ALBERT

Description: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de .

Description: The common age-related neurodegeneration of Parkinson's disease can result from dominant causes like increased dosage of vesicle-associated alpha-synuclein (SNCA) or recessive causes like deficiency of mitophagy factor PINK1. Interactions between these triggers and their convergence onto shared pathways are crucial, but currently conflicting evidence exists. Here, we crossed previously characterized mice with A53T-SNCA overexpression and with Pink1 deletion to generate double mutants (DMs). We studied their lifespan and behavior, histological and molecular anomalies at late and early ages. DM animals showed potentiated phenotypes in comparison with both single mutants (SMs), with reduced survival and strongly reduced spontaneous movements from the age of 3 months onwards. In contrast to SMs, a quarter of DM animals manifested progressive paralysis at ages 〉1 year and exhibited protein aggregates immunopositive for pSer129-SNCA, p62 and ubiquitin in spinal cord and basal brain. Brain proteome quantifications of ubiquitination sites documented altered degradation of SNCA and the DNA-damage marker H2AX at the age of 18 months. Global brain transcriptome profiles and qPCR validation experiments identified many consistent transcriptional dysregulations already at the age of 6 weeks, which were absent from SMs. The observed downregulations for Dapk1 , Dcaf17 , Rab42 and the novel SNCA-marker Lect1 as well as the upregulations for Dctn5 , Mrpl9 , Tmem181a , Xaf1 and H2afx reflect changes in ubiquitination, mitochondrial/synaptic/microtubular/cell adhesion dynamics and DNA damage. Thus, our study confirmed that SNCA-triggered neurotoxicity is exacerbated by the absence of PINK1 and identified a novel molecular signature that is detectable early in the course of this double pathology.

Description: Functional loss of SMN1 causes proximal spinal muscular atrophy (SMA), the most common genetic condition accounting for infant lethality. Hence, the hypomorphic copy gene SMN2 is the only resource of functional SMN protein in SMA patients and influences SMA severity in a dose-dependent manner. Consequently, current therapeutic approaches focus on SMN2 . Histone deacetylase inhibitors (HDACi), such as the short chain fatty acid VPA (valproic acid), ameliorate the SMA phenotype by activating the SMN2 expression. By analyzing blood SMN2 expression in 16 VPA-treated SMA patients, about one-third of individuals were identified as positive responders presenting increased SMN2 transcript levels. In 66% of enrolled patients, a concordant response was detected in the respective fibroblasts. Most importantly, by taking the detour of reprograming SMA patients' fibroblasts, we showed that the VPA response was maintained even in GABAergic neurons derived from induced pluripotent stem cells (iPS) cells. Differential expression microarray analysis revealed a complete lack of response to VPA in non-responders, which was associated with an increased expression of the fatty acid translocase CD36. The pivotal role of CD36 as the cause of non-responsiveness was proven in various in vitro approaches. Most importantly, knockdown of CD36 in SMA fibroblasts converted non- into pos-responders. In summary, the concordant response from blood to the central nervous system (CNS) to VPA may allow selection of pos-responders prior to therapy. Increased CD36 expression accounts for VPA non-responsiveness. These findings may be essential not only for SMA but also for other diseases such as epilepsy or migraine frequently treated with VPA.

Description: Experiments at 20–97 GPa and 2000 K in the system CaO–MgO–TiO 2 –SiO 2 constrain phase relations involving Mg-rich and Ca-rich perovskite solid solutions at conditions relevant to the Earth's deep Transition Zone and lower mantle. Bulk compositions were investigated with molar Ti/(Ti + Si) up to 0·5 within the quasi-ternary ‘perovskite plane’, which is defined by a reciprocal solution among the components MgSiO 3 , MgTiO 3 , CaSiO 3 , and CaTiO 3 . Multi-anvil experiments at 20 GPa and 2000 K on bulk compositions within the plane produce akimotoite coexisting with Ca-perovskites that lie close to the CaSiO 3 –CaTiO 3 join. Higher-pressure experiments using a laser-heated diamond anvil cell constrain the position of a two-perovskite field that extends into the perovskite plane from the solvus along the MgSiO 3 –CaSiO 3 binary join, where limited mutual solubility exists between MgSiO 3 and CaSiO 3 perovskites. On the join MgSiO 3 –MgTiO 3 , MgTiO 3 solubility in MgSiO 3 perovskite increases with pressure, with MgSi 0 · 8 Ti 0 · 2 O 3 perovskite stable at ~50 GPa. Limited reciprocal solution at ~25 GPa results in an expansive two-perovskite field that occupies much of the Si-rich portion of the perovskite plane. Solution of Ti into Mg-rich and Ca-rich perovskites enhances the solubility of reciprocal Ca and Mg components, respectively. Increase in pressure promotes reciprocal solution, and the two-phase field collapses rapidly with pressure toward the MgSiO 3 –CaSiO 3 join. We find that a single-phase, orthorhombic perovskite with near equimolar Ca and Mg is stable in a composition with Ti/(Ti + Si) of only 0·05 at 97 GPa, requiring that by this pressure the two-phase field occupies a small area close to the MgSiO 3 –CaSiO 3 join. On the basis of experiments at~1500 K, temperature has only a mild effect on the position of the Ca-rich limb of the solvus. Ca(Ti,Si)O 3 mineral inclusions in deep sublithospheric diamonds could not have formed in equilibrium with Mg-perovskite owing to their virtual lack of MgSiO 3 component at pressures of Mg-perovskite stability, but may have equilibrated with Transition Zone MgSiO 3 -rich phases at lower pressures; this observation can be extended generally to near-endmember CaSiO 3 inclusions. On an iron-free basis, the average bulk compositions of clinopyroxene–ilmenite and orthopyroxene–ilmenite megacrysts from kimberlites plot in single-perovskite fields at pressures greater than about 45 and 65 GPa, respectively, when projected onto the perovskite plane. We predict that the effect of iron will not be large, and estimate that single-phase perovskites may form at somewhat lower pressures than in the iron-free system. Thus, the origin of pyroxene–ilmenite megacrysts from single-phase perovskite solutions in the lower mantle is plausible on the basis of phase relations, although a lower pressure magmatic origin appears more likely. Deeply subducted Ti-rich lithologies such as ocean-island basalt will crystallize a single perovskite rather than a two-perovskite assemblage beginning at pressures of ~80 GPa. Normal mid-ocean ridge basalt and primitive mantle peridotite are expected to remain within a two-phase perovskite field until Mg-perovskite transforms to post-perovskite.

Description: Duchenne muscular dystrophy (DMD) is caused by mutations in the X-linked dystrophin ( DMD ) gene. The absence of dystrophin protein leads to progressive muscle weakness and wasting, disability and death. To establish a tailored large animal model of DMD, we deleted DMD exon 52 in male pig cells by gene targeting and generated offspring by nuclear transfer. DMD pigs exhibit absence of dystrophin in skeletal muscles, increased serum creatine kinase levels, progressive dystrophic changes of skeletal muscles, impaired mobility, muscle weakness and a maximum life span of 3 months due to respiratory impairment. Unlike human DMD patients, some DMD pigs die shortly after birth. To address the accelerated development of muscular dystrophy in DMD pigs when compared with human patients, we performed a genome-wide transcriptome study of biceps femoris muscle specimens from 2-day-old and 3-month-old DMD and age-matched wild-type pigs. The transcriptome changes in 3-month-old DMD pigs were in good concordance with gene expression profiles in human DMD, reflecting the processes of degeneration, regeneration, inflammation, fibrosis and impaired metabolic activity. In contrast, the transcriptome profile of 2-day-old DMD pigs showed similarities with transcriptome changes induced by acute exercise muscle injury. Our studies provide new insights into early changes associated with dystrophin deficiency in a clinically severe animal model of DMD.

Description: It is generally accepted that functionally important RNA structure is more conserved than sequence due to compensatory mutations that may alter the sequence without disrupting the structure. For small RNA molecules sequence–structure relationships are relatively well understood. However, structural bioinformatics of mRNAs is still in its infancy due to a virtual absence of experimental data. This report presents the first quantitative assessment of sequence–structure divergence in the coding regions of mRNA molecules based on recently published transcriptome-wide experimental determination of their base paring patterns. Structural resemblance in paralogous mRNA pairs quickly drops as sequence identity decreases from 100% to 85–90%. Structures of mRNAs sharing sequence identity below roughly 85% are essentially uncorrelated. This outcome is in dramatic contrast to small functional non-coding RNAs where sequence and structure divergence are correlated at very low levels of sequence similarity. The fact that very similar mRNA sequences can have vastly different secondary structures may imply that the particular global shape of base paired elements in coding regions does not play a major role in modulating gene expression and translation efficiency. Apparently, the need to maintain stable three-dimensional structures of encoded proteins places a much higher evolutionary pressure on mRNA sequences than on their RNA structures.

Description: The caseinolytic peptidase P (CLPP) is conserved from bacteria to humans. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder together with the chaperone CLPX. In spite of a known relevance for the mitochondrial unfolded protein response, its substrates and tissue-specific roles are unclear in mammals. Recessive CLPP mutations were recently observed in the human Perrault variant of ovarian failure and sensorineural hearing loss. Here, a first characterization of CLPP null mice demonstrated complete female and male infertility and auditory deficits. Disrupted spermatogenesis already at the spermatid stage and ovarian follicular differentiation failure were evident. Reduced pre-/post-natal survival and marked ubiquitous growth retardation contrasted with only light impairment of movement and respiratory activities. Interestingly, the mice showed resistance to ulcerative dermatitis. Systematic expression studies detected up-regulation of other mitochondrial chaperones, accumulation of CLPX and mtDNA as well as inflammatory factors throughout tissues. T-lymphocytes in the spleen were activated. Thus, murine Clpp deletion represents a faithful Perrault model. The disease mechanism probably involves deficient clearance of mitochondrial components and inflammatory tissue destruction.

Description: Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host- Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database ( http://mips.helmholtz-muenchen.de/HoPaCI/ ) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii . The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches.