Hexapod Hall scanner for high-resolution large area magnetic imaging

We demonstrate a six-axis scanning imaging apparatus using piezo bending actuators with a large scan range. The six axes of motion of the bending actuators together with the coupling mechanism to the translation stage allow complete control of the sensor position and orientation over the scanning surface, which is ideal for the use of planar sensors such as Hall devices. In particular, the design allows for in situ correction of the probe tilt angle so that the sensor distance to sample surface can be minimized. We investigate the impact of this alignment on the quality of the measured data using an InSb Hall sensor and a magnetic sample. We also demonstrate a synchronous commutation setup that can greatly enhance the magnetic image by reducing the Hall signal offset

An experimental comparison of three towed underwater video systems using species metrics, benthic impact and performance

Managing ecological systems, which operate over large spatial scales, is inherently difficult and often requires sourcing data from different countries and organizations. The assumption might be made that data collected using similar methodologies are comparable, but this is rarely tested. Here, benthic video data recorded using different towed underwater video systems (TUVSs) were experimentally compared. Three technically different TUVSs were compared on different seabed types (rocky, mixed ground and sandy) in Kingmere Marine Conservation Zone, off the south coast of England. For each TUVS, species metrics (forward facing camera), seabed impact (backward facing camera) and operational performance (strengths and limitations of equipment and video footage) were compared with the aim of providing recommendations on their future use and comparability of data between different systems. Statistically significant differences between species richness, density, cover and assemblage composition were detected amongst devices and were believed to be mostly due to their optical specifications. As a result of their high image definition and large field of vision both the benthic contacting heavy and benthic tending TUVS provided good quality footage and ecological measurements. However, the heaviest TUVS proved difficult to operate on irregular ground and was found to cause the most impact to the seabed. The lightest TUVS (benthic contacting light) struggled to maintain contact with the seabed. The benthic tending TUVS was able to fly over variable seabed relief and was comparably the least destructive. Results from this study highlight that particular care should be given to sled and optic specifications when developing a medium- or long-term marine protected area monitoring programme. Furthermore, when using data gathered from multiple sources to test ecological questions, different equipment specifications may confound observed ecological differences. A benthic tending TUVS is recommended for benthic surveys over variable habitat types, particularly in sensitive areas, such as marine protected areas

BioCatalogue: a universal catalogue of web services for the life sciences

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable ‘Web 2.0’-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community

Visualising biological data: a semantic approach to tool and database integration

<p>Abstract</p> <p>Motivation</p> <p>In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are <it>ad hoc </it>collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.</p> <p>Methods</p> <p>To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.</p> <p>Results</p> <p>The toolkit, named Utopia, is freely available from <url>http://utopia.cs.man.ac.uk/</url>.</p

BioXSD: the common data-exchange format for everyday bioinformatics web services

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types

Low-complexity regions within protein sequences have position-dependent roles

<p>Abstract</p> <p>Background</p> <p>Regions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis.</p> <p>Results</p> <p>In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms.</p> <p>Conclusions</p> <p>Our results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.</p

The EMBRACE web service collection

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions

MPP+-induced cytotoxicity in neuroblastoma cells: Antagonism and reversal by guanosine

Guanosine exerts neuroprotective effects in the central nervous system. Apoptosis, a morphological form of programmed cell death, is implicated in the pathophysiology of Parkinson’s disease (PD). MPP+, a dopaminergic neurotoxin, produces in vivo and in vitro cellular changes characteristic of PD, such as cytotoxicity, resulting in apoptosis. Undifferentiated human SH-SY5Y neuroblastoma cells had been used as an in vitro model of Parkinson’s disease. We investigated if extracellular guanosine affected MPP+-induced cytotoxicity and examined the molecular mechanisms mediating its effects. Exposure of neuroblastoma cells to MPP+ (10 μM–5 mM for 24–72 h) induced DNA fragmentation in a time-dependent manner (p < 0.05). Administration of guanosine (100 μM) before, concomitantly with or, importantly, after the addition of MPP+ abolished MPP+-induced DNA fragmentation. Addition of MPP+ (500 μM) to cells increased caspase-3 activity over 72 h (p < 0.05), and this was abolished by pre- or co-treatment with guanosine. Exposure of cells to pertussis toxin prior to MPP+ eliminated the anti-apoptotic effect of guanosine, indicating that this effect is dependent on a Gi protein-coupled receptor, most likely the putative guanosine receptor. The protection by guanosine was also abolished by the selective inhibitor of the enzyme PI-3-K/Akt/PKB (LY294002), confirming that this pathway plays a decisive role in this effect of guanosine. Neither MPP+ nor guanosine had any significant effect on α-synuclein expression. Thus, guanosine antagonizes and reverses MPP+-induced cytotoxicity of neuroblastoma cells via activation of the cell survival pathway, PI-3-K/Akt/PKB. Our results suggest that guanosine may be an effective pharmacological intervention in PD

Guanosine effect on cholesterol efflux and apolipoprotein E expression in astrocytes

The main source of cholesterol in the central nervous system (CNS) is represented by glial cells, mainly astrocytes, which also synthesise and secrete apolipoproteins, in particular apolipoprotein E (ApoE), the major apolipoprotein in the brain, thus generating cholesterol-rich high density lipoproteins (HDLs). This cholesterol trafficking, even though still poorly known, is considered to play a key role in different aspects of neuronal plasticity and in the stabilisation of synaptic transmission. Moreover, cell cholesterol depletion has recently been linked to a reduction in amyloid beta formation. Here we demonstrate that guanosine, which we previously reported to exert several neuroprotective effects, was able to increase cholesterol efflux from astrocytes and C6 rat glioma cells in the absence of exogenously added acceptors. In this effect the phosphoinositide 3 kinase/extracellular signal-regulated kinase 1/2 (PI3K/ERK1/2) pathway seems to play a pivotal role. Guanosine was also able to increase the expression of ApoE in astrocytes, whereas it did not modify the levels of ATP-binding cassette protein A1 (ABCA1), considered the main cholesterol transporter in the CNS. Given the emerging role of cholesterol balance in neuronal repair, these effects provide evidence for a role of guanosine as a potential pharmacological tool in the modulation of cholesterol homeostasis in the brain