Almost all human genes resulted from ancient duplication

Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins

PHOTOELECTROCATALYTIC PERFORMANCE OF MIXED OXIDE ELECTRODES FOR APPLICATIONS IN SOLAR CELLS

This thesis work is focused on the synthesis of TiO2 based hetero-nanostructured mixed metal oxides for their used as photo-anodes in different photo-electrochemical applications. Compared to single-phase photocatalysts, hetero-nanostructured mixed metal oxides can increase the efficiency of charges separation and lifetime, enhance the interfacial charge transfer to adsorbed substrate as well as improve the light-response range to the visible region.This thesis work is focused on the synthesis of TiO2 based hetero-nanostructured mixed metal oxides for their used as photo-anodes in different photo-electrochemical applications. Compared to single-phase photocatalysts, hetero-nanostructured mixed metal oxides can increase the efficiency of charges separation and lifetime, enhance the interfacial charge transfer to adsorbed substrate as well as improve the light-response range to the visible region

Morphology and dynamics of ice crystals and the effect of proteins

286 p.La tesis "Morfología y dinámica de los cristales de hielo y su efecto en las proteínas" se basa en una amplia gama de temas que abarcan el fundamento de la estructura del hielo (tanto su superficie como su morfología), la interacción de las proteínas con el hielo y las ciencias ambientales (formación de las nubes y la dinámica de los glaciares). El enfoque se centra en las interfaces hielo/vapor e hielo/agua.Mediante el microscopio electrónico de barrido ambiental (ESEM) a temperaturas inusualmente bajas, se ha logrado acceder a estudiar la morfología del hielo in-situ en diversas áreas del diagrama de fases (presión-temperatura). Además de reproducir las morfologías ya conocidas de cristales individuales e hielo poli-cristalino, se han observado formas ya conocidas de hielo, así como hielo poli-cristalino. Nuevas geometrías llamadas ¿pools¿, formas circulares de ¿m de diámetro, fueron encontradas en los límites del grano de la superficie del hielo poli-cristalino durante procesos de sublimación lento.Además, se estudiaron ocho soluciones diferentes de proteínas en condiciones de súper-enfriamiento mediante las técnicas de congelación de gota (drop freezing technique) y calorimetría diferencial de barrido (DSC). Únicamente, la (apo)ferritina y la ferritina han mostrado buenas características para la nucleación de hielo, es decir, la congelación bajo pequeño súper-enfriamiento (solo algunos grados debajo de 0 ºC), mientras que la mayoría de las soluciones de proteínas estudiadas se congelan por debajo de -15 ºC, como el agua pura.CIC NanoGUNE:nanoscience cooperative research center CFM: materials physics center ETH Zürich: Institute for Atmospheric and Climate Scienc

Energy-Momentum Distribution: Some Examples

In this paper, we elaborate the problem of energy-momentum in General Relativity with the help of some well-known solutions. In this connection, we use the prescriptions of Einstein, Landau-Lifshitz, Papapetrou and M\"{o}ller to compute the energy-momentum densities for four exact solutions of the Einstein field equations. We take the gravitational waves, special class of Ferrari-Ibanez degenerate solution, Senovilla-Vera dust solution and Wainwright-Marshman solution. It turns out that these prescriptions do provide consistent results for special class of Ferrari-Ibanez degenerate solution and Wainwright-Marshman solution but inconsistent results for gravitational waves and Senovilla-Vera dust solution.Comment: 20 pages, accepted for publication in Int. J. Mod. Phys.

Protein aggregates nucleate ice: the example of apoferritin

Biological material has gained increasing attention recently as a source of ice-nucleating particles that may account for cloud glaciation at moderate supercooling. While the ice-nucleation (IN) ability of some bacteria can be related to membrane-bound proteins with epitaxial fit to ice, little is known about the IN-active entities present in biological material in general. To elucidate the potential of proteins and viruses to contribute to the IN activity of biological material, we performed bulk freezing experiments with the newly developed drop freezing assay DRoplet Ice Nuclei Counter Zurich (DRINCZ), which allows the simultaneous cooling of 96 sample aliquots in a chilled ethanol bath. We performed a screening of common proteins, namely the iron storage protein ferritin and its iron-free counterpart apoferritin, the milk protein casein, the egg protein ovalbumin, two hydrophobins, and a yeast ice-binding protein, all of which revealed IN activity with active site densities > 0.1 mg−1 at −10 ∘C. The tobacco mosaic virus, a plant virus based on helically assembled proteins, also proved to be IN active with active site densities increasing from 100 mg−1 at −14 ∘C to 10 000 mg−1 at −20 ∘C. Among the screened proteins, the IN activity of horse spleen ferritin and apoferritin, which form cages of 24 co-assembled protein subunits, proved to be outstanding with active site densities > 10 mg−1 at −5 ∘C. Investigation of the pH dependence and heat resistance of the apoferritin sample confirmed the proteinaceous nature of its IN-active entities but excluded the correctly folded cage monomer as the IN-active species. A dilution series of apoferritin in water revealed two distinct freezing ranges, an upper one from −4 to −11 ∘C and a lower one from −11 to −21 ∘C. Dynamic light scattering measurements related the upper freezing range to ice-nucleating sites residing on aggregates and the lower freezing range to sites located on misfolded cage monomers or oligomers. The sites proved to persist during several freeze–thaw cycles performed with the same sample aliquots. Based on these results, IN activity seems to be a common feature of diverse proteins, irrespective of their function, but arising only rarely, most probably through defective folding or aggregation to structures that are IN active.This research has been supported by the Swiss National Foundation (grant nos. IZSEZ0_179149/1 and 200021_156581), the Basque government (Elkartek programmes ng 15 and ng 17), and the Spanish MINECO (grant no. MAT2013- 46006-R, programme MDM-2016-0618)

On homology searches by protein Blast and the characterization of the age of genes

BACKGROUND: It has been shown in a variety of organisms, including mammals, that genes that appeared recently in evolution, for example orphan genes, evolve faster than older genes. Low functional constraints at the time of origin of novel genes may explain these results. However, this observation has been recently attributed to an artifact caused by the inability of Blast to detect the fastest genes in different eukaryotic genomes. Distinguishing between these two possible explanations would be of great importance for any studies dealing with the taxon distribution of proteins and the origin of novel genes. RESULTS: Here we used simulations of protein sequences to examine the capacity of Blast to detect proteins of diverse evolutionary rates in the different species of an eukaryotic phylogenetic tree that included metazoans, fungi and plants. We simulated the evolution of protein genes with the same evolutionary rates than those observed in functional mammalian genes and with among-site rate heterogeneity. Under these conditions, we found that only a very small percentage of simulated ancestral eukaryotic proteins was affected by the Blast artifact. We show that the good detectability of Blast is due to the heterogeneity of protein evolutionary rates at different sites, since only a small conserved motif in a sequence suffices to detect its homologues. Our results indicate that Blast, at least when applied within eukaryotes, only misses homologues of extremely fast-evolving sequences, which are rare in the mammalian genome, as well as sequences evolving homogeneously or pseudogenes. CONCLUSION: Although great care should be exercised in the recognition of remote homologues, most functional mammalian genes can be detected in eukaryotic genomes by Blast. That is, the majority of functional mammalian genes are not as fast as for not being detected in other metazoans, fungi or plants, if they had been present in these organisms. Thus, the correlation previously found between age and rate seems not to be due to a pure Blast artifact, at least for mammals. This may have important implications to understand the mechanisms by which novel genes originate

Novel intron markers to study the phylogeny of closely related mammalian species

BACKGROUND: Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. RESULTS: In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. CONCLUSIONS: We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here

Regulation of sonic hedgehog-GLI1 downstream target genes PTCH1, Cyclin D2, Plakoglobin, PAX6 and NKX2.2 and their epigenetic status in medulloblastoma and astrocytoma

Abstract Background The Sonic hedgehog (Shh) signaling pathway is critical for cell growth and differentiation. Impairment of this pathway can result in both birth defects and cancer. Despite its importance in cancer development, the Shh pathway has not been thoroughly investigated in tumorigenesis of brain tumors. In this study, we sought to understand the regulatory roles of GLI1, the immediate downstream activator of the Shh signaling pathway on its downstream target genes PTCH1, Cyclin D2, Plakoglobin, NKX2.2 and PAX6 in medulloblastoma and astrocytic tumors. Methods We silenced GLI1 expression in medulloblastoma and astrocytic cell lines by transfection of siRNA against GLI1. Subsequently, we performed RT-PCR and quantitative real time RT-PCR (qRT-PCR) to assay the expression of downstream target genes PTCH1, Cyclin D2, Plakoglobin, NKX2.2 and PAX6. We also attempted to correlate the pattern of expression of GLI1 and its regulated genes in 14 cell lines and 41 primary medulloblastoma and astrocytoma tumor samples. We also assessed the methylation status of the Cyclin D2 and PTCH1 promoters in these 14 cell lines and 58 primary tumor samples. Results Silencing expression of GLI1 resulted up-regulation of all target genes in the medulloblastoma cell line, while only PTCH1 was up-regulated in astrocytoma. We also observed methylation of the cyclin D2 promoter in a significant number of astrocytoma cell lines (63%) and primary astrocytoma tumor samples (32%), but not at all in any medulloblastoma samples. PTCH1 promoter methylation was less frequently observed than Cyclin D2 promoter methylation in astrocytomas, and not at all in medulloblastomas. Conclusions Our results demonstrate different regulatory mechanisms of Shh-GLI1 signaling. These differences vary according to the downstream target gene affected, the origin of the tissue, as well as epigenetic regulation of some of these genes.http://deepblue.lib.umich.edu/bitstream/2027.42/78313/1/1471-2407-10-614.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78313/2/1471-2407-10-614.pdfPeer Reviewe

Tarnania fenestralis (Meigen, 1818) (Díptera: Micetophilidae) asociado al hongo Pleurotus eryngii (DC.) Quél.

Extensive natural mushroom cultivations of Pleurotus eryngii (DC.) Quél. were studied in their main productive area, the northwest of Segovia province, Spain, identifying a new parasite for this fungus, Tarnania fenestralis (Meigen, 1818) (Diptera: Micetophilidae). The prevalence of parasitization reaches 20.4% of the yield, the main damage being in the destruction of internal tissues of the carpophores, resulting in crop depreciation. Due to the high incidence of parasitization by the dipteran in the mushroom, as well as its abundance, the nematocerous fungivore T. fenestralis may be considered the main and most important parasite of extensive P. eryngii productions of all the zone in which the investigation is made.En el estudio de los parásitos que afectan a las producciones extensivas naturales de seta de cardo Pleurotus eryngii (DC.) Quél. en su principal área productiva: noroeste de Segovia, España; se identifica un nuevo parásito para este hongo, Tarnania fenestralis (Meigen, 1818) (Diptera: Micetophilidae). La prevalencia de parasitación encontrada es un 20,4% de la producción y su principal daño radica en la destrucción de los tejidos internos de los carpóforos, depreciando este recurso. Debido a la alta incidencia de parasitaciones del díptero en la seta, así como su abundancia, se considera al nematócero fungívoro T. fenestralis cómo el principal y más importante parásito de las producciones extensivas de P. eryngii de toda la zona en la que se realiza la investigación