Linking megathrust earthquakes to brittle deformation in a fossil accretionary complex

Seismological data from recent subduction earthquakes suggest that megathrust earthquakes induce transient stress changes in the upper plate that shift accretionary wedges into an unstable state. These stress changes have, however, never been linked to geological structures preserved in fossil accretionary complexes. The importance of coseismically induced wedge failure has therefore remained largely elusive. Here we show that brittle faulting and vein formation in the palaeo-accretionary complex of the European Alps record stress changes generated by subduction-related earthquakes. Early veins formed at shallow levels by bedding-parallel shear during coseismic compression of the outer wedge. In contrast, subsequent vein formation occurred by normal faulting and extensional fracturing at deeper levels in response to coseismic extension of the inner wedge. Our study demonstrates how mineral veins can be used to reveal the dynamics of outer and inner wedges, which respond in opposite ways to megathrust earthquakes by compressional and extensional faulting, respectively.

Coupled human and natural system dynamics as key to the sustainability of Lake Victoria's ecosystem services

East Africa’s Lake Victoria provides resources and services to millions of people on the lake’s shores and abroad. In particular, the lake’s fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria’s system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake’s social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks’ vulnerability to exploitation but reduce society’s vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.

Echinococcus granulosus infection dynamics in livestock of Greece

An epidemiological and molecular survey on the occurrence of Echinococcus hydatid cysts in livestock was conducted in Greece. In total 898 sheep, 483 goats, 38 buffaloes, 273 wild boars and 15 deer were examined and 30.2% (6.45% cyst fertility), 7.86% (3.2% cyst fertility), 42% (7.9% cyst fertility), 1.1% (0% cyst fertility), 0% of them were found infected, respectively. Infection rate in different geographical regions varied between 26.1 and 53.8% (cyst fertility 2.04 and 34.6%) in sheep, 7.33 and 13.3% (cyst fertility 0 and 3.2%) in goats. Genotyping, based on cox1 and nad1 analyses, demonstrated the predominance of E. granulosus s.s. (G1 genotype). The presence of one single genotype-complex within a relatively large spectrum of intermediate host species in Greece indicates the presence of a dominant transmission dog-sheep cycle involving additional host species which may act as disease reservoir for human infections.

Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations

We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution to investigate interaction and binding of α-tochoperol transfer protein (α-TTP) to phosphatidylinositol phosphate lipids (PIPs). Our calculations indicate that enrichment of membranes with such lipids facilitate membrane anchoring. Atomistic models suggest that PIP can be incorporated into the binding cavity of α-TTP and therefore confirm that such protein can work as lipid exchanger between the endosome and the plasma membrane. Comparison of the atomistic models of the α-TTP-PIPs complex with membrane-bound α-TTP revealed different roles for the various basic residues composing the basic patch that is key for the protein/ligand interaction. Such residues are of critical importance as several point mutations at their position lead to severe forms of ataxia with vitamin E deficiency (AVED) phenotypes. Specifically, R221 is main residue responsible for the stabilization of the complex. R68 and R192 exchange strong interactions in the protein or in the membrane complex only, suggesting that the two residues alternate contact formation, thus facilitating lipid flipping from the membrane into the protein cavity during the lipid exchange process. Finally, R59 shows weaker interactions with PIPs anyway with a clear preference for specific phosphorylation positions, hinting a role in early membrane selectivity for the protein. Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP.

Holocene biomass burning and global dynamics of the carbon cycle

Fire regimes have changed during the Holocene due to changes in climate, vegetation, and in human practices. Here, we hypothesise that changes in fire regime may have affected the global CO2 concentration in the atmosphere through the Holocene. Our data are based on quantitative reconstructions of biomass burning deduced from stratified charcoal records from Europe, and South-, Central- and North America, and Oceania to test the fire-carbon release hypothesis. In Europe the significant increase of fire activity is dated ≈6000 cal. yr ago. In north-eastern North America burning activity was greatest before 7500 years ago, very low between 7500–3000 years, and has been increasing since 3000 years ago. In tropical America, the pattern is more complex and apparently latitudinally zonal. Maximum burning occurred in the southern Amazon basin and in Central America during the middle Holocene, and during the last 2000 years in the northern Amazon basin. In Oceania, biomass burning has decreased since a maximum 5000 years ago. Biomass burning has broadly increased in the Northern and Southern hemispheres throughout the second half of the Holocene associated with changes in climate and human practices. Global fire indices parallel the increase of atmospheric CO2 concentration recorded in Antarctic ice cores. Future issues on carbon dynamics relatively to biomass burning are discussed to improve the quantitative reconstructions.

Computational fluid dynamics modelling in cardiovascular medicine.

This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges.

Modeling the Effects of Size on Patch Dynamics of an Inert Tracer

Mesoscale iron enrichment experiments have revealed that additional iron affects the phytoplankton productivity and carbon cycle. However, the role of initial size of fertilized patch in determining the patch evolution is poorly quantified due to the limited observational capability and complex of physical processes. Using a three-dimensional ocean circulation model, we simulated different sizes of inert tracer patches that were only regulated by physical circulation and diffusion. Model results showed that during the first few days since release of inert tracer, the calculated dilution rate was found to be a linear function with time, which was sensitive to the initial patch size with steeper slope for smaller size patch. After the initial phase of rapid decay, the relationship between dilution rate and time became an exponential function, which was also size dependent. Therefore, larger initial size patches can usually last longer and ultimately affect biogeochemical processes much stronger than smaller patches.

The dynamics of calmodulin signaling revealed using optical methods

The Ca2+-binding protein calmodulin (CaM) is a key transducer of Ca2+ oscillations by virtue of its ability to bind Ca 2+ selectively and then interact specifically with a large number of downstream enzymes and proteins. It remains unclear whether Ca2+ -dependent signaling alone can activate the full range of Ca 2+/CaM regulated processes or whether other regulatory schemes in the cell exist that allow specific targeting of CaM to subsets of Ca 2+/CaM binding sites or regions of the cell. Here we investigate the possibility that alterations of the availability of CaM may serve as a potential cellular mechanism for regulating the activation of CaM-dependent targets. By utilizing sensitive optical techniques with high spatial and temporal resolution, we examine the intracellular dynamics of CaM signaling at a resolution previously unattainable. After optimizing and characterizing both the optical methods and fluorescently labeled probes for intracellular measurements, the diffusion of CaM in the cytoplasm of HEK293 cells was analyzed. It was discovered that the diffusion characteristics of CaM are similar to that of a comparably sized inert molecule. Independent manipulation of experimental parameters, including increases in total concentrations of CaM and intracellular Ca2+ levels, did not change the diffusion of CaM in the cytoplasm. However, changes in diffusion were seen when the concentration of Ca2+/CaM-binding targets was increased in conjunction with elevated Ca2+. This indicates that CaM is not normally limiting for the activation of Ca 2+/CaM-dependent enzymes in HEK293 cells but reveals that the ratio of CaM to CaM-dependent targets is a potential mechanism for changing CaM availability. Next we considered whether cellular compartmentalization may act to regulate concentrations of available Ca2+/CaM in hippocampal neurons. We discovered changes in diffusion parameters of CaM under elevated Ca2+ conditions in the soma, neurite and nucleus which suggest that either the composition of cytoplasm is different in these compartments and/or they are composed of unique families of CaM-binding proteins. Finally, we return to the HEK293 cell and for the first time directly show the intracellular binding of CaM and CaMKII, an important target for CaM critical for neuronal function and plasticity. Furthermore, we analyzed the complex binding stoichiometry of this molecular interaction in the basal, activated and autophosphorylated states of CaMKII and determined the impact of this binding on CaM availability in the cell. Overall these results demonstrate that regulation of CaM availability is a viable cellular mechanism for regulating the output of CaM-dependent processes and that this process is tuned to the specific functional needs of a particular cell type and subcellular compartment. ^

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively “simple” individuals. By making simple assumptions about individuals’ decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors’ level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

The role of AKT-mediated phosphorylation in suppression of MAD1 and the development of new approach in protein complex detection

MAX dimerization protein 1 (MAD1) is a basic-helix-loop-helix transcription factors that recruits transcription repressor such as HDAC to suppress target genes transcription. It antagonizes to MYC because the promoter binding sites for MYC are usually also serve as the binding sites for MAD1 so they compete for it. However, the mechanism of the switch between MYC and MAD1 in turning on and off of genes' transcription is obscure. In this study, we demonstrated that AKT-mediated MAD1 phosphorylation inhibits MAD1 transcription repression function. The association between MAD1 and its target genes' promoter is reduced after been phosphorylated by AKT; therefore, consequently, allows MYC to occupy the binding site and activates transcription. Mutation of such phosphorylation site abrogates the inhibition from AKT. In addition, functional assays demonstrated that AKT suppressed MAD1-mediated transcription repression of its target genes hTERT and ODC. Cell cycle and cell growth were also been released from inhibition by MAD1 in the presents of AKT. Taken together, our study suggests that MAD1 is a novel substrate of AKT and AKT-mediated MAD1 phosphorylation inhibits MAD1function; therefore, activates MAD1 target genes expression. ^ Furthermore, analysis of protein-protein interaction is indispensable for current molecular biology research, but multiplex protein dynamics in cells is too complicated to be analyzed by using existing biochemical methods. To overcome the disadvantage, we have developed a single molecule level detection system with nanofluidic chip. Single molecule was analyzed based on their fluorescent profile and their profiles were plotted into 2 dimensional time co-incident photon burst diagram (2DTP). From this 2DTP, protein complexes were characterized. These results demonstrate that the nanochannel protein detection system is a promising tool for future molecular biology. ^

IDENTIFICATION AND ANALYSIS OF A NOVEL ROLE FOR THE TOUSLED-LIKE KINASE IN REGULATING MITOTIC SPINDLE DYNAMICS

Deregulation of kinase activity is one example of how cells become cancerous by evading evolutionary constraints. The Tousled kinase (Tsl) was initially identified in Arabidopsis thaliana as a developmentally important kinase. There are two mammalian orthologues of Tsl and one orthologue in C. elegans, TLK-1, which is essential for embryonic viability and germ cell development. Depletion of TLK-1 leads to embryonic arrest large, distended nuclei, and ultimately embryonic lethality. Prior to terminal arrest, TLK-1-depleted embryos undergo aberrant mitoses characterized by poor metaphase chromosome alignment, delayed mitotic progression, lagging chromosomes, and supernumerary centrosomes. I discovered an unanticipated requirement for TLK-1 in mitotic spindle assembly and positioning. Normally, in the newly-fertilized zygote (P0) the maternal pronucleus migrates toward the paternal pronucleus at the posterior end of the embryo. After pronuclear meeting, the pronuclear-centrosome complex rotates 90° during centration to align on the anteroposterior axis followed by nuclear envelope breakdown (NEBD). However, in TLK-1-depleted P0 embryos, the centrosome-pronuclear complex rotation is significantly delayed with respect to NEBD and chromosome congression, Additionally, centrosome positions over time in tlk-1(RNAi) early embryos revealed a defect in posterior centrosome positioning during spindle-pronuclear centration, and 4D analysis of centrosome positions and movement in newly fertilized embryos showed aberrant centrosome dynamics in TLK-1-depleted embryos. Several mechanisms contribute to spindle rotation, one of which is the anchoring of astral microtubules to the cell cortex. Attachment of these microtubules to the cortices is thought to confer the necessary stability and forces in order to rotate the centrosome-pronuclear complex in a timely fashion. Analysis of a microtubule end-binding protein revealed that TLK-1-depleted embryos exhibit a more stochastic distribution of microtubule growth toward the cell cortices, and the types of microtubule attachments appear to differ from wild-type embryos. Additionally, fewer astral microtubules are in the vicinity of the cell cortex, thus suggesting that the delayed spindle rotation could be in part due to a lack of appropriate microtubule attachments to the cell cortex. Together with recently published biochemical data revealing the Tousled-like kinases associate with components of the dynein microtubule motor complex in humans, these data suggest that Tousled-like kinases play an important role in mitotic spindle assembly and positioning.

Controls of sediment dynamics on the Galician slope reconstructed from three sediment cores (GeoB11035-1, GeoB130206-1, GeoB13071-1)

Controls of sediment dynamics at the Galician continental slope (NW Iberia) during the past 30 ka were reconstructed from three new gravity cores (GeoB11035-1, 130206-1, 13071-1) based on sedimentological (e.g. sortable silt, IRD), micropalaeontological (e.g. coccoliths), geochemical (AMS 14C, XRF) and geophysical (e.g. magnetic susceptibility) diagnostics. The data are consistent with existing regional knowledge that, during marine isotope stages 3-1, variations in detrital input, marine productivity and sea level were the essential drivers of sediment availability on the slope, whereas deep-water current velocities controlled sediment deposition: (1) the period prior to 30 cal ka BP is characterized by minor but systematic variations in various proxies which can be associated with D-O cycles; (2) between 30 and 18 cal ka BP, high detrital input and steady slope-parallel currents led to constant sedimentation; (3) from the LGM until 10 cal ka BP, the shelf-transgressive sea-level rise increased the detrital particle flux; sedimentation was influenced by significantly enhanced deep-water circulation during the Bølling/Allerød, and subsequent slowing during the Younger Dryas; (4) an abrupt and lasting change to hemipelagic sedimentation at ca. 10 cal ka BP was probably due to Holocene warming and decelerated transgression; (5) after 5 cal ka BP, additional input of detrital material to the slope is plausibly linked to the evolution of fine-grained depocentres on the Galician shelf, this being the first report of this close shelf-slope sedimentary linkage off NW Iberia. Furthermore, there is novel evidence of the nowadays strong outer shelf Iberian Poleward Current becoming established at about 15.5 cal ka BP. The data also demonstrate that small-scale morphologic features and local pathways of sediment export from the neighbouring shelf play an important role for sediment distribution on the NW Iberian slope, including a hitherto unknown sediment conduit off the Ría de Arousa. By implication, the impact of local morphology on along- and down-slope sediment dynamics is more complex than commonly considered, and deserves future attention.

Coastal erosion dynamics and storm characteristics of Bykovsky Peninsula

This study investigates the rate of erosion during the 1951-2006 period on the Bykovsky Peninsula, located north-east of the harbour town of Tiksi, north Siberia. Its coastline, which is characterized by the presence of ice-rich sediment (Ice Complex) and the vicinity of the Lena River Delta, retreated at a mean rate of 0.59 m/yr between 1951 and 2006. Total erosion ranged from 434 m of erosion to 92 m of accretion during these 56 years and exhibited large variability (sigma = 45.4). Ninety-seven percent of the rates observed were less than 2 m/yr and 81.6% were less than 1 m/yr. No significant trend in erosion could be recorded despite the study of five temporal subperiods within 1951-2006. Erosion modes and rates actually appear to be strongly dependant on the nature of the backshore material, erosion being stronger along low-lying coastal stretches affected by past or current thermokarst activity. The juxtaposition of wind records monitored at the town of Tiksi and erosion records yielded no significant relationship despite strong record amplitude for both data sets. We explain this poor relationship by the only rough incorporation of sea-ice cover in our storm extraction algorithm, the use of land-based wind records vs. offshore winds, the proximity of the peninsula to the Lena River Delta freshwater and sediment plume and the local topographical constraints on wave development.

Long-term dynamics of adaptive evolution in a globally important coccolithophore to ocean acidification

Recent evolution experiments have revealed that marine phytoplankton may adapt to global change, for example to ocean warming or acidification. Long-term adaptation to novel environments is a dynamic process and phenotypic change can take place thousands of generations after exposure to novel conditions. Using the longest evolution experiment performed in any marine species to date (4 yrs, = 2100 generations), we show that in the coccolithophore Emiliania huxleyi, long-term adaptation to ocean acidification is complex and initial phenotypic responses may revert for important traits. While fitness increased continuously, calcification was restored within the first 500 generations but later reduced in response to selection, enhancing physiological declines of calcification in response to ocean acidification. Interestingly, calcification was not constitutively reduced but revealed rates similar to control treatments when transferred back to present-day CO2 conditions. Growth rate increased with time in controls and adaptation treatments, although the effect size of adaptation assessed through reciprocal assay experiments varied. Several trait changes were associated with selection for higher cell division rates under laboratory conditions, such as reduced cell size and lower particulate organic carbon content per cell. Our results show that phytoplankton may evolve phenotypic plasticity that can affect biogeochemically important traits, such as calcification, in an unforeseen way under future ocean conditions.