Physiological and ecological hosts of Popenaias popeii (Bivalvia: Unionidae): laboratory studies identify more hosts than field studies

1. Freshwater mussels are critically endangered in North America, making it important to understand their environmental requirements at all life stages. As glochidia (larvae), they attach to fish hosts where they undergo substantial mortality, making this transition important in their life cycle. Larval host fish requirements have typically been described using data from laboratory infestations to determine suitable hosts. 2. Laboratory infestations circumvent many natural barriers that prevent infestation of physiologically compatible fishes by mussel larvae. While such methods are invaluable for identifying ‘physiological hosts,’ they cannot fully describe realised ‘ecological hosts’ in the field. 3. We studied Popenaias popeii in the Black River in New Mexico, because it is of conservation concern and it is the only mussel species present, facilitating identification of glochidial infestation. To explore the difference between physiological hosts and ecological hosts, we conducted a 3‐year field study of fishes infested by P. popeii glochidia. 4. Substantially fewer fish species were infested by P. popeii in the wild (10 of 20 observed) than had been identified as physiological hosts in laboratory trials (24 of 31). We combined data on fish abundance, proportion of fish hosts infested (prevalence) and the number of glochidia per fish (intensity) and identified three fish species that probably contributed substantially more to mussel recruitment by carrying more glochidia than other host species. 5. Similarities in behaviour among these fishes allowed us to hypothesise routes of infestation, such as benthos‐feeding by catostomids, that allow glochidia to infest these hosts at higher rates than other suitable hosts. Overall, this approach provides a method of quantifying the relative importance of different species of host fish in the mussel lifecycle.     

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Background

Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.

Results

Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.

Conclusions

Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users.     

Cell cycle population effects in perturbation studies

Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response (ESR), an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response in single cells, both the slow growth signature and ESR mainly reflect a redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed.     

Genetic variation in natural populations of Anthurium sinuatum and A. pentaphyllum var. pentaphyllum (Araceae) from north‐east Brazil using AFLP molecular markers

Genetic variation was investigated using AFLP markers in 12 populations of Anthurium sinuatum and A. pentaphyllum var. pentaphyllum (Araceae) in north‐east Brazil, Amazonia and the Brazilian Atlantic forest. Two unique genetic patterns characterized the populations of A. sinuatum as a group, but no correlation between genetic and geographical interpopulation distance was found; the Amazonian population was not separated from that in Ceará. The isolated Ceará brejo populations of A. sinuatum were genetically distinct, but genetic diversity levels were similar to populations elsewhere, with no evidence of genetic erosion. Anthurium pentaphyllum populations were significantly different from each other; Bayesian genetic structural analysis found no common genetic pattern, but revealed genetic clusters unique to subgroups and individual populations in the Atlantic forest and French Guiana. Anthurium pentaphyllum and A. sinuatum can be distinguished genetically, but individuals of both species formed intermediate genetic clusters that blurred their distinction. We suggest that genetic mixing of A. sinuatum and A. pentaphyllum has occurred in north‐east Brazil, possibly connected with cycles of humid forest expansion. The weak genetic structure in A. sinuatum is consistent with the natural fragmentation of continuous forest areas, possibly during the Holocene. This study highlights the scientific importance of the highly threatened brejo forests for tropical American biogeography. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 88–105.     

Effect of calcification on the mechanical stability of plaque based on a three-dimensional carotid bifurcation model

Background

This study characterizes the distribution and components of plaque structure by presenting a three-dimensional blood-vessel modelling with the aim of determining mechanical properties due to the effect of lipid core and calcification within a plaque. Numerical simulation has been used to answer how cap thickness and calcium distribution in lipids influence the biomechanical stress on the plaque.

Method

Modelling atherosclerotic plaque based on structural analysis confirms the rationale for plaque mechanical examination and the feasibility of our simulation model. Meaningful validation of predictions from modelled atherosclerotic plaque model typically requires examination of bona fide atherosclerotic lesions. To analyze a more accurate plaque rupture, fluid-structure interaction is applied to three-dimensional blood-vessel carotid bifurcation modelling. A patient-specific pressure variation is applied onto the plaque to influence its vulnerability.

Results

Modelling of the human atherosclerotic artery with varying degrees of lipid core elasticity, fibrous cap thickness and calcification gap, which is defined as the distance between the fibrous cap and calcification agglomerate, form the basis of our rupture analysis. Finite element analysis shows that the calcification gap should be conservatively smaller than its threshold to maintain plaque stability. The results add new mechanistic insights and methodologically sound data to investigate plaque rupture mechanics.

Conclusion

Structural analysis using a three-dimensional calcified model represents a more realistic simulation of late-stage atherosclerotic plaque. We also demonstrate that increases of calcium content that is coupled with a decrease in lipid core volume can stabilize plaque structurally.     

Factors affecting nest defence in female Canada Geese Branta canadensis

The effect of various characteristics of Canada Goose Branta canadensis females and clutch size on their nest defence intensity during incubation was studied in the field during five nesting seasons. Nests were approached by a human, and the leaving distance was measured. Risk-taking in post-encounter behaviour was categorized at three levels. Nesting success was significantly associated with nest tenacity, a variable derived from leaving distance, but not with post-encounter behaviour. Nest tenacity, as well as post-encounter behaviour, differed significantly between individuals. Intensity of post-encounter behaviour, but not nest tenacity, increased with increasing age of the female. Nest tenacity, standardized over the incubation period, increased with increasing clutch size, but post-encounter behaviour intensity did not. None of the nest defence variables was correlated with the structural size of the female. Nest tenacity, but not post-encounter behaviour intensity, increased during incubation. Nest tenacity did not differ between early and late breeders, but post-encounter behaviour was more intense in late breeders. There was no evidence of positive reinforcement of nest defence through repeated visits. Nest defence did not differ between lakes, lake types or nest site types, nor was it affected by the distance to the nearest neighbouring nest. The results supported several of the predictions extracted from parental investment theory.     

High resolution ultrasound-guided microinjection for interventional studies of early embryonic and placental development in vivo in mice

Background  

In utero microinjection has proven valuable for exploring the developmental consequences of altering gene expression, and for studying cell lineage or migration during the latter half of embryonic mouse development (from embryonic day 9.5 of gestation (E9.5)). In the current study, we use ultrasound guidance to accurately target microinjections in the conceptus at E6.5–E7.5, which is prior to cardiovascular or placental dependence. This method may be useful for determining the developmental effects of targeted genetic or cellular interventions at critical stages of placentation, gastrulation, axis formation, and neural tube closure.     

Food selection, food-seeking patterns and hunting success of captive Goosanders Mergus merganser and Red-breasted Mergansers M. serrator in relation to the behaviour of their prey

Food selection and food-seeking behaviour of hand-raised Goosanders Mergus merganser and Red-breasted Mergansers M. serrator were tested in experimental situations. When different combinations of two species of fish were presented simultaneously to hungry birds in a small trough where the prey was easily and equally available, neither duck species showed any preferences in prey selection. However, when these same fish species were presented to satiated birds, they showed definite preferences; the most preferred species were baltic salmon and brown trout followed in decreasing order by minnow, whitefish, sculpin, burbot and river lamprey. This was also the case when combinations of five to seven species were presented. However, under semi-natural conditions in a stream tank, the number of each species offish caught was related to their escape behaviour, not to the previously determined predator preferences. When salmon and minnows of different size were presented to hungry birds, they selected the larger fish regardless of species. In contrast, when satiated, they preferred small fish over large fish. Under the experimental conditions, the use of certain elements of foraging behaviour clearly differed between the two bird species: Mergus serrator spent more time hunting underwater than did M. merganser. Results are discussed in relation to the predator-prey situation existing under natural conditions in northern Swedish rivers.