Ecology of Thioploca spp.: Nitrate and sulfur storage in relation to chemical microgradients and influence of Thioploca spp. on the sedimentary nitrogen cycle

Microsensors, including a recently developed NO3 − biosensor, were applied to measure O2 and NO3 − profiles in marine sediments from the upwelling area off central Chile and to investigate the influence of Thioploca spp. on the sedimentary nitrogen metabolism. The studies were performed in undisturbed sediment cores incubated in a small laboratory flume to simulate the environmental conditions of low O2, high NO3 −, and bottom water current. On addition of NO3 −and NO2 −, Thioploca spp. exhibited positive chemotaxis and stretched out of the sediment into the flume water. In a core densely populated with Thioploca, the penetration depth of NO3 − was only 0.5 mm and a sharp maximum of NO3 − uptake was observed 0.5 mm above the sediment surface. In sediments with only fewThioploca spp., NO3 − was detectable down to a depth of 2 mm and the maximum consumption rates were observed within the sediment. No chemotaxis toward nitrous oxide (N2O) was observed, which is consistent with the observation that Thioploca does not denitrify but reduces intracellular NO3 − to NH4 +. Measurements of the intracellular NO3 − and S0 pools inThioploca filaments from various depths in the sediment gave insights into possible differences in the migration behavior between the different species. Living filaments containing significant amounts of intracellular NO3 − were found to a depth of at least 13 cm, providing final proof for the vertical shuttling of Thioploca spp. and nitrate transport into the sediment

Astrophysics in 2006

The fastest pulsar and the slowest nova; the oldest galaxies and the youngest stars; the weirdest life forms and the commonest dwarfs; the highest energy particles and the lowest energy photons. These were some of the extremes of Astrophysics 2006. We attempt also to bring you updates on things of which there is currently only one (habitable planets, the Sun, and the universe) and others of which there are always many, like meteors and molecules, black holes and binaries.Comment: 244 pages, no figure

Digital support interventions for the self-management of low back pain: a systematic review

Background: Low back pain (LBP) is a common cause of disability and is ranked as the most burdensome health condition globally. Self-management, including components on increased knowledge, monitoring of symptoms, and physical activity, are consistently recommended in clinical guidelines as cost-effective strategies for LBP management and there is increasing interest in the potential role of digital health. Objective: The study aimed to synthesize and critically appraise published evidence concerning the use of interactive digital interventions to support self-management of LBP. The following specific questions were examined: (1) What are the key components of digital self-management interventions for LBP, including theoretical underpinnings? (2) What outcome measures have been used in randomized trials of digital self-management interventions in LBP and what effect, if any, did the intervention have on these? and (3) What specific characteristics or components, if any, of interventions appear to be associated with beneficial outcomes? Methods: Bibliographic databases searched from 2000 to March 2016 included Medline, Embase, CINAHL, PsycINFO, Cochrane Library, DoPHER and TRoPHI, Social Science Citation Index, and Science Citation Index. Reference and citation searching was also undertaken. Search strategy combined the following concepts: (1) back pain, (2) digital intervention, and (3) self-management. Only randomized controlled trial (RCT) protocols or completed RCTs involving adults with LBP published in peer-reviewed journals were included. Two reviewers independently screened titles and abstracts, full-text articles, extracted data, and assessed risk of bias using Cochrane risk of bias tool. An independent third reviewer adjudicated on disagreements. Data were synthesized narratively. Results: Of the total 7014 references identified, 11 were included, describing 9 studies: 6 completed RCTs and 3 protocols for future RCTs. The completed RCTs included a total of 2706 participants (range of 114-1343 participants per study) and varied considerably in the nature and delivery of the interventions, the duration/definition of LBP, the outcomes measured, and the effectiveness of the interventions. Participants were generally white, middle aged, and in 5 of 6 RCT reports, the majority were female and most reported educational level as time at college or higher. Only one study reported between-group differences in favor of the digital intervention. There was considerable variation in the extent of reporting the characteristics, components, and theories underpinning each intervention. None of the studies showed evidence of harm. Conclusions: The literature is extremely heterogeneous, making it difficult to understand what might work best, for whom, and in what circumstances. Participants were predominantly female, white, well educated, and middle aged, and thus the wider applicability of digital self-management interventions remains uncertain. No information on cost-effectiveness was reported. The evidence base for interactive digital interventions to support patient self-management of LBP remains weak

The 3-D Structure of SN 1987A's inner Ejecta

Twenty years after the explosion of SN 1987A, we are now able to observe the three-dimensional spatially resolved inner ejecta. Detailed mapping of newly synthesised material and its radioactive decay daughter products sheds light on the explosion mechanism. This may reveal the geometry of the explosion and its connection to the equatorial ring and the outer rings around SN 1987A. We have used integral field spectroscopy to image the supernova ejecta and the equatorial ring in the emission lines of [Si I]+[Fe II] and He I. The spectral information can be mapped into a radial velocity image revealing the expansion of the ejecta both as projected onto the sky and perpendicular to the sky plane. The inner ejecta are spatially resolved in a North-South direction and are clearly asymmetric. We argue that the bulk of the ejecta is situated in the same plane as defined by the equatorial ring and does not form a bipolar structure as has been suggested. The exact shape of the ejecta is modelled and we find that an elongated triaxial ellipsoid fits the observations best. From our spectral analyses of the ejecta spectrum we find that most of the He I, [Si I] and [Fe I-II] emission originates in the core material which has undergone explosive nucleosynthesis. The He I emission may be the result of alpha-rich freeze-out if the positron energy is deposited locally. Our observations clearly indicate a non-symmetric explosion mechanism for SN 1987A. The elongation and velocity asymmetries point towards a large-scale spatial non-spherical distribution as predicted in recent explosion models. The orientation of the ejecta in the plane of the equatorial ring argues against a jet-induced explosion through the poles due to stellar rotation.Comment: Above abstract is abridged. 11 pages, 9 figures. Accepted July 1st 2010 by Astronomy and Astrophysic

Modifications to the foot-and-mouth disease virus 2A peptide; influence on polyprotein processing and virus replication

ABSTRACT Foot-and-mouth disease virus (FMDV) has a positive-sense single-stranded RNA (ssRNA) genome that includes a single, large open reading frame encoding a polyprotein. The cotranslational “cleavage” of this polyprotein at the 2A/2B junction is mediated by the 2A peptide (18 residues in length) using a nonproteolytic mechanism termed “ribosome skipping” or “StopGo.” Multiple variants of the 2A polypeptide with this property among the picornaviruses share a conserved C-terminal motif [D(V/I)E(S/T)NPG↓P]. The impact of 2A modifications within this motif on FMDV protein synthesis, polyprotein processing, and virus viability were investigated. Amino acid substitutions are tolerated at residues E 14 , S 15 , and N 16 within the 2A sequences of infectious FMDVs despite their reported “cleavage” efficiencies at the 2A/2B junction of only ca. 30 to 50% compared to that of the wild type (wt). In contrast, no viruses containing substitutions at residue P 17 , G 18 , or P 19 , which displayed little or no “cleavage” activity in vitro , were rescued, but wt revertants were obtained. The 2A substitutions impaired the replication of an FMDV replicon. Using transient-expression assays, it was shown that certain amino acid substitutions at residues E 14 , S 15 , N 16 , and P 19 resulted in partial “cleavage” of a protease-free polyprotein, indicating that these specific residues are not essential for cotranslational “cleavage.” Immunofluorescence studies, using full-length FMDV RNA transcripts encoding mutant 2A peptides, indicated that the 2A peptide remained attached to adjacent proteins, presumably 2B. These results show that efficient “cleavage” at the 2A/2B junction is required for optimal virus replication. However, maximal StopGo activity does not appear to be essential for the viability of FMDV. IMPORTANCE Foot-and-mouth disease virus (FMDV) causes one of the most economically important diseases of farm animals. Cotranslational “cleavage” of the FMDV polyprotein precursor at the 2A/2B junction, termed StopGo, is mediated by the short 2A peptide through a nonproteolytic mechanism which leads to release of the nascent protein and continued translation of the downstream sequence. Improved understanding of this process will not only give a better insight into how this peptide influences the FMDV replication cycle but may also assist the application of this sequence in biotechnology for the production of multiple proteins from a single mRNA. Our data show that single amino acid substitutions in the 2A peptide can have a major influence on viral protein synthesis, virus viability, and polyprotein processing. They also indicate that efficient “cleavage” at the 2A/2B junction is required for optimal virus replication. However, maximal StopGo activity is not essential for the viability of FMDV. </jats:p

Selection of functional 2A sequences within foot-and-mouth disease virus; requirements for the NPGP motif with a distinct codon bias

Foot-and-mouth disease virus (FMDV) has a positive-sense ssRNA genome including a single, large, open reading frame. Splitting of the encoded polyprotein at the 2A/2B junction is mediated by the 2A peptide (18 residues long), which induces a nonproteolytic, cotranslational “cleavage” at its own C terminus. A conserved feature among variants of 2A is the C-terminal motif N16P17G18/P19, where P19 is the first residue of 2B. It has been shown previously that certain amino acid substitutions can be tolerated at residues E14, S15, and N16 within the 2A sequence of infectious FMDVs, but no variants at residues P17, G18, or P19 have been identified. In this study, using highly degenerate primers, we analyzed if any other residues can be present at each position of the NPG/P motif within infectious FMDV. No alternative forms of this motif were found to be encoded by rescued FMDVs after two, three, or four passages. However, surprisingly, a clear codon preference for the wt nucleotide sequence encoding the NPGP motif within these viruses was observed. Indeed, the codons selected to code for P17 and P19 within this motif were distinct; thus the synonymous codons are not equivalent.</jats:p

Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholera and are stabilized by a double signaling domain receptor DosM

Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae’s cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array