Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p

COMPUCEA 2nd generation performance evaluation

COMPUCEA (Combined Procedure for Uranium Concentration and Enrichment Assay) is used for on-site analytical measurements in support of joint Euratom-IAEA inspections during physical inventory verification (PIV) campaigns in European Low-Enriched Uranium (LEU) fuel fabrication plants. The analyses provided on site during the PIV involve the accurate determination of the uranium element content and of the U-235 enrichment in verification samples (uranium product samples of solid form , i.e. powders, pellets) selected by the Safeguards inspectors. These samples are dissolved and then measured by energy-dispersive X-ray absorption edge spectrometry (L-edge densitometry) to obtain the uranium elemental content and gamma spectrometry with a Lanthanum-bromide detector for the U-235 abundance determination. The second generation of COMPUCEA equipment is compact, rugged and ready-to use directly after transport, no cooling of the detectors with liquid nitrogen is required. A software package for comfortable instrument control and data handling has been implemented. The paper describes the technique, setup and calibration procedure of the instrument. Results from PIV campaigns and comparisons between COMPUCEA results with data obtained by remote analysis with a qualified primary analytical method are presented, which demonstrate the performance of the technique. The achieved uncertainties are well within the international target values. First results obtained with a sandwich detector configuration for enhanced detection efficiency of the passive gamma spectrometry and a small separate X-ray fluorescence unit for the pre-screening of the samples for their Gd content are discussed.JRC.E.7-Nuclear Safeguards and Forensic

Transcriptional and Translational Regulatory Responses to Iron Limitation in the Globally Distributed Marine Bacterium Candidatus Pelagibacter ubique

Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity

Non-equilibrium induction of tin in germanium: towards direct bandgap Ge1−xSnx nanowires

The development of non-equilibrium group IV nanoscale alloys is critical to achieving new functionalities, such as the formation of a direct bandgap in a conventional indirect bandgap elemental semiconductor. Here, we describe the fabrication of uniform diameter, direct bandgap Ge1−xSnx alloy nanowires, with a Sn incorporation up to 9.2 at.%, far in excess of the equilibrium solubility of Sn in bulk Ge, through a conventional catalytic bottom-up growth paradigm using noble metal and metal alloy catalysts. Metal alloy catalysts permitted a greater inclusion of Sn in Ge nanowires compared with conventional Au catalysts, when used during vapour–liquid–solid growth. The addition of an annealing step close to the Ge-Sn eutectic temperature (230 °C) during cool-down, further facilitated the excessive dissolution of Sn in the nanowires. Sn was distributed throughout the Ge nanowire lattice with no metallic Sn segregation or precipitation at the surface or within the bulk of the nanowires. The non-equilibrium incorporation of Sn into the Ge nanowires can be understood in terms of a kinetic trapping model for impurity incorporation at the triple-phase boundary during growth

Understanding informal payments in health care: motivation of health workers in Tanzania

<p>Abstract</p> <p>Background</p> <p>There is growing evidence that informal payments for health care are fairly common in many low- and middle-income countries. Informal payments are reported to have a negative consequence on equity and quality of care; it has been suggested, however, that they may contribute to health worker motivation and retention. Given the significance of motivation and retention issues in human resources for health, a better understanding of the relationships between the two phenomena is needed. This study attempts to assess whether and in what ways informal payments occur in Kibaha, Tanzania. Moreover, it aims to assess how informal earnings might help boost health worker motivation and retention.</p> <p>Methods</p> <p>Nine focus groups were conducted in three health facilities of different levels in the health system. In total, 64 health workers participated in the focus group discussions (81% female, 19% male) and where possible, focus groups were divided by cadre. All data were processed and analysed by means of the NVivo software package.</p> <p>Results</p> <p>The use of informal payments in the study area was confirmed by this study. Furthermore, a negative relationship between informal payments and job satisfaction and better motivation is suggested. Participants mentioned that they felt enslaved by patients as a result of being bribed and this resulted in loss of self-esteem. Furthermore, fear of detection was a main demotivating factor. These factors seem to counterbalance the positive effect of financial incentives. Moreover, informal payments were not found to be related to retention of health workers in the public health system. Other factors such as job security seemed to be more relevant for retention.</p> <p>Conclusion</p> <p>This study suggests that the practice of informal payments contributes to the general demotivation of health workers and negatively affects access to health care services and quality of the health system. Policy action is needed that not only provides better financial incentives for individuals but also tackles an environment in which corruption is endemic.</p

Function and Regulation of Vibrio campbellii Proteorhodopsin: Acquired Phototrophy in a Classical Organoheterotroph

Proteorhodopsins (PRs) are retinal-binding photoproteins that mediate light-driven proton translocation across prokaryotic cell membranes. Despite their abundance, wide distribution and contribution to the bioenergy budget of the marine photic zone, an understanding of PR function and physiological significance in situ has been hampered as the vast majority of PRs studied to date are from unculturable bacteria or culturable species that lack the tools for genetic manipulation. In this study, we describe the presence and function of a horizontally acquired PR and retinal biosynthesis gene cluster in the culturable and genetically tractable bioluminescent marine bacterium Vibrio campbellii. Pigmentation analysis, absorption spectroscopy and photoinduction assays using a heterologous over-expression system established the V. campbellii PR as a functional green light absorbing proton pump. In situ analyses comparing PR expression and function in wild type (WT) V. campbellii with an isogenic ΔpR deletion mutant revealed a marked absence of PR membrane localization, pigmentation and light-induced proton pumping in the ΔpR mutant. Comparative photoinduction assays demonstrated the distinct upregulation of pR expression in the presence of light and PR-mediated photophosphorylation in WT cells that resulted in the enhancement of cellular survival during respiratory stress. In addition, we demonstrate that the master regulator of adaptive stress response and stationary phase, RpoS1, positively regulates pR expression and PR holoprotein pigmentation. Taken together, the results demonstrate facultative phototrophy in a classical marine organoheterotrophic Vibrio species and provide a salient example of how this organism has exploited lateral gene transfer to further its adaptation to the photic zone

Oceanic loading of wildfire-derived organic compounds from a small mountainous river

Copyright 2008 by the American Geophysical Union.Small mountainous rivers (SMRs) export substantial amounts of sediment into the world's oceans. The concomitant yield of organic carbon (OC) associated with this class of rivers has also been shown to be significant and compositionally unique. We report here excessively high loadings of polycyclic aromatic hydrocarbons (PAHs), lignin, and levoglucosan, discharged from the Santa Clara River into the Santa Barbara Channel. The abundance of PAHs, levoglucosan, and lignin in Santa Barbara Channel sediments ranged from 201.7 to 1232.3 ng gdw−1, 1.3 to 6.9 μg gdw−1, and 0.3 to 2.2 mg per 100 mg of the sedimentary OC, respectively. Assuming a constant rate of sediment accumulation, the annual fluxes of PAHs, levoglucosan, and lignin, to the Santa Barbara Channel were respectively, 885.5 ± 170.2 ng cm−2 a−1, 3.5 ± 1.9 μg cm−2 a−1 and 1.4 ± 0.3 mg per 100 mg OC cm−2 a−1, over ∼30 years. The close agreement between PAHs, levoglucosan, and lignin abundance suggests that the depositional flux of these compounds is largely biomass combustion-derived. To that end, use of the Santa Clara River as a model for SMRs suggests this class of rivers may be one of the largest contributors of pyrolyzed carbon to coastal systems and the open ocean. Wildfire associated carbon discharged from other high yield fluvial systems, when considered collectively, may be a significant source of lignin, pyrolytic PAHs, and other pyrogenic compounds to the ocean. Extrapolating these methods over geologic time may offer useful historical information about carbon sequestration and burial in coastal sediments and affect coastal carbon budgets

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves with more refined tools and expanded taxon sampling. We investigated mitochondrial origins with the benefit of new, deeply branching genome sequences from the ancient and prolific SAR11 clade of Alphaproteobacteria and publicly available alphaproteobacterial and mitochondrial genome sequences. Using the automated phylogenomic pipeline Hal, we systematically studied the effect of taxon sampling and missing data to accommodate small mitochondrial genomes. The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life