Purification and identification of a protein kinase activity modulated by ionizing radiation

ATBF1 was first discovered as a suppressor of AFP expression in hepatocytes. It is present in brain, adult liver, lung, and gastro-intestinal tract. Recently, it has been reported that ATBF1 regulates myoblastic differentiation and interacts with v-Myb in regulation of its transactivation. Using the yeast two-hybrid system, we searched for protein-protein interactions to uncover new functions for ATBF1. We present here experimental evidence that ATBF1 is a new regulatory factor for STAT3-mediated signal transduction through its interaction with PIAS3. PIAS3 was thus identified as an ATBF1-binding protein. In co-transfection experiments, the full-length ATBF1 was found to form complexes with PIAS3 in Hep G2 cells. In the luciferase assay, ATBF1 was found to have no influence on STAT3 signaling induced by IL-6 stimulation, but it did synergistically enhance PIAS3 inhibition of activated STAT3. In conclusion, ATBF1 can suppress the IL-6-mediated cellular response by acting together with PIAS3.     

Increased cell proliferation in the adult mouse hippocampus following chronic administration of group II metabotropic glutamate receptor antagonist, MGS0039

We have previously reported that MGS0039, a novel antagonist of group II metabotropic glutamate receptors (mGluRs), exerts antidepressant-like effects in experimental animal models. Recent studies suggest that the behavioral effects of chronic antidepressant treatment are mediated by the stimulation of neurogenesis in the hippocampus. In the present study, we examined the effects of MGS0039 on cell proliferation in the adult mouse hippocampus. MGS0039 (5 or 10mg/kg) or fluvoxamine was administered chronically to male ICR mice over a period of 14 days. Multiple bromodeoxyuridine (BrdU) administrations were performed after the last drug injection to label dividing cells. Immunohistochemical analyses after BrdU injections revealed that chronic MGS0039 treatment enhanced BrdU-positive cells in the dentate gyrus ( approximately 62% increase) in the same manner as chronic fluvoxamine treatment. This is the first in vivo study to demonstrate an increase in cell proliferation following a blockade of group II mGluRs. These findings raise the possibility that MGS0039 may exert antidepressant-like effects by modulating cell proliferation in the hippocampus.     

Many Independent Origins of trans Splicing of a Plant Mitochondrial Group II Intron

We examined the cis- vs. trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of land plants, using both Southern hybridization results (for 416 species) and intron sequence data from the literature. A total of 164 species (157 genera), all angiosperms, was found to have a trans-spliced form of the intron. Using a multigene land plant phylogeny, we infer that the intron underwent a transition from cis to trans splicing 15 times among the sampled angiosperms. In 10 cases, the intron was fractured between its 5 end and the intron-encoded matR gene, while in the other 5 cases the fracture occurred between matR and the 3 end of the intron. The 15 intron fractures took place at different time depths during the evolution of angiosperms, with those in Nymphaeales, Austrobaileyales, Chloranthaceae, and eumonocots occurring early in angiosperm evolution and those in Syringodium filiforme, Hydrocharis morsus-ranae, Najas, and Erodium relatively recently. The trans-splicing events uncovered in Austrobaileyales, eumonocots, Polygonales, Caryophyllales, Sapindales, and core Rosales reinforce the naturalness of these major clades of angiosperms, some of which have been identified solely on the basis of recent DNA sequence analyses.     

Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum

The chloroplast genome has experienced many architectural changes during the evolution of chlorophyte green algae, with the class Chlorophyceae displaying the lowest degree of ancestral traits. We have previously shown that the completely sequenced chloroplast DNAs (cpDNAs) of Chamydomonas reinhardtii (Chlamydomonadales) and Scenedesmus obliquus (Sphaeropleales) are highly scrambled in gene order relative to one another. Here, we report the complete cpDNA sequence of Stigeoclonium helveticum (Chaetophorales), a member of a third chlorophycean lineage. This genome, which encodes 97 genes and contains 21 introns (including four putatively trans-spliced group II introns inserted at novel sites), is remarkably rich in derived features and extremely rearranged relative to its chlorophycean counterparts. At 223,902 bp, Stigeoclonium cpDNA is the largest chloroplast genome sequenced thus far, and in contrast to those of Chlamydomonas and Scenedesmus, features no large inverted repeat. Interestingly, the pattern of gene distribution between the DNA strands and the bias in base composition along each strand suggest that the Stigeoclonium genome replicates bidirectionally from a single origin. Unlike most known trans-spliced group II introns, those of Stigeoclonium exhibit breaks in domains I and II. By placing our comparative genome analyses in a phylogenetic framework, we inferred an evolutionary scenario of the mutational events that led to changes in genome architecture in the Chlorophyceae.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Nucleotide sequence data reported are available in the GenBank database under the accession number DQ630521.     

Independence and interdependence in the nest-site choice by honeybee swarms: Agent-based models, analytical approaches and pattern formation

In a recent paper List, Elsholtz and Seeley (List et al., 2009) have devised an agent-based model of the nest-choice dynamics in swarms of honeybees, and have concluded that both interdependence and independence are needed for the bees to reach a consensus on the best nest site. We here present a simplified version of the model which can be treated analytically with the tools of statistical physics and which largely has the same features as the original dynamics. Based on our analytical approaches it is possible to characterize the co-ordination outcome exactly on the deterministic level, and to a good approximation if stochastic effects are taken into account, reducing the need for computer simulations on the agent-based level. In the second part of the paper we present a spatial extension, and show that transient non-trivial patterns emerge, before consensus is reached. Approaches in terms of Langevin equations for continuous field variables are discussed.     

Responses of coral reefs to increased amplitude of sea-level changes at the Mid-Pleistocene Climate Transition

We show responses of coral reefs to increased amplitude of sea-level changes at the Mid-Pleistocene Climate Transition (MPT) based on lithostratigraphic, sedimentologic and calcareous nannofossil biostratigraphic investigations on Pleistocene reef-complex deposits (Ryukyu Group) on the Motobu Peninsula, Okinawa-jima, Central Ryukyus. Our data show that reef growth started in earliest Quaternary time (1.45-1.65 Ma) and that extensive reef formation dates back to ∼ 0.8 Ma. The mode of Quaternary sedimentation changed at ∼ 0.8 Ma in the study area. Before this time, thick siliciclastics and mixed carbonate-siliciclastics accumulated, which were followed by the deposition of bioclastic sediments (detrital limestone). No indications have been found of episodic subaerial exposures in these deposits and no calcareous nannofossil biozones are lacking. Since the detrital limestone includes biogenic components characterizing fore-reef to shelf environments, the coastal areas of the northern Motobu Peninsula mostly lay in fore-reef to shelf environments for > 0.6 million years (between ∼ 0.8 Ma and 1.45-1.65 Ma), when the sediments had not been subaerially exposed due to sea-level changes characterized by relatively small amplitudes. Coral limestone that formed in the latest Early to Middle Pleistocene between 0.4 Ma and 0.8 Ma extends over the study area, ranging in elevation from 0 to 70 m. This coral limestone grades upward into fore-reef to shelf carbonates (rhodolith, Cycloclypeus-Operculina, and detrital limestones) which is in turn overlain by coral limestone. This succession, combined with configuration of the lithofacies and paleobathymetry inferred from lithology and biogenic components, implies that the reef-complex deposits formed responding to sea-level changes with amplitude of > 60 m. Consequently, we suggest that the change in the mode of sedimentation results from increased amplitude of sea-level fluctuations at ∼ 0.8 Ma. This timing corresponds roughly to the timing of the Mid-Pleistocene Climate Transition (MPT).     

Chloroplast heat shock protein Cpn60 from Chlamydomonas reinhardtii exhibits a novel function as a group II intron-specific RNA-binding protein

Intron-binding proteins in eukaryotic organelles are mainly encoded by the nuclear genome and are thought to promote the maturation of precursor RNAs. Here, we present a biochemical approach that enable the isolation of a novel nuclear-encoded protein from Chlamydomonas reinhardtii showing specific binding properties to organelle group II intron RNA. Using FPLC chromatography of chloroplast protein extracts, a 61-kDa RNA-binding protein was isolated and then tentatively identified by mass spectrometry as the chloroplast heat shock protein Cpn60. Heterologous Cpn60 protein was used in RNA protein gel mobility shift assays and revealed that the ATPase domains of Cpn60 mediates the specific binding of two group II intron RNAs, derived from the homologous chloroplast psaA gene and the heterologous mitochondrial LSU rRNA gene. The function of Cpn60 as a general organelle splicing factor is discussed.     

Juvenile ornithopod (Dinosauria: Rhabdodontidae) remains from the Upper Cretaceous (Lower Campanian, Gosau Group) of Muthmannsdorf (Lower Austria)

The fragmentary remains of a juvenile rhabdodontid ornithopod from the Coal-bearing Complex of the Gosau Group (Lower Campanian, Grünbach syncline) at Muthmannsdorf near Wiener Neustadt, Lower Austria are revised. The material, probably belonging to a single individual, includes a right dentary (lectotype of Iguanodon suessi Bunzel, 1871, designated herein), teeth, a fragmentary parietal, fragments of scapula, ?radius, femur, tibia, two vertebrae (lost) and a manual ungual.The lectotype dentary does not provide clear autapomorphies or sufficient diagnostic features to determine its position within the Rhabdodontidae at generic level. By this “Iguanodon suessi” Bunzel, 1871 and the genus “Mochlodon” Seeley, 1881, to which it was latter referred as type species, cannot be characterized sufficiently by differential diagnosis and these are best considered nomina dubia. Based upon combined character comparisons (mainly postcranial features) the Muthmannsdorf ornithopod is referred herein to Zalmoxes Weishampel, Jianu, Csiki and Norman, 2003, a genus so far known from the late Maastrichtian of Romania. It probably but not evidently represents a yet unnamed species, most closely related to Zalmoxes shqiperorum Weishampel, Jianu, Csiki and Norman, 2003. At the present state of knowledge the Austrian material is not further diagnostic at the species level and kept in open nomenclature as Zalmoxes sp.     

Searching for a needle in the haystack: comparing six methods to evaluate heteroplasmy in difficult sequence context

Mitochondrial DNA (mtDNA) mutations have been involved in disease, aging and cancer and furthermore exploited for evolutionary and forensic investigation. When investigating mtDNA mutations the peculiar aspects of mitochondrial genetics, such as heteroplasmy and threshold effect, require suitable approaches which must be sensitive enough to detect low-level heteroplasmy and, precise enough to quantify the exact mutational load. In order to establish the optimal approach for the evaluation of heteroplasmy, six methods were experimentally compared for their capacity to reveal and quantify mtDNA variants. Drawbacks and advantages of cloning, Fluorescent PCR (F-PCR), denaturing High Performance Liquid Chromatography (dHPLC), quantitative Real-Time PCR (qRTPCR), High Resolution Melting (HRM) and 454 pyrosequencing were determined. In particular, detection and quantification of a mutation in a difficult sequence context were investigated, through analysis of an insertion in a homopolymeric stretch (m.3571insC).