Setting Risk-Based Occupational Exposure Limits for No-Threshold Carcinogens

Several regulators have recently issued so-called risk-based occupational exposure limits for carcinogenic substances, and also reported estimates of the risk of fatality that exposure to the limit value would give rise to. This practice provides an opportunity to study how differences in the exposure limits set by different regulators are influenced by differences in the scientific judgment (what is the risk at different levels?) and in the policy judgment (how should large risks be accepted?). Based on a broad search, a list was compiled of exposure limits for carcinogens that the respective regulator associates with a numerical risk estimate. For benzene, such data was available from six regulators. The differences in estimates of the risk/exposure relationship and in risk tolerance were about equal in size for benzene, while the range for acceptability was somewhat wider. A similar pattern was observed, although less clearly, for substances with data from only two or three regulators. It is concluded that the science factor and the policy factor both contribute to differences in exposure limits for carcinogens. It was not possible to judge which of these two factors has the larger influence.     

Determinants of Rad21 localization at the centrosome in human cells

Cohesin proteins help maintain the physical associations between sister chromatids that arise in S-phase and are removed in anaphase. Recent studies found that cohesins also localize to the centrosomes, the organelles that organize the mitotic bipolar spindle. We find that the cohesin protein Rad21 localizes to centrosomes in a manner that is dependent upon known regulators of sister chromatid cohesion as well as regulators of centrosome function. These data suggest that Rad21 functions at the centrosome and that the regulators of Rad21 coordinate the centrosome and chromosomal functions of cohesin.     

The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective

Using profiles of phylogenetic profiles (P-cubic) we compared the evolutionary dynamics of different kinds of functional associations. Ordered from most to least evolutionarily stable, these associations were genes in the same operons, genes whose products participate in the same biochemical pathway, genes coding for physically interacting proteins and genes in the same regulons. Regulons showed the most plastic functional interactions with evolutionary stabilities barely better than those of unrelated genes. Further regulon analyses showed that global regulators contain less evolutionarily stable associations than local regulators. Genes co-repressed by global regulators had a higher evolutionary conservation than genes co-activated by global regulators. However, the reverse was true for genes co-repressed and co-activated by local regulators. Of all the regulon-related associations, the relationship between regulators and their target genes showed the most evolutionary stability. Different negative data sets built to contrast against each of the analysed kinds of modules also differed in evolutionary conservation revealing further underlying genome organization. Applying P-cubic analyses to other genomes might help visualize genome organization, understand the evolutionary importance and plasticity of functional associations and compare the quality of data sets expected to reflect functional interactions, such as those coming from high-throughput experiments.     

Many ways to be small: different environmental regulators of size generate distinct scaling relationships in Drosophila melanogaster

Static allometries, the scaling relationship between body and trait size, describe the shape of animals in a population or species, and are generated in response to variation in genetic or environmental regulators of size. In principle, allometries may vary with the different size regulators that generate them, which can be problematic since allometric differences are also used to infer patterns of selection on morphology. We test this hypothesis by examining the patterns of scaling in Drosophila melanogaster subjected to variation in three environmental regulators of size: nutrition, temperature and rearing density. Our data indicate that different environmental regulators of size do indeed generate different patterns of scaling. Consequently, flies that are ostensibly the same size may have very different body proportions. These data indicate that trait size is not simply a read-out of body size, but that different environmental factors may regulate body and trait size, and the relationship between the two, through different developmental mechanisms. It may therefore be difficult to infer selective pressures that shape scaling relationships in a wild population without first elucidating the environmental and genetic factors that generate size variation among members of the population.     

Low-molecular regulators of polypeptide hormone receptors containing LGR-repeats

During the last years the low-molecular non-peptidic regulators of the polypeptide hormone receptors containing LGR-repeats (LGR-receptors) were identified. The review summarizes and systematizes data on structure and molecular mechanisms realizing the effects of such regulators as agonists and antagonists of the luteinizing, follicle-stimulating and thyroid-stimulating hormones. The regulators interact with the serpentine domain of LGR-receptors and trigger the receptor-coupled signaling cascades. Low-molecular agonists and antagonists of the LGR-receptors are considered as a new generation of drugs that can demonstrate highly sensitive and selective regulation of the functional activity of signaling systems sensitive to pituitary glycoprotein hormones. These regulators are more available than these hormones and can be used orally.     

Molecular Analysis of Arp2/3 Complex Activation in Cells

Many forms of cellular motility are driven by the growth of branched networks of actin filaments, which push against a membrane. In the dendritic nucleation model, Arp2/3 complex is critical, binding to the side of an existing mother filament, nucleating a new daughter filament, and thus creating a branch. Spatial and temporal regulation of Arp2/3 activity is critical for efficient generation of force and movement. A diverse collection of Arp2/3 regulatory proteins has been identified. They bind to and/or activate Arp2/3 complex via an acidic motif with a conserved tryptophan residue. We tested this model for Arp2/3 regulator function in vivo, by examining the roles of multiple Arp2/3 regulators in endocytosis in living yeast cells. We measured the molecular composition of the actin network in cells with mutations that removed the acidic motifs of the four Arp2/3 regulators previously shown to influence the proper function of the actin network. Unexpectedly, we did not find a simple or direct correlation between defects in patch assembly and movement and changes in the composition and dynamics of dendritic nucleation proteins. Taken together our data does not support the simple hypothesis that the primary role for Arp2/3 regulators is to recruit and activate Arp2/3. Rather our data suggests that these regulators may be playing more subtle roles in establishing functional networks in vivo.     

A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition

Patient-specific analysis of molecular networks is a promising strategy for making individual risk predictions and treatment decisions in cancer therapy. Although systems biology allows the gene network of a cell to be reconstructed from clinical gene expression data, traditional methods, such as bayesian networks, only provide an averaged network for all samples. Therefore, these methods cannot reveal patient-specific differences in molecular networks during cancer progression. In this study, we developed a novel statistical method called NetworkProfiler, which infers patient-specific gene regulatory networks for a specific clinical characteristic, such as cancer progression, from gene expression data of cancer patients. We applied NetworkProfiler to microarray gene expression data from 762 cancer cell lines and extracted the system changes that were related to the epithelial-mesenchymal transition (EMT). Out of 1732 possible regulators of E-cadherin, a cell adhesion molecule that modulates the EMT, NetworkProfiler, identified 25 candidate regulators, of which about half have been experimentally verified in the literature. In addition, we used NetworkProfiler to predict EMT-dependent master regulators that enhanced cell adhesion, migration, invasion, and metastasis. In order to further evaluate the performance of NetworkProfiler, we selected Krueppel-like factor 5 (KLF5) from a list of the remaining candidate regulators of E-cadherin and conducted in vitro validation experiments. As a result, we found that knockdown of KLF5 by siRNA significantly decreased E-cadherin expression and induced morphological changes characteristic of EMT. In addition, in vitro experiments of a novel candidate EMT-related microRNA, miR-100, confirmed the involvement of miR-100 in several EMT-related aspects, which was consistent with the predictions obtained by NetworkProfiler.     

The endogenous allosteric regulators of receptors

The literature data devoted to endogenous allosteric regulators of membrane bound receptors are summarized in the present review. The allosteric processes are classified to (i) cooperative interaction, (ii) nonspecific, (iii) functional, and (iv) specific regulations according to target topography in a receptor. The specific endogenous allosteric regulators are described for GABAA, NMDA, muscarinic, nicotinic, serotonin, and opioid receptors. Substances of different chemical structure (peptides, lipids, and polycyclics) are able both to activate or inhibit binding and function of respective receptors. Some pathological processes appear to depend on endogenous receptor modulators. The role of the regulators is speculated in terms of receptor homeostasis, in particular, counteraction of receptor tolerance and/or sensitisation during physiological pulsation in a ligand' level in synaptic cleft.