The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition

The PYRIN domain is a conserved sequence motif identified in more than 20 human proteins with putative functions in apoptotic and inflammatory signalling pathways. The three-dimensional structure of the PYRIN domain from human ASC was determined by NMR spectroscopy. The structure determination reveals close structural similarity to death domains, death effector domains, and caspase activation and recruitment domains, although the structural alignment with these other members of the death-domain superfamily differs from previously predicted amino acid sequence alignments. Two highly positively and negatively charged surfaces in the PYRIN domain of ASC result in a strong electrostatic dipole moment that is predicted to be present also in related PYRIN domains. These results suggest that electrostatic interactions play an important role for the binding between PYRIN domains. Consequently, the previously reported binding between the PYRIN domains of ASC and ASC2/POP1 or between the zebrafish PYRIN domains of zAsc and Caspy is proposed to involve interactions between helices 2 and 3 of one PYRIN domain with helices 1 and 4 of the other PYRIN domain, in analogy to previously reported homophilic interactions between caspase activation and recruitment domains.     

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5‐aminoimidazole‐4‐carboxamideribotide. Solution NMR spectroscopy of ammonium chloride‐titrated samples was used to study the interaction of NH₃ with amino acids inside this channel. Although numerous residues showed ¹⁵N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using ¹H‐¹⁵N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon‐induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N′‐[(5′‐phosphoribulosyl)formimino]‐5‐aminoimidazole‐4‐carboxamide‐ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central β‐barrel of HisF and overlaps with the putative ammonia transport channel.     

Biomass Stock and Productivity of Primeval and Production Beech Forests: Greater Canopy Structural Diversity Promotes Productivity

Our knowledge of temperate broadleaf forest ecology is based mostly on the study of production forests, which lack the terminal stage of forest development and have a simpler stand structure than old-growth and primeval forests. How primeval and production forests differ in net primary production (NPP) is not well known. In three primeval and three nearby production forests of European beech (Fagus sylvatica) in the Slovakian Carpathians, we measured aboveground biomass stocks (live and dead), aboveground NPP (ANPP) and parameters characterizing canopy structural diversity (leaf area index and its spatial variation). Our study aims were (1) to explore the role of canopy structural diversity for ANPP and (2) to assess evidence of a productivity decline in the terminal stage. While aboveground live biomass stocks were on average 20% greater in the primeval forests (386 vs. 320 Mg ha^?1; insignificant difference at two sites), deadwood mass stocks were on average four times larger than in the production forests (86 vs. 19 Mg ha^?1). ANPP was similarly high in the primeval and production forests (10.0 vs. 9.9 Mg ha^?1 y^?1) and did not decrease towards the terminal stage. Production models indicate that, in the primeval forests, about 10% of ANPP (ca. 1 Mg ha^?1 y^?1) was generated by effects related to leaf area heterogeneity, evidencing a positive effect of structural diversity on forest productivity, even though species diversity was low. This study helps to better understand the impact of forest management on the productivity and carbon storage in temperate woodlands.     

The association between the caprellid Pariambus typicus Krøyer (Crustacea,Amphipoda) and ophiuroids

The work of Kazutsugu Hirayama over the past 25 yearspromoted the wide use of the marine rotifer Brachionusplicatilis as an experimental model in zooplanktonecology. His reports about the nature of geneticvariation in the B. plicatilis complex stimulated usto investigate how mate recognition maintains speciesboundaries. For the past several years, we haveexamined chemical communication between female andmale B. plicatilis. Here we report on the comparativebinding of polyclonal antibody against the materecognition pheromone (MRP) to three B. plicatilisstrains and three B. rotundiformis strains.Quantification of anti-MRP binding permitsinvestigation of how the female mating signal differsamong closely related Brachionus species and strains.Antibody binding reflects differentiation independentof the male receptor which has been describedelsewhere. Anti-MRP bound to females of all sixstrains and was localized in the corona. Antibodybinding greatly reduced mating in all three B. plicatilis strains. However, antibody bindingsignificantly reduced mating in only one of the B. rotundiformis strains. The MRP of both species has asimilar molecular weight, but the differential bindingsuggests that the mate recognition pheromone onfemales has differentiated in B. plicatilis and B. rotundiformis.     

Die Wirkung Des »Gibberellinantagonisten« 2-Chloräthyltrimethylammoniumchlorid (CCC) auf die Stecklingsbewurzelung Windender und nicht Windender Pflanzen

Summary Root initiation at cuttings is inhibited by application of gibberellin. CCC does not antagonize this inhibition. However, CCC stimulates root initiation at cuttings of three different species of twining plants known to be rich in endogenous gibberellin. CCC seems to be an antagonist for endogenous but not for exogenous gibberellin, which suggests that CCC influences gibberellin biosynthesis.     

Heat shock protein 27 as a prognostic and predictive biomarker in pancreatic ductal adenocarcinoma

A role of heat shock protein 27 (HSP27) as a potential biomarker has been reported in various tumour entities, but comprehensive studies in pancreatic cancer are lacking. Applying tissue microarray (TMA) analysis, we correlated HSP27 protein expression status with clinicopathologic parameters in pancreatic ductal adenocarcinoma specimens from 86 patients. Complementary, we established HSP27 overexpression and RNA-interference models to assess the impact of HSP27 on chemo- and radiosensitivity directly in pancreatic cancer cells. In the TMA study, HSP27 expression was found in 49% of tumour samples. Applying univariate analyses, a significant correlation was found between HSP27 expression and survival. In the multivariate Cox-regression model, HSP27 expression emerged as an independent prognostic factor. HSP27 expression also correlated inversely with nuclear p53 accumulation, indicating either protein interactions between HSP27 and p53 or TP53 mutation-dependent HSP27-regulation in pancreatic cancer. In the sensitivity studies, HSP27 overexpression rendered HSP27 low-expressing PL5 pancreatic cancer cells more susceptible towards treatment with gemcitabine. Vice versa, HSP27 protein depletion in HSP27 high-expressing AsPC-1 cells caused increased gemcitabine resistance. Importantly, HSP27 expression was inducible in pancreatic cancer cell lines as well as primary cells. Taken together, our study suggests a role for HSP27 as a prognostic and predictive marker in pancreatic cancer. Assessment of HSP27 expression could thus facilitate the identification of specific patient subpopulations that might benefit from individualized treatment options. Additional studies need to clarify whether modulation of HSP27 expression could represent an attractive concept to support the incorporation of hyperthermia in clinical treatment protocols for pancreatic cancer.     

Different structural organization of the encephalopsin gene in man and mouse

Encephalopsin, also called Panopsin, is a recently discovered extraretinal photoreceptor, which may play a role in non-visual photic processes such as the entrainment of circadian rhythm or the regulation of pineal melatonin production. Based on RT-PCR data and comparative genomic sequence analysis, we show that the human OPN3 gene consists of six exons and expresses various splice variants, while the murine homologue contains four exons and produces just one splice form. Furthermore, the human OPN3 gene overlaps with the neighboring KMO gene on a genomic as well as on an RNA level, whereas the corresponding genes in mouse lie close together but do not overlap. This finding is of particular interest, since differences in gene organization between man and mouse, that have been reported so far, occur within gene clusters, i.e. the number of genes within a certain cluster may differ between man and mouse. OPN3 provides an exception to this rule, since it is positionally uncoupled from other genes of the opsin family.     

Horizontal Gene Transfer in Aminoacyl-tRNA Synthetases Including Leucine-Specific Subtypes

Aminoacyl-tRNA synthetases catalyze a fundamental reaction for the flow of genetic information from RNA to protein. Their presence in all organisms known today highlights their important role in the early evolution of life. We investigated the evolutionary history of aminoacyl-tRNA synthetases on the basis of sequence data from more than 200 Archaea, Bacteria, and Eukaryota. Phylogenetic profiles are in agreement with previous observations that many genes for aminoacyl-tRNA synthetases were transferred horizontally between species from all domains of life. We extended these findings by a detailed analysis of the history of leucyl-tRNA synthetases. Thereby, we identified a previously undetected case of horizontal gene transfer from Bacteria to Archaea based on phylogenetic profiles, trees, and networks. This means that, finally, the last subfamily of aminoacyl-tRNA synthetases has lost its exceptional position as the sole subfamily that is devoid of horizontal gene transfer. Furthermore, the leucyl-tRNA synthetase phylogenetic tree suggests a dichotomy of the archaeal/eukaryotic-cytosolic and bacterial/eukaryotic-mitochondrial proteins. We argue that the traditional division of life into Prokaryota (non-chimeric) and Eukaryota (chimeric) is favorable compared to Woese’s trichotomy into Archaea/Bacteria/Eukaryota. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Yves Van de Peer]     

Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness

Within hosts, RNA viruses form populations that are genetically and phenotypically complex. Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood. Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts. We allowed West Nile virus (WNV) to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality. After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing. We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows. Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts. However, the selective pressures that control WNV populations seem to be bird species-dependent. Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7× more than sparrows, ~3.4× more than robins) and defective genomes (~1.4× greater than sparrows, ~2.7× greater than robins), but the lowest average mutation frequency (about equal to sparrows, ~2.6× lower than robins). Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection. These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations. Taken together, these results reveal important insights into how different hosts may contribute to the emergence of RNA viruses.