Phosphorylation of Adenosine with Trimetaphosphate Under Simulated Prebiotic Conditions

The phosphorylation of adenosine withtrimetaphosphate in solution, in solid phase and usingwet-dry cycles was carried out and it was found thatwet-dry cycles were the most efficient. The catalytic effectsof some metal ions on the phosphorylation were alsostudied and it was discovered that Ni(II) is the mosteffective. The combination of wet-dry cycles (4 cycles)and catalysis by Ni(II) led to an unprecedented highconversion of adenosine to phosphorylated products (30%)near neutral pH. The main phosphorylated products were2', 3'-cyclic AMP (10.4%) and 5'-ATP (13.0%).     

Sorbic Hydroxamic Acid, an Antifungal Agent Effective over a Wide pH Range

Sorbic hydroxamic acid was prepared from sorbic acid by esterification and treatment with hydroxylamine (mp 133 to 135 C, pK(a) 8.8). Its ultraviolet spectrum in acid solution had a single absorption maximum at 262 mmu; in alkaline solution the maximal absorption shifted to 255 mmu and significant absorption appeared at 280 to 300 mmu. At concentrations of 0.1% (w/v), sorbic hydroxamic acid prevented the growth of Aspergillus niger, Penicillium notatum, Botrytis cinerea, Cladosporium herbarum, and a Rhizopus species in grape juice over the pH range 3.6 to 9.2, although sorbic acid was not effective at pH 5.7 and above.     

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.     

Arabidopsis Coordinates the Diurnal Regulation of Carbon Allocation and Growth across a Wide Range of Photoperiods

In short photoperiods, plants accumulate starch more rapidly in the light and degrade it more slowly at night, ensuring that their starch reserves last until dawn. To investigate the accompanying changes in the timing of growth, Arabidopsis was grown in a range of photoperiods and analyzed for rosette biomass, photosynthesis, respiration, ribosome abundance, polysome loading, starch, and over 40 metabolites at dawn and dusk. The data set was used to model growth rates in the daytime and night, and to identify metabolites that correlate with growth. Modeled growth rates and polysome loading were high in the daytime and at night in long photoperiods, but decreased at night in short photoperiods. Ribosome abundance was similar in all photoperiods. It is discussed how the amount of starch accumulated in the light period, the length of the night, and maintenance costs interact to constrain growth at night in short photoperiods, and alter the strategy for optimizing ribosome use. Significant correlations were found in the day- time and the night between growth rates and the levels of the sugar-signal trehalose 6-phosphate and the amino acid biosynthesis intermediate shikimate, identifying these metabolites as hubs in a network that coordinates growth with diurnal changes in the carbon supply.     

Expressed Repeat Elements Improve RT-qPCR Normalization across a Wide Range of Zebrafish Gene Expression Studies

The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding mRNA targets. We assessed and compared the expression stability of a number of EREs to that of commonly used zebrafish reference genes in a diverse set of experimental conditions including a developmental time series, a set of different organs from adult fish and different treatments of zebrafish embryos including morpholino injections and administration of chemicals. Using geNorm and rank aggregation analysis we demonstrated that EREs have a higher overall expression stability compared to the commonly used reference genes. Moreover, we propose a limited set of ERE reference targets (hatn10, dna15ta1 and loopern4), that show stable expression throughout the wide range of experiments in this study, as strong candidates for inclusion as reference targets for qPCR normalization in future zebrafish expression studies. Our applied strategy to find and evaluate candidate expressed repeat elements for RT-qPCR data normalization has high potential to be used also for other species.     

Conserved Microsatellites in Ants Enable Population Genetic and Colony Pedigree Studies across a Wide Range of Species

Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.     

Prebiotic Synthesis of Nucleotides

If an RNA-only world preceded more complex forms oflife, then it is essential that the process wherebythe first nucleotides were made be considered. Presumably there were no enzymes and no templates tofacilitate the synthesis of the first nucleotides soanother form of chemical evolution must have beeninvolved. Answers to problems of this sort weresought vigorously in the 1960s and the early 1970s butmany issues were left unresolved. Progress made inthe last few years has added to this early work andbrings us closer to a satisfactory solution. In thisarticle key results, old and new, and some ideas as tohow further progress is likely to be made are discussed.There are reasons for optimism. Substantial progresshas been made on the synthesis of purines and ribose,phosphorylation and polyphosphorylation. Theoutstanding problems at this juncture relate to thesynthesis of ribose to the exclusion of the otheraldopentoses and to the problem of linking ribose tothe purine bases.     

Geothrix fermentans Secretes Two Different Redox-Active Compounds To Utilize Electron Acceptors across a Wide Range of Redox Potentials

The current understanding of dissimilatory metal reduction is based primarily on isolates from the proteobacterial genera Geobacter and Shewanella. However, environments undergoing active Fe(III) reduction often harbor less-well-studied phyla that are equally abundant. In this work, electrochemical techniques were used to analyze respiratory electron transfer by the only known Fe(III)-reducing representative of the Acidobacteria, Geothrix fermentans. In contrast to previously characterized metal-reducing bacteria, which typically reach maximal rates of respiration at electron acceptor potentials of 0 V versus standard hydrogen electrode (SHE), G. fermentans required potentials as high as 0.55 V to respire at its maximum rate. In addition, G. fermentans secreted two different soluble redox-active electron shuttles with separate redox potentials (-0.2 V and 0.3 V). The compound with the lower midpoint potential, responsible for 20 to 30% of electron transfer activity, was riboflavin. The behavior of the higher-potential compound was consistent with hydrophilic UV-fluorescent molecules previously found in G. fermentans supernatants. Both electron shuttles were also produced when cultures were grown with Fe(III), but not when fumarate was the electron acceptor. This study reveals that Geothrix is able to take advantage of higher-redox-potential environments, demonstrates that secretion of flavin-based shuttles is not confined to Shewanella, and points to the existence of high-potential-redox-active compounds involved in extracellular electron transfer. Based on differences between the respiratory strategies of Geothrix and Geobacter, these two groups of bacteria could exist in distinctive environmental niches defined by redox potential.     

Monte-Carlo Calculations for Methane and Argon over a Wide Range of Density and Temperature,Including the Two-Phase Vapor-Liquid Region

Abstract

The Gibbs-ensemble simulation technique provides a powerful method to calculate vapor-liquid phase behavior [1]. To evaluate the configurational energy of a system of molecules, commonly used experessions describe the interaction between two molecules. Contributions from higher-body forces are usually implicitly taken into account by adjusting two-body potential parameters to give agreement with experimental data. Explicit expressions for higher-body potentials are not commonly used in simulations [8]. The work by Smit et al. [9] gives the appropriate expressions to evaluate the pressure as well as the chemical potential from a density-dependent two-body potential in an NVT ensemble.

In the present work, contributions to the potential from two-body interactions are separated from those due to higher-body interactions; to take higher-body forces into account, a mean-field term, proportional to (density)^0.9, is added to the two-body potential. NPT-simulations over a wide range of temperature and density, as well as Gibbs-ensemble simulations, are used to evaluate phase behavior of argon and of methane. The results indicate that a simple mean-field correction to the “true” two-body Kihara potential provides good agreement between experiment and simulation.     

Radioactivity as a Significant Energy Source in Prebiotic Synthesis

Radioactivity in the continental crust (due mainly to the isotopes ²³⁸U,²³⁵U, ²³²Th and ⁴⁰K), as a energysource for chemical evolution in the early Archean (between 3.5 and 4 Ga bp), is reviewed.The most important radioactive sourcein the continental crust is due to theproduction and accumulation of radioactivegases within the crust voids (porosity). Thestudy of such mechanism has allowed us toreach a deeper understanding about the nature of the radioactive source and to describe itsbehavior, particularly with regard to prebiotic chemical evolution. An effectivetotal energy of 3 × 10^{18 Ja -1} hasbeen obtained for a depth of 1 km, 4 Ga ago. If a depth of 30 km is taken, the obtained valueis almost equal to the UV solar energyradiation (<150 nm). Within thevoids the radioactive source of thecontinental crust played a relevant role inprebiotic synthesis. In uraniumdeposits of the same age, the role ofradiactivity must have been even more relevantin favoring chemical evolution.     

Carbonyl Sulfide as a Prebiotic Activation Agent for Stereo- and Sequence-Selective,Amyloid-Templated Peptide Elongation

Origins of Life and Evolution of Biospheres - Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We...     

Ubiquity of Cysteine- and Metalloproteinase Activities in a Wide Range of Trypanosomatids

We have analysed the proteinase profiles of 11 species from 7 different genera of trypanosomatids by in situ detection of enzyme activities on SDS-PAGE gels containing co-polymerized gelatin as substrate, and the use of specific proteinase inhibitors. Our survey indicates that while cysteine- and metalloproteinases are distributed ubiquitously among trypanosomatids, there are marked differences between the enzyme profiles from the monogenetic (Crithidia, Herpetomonas, Leptomonas) and digenetic (Trypanosoma, Endotrypanum, Phytomonas, Leishmania) species. The detected metalloproteinase activities, ranging in size from 50–100 kDa, partitioned into the detergent-phase after Triton X-114 extraction, while most of cysteine proteinases, of three distinct molecular mass ranges (30–50 kDa, 80–100 kDa and 116–205 kDa), partitioned into the aqueous phase. Thus, within this group of organisms, the metalloproteinase activities seem to be predominantly membrane-associated proteins. We also show that the plant parasites of the genus Phytomonas exhibit a distinctive cysteine proteinase profile that might be exploited further as a criterion for taxonomy of the genus.