Human lymphoblastoid cell lines secreting antibodies with restricted HLA specificity

Peripheral B lymphocytes obtained from three healthy individuals who had been immunized against peripheral blood lymphocytes from appropriate HLA-incompatible donors were transformed by the use of Epstein-Barr virus. The transformed blastoid B cells were repeatedly subcultured by means of cluster picking, and the HLA antibody-producing cultures were identified by testing the culture supernatants by means of the cytotoxicity assay, using the corresponding donor cells. Thus far, four cell lines that secrete cytotoxic HLA antibodies (MP1, 3, 4, and 5) have been established. Specific immunoabsorption experiments revealed that the antibody activity is carried by lambda-type IgM for MP1, by kappa-type IgM for MP3 and MP5, and by both for MP4. Specificity analysis of a panel of HLA-pretyped cells indicated that MP1 detects DQw2, whereas MP5 recognizes B7. The specificity of MP3 was similar to a DQ specificity termed DC5 (probably equivalent to TA10) but not the same. In the case of MP4, both of the lambda-type and kappa-type antibodies appeared to be directed toward new HLA class 11 determinants.Abbreviations used in this paper HLA human major histocompatibility - EBV Epstein-Barr virus - B-LCL Blymphoblastoid cell line - NA not absorbed - PBS phosphate-buffered saline - SPA Sepharose protein A - NRS normal rabbit serum     

Thaimycins,new anthelmintic and antiprotozoal antibiotics produced by Streptomyces michiganensis var. amylolyticus var. nova

Summary A new microorganism, isolated in our laboratories and identified as Streptomyces michiganensis var. amylolyticus var. nova is described.Thaimycins can be obtained by submerged fermentation of this microorganism on a suitable culture medium.Three new related compounds, thaimycins A, B and C have been obtained and characterized by their physical and chemical properties.Data on the antiprotozoal and anthelmintic activities in vitro as well as in vivo are reported.     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Serum IgE reactivity profiling in an asthma affected cohort

Background

Epidemiological evidence indicates that atopic asthma correlates with high serum IgE levels though the contribution of allergen specific IgE to the pathogenesis and the severity of the disease is still unclear.

Methods

We developed a microarray immunoassay containing 103 allergens to study the IgE reactivity profiles of 485 asthmatic and 342 non-asthmatic individuals belonging to families whose members have a documented history of asthma and atopy. We employed k-means clustering, to investigate whether a particular IgE reactivity profile correlated with asthma and other atopic conditions such as rhinitis, conjunctivitis and eczema.

Results

Both case-control and parent-to-siblings analyses demonstrated that while the presence of specific IgE against individual allergens correlated poorly with pathological conditions, particular reactivity profiles were significantly associated with asthma (p<10E-09). An artificial neural network (ANN)-based algorithm, calibrated with the profile reactivity data, correctly classified as asthmatic or non-asthmatic 78% of the individual examined. Multivariate statistical analysis demonstrated that the familiar relationships of the study population did not affect the observed correlations.

Conclusions

These findings indicate that asthma is a higher-order phenomenon related to patterns of IgE reactivity rather than to single antibody reactions. This notion sheds new light on the pathogenesis of the disease and can be readily employed to distinguish asthmatic and non-asthmatic individuals on the basis of their serum reactivity profile.     

Genetic similarity of flag shoot and ascospore subpopulations of Erysiphe necator in Italy

The overwintering mode of the grape powdery mildew fungus, Erysiphe necator (syn. Uncinula necator), as mycelium in dormant buds (resulting in symptoms known as flag shoots) or as ascospores in cleistothecia, affects the temporal dynamics of epidemics early in the growing season. We tested whether distinct genetic groups (I and III) identified previously in E. necator correlate to overwintering modes in two vineyards in Tuscany, Italy, to determine whether diagnostic genetic markers could be used to predict overwintering. Samples from one vineyard were collected from flag shoots; the other vineyard, 60 km away, had no flag shoots, and mildew colonies were assumed to be derived from ascospores. Genetic markers putatively diagnostic for groups I and III showed that both types were common in the flag shoot subpopulation. Both genetic types were found in the ascospore population, although group III was dominant. We did not find strong genetic differentiation between the two subpopulations based on inter-simple sequence repeat markers. Although there was significant (P < 0.001) genetic differentiation between these subpopulations in 1997 and when 1997 and 1998 subpopulations were pooled (theta = 0.214 and 0.150, respectively), no differentiation was evident between vineyards in 1998 (theta = 0.138, P = 0.872). Moreover, we did not observe distinct lineages corresponding to overwintering modes, as observed in previous studies. We could not determine if differentiation resulted from biological differences or restricted gene flow between the two vineyards. Our samples were taken from both subpopulations early in the epidemic, while previous studies confounded overwintering mode and sampling time. These results do not support a strong correlation between overwintering and genetic groups, highlighting the need to base population biology studies on sound biological and epidemiological knowledge.     

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.     

Effects of Hydraulic Soil Properties on Vegetation Pattern Formation in Sloping Landscapes

Current models of vegetation pattern formation rely on a system of weakly nonlinear reaction–diffusion equations that are coupled by their source terms. While these equations, which are used to describe a spatiotemporal planar evolution of biomass and soil water, qualitatively capture the emergence of various types of vegetation patterns in arid environments, they are phenomenological and have a limited predictive power. We ameliorate these limitations by deriving the vertically averaged Richards’ equation to describe flow (as opposed to “diffusion”) of water in partially saturated soils. This establishes conditions under which this nonlinear equation reduces to its weakly nonlinear reaction–diffusion counterpart used in the previous models, thus relating their unphysical parameters (e.g., diffusion coefficient) to the measurable soil properties (e.g., hydraulic conductivity) used to parameterize the Richards equation. Our model is valid for both flat and sloping landscapes and can handle arbitrary topography and boundary conditions. The result is a model that relates the environmental conditions (e.g., precipitation rate, runoff and soil properties) to formation of multiple patterns observed in nature (such as stripes, labyrinth and spots).     

Modelling tissues in 3D: the next future of pharmaco-toxicology and food research?

The development and validation of reliable in vitro methods alternative to conventional in vivo studies in experimental animals is a well-recognised priority in the fields of pharmaco-toxicology and food research. Conventional studies based on two-dimensional (2-D) cell monolayers have demonstrated their significant limitations: the chemically and spatially defined three-dimensional (3-D) network of extracellular matrix components, cell-to-cell and cell-to-matrix interactions that governs differentiation, proliferation and function of cells in vivo is, in fact, lost under the simplified 2-D condition. Being able to reproduce specific tissue-like structures and to mimic functions and responses of real tissues in a way that is more physiologically relevant than what can be achieved through traditional 2-D cell monolayers, 3-D cell culture represents a potential bridge to cover the gap between animal models and human studies. This article addresses the significance and the potential of 3-D in vitro systems to improve the predictive value of cell-based assays for safety and risk assessment studies and for new drugs development and testing. The crucial role of tissue engineering and of the new microscale technologies for improving and optimising these models, as well as the necessity of developing new protocols and analytical methods for their full exploitation, will be also discussed.