Proteome approaches combined with Fourier transform infrared spectroscopy revealed a distinctive biofilm physiology in Bordetella pertussis

Proteome analysis was combined with whole-cell metabolic fingerprinting to gain insight into the physiology of mature biofilm in Bordetella pertussis, the agent responsible for whooping cough. Recent reports indicate that B. pertussis adopts a sessile biofilm as a strategy to persistently colonize the human host. However, since research in the past mainly focused on the planktonic lifestyle of B. pertussis, knowledge on biofilm formation of this important human pathogen is still limited. Comparative studies were carried out by combining 2-DE and Fourier transform infrared (FT-IR) spectroscopy with multivariate statistical methods. These complementary approaches demonstrated that biofilm development has a distinctive impact on B. pertussis physiology. Results from MALDI-TOF/MS identification of proteins together with results from FT-IR spectroscopy revealed the biosynthesis of a putative acidic-type polysaccharide polymer as the most distinctive trait of B. pertussis life in a biofilm. Additionally, expression of proteins known to be involved in cellular regulatory circuits, cell attachment and virulence was altered in sessile cells, which strongly suggests a significant impact of biofilm development on B. pertussis pathogenesis. In summary, our work showed that the combination of proteomics and FT-IR spectroscopy with multivariate statistical analysis provides a powerful tool to gain further insight into bacterial lifestyles.     

Extra-pair paternity and song characteristics in the willow warbler Phylloscopus trochilus

Complexity in bird song is often argued to be advantageous in processes of sexual selection, and numerous studies show that characteristics of song are associated with increased success in territory defence or mate attraction. Less evidence exists on the relationship between bird song characteristics and patterns of extra-pair paternity. We tested whether males that suffered from extra-pair paternity differed in song characteristics from males with no extra pair paternity in the willow warbler Phylloscopus trochilus . In the Scottish population that we studied, we found that 23.5% of young were not related to the social father, and that 47% of nests contained at least one extra pair young. Older males were less likely to suffer paternity loss. While song repertoire size was not related to loss of paternity, males with short songs suffered higher paternity loss than males with long songs. Although arrival date is a good correlate of social mate choice in this population, it was not related to extra-pair paternity. These results suggest that females use song length, or a trait correlated with this song characteristic, as a cue for choosing extra-pair partners in this species, or alternatively that variance in the success of mate guarding or female coercion is related to this song variable.     

Gamma carbonic anhydrases in plant mitochondria

Plant mitochondria contain non-phosphorylating bypasses of the respiratory chain, catalysed by the alternative oxidase (AOX) and alternative NADH dehydrogenases (NDH), as well as uncoupling (UCP) protein. Each of these components either circumvents or short-circuits proton translocation pathways, and each is encoded by a small gene family in Arabidopsis. Whole genome microarray experiments were performed with suspension cell cultures to examine the effects of various 3 h treatments designed to induce abiotic stress. The expression of over 60 genes encoding components of the classical, phosphorylating respiratory chain and tricarboxylic acid cycle remained largely constant when cells were subjected to a broad range of abiotic stresses, but expression of the alternative components responded differentially to the various treatments. In detailed time-course quantitative PCR analysis, specific members of both AOX and NDH gene families displayed coordinated responses to treatments. In particular, the co-expression of AOX1a and NDB2 observed under a number of treatments suggested co-regulation that may be directed by common sequence elements arranged hierarchically in the upstream promoter regions of these genes. A series of treatment sets were identified, representing the response of specific AOX and NDH genes to mitochondrial inhibition, plastid inhibition and abiotic stresses. These treatment sets emphasise the multiplicity of pathways affecting alternative electron transport components in plants.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s11103-005-5514-7     

Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction

A fundamental challenge to contemporary genetics is to distinguish rare missense alleles that disrupt protein functions from the majority of alleles neutral on protein activities. High-throughput experimental tools to securely discriminate between disruptive and non-disruptive missense alleles are currently missing. Here we establish a scalable cell-based strategy to profile the biological effects and likely disease relevance of rare missense variants in vitro. We apply this strategy to systematically characterize missense alleles in the low-density lipoprotein receptor (LDLR) gene identified through exome sequencing of 3,235 individuals and exome-chip profiling of 39,186 individuals. Our strategy reliably identifies disruptive missense alleles, and disruptive-allele carriers have higher plasma LDL-cholesterol (LDL-C). Importantly, considering experimental data refined the risk of rare LDLR allele carriers from 4.5- to 25.3-fold for high LDL-C, and from 2.1- to 20-fold for early-onset myocardial infarction. Our study generates proof-of-concept that systematic functional variant profiling may empower rare variant-association studies by orders of magnitude.     

Ageostrophic Frontal Processes Controlling Phytoplankton Production in the Catalano-Balearic Sea (Western Mediterranean)

Buoyancy-induced unstable boundary currents and the accompanying retrograde density fronts are often the sites of pronounced mesoscale activity, ageostrophic frontal processes, and associated high biological production in marginal seas. Biophysical model simulations of the Catalano-Balearic Sea (Western Mediterranean) illustrated that the unstable and nonlinear southward frontal boundary current along the Spanish coast resulted in a strain-driven frontogenesis mechanism. High upwelling velocities of up to 80 m d^-1 injected nutrients into the photic layer and promoted enhanced production on the less dense, onshore side of the front characterized by negative relative vorticity. Additional down-front wind stress and heat flux (cooling) intensified boundary current instabilities and thus ageostrophic cross-frontal circulation and augmented production. Specifically, entrainment of nutrients by relatively strong buoyancy-induced vertical mixing gave rise to a more widespread phytoplankton biomass distribution within the onshore side of the front. Mesoscale cyclonic eddies contributed to production through an eddy pumping mechanism, but it was less effective and more limited regionally than the frontal processes. The model was configured for the Catalano-Balearic Sea, but the mechanisms and model findings apply to other marginal seas with similar unstable frontal boundary current systems.     

Three New Species of Phytotelm-Breeding Melanophryniscus from the Atlantic Rainforest of Southern Brazil (Anura: Bufonidae)

Three new species of Melanophryniscus are described from the Serra do Mar mountain range of the state of Santa Catarina, southern Brazil. All species are found at intermediate to high altitudes and share phytotelm-breeding as their reproductive strategy. The new species are distinguished from other phytotelm-breeding Melanophryniscus based on different combinations of the following traits: snout-vent length, presence of white and/or yellow spots on forearms, mouth, belly and cloaca, pattern and arrangement of warts, and presence and number of corneous spines. The discovery of these species in a rather restricted geographical area suggests that the diversity of phytotelm-breeding species of Melanophryniscus might be severely underestimated. The conservation status of these species is of particular concern, given that one of them is at risk of extinction not only due to its restricted habitat, but also because of anthropogenic disturbances.