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

Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons.

The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals