Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis

A DNA sequence has been obtained for a 35.6-kb genomic segment from Heliobacillus mobilis that contains a major cluster of photosynthesis genes. A total of 30 ORFs were identified, 20 of which encode enzymes for bacteriochlorophyll and carotenoid biosynthesis, reaction-center (RC) apoprotein, and cytochromes for cyclic electron transport. Donor side electron-transfer components to the RC include a putative RC-associated cytochrome c553 and a unique four-large-subunit cytochrome bc complex consisting of Rieske Fe-S protein (encoded by petC), cytochrome b6 (petB), subunit IV (petD), and a diheme cytochrome c (petX). Phylogenetic analysis of various photosynthesis gene products indicates a consistent grouping of oxygenic lineages that are distinct and descendent from anoxygenic lineages. In addition, H. mobilis was placed as the closest relative to cyanobacteria, which form a monophyletic origin to chloroplast-based photosynthetic lineages. The consensus of the photosynthesis gene trees also indicates that purple bacteria are the earliest emerging photosynthetic lineage. Our analysis also indicates that an ancient gene-duplication event giving rise to the paralogous bchI and bchD genes predates the divergence of all photosynthetic groups. In addition, our analysis of gene duplication of the photosystem I and photosystem II core polypeptides supports a “heterologous fusion model” for the origin and evolution of oxygenic photosynthesis.

Estimating the probability for a protein to have a new fold: A statistical computational model

Structural genomics aims to solve a large number of protein structures that represent the protein space. Currently an exhaustive solution for all structures seems prohibitively expensive, so the challenge is to define a relatively small set of proteins with new, currently unknown folds. This paper presents a method that assigns each protein with a probability of having an unsolved fold. The method makes extensive use of protomap, a sequence-based classification, and scop, a structure-based classification. According to protomap, the protein space encodes the relationship among proteins as a graph whose vertices correspond to 13,354 clusters of proteins. A representative fold for a cluster with at least one solved protein is determined after superposition of all scop (release 1.37) folds onto protomap clusters. Distances within the protomap graph are computed from each representative fold to the neighboring folds. The distribution of these distances is used to create a statistical model for distances among those folds that are already known and those that have yet to be discovered. The distribution of distances for solved/unsolved proteins is significantly different. This difference makes it possible to use Bayes' rule to derive a statistical estimate that any protein has a yet undetermined fold. Proteins that score the highest probability to represent a new fold constitute the target list for structural determination. Our predicted probabilities for unsolved proteins correlate very well with the proportion of new folds among recently solved structures (new scop 1.39 records) that are disjoint from our original training set.

A Di-Leucine Sequence and a Cluster of Acidic Amino Acids Are Required for Dynamic Retention in the Endosomal Recycling Compartment of Fibroblasts

Insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase, is dynamically retained within the endosomal compartment of fibroblasts. The characteristics of this dynamic retention are rapid internalization from the plasma membrane and slow recycling back to the cell surface. These specialized trafficking kinetics result in <15% of IRAP on the cell surface at steady state, compared with 35% of the transferrin receptor, another transmembrane protein that traffics between endosomes and the cell surface. Here we demonstrate that a 29-amino acid region of IRAP's cytoplasmic domain (residues 56–84) is necessary and sufficient to promote trafficking characteristic of IRAP. A di-leucine sequence and a cluster of acidic amino acids within this region are essential elements of the motif that slows IRAP recycling. Rapid internalization requires any two of three distinct motifs: M15,16, DED64–66, and LL76,77. The DED and LL sequences are part of the motif that regulates recycling, demonstrating that this motif is bifunctional. In this study we used horseradish peroxidase quenching of fluorescence to demonstrate that IRAP is dynamically retained within the transferrin receptor-containing general endosomal recycling compartment. Therefore, our data demonstrate that motifs similar to those that determine targeting among distinct membrane compartments can also regulate the rate of transport of proteins from endosomal compartments. We propose a model for dynamic retention in which IRAP is transported from the general endosomal recycling compartment in specialized, slowly budding recycling vesicles that are distinct from those that mediate rapid recycling back to the surface (e.g., transferrin receptor-containing transport vesicles). It is likely that the dynamic retention of IRAP is an example of a general mechanism for regulating the distribution of proteins between the surface and interior of cells.

Oxidation states of the manganese cluster during the flash-induced S-state cycle of the photosynthetic oxygen-evolving complex.

The Mn K-edge x-ray absorption spectra for the pure S states of the tetranuclear Mn cluster of the oxygen-evolving complex of photosystem II during flash-induced S-state cycling have been determined. The relative S-state populations in samples given 0, 1, 2, 3, 4, or 5 flashes were determined from fitting the flash-induced electron paramagnetic resonance (EPR) multiline signal oscillation pattern to the Kok model. The edge spectra of samples given 0, 1, 2, or 3 flashes were combined with EPR information to calculate the pure S-state edge spectra. The edge positions (defined as the zero-crossing of the second derivatives) are 6550.1, 6551.7, 6553.5, and 6553.8 eV for S0, S1, S2, and S3, respectively. In addition to the shift in edge position, the S0--> S1 and S1--> S2 transitions are accompanied by characteristic changes in the shape of the edge, both indicative of Mn oxidation. The edge position shifts very little (0.3 eV) for the S2--> S3 transition, and the edge shape shows only subtle changes. We conclude that probably no direct Mn oxidation is involved in this transition. The proposed Mn oxidation state assignments are as follows: S0 (II, III, IV, IV) or (III, III, III, IV), S1 (III, III, IV, IV), S2 (III, IV, IV, IV), S3 (III, IV, IV, IV).

Role of aromatic residues in stabilization of the [Fe4S4] cluster in high-potential iron proteins (HiPIPs): physical characterization and stability studies of Tyr-19 mutants of Chromatium vinosum HiPIP.

The functional role of residue Tyr-19 of Chromatium vinosum HiPIP has been evaluated by site-directed mutagenesis experiments. The stability of the [Fe4S4] cluster prosthetic center is sensitive to side-chain replacements. Polar residues result in significant instability, while nonpolar residues (especially with aromatic side chains) maintain cluster stability. Two-dimensional NMR data of native and mutant HiPIPs are consistent with a model where Tyr-19 serves to preserve the structural rigidity of the polypeptide backbone, thereby maintaining a hydrophobic barrier for exclusion of water from the cluster cavity. Solvent accessibility results in more facile oxidation of the cluster by atmospheric oxygen, with subsequent rapid hydrolysis of the [Fe4S4]3+ core.

GU Monocerotis: A high-mass eclipsing overcontact binary in the young open cluster Dolidze 25

Context. The eclipsing binary GU Mon is located in the star-forming cluster Dolidze 25, which has the lowest metallicity measured in a Milky Way young cluster. Aims. GU Mon has been identified as a short-period eclipsing binary with two early B-type components. We set out to derive its orbital and stellar parameters. Methods. We present a comprehensive analysis, including B and V light curves and 11 high-resolution spectra, to verify the orbital period and determine parameters. We used the stellar atmosphere code FASTWIND to obtain stellar parameters and create templates for cross-correlation. We obtained a model to fit the light and radial-velocity curves using the Wilson-Devinney code iteratively and simultaneously. Results. The two components of GU Mon are identical stars of spectral type B1 V with the same mass and temperature. The light curves are typical of an EW-type binary. The spectroscopic and photometric analyses agree on a period of 0.896640 ± 0.000007 d. We determine a mass of 9.0 ± 0.6 M⊙ for each component and for temperatures of 28 000 ± 2000 K. Both values are consistent with the spectral type. The two stars are overfilling their respective Roche lobes, sharing a common envelope and, therefore the orbit is synchronised and circularised. Conclusions. The GU Mon system has a fill-out factor above 0.8, containing two dwarf B-type stars on the main sequence. The two stars are in a very advanced stage of interaction, with their extreme physical similarity likely due to the common envelope. The expected evolution of such a system very probably leads to a merger while still on the main sequence.

One money with several cycles? Evaluation of European business cycles using cluster analysis. ACES Cases No. 2009.3

Optimal currency area theory suggests that business cycle comovement is a sufficient condition for monetary union, particularly if there are low levels of labour mobility between potential members of the monetary union. Previous studies of co-movement of business cycle variables (mainly authored by Artis and Zhang in the late 1990s) found that there was a core of member states in the EU that could be grouped together as having similar business cycle comovements, but these studies always used Germany as the country against which to compare. In this study, the analysis of Artis and Zhang is extended and updated but correlating against both German and euro area macroeconomic aggregates and using more recent techniques in cluster analysis, namely model-based clustering techniques.

The surface brightness and colour-magnitude relations for Fornax cluster galaxies

We present BVI photometry of 190 galaxies in the central 4 x 3 deg(2) region of the Fornax cluster observed with the Michigan Curtis Schmidt Telescope. Results from the Fornax Cluster Spectroscopic Survey (FCSS) and the Flair-II Fornax Surveys have been used to confirm the membership status of galaxies in the Fornax Cluster Catalogue (FCC). In our catalogue of 213 member galaxies, 92 (43 per cent) have confirmed radial velocities. In this paper, we investigate the surface brightness-magnitude relation for Fornax cluster galaxies. Particular attention is given to the sample of cluster dwarfs and the newly discovered ultracompact dwarf galaxies (UCDs) from the FCSS. We examine the reliability of the surface brightness-magnitude relation as a method for determining cluster membership and find that at surface brightnesses fainter than 22 mag arcsec(-2), it fails in its ability to distinguish between cluster members and barely resolved background galaxies. Cluster members exhibit a strong surface brightness-magnitude relation. Both elliptical (E) galaxies and dwarf elliptical (dE) galaxies increase in surface brightness as luminosity decreases. The UCDs lie off the locus of the relation. B-V and V-I colours are determined for a sample of 113 cluster galaxies and the colour-magnitude relation is explored for each morphological type. The UCDs lie off the locus of the colour-magnitude relation. Their mean V - I colours (similar to1.09) are similar to those of globular clusters associated with NGC 1399. The location of the UCDs on both surface brightness and colour-magnitude plots supports the 'galaxy threshing' model for infalling nucleated dwarf elliptical (dE, N) galaxies.

Mixture modelling for cluster analysis

Cluster analysis via a finite mixture model approach is considered. With this approach to clustering, the data can be partitioned into a specified number of clusters g by first fitting a mixture model with g components. An outright clustering of the data is then obtained by assigning an observation to the component to which it has the highest estimated posterior probability of belonging; that is, the ith cluster consists of those observations assigned to the ith component (i = 1,..., g). The focus is on the use of mixtures of normal components for the cluster analysis of data that can be regarded as being continuous. But attention is also given to the case of mixed data, where the observations consist of both continuous and discrete variables.

Optical quantum computation using cluster states

We propose an approach to optical quantum computation in which a deterministic entangling quantum gate may be performed using, on average, a few hundred coherently interacting optical elements (beam splitters, phase shifters, single photon sources, and photodetectors with feedforward). This scheme combines ideas from the optical quantum computing proposal of Knill, Laflamme, and Milburn [Nature (London) 409, 46 (2001)], and the abstract cluster-state model of quantum computation proposed by Raussendorf and Briegel [Phys. Rev. Lett. 86, 5188 (2001)].

Cluster analysis of high-dimensional data: A case study

Normal mixture models are often used to cluster continuous data. However, conventional approaches for fitting these models will have problems in producing nonsingular estimates of the component-covariance matrices when the dimension of the observations is large relative to the number of observations. In this case, methods such as principal components analysis (PCA) and the mixture of factor analyzers model can be adopted to avoid these estimation problems. We examine these approaches applied to the Cabernet wine data set of Ashenfelter (1999), considering the clustering of both the wines and the judges, and comparing our results with another analysis. The mixture of factor analyzers model proves particularly effective in clustering the wines, accurately classifying many of the wines by location.

A pragmatic 2 × 2 × 2 factorial cluster randomized controlled trial of educational outreach visiting and case conferencing in palliative care—methodology of the Palliative Care Trial [ISRCTN 81117481]

The demand for palliative care is increasing, yet there are few data on the best models of care nor well-validated interventions that translate current evidence into clinical practice. Supporting multidisciplinary patient-centered palliative care while successfully conducting a large clinical trial is a challenge. The Palliative Care Trial (PCT) is a pragmatic 2 x 2 x 2 factorial cluster randomized controlled trial that tests the ability of educational outreach visiting and case conferencing to improve patient-based outcomes such as performance status and pain intensity. Four hundred sixty-one consenting patients and their general practitioners (GPs) were randomized to the following: (1) GP educational outreach visiting versus usual care, (2) Structured patient and caregiver educational outreach visiting versus usual care and (3) A coordinated palliative care model of case conferencing versus the standard model of palliative care in Adelaide, South Australia (3:1 randomization). Main outcome measures included patient functional status over time, pain intensity, and resource utilization. Participants were followed longitudinally until death or November 30, 2004. The interventions are aimed at translating current evidence into clinical practice and there was particular attention in the trial's design to addressing common pitfalls for clinical studies in palliative care. Given the need for evidence about optimal interventions and service delivery models that improve the care of people with life-limiting illness, the results of this rigorous, high quality clinical trial will inform practice. Initial results are expected in mid 2005. (c) 2005 Elsevier Inc. All rights reserved.

Cluster-state quantum computation

This article is a short introduction to and review of the cluster-state model of quantum computation, in which coherent quantum information processing is accomplished via a sequence of single-qubit measurements applied to a fixed quantum state known as a cluster state. We also discuss a few novel properties of the model, including a proof that the cluster state cannot occur as the exact ground state of any naturally occurring physical system, and a proof that measurements on any quantum state which is linearly prepared in one dimension can be efficiently simulated on a classical computer, and thus are not candidates for use as a substrate for quantum computation.

Community and cluster centre residential services for adults with intellectual disability: long-term results from an Australian-matched sample

Changes in residential accommodation models for adults with intellectual disability (ID) over the last 20 years in Australia, the United Kingdom and the United States have involved relocation from institutions primarily into dispersed homes in the community. But an evolving alternative service style is the cluster centre. This paper reports on the relocation of a matched group of 30 pairs of adults with moderate and severe IDs and challenging behaviour who were relocated from an institution into either dispersed housing in the community or cluster centres but under the same residential service philosophy. Adaptive and maladaptive behaviour, choice-making and objective life quality were assessed prior to leaving the institution and then after 12 and 24 months of living in the new residential model. Adaptive behaviour, choice-making and life quality increased for both groups and there was no change in level of maladaptive behaviour compared with levels exhibited in the institution. However, there were some significant differences between the community and cluster centre group as the community group increased some adaptive skills, choice-making and objective life quality to a greater extent than the cluster centre group. Both cluster centre and dispersed community living offer lifestyle and skill development advantages compared with opportunities available in large residential institutions. Dispersed community houses, however, offer increased opportunities for choice-making, acquisition of adaptive behaviours and improved life quality for long-term institutionalized adults with IDs.

Discovery of ultracompact dwarf galaxies in the Virgo Cluster

We have discovered nine ultracompact dwarf galaxies (UCDs) in the Virgo Cluster, extending samples of these objects outside the Fornax Cluster. Using the Two Degree Field (2dF) multifiber spectrograph on the Anglo-Australian Telescope, the new Virgo members were found among 1500 color-selected, starlike targets with 16: 0 < b(j) < 20.2 in a 2 degrees diameter field centered on M87 (NGC 4486). The newly found UCDs are comparable to the UCDs in the Fornax Cluster, with sizes less than or similar to 100 pc, -12.9 < M-B < -10.7, and exhibiting red absorption-line spectra, indicative of an older stellar population. The properties of these objects remain consistent with the tidal threshing model for the origin of UCDs from the surviving nuclei of nucleated dwarf elliptical galaxies disrupted in the cluster core but can also be explained as objects that were formed by mergers of star clusters created in galaxy interactions. The discovery that UCDs exist in Virgo shows that this galaxy type is probably a ubiquitous phenomenon in clusters of galaxies; coupled with their possible origin by tidal threshing, the UCD population is a potential indicator and probe of the formation history of a given cluster. We also describe one additional bright UCD with M-B = -12.0 in the core of the Fornax Cluster. We find no further UCDs in our Fornax Cluster Spectroscopic Survey down to bj 19.5 in two additional 2dF fields extending as far as 3 degrees from the center of the cluster. All six Fornax bright UCDs identified with 2dF lie within 0.degrees 5 (projected distance of 170 kpc) of the central elliptical galaxy NGC 1399.