2012). Das Verhältnis von FRET- zu Donor-Signal, das R/G-Ratio, dient zur sensitiven Klassifizierung des Integritätslevels einer siRNA Probe (Järve et al. 2007; Hirsch et al. 2011; Kim et al. 2010). Mit diesem System kann eine Degradierung von weniger als 5 % in der Küvette und in Zellen nachgewiesen werden.rnDie vorliegende Arbeit beschäftigt sich mit der Evaluierung von potentiellen FRET Farbstoffpaaren hinsichtlich deren Eignung für in vitro und in vivo Anwendung. Verschiedenste FRET-Paare, die das gesamte sichtbare Spektrum abdecken, wurden evaluiert und ermöglichen nun die Auswahl eines geeigneten Paares für die jeweilige Anwendung oder Kombination mit anderen Farbstoffen.rnMit Hilfe von Alexa555/Atto647N siRNA wurde ein erfolgreicher Einschluss von siRNA in Liposomen beobachtet. Eine anschließende Evaluierung der RNase-Protektion ergab für Liposomen, Nanohydrogele und kationische Peptide hervorragende protektive Eigenschaften. Basierend auf den Ergebnisse können diese und andere Transportsysteme nun für eine zelluläre Aufnahme optimiert werden.rnAtto488/Atto590 zeigte die besten Eigenschaften für Echtzeit-Integritätsmessungen in der Lebendzellmikroskopie. Verringerte Bleicheigenschaften und minimaler spektraler “Cross-Talk” ermöglichten es, transfizierte Zellen über einen Zeitraum von bis zu 8 Stunden zu beobachten. Mittels Atto488/Atto590 siRNA wurde die Einschleusung und Freisetzung in Zellen in Echtzeit untersucht. Dabei konnten Freisetzung und Verteilung in einzelnen Zellen beobachtet und analysiert werden. rnAuf eine anfängliche Phase mit hoher Freisetzungsrate folgte eine Phase mit geringerer Rate für den restlichen Beobachtungszeitraum. Die durchschnittliche Verweildauer im Zytosol betrug 24 und 58 Minuten, wobei zwischen lang- und kurzanhaltenden Ereignissen unterschieden werden konnte. Obwohl ein Import von siRNA in den Zellkern beobachtet wurde, konnte kein Schema bzw. genauer Zeitpunkt, in Bezug auf den Transfektionszeitraum für diese Ereignisse bestimmt werden. Die beobachteten Freisetzungsprozesse fanden sporadisch statt und Änderungen in der zellulären Verteilung geschahen innerhalb von wenigen Minuten. Einmal freigesetzte siRNA verschwand mit der Zeit wieder aus dem Zytosol und es blieben nur kleine Aggregate von siRNA mit immer noch geringer Integrität zurück.rn

Dynamics of Bora wind over the Adriatic sea: atmospheric water balance and role of air-sea fluxes and orography

The Bora wind is a mesoscale phenomenon which typically affects the Adriatic Sea basin for several days each year, especially during winter. The Bora wind has been studied for its intense outbreak across the Dinaric Alps. The properties of the Bora wind are widely discussed in the literature and scientific papers usually focus on the eastern Adriatic coast where strong turbulence and severe gust intensity are more pronounced. However, the impact of the Bora wind can be significant also over Italy, not only in terms of wind speed instensity. Depending on the synoptic pressure pattern (cyclonic or anticyclonic Bora) and on the season, heavy snowfall, severe storms, storm surges and floods can occur along the Adriatic coast and on the windward flanks of the Apennines. In the present work five Bora cases that occurred in recent years have been selected and their evolution has been simulated with the BOLAM-MOLOCH model set, developed at ISAC-CNR in Bologna. Each case study has been addressed by a control run and by several sensitivity tests, performed with the purpose of better understanding the role played by air-sea latent and sensible heat fluxes. The tests show that the removal of the fluxes induces modifications in the wind approching the coast and a decrease of the total precipitation amount predicted over Italy. In order to assess the role of heat fluxes, further analysis has been carried out: column integrated water vapour fluxes have been computed along the Italian coastline and an atmospheric water balance has been evaluated inside a box volume over the Adriatic Sea. The balance computation shows that, although latent heat flux produces a significant impact on the precipitation field, its contribution to the balance is relatively minor. The most significant and lasting case study, that of February 2012, has been studied in more detail in order to explain the impressive drop in the total precipitation amount simulated in the sensitivity tests with removed heat fluxes with respect to the CNTRL run. In these experiments relative humidity and potential temperature distribution over different cross-sections have been examined. With respect to the CNTRL run a drier and more stable boundary layer, characterised by a more pronounced wind shear at the lower levels, has been observed to establish above the Adriatic Sea. Finally, in order to demonstrate that also the interaction of the Bora flow with the Apennines plays a crucial role, sensitivity tests varying the orography height have been considered. The results of such sensitivity tests indicate that the propagation of the Bora wind over the Adriatic Sea, and in turn its meteorological impact over Italy, is influenced by both the large air-sea heat fluxes and the interaction with the Apennines that decelerate the upstream flow.

Active processes, morphology, and dynamics of icy debris fans: Landform evolution along rapidly degrading escarpments in alpine regions undergoing recent deglaciation

In the past few decades the impacts of climate warming have been significant in alpine glaciated regions. Many valley glaciers formerly linked as distributary glaciers to high-level icecaps have decoupled at their icefalls, exposing major escarpments and generating a suite of dynamic landforrns dominated by mass wasting. Ice-dominated landforms, here termed icy debris fans, develop rapidly by ice avalanching, rockfall, and icy debris flow. Field-based reconnaissance studies at two alpine settings, the Wrangell Mountains of Alaska and the Southern Alps of New Zealand, provide a preliminary morphogenetic model of spatial and temporal evolution of icy debris fans in a range of alpine settings. The influence of these processes on landform evolution is largely unrecognized in the literature dealing with post-glacial landform adjustment known as the paraglacial. A better understanding of these dynamic processes will be increasingly important because of the extreme geohazards characterizing these areas. Our field studies show that after glacier decoupling, icy debris fans begin to form along the base of bedrock escarpments at the mouths of catchments and prograde over valley glaciers. The presence of a distinct catchment, apex, and fan morphology distinguishes these landforms from other landforms common in periglacial hillslope settings receiving abundant clastic debris and ice. Ice avalanching is the most abundant process involved in icy debris fan formation. Fans developed below weakly incised catchments are dominated by ice avalanching and are composed primarily of ice with minor lithic detritus. Typically, avalanches fall into the fan catchments where sediments transform into grainflows that flow onto the fans. Once on the fans, avalanche deposits ablate rapidly, flattening and concentrating lithic fragments at the surface. Icy debris fans may become thick enough to become glaciers with splay crevasse systems. Fans developed below larger, more complex catchments are composed of higher proportions of lithic detritus resulting from temporary storage of ice and lithic detritus deposits within the catchment. Episodic outbursts of meltwater from the icecap may mix with the stored sediments and mobilize icy debris flows (mixture of ice and lithic clasts) onto the fans. Our observations indicate that the entire evolutionary cycle of icy debris fans probably occurs during an early paraglacial interval (i.e., decades to 100 years). Observations comparing avalanche frequency, volume, and fan morphologic evolution at the Alaska site between 2006 and 2010 illustrate complex response between icy debris fans even within the same cirque - where one fan may be growing while others are downwasting because of differences in ice supply controlled by their respective catchments and icecap contributions. As ice supply from the icecap diminishes through time, icy debris fans rapidly downwaste and eventually evolve into talus cones that receive occasional but ephemeral ice avalanches.

Reconstructing Iron Age Community Dynamics in Eskisehir Province, Central Turkey

Current understanding of the Iron Age polity of Phrygia in Central Anatolia is primarily based on excavations and survey in the region of the Phrygian capital of Gordion. In order to expand our knowledge of the Phrygian polity, we assess the scale and nature of Iron Age communities in the western (EskiAYehir) region of Phrygia. We address the challenge of interpreting ceramics derived from large-scale archaeological survey by utilizing Neutron Activation Analysis (NAA) of ceramics from 12 sites across the region collected by the EskiAYehir archaeological survey project as well as an excavated assemblage from Aar Hoyuk. While the uniformity in ceramic technology and styles suggest the region is part of the larger Phrygian community, NAA results reveal that (a) ceramic production was regionally highly localized with limited evidence of standardization during the Iron Age and (b) based on evidence of community interaction it is possible to establish a partial chronological sequence of development. These results have implications not only for understanding the internal dynamics within the Phrygian core but also for developing a methodology for comparing ancient polities using commensurate units of interacting communities. The present study is part of the larger Anatolian Iron Age Ceramics project (http://www.une.edu.au/a-ia).

Cultural Dynamics and Ceramic Resource Use at Late Bronze Age/Early Iron Age Troy, Northwestern Turkey

Changes in resource use over time can provide insight into technological choice and the extent of long-term stability in cultural practices. In this paper we re-evaluate the evidence for a marked demographic shift at the inception of the Early Iron Age at Troy by applying a robust macroscale analysis of changing ceramic resource use over the Late Bronze and Iron Age. We use a combination of new and legacy analytical datasets (NAA and XRF), from excavated ceramics, to evaluate the potential compositional range of local resources (based on comparisons with sediments from within a 10 km site radius). Results show a clear distinction between sediment-defined local and non-local ceramic compositional groups. Two discrete local ceramic resources have been previously identified and we confirm a third local resource for a major class of EIA handmade wares and cooking pots. This third source appears to derive from a residual resource on the Troy peninsula (rather than adjacent alluvial valleys). The presence of a group of large and heavy pithoi among the non-local groups raises questions about their regional or maritime origin. (C) 2012 Elsevier Ltd. All rights reserved.

Two patterns of adipokine and other biomarker dynamics in a long-term weight loss intervention

Long-term dietary intervention frequently induces a rapid weight decline followed by weight stabilization/regain. Here, we sought to identify adipokine biomarkers that may reflect continued beneficial effects of dieting despite partial weight regain.

Self-organised transients in a neural mass model of epileptogenic tissue dynamics

Stimulation of human epileptic tissue can induce rhythmic, self-terminating responses on the EEG or ECoG. These responses play a potentially important role in localising tissue involved in the generation of seizure activity, yet the underlying mechanisms are unknown. However, in vitro evidence suggests that self-terminating oscillations in nervous tissue are underpinned by non-trivial spatio-temporal dynamics in an excitable medium. In this study, we investigate this hypothesis in spatial extensions to a neural mass model for epileptiform dynamics. We demonstrate that spatial extensions to this model in one and two dimensions display propagating travelling waves but also more complex transient dynamics in response to local perturbations. The neural mass formulation with local excitatory and inhibitory circuits, allows the direct incorporation of spatially distributed, functional heterogeneities into the model. We show that such heterogeneities can lead to prolonged reverberating responses to a single pulse perturbation, depending upon the location at which the stimulus is delivered. This leads to the hypothesis that prolonged rhythmic responses to local stimulation in epileptogenic tissue result from repeated self-excitation of regions of tissue with diminished inhibitory capabilities. Combined with previous models of the dynamics of focal seizures this macroscopic framework is a first step towards an explicit spatial formulation of the concept of the epileptogenic zone. Ultimately, an improved understanding of the pathophysiologic mechanisms of the epileptogenic zone will help to improve diagnostic and therapeutic measures for treating epilepsy.

Uncovering the dynamics of cardiac systems using stochastic pacing and frequency domain analyses

Alternans of cardiac action potential duration (APD) is a well-known arrhythmogenic mechanism which results from dynamical instabilities. The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers. However, experiments have shown that such markers are not always accurate for the prediction of alternans. Using a mathematical ventricular cell model known to exhibit unstable dynamics of both membrane potential and Ca2+ cycling, we demonstrate that an accurate marker can be obtained by pacing at cycle lengths (CLs) varying randomly around a basic CL (BCL) and by evaluating the transfer function between the time series of CLs and APDs using an autoregressive-moving-average (ARMA) model. The first pole of this transfer function corresponds to the eigenvalue (λalt) of the dominant eigenmode of the cardiac system, which predicts that alternans occurs when λalt≤−1. For different BCLs, control values of λalt were obtained using eigenmode analysis and compared to the first pole of the transfer function estimated using ARMA model fitting in simulations of random pacing protocols. In all versions of the cell model, this pole provided an accurate estimation of λalt. Furthermore, during slow ramp decreases of BCL or simulated drug application, this approach predicted the onset of alternans by extrapolating the time course of the estimated λalt. In conclusion, stochastic pacing and ARMA model identification represents a novel approach to predict alternans without making any assumptions about its ionic mechanisms. It should therefore be applicable experimentally for any type of myocardial cell.