Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift

The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named 'schizorhodopsin (SzR)' has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pK(a)=12.3) is stabilised by the deprotonated counterion (presumably Asp184, pK(a)=3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral 'blue-shift' due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift

Prebiotic Organic Microstructures

Micro- and sub-micrometer spheres, tubules and fiber-filament soft structures have been synthesized in our experiments conducted with 3 MeV proton irradiations of a mixture of simple inorganic constituents, CO, N2 and H2O. We analysed the irradiation products, with scanning electron microscopy (SEM) and atomic force microscopy (AFM). These laboratory organic structures produced wide variety of proteinous and non-proteinous amino acids after HCl hydrolysis. The enantiomer analysis for D-, L- alanine confirmed that the amino acids were abiotically synthesized during the laboratory experiment. Considering hydrothermal activity, the presence of CO2 and H2, of a ferromagnesian silicate mineral environment, of an Earth magnetic field which was much less intense during Archean times than nowadays and consequently of a proton excitation source which was much more abundant, we propose that our laboratory organic microstructures might be synthesized during Archean times. We show similarities in morphology and in formation with some terrestrial Archean microstructures and we suggest that some of the observed Archean carbon spherical and filamentous microstructures might be composed of abiogenic organic molecules. We further propose a search for such prebiotic organic signatures on Mars. This article has been posted on Nature precedings on 21 July 2010 [1]. Extinct radionuclides as source of excitation have been replaced by cosmic radiations which were much more intense 3.5 Ga ago because of a much less intense Earth magnetic field. The new version of the article has been presented at the ORIGINS conference in Montpellier in july 2011 [2] and has since been published in Origins of Life and Evolution of Biospheres 42 (4) 307-316, 2012. 
DOI: 10.1007/s11084-012-9290-5 

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Demonstration of a Light-Driven SO42- Transporter and Its Spectroscopic Characteristics.

In organisms, ion transporters play essential roles in the generation and dissipation of ion gradients across cell membranes. Microbial rhodopsins selectively transport cognate ions using solar energy, in which the substrate ions identified to date have been confined to monovalent ions such as H+, Na+, and Cl-. Here we report a novel rhodopsin from the cyanobacterium Synechocystis sp. PCC 7509, which inwardly transports a polyatomic divalent sulfate ion, SO42-, with changes of its spectroscopic properties in both unphotolyzed and photolyzed states. Upon illumination, cells expressing the novel rhodopsin, named Synechocystis halorhodopsin (SyHR), showed alkalization of the medium only in the presence of Cl- or SO42-. That alkalization signal was enhanced by addition of a protonophore, indicating an inward transport of Cl- and SO42- with a subsequent secondary inward H+ movement across the membrane. The anion binding to SyHR was suggested by absorption spectral shifts from 542 to 536 nm for Cl- and from 542 to 556 nm for SO42-, and the affinities of Cl- and SO42- were estimated as 0.112 and 5.81 mM, respectively. We then performed time-resolved spectroscopic measurements ranging from femtosecond to millisecond time domains to elucidate the structure and structural changes of SyHR during the photoreaction. Based on the results, we propose a photocycle model for SyHR in the absence or presence of substrate ions with the timing of their uptake and release. Thus, we demonstrate SyHR as the first light-driven polyatomic divalent anion (SO42-) transporter and report its spectroscopic characteristics

System Size and Energy Dependence of Jet-Induced Hadron Pair Correlation Shapes in Cu+Cu and Au+Au Collisions at sqrt(s_NN) = 200 and 62.4 GeV

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from {dijets} in Cu+Cu and Au+Au collisions at sqrt(s_NN) = 62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from \Delta\phi=\pi in central and semi-central collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.Comment: 464 authors from 60 institutions, 6 pages, 3 figures, 2 tables. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Improved Measurement of Double Helicity Asymmetry in Inclusive Midrapidity pi^0 Production for Polarized p+p Collisions at sqrt(s)=200 GeV

We present an improved measurement of the double helicity asymmetry for pi^0 production in polarized proton-proton scattering at sqrt(s) = 200 GeV employing the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The improvements to our previous measurement come from two main factors: Inclusion of a new data set from the 2004 RHIC run with higher beam polarizations than the earlier run and a recalibration of the beam polarization measurements, which resulted in reduced uncertainties and increased beam polarizations. The results are compared to a Next to Leading Order (NLO) perturbative Quantum Chromodynamics (pQCD) calculation with a range of polarized gluon distributions.Comment: 389 authors, 4 pages, 2 tables, 1 figure. Submitted to Phys. Rev. D, Rapid Communications. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

SINE RNA Induces Severe Developmental Defects in Arabidopsis thaliana and Interacts with HYL1 (DRB1), a Key Member of the DCL1 Complex

The proper temporal and spatial expression of genes during plant development is governed, in part, by the regulatory activities of various types of small RNAs produced by the different RNAi pathways. Here we report that transgenic Arabidopsis plants constitutively expressing the rapeseed SB1 SINE retroposon exhibit developmental defects resembling those observed in some RNAi mutants. We show that SB1 RNA interacts with HYL1 (DRB1), a double-stranded RNA-binding protein (dsRBP) that associates with the Dicer homologue DCL1 to produce microRNAs. RNase V1 protection assays mapped the binding site of HYL1 to a SB1 region that mimics the hairpin structure of microRNA precursors. We also show that HYL1, upon binding to RNA substrates, induces conformational changes that force single-stranded RNA regions to adopt a structured helix-like conformation. Xenopus laevis ADAR1, but not Arabidopsis DRB4, binds SB1 RNA in the same region as HYL1, suggesting that SINE RNAs bind only a subset of dsRBPs. Consistently, DCL4-DRB4-dependent miRNA accumulation was unchanged in SB1 transgenic Arabidopsis, whereas DCL1-HYL1-dependent miRNA and DCL1-HYL1-DCL4-DRB4-dependent tasiRNA accumulation was decreased. We propose that SINE RNA can modulate the activity of the RNAi pathways in plants and possibly in other eukaryotes

Clinical and Functional Characterization of URAT1 Variants

Idiopathic renal hypouricaemia is an inherited form of hypouricaemia, associated with abnormal renal handling of uric acid. There is excessive urinary wasting of uric acid resulting in hypouricaemia. Patients may be asymptomatic, but the persistent urinary abnormalities may manifest as renal stone disease, and hypouricaemia may manifest as exercise induced acute kidney injury. Here we have identified Macedonian and British patients with hypouricaemia, who presented with a variety of renal symptoms and signs including renal stone disease, hematuria, pyelonephritis and nephrocalcinosis. We have identified heterozygous missense mutations in SLC22A12 encoding the urate transporter protein URAT1 and correlate these genetic findings with functional characterization. Urate handling was determined using uptake experiments in HEK293 cells. This data highlights the importance of the URAT1 renal urate transporter in determining serum urate concentrations and the clinical phenotypes, including nephrolithiasis, that should prompt the clinician to suspect an inherited form of renal hypouricaemia

Effects of acute ocean acidification on spatially-diverse polar pelagic foodwebs: insights from on-deck microcosms

The polar oceans are experiencing some of the largest levels of ocean acidification (OA) resulting from the uptake of anthropogenic carbon dioxide (CO2). Our understanding of the impacts this is having on polar marine communities is mainly derived from studies of single species in laboratory conditions, while the consequences for food web interactions remain largely unknown. This study carried out experimental manipulations of natural pelagic communities at different high latitude sites in both the northern (Nordic Seas) and southern hemispheres (Scotia and Weddell Seas). The aim of this study was to identify more generic responses and greater experimental reproducibility through implementing a series of short term (4 day), multilevel (3 treatment) carbonate chemistry manipulation experiments on unfiltered natural surface ocean communities, including grazing copepods. The experiments were successfully executed at six different sites, covering a diverse range of environmental conditions and differing plankton community compositions. The study identified the interaction between copepods and dinoflagellate cell abundance to be significantly altered by elevated levels of dissolved CO2 (pCO2), with dinoflagellates decreasing relative to ambient conditions across all six experiments. A similar pattern was not observed in any other major phytoplankton group. The patterns indicate that copepods show a stronger preference for dinoflagellates when in elevated pCO2 conditions, demonstrating that changes in food quality and altered grazing selectivity may be a major consequence of ocean acidification. The study also found that transparent exopolymeric particles (TEP) generally increased when pCO2 levels were elevated, but the response was dependent on the exact set of environmental conditions. Bacteria and nannoplankton showed a neutral response to elevated pCO2 and there was no significant relationship between changes in bacterial or nannoplankton abundance and that of TEP concentrations. Overall, the study illustrated that, although some similar responses exist, these contrasting high latitude surface ocean communities are likely to show different responses to the onset of elevated pCO2