Trimeric form of intracellular ATP synthase subunit β of Aggregatibacter actinomycetemcomitans binds human interleukin-1β

Bacterial biofilms resist host defenses and antibiotics partly because of their decreased metabolism. Some bacteria use proinflammatory cytokines, such as interleukin (IL)-1β, as cues to promote biofilm formation and to alter virulence. Although one potential bacterial IL-1β receptor has been identified, current knowledge of the bacterial IL-1β sensing mechanism is limited. In chronic biofilm infection, periodontitis, Aggregatibacter actinomycetemcomitans requires tight adherence (tad)-locus to form biofilms, and tissue destroying active lesions contain more IL-1β than inactive ones. The effect of IL-1β on the metabolic activity of A. actinomycetemcomitans biofilm was tested using alamarBlue™. The binding of IL-1β to A. actinomycetemcomitans cells was investigated using transmission electron microscopy and flow cytometry. To identify the proteins which interacted with IL-1β, different protein fractions from A. actinomycetemcomitans were run in native-PAGE and blotted using biotinylated IL-1β and avidin-HRP, and identified using mass spectroscopy. We show that although IL-1β slightly increases the biofilm formation of A. actinomycetemcomitans, it reduces the metabolic activity of the biofilm. A similar reduction was observed with all tad-locus mutants except the secretin mutant, although all tested mutant strains as well as wild type strains bound IL-1β. Our results suggest that IL-1β might be transported into the A. actinomycetemcomitans cells, and the trimeric form of intracellular ATP synthase subunit β interacted with IL-1β, possibly explaining the decreased metabolic activity. Because ATP synthase is highly conserved, it might universally enhance biofilm resistance to host defense by binding IL-1β during inflammation.     

Synthesis, vibrational spectra and X-ray structures of copper(I) thiourea complexes

Complex formation of thiourea with copper takes place as an intermediate step in the preparation of copper sulfide thin films by spray pyrolysis starting from aqueous solutions of copper(II) chloride and thiourea. The stoichiometry of the complex and that of the resulting thin film primarily depends on the molecular ratio of the starting materials. For comparison, the structures of all copper(I) thiourea complexes found in the Cambridge Structural Database are classified in this paper. In addition, syntheses, structural (single crystal XRD also at low temperature 193 K) and spectroscopic studies (FTIR and Raman) of six copper-thiourea complexes are now reported. The copper to thiourea stoichiometric ratio is 1:3 in four of these complexes, but their structures are basically different as dimerization or polymer formation takes place depending on whether the water of crystallisation is present or absent. The structure of bis(μ-thiourea)tetrakis(thiourea)dicopper(I) dichloride dihydrate, [Cu₂(tu)₆]Cl₂ · 2H₂O (1) was determined at room and also at low temperature. Bis(μ-thiourea)tetrakis(thiourea)dicopper(I) dibromide dihydrate, [Cu₂(tu)₆]Br₂ · 2H₂O (2) is isomorphous with 1, like the anhydrous compounds chlorotris(thiourea)copper(I), [Cu(tu)₃]Cl (3) and bromotris(thiourea)copper(I), [Cu(tu)₃]Br (4) are isomorphous. In the third isomorphous pair of complexes the copper to thiourea stoichiometric ratio is 1:1, viz. chloro(thiourea)copper(I) hemihydrate, [Cu(tu)]Cl · 0.5H₂O (5) and bromo(thiourea)copper(I) hemihydrate, [Cu(tu)]Br · 0.5H₂O (6). During the preparation of chloro(thiourea)copper(I) hemihydrate (5) a reaction by product α,α^′-dithiobisformamidinium dichloride, [SC(NH₂)₂]₂Cl₂ (7) was identified and structurally characterized which made it possible to suggest a reaction path leading to complex formation.     

Characterization of heterotrimeric nucleotide-depleted Gα(i)-proteins by Bodipy-FL-GTPγS fluorescence anisotropy

Recombinant heterotrimeric G-protein α_i1, α_i2 and α_i3 subunits were purified in GDP-depleting conditions by affinity chromatography using StrepII-tagged β₁γ₂ subunits. Real-time monitoring of fluorescence anisotropy of Bodipy-FL-GTPγS was used for characterization of nucleotide binding properties and inactivation of the purified proteins. All GDP-depleted α_i were unstable at room temperature and therefore nucleotide binding could be characterized only in a nonequilibrium state. In comparison to Mg²⁺, Mn²⁺ inhibited nucleotide binding to all α_i-heterotrimers studied and accelerated nucleotide release. Mn²⁺ had stabilizing effect on the nucleotide free state of the α_i1 subunit, whereas both Mn²⁺ as well as G-protein activation by mastoparan destabilized the α_i2 subunit.     

Life history trade-offs and relaxed selection can decrease bacterial virulence in environmental reservoirs

Pathogen virulence is usually thought to evolve in reciprocal selection with the host. While this might be true for obligate pathogens, the life histories of opportunistic pathogens typically alternate between within-host and outside-host environments during the infection-transmission cycle. As a result, opportunistic pathogens are likely to experience conflicting selection pressures across different environments, and this could affect their virulence through life-history trait correlations. We studied these correlations experimentally by exposing an opportunistic bacterial pathogen Serratia marcescens to its natural protist predator Tetrahymena thermophila for 13 weeks, after which we measured changes in bacterial traits related to both anti-predator defence and virulence. We found that anti-predator adaptation (producing predator-resistant biofilm) caused a correlative attenuation in virulence. Even though the direct mechanism was not found, reduction in virulence was most clearly connected to a predator-driven loss of a red bacterial pigment, prodigiosin. Moreover, life-history trait evolution was more divergent among replicate populations in the absence of predation, leading also to lowered virulence in some of the 'predator absent' selection lines. Together these findings suggest that the virulence of non-obligatory, opportunistic bacterial pathogens can decrease in environmental reservoirs through life history trade-offs, or random accumulation of mutations that impair virulence traits under relaxed selection.     

Biomine: predicting links between biological entities using network models of heterogeneous databases

ABSTRACT: BACKGROUND: Biological databases contain large amounts of data concerning the functions and associationsof genes and proteins. Integration of data from several such databases into a single repositorycan aid the discovery of previously unknown connections spanning multiple types ofrelationships and databases. RESULTS: Biomine is a system that integrates cross-references from several biological databases into agraph model with multiple types of edges, such as protein interactions, gene-diseaseassociations and gene ontology annotations. Edges are weighted based on their type,reliability, and informativeness. We present Biomine and evaluate its performance in linkprediction, where the goal is to predict pairs of nodes that will be connected in the future,based on current data. In particular, we formulate protein interaction prediction and diseasegene prioritization tasks as instances of link prediction. The predictions are based on aproximity measure computed on the integrated graph. We consider and experiment withseveral such measures, and perform a parameter optimization procedure where different edgetypes are weighted to optimize link prediction accuracy. We also propose a novel method fordisease-gene prioritization, defined as finding a subset of candidate genes that cluster togetherin the graph. We experimentally evaluate Biomine by predicting future annotations in thesource databases and prioritizing lists of putative disease genes. CONCLUSIONS: The experimental results show that Biomine has strong potential for predicting links when aset of selected candidate links is available. The predictions obtained using the entire Biominedataset are shown to clearly outperform ones obtained using any single source of data alone,when different types of links are suitably weighted. In the gene prioritization task, anestablished reference set of disease-associated genes is useful, but the results show that underfavorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and8.1 million relations between them, with focus on human genetics. Some of its functionalitiesare available in a public query interface at http://biomine.cs.helsinki.fi, allowing searching forand visualizing connections between given biological entities.     

MOLTING PHENOLOGY OF HARBOR SEALS ON TUGIDAK ISLAND, ALASKA

We documented the progression and timing of the annual molt of harbor seals on Tugidak Island, Alaska, from 1997 to 1999. In all years the timing of molting differed among age-sex classes. Yearlings molted first, subadults second, adult females third, and lastly adult males. Timing of molting was nearly identical in 1997–1998, whereas in 1999 molting occurred three to six days later for all age-sex classes except yearlings. Estimated dates when peak proportions of each age-sex class were molting ranged from 2 August (yearlings) to 2 September (adult males). The number of seals hauled out was positively related to the proportion of seals in the molt and negatively related to the proportion of seals in the postmolt. Population trend estimates, based on aerial counts conducted during a narrow window within the molting period, are likely biased toward certain age-sex classes. Statistical models used to estimate trend include covariates to help account for within-year variation in seal numbers, but do not account for compositional changes that occur during molting. Population modeling may elucidate the effects of within-year population structure on trend estimates. Monitoring molting phenology at additional sites is necessary to determine the extent of geographic variation in molting.     

Role of litter decomposition for the increased primary production in areas heavily grazed by reindeer: a litterbag experiment

Heavy grazing and trampling by reindeer increase nutrient cycling and primary production in areas where grasslands have replaced shrub and moss tundra. One way in which herbivores can affect nutrient cycling is through changing the litter decomposition processes. We studied the effect of herbivory on litter decomposition rate by reciprocal transplantation of litter between lightly grazed and heavily grazed areas, using the litterbag technique. We used litter from two of the most common species on the lightly grazed side, Betula nana and Empetrum nigrum , and two of the most common species on the heavily grazed side, Carex bigelowii and Deschampsia flexuosa . We found that herbivory improved litter quality by favouring species with easily decomposed litter. However, herbivory also improved litter quality by increasing the nitrogen content and lowering the C/N ratio of each species. Decomposition rates even correlated with the abundance of the plant category in question. Shrub litter decomposed faster in the lightly grazed area where shrubs were common, and graminoid litter decomposed faster in the heavily grazed area where graminoids were common. These results indicate that the decomposer micro-organisms are adapted to the most common litter types. This study shows that detailed information about the effect of herbivory on litter quality is important to understand differences between the short-term and long-term effects of herbivory on nutrient cycling and primary production.     

Effect of space allowance and earthen flooring on behaviour of farmed blue foxes

This study sought to evaluate the effect of cage space and earthen flooring on the behaviour of individually caged, farmed blue foxes (Alopex lagopus). Three different cage sizes [80 cm long (CL80), 120 cm long (CL120), 240 cm long (CL240); each 105 cm wide×70 cm high] with wire-mesh flooring, and one two-level cage (CL240E) with both wire-mesh (240 cm long×105 cm wide×70 cm high) and earthen flooring (80 cm long×105 cm wide×70 cm high) were employed. Quantitative ethograms were obtained from ten males in each group by videotaping the animals for 144 h monthly from August through November. Altogether 30 different behaviours were described. These were rather similar in all study groups. Examples of behavioural differences included pacing around with a neighbour and the incidence of scratching, which both declined with increasing cage space. Only the foxes in the cage with an earthen flooring (CL240E) exhibited digging behaviour, which averaged 11 min/24 h. The wire-mesh section was distinctly preferred to the earthen-floor section for most behaviours. Foxes in all groups were at their most active from 0800 to 1600 hours. Total activity, including several separate behaviours, declined as winter approached. Locomotor and oral stereotypies were infrequent, and no significant differences were found between the various cage options. For several hours before feeding, the foxes showed increasing levels of stereotypies, but afterwards, stereotypies abruptly declined. Received in revised form: 28 March 2001 Electronic Publication     

The formation of species pools: historical habitat abundance affects current local diversity

Aim Explanations of biogeographic diversity patterns have emphasized the role of large‐scale processes that determine species pools, whereas explanations of local patterns have not. We address the hypothesis that local diversity patterns are also primarily dependent on the size of the available species pools, which are expected to be large when the particular habitat type has been evolutionary more abundant, or in unproductive habitats due to shorter generation time and hence higher diversification rates. Location The Canary Islands. Methods We determined the geographic distribution and habitat requirements of all native vascular plant species in the Canary Islands. Species pools for each habitat type on particular islands were further split into two categories according to origin: either originating due to local diversification or due to natural immigration. The dependence of historical diversification and diversification rate on habitat type, area, age, altitude and distance to the mainland was tested with general linear mixed models weighed according to the Akaike information criterion. Results The largest portion of the local variation in plant species diversity was attributed to the historic (pre‐human) habitat area, although island age was also important. The diversification rate was higher in unproductive habitats of coastal scrub and summit vegetation. Main conclusion Our study supports the species pool hypothesis, demonstrating that natural local patterns of species diversity in different habitats mirror the abundance of those particular habitats in evolutionary history. It also supports the community‐level birth rate hypothesis, claiming that stressful conditions result in higher diversification rates. We conclude that much of the observed local variation in plant diversity can be attributed to the differing sizes of species pools evolved under particular habitat conditions, and that historic parameters are far more important determinants of local diversity than suggested by ecological theory.     

Intermediate filament proteins and epithelial differentiation in the embryonic ovary of the rat

Abstract. The development and sexual differentiation of gonads in female rat embryos and fetuses between the ages of 11 and 17 days was studied by immunocytochemical analysis of intermediate filament proteins and laminin by light and electron microscopy. In the 11-day-old pregonadal embryo, the surface epithelial cells in the ventral cortex of the mesonephros contained desmin but not cytokeratin or vimentin. The development of the gonad began on the following day by proliferative growth of the mesonephric surface cells, which like the subepithelial cells soon expressed vimentin in addition to desmin. The differentiation continued by formation of separate epithelial cell clusters, which joined into cords, irregular in shape and size. Desmin disappeared from the cord cells and cytokeratins appeared while vimentin remained in all somatic cell types. Desmin was especially abundant in some stromal cells adjacent to the epithelial tissues. After the segration of the basic ovarian tissues, vimentin and desmin decreased and cytokeratins appeared in the surface epithelial cells. New changes in cytokeratin expression appeared with the differentiation of the embryonic cords in a sex-specific manner with gradual decrease of reactivity for cytokeratin 18. No immunoreaction to the neurofilament proteins was found at the present ages, and the germ cells were negative for intermediate filaments. The results show that desmin is expressed in several primitive ovarian and mesonephric cells even though they are not myogenic. The sexual differences emerge after the incipient formation of the genetically female gonad, as different organization of the internal epithelial tissue with different timing of changes in intermediate filament proteins when compared with the male gonad.