Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population

Horizontal flow fields observed in Hinode G-band images. I. Methods

Context: The interaction of plasma motions and magnetic fields is an important mechanism, which drives solar activity in all its facets. For example, photospheric flows are responsible for the advection of magnetic flux, the redistribution of flux during the decay of sunspots, and the built-up of magnetic shear in flaring active regions. Aims: Systematic studies based on G-band data from the Japanese Hinode mission provide the means to gather statistical properties of horizontal flow fields. This facilitates comparative studies of solar features, e.g., G-band bright points, magnetic knots, pores, and sunspots at various stages of evolution and in distinct magnetic environments, thus, enhancing our understanding of the dynamic Sun. Methods: We adapted Local Correlation Tracking (LCT) to measure horizontal flow fields based on G-band images obtained with the Solar Optical Telescope on board Hinode. In total about 200 time-series with a duration between 1-16 h and a cadence between 15-90 s were analyzed. Selecting both a high-cadence (dt = 15 s) and a long-duration (dT = 16 h) time-series enabled us to optimize and validate the LCT input parameters, hence, ensuring a robust, reliable, uniform, and accurate processing of a huge data volume. Results: The LCT algorithm produces best results for G-band images having a cadence of 60-90 s. If the cadence is lower, the velocity of slowly moving features will not be reliably detected. If the cadence is higher, the scene on the Sun will have evolved too much to bear any resemblance with the earlier situation. Consequently, in both instances horizontal proper motions are underestimated. The most reliable and yet detailed flow maps are produced using a Gaussian kernel with a size of 2560 km x 2560 km and a full-width-at-half-maximum (FWHM) of 1200 km (corresponding to the size of a typical granule) as sampling window.Comment: 12 pages, 8 figures, 4 tables, accepted for publication in Astronomy and Astrophysic

Role of Extracellular Carbonic Anhydrase in Dissolved Inorganic Carbon Uptake in Alkaliphilic Phototrophic Biofilm

Alkaline Soda Lakes are extremely productive ecosystems, due to their high dissolved inorganic carbon (DIC) concentrations. Here, we studied the dynamics of the carbonate system, in particular, the role of extracellular carbonic anhydrase (eCA) of an alkaliphilic phototrophic biofilm composed of bacteria enriched from soda lake benthic mats. By using measurements with microsensors and membrane inlet mass spectrometry, combined with mathematical modeling, we show how eCA controls DIC uptake. In our experiments, the activity of eCA varied four-fold, and was controlled by the bicarbonate concentration during growth: a higher bicarbonate concentration led to lower eCA activity. Inhibition of eCA decreased both the net and the gross photosynthetic productivities of the investigated biofilms. After eCA inhibition, the efflux of carbon dioxide (CO2) from the biofilms increased two- to four-fold. This could be explained by the conversion of CO2, leaking from cyanobacterial cells, by eCA, to bicarbonate. Bicarbonate is then taken up again by the cyanobacteria. In suspensions, eCA reduced the CO2 leakage to the bulk medium from 90 to 50%. In biofilms cultivated at low bicarbonate concentration (similar to 0.13 mM), the oxygen production was reduced by a similar ratio upon eCA inhibition. The role of eCA in intact biofilms was much less significant compared to biomass suspensions, as CO2 loss to the medium is reduced due to mass transfer resistance

Simulation of a flux emergence event and comparison with observations by Hinode

We study the observational signature of flux emergence in the photosphere using synthetic data from a 3D MHD simulation of the emergence of a twisted flux tube. Several stages in the emergence process are considered. At every stage we compute synthetic Stokes spectra of the two iron lines Fe I 6301.5 {\AA} and Fe I 6302.5 {\AA} and degrade the data to the spatial and spectral resolution of Hinode's SOT/SP. Then, following observational practice, we apply Milne-Eddington-type inversions to the synthetic spectra in order to retrieve various atmospheric parameters and compare the results with recent Hinode observations. During the emergence sequence, the spectral lines sample different parts of the rising flux tube, revealing its twisted structure. The horizontal component of the magnetic field retrieved from the simulations is close to the observed values. The flattening of the flux tube in the photosphere is caused by radiative cooling, which slows down the ascent of the tube to the upper solar atmosphere. Consistent with the observations, the rising magnetized plasma produces a blue shift of the spectral lines during a large part of the emergence sequence.Comment: A&A Letter, 3 figure

Simulation of the Formation of a Solar Active Region

We present a radiative magnetohydrodynamics simulation of the formation of an Active Region on the solar surface. The simulation models the rise of a buoyant magnetic flux bundle from a depth of 7.5 Mm in the convection zone up into the solar photosphere. The rise of the magnetic plasma in the convection zone is accompanied by predominantly horizontal expansion. Such an expansion leads to a scaling relation between the plasma density and the magnetic field strength such that $B\propto\varrho^{1/2}$. The emergence of magnetic flux into the photosphere appears as a complex magnetic pattern, which results from the interaction of the rising magnetic field with the turbulent convective flows. Small-scale magnetic elements at the surface first appear, followed by their gradual coalescence into larger magnetic concentrations, which eventually results in the formation of a pair of opposite polarity spots. Although the mean flow pattern in the vicinity of the developing spots is directed radially outward, correlations between the magnetic field and velocity field fluctuations allow the spots to accumulate flux. Such correlations result from the Lorentz-force driven, counter-streaming motion of opposite-polarity fragments. The formation of the simulated Active Region is accompanied by transient light bridges between umbrae and umbral dots. Together with recent sunspot modeling, this work highlights the common magnetoconvective origin of umbral dots, light bridges and penumbral filaments.Comment: Accepted for publication in Ap

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

Background: Anaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute approximately 50% of the nitrogen in the atmosphere. It is currently unknown which proteins constitute the organellar proteome and how anammox bacteria are able to specifically target organellar and cell-envelope proteins to their correct final destinations. Experimental approaches are complicated by the absence of pure cultures and genetic accessibility. However, the genome of the anammox bacterium Candidatus "Kuenenia stuttgartiensis" has recently been sequenced. Here, we make use of these genome data to predict the organellar sub-proteome and address the molecular basis of protein sorting in anammox bacteria. Results: Two training sets representing organellar (30 proteins) and cell envelope (59 proteins) proteins were constructed based on previous experimental evidence and comparative genomics. Random forest (RF) classifiers trained on these two sets could differentiate between organellar and cell envelope proteins with ~89% accuracy using 400 features consisting of frequencies of two adjacent amino acid combinations. A physicochemically distinct organellar sub-proteome containing 562 proteins was predicted with the best RF classifier. This set included almost all catabolic and respiratory factors encoded in the genome. Apparently, the cytoplasmic membrane performs no catabolic functions. We predict that the Tat-translocation system is located exclusively in the organellar membrane, whereas the Sec-translocation system is located on both the organellar and cytoplasmic membranes. Canonical signal peptides were predicted and validated experimentally, but a specific (N- or C-terminal) signal that could be used for protein targeting to the organelle remained elusive. Conclusions: A physicochemically distinct organellar sub-proteome was predicted from the genome of the anammox bacterium K. stuttgartiensis. This result provides strong in silico support for the existing experimental evidence for the existence of an organelle in this bacterium, and is an important step forward in unravelling a geochemically relevant case of cytoplasmic differentiation in bacteria. The predicted dual location of the Sec-translocation system and the apparent absence of a specific N- or C-terminal signal in the organellar proteins suggests that additional chaperones may be necessary that act on an as-yet unknown property of the targeted proteins

Забезпечення якості медичної допомоги в умовах запровадження в Україні обов'язкового медичного страхування (адміністративно-правові принципи та складові елементи)

Аналізуються адміністративно правові принципи та складові елементи забезпечення якості медичної допомоги в умовах запровадження в Україні обов’язкового медичного страхування. Особлива увага приділена питанням контролю якості медичної допомоги. Ключові слова: якість надання медичної допомоги, обов’язкове медичне страхування.Анализируются административно правовые принципы и составляющие части обеспечения качества медицинской помощи в условиях утверждения в Украине обязательного медицинского страхования. Особое внимание уделено вопросам контроля качества оказания медицинской помощи. Ключевые слова: качество медицинской помощи, обязательное медицинское страхование.Administrative and legal principles and component parts of providing medical care quality in conditions of introducing compulsory medical insurance in Ukraine are analyzed in the article. Special attention is paid to the control provision of medical care quality. Key words: medical care quality, compulsory medical insurance

Psychiatry during the Nazi era: ethical lessons for the modern professional

For the first time in history, psychiatrists during the Nazi era sought to systematically exterminate their patients. However, little has been published from this dark period analyzing what may be learned for clinical and research psychiatry. At each stage in the murderous process lay a series of unethical and heinous practices, with many psychiatrists demonstrating a profound commitment to the atrocities, playing central, pivotal roles critical to the success of Nazi policy. Several misconceptions led to this misconduct, including allowing philosophical constructs to define clinical practice, focusing exclusively on preventative medicine, allowing political pressures to influence practice, blurring the roles of clinicians and researchers, and falsely believing that good science and good ethics always co-exist. Psychiatry during this period provides a most horrifying example of how science may be perverted by external forces. It thus becomes crucial to include the Nazi era psychiatry experience in ethics training as an example of proper practice gone awry

Intermittency in the photosphere and corona above an active region

Recent studies undoubtedly demonstrate that the magnetic field in the photosphere and corona is an intermittent structure, which offers new views on the underlying physics. In particular, such problems as the existence in the corona of localized areas with extremely strong resistivity (required to explain magnetic reconnection of all scales) and the interchange between small and large scales (required in study of the photosphere/corona coupling), to name a few, can be easily captured by the concept of intermittency. This study is focused on simultaneous time variations of intermittency properties derived in the photosphere, chromosphere and corona. We analyzed data for NOAA AR 10930 acquired between Dec 08, 2006 12:00 UT and Dec 13, 2006 18:45 UT. Photospheric intermittency was inferred from Hinode magnetic field measurements, while intermittency in the transition region and corona was derived from Nobeyama 9 GHz radio polarization measurements, high cadence Hinode/XRT/Be-thin data as well as GOES 1-8\AA flux. Photospheric dynamics and its possible relationship with the intermittency variations were also analyzed by calculating the kinetic vorticity. For this case study we found the following chain of events. Intermittency of the photospheric magnetic field peaked after the specific kinetic vorticity of plasma flows in the AR reached its maximum level (4 hour time delay). In turn, gradual increase of coronal intermittency occurred after the peak of the photospheric intermittency. The time delay between the peak of photospheric intermittency and the occurrence of the first strong (X3.4) flare was approximately 1.3 days. Our analysis seems to suggest that the enhancement of intermittency/complexity first occurs in the photosphere and is later transported toward the corona

An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by 31P NMR

The cytoplasm of anaerobic ammonium oxidizing (anammox) bacteria consists of three compartments separated by membranes. It has been suggested that a proton motive force may be generated over the membrane of the innermost compartment, the “anammoxosome”. 31P nuclear magnetic resonance (NMR) spectroscopy was employed to investigate intracellular pH differences in the anammox bacterium Kuenenia stuttgartiensis. With in vivo NMR, spectra were recorded of active, highly concentrated suspensions of K. stuttgartiensis in a wide-bore NMR tube. At different external pH values, two stable and distinct phosphate peaks were apparent in the recorded spectra. These peaks were equivalent with pH values of 7.3 and 6.3 and suggested the presence of a proton motive force over an intracytoplasmic membrane in K. stuttgartiensis. This study provides for the second time—after discovery of acidocalcisome-like compartments in Agrobacterium tumefaciens—evidence for an intracytoplasmic pH gradient in a chemotrophic prokaryotic cell