Kinematics of dense gas in the L1495 filament

We study the kinematics of the dense gas of starless and protostellar cores traced by the N2D+(2-1), N2H+(1-0), DCO+(2-1), and H13CO+(1-0) transitions along the L1495 filament and the kinematic links between the cores and the surrounding molecular cloud. We measure velocity dispersions, local and total velocity gradients and estimate the specific angular momenta of 13 dense cores in the four transitions using the on-the-fly observations with the IRAM 30 m antenna. To study a possible connection to the filament gas, we use the fit results of the C18O(1-0) survey performed by Hacar et al. (2013). All cores show similar properties along the 10 pc-long filament. N2D+(2-1) shows the most centrally concentrated structure, followed by N2H+(1-0) and DCO+(2-1), which show similar spatial extent, and H13CO+(1-0). The non-thermal contribution to the velocity dispersion increases from higher to lower density tracers. The change of magnitude and direction of the total velocity gradients depending on the tracer used indicates that internal motions change at different depths within the cloud. N2D+ and N2H+ show smaller gradients than the lower density tracers DCO+ and H13CO+, implying a loss of specific angular momentum at small scales. At the level of cloud-core transition, the core's external envelope traced by DCO+ and H13CO+ is spinning up, consistent with conservation of angular momentum during core contraction. C18O traces the more extended cloud material whose kinematics is not affected by the presence of dense cores. The decrease in specific angular momentum towards the centres of the cores shows the importance of local magnetic fields to the small scale dynamics of the cores. The random distributions of angles between the total velocity gradient and large scale magnetic field suggests that the magnetic fields may become important only in the high density gas within dense cores.Comment: Accepted for publication in A&A. The abstract is shortene

Molecular dissection of translation initiation factor IF2. Evidence for two structural and functional domains.

By means of limited proteolysis of Bacillus stearothermophilus initiation factor IF2 and genetic manipulation of its structural gene, infB, we have been able to produce (or hyperproduce) and purify two polypeptide fragments corresponding to two structurally and functionally separate domains of the protein. The first is the G-domain (approximately 41 kDa), which makes up the central part of the molecule and contains the conserved structural elements found in all GTP/GDP-binding sites of G-proteins. This domain is resistant to proteolysis in the presence of GTP or GDP, retains the capacity to interact with the 50 S subunit, binds weakly to the 30 S subunit, and displays ribosome-dependent GTPase activity with an approximately 2-fold higher Km for GTP and the same Vmax as compared with intact IF2. The second is the C-domain (approximately 24 kDa), which corresponds to the COOH-terminal part of IF2 and constitutes an extraordinarily compact domain containing the fMet-tRNA binding site of IF2. In spite of its negligible affinity for the ribosomes, the C-domain weakly stimulates the ribosomal binding of fMet-tRNA, presumably by affecting the conformation of the initiator tRNA molecule

Ribosomal selection of mRNAs with degenerate initiation triplets

To assess the influence of degenerate initiation triplets on mRNA recruitment by ribosomes, five mRNAs identical but for their start codon (AUG, GUG, UUG, AUU and AUA) were offered to a limiting amount of ribosomes, alone or in competition with an identical AUGmRNA bearing a mutation conferring different electrophoretic mobility to the product. Translational efficiency and competitiveness of test mRNAs toward this AUGmRNA were determined quantifying the relative amounts of the electrophoretically separated wt and mutated products synthesized in vitro and found to be influenced to different extents by the nature of their initiation triplet and by parameters such as temperature and nutrient availability in the medium. The behaviors of AUAmRNA, UUGmRNA and AUGmRNA were the same between 20 and 40°C whereas the GUG and AUUmRNAs were less active and competed poorly with the AUGmRNA, especially at low temperature. Nutrient limitation and preferential inhibition by ppGpp severely affected activity and competitiveness of all mRNAs bearing non-AUG starts, the UUGmRNA being the least affected. Overall, our data indicate that beyond these effects exclusively due to the degenerate start codons within an optimized translational initiation region, an important role is played by the context in which the rare start codons are present

Strategies for Oligoribonucleotide Synthesis According to the Phosphoramidite Method

Advances in oligoribonucleotide synthesis have lagged behind those in oligodeoxyribonucleotide synthesis because of the difficulty in identifying orthogonal protecting groups for the 2′‐ and 5′‐hydroxyls. Adaptation of the phosphoramidite method for DNA synthesis to RNA synthesis has greatly improved our understanding of RNA. It allows site‐specific introduction of modified nucleosides to any position in an RNA molecule, as well as introduction of variations at multiple sites in the molecule. This overview discusses issues that are relevant to RNA synthesis by the phosphoramidite approach, including supports used, activation of the ribonucleoside phosphoramidites, and protection of the nucleobase, phosphate, and 2′‐ and 5′‐hydroxyls.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143793/1/cpnc0305.pd

Dietary nitrate increases arginine availability and protects mitochondrial complex I and energetics in the hypoxic rat heart

This is the final version. It was first published by Wiley in The Journal of Physiology at http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2014.275263/abstract.Hypoxic exposure is associated with impaired cardiac energetics in humans and altered mitochondrial function, with suppressed complex I-supported respiration, in rat heart. This response might limit reactive oxygen species (ROS) generation, but at the cost of impaired electron transport chain (ETC) activity. Dietary nitrate supplementation improves mitochondrial efficiency and can promote tissue oxygenation by enhancing blood flow. We therefore hypothesised that ETC dysfunction, impaired energetics and oxidative damage in the hearts of rats exposed to chronic hypoxia could be alleviated by sustained administration of a moderate dose of dietary nitrate. Male Wistar rats (n=40) were given water supplemented with 0.7 mmol/L NaCl (as control) or 0.7 mmol/L NaNO3, elevating plasma nitrate levels by 80%, and were exposed to 13% O2 (hypoxia) or normoxia (n=10 per group) for 14 days. Respiration rates, ETC protein levels, mitochondrial density, ATP content and protein carbonylation were measured in cardiac muscle. Complex I respiration rates and protein levels were 33% lower in hypoxic/NaCl rats compared with normoxic/NaCl controls. Protein carbonylation was 65% higher in hearts of hypoxic rats compared with controls, indicating increased oxidative stress, whilst ATP levels were 62% lower. Respiration rates, complex I protein and activity, protein carbonylation and ATP levels were all fully protected in the hearts of nitrate-supplemented hypoxic rats. Both in normoxia and hypoxia, dietary nitrate suppressed cardiac arginase expression and activity and markedly elevated cardiac L-arginine concentrations, unmasking a novel mechanism of action by which nitrate enhances tissue NO bioavailability. Dietary nitrate therefore alleviates metabolic abnormalities in the hypoxic heart, improving myocardial energetics

Progress of the National Air Quality Cooperation Programme (NSL)

Om de luchtkwaliteit in Nederland te verbeteren is het Nationaal Samenwerkingsprogramma Luchtkwaliteit (NSL) opgezet. In dit programma werken de Rijksoverheid en decentrale overheden samen om te zorgen dat Nederland overal tijdig aan de grenswaarden voor fijnstof (2011) en stikstofdioxide (2015) zal voldoen. Om de voortgang te volgen is bij het NSL een monitoringsprogramma opgezet. Centraal onderdeel daarvan is een rekeninstrument waarvoor de overheden de brongegevens aanleveren. De daaruitvolgende rekenresultaten zijn vervolgens door het Bureau Monitoring (samenwerkingsverband RIVM en InfoMil) samengevoegd in voorliggende voortgangsrapportage. De prognoses voor 2011 en 2015 laten zien dat voor een groot deel van Nederland de resultaten onder de Europese grenswaarden voor PM10 (fijnstof) en NO2 liggen. Op een aantal plekken zijn er wel nieuwe of grotere overschrijdingen van de PM10- en NO2-grenswaarden zichtbaar. Bij de fijnstof (PM10) overschrijdingen gaat het hoofdzakelijk om locaties bij veehouderijen en een aantal industriele gebieden. Vooral nabij veehouderijen is op een aantal plekken nog sprake van grote overschrijdingen die lastig voor medio 2011 op te lossen zijn. De huidige prognose voor de concentraties stikstofdioxide in 2015 laat een minder gunstige ontwikkeling zien ten opzichte van wat is berekend in de vaststelling van het NSL. Dit komt voor een belangrijk deel door tegenvallende verkeersemissies wat heeft geleid tot een aantal nieuwe overschrijdingen. De nu in de prognoses berekende concentraties liggen op veel locaties net onder de grenswaarde. Met veel concentraties net onder de grenswaarde neemt het aantal overschrijdingen snel toe bij een tegenvaller in een van de gemaakte aannamen. In combinatie met een grote en deels onbekende onzekerheid in de rekenresultaten vormt dit een risico voor het behalen van de doelstelling van het NSL.The NSL has been put in place to improve air quality in the Netherlands and to ensure that the Netherlands meets the date of compliance with the EU limit values for particulate matter and nitrogen dioxide. Local, regional and national authorities work together within the framework of this programme to ensure that these goals are met. A monitoring programme, centred around a specially designed assessment tool, has been set up to monitor the progress. This tool uses data that the participating authorities are required to provide as part of the annual monitoring cycle. The results of the tool have been bundled by the Bureau Monitoring into this progress report. The prognosis for 2011 and 2015, based on the results obtained using the assessment tool, are that the concentrations of PM10 and NO2 fall below the EU limit values in most parts of the Netherlands. However, exceedances of the limit values do occur at specific locations. For PM10, these exceedances mostly occur close to a number of industrial sites and stock farms. Particularly high exceedances in the vicinity of these stock farms will make it difficult to meet the limit values by mid 2011 at these locations. The prognostications for NO2 show a less favourable decline in NO2 concentrations than was modelled at the establishment of the NSL. This is mostly due to the decline in traffic emissions falling short of expectations, resulting in new exceedances. At many locations, the calculated concentrations in the prognostications fall just under the limit value and, consequently, there will be a large increase in the number of exceedances when one or more of the premises become less favourable. This possibility, together with the large and partially unknown uncertainty in the calculation results, add up to a risk for not meeting the limit values by the date of compliance.VRO