Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time<5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (>80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q²=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.     

Functional architecture of RNA polymerase I

Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming.     

N‐Acylated Alanine Methyl Esters (NAMEs) from Roseovarius tolerans,Structural Analogs of Quorum‐Sensing Autoinducers,N‐Acylhomoserine Lactones

The Roseobacter clade is one of the most important bacteria group living in the ocean. Liquid cultures of Roseovarius tolerans EL 164 were investigated for the production of autoinducers such as N‐acylhomoserine lactones (AHLs) and other secondary metabolites. The XAD extracts were analyzed by GC/MS. Two AHLs, Z7‐C14 : 1‐homoserine lactone (HSL) and C15 : 1‐HSL, were identified. Additionally, the extract contained five compounds with molecular‐ion peaks at m/z 104, 145, and 158, thus exhibiting mass spectra similar to those of AHLs with corresponding peaks at m/z 102, 143, and 156. Isolation of the main compound by column chromatography, NMR analysis, dimethyl disulfide derivatization for the determination of the location of the C?C bond and finally synthesis of the compound with the proposed structure confirmed the compound to be (Z)‐N‐(hexadec‐9‐enoyl)alanine methyl ester. Four additional minor compounds were identified as C14 : 0‐, C15 : 0‐, C16 : 0‐, and C17 : 1‐N‐acylated alanine methyl esters (NAMEs). All NAMEs have not been described from natural sources before. A BLASTp search showed the presence of AHL‐producing luxI genes, but no homologous genes potentially responsible for the structurally closely related NAMEs were found. The involvement of the NAMEs in chemical communication processes of the bacteria is discussed.     

Predictive Model for Inactivation of Feline Calicivirus, a Norovirus Surrogate, by Heat and High Hydrostatic Pressure

Noroviruses, which are members of the Caliciviridae family, represent the leading cause of nonbacterial gastroenteritis in developed countries; such norovirus infections result in high economic costs for health protection. Person-to-person contact, contaminated water, and foods, especially raw shellfish, vegetables, and fruits, can transmit noroviruses. We inactivated feline calicivirus, a surrogate for the nonculturable norovirus, in cell culture medium and mineral water by heat and high hydrostatic pressure. Incubation at ambient pressure and 75°C for 2 min as well as treatment at 450 MPa and 15°C for 1 min inactivated more than 7 log₁₀ PFU of calicivirus per ml in cell culture medium or mineral water. The heat and pressure time-inactivation curves obtained with the calicivirus showed tailing in the logarithmic scale. Modeling by nth-order kinetics of the virus inactivation was successful in predicting the inactivation of the infective virus particles. The developed model enables the prediction of the calicivirus reduction in response to pressures up to 500 MPa, temperatures ranging from 5 to 75°C, and various treatment times. We suggest high pressure for processing of foods to reduce the health threat posed by noroviruses.     

Can we see inside? Predicting strategic behavior given limited information

Evolutionary theory predicts that observable traits should evolve to reliably indicate unobservable behavioral tendencies in coordination games but not social dilemmas. We conducted a two-part study to test this idea. First, we recorded 60-s videos of participants, and then these participants played a stag hunt game or a prisoner’s dilemma. Subsequently, raters viewed these videos, with the sound either off or on, and they guessed player choices. Raters showed a significant tendency to guess that attractive players chose stag. In contrast to the prediction, rater accuracy was at chance regardless of whether the sound of the video was off or on. For prisoner’s dilemma players, raters showed a significant tendency to guess that women cooperated at a higher rate than men. Again in contrast to the prediction, accuracy was significantly above chance in this case. To calibrate the importance of this accuracy rate, we developed two models that suggest the accuracy we observed in the prisoner’s dilemma case is probably not high enough to support the evolution of cooperation. Altogether, our results show that raters tried to achieve a meaningful degree of accuracy about players by using the limited information available in the videos, but they could not do so.     

Ethological analyses of the effects of naloxone and the opiate antagonist ICI 154, 129 on social interactions in male house mice

The influences of the mu blocker naloxone and the novel opioid delta receptor antagonist ICI, 154, 129 on videotaped encounters between individually-housed, male Swiss mice and anosmic male ‘standard opponents’ were assessed using a variety of ethological analyses. The effects of drugs were studied on individual elements and on the times allocated by subjects to broad categories of behaviour. Neither of the drugs significantly altered times allocated to broad categories of behaviour. Both doses of both compounds significantly increased the incidences of some ‘fearful’/defensive postures. A more detailed analysis considered the effects of the drugs on the sequences of postures used in the resident's behaviour. This involved the generation of ‘dendrograms’ which provided support for the view that both naloxone and ICI 154, 129 altered the associations between behavioural elements seen in saline controls (especially at higher doses) and that the effects of these antagonists were qualitatively different.     

A fourth gene from the Candida albicans CDR family of ABC transporters

Using primers derived from a region of the Candida albicans CDR1 (Candida drug resistance) gene that is conserved in other ABC (ATP-binding cassette) transporters, a DNA fragment from a previously unknown CDR gene was obtained by polymerase chain reaction (PCR). After screening a C. albicans genomic library with this fragment as a probe, the complete CDR4 gene was isolated and sequenced. CDR4 codes for a putative ABC transporter of 1490 amino acids with a high degree of homology to Cdr1p, Cdr2p and Cdr3p from C. albicans (62, 59 and 57% amino acid sequence identity, respectively). Cdr4p has a predicted structure typical for cluster I.1 of yeast ABC transporters, characterized by two homologous halves, each comprising an N-terminal hydrophilic domain with consensus sequences for ATP binding and a C-terminal hydrophobic domain with six transmembrane helices. In contrast to the CDR1/CDR2 genes, the genetic structure of the CDR4 gene was conserved in 59 C. albicans isolates from six different patients. Northern hybridization analysis showed that the CDR4 gene was expressed in most isolates, but no correlation between CDR4 mRNA levels and the degree of fluconazole resistance of the isolates was found. In addition, a C. albicans mutant in which both copies of the CDR4 gene were disrupted by insertional mutagenesis was not hypersusceptible to fluconazole as compared to the parent strain. Unlike CDR1 and CDR2, CDR4 does not, therefore, seem to be involved in fluconazole resistance in C. albicans.     

Effects of depth, sediment and grazers on the degradation of drifting filamentous algae (Cladophora glomerata and Pilayella littoralis)

Eutrophication in the northern Baltic Sea promotes growth of annual filamentous algae. The algae detach, gather at the bottom and give rise to algal mats of varying size, density, composition and condition. Dense mats of filamentous algae induce anoxia, which in turn leads to faunal mortality. By a set of field experiments, we have studied the fate of the abundant Cladophora glomerata after detaching from the rocky substrate, and the effect of water depth and sediment on its decay. Further, we have studied the importance of common mesograzers (Gammarus and Idotea) on the rate of degradation of C. glomerata and Pilayella littoralis.Our results show that loose algae at shallow sites (8 m) decompose faster than algae in deeper (18 m) areas. Drifting C. glomerata on the sediment is more rapidly broken down and dissolved than algae floating in the water column, which depends on higher microbiological activity. Dominant amphipods (Gammarus spp) colonise near-shore drift algae quickly, and juvenile bivalves (Cerastoderma glaucum) utilise algae in the water column for settling. Moderate natural densities of grazers (Gammarus spp and Idotea baltica) in the drifting algae did not increase the degradation rates of C. glomerata and P. littoralis. C. glomerata was completely decomposed in 4 months.Our experiments demonstrate the effects of position (depth, water/sediment) and grazing on the degradation of drifting filamentous algae. Mass developments of opportunistic algae occur annually in the study area, and information on the destiny of detached drift algae may help us to predict their longevity and the damage they cause, and hence, to decide on long-term measures needed to improve environmental conditions.