Impact of faunal complexity on nutrient supply in field mesocosms from a spruce forest soil

A field study in an acidic spruce forest soil using soil mesocosms was conducted to investigate the effects of mesofauna and macrofauna on exchangeable cations, organic matter content, base saturation, and Ca-lactate extractable nutrients. In the field, intact soil monoliths were taken from the ground, defaunated by deep-freezing and wrapped in nets of various mesh-sizes to control immigration of different faunal size classes. The monoliths were then replanted in the field. Three types of treatments for the mesocosms were prepared: (1) microbiota only, (2) microbiota and mesofauna, (3) microbiota, mesofauna, and macrofauna (=complex fauna). After eight months the mesocosms and unmanipulated control plots (treatment 4) were destructively sampled and submitted to chemical analysis. Generally, the exchangeable base cations and Mn²⁺ showed higher contents with increasing faunal complexity, whereas the exchangeable acidic cations of Fe³⁺ and Al³⁺ decreased in the monoliths with complex fauna. These effects were significant for K⁺, Mg²⁺ and Mn²⁺ in the L/F-layer and for Ca²⁺, Mn²⁺, Al³⁺ and Fe³⁺ in the H-layer. As a possible explanation a rise of ion-binding sites in the course of enhanced humification processes is discussed.In the L/F-layer base cations showed higher concentrations in the monoliths with complex fauna as compared to the control plot, which contained intact roots. This might be due to nutrient uptake by roots in the control plot or enhanced mineralization in the monoliths with complex fauna, where roots had been cut.     

Specific contacts between the FLP protein of the yeast 2-micron plasmid and its recombination site

Contact points between the FLP protein of the yeast 2-micron plasmid and its recombination site have been defined. Important features of the region previously defined as the minimal recombination site in vitro include a pair of 13-base pair inverted repeats separated by an 8-base pair spacer. The two FLP protein-binding sites within this region are 12 base pairs in length. In each case they include the internal 11 base pairs of one of the 13-base pair repeats, as well as the adjacent base pair within the spacer. The internal 6 base pairs within the spacer are not involved in binding or recognition by FLP protein. When the size of the spacer is increased or decreased by one base pair, the distance between the cleavage points is also increased or decreased correspondingly by one base pair. Points of cleavage are unaffected by changes in the spacer sequence. Specific contact points involving purine residues, identified by methylation protection and recombination interference experiments, are located in both the major and minor grooves of the DNA. Additional contact points between FLP protein and phosphate groups in the phosphate-deoxyribose backbone are clustered near the cleavage sites.     

Slow upward drift of VO2 during constant-load cycling in untrained subjects

The oxygen uptake kinetics during constant-load exercise when sitting on a bicycle ergometer were determined in 7 untrained subjects by measuring breath-by-breath VO2 during continuous exercise to volitional exhaustion (mean endurance time = 1160 +/- 172 s) at a pedal frequency of 70 revolutions.min-1. The power output, averaging 189.5 W, was set at 82.5% of that eliciting the individual VO2max during a 5 min incremental exercise test. Throughout the exercise period, the VO2 kinetics could be appropriately described by a two-component exponential equation of the form: VO2(t) = Ya[1 - exp(-kat)] + Yb[1 - exp(-kbt)] where VO2 is net oxygen consumption and t the time from work onset. VO2 measured at the end of exercise was close to VO2max (98% VO2max) and the mean values of Ya, ka, Yb and kb amounted to 1195 ml O2.min-1, 0.034 s-1, 1562 ml O2.min-1, and 0.005 s-1 respectively. The initial rate of increase in VO2 predicted from the above equation is slower than that calculated, for the same work intensity, on the basis of the data obtained by Morton (1985) in trained subjects. For t greater than 480 s, however, the two models yield substantially equal results.     

Evidence against a PGF4a prostaglandin structure in trout tissue--a correction

Analysis of the oxygenated products generated from docosahexaenoic acid by trout gill tissue and reinterpretation of the mass spectrum of the proposed novel prostanoid indicate that the compounds identified as n-3 prostaglandins are trihydroxylated derivatives of the precursor polyunsaturated fatty acids.     

Lateral Growth Limitation of Corneal Fibrils and Their Lamellar Stacking Depend on Covalent Collagen Cross-linking by Transglutaminase-2 and Lysyl Oxidases,Respectively

Corneal stroma contains an extracellular matrix of orthogonal lamellae formed by parallel and equidistant fibrils with a homogeneous diameter of ∼35 nm. This is indispensable for corneal transparency and mechanical functions. However, the mechanisms controlling corneal fibrillogenesis are incompletely understood and the conditions required for lamellar stacking are essentially unknown. Under appropriate conditions, chick embryo corneal fibroblasts can produce an extracellular matrix in vitro resembling primary corneal stroma during embryonic development. Among other requirements, cross-links between fibrillar collagens, introduced by tissue transglutaminase-2, are necessary for the self-assembly of uniform, small diameter fibrils but not their lamellar stacking. By contrast, the subsequent lamellar organization into plywood-like stacks depends on lysyl aldehyde-derived cross-links introduced by lysyl oxidase activity, which, in turn, only weakly influences fibril diameters. These cross-links are introduced at early stages of fibrillogenesis. The enzymes are likely to be important for a correct matrix deposition also during repair of the cornea.     

Interactively illustrating polymerization using three-level model fusion

Background

Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. Illustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments.

Results

In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at different time scales. We integrate physical and empirical modeling, according to which approach best suits the different involved levels of detail, and we additionally enable a form of interactive steering, while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a first evaluation with domain experts.

Conclusion

We conclude that our approach provides a new, hybrid modeling approach for illustrating the process of emergence in physiology, embedded in a densely filled environment. Our approach of a complementary fusion of three systems combines the strong points from the different modeling approaches and is capable to bridge different spatial and temporal scales.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-345) contains supplementary material, which is available to authorized users.     

Dominance of Epiphytic Filamentous Thiothrix spp. on an Aquatic Macrophyte in a Hydrothermal Vent Flume in Sedge Bay, Yellowstone Lake, Wyoming

Sublacustrine hydrothermal vents, geysers, and fumaroles impart regions of Yellowstone Lake with distinctive chemical compositions that generate unique freshwater habitats and support diverse microbial life. Some microbial communities within Sedge Bay manifest themselves as accumulations of white-colored films on the surfaces of aquatic macrophytes located within the hydrothermal flow of vents. It was hypothesized that the white films were the product of microbial growth, particularly sulfur-oxidizing bacteria. An investigation of the relevant biological compounds in the vent waters was conducted. Microscopy, non-culture molecular techniques, and phylogenetic analysis were used to assay the bacterial diversity associated with the films. Microscopic analysis of the white films revealed the presence of long filaments (>200 μm) that contained sulfur granules. Filaments with these characteristics were not detected on the normal macrophyte samples. Nucleic acids were extracted from the surface of macrophyte coated with the white film (SB1, SB2) and from the surface of an uncoated macrophyte (SC). 16S ribosomal (rRNA) genes were amplified with the polymerase chain reaction (PCR) and cloned. Amplified ribosomal DNA restriction analysis (ARDRA) was used to examine 100 clones from each library and identify unique phylotypes. S_Chao1 and the Shannon Index, mathematical measures of richness and heterogeneity, were employed to assess the ARDRA pattern diversity of each sample. The SC community contained 50 unique phylotypes, predominantly cyanobacteria and proteobacteria, and was the most heterogeneous. SB1 and SB2 communities were less heterogeneous and dominated by Thiothrix. Dilution to extinction PCR conducted with specific primers indicated that the relative abundance of Thiothrix 16S rRNA gene copies in all three samples were similar. However, reduced sulfur compounds from the vent resulted in a more narrow habitat that supported the sulfur-oxidizing Thiothrix in the white film to the exclusion of cyanobacteria and other proteobacteria found on the normal macrophyte. The majority of 16S rRNA gene sequences obtained in this study displayed similarities ≤98% to any known sequence in public data bases which suggests an abundance of new bacterial species in Sedge Bay.     

Implications of coral harvest and transplantation on reefs in northwestern Dominica

In June, 2002, the government of Dominica requested assistance in evaluating the coral culture and transplantation activities being undertaken by Oceanographic Institute of Dominica (OID), a coral farm culturing both western Atlantic and Indo-Pacific corals for restoration and commercial sales. We assessed the culture facilities of OID, the condition of reefs, potential impacts of coral collection and benefits of coral transplantation. Coral reefs (9 reefs, 3-20 m depth) were characterized by 35 species of scleractinian corals and a live coral cover of 8-35%. Early colonizing, brooders such as Porites astreoides (14.8% of all corals), P. porites (14.8%), Meandrina meandrites (14.7%) and Agaricia agaricites (9.1%) were the most abundant corals, but colonies were mostly small (mean = 25 cm diameter). Montastraea annularis (complex) was the other dominant taxa (20.8% of all corals) and colonies were larger (mean = 70 cm). Corals (pooled species) were missing an average of 20% of their tissue, with a mean of 1.4% recent mortality. Coral diseases affected 6.4% of all colonies, with the highest prevalence at Cabrits West (11.0%), Douglas Bay (12.2%) and Coconut Outer reef (20.7%). White plague and yellow band disease were causing the greatest loss of tissue, especially among M. annularis (complex), with localized impacts from corallivores, overgrowth by macroalgae, storm damage and sedimentation. While the reefs appeared to be undergoing substantial decline, restoration efforts by OlD were unlikely to promote recovery. No Pacific species were identified at OID restoration sites, yet species chosen for transplantation with highest survival included short-lived brooders (Agaricia and Porites) that were abundant in restoration sites, as well as non-reef builders (Palythoa and Erythropodium) that monopolize substrates and overgrow corals. The species of highest value for restoration (massive broadcast spawners) showed low survivorship and unrestored populations of these species were most affected by biotic stressors and human impacts, all of which need to be addressed to enhance survival of outplants. Problems with culture practices at OID, such as high water temperature, adequate light levels and persistent overgrowth by macroalgae could be addressed through simple modifications. Nevertheless, coral disease and other stressors are of major concern to the most important reef builders, as these species are less amenable to restoration, collection could threaten their survival and losses require decades to centuries to replace.     

European regulatory framework and practices for veterinary Leptospira vaccine potency testing

In Europe, the legal basis for requirements for medicinal products is described in the European Pharmacopoeia (Ph. Eur.) In the European Union, the Ph. Eur. is supplemented by several guidelines issued by the European Medicines Agency. Immunological veterinary products must comply with the Ph. Eur. monograph on veterinary vaccines and the accompanying texts, as well as specific monographs. The Ph. Eur. includes monographs on canine leptospirosis and bovine leptospirosis vaccines (inactivated). Both monographs require that an immunogenicity test be performed once in the target species during the life of a vaccine. The hamster challenge test is applied for batch potency testing of canine vaccines. Alternatively, serological tests or suitable validated in vitro tests to determine the content of one or more antigenic components indicative of protection may be performed. Vaccines for use in cattle are tested in a serological test in guinea pigs. The acceptance criteria in alternative tests are set with reference to a batch of vaccine that has given satisfactory results in the immunogenicity test. At a January 2012 European workshop, the suitability of the hamster potency test was questioned and unanimous agreement was reached that moving toward complete in vitro testing is possible and should be promoted.