Changes in activation sequence of embryonic chick atria correlate with developing myocardial architecture

To characterize developmental changes in impulse propagation within atrial musculature, we performed high-speed optical mapping of activation sequence of the developing chick atria using voltage-sensitive dye. The activation maps were correlated with detailed morphological studies using scanning electron microscopy, histology, and whole mount confocal imaging with three-dimensional reconstruction. A preferential pathway appeared during development within the roof of the atria, transmitting the impulse rapidly from the right-sided sinoatrial node to the left atrium. The morphological substrate of this pathway, the bundle of Bachman, apparent from stage 29 onward, was a prominent ridge of pectinate muscles continuous with the terminal crest. Further acceleration of impulse propagation was noted along the ridges formed by the developing pectinate muscles, ramifying from the terminal crest toward the atrioventricular groove. In contrast, when the impulse reached the interatrial septum, slowing was often observed, suggesting that the septum acts as a barrier or sink for electrical current. We conclude that these inhomogeneities in atrial impulse propagation are consistent with existence of a specialized network of fast-conducting tissues. The purpose of these preferential pathways appears to be to assure synchronous atrial activation and contraction rather than rapid impulse conduction between the sinoatrial and atrioventricular nodes.     

On the potential of fatty acids as trophic markers in Arctic grazers: feeding experiments with sea urchins and amphipods fed nine diets of macroalgae

To elucidate dietary preferences of benthic grazers at the Arctic Kongsfjorden by means of fatty acid trophic markers, ten different parallel treatments (starvation, 3 species of red macroalgae, 4 species of brown macroalgae and 2 species of green macroalgae) were offered as mono-algal diet to specimens of the dominant sea urchin Strongylocentrotus droebachiensis (Echinodermata, Echinoidea) and the gammarid amphipod Gammarellus homari (Crustacea, Amphipoda). At the end of the 3-week feeding experiments, amphipods and sea urchins (soft tissue) were deep-frozen and analysed for total lipid contents as well as fatty acid (FA) compositions. In addition, FA profiles of the algal species were determined and screened for specific FA patterns or single FAs qualifying as potential trophic markers in the grazers. Despite their diets of nine algal species with different FA compositions, FA patterns of the sea urchins and amphipods revealed a pronounced similarity between treatments. This strong similarity was also observed in the faecal pellets of the sea urchins. Hence, deviating FA compositions of the macroalgae were neither reflected in the FA patterns of the grazers’ tissue nor in their faecal pellets. Suitable algal FA trophic markers could thus not be identified in the two grazers from Kongsfjorden. The rather low lipid levels, especially in the amphipods, as well as a pronounced degradation and modification of FAs may explain that the FA trophic marker approach did not provide evidence of dietary preferences. Future experiments may obtain a higher resolution of potential FA trophic markers by analysing separate lipid classes or single tissues of lipid-poor grazers. Alternatively, different methods are needed to reveal high-resolution trophic relationships between macroalgae and herbivores in Kongsfjorden.     

A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer

Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer.     

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

p53 and p19(ARF) are tumor suppressors frequently mutated in human tumors. In a high-throughput screen in mice for mutations collaborating with either p53 or p19(ARF) deficiency, we identified 10,806 retroviral insertion sites, implicating over 300 loci in tumorigenesis. This dataset reveals 20 genes that are specifically mutated in either p19(ARF)-deficient, p53-deficient or wild-type mice (including Flt3, mmu-mir-106a-363, Smg6, and Ccnd3), as well as networks of significant collaborative and mutually exclusive interactions between cancer genes. Furthermore, we found candidate tumor suppressor genes, as well as distinct clusters of insertions within genes like Flt3 and Notch1 that induce mutants with different spectra of genetic interactions. Cross species comparative analysis with aCGH data of human cancer cell lines revealed known and candidate oncogenes (Mmp13, Slamf6, and Rreb1) and tumor suppressors (Wwox and Arfrp2). This dataset should prove to be a rich resource for the study of genetic interactions that underlie tumorigenesis.     

ClC-3 and IClswell are required for normal neutrophil chemotaxis and shape change

Polymorphonuclear leukocytes undergo directed movement to sites of infection, a complex process known as chemotaxis. Extension of the polymorphonuclear leukocyte (PMN) leading edge toward a chemoattractant in association with uropod retraction must involve a coordinated increase/decrease in membrane, redistribution of cell volume, or both. Deficits in PMN phagocytosis and trans-endothelial migration, both highly motile PMN functions, suggested that the anion transporters, ClC-3 and ICl(swell), are involved in cell motility and shape change ( Moreland, J. G., Davis, A. P., Bailey, G., Nauseef, W. M., and Lamb, F. S. (2006) J. Biol. Chem. 281, 12277-12288 ). We hypothesized that ClC-3 and ICl(swell) are required for normal PMN chemotaxis through regulation of cell volume and shape change. Using complementary chemotaxis assays, EZ-TAXIScantrade mark and dynamic imaging analysis software, we analyzed the directed cell movement and morphology of PMNs lacking normal anion transporter function. Murine Clcn3(-/-) PMNs and human PMNs treated with anion transporter inhibitors demonstrated impaired chemotaxis in response to formyl peptide. This included decreased cell velocity and failure to undergo normal cycles of elongation and retraction. Impaired chemotaxis was not due to a diminished number of formyl peptide receptors in either murine or human PMNs, as measured by flow cytometry. Murine Clcn3(-/-) and Clcn3(+/+) PMNs demonstrated a similar regulatory volume decrease, indicating that the ICl(swell) response to hypotonic challenge was intact in these cells. We further demonstrated that ICl(swell) is essential for shape change during human PMN chemotaxis. We speculate that ClC-3 and ICl(swell) have unique roles in regulation of PMN chemotaxis; ICl(swell) through direct effects on PMN volume and ClC-3 through regulation of ICl(swell).     

Testing the potential seed availability in dung samples: comparison of two seedling emergence methods

To optimize the estimation of species composition and viable seed content of herbivore faeces and to make different approaches comparable, two seedling emergence methods are evaluated. The Ter Heerdt method (TH) employs concentrated samples, potentially increasing and accelerating seedling emergence, as shown for soil samples (95% of all seedlings emerged within 6 weeks). Samples are kept under controlled conditions (glasshouse or climate room). Secondly, a common garden method (CG) using unconcentrated samples so that seasonal changes could fulfill the germination requirements of a broad species spectrum (experiment duration approximately 15 months) was applied. The methods were tested by the use of sheep faeces samples, collected during a six-day grazing period in a threatened dry grassland (Allio-Stipetum capillatae).Both methods proved largely similar in species composition (QS=0.81) and viable seed content (QS=0.69). More species (e.g. monocotyls) and a higher seedling emergence of hard-seeded species (Fabaceae and Cistaceae) were found in the CG method. Besides a higher emergence of some small-seeded winter annuals, few other species emerged exclusively by use of the TH method. Nevertheless, all species detected by only one method were found in low individual numbers (4).Depending on research interest and availability of space and time, the most appropriate method can be chosen. If the main focus is on the species composition, unconcentrated faeces samples can be studied by CG. In case the overall viable seed content is more important and/or a shorter time period is available, TH serves as a suitable alternative.     

Trans-Uterine Tracer Injections in Mammalian Foetuses

Intra-uterine manipulation of mammalian foetuses for experimental purposes was first described at the beginning of this century (Wolff, 1919). Though numerous publications have appeared since which bear witness to the feasibility of intra-uterine manipulation, its application has remained rather restricted. In this paper we describe a technique for the trans-uterine injection of neuronal tracers into rat foetuses. Uterine wall and foetal membranes are pierced only with a micro pipette, and are thus left virtually intact, preventing loss of amniotic fluid. Surgical mortality is 24% overall, but the experimental success rate is much lower (23%). Even so these results are comparable to more complicated procedures, because the technique is simple (i.e. requires no micro surgical skill), and because up to 6 foetuses can be injected per dam. Technical problems, such as foetal anaesthesia and the detection of false-negative results due to imponderable factors are discussed.