Spectral mixture analysis of EELS spectrum-images

Recent advances in detectors and computer science have enabled the acquisition and the processing of multidimensional datasets, in particular in the field of spectral imaging. Benefiting from these new developments, earth scientists try to recover the reflectance spectra of macroscopic materials (e.g., water, grass, mineral types...) present in an observed scene and to estimate their respective proportions in each mixed pixel of the acquired image. This task is usually referred to as spectral mixture analysis or spectral unmixing (SU). SU aims at decomposing the measured pixel spectrum into a collection of constituent spectra, called endmembers, and a set of corresponding fractions (abundances) that indicate the proportion of each endmember present in the pixel. Similarly, when processing spectrum-images, microscopists usually try to map elemental, physical and chemical state information of a given material. This paper reports how a SU algorithm dedicated to remote sensing hyperspectral images can be successfully applied to analyze spectrum-image resulting from electron energy-loss spectroscopy (EELS). SU generally overcomes standard limitations inherent to other multivariate statistical analysis methods, such as principal component analysis (PCA) or independent component analysis (ICA), that have been previously used to analyze EELS maps. Indeed, ICA and PCA may perform poorly for linear spectral mixture analysis due to the strong dependence between the abundances of the different materials. One example is presented here to demonstrate the potential of this technique for EELS analysis.Comment: Manuscript accepted for publication in Ultramicroscop

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions

Calmodulin, the ubiquitous calcium-activated second messenger in eukaryotes, is an extremely versatile molecule involved in many biological processes: muscular contraction, synaptic plasticity, circadian rhythm, and cell cycle, among others. The protein is structurally organised into two globular lobes, joined by a flexible linker. Calcium modulates calmodulin activity by favoring a conformational transition of each lobe from a closed conformation to an open conformation. Most targets have a strong preference for one conformation over the other, and depending on the free calcium concentration in a cell, particular sets of targets will preferentially interact with calmodulin. In turn, targets can increase or decrease the calcium affinity of the calmodulin molecules to which they bind. Interestingly, experiments with the tryptic fragments showed that most targets have a much lower affinity for the N-lobe than for the C-lobe. Hence, the latter predominates in the formation of most calmodulin-target complexes. We showed that a relatively simple allosteric mechanism, based the classic MWC model, can capture the observed modulation of both the isolated C-lobe, and intact calmodulin, by individual targets. Moreover, our model can be naturally extended to study how the calcium affinity of a single pool of calmodulin is modulated by a mixture of competing targets in vivo

Differentiated, promoter-specific response of [4Fe-4S] NsrR DNA-binding to reaction with nitric oxide

NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA-binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ~2 NO per cluster, while for the hmpA1 and nsrR promoters, ~4 and ~8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8 – 10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ~2 NO per cluster, along with two further intermediates at ~4 and ~6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA-binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes

Mass spectrometric identification of [4Fe-4S](NO)x intermediates of nitric oxide sensing by regulatory iron-sulfur cluster proteins

Nitric oxide (NO) can function as both a cytotoxin and a signalling molecule. In both cases, reaction with iron–sulfur (Fe–S) cluster proteins plays an important role because Fe–S clusters are reactive towards NO and so are a primary site of general NO-induced damage (toxicity). This sensitivity to nitrosylation is harnessed in the growing group of regulatory proteins that function in sensing of NO via an Fe–S cluster. Although information about the products of cluster nitrosylation is now emerging, detection and identification of intermediates remains a major challenge, due to their transient nature and the difficulty in distinguishing spectroscopically similar iron-NO species. Here we report studies of the NO-sensing Fe–S cluster regulators NsrR and WhiD using non-denaturing mass spectrometry, in which non-covalent interactions between the protein and Fe/S/NO species are preserved. The data provide remarkable insight into the nitrosylation reactions, permitting identification, for the first time, of protein-bound mono-, di- and tetranitrosyl [4Fe–4S] cluster complexes ([4Fe–4S](NO), [4Fe–4S])(NO) 2 and [4Fe–4S](NO) 4 ) as intermediates along pathways to formation of product Roussin's red ester (RRE) and Roussin's black salt (RBS)-like species. The data allow the nitrosylation mechanisms of NsrR and WhiD to be elucidated and clearly distinguished

A novel three-dimensional macrocellular carbonaceous biofuel cell

Here we report the first membrane-free biofuel cell obtained using three-dimensional carbonaceous foam electrodes. We first developed a new synthetic pathway to produce a new carbonaceous foam electrode material bearing porosity both on the meso and macroporous scales. We proved that by increasing the porosity of our three-dimensional foams we could increase the current density of our modified electrodes. Then, by choosing the right combination of enzyme and mediator, and the right loading of active components, we achieved high current densities for an anodic system. Finally, we combined the improved cathode and anode to build a new membrane-free hybrid enzymatic biofuel cell consisting of a mediated anode and a mediator-free cathode

Quantum State Diffusion and Time Correlation Functions

In computing the spectra of quantum mechanical systems one encounters the Fourier transforms of time correlation functions, as given by the quantum regression theorem for systems described by master equations. Quantum state diffusion (QSD) gives a useful method of solving these problems by unraveling the master equation into stochastic trajectories; but there is no generally accepted definition of a time correlation function for a single QSD trajectory. In this paper we show how QSD can be used to calculate these spectra directly; by formally solving the equations which arise, we arrive at a natural definition for a two-time correlation function in QSD, which depends explicitly on both the stochastic noise of the particular trajectory and the time of measurement, and which agrees in the mean with the ensemble average definition of correlation functions.Comment: 16 pages standard LaTeX + 1 figure (uuencoded postscript) Numerous minor revisions and clarifications. To appear in J. Mod. Optic

Spin Hall effect of light in a random medium

We show that optical beams propagating in transversally disordered materials exhibit a spin Hall effect and a spin-to-orbital conversion of angular momentum as they deviate from paraxiality. We theoretically describe these phenomena on the basis of the microscopic statistical approach to light propagation in random media, and show that they can be detected via polarimetric measurements under realistic experimental conditionsComment: 5 pages, 4 figure

Generation of 34S-substituted protein-bound [4Fe-4S] clusters using 34S-L-cysteine

The ability to specifically label the sulphide ions of protein-bound iron–sulphur (FeS) clusters with 34S isotope greatly facilitates structure–function studies. In particular, it provides insight when using either spectroscopic techniques that probe cluster-associated vibrations, or non-denaturing mass spectrometry, where the ∼+2 Da average increase per sulphide enables unambiguous assignment of the FeS cluster and, where relevant, its conversion/degradation products. Here, we employ a thermostable homologue of the O-acetyl-L-serine sulfhydrylase CysK to generate 34S-substituted L-cysteine and subsequently use it as a substrate for the L-cysteine desulfurase NifS to gradually supply 34S2− for in vitro FeS cluster assembly in an otherwise standard cluster reconstitution protocol