Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments

The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a few organisms. Genes for IPCT and DIPPS were found in the genomes of 33 organisms, all with thermophilic/hyperthermophilic lifestyles. Phylogeny of IPCT/DIPPS revealed an incongruent topology with 16S RNA phylogeny, thus suggesting horizontal gene transfer. The phylogenetic tree of the DIPPS domain was rooted by using phosphatidylinositol phosphate synthase sequences as out-group. The root locates at the separation of genomes with fused and split genes. We propose that the gene encoding DIPPS was recruited from the biosynthesis of phosphatidylinositol. The last DIP-synthesizing ancestor harboured separated genes for IPCT and DIPPS and this architecture was maintained in a crenarchaeal lineage, and transferred by horizontal gene transfer to hyperthermophilic marine Thermotoga species. It is plausible that the driving force for the assembly of those two genes in the early ancestor is related to the acquired advantage of DIP producers to cope with high temperature. This work corroborates the view that Archaea were the first hyperthermophilic organisms.     

Cdk activity couples epigenetic centromere inheritance to cell cycle progression

Centromeres form the site of chromosome attachment to microtubules during mitosis. Identity of these loci is maintained epigenetically by nucleosomes containing the histone H3 variant CENP-A. Propagation of CENP-A chromatin is uncoupled from DNA replication initiating only during mitotic exit. We now demonstrate that inhibition of Cdk1 and Cdk2 activities is sufficient to trigger CENP-A assembly throughout the cell cycle in a manner dependent on the canonical CENP-A assembly machinery. We further show that the key CENP-A assembly factor Mis18BP1(HsKNL2) is phosphorylated in a cell cycle-dependent manner that controls its centromere localization during mitotic exit. These results strongly support a model in which the CENP-A assembly machinery is poised for activation throughout the cell cycle but kept in an inactive noncentromeric state by Cdk activity during S, G2, and M phases. Alleviation of this inhibition in G1 phase ensures tight coupling between DNA replication, cell division, and subsequent centromere maturation.     

Multifunctionalized CMCht/PAMAM dendrimer nanoparticles modulate the cellular uptake by astrocytes and oligodendrocytes in primary cultures of glial cells

The efficiency of the treatments involving CNS disorders is commonly diminished by the toxicity, reduced stability and lack of targeting of the administered neuroactive compounds. In this study, we have successfully multifunctionalized CMCht/PAMAM dendrimer nanoparticles by coupling the CD11b antibody and loading MP into the nanoparticles. The modification of the new antibody-conjugated nanoparticles was confirmed by S-TEM observation and (1) H NMR and FTIR spectroscopy. Cytotoxicity assays revealed that the conjugates did not affect the viability of both primary cultures of glial and microglial cells. Trace analyses of FITC-labelled nanoparticles revealed that the uptake of antibody-conjugated nanoparticles was conserved in microglial cells but significantly decreased in astrocytes and oligodendrocytes. Thus, this study demonstrates that antibody conjugation contributes to a modulation of the internalization of these nanocarriers by different cell types, which might be of relevance for specific targeting of CNS cell populations.     

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.     

The spectral networks paradigm in high throughput mass spectrometry

High-throughput proteomics is made possible by a combination of modern mass spectrometry instruments capable of generating many millions of tandem mass (MS(2)) spectra on a daily basis and the increasingly sophisticated associated software for their automated identification. Despite the growing accumulation of collections of identified spectra and the regular generation of MS(2) data from related peptides, the mainstream approach for peptide identification is still the nearly two decades old approach of matching one MS(2) spectrum at a time against a database of protein sequences. Moreover, database search tools overwhelmingly continue to require that users guess in advance a small set of 4-6 post-translational modifications that may be present in their data in order to avoid incurring substantial false positive and negative rates. The spectral networks paradigm for analysis of MS(2) spectra differs from the mainstream database search paradigm in three fundamental ways. First, spectral networks are based on matching spectra against other spectra instead of against protein sequences. Second, spectral networks find spectra from related peptides even before considering their possible identifications. Third, spectral networks determine consensus identifications from sets of spectra from related peptides instead of separately attempting to identify one spectrum at a time. Even though spectral networks algorithms are still in their infancy, they have already delivered the longest and most accurate de novo sequences to date, revealed a new route for the discovery of unexpected post-translational modifications and highly-modified peptides, enabled automated sequencing of cyclic non-ribosomal peptides with unknown amino acids and are now defining a novel approach for mapping the entire molecular output of biological systems that is suitable for analysis with tandem mass spectrometry. Here we review the current state of spectral networks algorithms and discuss possible future directions for automated interpretation of spectra from any class of molecules.     

Thrombospondin-1 binds to ApoER2 and VLDL receptor and functions in postnatal neuronal migration

Apolipoprotein E receptor 2 (ApoER2), very low-density lipoprotein receptor (VLDLR), and Dab1 are the main components of the Reelin signalling cascade. Reelin is the sole ligand defined so far in signalling through this pathway. Postnatal migration of neuronal precursors from the subventricular zone (SVZ) to the olfactory bulb (OB), however, depends on ApoER2 and Dab1, but functions independently of Reelin. Here, we show that thrombospondin-1 (THBS-1) is a novel physiological ligand for ApoER2 and VLDLR. THBS-1 is present in the SVZ and along the entire rostral migratory stream (RMS). It binds to ApoER2 and VLDLR and induces phosphorylation of Dab1. In contrast to Reelin, it does not induce Dab1 degradation or Akt phosphorylation, but stabilizes neuronal precursor chains derived from subventricular explants. Lack of THBS-1 results in anatomical abnormalities of the RMS and leads to a reduction of postnatal neuronal precursors entering the OB.     

Genetic parameters of intra- and inter-specific hybrids of Eucalyptus globulus and E. nitens

Intra-specific hybrids within Eucalyptus nitens and E. globulus were compared directly with inter-specific E. nitens × globulus using common parents. Diameter (age 2, 4, 6, 10 years) and Pilodyn (age 6 years) were used as indirect measures of growth and wood density, respectively. Genetic parameters were estimated for all cross types and traits. A direct comparison of the general combining ability with the general hybridising ability was made. Heterosis was estimated for intra- and inter-specific hybrids. The intra-specific hybrids in both species exhibit intermediate heritabilities and levels of additive genetic variance. The inter-specific F1 E. nitens × globulus exhibited high incidence of abnormalities at young ages and high levels of later age mortality. The mean performance of surviving inter-specific F1 hybrids was generally intermediate for all traits, to varying degrees, between the parental intra-specific crosses, and there is little evidence for significant heterosis. Different provenances of E. globulus may exhibit different responses to hybridisation. In this case, the inter-specific F1 hybrids, using Taranna E. globulus, appear to perform worse on average than those using King Island provenance for growth traits. There is evidence that specific hybrid families are produced that outperform most of the pure species families for one or other of the traits examined; however, there is no reliable quantitative genetic method of predicting which parents should be used.     

Sampling strategies for biotope definition: minimal sampling area for selected groups of macroinvertebrates in the rocky subtidal of São Miguel, Azores

Azorean rocky shores are mainly characterized by patchy algae-based communities with variable associated macrofauna. Characterization studies should therefore include quantitative information for both algae and macroinvertebrates. Unlike for the algae, minimal sampling areas are undefined for macroinvertebrates in the Azores. The present study defines the minimal area to be used for the assessment of the abundance of conspicuous benthic macroinvertebrate abundance. This study proposes methodologies to be used for a selected group of invertebrates when simultaneously undertaking quantifications of macroalgae.