Further Evidence for Collimated Particle Beams from Pulsars, and Precession

We follow up on our (Radhakrishnan & Deshpande, 2001: RD01) radically different interpretation of the observed structures and morphologies in the x-ray observations of the nebulae around young pulsars (PWNe). In our general model for PWNe (RD01), originally motivated by the Chandra observations of the Vela X-ray nebula, the bright arcs, the jet-like feature and the diffuse components in such nebulae can be explained together in detail, wherein the arcs are understood as traces of the particle beams from the two magnetic poles at the shock front. We consider this as important evidence for collimated particle beams from pulsars' magnetic poles. In this paper, we discuss the variability in the features in the Vela X-ray nebula observed by Pavlov et al. (2003), and assess the relevance and implication of our model to the observations on the Crab and other remnants. Our basic picture after incorporating the signatures of free precession of the central compact object can readily account for the variability and significant asymmetries, including the bent jet-like features, in the observed morphologies. The implications of these findings are discussed.Comment: Minor revision; 12 (9+3) pages, 3 figures; To appear in Ap

what is life the emergence of life in a mineral world

The premise of this talk is that, apart from liquid water and carbon molecules, specific environmental components and conditions were essential for the origin of life, i.e. phosphate, reactive rock..

RNA Oligomerisation without Added Catalyst from 2 ',3 '-Cyclic Nucleotides by Drying at Air-Water Interfaces

For the emergence of life, the abiotic synthesis of RNA from its monomers is a central step. We found that in alkaline, drying conditions in bulk and at heated air-water interfaces, 2 ',3 '-cyclic nucleotides oligomerised without additional catalyst, forming up to 10-mers within a day. The oligomerisation proceeded at a pH range of 7-12, at temperatures between 40-80 degrees C and was marginally enhanced by K+ ions. Among the canonical ribonucleotides, cGMP oligomerised most efficiently. Quantification was performed using HPLC coupled to ESI-TOF by fitting the isotope distribution to the mass spectra. Our study suggests a oligomerisation mechanism where cGMP aids the incorporation of the relatively unreactive nucleotides C, A and U. The 2 ',3 '-cyclic ribonucleotides are byproducts of prebiotic phosphorylation, nucleotide syntheses and RNA hydrolysis, indicating direct recycling pathways. The simple reaction condition offers a plausible entry point for RNA to the evolution of life on early Earth

Cyclic AMP in Mycobacteria: Characterization and Functional Role of the Rv1647 Ortholog in Mycobacterium smegmatis▿

Mycobacterial genomes are endowed with many eukaryote-like nucleotide cyclase genes encoding proteins that can synthesize 3′,5′-cyclic AMP (cAMP). However, the roles of cAMP and the need for such redundancy in terms of adenylyl cyclase genes remain unknown. We measured cAMP levels in Mycobacterium smegmatis during growth and under various stress conditions and report the first biochemical and functional characterization of the MSMEG_3780 adenylyl cyclase, whose orthologs in Mycobacterium tuberculosis (Rv1647) and Mycobacterium leprae (ML1399) have been recently characterized in vitro. MSMEG_3780 was important for producing cAMP levels in the logarithmic phase of growth, since the ΔMSMEG_3780 strain showed lower intracellular cAMP levels at this stage of growth. cAMP levels decreased in wild-type M. smegmatis under conditions of acid stress but not in the ΔMSMEG_3780 strain. This was correlated with a reduction in MSMEG_3780 promoter activity, indicating that the effect of the reduction in cAMP levels on acid stress was caused by a decrease in the transcription of MSMEG_3780. Complementation of the ΔMSMEG_3780 strain with the genomic integration of MSMEG_3780 or the Rv1647 gene could restore cAMP levels during logarithmic growth. The Rv1647 promoter was also acid sensitive, emphasizing the biochemical and functional similarities in these two adenylyl cyclases. This study therefore represents the first detailed biochemical and functional analysis of an adenylyl cyclase that is important for maintaining cAMP levels in mycobacteria and underscores the subtle roles that these genes may play in the physiology of the organism

Cyclic AMP in Mycobacteria: Characterization and Functional Role of the Rv1647 Ortholog in Mycobacterium smegmatis{triangledown}

Mycobacterial genomes are endowed with many eukaryote-like nucleotide cyclase genes encoding proteins that can synthesize 3',5'-cyclic AMP (cAMP). However, the roles of cAMP and the need for such redundancy in terms of adenylyl cyclase genes remain unknown. We measured cAMP levels in Mycobacterium smegmatis during growth and under various stress conditions and report the first biochemical and functional characterization of the MSMEG_3780 adenylyl cyclase, whose orthologs in Mycobacterium tuberculosis (Rv1647) and Mycobacterium leprae (ML1399) have been recently characterized in vitro. MSMEG_3780 was important for producing cAMP levels in the logarithmic phase of growth, since the {Delta}MSMEG_3780 strain showed lower intracellular cAMP levels at this stage of growth. cAMP levels decreased in wild-type M. smegmatis under conditions of acid stress but not in the {Delta}MSMEG_3780 strain. This was correlated with a reduction in MSMEG_3780 promoter activity, indicating that the effect of the reduction in cAMP levels on acid stress was caused by a decrease in the transcription of MSMEG_3780. Complementation of the {Delta}MSMEG_3780 strain with the genomic integration of MSMEG_3780 or the Rv1647 gene could restore cAMP levels during logarithmic growth. The Rv1647 promoter was also acid sensitive, emphasizing the biochemical and functional similarities in these two adenylyl cyclases. This study therefore represents the first detailed biochemical and functional analysis of an adenylyl cyclase that is important for maintaining cAMP levels in mycobacteria and underscores the subtle roles that these genes may play in the physiology of the organism

High-Fidelity Templated Ligation of RNA via 2′,3′-cyclic Phosphate

The templated ligation of oligonucleotides offers a mode of replication in an RNA world. The 2′,3′-cyclic phosphate (>P) is a prebiotically available activation group for RNA and the product of backbone hydrolysis. Using gel electrophoresis and liquid chromatography, we found that the templated ligation of RNA with >P activation proceeds in alkaline (pH 9-11) low-salt aqueous solutions with 1 mM MgCl2 in temperatures ranging from 20 to 25 °C within a few days. Under the optimum conditions of pH 10 and 5 °C, the ligation yielded 40% after 7 days. No additional catalysts were required. In contrast to previous reports, we found an equimolar mixture of 2′-5′ and 3′-5′ linked oligomers in the used conditions. We probed the nucleotide specificity at the ligation site and found that one mutation reduced the ligation yield by 82-92%. We extrapolated these results to a per-nucleotide replication fidelity of 95-98% when ligating 4- to 6-mers. With splinted oligomers, five ligations created a 96 mer strand, demonstrating a possible assembly pathway for long ribozymes. With the low salt requirements, strand separation will be compatible with the ligation conditions using non-equilibrium settings. The findings suggest that templated ligation mediated by 2′,3′-cyclic phosphate in alkaline conditions offer a slow, but precise replication and elongation reaction for RNA on early Earth

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

International audienceThe exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor

RNA polymerisation without catalyst from 2’,3’-cyclic nucleotides by drying at air-water interfaces

For the emergence of life, the abiotic synthesis of RNA from its monomers is a central step. We found alkaline, uncatalysed drying conditions in bulk and at heated air-water interfaces where 2´,3´-cyclic nucleotides polymerised, forming up to 10-mers within a day. The polymerisation proceeded at a pH range of 7-12 at temperatures between 40-80 °C and was marginally enhanced by K+ ions. Among the canonical ribonucleotides, cGMP polymerised most efficiently. Quantification was performed using HPLC coupled to ESI-TOF by fitting the isotope distribution to the mass spectra. Our study suggests a polymerisation mechanism where cGMP aids the incorporation of the relatively unreactive nucleotides C, A and U. The 2´,3´-cyclic nucleotides are byproducts of prebiotic phosphorylation, nucleotide syntheses and RNA hydrolysis, indicating direct recycling pathways. The simple reaction condition offers a plausible entry point for RNA to the evolution of life on early Earth

Photochemistry of organic molecules in the Solar System: experimental studies outside the International Space Station. The cases of glycine, and nucleobases

Solar UV radiation is a major source of energy for initiating chemical evolution towards complex organic structures, but it can also photo-dissociate even the most complex molecules. Thus, solar UV can erase the organic traces of past life at the surface of planets, such as Mars, destroy organic molecules present on meteorites and micrometeorites, influence the production of distributed sources in comets or initiate chemistry in Titan's atmosphere. In the interstellar medium, the UV radiation field emitted by stars in the galaxy is also responsible for the chemical evolution and the extraordinary diversity of organic molecules detected. PSS (Photochemistry on the Space Station) was a Low Earth Orbit (LEO) experiment, implemented from mid-2014 to early 2016 on the EXPOSE-R2 platform outside the International Space Station. Its goal was to improve our knowledge about the chemical nature and evolution of organic molecules with astrobiological implications in space environments. It was a new step in a series of experiments conducted outside the MIR space station, in the ESA BIOPAN and previous EXPOSE facilities. In PSS, both vented and sealed cells were used allowing exposure of both solid and gaseous samples. Five kinds of experiments was carried out exposing molecules related to different environmental factors of astrobiological significance: the interstellar medium, comets & meteorites, Titan, Mars, as well as a set of samples to test the stability of biochips in space. In this talk we will describe the PSS experiment and focus on some results related to the stability of some prebioticaly relevant compounds such as glycine, the simplest amino acid, and nucleobases such as uracil, guanine and adenine. These molecules were both exposed in Low Earth Orbit and studied in the laboratory in order to derive their photochemical lifetime if they are ejected from comets on dust particles and orbit around the Sun before reaching the Earth as micrometeorites. The results can lead to better understand the contribution of cometary particles in the establishment of an organic reservoir on primitive Earth

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

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