Fish habitat modelling as a tool for river management

This paper presents an integrated modelling approach to simulate and assess ecological effects of physical habitat changes in rivers. An ecohydraulic simulation tool was created by combining a 1D hydraulic model based on HEC-RAS software and the fish habitat module of CASiMiR, a fuzzy logic-based ecohydraulic modelling system. This tool was applied on a river stretch commonly occurring in Belgium and elsewhere in Europe. In particular the effect of weir removal on habitat suitability for bullhead (Cottus gobio L.) was simulated. Physical conditions of the studied stretch after weir removal were simulated with a hydraulic model. CASiMiR linked these conditions to ecological expert knowledge to calculate habitat suitability for three life stages of bullhead at four different flow rates based on fuzzy logic. Results indicated that after weir removal, habitat suitability increased significantly for all life stages and all flow rates. The presented approach is promising regarding fish community assessment and ecological river engineering.     

Analyzing ungulate long bones as a tool for habitat reconstruction

The long bones (humerus, radius, metacarpus, femur, tibia, metatarsus) of 51 extant bovid and 7 equid specimens were measured in order to test the hypothesis that they show adaptations to different habitats. We performed factor analyses (FAs) with principal component extraction method and plotted the extracted factors (Fs) in simple scatterplots. The preferred habitats (grassland, forest, mountainous regions) were labeled in the plots, and our results show three clearly separated clusters for F2 vs. F3. According to our interpretation, F1 reflects the body size of the specimens while F2 is most probably reflecting cursorial adaptations. F3 is largely affected by dimensional bone characteristics adapted to maneuver in the environment, and therefore, F3 is somehow linked to habitat. The investigated equids are plotting within the cluster of bovids preferring grassland habitats, which is surprising because of different constructions of the metapodials in perissodactyls and ruminants. Performed linear discriminant analyses (LDAs) are supporting our FA results. This approach combines biometrics with statistics and presents a tool, which easily can be applied helping to identify the paleo-habitat or the paleo-ecology of extinct bovids with implications on fossil localities.     

Cell tracking velocimetry as a tool for defining saturation binding of magnetically conjugated antibodies.

BACKGROUND: Continuous flow immunomagnetic separation is an attractive alternative to current batch mode immunomagnetic separation methods because it is capable of high sorting speeds at mild cell conditions, and grants the operator better control of separation process. The control of the separation is dependent on knowledge of the amount of magnetic label attached to the cell (magnetic labeling intensity), however. Determination of the magnetic labeling is accomplished by measuring cell magnetophoretic mobility using a newly developed technique of Cell Tracking Velocimetry (CTV). METHODS: Flow cytometry was used to define the antibody binding characteristics of a fluorescently tagged primary antibody. Subsequently, CTV was used to measure antibody-binding characteristics of a magnetically tagged secondary antibody. RESULTS: The results of this study show that CTV is capable of providing valuable information concerning the cell labeling by magnetically tagged antibodies. It was demonstrated that the magnetically conjugated antibody binding curve exhibits the same exponential increase to saturation characteristics as that seen with the fluorescently tagged antibody. Further, it was shown that the intensity of the secondary magnetic labeling is directly proportional to the intensity of the primary fluorescent label. CONCLUSIONS: CTV is an accurate tool for evaluation of magnetically conjugated antibodies. The ability to determine the intensity of magnetic labeling is necessary for the development of continuous flow immunomagnetic separations based on cell magnetophoresis.     

Evidences of habitat displacement between two common soft-bottom SW Atlantic intertidal crabs

The intertidal burrowing crab Chasmagnathus granulatus Dana is the dominant species in soft sediments and vegetated intertidal areas along the SW Atlantic estuaries (southern Brazil 28°S to the northern Argentinean Patagonia 41°S) where it produces dense and extensive burrowing beds. The mud crab Cyrtograpsus angulatus Dana coexists with Ch. granulatus in this area, but it also inhabits areas to the south (northern and central Argentinean Patagonia). A survey covering both areas showed that C. angulatus rarely live in burrows when coexisting with Ch. granulatus, but form large burrowing beds when not coexisting with Ch. granulatus. When both species coexisted, burrowing beds of C. angulatus are restricted to sandy-muddy areas. Only rarely are burrows of C. angulatus found within Ch. granulatus beds. However, when Ch. granulatus were experimentally excluded within their burrowing beds, new settlers of C. angulatus made burrows and maintained them until they reached large size. Paired (inside and outside Ch. granulatus burrowing bed) sampling during high tide using beach nets showed that C. angulatus rarely venture inside the Ch. granulatus crab beds. Other field experiments showed that adults Ch. granulatus always displace C. angulatus from burrows. Furthermore, in several sites located south of the limit of distribution of Ch. granulatus at the Patagonian coast, soft bare intertidals are dominated by burrowing beds of C. angulatus mixed with the congener C. altimanus Dana. Together, these evidences suggest that the mud crab C. angulatus is displaced from soft bottom areas by the burrowing crab Ch. granulatus. It is an example of competitive exclusion through aggressive interference in soft-bottom habitats when the shared resource is the access to sediment surface, a two-dimensional well-defined resource.     

基质辅助激光解吸电离飞行时间质谱技术作为常见益生菌菌种鉴定辅助工具的研究

目的评价基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)技术用于常见益生菌菌株鉴定及潜在益生菌菌株筛选的可行性。方法利用16S rDNA序列分析在方法学上对MALDI-TOF MS技术的鉴定能力进行研究;通过MALDI-TOF MS技术对现有保藏菌株的鉴定结果研究MALDI-TOF MS技术的鉴定准确性及优越性。结果 MALDI-TOF MS技术具备较16S rDNA序列分析更高的菌株鉴定能力;MALDI-TOF MS技术的鉴定结果准确、稳定。结论 MALDI-TOF MS技术可以作为准确、快速、廉价及可高通量操作的菌株鉴定方法应用于常见益生菌菌株的鉴定及潜在益生菌菌株的筛选。     

Dispersal of common dormiceMuscardinus avellanarius in a habitat mosaic

In the eastern part of Saxony (Germany), common dormiceMuscardinus avellanarius (Linnaeus, 1758) were found in very small woods (average area of 10 woods was 2.9 ± 1.4 ha) isolated within agricultural fields for more than 100 years (average distance to the next, larger wood 268 ± 84 m). Dormice reproduced even in wood islands smaller than two hectares. Altogether 6 marked dormice were recorded migrating across the open landscape. Of these, 5 were juveniles. Minimum and maximum distances in treeless areas between points of capture and recapture were 250 and 500 m respectively. These migrations over open ground seem to be rare but normal events and explain the presence of common dormice in very small patches of woodland in habitat mosaics.     

Leaf energy balance modelling as a tool to infer habitat preference in the early angiosperms

Despite more than a century of research, some key aspects of habitat preference and ecology of the earliest angiosperms remain poorly constrained. Proposed growth ecology has varied from opportunistic weedy species growing in full sun to slow-growing species limited to the shaded understorey of gymnosperm forests. Evidence suggests that the earliest angiosperms possessed low transpiration rates: gas exchange rates for extant basal angiosperms are low, as are the reconstructed gas exchange rates for the oldest known angiosperm leaf fossils. Leaves with low transpirational capacity are vulnerable to overheating in full sun, favouring the hypothesis that early angiosperms were limited to the shaded understorey. Here, modelled leaf temperatures are used to examine the thermal tolerance of some of the earliest angiosperms. Our results indicate that small leaf size could have mitigated the low transpirational cooling capacity of many early angiosperms, enabling many species to survive in full sun. We propose that during the earliest phases of the angiosperm leaf record, angiosperms may not have been limited to the understorey, and that some species were able to compete with ferns and gymnosperms in both shaded and sunny habitats, especially in the absence of competition from more rapidly growing and transpiring advanced lineages of angiosperms.     

Mangroves as a habitat for fish and prawns

Mangrove inlets and creeks in Selangor, Malaysia are the habitat for 119 species of fish and 9 species of prawns. The majority of fish and all prawns sampled in the inlets were juveniles. The common fish species in the inlets in terms of weight wereArius sagor, Ambassis gymnocephalus, Liza subviridis, Toxotes jaculator, Sphyraena barracuda andLates calcarifer. Prawns were represented by juvenilePenaeus penicillatus, P. merguiensis, P. indicus, Metapenaeus brevicornis andM. affinis. Samples from enclosure traps set on mudflats during ebbing water captured 37 species of fish and 11 species of prawns. The role of mangroves as nursery and feeding grounds for fish and prawns is reviewed in the light of recent work in Selangor. It is apparent that mangroves support fisheries by providing habitat and food.     

Experiments on habitat selection in voles: Implications for the inverse distribution of two common European species

Summary Several pairs of species of microtine rodents show inverse distributions or abundance. Here I determine if the inverse abundance relationship of the bank vole Clethrionomys glareolus (a forest species) and the field vole Microtus agrestis (an open field species) could be explained by habitat selection. Habitat selection was examined by choice experiments with combinations of soil and vegetation types, and with separate habitat factors. The effects of early experience and social behaviour were also studied, e.g. in a large outdoor enclosure. M. agrestis showed a stronger dependence on shelter (e.g. easily excavated soil or thick grassy vegetation) than C. glareolus, while the presence of preferred food did not affect habitat selection for either species. In both species, laboratory-bred specimens showed considerably fewer preferences. Habitat selection in subadult C. glareolus was influenced by social clumping, while territorial behaviour made more even distributions in M. agrestis.The less rigid habitat selection and weaker territorial behaviour observed in the forest species (Clethrionomys) compared with a species from temporary habitats (Microtus) is not consistent with present concepts of r- and K-selection.     

The ecology of European ponds: defining the characteristics of a neglected freshwater habitat

There is growing awareness in Europe of the importance of ponds, and increasing understanding of the contribution they make to aquatic biodiversity and catchment functions. Collectively, they support considerably more species, and specifically more scarce species, than other freshwater waterbody types. Ponds create links (or stepping stones) between existing aquatic habitats, but also provide ecosystem services such as nutrient interception, hydrological regulation, etc. In addition, ponds are powerful model systems for studies in ecology, evolutionary biology and conservation biology, and can be used as sentinel systems in the monitoring of global change. Ponds have begun to receive greater protection, particularly in the Mediterranean regions of Europe, as a result of the identification of Mediterranean temporary ponds as a priority in the EU Habitats Directive. Despite this, they remain excluded from the provisions of the Water Framework Directive, even though this is intended to ensure the good status of all waters. There is now a need to strengthen, develop and coordinate existing initiatives, and to build a common framework in order to establish a sound scientific and practical basis for pond conservation in Europe. The articles presented in this issue are intended to explore scientific problems to be solved in order to increase the understanding and the protection of ponds, to highlight those aspects of pond ecology that are relevant to freshwater science, and to bring out research areas which are likely to prove fruitful for further investigation. Guest editors: R. Céréghino, J. Biggs, B. Oertli and S. Declerck The ecology of European ponds: defining the characteristics of a neglected freshwater habitat     

Logistic regression methods for retrospective case-control studies using complex sampling procedures

There are a number of possible designs for case-control studies. The simplest uses two separate simple random samples, but an actual study may use more complex sampling procedures. Typically, stratification is used to control for the effects of one or more risk factors in which we are interested. It has been shown (Anderson, 1972, Biometrika 59, 19-35; Prentice and Pyke, 1979, Biometrika 66, 403-411) that the unconditional logistic regression estimators apply under stratified sampling, so long as the logistic model includes a term for each stratum. We consider the case-control problem with stratified samples and assume a logistic model that does not include terms for strata, i.e., for fixed covariates the (prospective) probability of disease does not depend on stratum. We assume knowledge of the proportion sampled in each stratum as well as the total number in the stratum. We use this knowledge to obtain the maximum likelihood estimators for all parameters in the logistic model including those for variables completely associated with strata. The approach may also be applied to obtain estimators under probability sampling.     

Gradients of salinity stress, environmental stability and water chemistry as a templet for defining habitat types and physiological strategies in inland salt waters

The search for pattern in the geographic occurrence of salt lake flora and fauna often reveals strong associations of specific taxa with certain types of water chemistry. Solute composition, along with salinity and habitat stability, may provide a templet shaping the distribution of many organisms inhabiting saline lakes. A review of studies demonstrating habitat associations, specific solute tolerance, and ionic and osmotic adaptations provide evidence of fidelity to particular conditions of environmental chemistry across a wide taxonomic spectrum. Under low salinity conditions, some species show osmoregulatory adaptability to varied solute composition but the capacity for such flexibility is reduced with increased salinity and only certain taxa are found in hypersaline waters dominated by a particular solute. Anionic ratios of chloride, bicarbonate–carbonate, and sulfate appear to be especially important determinants of distribution. Specific solute tolerance presents an alternative explanation to disrupted hydrographic connections in describing how biogeographic distributions may be restricted to certain aquatic habitats in arid regions. Physiological adaptations to chemistry, exemplified in the brine fly genus Ephydra, may be an integral part of the evolution, ecology and diversification of saline water organisms.