Maximum-likelihood absorption tomography

Maximum-likelihood methods are applied to the problem of absorption tomography. The reconstruction is done with the help of an iterative algorithm. We show how the statistics of the illuminating beam can be incorporated into the reconstruction. The proposed reconstruction method can be considered as a useful alternative in the extreme cases where the standard ill-posed direct-inversion methods fail.Comment: 7 pages, 5 figure

Holographic Methods as Local Probes of the Atomic Order in Solids

In the last fifteen years several techniques based on the holographic principle have been developed for the study of the 3D local order in solids. These methods use various particles: electrons, hard x-ray photons, gamma photons, or neutrons to image the atoms. Although the practical realisation of the various imaging experiments is very different, there is a common thread; the use of inside reference points for holographic imaging. In this paper we outline the basics of atomic resolution holography using inside reference points, especially concentrating to the hard x-ray case. Further, we outline the experimental requirements and what has been practically realized in the last decade. At last we give examples of applications and future perspectives.Comment: 14 pages, 6 figure

A Zala és befolyói makroszkopikus gerinctelen faunája | On the macroinvertebrate fauna of river Zala and its inflows

A Zala és befolyói makroszkopikus gerinctelen faunája kevéssé is-mert, habár számos faunisztikai jellegű gyűjtést végeztek ezen a területen. Dolgozatunkban átfogó irodalmi áttekintést adunk a Zala és befolyói makrogerinctelen faunájáról, illetve saját, 2007-ben végzett faunisztikai felmérésünk eredményeit mutatjuk be. | Although many faunistical investigations were carried out in this area, the aquatic macroinvertebrate fauna of River Zala and its inflows is poorly known. In this paper a compilation is given on the macroinvertebrate fauna of River Zala and its inflows, and the results of own faunistical investigations carried out in 2007 are presented

Amphibious Seismic Survey Images Plate Interface at 1960 Chile Earthquake

The southern central Chilean margin at the site of the largest historically recorded earthquake in the Valdivia region, in 1960 (Mw = 9.5), is part of the 5000-km-long active subduction system whose geodynamic evolution is controversially debated and poorly understood. Covering the area between 36° and 40°S, the oceanic crust is segmented by prominent fracture zones. The offshore forearc and its onshore continuation show a complex image with segments of varying geophysical character, and several fault systems active during the past 24 m.y. In autumn 2001, the project SPOC was organized to study the Subduction Processes Off Chile, with a focus on the seismogenic coupling zone and the forearc. The acquired seismic data crossing the Chilean subduction system were gathered in a combined offshore-onshore survey and provide new insights into the lithospheric structure and evolution of active margins with insignificant frontal accretion

Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria

Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers

DODAB and DODAC bilayer-like aggregates in the micromolar surfactant concentration domain

In the millimolar concentration domain (typically 1 mM), dioctadecyldimethylammonium bromide and chloride (DODAX, X representing Br- or Cl- counterions) molecules assemble in water as large unilamellar vesicles. Differential scanning calorimetry (DSC) is a suitable technique to obtain the melting temperature (Tm) characteristic of surfactant bilayers, while fluorescence spectroscopy detects formation of surfactant aggregates, like bilayers. These two techniques were combined to investigate the assemble of DODAX molecules at micromolar concentrations, from 10 to 100 micromolar. At 1 mM surfactant, Tm ~ 45 ºC and 49 oC, respectively for DODAB and DODAC. DSC and fluorescence of Nile Red were used to show the formation of DODAX aggregates, at the surfactant concentration as low as 10 micromolar, whose Tm decreases monotonically with increasing DODAX concentration to attain the value for the ordinary vesicles. The data indicate that these aggregates are organized as bilayer-like structures.Fundação para a Ciência e a Tecnologia (FCT

Extrinsic Fluorescent Dyes as Tools for Protein Characterization

Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. The main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. In recent time, the use of extrinsic fluorescent dyes such as ANS, Bis-ANS, Nile Red, Thioflavin T and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. The intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization