RhoA signaling modulates cyclin D1 expression in human lung fibroblasts; implications for idiopathic pulmonary fibrosis

Background

To elucidate further the pathogenesis of sporadic, idiopathic pulmonary arterial hypertension (IPAH) and identify potential therapeutic avenues, differential gene expression in IPAH was examined by suppression subtractive hybridisation (SSH).

Methods

Peripheral lung samples were obtained immediately after removal from patients undergoing lung transplant for IPAH without familial disease, and control tissues consisted of similarly sampled pieces of donor lungs not utilised during transplantation. Pools of lung mRNA from IPAH cases containing plexiform lesions and normal donor lungs were used to generate the tester and driver cDNA libraries, respectively. A subtracted IPAH cDNA library was made by SSH. Clones isolated from this subtracted library were examined for up regulated expression in IPAH using dot blot arrays of positive colony PCR products using both pooled cDNA libraries as probes. Clones verified as being upregulated were sequenced. For two genes the increase in expression was verified by northern blotting and data analysed using Student's unpaired two-tailed t-test.

Results

We present preliminary findings concerning candidate genes upregulated in IPAH. Twenty-seven upregulated genes were identified out of 192 clones examined. Upregulation in individual cases of IPAH was shown by northern blot for tissue inhibitor of metalloproteinase-3 and decorin (P < 0.01) compared with the housekeeping gene glyceraldehydes-3-phosphate dehydrogenase.

Conclusion

Four of the up regulated genes, magic roundabout, hevin, thrombomodulin and sucrose non-fermenting protein-related kinase-1 are expressed specifically by endothelial cells and one, muscleblind-1, by muscle cells, suggesting that they may be associated with plexiform lesions and hypertrophic arterial wall remodelling, respectively.     

Selection on Arctic charr generated by competition from brown trout

We experimentally explored population‐ and individual‐level effects on Arctic charr (Salvelinus alpinus) resulting from resource competition with its common European competitor, the brown trout (Salmo trutta). At the population level, we compared performance of the two species in their natural sympatric state with that of Arctic charr in allopatry. At the individual level, we established selection gradients for morphological traits of Arctic charr in allopatric and in sympatric conditions. We found evidence for interspecific competition likely by interference at the population level when comparing differences in average performance between treatments. The growth and feeding rates did not differ significantly between allopatric and sympatric Arctic charr despite lower charr densities (substitutive design) in sympatric enclosures indicating that inter‐ and intraspecific competition are of similar strength. The two species showed distinct niche segregation in sympatry, and brown trout grew faster than Arctic charr. Arctic charr did not expand their niche in allopatry, indicating that the two species compete to a limited degree for the same resources and that interference may suppress the growth of charr in sympatric enclosures. At the individual level, however, we found directional selection in sympatric enclosures against individual Arctic charr with large head and long fins and against individuals feeding on zoobenthos rather than zooplankton indicating competition for common resources (possibly exploitative) between trout and these charr individuals. In allopatric enclosures these relations were not significant. Diets were correlated to the morphology supporting selection against the benthic‐feeding type, i.e. individuals with morphology and feeding behaviour most similar to their competitor, the benthic feeding brown trout. Thus, this study lends support to the hypothesis that Arctic charr have evolved in competition with brown trout, and through ecological character displacement adapted to their present niche.     

Life history characteristics of brown trout in lakes at different stages of acidification

In 66 Norwegian lakes with allopatric populations of brown trout Salmo trutta that ranged from highly acidified to non-acid (pH 4·7–6·6) there was a significant inverse correlation between mean age and relative abundance (CPUE). As mean annual survival rates were not significantly related to CPUE, this population response may indicate that recruitment was lower in low-density lakes. Age-specific masses were significantly higher in populations that had declined in abundance than in unaffected populations. Mean body mass at sexual maturity in both males and females was inversely correlated with CPUE. Between populations, high age at maturity was associated with high survival rates in both sexes. Age at maturity correlated positively with specific growth rate between the ages of 1 and 2 years in females only.     

The Importance of Detritivore Species Diversity for Maintaining Stream Ecosystem Functioning Following the Invasion of a Riparian Plant

The strength of linkages between riparian plants and stream communities can be expected to be influenced by invading plants. While most studies so far have been focussed on the effects of the leaf litter quality of the invader, this study addresses the impact of detritivores on the pool of detritus. In a natural setting, we found that species richness of shredding macroinvertebrates significantly influenced the breakdown rate of an invasive weed species, the Japanese knotweed (Fallopia japonica), which has become a major plant invader along streams and rivers in Europe and North America. Our findings imply that a reduction of the diversity of shredder species, which may be the result of disturbances, could negatively influence stream ecosystems' capacity of processing knotweed leaves. Although the knotweed showed breakdown rates similar to those of common native tree and shrub species, other exotic leaf species might show considerably slower rates and hence have greater consequences for the ecosystems. We have, in this study, indicated a technique by which the effects of other non-indigenous plants on ecosystem functioning might be considered.     

A new flow-through bioassay for testing low-emission antifouling coatings

Current antifouling (AF) technologies are based on the continuous release of biocides into the water, and consequently discharge into the environment. Major efforts to develop more environmentally friendly coatings require efficient testing in laboratory assays, followed by field studies. Barnacles are important fouling organisms worldwide, increasing hydrodynamic drag on ships and damaging coatings on underwater surfaces, and thus are extensively used as models in AF research, mostly in static, laboratory-based systems. Reliable flow-through test assays for the screening of biocide-containing AF paints, however, are rare. Herein, a flow-through bioassay was developed to screen for diverse low-release biocide paints, and to evaluate their effects on pre- and post-settlement traits in barnacles. The assay distinguishes between the effects from direct surface contact and bulk-water effects, which are crucial when developing low-emission AF coatings. This flow-through bioassay adds a new tool for rapid laboratory-based first-stage screening of candidate compounds and novel AF formulations.     

Composition of riparian litter input regulates organic matter decomposition: Implications for headwater stream functioning in a managed forest landscape

Although the importance of stream condition for leaf litter decomposition has been extensively studied, little is known about how processing rates change in response to altered riparian vegetation community composition. We investigated patterns of plant litter input and decomposition across 20 boreal headwater streams that varied in proportions of riparian deciduous and coniferous trees. We measured a suite of in‐stream physical and chemical characteristics, as well as the amount and type of litter inputs from riparian vegetation, and related these to decomposition rates of native (alder, birch, and spruce) and introduced (lodgepole pine) litter species incubated in coarse‐ and fine‐mesh bags. Total litter inputs ranged more than fivefold among sites and increased with the proportion of deciduous vegetation in the riparian zone. In line with differences in initial litter quality, mean decomposition rate was highest for alder, followed by birch, spruce, and lodgepole pine (12, 55, and 68% lower rates, respectively). Further, these rates were greater in coarse‐mesh bags that allow colonization by macroinvertebrates. Variance in decomposition rate among sites for different species was best explained by different sets of environmental conditions, but litter‐input composition (i.e., quality) was overall highly important. On average, native litter decomposed faster in sites with higher‐quality litter input and (with the exception of spruce) higher concentrations of dissolved nutrients and open canopies. By contrast, lodgepole pine decomposed more rapidly in sites receiving lower‐quality litter inputs. Birch litter decomposition rate in coarse‐mesh bags was best predicted by the same environmental variables as in fine‐mesh bags, with additional positive influences of macroinvertebrate species richness. Hence, to facilitate energy turnover in boreal headwaters, forest management with focus on conifer production should aim at increasing the presence of native deciduous trees along streams, as they promote conditions that favor higher decomposition rates of terrestrial plant litter.     

Structural mapping of an aggregation nucleation site in a molten globule intermediate.

Protein aggregation plays an important role in biotechnology and also causes numerous diseases. Human carbonic anhydrase II is a suitable model protein for studying the mechanism of aggregation. We found that a molten globule state of the enzyme formed aggregates. The intermolecular interactions involved in aggregate formation were localized in a direct way by measuring excimer formation between each of 20 site-specific pyrene-labeled cysteine mutants. The contact area of the aggregated protein was very specific, and all sites included in the intermolecular interactions were located in the large beta-sheet of the protein, within a limited region between the central beta-strands 4 and 7. This substructure is very hydrophobic, which underlines the importance of hydrophobic interactions between specific beta-sheet containing regions in aggregate formation.     

A null model for randomization tests of nestedness in species assemblages

Analysis of the degree of order in species assemblages in terms of nested subsets has received increased interest during the last decade. However, recently a series of papers have questioned the validity of methods employed for testing whether observed patterns deviate from random expectations. The current view seems to be that the randomization procedure should control for both number of species per site and species frequencies. The randomization procedures used also choose to keep the total number of observations constant in each resample. In this paper I question some of these assumptions when analyzing species-by-site matrices for detecting whether the biota is significantly nested or not. My basic assumption is that the observed species frequency is only an estimate of the probability of occurrence for the particular species. For a test of degree of nestedness all sites should be regarded as being equal. To what extent size, isolation or habitat quality may influence species distribution is a secondary question if nestedness can be statistically proven. This implies that generation of random matrices should only consider the frequency of the species (as an estimate of their probability of occurring in any patch). Such matrices are computationally simple and besides providing a test of nestedness also open the possibility of testing whether the range in species richness is smaller or larger than expected under random expectations. The choice of null model for the test should always be viewed in relation to the question asked. If nestedness is concerned the methods proposed here should be used. However, if other questions are at hand the restrictions of previous approaches may be valid. This is for instance the case if pairwise species co-occurrences are analyzed. In this case, the richness of each site should obviously be incorporated in the randomization to control for the higher probability of co-occurrence at species-rich sites.