Accuracy of body mass estimates of formalin-preserved fish – a review

This paper highlights possible effects of physical and chemical mechanisms of formalin fixation and preservation on biological tissue and reviews the consequent potential inaccuracies on estimates of body mass of small fishes fixed and preserved in formalin. Twenty-six papers including 65 independent experiments with 35 species which examine effects of formalin on body mass estimates on small fishes are included. The effect of the formalin on the specimens depends on the salinity of the water used to dilute the commercial formalin (usually 1:9 formalin: water) before being used to fixate and preserve fish. Mean wet body mass of the specimens from the studies using seawater or fresh water diluted formalin deceases by 13% and increases by 7%, respectively, from before to after being immersed in formalin. The same trend is found with condition factor in the few papers that report this parameter. Body length decreases on average by c. 2% in fixated and preserved fish regardless of whether the formalin is diluted in seawater or fresh water.     

Estimating the variation,autocorrelation, and environmental sensitivity of phenotypic selection

Despite considerable interest in temporal and spatial variation of phenotypic selection, very few methods allow quantifying this variation while correctly accounting for the error variance of each individual estimate. Furthermore, the available methods do not estimate the autocorrelation of phenotypic selection, which is a major determinant of eco‐evolutionary dynamics in changing environments. We introduce a new method for measuring variable phenotypic selection using random regression. We rely on model selection to assess the support for stabilizing selection, and for a moving optimum that may include a trend plus (possibly autocorrelated) fluctuations. The environmental sensitivity of selection also can be estimated by including an environmental covariate. After testing our method on extensive simulations, we apply it to breeding time in a great tit population in the Netherlands. Our analysis finds support for an optimum that is well predicted by spring temperature, and occurs about 33 days before a peak in food biomass, consistent with what is known from the biology of this species. We also detect autocorrelated fluctuations in the optimum, beyond those caused by temperature and the food peak. Because our approach directly estimates parameters that appear in theoretical models, it should be particularly useful for predicting eco‐evolutionary responses to environmental change.     

Winter climate change: Ice encapsulation at mild subfreezing temperatures kills freeze-tolerant lichens

While it has been widely proven that many lichens are extremely freeze-tolerant in the dry state, little is known about how moist lichens respond to freezing under oxic and anoxic conditions. In circumpolar areas where lichens are an important component of boreal and Arctic ecosystems, winter climate is changing, leading to increased frequency of winter thaw and ground-icing events. It is imperative to elucidate in further detail how northern vegetation responds to being encapsulated in ice. A winter icing simulation experiment was therefore undertaken, encapsulating two reindeer lichens (Cladonia stellaris and Cladonia rangiferina) and two epiphytic lichens (Parmeliopsis ambigua and Melanohalea olivacea) in ice at temperatures just below freezing for a maximum period of 98 d. Photosynthetic and chlorophyll fluorescence rates decreased strongly, clearly suggesting that the algal partner of the lichens was dying. Low but detectable respiration rates indicate that the fungal partner maintained some physiological activity. Ethanol accumulated in the lichens during ice encapsulation as a result of anaerobic respiration. The algae probably were dying from a combination of depletion of carbon reserves and toxic levels of ethanol and other stress metabolites. This experiment shows that boreal and Arctic-alpine lichens are sensitive to a warmer and more fluctuating winter climate. Increasing frequency of winter icing events may therefore have extensive and hitherto unknown effects on lichen-dominated ecosystems, their herbivores and the indigenous peoples whose livelihoods largely depend on them.     

Data fusion in metabolomic cancer diagnostics

We have recently shown that fluorescence spectroscopy of plasma samples has promising abilities regarding early detection of colorectal cancer. In the present paper, these results were further developed by combining fluorescence with the biomarkers, CEA and TIMP-1 and traditional metabolomic measurements in the form of ¹H NMR spectroscopy. The results indicate that using an extensive profile established by combining such measurements together with the biomarkers is better than using single markers.     

A new sorediate,fumarprotocetraric acid‐producing lichen species of Menegazzia (Parmeliaceae,Ascomycota) from New Zealand

A new sorediate lichen, Menegazzia hypernota Bjerke, is described from New Zealand. This new species is characterised by convex, crescent‐shaped to fabi‐form soralia that are occasionally associated with perforations; apothecia with 2‐spored asci; the small perforations; the numerous secondary lobules; the presence of inconspicuous, yellow spots in the internal cavity; and fumarprotocetraric acid as principal medullary constituent. Menegazzia caliginosa, a species associated with M. hypernota, is reported for the first time from the Auckland Islands.     

Effects of gradual expansign on arterial stenosis

The blood flow through an arterial stenosis can theoretically be increased by gradual expansion of the stenosis. This hypothesis was tested by comparing the flow through abruptly expanding and gradually expanding stenosed plastic conduits. The conduits were tested in non-pulsatile flow with water and bank blood and in pulsatile flow in dog's descending aorta. It was found that:

1. (a)
   The pressure drop in arterial stenoses is larger than that predicted by non-pulsatile theory.     

Alignment-independent comparisons of human gastrointestinal tract microbial communities in a multidimensional 16S rRNA gene evolutionary space

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities.     

House-level risk factors associated with the colonization of broiler flocks with Campylobacter spp. in Iceland, 2001 – 2004

Background

The most predominant beta2-integrin lymphocyte function-associated antigen-1 (LFA-1, CD11a/CD18, alphaLbeta2), expressed on all leukocytes, is essential for many adhesive functions of the immune system. Interestingly, RTX toxin-producing bacteria specifically target this leukocyte beta2-integrin which exacerbates lesions and disease development.

Results

This study reports the sequencing of the wild boar beta2-integrin CD11a and CD18 cDNAs. Predicted CD11a and CD18 subunits share all the main structural characteristics of their mammalian homologues, with a larger interspecies conservation for the CD18 than the CD11a. Besides these strong overall similarities, wild boar and domestic pig LFA-1 differ by 2 (CD18) and 1 or 3 (CD11a) substitutions, of which one is located in the crucial I-domain (CD11a, E168D).

Conclusion

As most wild boars are seropositive to the RTX toxin-producing bacterium Actinobacillus pleuropneumoniae and because they have sustained continuous natural selection, future studies addressing the functional impact of these polymorphisms could bring interesting new information on the physiopathology of Actinobacillus pleuropneumoniae-associated pneumonia in domestic pigs.