Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily,but exhibits an unusual active site

Background  

Catalytic domains of Type II restriction endonucleases (REases) belong to a few unrelated three-dimensional folds. While the PD-(D/E)XK fold is most common among these enzymes, crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI). Bioinformatics analyses supported by mutagenesis experiments suggested that some REases belong to the HNH fold (e.g. R.KpnI), and that a small group represented by R.Eco29kI belongs to the GIY-YIG fold. However, for a large fraction of REases with known sequences, the three-dimensional fold and the architecture of the active site remain unknown, mostly due to extreme sequence divergence that hampers detection of homology to enzymes with known folds.     

A rhodopsin immunoanalog in the related photosensitive protozoans Blepharisma japonicum and Stentor coeruleus

Immunoblotting of isolated cell membrane fractions from ciliates Blepharisma japonicum and Stentor coeruleus with a polyclonal antibody raised against rhodopsin revealed one strong protein band of about 36 kDa, thought to correspond to protozoan rhodopsin. Inspection of both ciliates labeled with the same antibody using a confocal microscope confirmed the immunoblotting result and demonstrated the presence of these rhodopsin-like molecules localized within the cell membrane area. Immunoblot analysis of the ciliate membrane fractions resolved by two-dimensional gel electrophoresis identified two distinct 36 kDa spots at pIs of 4.5 and 7.0 for Blepharisma, and three spots at pIs of 4.4, 5.0 and 6.0 for Stentor, indicating a possible mixture of phosphorylated rhodopsin species in these cells. The obtained results suggest that both Blepharisma and the related ciliate Stentor contain within the cell membrane the rhodopsin-like proteins, which may be involved as receptor molecules in the sensory transduction pathway mediating motile photoresponses in these protists as in other species of lower eukaryota.     

Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases

Background  

Alteration in epigenetic methylation can affect gene expression and other processes. In Prokaryota, DNA methyltransferase genes frequently move between genomes and present a potential threat. A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs. Here we examined whether McrBC competes with genome methylation systems through host killing by chromosome cleavage.     

Interactions between phytoplankton and zooplankton in the hypertrophic Swarzedzkie Lake in western Poland

The hypertrophic Swarzdzkie Lake, Poland, is characterized byhigh species diversity, abundance and biomass of both phytoplanktonand zooplankton (up to 99.5 mg WW L^–1 and 817.75 µgDW L^–1, respectively). The community grazing rate calculatedwith the use of two empirical models, and based on herbivorouscrustaceans, peaked in spring and early autumn up to 150.6%of water filtered per day, and was the lowest during winter.Simple statistics revealed a positive correlation between zooplanktonbiomass and chlorophyll a concentration (r = 0.404, P = 0.033)and between zooplankton abundance and phytoplankton biomass(r = 0.42, P = 0.028). Canonical statistics indicated, however,that the relationship exists only with size groups and/or livingforms of a few taxonomical groups of phytoplankton. Redundancyanalysis (RDA) confirmed a positive influence of the communitygrazing rate on micro- and nanoplanktonic Cryptophyceae, butnot on the microplanktonic Cyanobacteria, as was suggested bycanonical correlation analysis. RDA also indicated a weak negativeinfluence on nanoplanktonic Euglenophyceae and Chlorophyceaeexerted by filtering crustaceans. Some taxonomically diverseflagellated nanoplanktonic algae were grazing sensitive, whereasmicroplanktonic cryptophytes and coenobial green algae weresignificantly grazing resistant.     

Magnitude of mesozooplankton variability: a case study from the Marginal Ice Zone of the Barents Sea in spring

Zooplankton was studied on eight stations in the marginal icezone (MIZ) of the Barents Sea, in May 1999, along two transectsacross the ice edge. On each station, physical background measurementsand zooplankton samples were taken every 6 h over a 24 h periodat five discrete depth intervals. Cluster analysis revealedseparation of open water stations from all ice stations as wellas high similarity level among replicates belonging to particularstation. Based on five replicates per station, analysis of variance(ANOVA) confirmed significant differences (P < 0.05) in abundancesof the main mesozooplankton taxa among stations. Relations betweenthe zooplankton community and environmental parameters wereestablished using redundancy analysis (CANOCO). In total, 55%of mesozooplankton variability within studied area was explainedby eight variables with significant conditional effects: depthstratum, fluorescence, temperature, salinity, bottom depth,latitude, bloom situation, and ice concentration. GLM modelssupported supposition about clear and negative relationshipbetween concentration of Oithona similis, and overall mesozooplanktondiversity. The analyses showed a dynamic relationship betweenmesozooplankton distribution and hydrological conditions onshort-term scale. Furthermore, our study demonstrated that variabilityin the physical environment of dynamic MIZ of the Barents Seahas measurable effect on the Arctic pelagic ecosystem.     

Evolutionary Acceleration and Divergence in <Emphasis Type="Italic">Procolobus kirkii</Emphasis>

We investigated the role of geographical insularity in divergence and speciation of Procolobus kirkii by examining cranial morphology. The sample (n = 369) included museum specimens of Procolobus spp. and recently deceased individuals of P. kirkii from the main island of Zanzibar and 2 smaller islands in the archipelago. Geometric morphometrics evinced pronounced divergence of Procolobus kirkii from mainland Procolobus, including members of P. badius ssp., P. pennantii ssp., P. rufomitratus, P. gordonorum and also representatives of the assemblage of red colobus populations from Central Equatorial Africa. Procolobus kirkii has a small cranium, consistent with the island rule for large mammals, reduced sexual dimorphism consistent with Rensch’s rule, and a distinct cranial form. Analyses of phenotypic variance of Procolobus kirkii gave no evidence for population bottlenecks in the history of the species, but there is a clear indication that the species has experienced accelerated morphological evolution of size, probably as a result of insularity. Their highly distinctive morphology lends weight to the argument that they are a unique insular endemic species in need of active conservation. An erratum to this article can be found at     

Optimization of a synthetic siRNA delivery for the treatment of rhabdomyosarcoma

Silencing of a target-genes by small interfering RNA (siRNA) has emerged as a powerful new tool not only for basic research but also with potential therapeutic benefits. This paper demonstrates that optimal delivery strategy is crucial for effective target-gene silencing. Using lipofection, under defined conditions, we were able to markedly down-regulate expression of the selected genes involved in rhabdomyosarcoma metastasis: MET, CXCR4, LIFR and PAX3-FKHR.     

Blue Tits Cyanistes caeruleus breeding in a House Martin Delichon urbicum nest

This paper describes a breeding attempt by Blue Tits Cyanistes caeruleus in the nest of House Martins Delichon urbicum on the wall of a block of flats in Wroc?aw, Poland. Urban environments may provide novel competition and costs for breeding birds.     

PDMP,a ceramide analogue,acts as an inhibitor of mTORC1 by inducing its translocation from lysosome to endoplasmic reticulum

Mammalian or mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth, metabolism, and cell differentiation. Recent studies have revealed that the recruitment of mTORC1 to lysosomes is essential for its activation. The ceramide analogue 1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP), a well known glycosphingolipid synthesis inhibitor, also affects the structures and functions of various organelles, including lysosomes and endoplasmic reticulum (ER). We investigated whether PDMP regulates the mTORC1 activity through its effects on organellar behavior. PDMP induced the translocation of mTORC1 from late endosomes/lysosomes, leading to the dissociation of mTORC1 from its activator Rheb in MC3T3-E1 cells. Surprisingly, we found mTORC1 translocation to the ER upon PDMP treatment. This effect of PDMP was independent of its action as the inhibitor, since two stereoisomers of PDMP, with and without the inhibitor activity, showed essentially the same effect. We confirmed that PDMP inhibits the mTORC1 activity based on the decrease in the phosphorylation of ribosomal S6 kinase, a downstream target of mTORC1, and the increase in LC3 puncta, reflecting autophagosome formation. Furthermore, PDMP inhibited the mTORC1-dependent osteoblastic cell proliferation and differentiation of MC3T3-E1 cells. Accordingly, the present results reveal a novel mechanism of PDMP, which inhibits the mTORC1 activity by inducing the translocation of mTOR from lysosomes to the ER.