Spatial proximity of translocation-prone gene loci in human lymphomas

Cancer cells frequently have disease-specific chromosome rearrangements. It is poorly understood why translocations between chromosomes recur at specific breakpoints in the genome. Here we provide evidence that higher-order spatial genome organization is a contributing factor in the formation of recurrent translocations. We show that MYC, BCL and immunoglobulin loci, which are recurrently translocated in various B-cell lymphomas, are preferentially positioned in close spatial proximity relative to each other in normal B cells. Loci in spatial proximity are non-randomly positioned towards the nuclear interior in normal B cells. This locus proximity is the consequence of higher-order genome structure rather than a property of individual genes. Our results suggest that the formation of specific translocations in human lymphomas, and perhaps other tissues, is determined in part by higher-order spatial organization of the genome.     

Contributions of microbial biofilms to ecosystem processes in stream mesocosms

In many aquatic ecosystems, most microbes live in matrix-enclosed biofilms and contribute substantially to energy flow and nutrient cycling. Little is known, however, about the coupling of structure and dynamics of these biofilms to ecosystem function. Here we show that microbial biofilms changed the physical and chemical microhabitat and contributed to ecosystem processes in 30-m-long stream mesocosms. Biofilm growth increased hydrodynamic transient storage-streamwater detained in quiescent zones, which is a major physical template for ecological processes in streams-by 300% and the retention of suspended particles by 120%. In addition, by enhancing the relative uptake of organic molecules of lower bioavailability, the interplay of biofilm microarchitecture and mass transfer changed their downstream linkage. As living zones of transient storage, biofilms bring hydrodynamic retention and biochemical processing into close spatial proximity and influence biogeochemical processes and patterns in streams. Thus, biofilms are highly efficient and successful ecological communities that may also contribute to the influence that headwater streams have on rivers, estuaries and even oceans through longitudinal linkages of local biogeochemical and hydrodynamic processes.     

Morphological changes to Escherichia coli O157:H7, commensal E. coli and Salmonella spp in response to marginal growth conditions,with special reference to mildly stressing temperatures

Certain rod-shaped bacteria have been reported to form elongated filamentous cells when exposed to marginal growth conditions, including refrigeration temperatures. To expand upon these observations, the filamentation of commensal Escherichia coli, E. coli O157:H7 and Salmonella spp was investigated, following exposure to certain, mildly stressing, levels of temperature, pH or water activity (aw), with levels of cellular protein being monitored during cell elongation, in some experiments. Our studies indicated that cellular filamentation could be demonstrated in all 15 strains of the above organisms tested, following exposure to marginal conditions achieved by incubation at high or low temperatures, high or low pH values and low aw. The level of environmental stress causing filamentation tended to be specific to the particular organisms. For example, Salmonella spp formed filamentous cells at 44 degrees C, whereas E. coli strains, including O157, grew by binary fission at that temperature, but formed filamentous cells at 46 degrees C. In addition, plate count techniques to enumerate bacteria during filamentation, failed to reflect the increase in cell biomass that was occurring, whereas measurements of protein concentration demonstrated the increase quite strikingly. These findings have important implications for our understanding of the ability of food-borne pathogens to cause disease, since the infectious dose of a microorganism implicated in an outbreak of such disease is typically determined by a viable count method, which could underestimate the number of potential infectious units present in a food that had been stored in such a way as to provide marginal growth conditions.     

Distribution of some similarity coefficients for dyadic binary data in the case of associated attributes

Parameters are derived of distributions of three coefficients of similarity between pairs (dyads) of operational taxonomic units for multivariate binary data (presence/absence of attributes) under statistical independence. These are applied to test independence for dyadic data. Association among attributes within operational taxonomic units is allowed. It is also permissible for the two units in the dyad to be drawn from different populations having different presence probabilities of attributes. The variance of the distribution of the similarity coefficients under statistical independence is shown to be relatively large in many empirical situations. This result implies that the practical interpretation of these coefficients requires much care. An application using the Jaccard index is given for the assessment of consensus between psychotherapists and their clients.

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La distribution des coefficients de similarité pour les données binaires et les attributs associés

Résumé Les paramètres de la distribution de trois coefficients de similarité entre paires d'éléments taxinomiques opérationels de données multivariables binaires (présence/absence) ont été dérivés dans l'hypothèse d'indépendance statistique. Ces paramètres sont utilisés dans un test d'indépendance pour les données dyadiques. L'existence est autorisée, dans la population d'éléments, d'une association entre plusieurs attributs. Il est également permis que les deux éléments de la dyade soient tirés de deux populations différentes, ayant différentes probabilit és quant à la présence des attributs. Dans beaucoup de situations empiriques, la variance des coefficients de similarité peut être relativement élevée dans le cas d'indépendance statistique. Par conséquence, ces coefficients doivent être interprétés avec précaution. Un exemple est donné pour le coefficient de Jaccard, qui a été employé dans une recherche sur la concordance entre des psychothérapeutes et leurs clients.

     

Estimation and Prediction for Stochastic Blockmodels for Graphs with Latent Block Structure

a posteriori blockmodeling for graphs is proposed. The model assumes that the vertices of the graph are partitioned into two unknown blocks and that the probability of an edge between two vertices depends only on the blocks to which they belong. Statistical procedures are derived for estimating the probabilities of edges and for predicting the block structure from observations of the edge pattern only. ML estimators can be computed using the EM algorithm, but this strategy is practical only for small graphs. A Bayesian estimator, based on the Gibbs sampling, is proposed. This estimator is practical also for large graphs. When ML estimators are used, the block structure can be predicted based on predictive likelihood. When Gibbs sampling is used, the block structure can be predicted from posterior predictive probabilities. A side result is that when the number of vertices tends to infinity while the probabilities remain constant, the block structure can be recovered correctly with probability tending to 1.