Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Putative odour receptors localize in cilia of olfactory receptor cells in rat and mouse: a freeze-substitution ultrastructural study

Two different polyclonal antibodies were raised to synthetic peptides corresponding to distinct putative odour receptors of rat and mouse. Both antibodies selectively labelled olfactory cilia as seen with cryofixation and immunogold ultrastructural procedures. Regions of the olfactory organ where label was detected were consistent with those found at LM levels. Immunopositive cells were rare; only up to about 0.4% of these receptor cells were labelled. Despite chemical, species, and topographic differences both antibodies behaved identically in their ultrastructural labelling patterns. For both antibodies, labelling was very specific for olfactory cilia; both bound amply to the thick proximal and the thinner and long distal parts of the cilia. Dendritic knobs showed little labelling if any. Dendritic receptor cell structures below the knobs, supporting cell structures, and respiratory cilia did not immunolabel. There were no obvious differences in morphology between labelled and unlabelled receptor cells and their cilia. Labelling could be followed up to a distance of about 15 μm from the knobs along the distal parts of the cilia. When labelled cells were observed, this signal was detectable in two, sometimes three, sections taken through these cells while being consistently absent in neighbouring cells. This pattern argues strongly for the specificity of the labelling. In conclusion, very few receptor cells labelled with the antibodies to putative odour receptors. Additionally the olfactory cilia, the cellular regions that first encounter odour molecules and that are thought to transduce the odorous signal, displayed the most intense labelling with both antibodies. Consequently, the results showed these cilia as having many copies of the putative receptors. Finally, similar patterns of subcellular labelling were displayed in two different species, despite the use of different antibodies. Thus, this study provides compelling evidence that the heptahelical putative odour receptors localize in the olfactory cilia.     

A histochemical and electrophysiological study of the action of diazoxon on cholinesterase activity and nerve conduction in ganglia of the cockroach Periplaneta americana L

When sixth abdominal or metathoracic ganglia of the cockroach Periplaneta americana L. were irrigated continuously with diazoxon (O, O-diethyl O-(2-isopropyl-6-methyl-4-pyrimidinyl) phosphate) solution in situ, the log. of the time required to block conduction in certain nerve pathways in the ganglia was directly proportional to the log. of the concentration of diazoxon applied. Inhibition of cholinesterase began peripherally before function was affected, and had begun to affect the neuropile by the time that conduction was first blocked. Longer exposure to diazoxon disrupted nerve function even more, especially in the sixth abdominal ganglion, and inhibited more cholinesterase, but much longer exposure was needed to inhibit nearly all the cholinesterase. Irrigation with saline, begun when block first occurred, failed to restore completely either nerve function or cholinesterase activity. The cholinesterase activity of ganglia from cockroaches treated topically with an LD90 of diazoxon and examined at intervals after treatment decreased steadily to a level similar to that of ganglia treated directly with diazoxon until conduction was just blocked, but rarely became less, even in moribund insects. Nerve function in metathoracic ganglia became badly affected and remained so in all cockroaches that failed to recover, but sixth abdominal ganglia, though usually badly affected for a time, always recovered normal function, even in prostrate cockroaches. The condition of a poisoned insect, therefore, corresponded much more closely to the functional condition of the metathoracic ganglion than to that of the sixth abdominal ganglion. Applying the insecticide close to a ganglion advanced the time of onset of symptoms but affected the final outcome very little. It was calculated that the highest concentration of diazoxon in the haemo-lymph in contact with the nervous systems of cockroaches treated topically with LDgo's of diazoxon was about 10^-5M.     

Response of fauna in seagrass to habitat edges,patch attributes and hydrodynamics

This study has investigated the taxon‐specific responses of fauna to patch edges, and how these relate to patch attributes (patch size, seagrass biomass and water depth), and hydrodynamics in the seagrass habitat. Faunal abundances were sampled at the edge, 2 m in from the edge, and in the middle of 10 seagrass patches of variable size in Port Phillip Bay, Australia. Five of nine taxa showed edge effects. There were higher abundances at the edge compared with the middle for porcellid harpacticoids, and an increase in abundance from the edge to the middle of the patches for tanaids and isopods. For caprellid and gammarid amphipods, the edge effect varied across patches. Changes in current within the patch and patch size were related to the variability in the edge effect pattern of caprellids. None of the measured environmental variables (seagrass biomass, current and water depth) or patch size had a role in the variable edge effect pattern of gammarid amphipods. At the patch level, the distribution of six of nine taxa in this study, namely isopods, polychaetes, ‘other harpacticoids’, porcellid harpacticoids, cumaceans and gammarid amphipods, was related to differences in average water depth, average seagrass biomass and patch size. Our study indicates that the faunal response to edges cannot be generalized across seagrass habitat, and the implications of habitat area loss will vary depending on the taxon under consideration.     

Assessment of soil calcium status in red spruce forests in the northeastern United States

Long-term changes in concentrations of available Ca in soils of redspruce forests have been documented, but remaining questions aboutthe magnitude and regional extent of these changes have precluded anassessment of the current and future status of soil Ca. To addressthis problem, soil samples were collected in 1992—93from 12 sites in New York, Vermont, New Hampshire, and Maine toprovide additional data necessary to synthesize all availableresearch results on soil Ca in red spruce forests. Sites werechosen to encompass the range of environmental conditionsexperienced by red spruce. Concentrations of exchangeableCa ranged from 2.13 to 21.6 cmol_ckg^–1 in the Oa horizon, and from 0.11 to 0.68cmol_c kg^–1 in the upper 10 cm of theB horizon. These measurements expanded the range of exchangeable Ca reported in the literature for both horizons in northeastern redspruce forests. Exchangeable Ca was the largest Ca fraction in theforest floor at most sites (92% ofacid-extractableCa), but mineral Ca was the largest fraction at the three sites that also had the highest mineral-matter concentrations. Theprimary factor causing variability in Ca concentrations among siteswas the mineralogy of parent material, but exchangeable concentrationsin the B horizon of all sites were probably reduced by acidicdeposition. Because the majority of Ca in the forest floor isin a readily leachable form, and Ca inputs to the forest floor from the mineral soil and atmospheric deposition have beendecreasing in recent decades, the previously documented decreasesin Ca concentrations in the forest floor over previous decades mayextend into the future.     

Les génotypes responsables de mucoviscidose ou d’absence bilatérale des canaux déférents ABCD

Over the last decade, the genetic basis for CBAVD has been identified by its association with CFTR gene mutations, and CBAVD is now generally considered to be a mild or incomplete form of CF. In this review, the author summarizes the main results of compilation of CFTR gene analysis conducted in French laboratories for 3,923 patients with CF and 800 males with CABVD. The degree of clinical expression can be affected by several variables, including the molecular mechanisms by which the various CFTR mutations impair or disrupt the function of the CFTR chloride channel. Phenotypic expression of CFTR mutational genotypes varies from severe, progressive pulmonary disease with pancreatic insufficiency (CF-PI), to mild pulmonary disease with pancreatic sufficiency (PS) or singleorgan forms of “CFTR-opathies”. In CF, a total of 310 different CFTR mutations accounting for 94% of 7,846 CF alleles have generated almost 500 different genotypes, comprising 2 severe mutations in 88% of cases (CF-PI), one severe mutation in trans to a mild mutation in 11% (CF-PS), and 2 mild mutations in 1% of identified genotypes. In CBAVD, 137 mutations scattered over the whole gene were identified in 60% of 1,600 CBAVD alleles during the study. Among the 150 characterized mutational CFTR genotypes, compound heterozygosity was the rule, and the most frequent CBAVD combinations were ΔF508/5T (35%), ΔF508/other mutation (30%, including ΔF508/R117H-7T: 5,6%), and 5T/other mutation (17%). No combination of two severe mutations was found in CBAVD (0%); by contrast with the CF population, 88% of genotypes identified in CBAVD comprised a severe mutation in trans to a mild mutation, and 12% consisted of 2 mild mutations. A total of 22 genotypes were shared by both CF and CBAVD. The role of the 5T allele as a splicing variant with variable, incomplete disease penetrance in CBAVD is reviewed. Other haplotype backgrounds, such as the TG12 sequence and the M470V polymorphism, may influence CFTR splicing and/or function. This study confirms the high molecular heterogeneity of CFTR mutations in CBAVD and emphasizes the importance of extensive CFTR analysis in these patients. Longterm follow-up studies of CBAVD patients are necessary in order to predict the phenotypic consequences of numerous CFTR mutational genotypes.     

Population trends of European common birds are predicted by characteristics of their climatic niche

Temperate species are projected to experience the greatest temperature increases across a range of modelled climate change scenarios, and climate warming has been linked to geographical range and population changes of individual species at such latitudes. However, beyond the multiple modelling approaches, we lack empirical evidence of contemporary climate change impacts on populations in broad taxonomic groups and at continental scales. Identifying reliable predictors of species resilience or susceptibility to climate warming is of critical importance in assessing potential risks to species, ecosystems and ecosystem services. Here we analysed long‐term trends of 110 common breeding birds across Europe (20 countries), to identify climate niche characteristics, adjusted to other environmental and life history traits, that predict large‐scale population changes accounting for phylogenetic relatedness among species. Beyond the now well‐documented decline of farmland specialists, we found that species with the lowest thermal maxima (as the mean spring and summer temperature of the hottest part of the breeding distribution in Europe) showed the sharpest declines between 1980 and 2005. Thermal maximum predicted the recent trends independently of other potential predictors. This study emphasizes the need to account for both land‐use and climate changes to assess the fate of species. Moreover, we highlight that thermal maximum appears as a reliable and simple predictor of the long‐term trends of such endothermic species facing climate change.