Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis.

The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from Mycobacterium smegmatis This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel

Effects of high CO2 and warming on a Baltic Sea microzooplankton community

Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure

Chemoenzymatic Hydrogen Production from Methanol through the Interplay of Metal Complexes and Biocatalysts

Microbial methylotrophic organisms can serve as great inspiration in the development of biomimetic strategies for the dehydrogenative conversion of C1 molecules under ambient conditions. In this Concept article, a concise personal perspective on the recent advancements in the field of biomimetic catalytic models for methanol and formaldehyde conversion, in the presence and absence of enzymes and co-factors, towards the formation of hydrogen under ambient conditions is given. In particular, formaldehyde dehydrogenase mimics have been introduced in stand-alone C1-interconversion networks. Recently, coupled systems with alcohol oxidase and dehydrogenase enzymes have been also developed for in situ formation and decomposition of formaldehyde and/or reduced/oxidized nicotinamide adenine dinucleotide (NADH/ NAD+). Although C1 molecules are already used in many industries for hydrogen production, these conceptual bioinspired low-temperature energy conversion processes may lead one day to more efficient energy storage systems enabling renewable and sustainable hydrogen generation for hydrogen fuel cells under ambient conditions using C1 molecules as fuels for mobile and miniaturized energy storage solutions in which harsh conditions like those in industrial plants are not applicable.Peer reviewe

HPC-oriented Canonical Workflows for Machine Learning Applications in Climate and Weather Prediction

Machine learning (ML) applications in weather and climate are gaining momentum as big data and the immense increase in High-performance computing (HPC) power are paving the way. Ensuring FAIR data and reproducible ML practices are significant challenges for Earth system researchers. Even though the FAIR principle is well known to many scientists, research communities are slow to adopt them. Canonical Workflow Framework for Research (CWFR) provides a platform to ensure the FAIRness and reproducibility of these practices without overwhelming researchers. This conceptual paper envisions a holistic CWFR approach towards ML applications in weather and climate, focusing on HPC and big data. Specifically, we discuss Fair Digital Object (FDO) and Research Object (RO) in the DeepRain project to achieve granular reproducibility. DeepRain is a project that aims to improve precipitation forecast in Germany by using ML. Our concept envisages the raster datacube to provide data harmonization and fast and scalable data access. We suggest the Juypter notebook as a single reproducible experiment. In addition, we envision JuypterHub as a scalable and distributed central platform that connects all these elements and the HPC resources to the researchers via an easy-to-use graphical interface

Resolution of Clinical and Laboratory Abnormalities after Diagnosis of Ventilator-Associated Pneumonia in Trauma Patients

Background: Guidelines advise that patients with ventilator-associated pneumonia (VAP) should respond clinically by Day 3 of antibiotics. White blood cell (WBC) count, maximum temperature (Tmax), and PaO2:FIO2 ratio are all said to respond significantly by Day 6. Resolution of abnormalities has not been evaluated in trauma patients. Methods: Retrospective review of trauma patients with VAP. The WBC count, Tmax, and PaO2:FIO2 were evaluated for 16 days after diagnosis. Patients were grouped into uncomplicated VAP, complicated VAP (those with inadequate empirical therapy [IEAT], VAP relapse/superinfection, or acute respiratory distress syndrome), and concurrent infection +VAP (those also infected at another site). Results: There were 126 patients (uncomplicated VAP= 29, complicated VAP = 69, and concurrent infection + VAP = 28). The mean Tmax in patients with uncomplicated VAP decreased significantly from diagnosis to Day 4 (Day 1: 39 – 0.5°C vs. Day 4: 38.6 – 0.7°C; p = 0.028) but never normalized. Their WBC counts and PaO2:FIO2 did not change significantly over the 16-day follow-up and never normalized.When comparing the three groups, the probability of resolving all three abnormalities was not different (p = 0.5). Conclusions: Clinical and laboratory abnormalities in critically injured patients with VAP do not resolve as quickly as suggested in the guidelines. Future studies should evaluate new methods to determine the response to antibiotic therapy in critically injured patients with VAP

Fate of Cajal–Retzius Neurons in the Postnatal Mouse Neocortex

Cajal–Retzius (CR) neurons play a critical role in cortical neuronal migration, but their exact fate after the completion of neocortical lamination remains a mystery. Histological evidence has been unable to unequivocally determine whether these cells die or undergo a phenotypic transformation to become resident interneurons of Layer 1 in the adult neocortex. To determine their ultimate fate, we performed chronic in vivo two-photon imaging of identified CR neurons during postnatal development in mice that express the green fluorescent protein (GFP) under the control of the early B-cell factor 2 (Ebf2) promoter. We find that, after birth, virtually all CR neurons in mouse neocortex express Ebf2. Although postnatal CR neurons undergo dramatic morphological transformations, they do not migrate to deeper layers. Instead, their gradual disappearance from the cortex is due to apoptotic death during the second postnatal week. A small fraction of CR neurons present at birth survive into adulthood. We conclude that, in addition to orchestrating cortical layering, a subset of CR neurons must play other roles beyond the third postnatal week

Spitzer view on the evolution of star-forming galaxies from z=0 to z~3

We use a 24 micron selected sample containing more than 8,000 sources to study the evolution of star-forming galaxies in the redshift range from z=0 to z~3. We obtain photometric redshifts for most of the sources in our survey using a method based on empirically-built templates spanning from ultraviolet to mid-infrared wavelengths. The accuracy of these redshifts is better than 10% for 80% of the sample. The derived redshift distribution of the sources detected by our survey peaks at around z=0.6-1.0 (the location of the peak being affected by cosmic variance), and decays monotonically from z~1 to z~3. We have fitted infrared luminosity functions in several redshift bins in the range 0<z<~3. Our results constrain the density and/or luminosity evolution of infrared-bright star-forming galaxies. The typical infrared luminosity (L*) decreases by an order of magnitude from z~2 to the present. The cosmic star formation rate (SFR) density goes as (1+z)^{4.0\pm0.2} from z=0 to z=0.8. From z=0.8 to z~1.2, the SFR density continues rising with a smaller slope. At 1.2<z<3, the cosmic SFR density remains roughly constant. The SFR density is dominated at low redshift (z<0.5) by galaxies which are not very luminous in the infrared (L_TIR<1.e11 L_sun, where L_TIR is the total infrared luminosity, integrated from 8 to 1000 micron). The contribution from luminous and ultraluminous infrared galaxies (L_TIR>1.e11 L_sun) to the total SFR density increases steadily from z~0 up to z~2.5, forming at least half of the newly-born stars by z~1.5. Ultraluminous infrared galaxies (L_TIR>1.e12 L_sun) play a rapidly increasing role for z>~1.3.Comment: 28 pages, 17 figures, accepted for publication in Ap