HP1: facts,open questions,and speculation

The demonstration, over a decade ago, that HP1 is a highly conserved constituent of heterochromatin was accompanied by the explicit view that this protein plays a pivotal role in epigenetic regulation (P.B. Singh, J.R. Miller, J. Pearce, R. Kothary, R.D. Burton, R. Paro, T.C. James, and S.J. Gaunt, 1991, Nucleic Acids Res. 19, 789-794). Recent studies have confirmed this view, unveiling specific interactions of HP1 with a variety of histone and nonhistone proteins. We discuss here some of these observations, concentrating on structure-function relationships and intracellular dynamics. Integrating the available information, we also present a hypothetical model describing how HP1, acting as a bifunctional cross-linker, could organize peripheral heterochromatin and contribute in the compartmentalization of the cell nucleus.     

Technical and Policy Challenges in Developing and Implementing Risk-Based Environmental Regulations

The reform in environmental regulations being considered at both federal and state levels is intended to enhance the value and effectiveness of a rule by incorporating risk assessment and cost benefit analysis in the rule making process or regulatory implementation. Although a risk based approach may not provide a panacea to all environmental problem solving, it offers some obvious advantages over the status quo. In particular, it establishes a scientifically defensible basis for evaluating the trade off between risks, costs and benefits in making prudent environmental decisions and developing effective regulatory policies. This paper presents a conceptual framework for risk reduction, summarizes the current status in risk-based legislation at the federal level, provides examples of how various states are using risk based approaches in their regulatory programs, addresses aspects of technical and policy challenges in rule making and other policy and enforcement decisions and provides suggestions for meeting these challenges.     

A morphometric approach to the geographic variation of the terrestrial isopod species Armadillo tuberculatus (Isopoda: Oniscidea)

The terrestrial isopod species Armadillo tuberculatus Vogl, 1876 (Crustacea, Isopoda, Oniscidea) is a widely polymorphic species distributed in the south-central Aegean region (Greece) with a different morph on each island. Variation consists in coloration, size of cuticular tubercules, shape of telson and the shape of the male first pleopod exopodite (secondary sexual character of taxonomic importance). We studied the allometric growth of a cuticular tubercule in 17 populations (for both male and female individuals) and the shape variation of the first male pleopod exopodite in 10 populations using Elliptic Fourier Analysis, in order to test for patterns of intraspecific variation and possible relationships between morphs. In addition, Thin Plate Spline analysis was used for the calculation of the minimum bending energy between different exopodite shapes, which was then used for estimating the minimum spanning network (MSN) connecting them. The different allometric growth rates of the tubercule among island groups were significantly related to island latitude and climatic factors. On the other hand, the clustering of islands and the MSN based on male exopodite shape differences were not related to the palaeogeography of the Aegean region or to the present geographic distances of islands. These results are interpreted as evidence for non-adaptive radiation of the morphs.     

Abacavir-Reactive Memory T Cells Are Present in Drug Na?ve Individuals

BackgroundFifty-five percent of individuals with HLA-B*57:01 exposed to the antiretroviral drug abacavir develop a hypersensitivity reaction (HSR) that has been attributed to naïve T-cell responses to neo-antigen generated by the drug. Immunologically confirmed abacavir HSR can manifest clinically in less than 48 hours following first exposure suggesting that, at least in some cases, abacavir HSR is due to re-stimulation of a pre-existing memory T-cell population rather than priming of a high frequency naïve T-cell population.MethodsTo determine whether a pre-existing abacavir reactive memory T-cell population contributes to early abacavir HSR symptoms, we studied the abacavir specific naïve or memory T-cell response using HLA-B*57:01 positive HSR patients or healthy controls using ELISpot assay, intra-cellular cytokine staining and tetramer labelling.ResultsAbacavir reactive CD8+ T-cell responses were detected in vitro in one hundred percent of abacavir unexposed HLA-B*57:01 positive healthy donors. Abacavir-specific CD8+ T cells from such donors can be expanded from sorted memory, and sorted naïve, CD8+ T cells without need for autologous CD4+ T cells.ConclusionsWe propose that these pre-existing abacavir-reactive memory CD8+ T-cell responses must have been primed by earlier exposure to another foreign antigen and that these T cells cross-react with an abacavir-HLA-B*57:01-endogenous peptide ligand complex, in keeping with the model of heterologous immunity proposed in transplant rejection.     

Microbial transformation of pentachloronitrobenzene under nitrate reducing conditions

The effect of pentachloronitrobenzene (PCNB) on denitrification was assessed with two denitrifying cultures (PCNB-free control and PCNB-acclimated) developed from a contaminated estuarine sediment. PCNB was transformed to pentachloroaniline (PCA) in the PCNB-acclimated culture repeatedly amended with 0.1 μM PCNB, but further dechlorination or degradation of PCA was not observed for almost 1 year. The effect of PCNB on denitrification was also investigated with the PCNB-free control culture. PCNB at an initial concentration of 13 μM was transformed to PCA simultaneously with nitrate reduction but only after the nitrate concentration was at or below 20 mg N/l. PCNB addition at an initial concentration of 13 μM to the control denitrifying culture developed as PCNB-free culture resulted in a transient accumulation of nitric oxide (NO) and nitrous oxide (N₂O). Similarly to the PCNB-acclimated culture, PCNB transformation to PCA started when the nitrate concentration decreased to about 20 mg N/l. A low degree of nitro group removal resulting in the formation of pentachlorobenzene (PeCB) was also observed in the control culture when amended with 13 μM PCNB. Further transformation or degradation of PCA was not observed in all cultures maintained under active nitrate reducing conditions. Based on the results of this study, the presence of nitrate at low concentrations in anoxic/anaerobic soil and sediments is not expected to negatively affect the biotransformation of PCNB to PCA, but dechlorination or degradation of PCA is not expected under active nitrate reducing conditions.     

Crossing paths with Notch in the hyper-network

The development of complex and diverse metazoan morphologies is coordinated by a surprisingly small number of evolutionarily conserved signaling mechanisms. These signals can act in parallel but often appear to function as an integrated hyper-network. The nodes defining this complex molecular circuitry are poorly understood, but the biological significance of pathway cross-talk is profound. The importance of such large-scale signal integration is exemplified by Notch and its ability to cross-talk with all the major pathways to influence cell differentiation, proliferation, survival and migration. The Notch pathway is, thus, a useful paradigm to illustrate the complexity of pathway cross-talk: its pervasiveness, context dependency, and importance in development and disease.     

Inhibin secretion in women with the polycystic ovary syndrome before and after treatment with progesterone

Objectives  

It has been suggested that inhibin secretion is altered in women with the polycystic ovary syndrome (PCOS). However, the contribution of a preceding luteal phase has not been taken into account. The aim of the present study was to investigate whether progesterone in the context of a simulated luteal phase affects basal and FSH-induced inhibin secretion in women with PCOS and elevated LH.     

Literature mining, ontologies and information visualization for drug repurposing

The immense growth of MEDLINE coupled with the realization that a vast amount of biomedical knowledge is recorded in free-text format, has led to the appearance of a large number of literature mining techniques aiming to extract biomedical terms and their inter-relations from the scientific literature. Ontologies have been extensively utilized in the biomedical domain either as controlled vocabularies or to provide the framework for mapping relations between concepts in biology and medicine. Literature-based approaches and ontologies have been used in the past for the purpose of hypothesis generation in connection with drug discovery. Here, we review the application of literature mining and ontology modeling and traversal to the area of drug repurposing (DR). In recent years, DR has emerged as a noteworthy alternative to the traditional drug development process, in response to the decreased productivity of the biopharmaceutical industry. Thus, systematic approaches to DR have been developed, involving a variety of in silico, genomic and high-throughput screening technologies. Attempts to integrate literature mining with other types of data arising from the use of these technologies as well as visualization tools assisting in the discovery of novel associations between existing drugs and new indications will also be presented.