A burst from the direction of UZ Fornacis with XMM-Newton

The XMM-Newton pointing towards the magnetic cataclysmic variable UZ For finds the source to be a factor > 10^3 fainter than previous EXOSAT and ROSAT observations. The source was not detected for the majority of a 22 ksec exposure with the EPIC cameras, suggesting that the accretion rate either decreased, or stopped altogether. However a 1.1 ksec burst was detected from UZ For during the observation. Spectral fits favour optically thin, kT = 4.4 keV thermal emission. Detection of the burst by the on-board Optical Monitor indicates that this was most probably an accretion event. The 0.1-10 keV luminosity of 2.1 x 10^30 erg/s is typical for accretion shock emission from high state polars and would result from the potential energy release of ~ 10^16 g of gas. There is no significant soft excess due to reprocessing in the white dwarf atmosphere.Comment: 7 pages, 2 postscript figures, ApJL, in pres

Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic Sediments

In this report, we describe the selective cloning of large DNA fragments from magnetotactic metagenomes from various aquatic habitats. This was achieved by a two-step magnetic enrichment which allowed the mass collection of environmental magnetotactic bacteria (MTB) virtually free of nonmagnetic contaminants. Four fosmid libraries were constructed and screened by end sequencing and hybridization analysis using heterologous magnetosome gene probes. A total of 14 fosmids were fully sequenced. We identified and characterized two fosmids, most likely originating from two different alphaproteobacterial strains of MTB that contain several putative operons with homology to the magnetosome island (MAI) of cultivated MTB. This is the first evidence that uncultivated MTB exhibit similar yet differing organizations of the MAI, which may account for the diversity in biomineralization and magnetotaxis observed in MTB from various environments

Intrinsic and extrinsic diffusion of indium in germanium

Diffusion experiments with indium (In) in germanium (Ge) were performed in the temperature range between 550 and 900°C. Intrinsic and extrinsic doping levels were achieved by utilizing various implantation doses. Indium concentration profiles were recorded by means of secondary ion mass spectrometry and spreading resistance profiling. The observed concentration independent diffusion profiles are accurately described based on the vacancy mechanism with a singly negatively charged mobile In-vacancy complex. In accord with the experiment, the diffusion model predicts an effective In diffusion coefficient under extrinsic conditions that is a factor of 2 higher than under intrinsic conditions. The temperature dependence of intrinsic In diffusion yields an activation enthalpy of 3.51 eV and confirms earlier results of Dorner et al. [Z. Metallk. 73, 325 (1982)]. The value clearly exceeds the activation enthalpy of Ge self- diffusion and indicates that the attractive interaction between In and a vacancy does not extend to third nearest neighbor sites which confirms recent theoretical calculations. At low temperatures and high doping levels, the In profiles show an extended tail that could reflect an enhanced diffusion at the beginning of the annealing

Proteasome assembly from 15S precursors involves major conformational changes and recycling of the Pba1-Pba2 chaperone

The chaperones Ump1 and Pba1-Pba2 promote efficient biogenesis of 20S proteasome core particles from its subunits via 15S intermediates containing alpha and beta subunits, except beta7. Here we elucidate the structural role of these chaperones in late steps of core particle biogenesis using biochemical, electron microscopy, cross-linking and mass spectrometry analyses. In 15S precursor complexes, Ump1 is largely unstructured, lining the inner cavity of the complex along the interface between alpha and beta subunits. The alpha and beta subunits form loosely packed rings with a wider alpha ring opening than in the 20S core particle, allowing for the Pba1-Pba2 heterodimer to be partially embedded in the central alpha ring cavity. During biogenesis, the heterodimer is expelled from the alpha ring by a restructuring event that organizes the beta ring and leads to tightening of the alpha ring opening. In this way, the Pba1-Pba2 chaperone is recycled for a new round of proteasome assembly

Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae

BACKGROUND: Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera Acholeplasma and ‘Candidatus Phytoplasma’. Acholeplasmas are ubiquitous saprophytic bacteria. Several isolates are derived from plants or animals, whereas phytoplasmas are characterised as intracellular parasitic pathogens of plant phloem and depend on insect vectors for their spread. The complete genome sequences for eight strains of this family have been resolved so far, all of which were determined depending on clone-based sequencing. RESULTS: The A. oculi strain 19L chromosome was sequenced using two independent approaches. The first approach comprised sequencing by synthesis (Illumina) in combination with Sanger sequencing, while single molecule real time sequencing (PacBio) was used in the second. The genome was determined to be 1,587,120 bp in size. Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence. High-quality sequences were obtained by both strategies differing in six positions, which are interpreted as reliable variations present in the culture population. Our genome analysis revealed 1,471 protein-coding genes and highlighted the absence of the F(1)F(O)-type Na(+) ATPase system and GroEL/ES chaperone. Comparison of the four available Acholeplasma sequences revealed a core-genome encoding 703 proteins and a pan-genome of 2,867 proteins. CONCLUSIONS: The application of two state-of-the-art sequencing technologies highlights the potential of single molecule real time sequencing for complete genome determination. Comparative genome analyses revealed that the process of losing particular basic genetic features during genome reduction occurs in both genera, as indicated for several phytoplasma strains and at least A. oculi. The loss of the F(1)F(O)-type Na(+) ATPase system may separate Acholeplasmataceae from other Mollicutes, while the loss of those genes encoding the chaperone GroEL/ES is not a rare exception in this bacterial class. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-931) contains supplementary material, which is available to authorized users

EVALUATING THE EFFECTS OF MONENSIN OVERDOSE IN DAIRY CATTLE

Monensin is approved as a feed additive by the FDA Center for Veterinary Medicine to increase milk production efficiency in lactating dairy cattle. To assess the effects of a gross error in mixing monensin into cattle feed, a 10-fold overdose was given for three consecutive days to naïve cows as well as cows previously dosed with monensin within the label range. Cows were evaluated during the overdose and for a subsequent 4 week observation period. Physiological variables were analyzed, including dry matter intake, body weight, body condition score, and serum chemistry profile. Production variables were analyzed, including milk yield and milk composition. Cows were blocked according to pre-treatment milk output, days in milk, and body condition. Results were analyzed using linear mixed model methodology with a baseline covariate. The study provided information for the veterinarian and the dairy farmer for determining whether an overdose may have occurred, for assessing the prognosis, and for deciding whether to continue feeding monensin immediately following an overdose

Cooperative object transport with a swarm of e-puck robots: robustness and scalability of evolved collective strategies

Cooperative object transport in distributed multi-robot systems requires the coordination and synchronisation of pushing/pulling forces by a group of autonomous robots in order to transport items that cannot be transported by a single agent. The results of this study show that fairly robust and scalable collective transport strategies can be generated by robots equipped with a relatively simple sensory apparatus (i.e. no force sensors and no devices for direct communication). In the experiments described in this paper, homogeneous groups of physical e-puck robots are required to coordinate and synchronise their actions in order to transport a heavy rectangular cuboid object as far as possible from its starting position to an arbitrary direction. The robots are controlled by dynamic neural networks synthesised using evolutionary computation techniques. The best evolved controller demonstrates an effective group transport strategy that is robust to variability in the physical characteristics of the object (i.e. object mass and size of the longest object’s side) and scalable to different group sizes. To run these experiments, we designed, built, and mounted on the robots a new sensor that returns the agents’ displacement on a 2D plane. The study shows that the feedback generated by the robots’ sensors relative to the object’s movement is sufficient to allow the robots to coordinate their efforts and to sustain the transports for an extended period of time. By extensively analysing successful behavioural strategies, we illustrate the nature of the operational mechanisms underpinning the coordination and synchronisation of actions during group transport

Regulation of S1PR2 by the EBV oncogene LMP1 in aggressive ABC subtype diffuse large B cell lymphoma.

The Epstein-Barr virus (EBV) is found almost exclusively in the activated B cell (ABC) subtype of diffuse large B cell lymphoma (DLBCL), yet its contribution to this tumour remains poorly understood. We have focussed on the EBV-encoded latent membrane protein-1 (LMP1), a constitutively activated CD40 homologue expressed in almost all EBV-positive DLBCL and which can disrupt germinal centre (GC) formation and drive lymphomagenesis in mice. Comparison of the transcriptional changes that follow LMP1 expression with those that follow transient CD40 signalling in human GC B cells enabled us to define pathogenic targets of LMP1 aberrantly expressed in ABC-DLBCL. These included the down-regulation of S1PR2, a sphingosine-1-phosphate (S1P) receptor that is transcriptionally down-regulated in ABC-DLBCL, and when genetically ablated leads to DLBCL in mice. Consistent with this we found that LMP1-expressing primary ABC-DLBCL were significantly more likely to lack S1PR2 expression than were LMP1-negative tumours. Furthermore, we showed that the down-regulation of S1PR2 by LMP1 drives a signalling loop leading to constitutive activation of the phosphatidylinositol-3-kinase (PI3-K) pathway. Finally, core LMP1-PI3-K targets were enriched for lymphoma-related transcription factors and genes associated with shorter overall survival in patients with ABC-DLBCL. Our data identify a novel function for LMP1 in aggressive DLBCL

Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

Background: In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications. Methodology: We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection. Conclusions: With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approac

Ant-like task allocation and recruitment in cooperative robots

One of the greatest challenges in robotics is to create machines that are able to interact with unpredictable environments in real time. A possible solution may be to use swarms of robots behaving in a self-organized manner, similar to workers in an ant colony. Efficient mechanisms of division of labour, in particular series-parallel operation and transfer of information among group members, are key components of the tremendous ecological success of ants. Here we show that the general principles regulating division of labour in ant colonies indeed allow the design of flexible, robust and effective robotic systems. Groups of robots using ant-inspired algorithms of decentralized control techniques foraged more efficiently and maintained higher levels of group energy than single robots. But the benefits of group living decreased in larger groups, most probably because of interference during foraging. Intriguingly, a similar relationship between group size and efficiency has been documented in social insects. Moreover, when food items were clustered, groups where robots could recruit other robots in an ant-like manner were more efficient than groups without information transfer, suggesting that group dynamics of swarms of robots may follow rules similar to those governing social insects