Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Punctuated Chirality

Most biomolecules occur in mirror, or chiral, images of each other. However, life is homochiral: proteins contain almost exclusively levorotatory (L) amino acids, while only dextrorotatory (R) sugars appear in RNA and DNA. The mechanism behind this fundamental asymmetry of life remains an open problem. Coupling the spatiotemporal evolution of a general autocatalytic polymerization reaction network to external environmental effects, we show through a detailed statistical analysis that high intensity and long duration events may drive achiral initial conditions towards chirality. We argue that life's homochirality resulted from sequential chiral symmetry breaking triggered by environmental events, thus extending the theory of punctuated equilibrium to the prebiotic realm. Applying our arguments to other potentially life-bearing planetary platforms, we predict that a statistically representative sampling will be racemic on average.Comment: 13 pages, 4 color figures. Final version published in Origins of Life and Evolution of Biospheres. Typos corrected, figures improved, and a few definitions and word usage clarifie

Expenditure Reform in Industrialised Countries: A Case Study Approach

This study examines reforms of public expenditure in industrialised countries over the past two decades. We distinguish ambitious and timid reformers and analyse in detail reform experiences in eight case studies of ambitious reform episodes. We find that ambitious reform countries reduce spending on transfers, subsidies and public consumption while largely sparing education spending. Such expenditure retrenchment is also typically part of a comprehensive reform package that includes improvements in fiscal institutions as well as structural and other macroeconomic reforms. The study finds that ambitious expenditure retrenchment and reform coincides with large improvements in fiscal and economic growth indicators

Microwave sensor system for continuous monitoring of adhesive curing processes

A microwave sensor system has been developed for monitoring adhesive curing processes. The system provides continuous, real-time information about the curing progress without interfering with the reaction. An open-coaxial resonator is used as the sensor head, and measurements of its resonance frequency and quality factor are performed during cure to follow the reaction progress. Additionally, the system provides other interesting parameters such as reaction rate or cure time. The adhesive dielectric properties can also be computed off-line, which gives additional information about the process. The results given by the system correlate very well with conventional measurement techniques such as differential scanning calorimetry, combining accuracy and rate with simplicity and an affordable cost. © 2012 IOP Publishing Ltd.The authors thank Rut Benavente Martinez for her assistance in the DSC experiments. The contract of BG-B is financed by the Ministry of Science and Innovation of Spain, through the 'Torres Quevedo' Sub-programme, which is also co-financed by the European Social Fund (ESF). This work has been financed by the Ministry of Science and Innovation of Spain through the project MONIDIEL (TEC2008-04109).García Baños, B.; Catalá Civera, JM.; Penaranda-Foix, FL.; Canós Marín, AJ.; Sahuquillo Navarro, O. (2012). Microwave sensor system for continuous monitoring of adhesive curing processes. Measurement Science and Technology. 23(3). https://doi.org/10.1088/0957-0233/23/3/035101S233Jost, M., & Sernek, M. (2008). Shear strength development of the phenol–formaldehyde adhesive bond during cure. Wood Science and Technology, 43(1-2), 153-166. doi:10.1007/s00226-008-0217-2Costa, M. L., Botelho, E. C., Paiva, J. M. F. de, & Rezende, M. C. (2005). Characterization of cure of carbon/epoxy prepreg used in aerospace field. 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MIKON - 2000. Conference Proceedings (IEEE Cat. No.00EX428). doi:10.1109/mikon.2000.913931Canos, A. J., Catala-Civera, J. M., Penaranda-Foix, F. L., & Reyes-Davo, E. (2006). A novel technique for deembedding the unloaded resonance frequency from measurements of microwave cavities. IEEE Transactions on Microwave Theory and Techniques, 54(8), 3407-3416. doi:10.1109/tmtt.2006.877833Marks, R. B., & Williams, D. F. (1992). A general waveguide circuit theory. Journal of Research of the National Institute of Standards and Technology, 97(5), 533. doi:10.6028/jres.097.024Harrington, R. F. (1967). Matrix methods for field problems. Proceedings of the IEEE, 55(2), 136-149. doi:10.1109/proc.1967.5433Baker-Jarvis, J., Janezic, M. D., Domich, P. D., & Geyer, R. G. (1994). Analysis of an open-ended coaxial probe with lift-off for nondestructive testing. IEEE Transactions on Instrumentation and Measurement, 43(5), 711-718. doi:10.1109/19.328897Taylor, B. N. (1994). 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Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

BACKGROUND: Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. RESULTS: We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. CONCLUSIONS: In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny . Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes