Erratum: The chemistry of transient molecular cloud cores

We assume that some, but not all, of the structure observed in molecular clouds is associated with transient features which are not bound by self-gravity. We investigate the chemistry of a transient density fluctuation, with properties similar to those of a core within a molecular cloud. We run a multipoint chemical code through a core's condensation from a diffuse medium to its eventual dispersion, over a period of ∼1 Myr. The dynamical description adopted for our study is based on an understanding of a particular mechanism, involving slow-mode wave excitation, for transient structure formation which so far has been studied in detail only with plane-parallel models in which self-gravity has not been included. We find a significant enhancement of the chemical composition of the core material on its return to diffuse conditions, whilst the expansion of the core as it disperses moves this material out to large distances from the core centre. This process transports molecular species formed in the high-density regions out into the diffuse medium. Chemical enrichment of the cloud as a whole also occurs, as other cores of various sizes, life-spans and separations evolve throughout. Enrichment is strongly affected by freeze-out on to dust grains, which takes place in high-density, high visual extinction regions. As the core disperses after reaching its peak density and the visual extinction drops below a critical value, grain mantles are evaporated back into the gas phase, initiating more chemistry. The influence of the sizes, masses and cycle periods of cores will be large both for the level of chemical enrichment of a dark cloud and ultimately for the low-mass star formation rate. The cores in which stars form are almost certainly bound by their self-gravity and are not transient in the sense that the cores on which most of our study is focused are transient. Obviously, enrichment of the chemistry of low-density material will not take place if self-gravity prevents the re-expansion of a core. We also consider the case of a self-gravitating core, by holding its peak density conditions for a further 0.4 Myr. We find that the differences near the peak densities between transient and gravitationally bound cores are generally small, and the resultant column densities for objects near the peak densities do not provide definitive criteria for discriminating between transient and bound cores. However, increases in fractional abundances due to reinjection of mantle-borne species may provide a criterion for detection of a non-bound core

The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket

© 2015 International Union of Crystallography. Staphylococcus aureus is a common and serious cause of infection in humans. The bacterium expresses a cell-surface receptor that binds to, and strips haem from, human haemoglobin (Hb). The binding interface has previously been identified; however, the structural changes that promote haem release from haemoglobin were unknown. Here, the structure of the receptor-Hb complex is reported at 2.6 Å resolution, which reveals a conformational change in the α-globin F helix that disrupts the haem-pocket structure and alters the Hb quaternary interactions. These features suggest potential mechanisms by which the S. aureus Hb receptor induces haem release from Hb

Improved growth and morphological plasticity of <i>Haloferax volcanii</i>.

Some microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeon Haloferax volcanii commonly forms discoid-shaped ('plate') cells in culture, but may also be present as rods, and can develop into motile rods in soft agar, or longer filaments in certain biofilms. Here we report improvement of H. volcanii growth in both semi-defined and complex media by supplementing with eight trace element micronutrients. With these supplemented media, transient development of plate cells into uniformly shaped rods was clearly observed during the early log phase of growth; cells then reverted to plates for the late log and stationary phases. In media prepared with high-purity water and reagents, without supplemental trace elements, rods and other complex elongated morphologies ('pleomorphic rods') were observed at all growth stages of the culture; the highly elongated cells sometimes displayed a substantial tubule at one or less frequently both poles, as well as unusual tapered and highly curved forms. Polar tubules were observed forming by initial mid-cell narrowing or tubulation, causing a dumbbell-like shape, followed by cell division towards one end. Formation of the uniform early log-phase rods, as well as the pleomorphic rods and tubules were dependent on the function of the tubulin-like cytoskeletal protein, CetZ1. Our results reveal the remarkable morphological plasticity of H. volcanii cells in response to multiple culture conditions, and should facilitate the use of this species in further studies of archaeal biology

Red blood cells (RBCs) visualisation in bifurcations and bends

Bifurcating networks are commonly found in nature. One example is the microvascular system, composed of blood vessels consecutively branching into daughter vessels, driving the blood into the capillaries, where the red blood cells (RBCs) are responsible for delivering O 2 and up taking cell waste and CO 2 . In this preliminary study, we explore a microfluidic bifurcating geometry inspired by such biological models, for investigating RBC partitioning as well as RBC-plasma separation favored by the consecutive bifurcating channels. A biomimetic design rule [1] based on Murray’s law [2] was used to set the channels’ dimensions along the network, which consists of consecutive bifurcating channels of reducing diameter. The ability to apply differential flow resistances by controlling the flow rates at the end of the network allowed us to monitor the formation of a cell-free layer (CFL) for different flow conditions at haematocrits of 1% and 5%. We have also compared the values of CFL thickness determined directly by the measurement on the projection image created from a stack of images or indirectly by analyzing the intensity profile in the same projection. The results obtained from this study confirm the potential to study RBC partitioning along bifurcating networks, which could be of particular interest for the separation of RBCs from plasma in point-of-care devices.JF would like to thank Professor Graça Minas and her coworkers for providing the laboratory facilities and technical help during the experiments.info:eu-repo/semantics/publishedVersio

Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.

As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S. pneumoniae and an 18-base-pair DNA binding site-the E-site-found by our DNA mapping studies to bind drug strongly in the presence of topoisomerase IV (Leo et al. 2005 J. Biol. Chem. 280, 14 252-14 263, doi:10.1074/jbc.M500156200). Although the degree of antibiotic resistance towards fluoroquinolones is much lower than that of β-lactams and a range of ribosome-bound antibiotics, there is a pressing need to increase the diversity of members of this successful clinically used class of drugs. The quinolone moiety of the new 7,8-bridged agents ACHN-245 and ACHN-454 binds similarly to that of clinafloxocin, levofloxacin, moxifloxacin and trovofloxacin but the cyclic scaffold offers the possibility of chemical modification to produce interactions with other topoisomerase residues at the active site

Permutation entropy and statistical complexity analysis of turbulence in laboratory plasmas and the solar wind

The Bandt-Pompe permutation entropy and the Jensen-Shannon statistical complexity are used to analyze fluctuating time series of three different turbulent plasmas: the magnetohydrodynamic (MHD) turbulence in the plasma wind tunnel of the Swarthmore Spheromak Experiment (SSX), drift-wave turbulence of ion saturation current fluctuations in the edge of the Large Plasma Device (LAPD), and fully developed turbulent magnetic fluctuations of the solar wind taken from the Wind spacecraft. The entropy and complexity values are presented as coordinates on the CH plane for comparison among the different plasma environments and other fluctuation models. The solar wind is found to have the highest permutation entropy and lowest statistical complexity of the three data sets analyzed. Both laboratory data sets have larger values of statistical complexity, suggesting that these systems have fewer degrees of freedom in their fluctuations, with SSX magnetic fluctuations having slightly less complexity than the LAPD edge Isat. The CH plane coordinates are compared to the shape and distribution of a spectral decomposition of the wave forms. These results suggest that fully developed turbulence (solar wind) occupies the lower-right region of the CH plane, and that other plasma systems considered to be turbulent have less permutation entropy and more statistical complexity. This paper presents use of this statistical analysis tool on solar wind plasma, as well as on an MHD turbulent experimental plasma

Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH

Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc

A proton-cyclotron wave storm generated by unstable proton distribution functions in the solar wind

We use audification of 0.092 s cadence magnetometer data from the Wind spacecraft to identify waves with amplitudes >0.1 nT near the ion gyrofrequency (~0.1 Hz) with duration longer than 1 hr during 2008. We present one of the most common types of event for a case study and find it to be a proton-cyclotron wave storm, coinciding with highly radial magnetic field and a suprathermal proton beam close in density to the core distribution itself. Using linear Vlasov analysis, we conclude that the long-duration, large-amplitude waves are generated by the instability of the proton distribution function. The origin of the beam is unknown, but the radial field period is found in the trailing edge of a fast solar wind stream and resembles other events thought to be caused by magnetic field footpoint motion or interchange reconnection between coronal holes and closed field lines in the corona