The canonical NF-kappaB pathway is required for formation of luminal mammary neoplasias and is activated in the mammary progenitor population.

The role of the canonical NF-kappaB pathway in mammary tumorigenesis was investigated using a transgenic (TG) mouse expressing a dominant-negative inhibitor of kappaB (IkappaBalpha(SR (S32A/S36A))) in the mammary gland under the control of the mouse mammary tumor virus promoter (MMTV). TG and control mice were subjected to a chemical carcinogenesis protocol. Hyperkeratinized squamous metaplasias (cytokeratin-6+/p63+) sometimes with a basaloid island component, were found in both TG and control mice whereas luminal (cytokeratin-19+/MUC1+) ErbB2+ papillary and adenomatous lesions developed almost exclusively in control mice. p65/RelA- and NF-kappaB DNA-binding activity were detected in mammary luminal lesions, but rarely in squamous metaplasias. Analysis of NF-kappaB family proteins and target genes using microarray data from a cohort of human mammary tumors revealed the expression of a canonical NF-kappaB pathway, but not non-canonical pathway proteins in HER2+ luminal cancers. HER2+ tumors also showed differential regulation of specific NF-kappaB target genes relative to basal and ER+ luminal cancers. Isolation of mammary cell populations enriched for stem and progenitor cell characteristics from an NF-kappaB-EGFP reporter mouse by fluorescence-activated cell sorting demonstrated that luminal progenitors contain activated NF-kappaB whereas the mammary stem cell-enriched population, does not. Together these data suggest that the canonical NF-kappaB pathway is active in normal luminal progenitor cells before transformation and is required for the formation of mammary luminal-type epithelial neoplasias.

Protein repeats: structures, functions, and evolution.

Internal repetition within proteins has been a successful strategem on multiple separate occasions throughout evolution. Such protein repeats possess regular secondary structures and form multirepeat assemblies in three dimensions of diverse sizes and functions. In general, however, internal repetition affords a protein enhanced evolutionary prospects due to an enlargement of its available binding surface area. Constraints on sequence conservation appear to be relatively lax, due to binding functions ensuing from multiple, rather than, single repeats. Considerable sequence divergence as well as the short lengths of sequence repeats mean that repeat detection can be a particularly arduous task. We also consider the conundrum of how multiple repeats, which show strong structural and functional interdependencies, ever evolved from a single repeat ancestor. In this review, we illustrate each of these points by referring to six prolific repeat types (repeats in beta-propellers and beta-trefoils and tetratricopeptide, ankyrin, armadillo/HEAT, and leucine-rich repeats) and in other less-prolific but nonetheless interesting repeats.

XplorMed: a tool for exploring MEDLINE abstracts.

The most frequent access to the MEDLINE database of scientific abstracts is by keyword search. However, this is often not sufficient because although the user might find all the useful abstracts, these are buried in hundreds that are irrelevant. The exploratory tool XplorMed has been developed to analyse the result of any MEDLINE query. It suggests main groups of related topics and documents, sparing the user the need of reading all abstracts.

Coexistence of multiple propagating wave-fronts in a regulated enzyme reaction model: link with birhythmicity and multi-threshold excitability.

We analyze the spatial propagation of wave-fronts in a biochemical model for a product-activated enzyme reaction with non-linear recycling of product into substrate. This model was previously studied as a prototype for the coexistence of two distinct types of periodic oscillations (birhythmicity). The system is initially in a stable steady state characterized by the property of multi-threshold excitability, by which it is capable of amplifying in a pulsatory manner perturbations exceeding two distinct thresholds. In such conditions, when the effect of diffusion is taken into account, two distinct wave-fronts are shown to propagate in space, with distinct amplitudes and velocities, for the same set of parameter values, depending on the magnitude of the initial perturbation. Such a multiplicity of propagating wave-fronts represents a new type of coexistence of multiple modes of dynamic behavior, besides the coexistence involving, under spatially homogeneous conditions, multiple steady states, multiple periodic regimes, or a combination of steady and periodic regimes.

Network organization of cell metabolism: monosaccharide interconversion.

The structural properties of carbohydrate metabolism are being studied. The present contribution focuses mainly on those processes involving the transfer of carbon fragments among sugars. It is shown how enzymatic activities fix the way the system self-organizes stoichiometrically at the steady state. It is proven that there exists a specific correspondence between the set of all possible enzymic activities, the activity set, and the set of stoichiometrically compatible flux distributions through the pathway. On the one hand, there are enzymic activities that do not allow a stoichiometrically feasible coupling at the steady state of the reactions involved in the conversion. On the other hand, there are enzymic activities that are related to one or more flux distributions at the steady state (i.e. with one or several rate vectors respectively). For this latter group, it can be demonstrated that the structure of the system depends on other non-structural factors, such as boundary constraints and the kinetic parameters. As a consequence, it is suggested that this kind of metabolic process must be viewed as a complex reaction network instead of a sequential number of steps. Some implications of these derivations are illustrated for the particular conversion of CO2 --> C3. General remarks are also discussed within the framework of network models of cell metabolism.