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.     

Bud dormancy and vegetative growth in Salix polaris as affected by temperature and photoperiod

Summary Vegetative growth of two ecotypes (lat. 78° 15N and 69°37N) of Salix polaris L. was studied in phytotron experiments. Dormancy of the winter buds was broken by chilling at 0.5°C for 14 to 42 days. Chilling requirement increased with decreasing growth temperature. The optimum temperature for bud break and shoot growth was about 15°C for both ecotypes. Cessation of apical shoot growth and abscission of shoot tip was not prevented by long photoperiods. However, at high temperature, 15°C or more, and in 18 to 24 h photoperiod, two or three growth flushes occurred frequently in both ecotypes. Leaf abscission in the arctic ecotype from lat. 78°N was not affected by photoperiod when grown at 6°C, but was stimulated by short photoperiod when grown at 15°C. In the ecotype from lat. 69°N leaf abscission was enhanced by short photoperiod even at 6°C.     

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.     

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.     

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.     

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.     

Effective size in management and conservation of subdivided populations

A numerical method for computing the eigenvalue variance effective size of a subdivided population connected by any fixed pattern of migration is described. Using specific examples it is shown that total effective size of a subdivided population can become less than the sum of the subpopulation sizes as a result of directionalities in the pattern of migration. For an extension of the model with threshold harvesting and local deterministic logistic population dynamic we consider the problem of maximizing the total harvesting yield with constraints on the total effective size. For some simple source-sink systems and more complicated population structures where subpopulations differ in their degree of isolation, it is shown to be optimal, for a given total effective size, to raise the harvesting thresholds relatively more in small and in isolated populations. Finally, we show how the method applies to populations which are supplemented, either intentionally or unintentionally. It is shown that the total effective size can be reduced by several orders of magnitude if the captive component of a population is much smaller than the wild component, even with symmetric backward migration.     

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.     

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.     

Preoperative mannan-binding lectin pathway and prognosis in colorectal cancer

Purpose: Deficiency of the mannan-binding lectin (MBL) pathway of innate immunity is associated with increased susceptibility to infections. In patients with colorectal cancer (CRC), postoperative infection is associated with poor prognosis. The aim of the present study was to evaluate (1) the relation between the MBL pathway and postoperative infectious complications and survival of patients resected for CRC, and (2) the role of MBL in acute phase response compared to C-reactive protein (CRP). Methods: Preoperative MBL concentration, MBL-associated serine protease (MBL/MASP) activity and CRP were determined in serum from 611 patients and 150 healthy controls. The patients were observed for 8 years. Postoperative infections, recurrence and survival were recorded. Results: The MBL pathway components were increased in the patients compared with the healthy controls (p<0.0001). Low MBL levels were predictive of pneumonia (p=0.01), and pneumonia (n=87) was associated with poor survival (p=0.003; HR=1.5; 95% CI, 1.1 to 1.9). MBL and MBL/MASP activity showed no correlation with CRP (Spearmans =0.02; 95% CI, –0.06 to 0.10). Conclusion: Low preoperative MBL levels are predictive of pneumonia, which is associated with poorer survival. MBL concentration and MBL/MASP activity was not predictive of other postoperative infections or long-term prognosis, and showed no correlation with CRP.