Eight PCR primers to amplify EST‐linked microsatellites in the Eastern oyster,Crassostrea virginica genome

Twenty‐four microsatellite repeat sequences were identified by screening a total of 4446 eastern oyster, Crassostrea virginica, expressed sequence tags. Polymerase chain reaction primers were designed to amplify 12 of these loci. After optimizing reaction parameters, eight loci showed high variability with consistent amplification that could be scored unambiguously. Ninety two C. virginica from the James River, VA, were genotyped at these loci. Number of alleles per locus ranged from 11 to 53, expected and observed heterozygosities ranged from 0.69 to 0.97, and from 0.30 to 0.99, respectively. Discrepancies between expected and observed heterozygosities were common and likely caused by null alleles.     

Plastic resource polymorphism: effects of resource availability on Arctic char (Salvelinus alpinus) morphology

Resource polymorphism has been suggested to be a platform for speciation. In some cases resource polymorphism depends on phenotypic plasticity but in other cases on genetic differences between morphotypes, which in turn has been suggested to be the ongoing development of a species pair. Here we study environmentally induced morphological differences in two age classes of Arctic char ( Salvelinus alpinus ) influencing char performance and diet in relation to resource availability. We found that structurally complex habitats with relatively lower zooplankton densities gave rise to individuals with a deeper body, and a downward positioned tip of the snout compared with individuals from structurally simple habitats with relatively higher zooplankton densities for both age classes. Environment also had an effect on foraging efficiency on zooplankton, with fish from structurally simple habitats had a higher foraging rate than fish from structurally complex habitats. Diet analyses showed that resource use in char mainly depends on the relative abundance of different resources. Therefore, to gain further understanding of resource polymorphism we suggest that future studies must include population dynamic feedbacks by the resources on the consumers.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 341–351.     

Antibiotic Activity of the Chrysophyte Ochromonas malhamensis

The effects were studied of extracts from the chrysophyte Ochromonas malhamensis on Staphylococcus aureus, Bacillus megaterium, Bacillus subtilis and Escherichia coli. The extracts contained three different antibiotically active substances, one of which was produced during the extraction. The other two had no effect on E. coli, but inhibited the growth of the three other bacteria. The present experiments show that one of the products increases its antibiotic activity when exposed to visible light, and that its activity is enhanced by boiling the extracts for 5 minutes. The other active substance is not affected by light, but shows increased activity after being boilt for 5 minutes.     

Experimental taxonomy of Bulinus (Gastropoda: Planorbidae): the West and North African species reconsidered, based upon an electrophoretic study of several enzymes per individual

Horizontal starch gel electrophoresis was used to score mobilities of seven different enzymes in species of Bulinus from North and West Africa. An account of the intra- and inter-population variation observed was given. Based on the data obtained it was suggested that enzymic data should be used as taxonomic characters in parallel with morphological and anatomical characters. It is suggested that enzymic characters could be used to place taxa into synonymy if the data are collected in such a way that one can write up an enzyme profile for the single individual. The nine taxa of Bulinus known to occur in North and West Africa were revised, the taxon B. jousseaumei was synonymized with B. globosus , and the two taxa B. guernei and B. rohlfsi were synonymized with B. truncatus. As a result of the revision only six species could be recognized as valid from the area, these being B. forskalii, B. globosus, B. senegalensis, B. truncatus, B. ugandae and B. umbilicatus. Finally, some enzymic characters are suggested that may be used for a reliable identification of these morphologically very difficult taxa.     

The effect of water colour on lake hydrodynamics: a modelling study

1. The one‐dimensional equation solver, PROgram for Boundary layers in the Environment, was used to simulate the temperature structure of Lake Erken, a medium‐sized Swedish lake, assuming differing extinction coefficients for a series of modelled years driven by observed meteorological data and by a set of idealized meteorological data. 2. Results suggested that, as expected, larger extinction coefficients initially led to surface waters becoming warmer. The reverse was true late in the summer, however, as the warming induced by greater absorption of solar radiation was outweighed by the cooling effects of entrained colder hypolimnetic water. 3. There was between a two‐ and fourfold inter‐annual variation in the effects on key physical lake parameters, induced by changing extinction coefficient, such as maximum heat flux, heat content and Schmidt stability. 4. The change in surface heat flux induced by a change in extinction coefficient was up to almost 50 W m⁻². 5. In the summer, changes in extinction coefficient from 0.5 to 0.2 m⁻¹ led to a dramatic shift in the duration of the stratified period as well as to enormous changes in Schmidt stability and hypolimnetic temperature. 6. Future changes to extinction coefficients of small and medium‐sized lakes are likely to have wide‐ranging effects on lake thermal structure and ecology.     

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores and P values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.     

Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215‐bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite F_ST = 0.205, P < 0.001; global mitochondrial control region Φ_ST = 0.399, P < 0.001). Microsatellite‐based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human‐mediated introductions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Treeline shifts in the Ural mountains affect soil organic matter dynamics

Historical photographs document that during the last century, forests have expanded upwards by 60–80 m into former tundra of the pristine Ural mountains. We assessed how the shift of the high‐altitude treeline ecotone might affect soil organic matter (SOM) dynamics. On the gentle slopes of Mali Iremel in the Southern Urals, we (1) determined the differences in SOM stocks and properties from the tundra at 1360 m above sea level (a.s.l.) to the subalpine forest at 1260 m a.s.l., and (2) measured carbon (C) and nitrogen (N) mineralization from tundra and forest soils at 7 and 20 °C in a 6‐month incubation experiment. C stocks of organic layers were 3.6±0.3 kg C m^?2 in the tundra and 1.9±0.2 kg C m^?2 in the forest. Mineral soils down to the bedrock stored significantly more C in the forest, and thus, total soil C stocks were slightly but insignificantly greater in the forest (+3 kg C m^?2). Assuming a space for time approach based on tree ages suggests that the soil C sink due to the forest expansion during the last century was at most 30 g C m^?2 yr^?1. Diffuse reflective infrared spectroscopy and scanning calorimetry revealed that SOM under forest was less humified in both organic and mineral horizons and, therefore, contained more available substrate. Consistent with this result, C mineralization rates of organic layers and A horizons of the forest were two to four times greater than those of tundra soils. This difference was similar in magnitude to the effect of increasing the incubation temperature from 7 to 20 °C. Hence, indirect climate change effects through an upward expansion of forests can be much larger than direct warming effects (Δ0.3 K across the treeline). Net N mineralization was 2.5 to six times greater in forest than in tundra soils, suggesting that an advancing treeline likely increases N availability. This may provide a nutritional basis for the fivefold increase in plant biomass and a tripling in productivity from the tundra to the forest. In summary, our results suggest that an upward expansion of forest has small net effects on C storage in soils but leads to changes in SOM quality, accelerates C cycling and increases net N mineralization, which in turn might stimulate plant growth and thus C sequestration in tree biomass.     

Influence of sediment organic enrichment and water alkalinity on growth of aquatic isoetid and elodeid plants

1. Lake eutrophication has increased phytoplankton blooms and sediment organic matter. Among higher plants, small, oligotrophic rosette species (isoetids) have disappeared, while a few tall, eutrophic species (elodeids) may have persisted. Despite recent reduction of nutrient loading in restored lakes, the vegetation has rarely regained its former composition and coverage. Patterns of recovery may depend on local alkalinity because HCO₃^? stimulates photosynthesis of elodeids and not of isoetids. In laboratory growth experiments with two isoetids (Lobelia dortmanna and Littorella uniflora) and two elodeids (Potamogeton crispus and P. perfoliatus), we test whether organic enrichment of lake sediments has a long‐lasting influence by: (i) reducing plant growth because of oxygen stress on plant roots and (ii) inhibiting growth more for isoetids than elodeids. We also test whether (iii) increasing alkalinity (from 0.17 to 3.20 meq. L^?1) enhances growth and reduces inhibition of organic sediment enrichment for elodeids but not for isoetids. 2. In low organic sediments, higher oxygen release from roots of isoetids than elodeids generated oxic conditions to greater sediment depth for Lobelia (4.3 cm) and Littorella (3.0 cm) than for Potamogeton species (1.6–2.2 cm). Sediment oxygen penetration depth fell rapidly to 0.4–1.0 cm for all four species at even modest organic enrichment and oxygen consumption in the sediments. Roots became shorter and isoetid roots became thicker to better supply oxygen to apical meristems. 3. Growth of elodeids was strongly inhibited across all levels of organic enrichment of sediments being eight‐fold lower at the highest enrichment compared to the unenriched control. Leaf biomass of isoetids increased three‐fold by moderate organic enrichment presumably because of greater CO₂ supply from sediments being their main CO₂ source. At higher organic enrichment, isoetid biomass was reduced, leaf chlorophyll declined up to 10‐fold, root length declined from 7 to <2 cm and mortality rose (up to 50%) signalling high plant stress. 4. Lobelia was not affected by HCO₃^? addition in accordance with its use of sediment CO₂. Biomass of elodeids increased severalfold by rising alkalinity from 0.17 to 3.20 meq. L^?1 in accordance with their use of HCO₃^? for photosynthesis, while the negative impact of organically enriched sediments remained. 5. Overall, root development of all four species was so strongly restricted in sediments enriched with labile organic matter that plants if growing in situ may lose root anchorage. Other experiments demonstrate that this risk is enhanced by greater water content and reduced consolidation in organically rich sediments. Therefore, formation of more muddy and oxygen‐demanding sediments during eutrophication will impede plant recovery in restored lakes while high local alkalinity will help elodeid recovery.