A mammalian DNA methylation landscape.

A study of 348 species offers clues into the diversity of mammalian life spans

Origin and evolution of eukaryotic transcription factors

Transcription factors (TFs) have a central role in genome regulation directing gene transcription through binding specific DNA sequences. Eukaryotic genomes encode a large diversity of TF classes, each defined by unique DNA-interaction domains. Recent advances in genome sequencing and phylogenetic placement of diverse eukaryotic and archaeal species are re-defining the evolutionary history of eukaryotic TFs. The emerging view from a comparative genomics perspective is that the Last Eukaryotic Common Ancestor (LECA) had an extensive repertoire of TFs, most of which represent eukaryotic evolutionary novelties. This burst of TF innovation coincides with the emergence of genomic nuclear segregation and complex chromatin organization

Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family

The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally show how retrotransposon-encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host genome, in the myriapod Strigamia maritima. Consistently, young MBD-encoding Copia retrotransposons (CopiaMBD) accumulate in regions with higher CpG densities than other LTR-retrotransposons also present in the genome. This would suggest that retrotransposons use MBDs to integrate into heterochromatic regions in Strigamia, avoiding potentially harmful insertions into host genes. In contrast, CopiaMBD insertions in the spider Stegodyphus dumicola genome disproportionately accumulate in methylated gene bodies compared with other spider LTR-retrotransposons. Given that transposons are not actively targeted by DNA methylation in the spider genome, this distribution bias would also support a role for MBDs in the integration process. Together, these data show that retrotransposons can co-opt host-derived epigenome readers, potentially harnessing the host epigenome landscape to advantageously tune the retrotransposition process

Synchronous versus asynchronous modeling of gene regulatory networks

Motivation: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, protein–protein and gene–protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes

Use of flow-cytometry to distinguish between haploid and diploid strains of Aspergillus fumigatus

Many filamentous fungi with general interest such as plant/human pathogens and enzyme/antibiotic producers lack a sexual cycle. Since sexual crosses are unavailable in these species, the parasexual analysis, apart from physical mapping, is the only way of mapping the chromosomes. The use of the parasexual cycle requires a method to distinguish between haploids and diploids. Here, we report the use of flow-cytometry to distinguish clearly between haploid and diploid strains of Aspergillus fumigatus, a very rapid, simple and accurate technique that can be applied to parasexual analysis in other filamentous fungi

Bioactivity of wollastonite/aerogels composites obtained from a TEOS-MTES matrix

Organic-inorganic hybrid materials were synthesized by controlled hydrolysis of tetraethoxysilane (TEOS), methyltrimethoxysilane (MTES), synthetic wollastonite powders and polydimethylsiloxane (PDMS) in an ethanol solution. Aerogels were prepared from acid hydrolysis of TEOS and MTES with different volume ratio in ethanol, followed by addition of wollastonite powder and PDMS in order to obtain aerogels with 20 wt% of PDMS and 5 wt% of CaO of the total silica. Finally, when the wet gels were obtained, they were supercritically dried at 260°C and 90 bar, in ethanol. In order to obtain its bioactivity, one method for surface activation is based on a wet chemical alkaline treatment. The particular interest of this study is that we introduce hybrid aerogels, in a 1 M solution of NaOH, for 30 s at room temperature. We evaluate the bioactivity of TEOS-MTES aerogel when immersed in a static volume of simulated body fluid (SBF). An apatite layer of spherical-shaped particles of uniform size smaller than 5 microns is observed to form on the surface of the aerogels after 25 days soaking in SBF.Ministerio de Ciencia e Innovación MAT2005-01583Junta de Andalucía TEP 79

Relative influence of environmental factors on biodiversity and behavioural traits of a rare mesopelagic fish, Trachipterus trachypterus (gmelin, 1789), in a continental shelf front of the Mediterranean Sea

Coastal environments can be influenced by water body masses with particular physical, chemical, and biological properties that create favourable conditions for the development of unique planktonic communities. In this study, we investigated a continental shelf front at Ponza Island (Tyrrhenian Sea) and discussed its diversity and complexity in relation to major environmental parameters. Moon phase and current direction were found to play a significant role in shaping species abundance and behaviour. During in situ observations, we also provided the first data on the behaviour of juveniles of a rare mesopelagic species, Trachipterus trachypterus, suggesting the occurrence of Batesian mimicry

Caracterización química y cuantificación del rendimiento de extracción de pigmento en siete accesiones mexicanas de Bixa orellana

Achiote (Bixa orellana) is a plant used for obtaining a natural dye rich on carotenoids (mainly bixin and norbixin); it is also the plant species with the highest content of tocotrienols in nature. In the present work, the pigment extraction yield of seven Mexican accessions of Bixa orellana was quantified. Also color parameters and content of tocotrienols, tocopherols, norbixin, bixin, total phenolic compounds and antioxidant capacity were evaluated in the corresponding annatto extracts. The highest percentage of pigment extraction yield was obtained with KOH (4.84%). Accessions 43 (L*= 4.01 ± 0.79, C*= 7.33 ± 1.07, h= 25.76 ± 6.35) and 50 (L*= 3.17 ± 0.64, C*= 6.81 ± 0.53, h= 26.41 ± 4.41) had the lowest color values, meaning these accessions had a darker and redder color. Four accessions showed the highest content of bixin: accession 48 (3.1%), 45 (2.6%) 43 (2.4%) and 47 (2.2%). Accession 50 had showed the highest content of total phenolic compounds and of tocotrienols (T3), mainly the isoform δ-T3 (5.03 ± 0.64 mg g−1 Seed Dry Weight), as well as the highest antioxidant capacity.El achiote (Bixa orellana) es una planta utilizada para obtener un colorante natural rico en carotenoides (principalmente bixina y norbixina); además, es la especie vegetal con el mayor contenido de tocotrienoles. En este trabajo, se determinó el rendimiento de extracción de pigmento de siete accesiones mexicanas de Bixa orellana. También se evaluaron los parámetros de color y el contenido de tocotrienoles, tocoferoles, norbixina, bixina, compuestos fenólicos totales y la capacidad antioxidante en extractos de annato. El mayor porcentaje de rendimiento de extracción de pigmento fue obtenido con KOH (4.847905%). Las accesiones 43 (L*= 4.01 ± 0.79, C*= 7.33 ± 1.07, h= 25.76 ± 6.35) y 50 (L*= 3.17 ± 0.64, C*= 6.81 ± 0.53, h= 26.41 ± 4.41) presentaron los valores más bajos de los párametros de color, lo que significa que estas accesiones tuvieron un color más oscuro y más rojo. Cuatro accesiones mostraron el mayor contenido de bixina: accesión 48 (3.1%), 45 (2.6%) 43 (2.4%) and 47 (2.2%). La accession 50 mostró el mayor contenido de compuestos fenólicos totales y de tocotrienoles (T3), principalmente la isoforma δ-T3 (5.03 ± 0.64 mg g-1 Peso Seco), así como también la mayor capacidad antioxidante.Fil: Raddatz Mota, D.. Universidad Autónoma Metropolitana; MéxicoFil: Pérez Flores, L. J.. Universidad Autónoma Metropolitana; MéxicoFil: Carrari, Fernando Oscar. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Insani, Ester Marina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Asis, Ramón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Mendoza Espinoza, J. A.. Universidad Nacional Autónoma de México; MéxicoFil: Díaz de León Sánchez, F.. Universidad Autónoma Metropolitana; MéxicoFil: Rivera Cabrera, F.. Universidad Autónoma Metropolitana; Méxic