Towards a biogeographic regionalization of the European biota

Aim To determine if it is possible to generate analytically derived regionalizations for multiple groups of European plants and animals and to explore potential influences on the regions for each taxonomic group. Location Europe. Methods We subjected range maps of trees, butterflies, reptiles, amphibians, birds and mammals to k‐means clustering followed by v‐fold cross‐validation to determine the pattern and number of regions (clusters). We then used the mean range sizes of species in each group as a correlate of the number of regions obtained for each taxon, and climate and species richness gradients as correlates of the spatial arrangement of the group‐specific regions. We also included the pattern of tree clusters as a predictor of animal clusters in order to test the ‘habitat templet’ concept as an explanation of animal distribution patterns. Results Spatially coherent clusters were found for all groups. The number of regions ranged from three to eight and was strongly associated with the mean range sizes of the species in each taxon. The cluster patterns of all groups were associated with various combinations of climate, underlying species richness gradients and, in the case of animals, the arrangement of tree clusters, although the rankings of the correlates differed among groups. In four of five groups the tree pattern was the strongest single predictor of the animal cluster patterns. Main conclusions Despite a long history of human disturbance and habitat modification, the European biota retains a discernable biogeographic structure. The primary driver appears to be aspects of climate related to water–energy balance, which also influence richness gradients. For many animals, the underlying habitat structure, as measured by tree distributions, appears to have a strong influence on their biogeographic structure, highlighting the need to preserve natural forest formations if we want to preserve the historical signal found in geographic distributions.     

Bacterial outer membrane protein analysis by electrophoresis and microchip technology

Outer membrane proteins are indispensable components of bacterial cells and participate in several relevant functions of the microorganisms. Changes in the outer membrane protein composition might alter antibiotic sensitivity and pathogenicity. Furthermore, the effects of various factors on outer membrane protein expression, such as antibiotic treatment, mutation, changes in the environment, lipopolysaccharide modification and biofilm formation, have been analyzed. Traditionally, the outer membrane protein profile determination was performed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Converting this technique to capillary electrophoresis format resulted in faster separation, lower sample consumption and automation. Coupling capillary electrophoresis with mass spectrometry enabled the fast identification of bacterial proteins, while immediate quantitative analysis permitted the determination of up- and downregulation of certain outer membrane proteins. Adapting capillary electrophoresis to microchip format ensured a further ten- to 100-fold decrease in separation time. Application of different separation techniques combined with various sensitive detector systems has ensured further opportunities in the field of high-throughput bacterial protein analysis. This review provides an overview using selected examples of outer membrane proteins and the development and application of the electrophoretic and microchip technologies for the analysis of these proteins.     

Zonobiomes, zonoecotones and azonal vegetation along the Pacific coast of North America

In this study of the Pacific coast of North America, from Baja California to Alaska, we evaluated the hypothesis that the floristic composition of azonal vegetation determines areas and distribution limits similar to those of the corresponding zonobiomes (ZB), and does so in response to the same macroclimatic changes occurring on the continental scale. To this end, 686 vascular plants of the different habitats found in 279 sites along this coastal strip were recorded. Using an objective classification system (Average Linkage Clustering) and factorial analysis, floristic data acquired in fieldwork were classified into groups, which were in turn related to regional macroclimates. Our main finding was that the azonal coastal vegetation follows a distribution model that is closely linked to the corresponding macroclimate. The four ZB of the northern Pacific coast show a flora and azonal vegetation characteristic to each zonobiome; the latitudinal limits of the azonal vegetation practically coinciding with those already established for the zonal vegetation. The Boreal and Temperate ZB show high percentages of broadly distributed elements. The floristically richest zonobiome in terms of endemic taxa is the Mediterranean zonobiome, whereas the flora of Baja California is characterized by a high number of taxa related to Neotropical flora, especially to those showing links with South America. Data on the geographical distribution and habitats of the 247 most significant coastal species are also provided.     

High levels of acute phase proteins and soluble 70 kDa heat shock proteins are independent and additive risk factors for mortality in colorectal cancer

Recently, we reported that high soluble Hsp70 (sHsp70) level was a significant predictor of mortality during an almost 3-year-long follow-up period in patients with colorectal cancer. This association was the strongest in the group of <70-year-old female patients as well as in those who were in a less advanced stage of the disease at baseline. According to these observations, measurement of the serum level of sHsp70 is a useful, stage-independent prognostic marker in colorectal cancer, especially in patients without distant metastasis. Since many literature data indicated that measurement of C-reactive protein (CRP) and other acute phase proteins (APPs) may also be suitable for predicting the mortality of patients with colorectal cancer, it seemed reasonable to study whether the effect of sHsp70 and other APPs are related or independent. In order to answer this question, we measured the concentrations of CRP as well as of other complement-related APPs (C1 inhibitor, C3, and C9) along with that of the MASP-2 complement component in the sera of 175 patients with colorectal cancer and known levels of sHsp70, which have been used in our previous study. High (above median) levels of CRP, C1 esterase inhibitor (C1-INH), and sHsp70 were found to be independently associated with poor patient survival, whereas no such association was observed with the other proteins tested. According to the adjusted Cox proportional hazards analysis, the additive effect of high sHsp70, CRP, and C1-INH levels on the survival of patients exceeded that of high sHsp70 alone, with a hazard ratio (HR) of 2.83 (1.13–70.9). In some subgroups of patients, such as in females [HR 4.80 (1.07–21.60)] or in ≤70-year-old patients [HR 11.53 (2.78–47.70)], even greater differences were obtained. These findings indicate that the clinical mortality–prediction value of combined measurements of sHsp70, CRP, and C1-INH with inexpensive methods can be very high, especially in specific subgroups of patients with colorectal cancer.     

Remodeling of the vascular tunica media is essential for development of collateral vessels in the canine heart

Previous studies have shown that neointima formation and adventitial remodeling play an important role in the enlargement of collateral vessels (CVs) during coronary arteriogenesis in the dog heart. In this study, we investigated the importance of remodeling of the tunica media in the same model. Basal membrane (BM), contractile and cytoskeletal components of smooth muscle cells (SMCs) were studied in growth of coronary CVs induced by chronic occlusion of the left circumflex (LCX) coronary artery by routine histology, electron microscopy (EM), and immunoconfocal microscopy using antibodies against α-smooth actin (α-SM actin), calponin, desmin, and laminin. In addition, matrix metalloproteinase-2 (MMP-2) and tissue inhibitor-1 of matrix metalloproteinase (TIMP-1) were investigated. The data showed that (1) in normal small arteries (NVs) laminin formed a network in which SMCs were encaged;α-SM actin, calponin and desmin were evenly expressed in SMCs; (2) in early (2 weeks) growing CVs the laminin network was disrupted, desmin was significantly reduced in SMCs, but α-SM actin and calponin still highly expressed; (3) in actively (6 weeks) growing CVs laminin was still weak in the tunica media (TM), but without network-like structure. Desmin was further reduced in SMCs of TM, whereas α-SM actin and calponin showed little changes, although they were significantly decreased in intimal SMCs; (4) in mature CVs, the network-like structure was re-formed, and α-SM actin, calponin, and desmin were all similar to that in normal vessels; (5) histology for BM confirmed laminin staining; (6) EM revealed that in NVs the SMCs contained abundant contractile filaments and were surrounded by a layer of BM whereas in growing CVs, BM structure was not observed, but the SMCs in the media still contained many myofilaments; (7) MMP-2 was highly expressed in the media of early growing vessels, but decreased in TM of actively growing vessels where TIMP-1 expression was high. In conclusion, our data revealed features of TM of growing CVs. Disruption and degradation of BM facilitate SMC proliferation, and together with reduction of desmin and fragmentation of the internal elastic lamina enable the vascular wall to expand and enlarge when blood pressure and shear stress increase. MMP2 may be an important player in regulating SMC phenotype, proliferation, migration and maintaining integrity of the vascular wall through governing proteolysis during arteriogenesis. (Mol Cell Biochem 264: 201–210, 2004)     

Characteristics of bovine early puerperal uterine contractility recorded under farm conditions

A non-invasive, digital technique was used to measure and quantify intrauterine pressure (IUP) changes in early postpartum dairy cows kept under farm conditions in order to document physiological changes in uterine contractility after uncomplicated calvings. In addition, possible relationships between characteristics of uterine contractility and blood ionized calcium (Ca(2+))-concentrations were investigated. Recordings of uterine contractility were made by using a transcervically inserted open tip catheter in 12 healthy cows during their first 48h after calving. The IUP recording technique appeared easily applicable under farm conditions. Although mean frequency (FREQ), amplitude (AMP) and area under the curve (AUC) of the myometrial contractions significantly decreased due to time, untreated early postpartum cows showed a high variability in characteristics of uterine contractility. There was no correlation between blood Ca2+ -concentrations and any of the contractility parameters.     

A true autoactivating enzyme. Structural insight into mannose-binding lectin-associated serine protease-2 activations

Few reports have described in detail a true autoactivation process, where no extrinsic cleavage factors are required to initiate the autoactivation of a zymogen. Herein, we provide structural and mechanistic insight into the autoactivation of a multidomain serine protease: mannose-binding lectin-associated serine protease-2 (MASP-2), the first enzymatic component in the lectin pathway of complement activation. We characterized the proenzyme form of a MASP-2 catalytic fragment encompassing its C-terminal three domains and solved its crystal structure at 2.4 A resolution. Surprisingly, zymogen MASP-2 is capable of cleaving its natural substrate C4, with an efficiency about 10% that of active MASP-2. Comparison of the zymogen and active structures of MASP-2 reveals that, in addition to the activation domain, other loops of the serine protease domain undergo significant conformational changes. This additional flexibility could play a key role in the transition of zymogen MASP-2 into a proteolytically active form. Based on the three-dimensional structures of proenzyme and active MASP-2 catalytic fragments, we present model for the active zymogen MASP-2 complex and propose a mechanism for the autoactivation process.     

Nuclear caspase-3 and capase-7 activation, and Poly(ADP-ribose) polymerase cleavage are early events in camptothecin-induced apoptosis

Chemotherapy-induced apoptosis by DNA-damaging drugs is thought to be generally dependent on the release of cytochrome c and the subsequent activation of caspase-9 and -3. However, the molecular mechanism of how damaged DNA triggers the apoptotic process is not clear. To better understand the mechanisms underlying this process, we examined drug-induced apoptosis in cultured H-460 cells. Using cell fractionation, western blotting, and immunofluorescence assays, we show that the activation of nuclear caspases-7 and -3, and poly(ADP-ribose) polymerase (PARP) cleavage, are early events in camptothecin-induced apoptosis. Moreover, we demonstrate that these events precede the release of cytochrome c and apoptotic inducing factor, and the activation of caspases 2, 8, 9 and 12. Together our results suggest that drugs acting at the DNA level can initiate apoptosis via nuclear caspase activation. An erratum to this article is available at .     

On the selection of phylogenetic eigenvectors for ecological analyses

Among the statistical methods available to control for phylogenetic autocorrelation in ecological data, those based on eigenfunction analysis of the phylogenetic distance matrix among the species are becoming increasingly important tools. Here, we evaluate a range of criteria to select eigenvectors extracted from a phylogenetic distance matrix (using phylogenetic eigenvector regression, PVR) that can be used to measure the level of phylogenetic signal in ecological data and to study correlated evolution. We used a principal coordinate analysis to represent the phylogenetic relationships among 209 species of Carnivora by a series of eigenvectors, which were then used to model log‐transformed body size. We first conducted a series of PVRs in which we increased the number of eigenvectors from 1 to 70, following the sequence of their associated eigenvalues. Second, we also investigated three non‐sequential approaches based on the selection of 1) eigenvectors significantly correlated with body size, 2) eigenvectors selected by a standard stepwise algorithm, and 3) the combination of eigenvectors that minimizes the residual phylogenetic autocorrelation. We mapped the mean specific component of body size to evaluate how these selection criteria affect the interpretation of non‐phylogenetic signal in Bergmann's rule. For comparison, the same patterns were analyzed using autoregressive model (ARM) and phylogenetic generalized least‐squares (PGLS). Despite the robustness of PVR to the specific approaches used to select eigenvectors, using a relatively small number of eigenvectors may be insufficient to control phylogenetic autocorrelation, leading to flawed conclusions about patterns and processes. The method that minimizes residual autocorrelation seems to be the best choice according to different criteria. Thus, our analyses show that, when the best criterion is used to control phylogenetic structure, PVR can be a valuable tool for testing hypotheses related to heritability at the species level, phylogenetic niche conservatism and correlated evolution between ecological traits.