Towards a metadata standard for field spectroscopy

This thesis identifies the core components for a field spectroscopy metadata standard to facilitate discoverability, interoperability, reliability, quality assurance and extended life cycles for datasets being exchanged in a variety of data sharing platforms. The research is divided into five parts: 1) an overview of the importance of field spectroscopy, metadata paradigms and standards, metadata quality and geospatial data archiving systems; 2) definition of a core metadataset critical for all field spectroscopy applications; 3) definition of an extended metadataset for specific applications; 4) methods and metrics for assessing metadata quality and completeness in spectral data archives; 5) recommendations for implementing a field spectroscopy metadata standard in data warehouses and ‘big data’ environments. Part 1 of the thesis is a review of the importance of field spectroscopy in remote sensing; metadata paradigms and standards; field spectroscopy metadata practices, metadata quality; and geospatial data archiving systems. The unique metadata requirements for field spectroscopy are discussed. Conventional definitions and metrics for measuring metadata quality are presented. Geospatial data archiving systems for data warehousing and intelligent information exchange are explained. Part 2 of the thesis presents a core metadataset for all field spectroscopy applications, derived from the results of an international expert panel survey. The survey respondents helped to identify a metadataset critical to all field spectroscopy campaigns, and for specific applications. These results form the foundation of a field spectroscopy metadata standard that is practical, flexible enough to suit the purpose for which the data is being collected, and/or has sufficient legacy potential for long-term sharing and interoperability with other datasets. Part 3 presents an extended metadataset for specific application areas within field spectroscopy. The key metadata is presented for three applications: tree crown, soil, and underwater coral reflectance measurements. The performance of existing metadata standards in complying with the field spectroscopy metadataset was measured. Results show they consistently fail to accommodate the needs of both field spectroscopy scientists in general as well as the three application areas. Part 4 presents criteria for measuring the quality and completeness of field spectroscopy metadata in a spectral archive. Existing methods for measuring quality and completeness of metadata were scrutinized against the special requirements of field spectroscopy datasets. Novel field spectroscopy metadata quality parameters were defined. Two spectral libraries were examined as case studies of operationalized metadata. The case studies revealed that publicly available datasets are underperforming on the quality and completeness measures. Part 5 presents recommendations for adoption and implementation of a field spectroscopy standard, both within the field spectroscopy community and within the wider scope of IT infrastructure for storing and sharing field spectroscopy metadata within data warehouses and big data environments. The recommendations are divided into two main sections: community adoption of the standard, and integration of standardized metadatasets into data warehouses and big data platforms. This thesis has identified the core components of a metadata standard for field spectroscopy. The metadata standard serves overall to increase the discoverability, reliability, quality, and life cycle of field spectroscopy metadatasets for wide-scale data exchange

Modulation of the <i>Neisseria gonorrhoeae </i>drug efflux conduit MtrE

We acknowledge funding through the Wellcome Trust Interdisciplinary Research Funds (grant WT097818MF), the Scottish Universities’ Physics Alliance (SUPA), Tenovus Tayside (grant T16/30) and the Tayside Charitable Trust. O.N.V. has been funded through a BBSRC CASE award (BB/J013072/1).Widespread antibiotic resistance, especially of Gram-negative bacteria, has become a severe concern for human health. Tripartite efflux pumps are one of the major contributors to resistance in Gram-negative pathogens, by efficiently expelling a broad spectrum of antibiotics from the organism. In Neisseria gonorrhoeae, one of the first bacteria for which pan-resistance has been reported, the most expressed efflux complex is MtrCDE. Here we present the electrophysiological characterisation of the outer membrane component MtrE and the membrane fusion protein MtrC, obtained by a combination of planar lipid bilayer recordings and in silico techniques. Our in vitro results show that MtrE can be regulated by periplasmic binding events and that the interaction between MtrE and MtrC is sufficient to stabilize this complex in an open state. In contrast to other efflux conduits, the open complex only displays a slight preference for cations. The maximum conductance we obtain in the in vitro recordings is comparable to that seen in our computational electrophysiology simulations conducted on the MtrE crystal structure, indicating that this state may reflect a physiologically relevant open conformation of MtrE. Our results suggest that the MtrC/E binding interface is an important modulator of MtrE function, which could potentially be targeted by new efflux inhibitors.Publisher PDFPeer reviewe

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities

Sitting at the edge: How biomolecules use hydrophobicity to tune their interactions and function

Water near hydrophobic surfaces is like that at a liquid-vapor interface, where fluctuations in water density are substantially enhanced compared to that in bulk water. Here we use molecular simulations with specialized sampling techniques to show that water density fluctuations are similarly enhanced, even near hydrophobic surfaces of complex biomolecules, situating them at the edge of a dewetting transition. Consequently, water near these surfaces is sensitive to subtle changes in surface conformation, topology, and chemistry, any of which can tip the balance towards or away from the wet state, and thus significantly alter biomolecular interactions and function. Our work also resolves the long-standing puzzle of why some biological surfaces dewet and other seemingly similar surfaces do not.Comment: 12 pages, 4 figure

Water in Cavity−Ligand Recognition

We use explicit solvent molecular dynamics simulations to estimate free energy, enthalpy, and entropy changes along the cavity-ligand association coordinate for a set of seven model systems with varying physicochemical properties. Owing to the simplicity of the considered systems we can directly investigate the role of water thermodynamics in molecular recognition. A broad range of thermodynamic signatures is found in which water (rather than cavity or ligand) enthalpic or entropic contributions appear to drive cavity-ligand binding or rejection. The unprecedented, nanoscale picture of hydration thermodynamics can help the interpretation and design of protein-ligand binding experiments. Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models

Photoinduced Excited State Electron Transfer at Liquid/Liquid Interfaces

Several aspects of the photoinduced electron transfer (ET) reaction betweencoumarin 314 (C314) and N,N-dimethylaniline (DMA) at the water/DMA interface areinvestigated by molecular dynamics simulations. New DMA and water/DMA potentialenergy surfaces are developed and used to characterize the neat water/DMA interface.The adsorption free energy, the rotational dynamics and the solvation dynamics of C314at the liquid/liquid interface are investigated and are generally in reasonable agreementwith available experimental data. The solvent free energy curves for the ET reactionbetween excited C314 and DMA molecules are calculated and compared with thosecalculated for a simple point charge model of the solute. It is found that thereorganization free energy is very small when the full molecular description of the soluteis taken into account. An estimate of the ET rate constant is in reasonable agreement withexperiment. Our calculations suggest that the polarity of the surface “reported” by thesolute, as reflected by solvation dynamics and the reorganization free energy, is strongly solute-dependent