OMERO: flexible, model-driven data management for experimental biology

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.     

Habitat quality and connectivity in agricultural landscapes: The role of land use systems at various scales in time

Connectivity is a key concept of landscape ecology as it relates to flows and movements of organisms as driven by landscape structure. More and more aspects of landscape heterogeneity are considered in measuring connectivity, as the diversity of crops in agricultural landscapes. In this paper, we explored the value of considering changes and cumulated effects of connectivity over time. As an example, we analysed connectivity among patches influenced by maize over 7 years in an agricultural landscape in Brittany, France.Clear temporal patterns appeared: maize is concentrated in certain parts of the landscape, but over the period the whole area, 70% of the landscape, used for maize was connected. Instead of discrete patches, maize may produce large clusters allowing movement from patch to patch from year to year. This reinforces the importance of understanding land use allocation rules within farms and landscapes to evaluate the ecological effects of agriculture.     

Anatomy of flower and fruit of <i>Vassobia breviflora</i> (Solanaceae) in the south of the southern Yungas (Argentina)

Solanaceae is a family with nearly 2400 species of cosmopolitan distribution. Vassobia breviflora is the only species of the genus present in Argentina. The goal of this work was to review and characterize the anatomy of the flower and fruit of V. breviflora from samples collected in populations of Yungas in the argentine Northwest. Conventional anatomical techniques were applied. The results showed that most flower, fruit and seed structures did not differ from those previously reported regarding the structural organization described for other species of the Solanaceae family. However, for the first time, we described the androecium, fruit, seed, floral and fruit pedicels, five types of tricomes and five types of stomata in the perianth. We found some differences in the shape of the transmission tissue and in the type of ovule with respect to that previously reported. Also, we located the parenchyma and the epidermic secretory cells of the nectary. In the context of the family Solanaceae, we discussed the function and diagnostic value of the described structures.     

Prediction uncertainty of environmental change effects on temperate European biodiversity

Observed patterns of species richness at landscape scale (gamma diversity) cannot always be attributed to a specific set of explanatory variables, but rather different alternative explanatory statistical models of similar quality may exist. Therefore predictions of the effects of environmental change (such as in climate or land cover) on biodiversity may differ considerably, depending on the chosen set of explanatory variables. Here we use multimodel prediction to evaluate effects of climate, land-use intensity and landscape structure on species richness in each of seven groups of organisms (plants, birds, spiders, wild bees, ground beetles, true bugs and hoverflies) in temperate Europe. We contrast this approach with traditional best-model predictions, which we show, using cross-validation, to have inferior prediction accuracy. Multimodel inference changed the importance of some environmental variables in comparison with the best model, and accordingly gave deviating predictions for environmental change effects. Overall, prediction uncertainty for the multimodel approach was only slightly higher than that of the best model, and absolute changes in predicted species richness were also comparable. Richness predictions varied generally more for the impact of climate change than for land-use change at the coarse scale of our study. Overall, our study indicates that the uncertainty introduced to environmental change predictions through uncertainty in model selection both qualitatively and quantitatively affects species richness projections.     

Dichotomy of AML1-ETO Functions: Growth Arrest versus Block of Differentiation

The fusion gene AML1-ETO is the product of t(8;21)(q22;q22), one of the most common chromosomal translocations associated with acute myeloid leukemia. To investigate the impact of AML1-ETO on hematopoiesis, tetracycline-inducible AML1-ETO-expressing cell lines were generated using myeloid cells. AML1-ETO is tightly and strongly induced upon tetracycline withdrawal. The proliferation of AML1-ETO(+) cells was markedly reduced, and most of the cells eventually underwent apoptosis. RNase protection assays revealed that the amount of Bcl-2 mRNA was decreased after AML1-ETO induction. Enforced expression of Bcl-2 was able to significantly delay, but not completely overcome, AML1-ETO-induced apoptosis. Prior to the onset of apoptosis, we also studied the ability of AML1-ETO to modulate differentiation. AML1-ETO expression altered granulocytic differentiation of U937T-A/E cells. More significantly, this change of differentiation was associated with the down-regulation of CCAAT/enhancer binding protein alpha (C/EBPalpha), a key regulator of granulocytic differentiation. These observations suggest a dichotomy in the functions of AML1-ETO: (i) reduction of granulocytic differentiation correlated with decreased expression of C/EBPalpha and (ii) growth arrest leading to apoptosis with decreased expression of CDK4, c-myc, and Bcl-2. We predict that the preleukemic AML1-ETO(+) cells must overcome AML1-ETO-induced growth arrest and apoptosis prior to fulfilling their leukemogenic potential.     

Adaptation of Cryo‐Sectioning for IEM Labeling of Asymmetric Samples: A Study Using Caenorhabditis elegans

Cryo‐sectioning procedures, initially developed by Tokuyasu, have been successfully improved for tissues and cultured cells, enabling efficient protein localization on the ultrastructural level. Without a standard procedure applicable to any sample, currently existing protocols must be individually modified for each model organism or asymmetric sample. Here, we describe our method that enables reproducible cryo‐sectioning of Caenorhabditis elegans larvae/adults and embryos. We have established a chemical‐fixation procedure in which flat embedding considerably simplifies manipulation and lateral orientation of larvae or adults. To bypass the limitations of chemical fixation, we have improved the hybrid cryo‐immobilization–rehydration technique and reduced the overall time required to complete this procedure. Using our procedures, precise cryo‐sectioning orientation can be combined with good ultrastructural preservation and efficient immuno‐electron microscopy protein localization. Also, GFP fluorescence can be efficiently preserved, permitting a direct correlation of the fluorescent signal and its subcellular localization. Although developed for C. elegans samples, our method addresses the challenge of working with small asymmetric samples in general, and thus could be used to improve the efficiency of immuno‐electron localization in other model organisms.      

Functional landscape heterogeneity and animal biodiversity in agricultural landscapes

Biodiversity in agricultural landscapes can be increased with conversion of some production lands into 'more-natural'- unmanaged or extensively managed - lands. However, it remains unknown to what extent biodiversity can be enhanced by altering landscape pattern without reducing agricultural production. We propose a framework for this problem, considering separately compositional heterogeneity (the number and proportions of different cover types) and configurational heterogeneity (the spatial arrangement of cover types). Cover type classification and mapping is based on species requirements, such as feeding and nesting, resulting in measures of 'functional landscape heterogeneity'. We then identify three important questions: does biodiversity increase with (1) increasing heterogeneity of the more-natural areas, (2) increasing compositional heterogeneity of production cover types and (3) increasing configurational heterogeneity of production cover types? We discuss approaches for addressing these questions. Such studies should have high priority because biodiversity protection globally depends increasingly on maintaining biodiversity in human-dominated landscapes.     

Colorimetric detection of residual quaternary ammonium compounds on dry surfaces and prediction of antimicrobial activity using bromophenol blue

Controlling and monitoring the residual activity of quaternary ammonium compounds (QACs) are critical for maintaining safe yet effective levels of these agents in the environment. This study investigates the utility of bromophenol blue (BPB) as a safe, rapid and user-friendly indicator to detect in situ residual QACs dried on hard, non-porous surfaces, as well a means to assess their antimicrobial efficacy. At pH 7, BPB has a purple colour which turns blue upon its complexation with QACs such as didecyldimethylammonium chloride (DDAC). BPB itself has no antimicrobial properties up to 400 ppm. Within the range of 0–400 ppm, BPB colour change was tied to specific DDAC antimicrobial performances with a detection threshold of 100 ppm. BPB concentration and application volume could be adjusted such that a colour shift from purple to blue correlated with a set percent reduction (>99·9%) in test bacteria (Staphylococcus aureus and Klebsiella aerogenes). The BPB solutions developed in this study yielded similar colour shifts on polycarbonate and stainless steel surfaces and did not cross-react with chemical ingredients commonly found in sanitizers and disinfectant products. Overall, this study suggests that BPB provides a simple solution to safely monitor the post-application level and biocidal activity of residual dried QACs on surfaces.     

Expression of the alpha 1-proteinase inhibitor gene family during evolution of the genus Mus

alpha 1-Proteinase inhibitors (alpha 1-PIs) are members of the serpin superfamily of proteinase inhibitors, and are important in the maintenance of homeostasis in a wide variety of animal taxa. Previous studies have shown that in mice (genus Mus), evolution of alpha 1-PIs is characterized by gene amplification, region-specific concerted evolution, and rapid accumulation of amino acid substitutions. The latter occurs primarily in the reactive center, which is the region of the alpha 1-PI molecule that determines the inhibitor's specificity for target proteinases. The P1 residue within the reactive center, which is methionine in so-called orthodox alpha 1-PIs and an amino acid other than methionine in unorthodox alpha 1-PIs, is a primary determinant of inhibitor specificity. In the present study, we find that the expression of mRNAs encoding unorthodox alpha 1-PIs is polymorphic within Mus species, i.e., among individuals or inbred strains. This is in striking contrast to mRNAs that encode orthodox alpha 1-PIs, whose concentrations are relatively invariant. The intraspecies variations in mRNA expression represent polymorphisms in the structure of the alpha 1- PI gene family. The results, taken together with previously described aspects of alpha 1-PI evolution, indicate that the dissimilar levels of polymorphism exhibited by orthodox and unorthodox alpha 1-PIs, which likely have distinct physiological functions, may reflect different levels of selective constraint. The significance of this finding to the evolution of gene families is discussed.