Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

Two new species and a phylogenetic analysis of the genus Tectidrilus (0Iigochaeta, Tubifcidae)

Tectidrilus probus sp.n. and Tectidrilus profusus sp.n. are described from offshore localities in southern California. Both species appear closely related to T. diversus Ersëus, 1982, which occurs in the same area, but they differ from the latter by possessing small oesophageal diverticula; T. probus differs also by its very small spermathecal vestibules. Tectidrilus profusus is a highly apomorphic form with elaborate, partly muscular, male ducts and spermathecae. Monophyly of Tectidrilus is supported by the short clitellum and the unisetal 'bundles' in postclitellar segments. Patterns of apomorphic character states within the genus are analyzed under the principle of Camin-Sokal parsimony (irreversibility of character states), giving three equally parsimonious cladograms. In the strict consensus tree of these cladograms, eight of the twelve members of Tectidrilus form an apomorphic group defined by the papillated body wall, but the individual species within this group cannot be unequivocally resolved from each other.     

The relative importance of lethal and non-lethal effects of fish on insect colonisation of ponds

1. We hypothesised that adult insects actively monitor potential habitats for the presence of fish by means of chemical cues and avoid sites that pose significant risks. This was examined by quantifying colonisation of insects in outdoor pools with no fish (controls), fish (direct predation effect) or caged fish (chemical predator cues).
2. A significant direct effect of predation was found, but no indirect effect (avoidance of chemical cue pools), on the total biomass of colonising insects. However, predatory insects avoided fish-cue pools, thus releasing non-predatory insects from predation. This resulted in significantly greater biomass of non-predatory insects in fish-cue pools than control pools.
3. Fish reduced the number of species of colonising insects in pools through predation. This negative influence of fish implies that caution is necessary when stocking wetlands and ponds with fish if the goal is to maximise biodiversity.
4. Our data suggest that although predatory aquatic insects may use chemical signals to assess the quality of potential habitats with respect to predation risk, direct predation is the main method by which fish affect insect assemblages in ponds. Because fish and invertebrate predators may both have strong effects on prey mortality, behavioural adjustment by insects to the actual predator regime within a habitat should be more important than avoiding colonisation of habitats with fish.     

Marine Oligochaeta from the Koster Area, West Coast of Sweden, with Descriptions of Two New Enchytraeid Species

A total of 28 species of marine Oligochaeta (belonging to the families Naididae, Tubificidae and Enchytraeidae) are reported from eulittoral and sublittoral sediment samples taken in the Koster area on the Swedish West Coast. Lumbricillus algensis sp.n. and Grania ovitheca sp.n. are described and their morphological and taxonomical relations to other enchytraeids are discussed. L. algensis is characterized mainly by its spermathecae, which project into segment VI, and by its very large penial bulbs. G. ovitheca possesses no dorsal setae, the ventral setae being present posterior to the clitellum only, and its spermathecae consist of a narrow duct and a large egg-shaped to oval ampulla, filling most of the coelom of segment V. Four sublittoral species, Limnodriloides barnardi (Tubificidae), Lumbricillus semifuscus, Marionina sublitoralis and Grania roscoffensis (all Enchytraeidae) are reported as new to the Swedish fauna.     

Taxonomic Studies on the Marine Genera Aktedrilus Knöllner and Bacescuella Hrabe' (Oligochaeta, Tubificidae), with Descriptions of Seven New Species

The taxonomy and morphology of Aktedrilus Knöllner, 1935 and Bacescuella Hrabe' 1973 (subfamily Phallodrilinae), both common genera of the marine, littoral meiofauna, were studied on the basis of material from various geographical areas. A. monospermathecus Knöllner, 1935 is redescribed from France and Scotland. A. magnus sp.n., A. hrevis sp.n., A. curvipenis sp.n. and A. floridensis sp.n. are described from Italy, Brazil, France and Florida, respectively. Two very closely related forms are described from the Pacific: A. locyi sp.n. (California) and A. parviprostatus sp.n. (Great Barrier Reef). B. mediterranea sp.n. is described from Italy, and new European records are given forB. arclica Erséus, 1978 andfi. parvithecata Erséus, 1978. Both genera are characterized by having two pairs of prostate glands, well developed penes, and unpaired, mid-dorsal spermatheca (if present). The species of Bacescuella transfer their sperm by means of external spermatophores, structures that are not developed in Aktedrilus. The eight species of Aktedrilus are largely distinguished by means of the morphology of the spermatheca, penes and prostates. The four species of Bacescuella differ principally from each other in the length of the vasa deferentia, and in the morphology of the prostates and copulatory organs. Most Bacescuella species lack spermatheca.     

Modelling expected trout ranges under current and future water temperature regimes in the Eastern Cape,South Africa

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.     

Bronchoabsorption; a novel bronchoscopic technique to improve biomarker sampling of the airway

Background

Current techniques used to obtain lung samples have significant limitations and do not provide reproducible biomarkers of inflammation. We have developed a novel technique that allows multiple sampling methods from the same area (or multiple areas) of the lung under direct bronchoscopic vision. It allows collection of mucosal lining fluid and bronchial brushing from the same site; biopsy samples may also be taken. The novel technique takes the same time as standard procedures and can be conducted safely.

Methods

Eight healthy smokers aged 40–65 years were included in this study. An absorptive filter paper was applied to the bronchial mucosa under direct vision using standard bronchoscopic techniques. Further samples were obtained from the same site using bronchial brushings. Bronchoalveolar lavage (BAL) was obtained using standard techniques. Chemokine (C-C Motif) Ligand 20 (CCL20), CCL4, CCL5, Chemokine (C-X-C Motif) Ligand 1 (CXCL1), CXCL8, CXCL9, CXCL10, CXCL11, Interleukin 1 beta (IL-1β), IL-6, Vascular endothelial growth factor (VEGF), Matrix metalloproteinase 8 (MMP-8) and MMP-9 were measured in exudate and BAL. mRNA was collected from the bronchial brushings for gene expression analysis.

Results

A greater than 10 fold concentration of all the biomarkers was detected in lung exudate in comparison to BAL. High yield of good quality RNA with RNA integrity numbers (RIN) between 7.6 and 9.3 were extracted from the bronchial brushings. The subset of genes measured were reproducible across the samples and corresponded to the inflammatory markers measured in exudate and BAL.

Conclusions

The bronchoabsorption technique as described offers the ability to sample lung fluid direct from the site of interest without the dilution effects caused by BAL. Using this method we were able to successfully measure the concentrations of biomarkers present in the lungs as well as collect high yield mRNA samples for gene expression analysis from the same site. This technique demonstrates superior sensitivity to standard BAL for the measurement of biomarkers of inflammation. It could replace BAL as the method of choice for these measurements. This method provides a systems biology approach to studying the inflammatory markers of respiratory disease progression.

Trial registration

NHS Health Research Authority (13/LO/0256).     

Responses of riparian trees and shrubs to flow regulation along a boreal stream in northern Sweden

1. Flow dynamics is a major determinant of riparian plant communities. Therefore, flow regulation may heavily affect riparian ecosystems. Despite the large number of dams worldwide, little specific information is available on the longitudinal impacts of dams on vegetation, for example how far downstream and at what degree of regulation a dam on a river can influence riparian woodlands. 2. We quantified the long‐term responses of riparian trees and shrubs to flow regulation by identifying their lateral distribution and habitat conditions along a boreal river in northern Sweden that has been regulated by a single dam since 1948. The regulation has reduced annual flow fluctuations, this effect being largest at the dam, downstream from which it progressively decreases following the entrance of free‐flowing tributaries. 3. We related changes in the distribution patterns, composition, abundance and richness of tree and shrub species to the degree of regulation along the river downstream from the dam. Regulation has triggered establishment of trees and shrubs closer to the channel, making it possible to measure ecological impacts of flow regulation as differences in vegetation attributes relative to the positions of tree and shrub communities established before and after regulation. 4. Trees and shrubs had migrated towards the mid‐channel along the entire study reach, but the changes were largest immediately downstream of the dam. Shrubs were most impacted by flow regulation in terms of lateral movement, but the effect on trees extended furthest downstream. 5. The species composition of trees progressively returned to its pre‐regulation state with distance downstream, but entrance of free‐flowing tributaries and variation in channel morphology and substratum caused local deviations. Species richness after regulation increased for trees but decreased for shrubs. The changes in species composition and richness of trees and shrubs showed no clear downstream patterns, suggesting that other factors than the degree of regulation were more important in governing life form.     

Multiple effects of temperature,photoperiod and food quality on the performance of a pine sawfly

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Size-dependent effects of an invasive herbivorous snail (Pomacea canaliculata) on macrophytes and periphyton in Asian wetlands

1. The invasive golden apple snail (Pomacea canaliculata), native to South America, is a serious pest on rice seedlings in south‐east Asia and has also been shown to consume large amounts of macrophytes in natural wetlands, with large effects on ecosystem functioning. Earlier studies suggest that the snail undergoes an ontogenetic diet shift, feeding on algae and detritus as juveniles and shifting to aquatic macrophytes as adults. 2. Here, we study the effects of snail populations with a size‐structure typical of either populations at an invasive front or the size‐structure of established populations. In an enclosure experiment performed in a wetland in Laos, we compared treatments with small snails only (3 mm; invasive treatment) to treatments with small, medium sized (10 mm) and adult (>25 mm) snails (established treatment). The effects of snail grazing on three aquatic macrophyte species and periphytic algae were quantified. 3. We found that snails of all sizes had a strong negative effect on the biomass of all macrophyte species and periphytic algae. There was no evidence of an ontogenetic diet change, i.e. snails in both the invasive and established treatments affected macrophyte biomass. Foraging was size‐dependent in that small snails had higher relative foraging capacity (g plant consumed per g of snail) compared with medium and adult snails. Small snails, therefore, depressed growth of medium snails at increasing densities through exploitative competition for preferred resources, while adult snails did not grow at all in the presence of small snails. 4. Density dependence is common in freshwater invertebrates, including gastropod populations, but differences in size dependent foraging‐ and competitive‐ability have rarely been demonstrated in this group of organisms. Knowledge about intra‐specific differences in ecological performance may, however, both deepen our understanding of the processes that underlie population dynamics in invertebrates such as gastropods, and help develop control strategies for invasive golden apple snails.