Predictions from a stochastic polymer model for the MinDE dynamics in E.coli

The spatiotemporal oscillations of the Min proteins in the bacterium Escherichia coli play an important role in cell division. A number of different models have been proposed to explain the dynamics from the underlying biochemistry. Here, we extend a previously described discrete polymer model from a deterministic to a stochastic formulation. We express the stochastic evolution of the oscillatory system as a map from the probability distribution of maximum polymer length in one period of the oscillation to the probability distribution of maximum polymer length half a period later and solve for the fixed point of the map with a combined analytical and numerical technique. This solution gives a theoretical prediction of the distributions of both lengths of the polar MinD zones and periods of oscillations -- both of which are experimentally measurable. The model provides an interesting example of a stochastic hybrid system that is, in some limits, analytically tractable.Comment: 16 page

A model of fasciculation and sorting in mixed populations of axons

We extend a recently proposed model (Chaudhuri et al., EPL 87, 20003 (2009)) aiming to describe the formation of fascicles of axons during neural development. The growing axons are represented as paths of interacting directed random walkers in two spatial dimensions. To mimic turnover of axons, whole paths are removed and new walkers are injected with specified rates. In the simplest version of the model, we use strongly adhesive short-range inter-axon interactions that are identical for all pairs of axons. We generalize the model to adhesive interactions of finite strengths and to multiple types of axons with type-specific interactions. The dynamic steady state is characterized by the position-dependent distribution of fascicle sizes. With distance in the direction of axon growth, the mean fascicle size and emergent time scales grow monotonically, while the degree of sorting of fascicles by axon type has a maximum at a finite distance. To understand the emergence of slow time scales, we develop an analytical framework to analyze the interaction between neighboring fascicles.Comment: 19 pages, 13 figures; version accepted for publication in Phys Rev

Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA

We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryos. Using immunofluorescence analysis, an in vitro mitochondrial uptake assay and sub‐fractionation of human mitochondria we show hSuv3p to be a soluble protein localised in the mitochondrial matrix. We expressed and purified recombinant hSuv3p protein from a bacterial expression system. The purified enzyme was capable of hydrolysing ATP with a Km of 41.9 µM and the activity was only modestly stimulated by polynucleotides. hSuv3p unwound partly hybridised dsRNA and dsDNA structures with a very strong preference for the latter. The presented analysis of the hSuv3p NTPase/helicase suggests that new functions of the protein have been acquired in the course of evolution

Abnormally high acoustic sea-floor backscatter patterns in active methane venting areas, Dnepr paleo-delta, northwestern Black Sea

During the 58th and 60th cruise of R.V. Vodyanitskiy, conducted in the framework of the EU-funded CRIMEA project, almost 3000 active bubble-releasing seeps were detected with an adapted split-beam echosounder within the 1540 km2 of the studied Dnepr paleo-delta area. The distribution of these active seeps is not random, but is controlled by morphology, by underlying stratigraphy and sediment properties, and by the presence of gas hydrates acting as a seal and preventing upward migrating gas to be released as bubbles in the water column (Naudts et al., 2006).Here we present the relation between acoustic sea-floor backscatter and the distribution of more than 600 active methane seeps detected within a small area on the continental shelf. This study is further sustained by visual sea-floor observations, highresolution seismic data, pore-water data and grain-size analysis.The backscatter data indicate that seeps are generally not located within highbackscatter areas, but rather surround them. Most seeps are located within shallow pockmarks which are characterized by medium-backscatter values, whereas deeper pockmarks have high-backscatter values with much lower seep densities. The seismic data show the presence of a distinct gas front (free gas); shallow gas fronts correspond to high- and medium-backscatter areas, which are associated with gas seeps, whereas deep gas fronts correspond to low-backscatter areas without seeps. The presence of shallow gas is also confirmed by the pore-water data, showing higher amounts of dissolved-methane concentrations for areas with medium- to high-backscatter values.Visual observations showed that the high-backscatter areas correspond to white Beggiatoa mats. These thiotrophic bacterial mats are indicators for the anaerobic oxidation of methane (AOM) which results in the formation of methane-derived carbonates (MDAC’s). AOM was also confirmed by the pore-water data. No clear correlation with grain-size distribution could be established.Based on the integration of all datasets, we conclude that the observed highbackscatter anomalies are a result of methane-derived authigenic carbonates (MDAC’s). The carbonate formation appears to lead to a gradual (self)-sealing of the seeps (Hovland, 2002), followed by a relocation of the bubble-releasing holes. Furthermore, the degree of MDAC-formation is directly linked to the backscatter intensity and seep activity which makes it possible to use the backscatter strength as a proxy for the seep activity and distribution

Anomalous seafloor backscatter patterns in methane venting areas, Dnepr paleo-delta, NW Black Sea

The relation between acoustic seafloor backscatter and seep distribution is examined by integrating multibeam backscatter data and seep locations detected by single-beam echosounder. This study is further supported by side scan sonar recordings, high-resolution 5 kHz seismic data, pore-water analysis, grain-size analysis and visual seafloor observations. The datasets were acquired during the 2003 and 2004 expeditions of the EC-funded CRIMEA project in the Dnepr paleo-delta area, northwestern Black Sea. More than 600 active methane seeps were hydro-acoustically detected within a small (3.96 km by 3.72 km) area on the continental shelf of the Dnepr paleo-delta in water depths ranging from -72 m to -156 m. Multibeam and side scan sonar recordings show backscatter patterns that are clearly associated with seepage or with a present dune area. Seeps generally occur within medium- to high backscatter areas which often coincide with pockmarks. High-resolution seismic data reveal the presence of an undulating gas front, i.e. the top of the free gas in the subsurface, which domes up towards and intersects the seafloor at locations where gas seeps and medium- to high-backscatter values are detected. Pore-water analysis of 4 multi-cores, taken at different backscatter intensity sites, shows a clear correlation between backscatter intensity and dissolved methane fluxes. All analyzed chemical species indicate increasing anaerobic oxidation of methane (AOM) from medium- to high-backscatter locations. This is confirmed by visual seafloor observations, showing bacterial mats and authigenic carbonates formed by AOM. Grain-size analysis of the 4 multi-cores only reveals negligible variations between the different backscatter sites. Integration of all datasets leads to the conclusion that the observed backscatter patterns are the result of ongoing methane seepage and the precipitation of methane-derived authigenic carbonates (MDACs) caused by AOM. The carbonate formation also appears to lead to a gradual (self-)sealing of the seeps by cementing fluid pathways/horizons followed by a relocation of the bubble-releasing locations

Current Results of the EC-sponsored Catchment Modelling (CatchMod) Cluster

To support the Water Framework Directive implementation, much research has been commissioned at both national and European levels. CatchMod is a cluster of these projects, which is focusing on the development of computational catchment models and related tools. This paper presents an overview of the results of the CatchMod cluster to dat

Significance of anaerobic methane oxidation in methane-rich sediments overlying the Blake Ridge gas hydrates

A unique set of geochemical pore-water data, characterizing the sulfate reduction and uppermost methanogenic zones, has been collected at the Blake Ridge (offshore southeastern North America) from Ocean Drilling Program (ODP) Leg 164 cores and piston cores. The δ13 C values of dissolved CO2(Σ CO2) are as 13 C-depleted as –37.7‰ PDB (Site 995) at the sulfate-methane interface, reflecting a substantial contribution of isotopically light carbon from methane. Although the geochemical system is complex and difficult to fully quantify, we use two methods to constrain and illustrate the intensity of anaerobic methane oxidation in Blake Ridge sediments. An estimate using a two-component mixing model suggests that ~24% of the carbon residing in the Σ CO2 pool is derived from biogenic methane. Independent diagenetic modeling of a methane concentration profile (Site 995) indicates that peak methane oxidation rates approach 0.005 μmol cm–3 yr–1, and that anaerobic methane oxidation is responsible for consuming ~35% of the total sulfate flux into the sediments. Thus, anaerobic methane oxidation is a significant biogeochemical sink for sulfate, and must affect interstitial sulfate concentrations and sulfate gradients. Such high proportions of sulfate depletion because of anaerobic methane oxidation are largely undocumented in continental rise sediments with overlying oxic bottom waters. We infer that the additional amount of sulfate depleted through anaerobic methane oxidation, fueled by methane flux from below, causes steeper sulfate gradients above methane-rich sediments. Similar pore water chemistries should occur at other methane-rich, continental-rise settings associated with gas hydrates

Teaching Index Numbers to economists

Economic statistics are frequently reported in the form of index numbers. This article considers how the field of Index Numbers should be approached in the teaching of a general economic degree. While the topic finds a natural home in statistics modules, it is emphasised that the area can also be referred to in the teaching of other areas of economics. It is also emphasised that the differences between Index Numbers theory and the practice of compiling economic statistics such as inflation can help students gain a better understanding of applied economic statistics. Methods for assessing learning in the area are also considered and available material to support teaching is also summarised