Characterization of the active site and calcium binding in cytochromecnitrite reductases

The decahaem homodimeric cytochrome c nitrite reductase (NrfA) is expressed within the periplasm of a wide range of Gamma-, Delta- and Epsilon-proteobacteria and is responsible for the six-electron reduction of nitrite to ammonia. This allows nitrite to be used as a terminal electron acceptor, facilitating anaerobic respiration while allowing nitrogen to remain in a biologically available form. NrfA has also been reported to reduce nitric oxide (a reaction intermediate) and sulfite to ammonia and sulfide respectively, suggesting a potential secondary role as a detoxification enzyme. The protein sequences and crystal structures of NrfA from different bacteria and the closely related octahaem nitrite reductase from Thioalkalivibrio nitratireducens (TvNir) reveal that these enzymes are homologous. The NrfA proteins contain five covalently attached haem groups, four of which are bis-histidine-co-ordinated, with the proximal histidine being provided by the highly conserved CXXCH motif. These haems are responsible for intraprotein electron transfer. The remaining haem is the site for nitrite reduction, which is ligated by a novel lysine residue provided by a CXXCK haem-binding motif. The TvNir nitrite reductase has five haems that are structurally similar to those of NrfA and three extra bis-histidine-coordinated haems that precede the NrfA conserved region. The present review compares the protein sequences and structures of NrfA and TvNir and discusses the subtle differences related to active-site architecture and Ca2+ binding that may have an impact on substrate reduction

The Reach-Avoid Problem for Constant-Rate Multi-Mode Systems

A constant-rate multi-mode system is a hybrid system that can switch freely among a finite set of modes, and whose dynamics is specified by a finite number of real-valued variables with mode-dependent constant rates. Alur, Wojtczak, and Trivedi have shown that reachability problems for constant-rate multi-mode systems for open and convex safety sets can be solved in polynomial time. In this paper, we study the reachability problem for non-convex state spaces and show that this problem is in general undecidable. We recover decidability by making certain assumptions about the safety set. We present a new algorithm to solve this problem and compare its performance with the popular sampling based algorithm rapidly-exploring random tree (RRT) as implemented in the Open Motion Planning Library (OMPL).Comment: 26 page

The Mid-Late Holocene Evolution of Southern Walland Marsh and the Origin of the ‘Midley Sand’

This paper documents new litho-, bio- and chronostratigraphic information and sedimentological data from sites at Sandyland on Broomhill Level, Midley and Lydd. These locations are situated between former tidal inlets at Romney and Rye which were instrumental in driving Foreland and Marshland environmental change during the last 2000 years. Peat formation commenced c. 4500 cal. yr BP at Sandyland and after 3700 cal. yr BP at Lydd. At Sandyland, eutrophic fen carr communities were replaced by acidic, nutrient-poor Myrica-dominated vegetation from c. 4100 cal. yr BP, a shift reported from other sites on Walland Marsh and from neighbouring areas. At Lydd, there was no local development of Myrica, probably due to the proximity of the site to tidal channels associated with an opening in the barrier at Hythe. Inundation occurred sometime after c. 2300 cal. yr BP at both sites although the upper contacts of the peat are sharp and have probably been eroded. The sedimentological investigations of the surface outcrops of ‘Midley Sand’ at Sandyland and Midley, combined with other stratigraphic and palaeogeographic evidence, are consistent with deposition in a tidal channel. The data support the existence of an open-ended channel connecting the inlets at Romney and Rye between AD 700 and the 12th century AD, which had already begun to infill and become reclaimed prior to the storms of the 13th century AD. The Wainway Channel appears to be a later feature which developed in the area after the closure of the Romney inlet and enlargement of the Rye inlet as a result of these storms

Lazy Abstraction-Based Controller Synthesis

We present lazy abstraction-based controller synthesis (ABCS) for continuous-time nonlinear dynamical systems against reach-avoid and safety specifications. State-of-the-art multi-layered ABCS pre-computes multiple finite-state abstractions of varying granularity and applies reactive synthesis to the coarsest abstraction whenever feasible, but adaptively considers finer abstractions when necessary. Lazy ABCS improves this technique by constructing abstractions on demand. Our insight is that the abstract transition relation only needs to be locally computed for a small set of frontier states at the precision currently required by the synthesis algorithm. We show that lazy ABCS can significantly outperform previous multi-layered ABCS algorithms: on standard benchmarks, lazy ABCS is more than 4 times faster

Sedimentary macrofossil records reveal ecological change in English lakes: implications for conservation

Aquatic macrophytes play a key role in providing habitat, refuge and food for a range of biota in shallow lakes. However, many shallow lakes have experienced declines in macrophyte vegetation in recent decades, principally due to eutrophication. As changes in macrophyte composition and abundance can affect overall ecological structure and function of a lake, an assessment of the timing and nature of such changes is crucial to our understanding of the wider lake ecosystem. In the typical absence of historical plant records, the macro-remains of macrophytes preserved in lake sediments can be used to assess long-term changes in aquatic vegetation. We generated recent (150–200 years) plant macrofossil records for six English lakes subject to conservation protection to define past macrophyte communities, assess trajectories of ecological change and consider the implications of our findings for conservation targets and strategies. The data for all six lakes reveal a diverse submerged macrophyte community, with charophytes as a key component, in the early part of the sedimentary records. The stratigraphies indicate considerable change to the aquatic vegetation over the last two centuries with a general shift towards species more typically associated with eutrophic conditions. A common feature is the decline in abundance of low-growing charophytes and an increase in tall canopy-forming angiosperms such as fine-leaved Potamogeton species, Zannichellia palustris and Callitriche species. We hypothesise, based on findings from long-term datasets and palaeoecological records from enriched shallow lakes where plants are now absent, that the observed shifts provide a warning to managers that the lakes are on a pathway to complete macrophyte loss such that nutrient load reduction is urgently needed. It is the sound understanding of present-day plant ecology that affords such reliable interpretation of the fossil data which, in turn, provide valuable context for current conservation decisions

The coming and going of a marl lake: multi-indicator palaeolimnology reveals abrupt ecological change and alternative views of reference conditions

Eutrophication is the most pressing threat to highly calcareous (marl) lakes in Europe. Despite their unique chemistry and biology, comprehensive studies into their unimpacted conditions and eutrophication responses are underrepresented in conservation literature. A multi-indicator palaeolimnological study spanning ca. 1260–2009 was undertaken at Cunswick Tarn (UK), a small, presently eutrophic marl lake, in order to capture centennial timescales of impact. Specific aims were to (1) establish temporal patterns of change (gradual/abrupt) across biological groups, thereby testing theories of resistance of marl lake benthic communities to enrichment, and (2) compare the core record of reference condition with prevailing descriptions of high ecological status. Analyses of sediment calcium (Ca), phosphorus (P), pigments, diatoms, testate amoebae, cladocerans, and macrofossils, revealed three abrupt changes in ecosystem structure. The first (1900s), with biomass increases in charophytes and other benthic nutrient-poor indicators, supported ideas of resistance to eutrophication in Chara lakes. The second transition (1930s), from charophyte to angiosperm dominance, occurred alongside reductions in macrophyte cover, increases in eutrophic indicators, and a breakdown in marling, in support of ideas of threshold responses to enrichment. Core P increased consistently into the 1990s when rapid transitions into pelagic shallow lake ecology occurred and Cunswick Tarn became biologically unidentifiable as a marl lake. The moderate total P at which these changes occurred suggests high sensitivity of marl lakes to eutrophication. Further, the early record challenges ideas of correlation between ecological condition, charophyte biomass and sediment Ca. Instead, low benthic production, macrophyte cover, and Ca sedimentation, was inferred. Management measures must focus on reducing external nutrient and sediment loads at early stages of impact in order to preserve marl lakes

Subbarrel patterns in somatosensory cortical barrels can emerge from local dynamic instabilities

Complex spatial patterning, common in the brain as well as in other biological systems, can emerge as a result of dynamic interactions that occur locally within developing structures. In the rodent somatosensory cortex, groups of neurons called "barrels" correspond to individual whiskers on the contralateral face. Barrels themselves often contain subbarrels organized into one of a few characteristic patterns. Here we demonstrate that similar patterns can be simulated by means of local growth-promoting and growth-retarding interactions within the circular domains of single barrels. The model correctly predicts that larger barrels contain more spatially complex subbarrel patterns, suggesting that the development of barrels and of the patterns within them may be understood in terms of some relatively simple dynamic processes. We also simulate the full nonlinear equations to demonstrate the predictive value of our linear analysis. Finally, we show that the pattern formation is robust with respect to the geometry of the barrel by simulating patterns on a realistically shaped barrel domain. This work shows how simple pattern forming mechanisms can explain neural wiring both qualitatively and quantitatively even in complex and irregular domains. © 2009 Ermentrout et al

Preliminary Limits on the WIMP-Nucleon Cross Section from the Cryogenic Dark Matter Search (CDMS)

We are conducting an experiment to search for WIMPs, or weakly-interacting massive particles, in the galactic halo using terrestrial detectors. This generic class of hypothetical particles, whose properties are similar to those predicted by extensions of the standard model of particle physics, could comprise the cold component of non-baryonic dark matter. We describe our experiment, which is based on cooled germanium and silicon detectors in a shielded low-background cryostat. The detectors achieve a high degree of background rejection through the simultaneous measurement of the energy in phonons and ionization. Using exposures on the order of one kilogram-day from initial runs of our experiment, we have achieved (preliminary) upper limits on the WIMP-nucleon cross section that are comparable to much longer runs of other experiments.Comment: 5 LaTex pages, 5 eps figs, epsf.sty, espcrc2dsa2.sty. Proceedings of TAUP97, Gran Sasso, Italy, 7-11 Sep 1997, Nucl. Phys. Suppl., A. Bottino, A. di Credico and P. Monacelli (eds.). See also http://cfpa.berkeley.ed

Equivalence of switching linear systems by bisimulation

A general notion of hybrid bisimulation is proposed for the class of switching linear systems. Connections between the notions of bisimulation-based equivalence, state-space equivalence, algebraic and input–output equivalence are investigated. An algebraic characterization of hybrid bisimulation and an algorithmic procedure converging in a finite number of steps to the maximal hybrid bisimulation are derived. Hybrid state space reduction is performed by hybrid bisimulation between the hybrid system and itself. By specializing the results obtained on bisimulation, also characterizations of simulation and abstraction are derived. Connections between observability, bisimulation-based reduction and simulation-based abstraction are studied.\ud \u

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate