Small-molecule inhibitors of bacterial AddAB and RecBCD helicase-nuclease DNA repair enzymes

The AddAB and RecBCD helicase-nucleases are related enzymes prevalent among bacteria but not eukaryotes and are instrumental in the repair of DNA double-strand breaks and in genetic recombination. Although these enzymes have been extensively studied both genetically and biochemically, inhibitors specific for this class of enzymes have not been reported. We developed a high-throughput screen based on the ability of phage T4 gene 2 mutants to grow in Escherichia coli only if the host RecBCD enzyme, or a related helicase-nuclease, is inhibited or genetically inactivated. We optimized this screen for use in 1536-well plates and screened 326,100 small molecules in the NIH molecular libraries sample collection for inhibitors of the Helicobacter pylori AddAB enzyme expressed in an E. coli recBCD deletion strain. Secondary screening used assays with cells expressing AddAB or RecBCD and a viability assay that measured the effect of compounds on cell growth without phage infection. From this screening campaign, 12 compounds exhibiting efficacy and selectivity were tested for inhibition of purified AddAB and RecBCD helicase and nuclease activities and in cell-based assays for recombination; seven were active in the 0.1-50 μM range in one or another assay. Compounds structurally related to two of these were similarly tested, and three were active in the 0.1-50 μM range. These compounds should be useful in further enzymatic, genetic, and physiological studies of these enzymes, both purified and in cells. They may also lead to useful antibacterial agents, since this class of enzymes is needed for successful bacterial infection of mammals.     

Isolation and characterization of mouse and human esophageal epithelial cells in 3D organotypic culture

This protocol describes the isolation and characterization of mouse and human esophageal epithelial cells and the application of 3D organotypic culture (OTC), a form of tissue engineering. This model system permits the interrogation of mechanisms underlying epithelial-stromal interactions. We provide guidelines for isolating and cultivating several sources of epithelial cells and fibroblasts, as well as genetic manipulation of these cell types, as a prelude to their integration into OTC. The protocol includes a number of important applications, including histology, immunohistochemistry/immunofluorescence, genetic modification of epithelial cells and fibroblasts with retroviral and lentiviral vectors for overexpression of genes or RNA interference strategies, confocal imaging, laser capture microdissection, RNA microarrays of individual cellular compartments and protein-based assays. The OTC (3D) culture protocol takes 15 d to perform.     

Characterization of a Bacillus subtilis 64-kDa DNA polymerase X potentially involved in DNA repair

Bacillus subtilis gene yshC encodes a 64-kDa family X DNA polymerase (PolXBs), which contains all the critical residues involved in DNA and nucleotide binding as well as those responsible for catalysis of DNA polymerization, conserved in most family X members. Biochemical analyses of the purified enzyme indicate that PolXBs is a monomeric and strictly template-directed DNA polymerase, preferentially acting on DNA structures containing gaps from one to a few nucleotides and bearing a phosphate group at the 5' end of the downstream DNA. The fact that PolXBs is able to conduct filling of a single-nucleotide gap, allowing further sealing of the resulting nick by a DNA ligase, points to a putative role in base excision repair during the B. subtilis life cycle.     

Genetic races associated with the genera and sections of host species in the holoparasitic plant Cytinus (Cytinaceae) in the Western Mediterranean basin

* Speciation via race formation is an important evolutionary process in parasites, producing changes that favour their development on particular host species. Here, the holoparasitic plant Cytinus, which has diverse host species in the family Cistaceae, has been used to study the occurrence of such races. * Amplified fragment length polymorphism (AFLP) analyses were performed on 174 individuals of 22 populations parasitizing 10 Cistaceae species in the Western Mediterranean basin. * Neighbour-joining, multivariate ordination analyses, and individual-based Bayesian analyses, clustered Cytinus populations into five well-characterized genetic races that, overall, agreed with the taxonomic sections of their hosts. In the AMOVA, among-races differences accounted for almost 50% of the genetic variation. The isolation-by-distance model was not supported by a Mantel test among Cytinus populations (r = 0.012; P = 0.456). All races showed low within-population genetic diversity, probably as a result of restricted pollen flow aggravated by flowering asynchrony, restricted seed dispersion, or stochastic processes. * The genetic differentiation among the five races of Cytinus is congruent with the view that these races are well-characterized lineages that have evolved independently as a result of selective pressures imposed by their hosts. This pattern, with genetically distinctive groups associated with the infrageneric sections of the host species, has not been reported previously for parasitic angiosperms.     

“Fluorescent glycogen” formation with sensibility for <Emphasis Type="Italic">in vivo</Emphasis> and <Emphasis Type="Italic">in vitro</Emphasis> detection

There are presently many methods of detecting complex carbohydrates, and particularly glycogen. However most of them require radioisotopes or destruction of the tissue and hydrolysis of glycogen to glucose. Here we present a new method based on the incorporation of 2-NBDG (2-{N-[7-nitrobenz-2-oxa-1, 3-diazol 4-yl] amino}-2-deoxyglucose), a D-glucose fluorescent derivative, into glycogen. Two kinds of approaches were carried out by using Clone 9 rat hepatocytes as a cellular model; (1) Incubation of cell lysates with 2-NBDG, carbohydrate precipitation in filters and measurement of fluorescence in a microplate reader (2) Incubation of living hepatocytes with 2-NBDG and recording of fluorescence images by confocal microscopy. 2-NBDG labeled glycogen in both approaches. We confirmed this fact by comparison to the labeling obtained with a specific monoclonal anti-glycogen antibody. Also drugs that trigger glycogen synthesis or degradation induced an increase or decrease of fluorescence, respectively. This is a simple but efficient method of detecting glycogen with 2-NBDG. It could be used to record changes in glycogen stores in living cells and cell-free systems and opens the prospect of understanding the role of this important energy reserve under various physiological and pathophysiological conditions.     

An ensemble model for predicting Rhopalosiphum padi abundance

A novel modeling method is proposed to predict the abundance of the main vector of barley yellow dwarf virus in autumn sown cereal crops. An ensemble model based on artificial neural networks (ANN) was developed to predict the number of Rhopalosiphum padi (L.) (Homoptera: Aphididae) caught in traps during the autumn flight period at Lincoln, Canterbury, New Zealand, over the period 1982–2003. Artificial neural networks were trained using historical weather data and aphid data collected from a suction trap. Model results were compared with those obtained using multiple regression (MR) models using the same independent variables. Both ANN and MR models were validated by leave‐one‐out validation, in other words, by sequentially jackknifing each year out of the data set, fitting a model to the remaining data, then using that model to predict the number of aphids for each jackknifed year. A linear ensemble of ANN models further improved the predictions and represented the trends in the number of aphids over the 22‐year period very well. The r² between the predicted and observed numbers of aphids for the ANN models changed from 0.68 to 0.83 using the linear ensemble model, but the ensemble approach did not change the prediction for the MR models. The absolute mean error (ABSME) of prediction was much lower for the ANN ensemble predictions compared to that for the MR models. The ABMSE for the ANN models dropped from 109 to 86 aphids compared to an ABMSE reduction from 245 to 220 aphids for the MR models. We discuss the potential for ensemble models for predicting insect abundance when long‐term historical data are available.     

Evaluation of quantitative models of the effect of insulin on lipolysis and glucose disposal

The effects of insulin on the suppression of lipolysis are neither fully understood nor quantified. We examined a variety of mathematical models analogous to the minimal model of glucose disposal (MMG) to quantify the combined influence of insulin on lipolysis and glucose disposal during an insulin-modified frequently sampled intravenous glucose tolerance test. The tested models, which include two previously published ones, consisted of separate compartments for plasma free fatty acids (FFA), glucose, and insulin. They differed in the number of compartments and in the action of insulin to suppress lipolysis that decreased the plasma FFA level. In one category of models, a single insulin compartment acted on both glucose and FFA simultaneously. In a second category, there were two insulin compartments, each acting on FFA and glucose independently. For each of these two categories, we tested 11 variations of how insulin suppressed lipolysis. We also tested a model with an additional glucose compartment that acted on FFA. These 23 models were fit to the plasma FFA and glucose concentrations of 102 subjects individually. Using Bayesian model comparison methods, we selected the model that best balanced fit and minimized model complexity. In the best model, insulin suppressed lipolysis via a Hill function through a remote compartment that acted on both glucose and FFA simultaneously, and glucose dynamics obeyed the classic MMG.     

Pulping cardoon (Cynara cardunculus) with peroxyformic acid (MILOX) in one single stage

In this work, depithed cardoon stalk (Cynara cardunculus) has been used with the objective of obtaining bleachable pulps. The material, once properly prepared, was subjected to one-step peroxyformic acid delignification. In order to study the process, a face-centred second order factorial design was developed which allowed the determination of the influences of four variables: concentrations of formic acid and hydrogen peroxide in the cooking liquor and the time and temperature of the treatment.

Empirical mathematical models have been obtained which predict the yield, kappa index, residual lignin content, and viscosity of the pulps. These models demonstrate that in general the delignification was extensive, producing pulps with kappa indexes less than 25 in the majority of cases, with good yields in the range of 45–60%. However, the pulps seem to have been degraded in the reaction media, as can be deduced from the low viscosity values found: 260–520 mL/g.