Partitioning the variation in a plot‐by‐species data matrix that is related to n sets of explanatory variables

Abstract. Variation partitioning by (partial) constrained ordination is a popular method for exploratory data analysis, but applications are mostly restricted to simple ecological questions only involving two or three sets of explanatory variables, such as climate and soil, this because of the rapid increase in complexity of calculations and results with an increasing number of explanatory variable sets. The existence is demonstrated of a unique algorithm for partitioning the variation in a set of response variables on n sets of explanatory variables; it is shown how the 2n– 1 non‐overlapping components of variation can be calculated. Methods for evaluation and presentation of variation partitioning results are reviewed, and a recursive algorithm is proposed for distributing the many small components of variation over simpler components. Several issues related to the use and usefulness of variation partitioning with n sets of explanatory variables are discussed with reference to a worked example.     

Disentangling complex fine‐scale ecological patterns by path modelling using GLMM and GIS

Question: How can statistical modelling tools (GLMM) and GIS be used as an aid in understanding complex ecological patterns? This general question was approached by using bryophyte demography data as an example. More specifically, we asked what is the contribution of terrain shape to explaining the performance and fate of plant individuals, controlling for all other known relationships? Location: Norway. Methods: Information on demography was obtained for 140 populations of the perennial clonal bryophyte Hylocomium splendens in Norway spruce forests during an 11‐year period (1992‐2002). Performance (size and branching pattern) was recorded for mature segments and fate was recorded for growing points. Positions of each of the more than 30 000 recorded bryophyte ramets were coupled with (micro‐) topographic characteristics (slope and convexity) derived from fine‐scale digital elevation models in a GIS framework. Carefully planned sequences of generalised linear mixed models (GLMM) were performed to test predictions from a conceptual path model. Results: We demonstrate strong dependence of size on branching, fate and on vertical position in the bryophyte carpet, and an effect of vertical position on branching pattern. Micro‐topography contributed to explaining plant performance by four different mechanisms: (1) a direct effect of slope on the segment's vertical position in the carpet; (2‐3) direct effects of both slope and convexity on fates of individuals via controls on risk of burial; and (4) an indirect effect of convexity on branching pattern via a direct effect on size. No indication of a direct effect of terrain on branching was found. Conclusions: Our study exemplifies the usefulness of GLMM for disentangling complex ecological relationships. Specifically, we recognise micro‐topography as a potentially important factor for plant demography in general and for performance and fate of individuals in particular.     

Epizoochorous seed dispersal in relation to seed availability – an experiment with a red fox dummy

Questions: Is the red fox a potential vector for epizoochorous seed dispersal? Can seed attachment and retention be predicted from plant and seed traits? Location: Grasslands in southern Norway. Methods: Epizoochorous seed attachment on the red fox was studied by walking a dummy fox through the vegetation and comparing seeds found on the dummy with the estimated seed availability in the vegetation. Seed retention, i.e. the ability of different seeds to stay on the fox, was estimated in a separate experiment. Seed attachment and retention were related to plant and seed traits using statistical models that account for heteroscedasticity and zero‐inflated data. Results: The majority of seeds attached to the fox originated from a few species, but also species without specific seed traits that are supposed to enhance epizoochory attached at least some seeds to the fox. The probability of seed attachment was positively related to plant height, bristle and hooked seed appendages, and negatively related to winged appendages, seed mass, and seed sphericity. Seed retention was positively related to the seed traits bristles, hooks and pappus. For several species, the results indicate a high potential for dispersal over long distances. Conclusions: In modern agricultural landscapes, large herbivores are often restricted in their mobility or are found at low densities, and other animal vectors may therefore be important for seed dispersal. In our study, a range of plant species were able to disperse by attaching seeds to, and having their seeds retained in, the fox fur some distance. We suggest that the red fox may be an important vector for epizoochorous seed dispersal in the agricultural landscape.     

Anti-dsDNA Antibodies Promote Initiation,and Acquired Loss of Renal Dnase1 Promotes Progression of Lupus Nephritis in Autoimmune (NZBxNZW)F1 Mice

Background

Lupus nephritis is characterized by deposition of chromatin fragment-IgG complexes in the mesangial matrix and glomerular basement membranes (GBM). The latter defines end-stage disease.

Methodology/Principals

In the present study we determined the impact of antibodies to dsDNA, renal Dnase1 and matrix metalloprotease (MMP) mRNA levels and enzyme activities on early and late events in murine lupus nephritis. The major focus was to analyse if these factors were interrelated, and if changes in their expression explain basic processes accounting for lupus nephritis.

Findings

Early phases of nephritis were associated with chromatin-IgG complex deposition in the mesangial matrix. A striking observation was that this event correlated with appearance of anti-dsDNA antibodies and mild or clinically silent nephritis. These events preceded down-regulation of renal Dnase1. Later, renal Dnase1 mRNA level and enzyme activity were reduced, while MMP2 mRNA level and enzyme activity increased. Reduced levels of renal Dnase1 were associated in time with deficient fragmentation of chromatin from dead cells. Large fragments were retained and accumulated in GBM. Also, since chromatin fragments are prone to stimulate Toll-like receptors in e.g. dendritic cells, this may in fact explain increased expression of MMPs.

Significance

These scenarios may explain the basis for deposition of chromatin-IgG complexes in glomeruli in early and late stages of nephritis, loss of glomerular integrity and finally renal failure.     

The CW domain, a new histone recognition module in chromatin proteins

Post-translational modifications of the N-terminal histone tails, including lysine methylation, have key roles in regulation of chromatin and gene expression. A number of protein modules have been identified that recognize differentially modified histone tails and provide their proteins with the capacity to sense such modifications. Here, we identify the CW domain of plant and animal chromatin-related proteins as a novel module that recognizes different methylated states of lysine 4 on histone H3 (H3K4me). The solution structure of the CW domain of the Arabidopsis ASH1 HOMOLOG2 (ASHH2) histone methyltransferase provides insight into how different CW domains can distinguish different methylated histone tails. We provide evidence that ASHH2 is acting on H3K4me-marked genes, allowing for ASHH2-dependent H3K36 tri-methylation, which contributes to sustained expression of tissue-specific and developmentally regulated genes. This suggests that ASHH2 is a combined 'reader' and 'writer' of the histone code. We propose that different CW domains, dependent on their specificity for different H3K4 methylations, are important for epigenetic memory or participate in switching between permissive and repressive chromatin states.     

Matrix Metalloproteinase 7 Is Associated with Symptomatic Lesions and Adverse Events in Patients with Carotid Atherosclerosis

Background

Atherosclerosis is a major cause of cerebrovascular disease. Matrix metalloproteinases (MMPs) play an important role in matrix degradation within the atherosclerotic lesion leading to plaque destabilization and ischemic stroke. We hypothesized that MMP-7 could be involved in this process.

Methods

Plasma levels of MMP-7 were measured in 182 consecutive patients with moderate (50–69%) or severe (≥70%) internal carotid artery stenosis, and in 23 healthy controls. The mRNA levels of MMP-7 were measured in atherosclerotic carotid plaques with different symptomatology, and based on its localization to macrophages, the in vitro regulation of MMP-7 in primary monocytes was examined.

Results

Our major findings were (i) Patients with carotid atherosclerosis had markedly increased plasma levels of MMP-7 compared to healthy controls, with particularly high levels in patients with recent symptoms (i.e., within the last 2 months). (ii) A similar pattern was found within carotid plaques with markedly higher mRNA levels of MMP-7 than in non-atherosclerotic vessels. Particularly high protein levels of MMP-7 levels were found in those with the most recent symptoms. (iii) Immunhistochemistry showed that MMP-7 was localized to macrophages, and in vitro studies in primary monocytes showed that the inflammatory cytokine tumor necrosis factor-α in combination with hypoxia and oxidized LDL markedly increased MMP-7 expression. (iv) During the follow-up of patients with carotid atherosclerosis, high plasma levels of MMP-7 were independently associated with total mortality.

Conclusion

Our findings suggest that MMP-7 could contribute to plaque instability in carotid atherosclerosis, potentially involving macrophage-related mechanisms.     

Understorey vegetation development in North Finnish Picea forests after disturbance: re‐analysis of Sirén's data

Abstract. Sirén (1955) studied understorey species composition, tree stand properties and humus‐layer thickness in 64 unlogged forest stands on topographically and pedologically comparable sites. The stands were of even age (6 – 300 yr), stocked with the first or second tree generation after wildfire. The view of Sirén and several authors after him, that the vegetation of old‐growth boreal Picea forests is homogeneous on a broad scale, was examined by applying, in parallel, the partial variants of two ordination methods (DCA and PCA) to Sirén's vegetation data. Two main vegetation gradients were found: a major gradient running from recently burnt plots with prominence of pioneer species to plots with stand age > 100 yr, a well stocked tree layer and a thick humus layer, dominance of feather‐mosses and ample occurrence of shade‐tolerant as well as light‐preferring vascular plant species, and a second gradient along which first‐ and second‐generation plots segregate. The more prominent element of Betula trees in first‐ than in second‐generation stands < 100 yr contributed to the latter. A minor third gradient related to humus‐layer thickness was recovered by partial DCA only. The main vegetation gradient reappeared in separate ordinations of data from 47 mature forest stands (> 100 yr), but without being correlated with forest age. Variation among mature‐forest stands in the importance of pioneer species is considered mainly to be brought about by fine‐scale disturbance processes such as tree uprooting. Increasing importance of factors operating on within‐stand scales [development of a varied gap structure and stronger gradients in tree influence (radiation at ground level), soil moisture, soil depth and nutrient availability] with time is also reflected in the second and third mature‐forest ordination axes. Possible implications of the results for conservation of biological diversity and monitoring of changes in boreal forests are discussed.