On the action potential as a propagating density pulse and the role of anesthetics

The Hodgkin-Huxley model of nerve pulse propagation relies on ion currents through specific resistors called ion channels. We discuss a number of classical thermodynamic findings on nerves that are not contained in this classical theory. Particularly striking is the finding of reversible heat changes, thickness and phase changes of the membrane during the action potential. Data on various nerves rather suggest that a reversible density pulse accompanies the action potential of nerves. Here, we attempted to explain these phenomena by propagating solitons that depend on the presence of cooperative phase transitions in the nerve membrane. These transitions are, however, strongly influenced by the presence of anesthetics. Therefore, the thermodynamic theory of nerve pulses suggests a explanation for the famous Meyer-Overton rule that states that the critical anesthetic dose is linearly related to the solubility of the drug in the membranes.Comment: 13 pages, 8 figure

Optimizing Resistance Coefficients for Large Bed Element Streams

This is a report of a comparison of Darcy resistance coefficients calculafed for previously reported laboratory data and those calculated for large bed element streams. Large bed element (LBE) streams exist frequently in nature where rocks derived from valley walls or from channels cutting through ancient glacial or fluvial deposits are moved only under conditions of extreme flood. The height of bed elements is a significant part of the mean depth of flow. The stream gradients are high and are quite stable for all but the highest flows

The Evolution of X-ray Bursts in the "Bursting Pulsar" GRO J1744-28

GRO J1744-28, commonly known as the `Bursting Pulsar', is a low mass X-ray binary containing a neutron star and an evolved giant star. This system, together with the Rapid Burster (MXB 1730-33), are the only two systems that display the so-called Type II X-ray bursts. These type of bursts, which last for 10s of seconds, are thought to be caused by viscous instabilities in the disk; however the Type II bursts seen in GRO J1744-28 are qualitatively very different from those seen in the archetypal Type II bursting source the Rapid Burster. To understand these differences and to create a framework for future study, we perform a study of all X-ray observations of all 3 known outbursts of the Bursting Pulsar which contained Type II bursts, including a population study of all Type II X-ray bursts seen by RXTE. We find that the bursts from this source are best described in four distinct phenomena or `classes' and that the characteristics of the bursts evolve in a predictable way. We compare our results with what is known for the Rapid Burster and put out results in the context of models that try to explain this phenomena.Comment: Accepted to MNRAS Aug 17 201

Combining education and science outcomes : the marine studies programme and Tūhua marine reserve monitoring

Tūhua (Mayor Island) lies 35 kilometres off shore in the Bay of Plenty, New Zealand. It has a long history of Māori occupation and is of high cultural significance to these traditional owners. Tūhua was once world-renowned for big game fishing, but after incremental declines in local fish populations, in 1993 a no-take marine reserve was gazetted and has been the subject of annual marine monitoring surveys since that time. Continued monitoring has only been possible because of the creation of an innovative science/education partnership between the Tūhua Trust Board, representing the indigenous Māori owners of the island, the Department of Conservation (DOC), responsible for managing the reserve, and the Marine Studies Department of Bay of Plenty Polytechnic (BOPP). The Polytechnic\u27s Marine Studies course is a successful undergraduate diploma/degree education programme, combining strong practical elements with academic rigour. Second year Marine Studies students and staff members undertake the marine monitoring surveys at Tūhua on an annual extended field trip. Managers expected the marine reserve would demonstrate growth in fish numbers in comparison to the adjacent less protected areas. However little change in key indicator species was apparent after ten years of protection and this precipitated a review of the methodology and marine management policies. Twenty years after protection, there are now clear differences. Interwoven with this hard science discourse are the perceptions of the students involved in the annual monitoring programme. On the extended monitoring field trip, the students and staff members live on the island for ten days in basic conditions and are immersed in a natural learning environment. Results of a series of questionnaires suggest that the students involved increase not only their skill sets but also have increased self-confidence, motivation and conservation awareness. Science and education outcomes have been successfully combined into a readily transferable model over twenty years at this ecologically and culturally significant island location.Keith E. Gregor: Marine Studies Department, Bay of Plenty PolytechnicKim D. Youg: Conservation Ecology Research Unit, Department of Zoology and Entomology, University of PretoriaDaniel C. Rapson: Tauranga Management Area, Department of ConservationJacob McC. Overton: Landcare Researc

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology

This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).
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Propagation modes of 3D scour below a submarine pipeline in oblique steady currents and waves

This paper presents experimental results on 3D scour propagation along a pipeline under oblique-incidence currents and waves. Different modes of 3D scour propagation were discovered after the local scour was initiated below the pipeline. These modes include scour propagation throughout the whole pipeline, onset of scour at multiple locations due to piping, termination of scour propagation induced by backfill and no scour propagation. The critical conditions for these scour propagation modes were determined in terms of flow incident angle, embedment depth and Shields parameter (or KC number). © 2016 Taylor & Francis Group, London

Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods

Significant computational efforts have been focused toward exposing the molecular mechanisms of anesthesia in recent years. In the past decade, this has been aided considerably by a momentous increase in the number of high-resolution structures of ion channels, which are putative targets for the anesthetic agents, as well as advancements in high-performance computing technologies. In this review, typical simulation methods to investigate the behavior of model membranes and membrane-protein systems are briefly reviewed, and related computational studies are surveyed. Both lipid- and protein-mediated mechanisms of anesthetic action are scrutinized, focusing on the behavior of ion channels in the latter case