Interactions between surfactants and silver nanoparticles of varying charge.

The interaction between silver nanoparticles (Ag NPs) of different surface charge and surfactants relevant to the laundry cycle has been investigated to understand changes in speciation, both in and during transport from the washing machine. Ag NPs were synthesized to exhibit either a positive or a negative surface charge in solution conditions relevant for the laundry cycle (pH 10 and pH 7). These particles were characterized in terms of size and surface charge and compared to commercially laser ablated Ag NPs. The surfactants included anionic sodium dodecylbenzenesulfonate (LAS), cationic dodecyltrimethylammoniumchloride (DTAC) and nonionic Berol 266 (Berol). Surfactant-Ag NP interactions were studied by means of dynamic light scattering, Raman spectroscopy, zeta potential, and Quartz Crystal Microbalance. Mixed bilayers of CTAB and LAS were formed through a co-operative adsorption process on positively charged Ag NPs with pre-adsorbed CTAB, resulting in charge reversal from positive to negative zeta potentials. Adsorption of DTAC on negatively charged synthesized Ag NPs and negatively charged commercial Ag NPs resulted in bilayer formation and charge reversal. Weak interactions were observed for nonionic Berol with all Ag NPs via hydrophobic interactions, which resulted in decreased zeta potentials for Berol concentrations above its critical micelle concentration. Differences in particle size were essentially not affected by surfactant adsorption, as the surfactant layer thicknesses did not exceed more than a few nanometers. The surfactant interaction with the Ag NP surface was shown to be reversible, an observation of particular importance for hazard and environmental risk assessments.

Neonatal mortality and morbidity in extremely preterm small for gestational age infants: a population based study.

AIM: To assess if growth restricted (small for gestational age, SGA) extremely preterm infants have excess neonatal mortality and morbidity. METHODS: This was a cohort study of all infants born alive at 22-27 weeks' post menstrual age in Norway during 1999-2000. Outcomes were compared between those who were SGA, defined as a birth weight less than the fifth percentile for post menstrual age, and those who had weights at or above the fifth percentile. RESULTS: Of 365 infants with a post menstrual age of <28 weeks, 31 (8%) were SGA. Among infants with a post menstrual age of <28 weeks, only chronic lung disease was associated with SGA status (OR 2.7, 95% CI 1.0 to 7.2). SGA infants with a post menstrual age of 26-27 weeks had excess neonatal mortality (OR 3.8, 95% CI 1.3 to 11), chronic lung disease and a significantly higher mean number of days (age) before tolerating full enteral nutrition. SGA infants with a post menstrual age of 22-25 weeks had an excess risk of necrotising enterocolitis. CONCLUSION: Extremely preterm SGA infants had excess neonatal mortality and morbidity in terms of necrotising enterocolitis and chronic lung disease.

Uranium colloid analysis by single particle inductively coupled plasma-mass spectrometry.

Uranium single particle analysis has been performed by inductively coupled plasma-mass spectrometry (ICP-MS) and the performances are compared with that provided by scanning electron microscopy and single particle counting. The transient signal induced by the flash of ions due to the ionisation of an uranium colloidal particle in the plasma torch can be detected and measured for selected uranium ion masses ((238)U(+), (235)U(+) or (254)[(238)U(16)O](+)) by the mass spectrometer. The signals recorded via time scanning are analysed as a function of particle size or fraction of the studied element or isotope in the colloid phase. The frequency of the flashes is directly proportional to the concentration of particles in the colloidal suspension. The feasibility tests were performed on uranium dioxide particles. The study also describes the experimental conditions and the choice of mass to detect uranium colloids in a single particle analysis mode.

Three-block bi-focal PLS (3BIF-PLS) and its application in QSAR.

When X and Y are multivariate, the two-block partial least squares (PLS) method is often used. In this paper, we outline an extension addressing a special case of the three-block (X/Y/Z) problem, where Z sits "under" Y. We have called this approach three-block bi-focal PLS (3BIF-PLS). It views the X/Y relationship as the dominant problem, and seeks to use the additional information in Z in order to improve the interpretation of the Y-part of the X/Y association. Two data sets are used to illustrate 3BIF-PLS. Example I relates to single point mutants of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 and their ability to transform halogenated hydrocarbons, some of which are found as organic pollutants in soil. Example II deals with soil remediation capability of bacteria. Whole bacterial communities are monitored over time using "DNA-fingerprinting" technology to see how pollution affects population composition. Since the data sets are large, hierarchical multivariate modelling is invoked to compress data prior to 3BIF-PLS analysis. It is concluded that the 3BIF-PLS approach works well. The paper contains a discussion of pros and cons of the method, and hints at further developmental opportunities.

Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors.

A library of thrombin inhibitors has been designed using statistical molecular design. An aromatic scaffold was used, with three varied positions corresponding to three pockets at the active site of thrombin (the S-, P-, and D-pockets). The selection was performed in the building block space, and previously acquired data were included in the design procedure. The design resulted in six, four, and six building blocks for the first (S), second (P), and third (D) pockets, respectively. A second round of selection applied to the combined selected building blocks resulted in a subset of 18 compounds. The selected library was synthesized in parallel and biologically evaluated. The compounds were analyzed with respect to their inhibition (pIC(50)) of thrombin; membrane permeability, estimated by migration behavior in micellar media (CE log k') and pK(a); and specificity with respect to inhibition (K(i)) of trypsin. Multivariate QSAR studies of the responses yielded valuable results and information that could only be found using statistical molecular design in combination with multivariate analysis.

The Escherichia coli SeqA protein binds specifically to two sites in fully and hemimethylated oriC and has the capacity to inhibit DNA replication and affect chromosome topology.

The SeqA protein was identified as a factor that prevents reinitiation of newly replicated, hemimethylated origins. SeqA also seems to inhibit initiation of fully methylated origins, thus contributing to the regulation of chromosomal replication. The SeqA protein was found to bind to two sites in the left part of the origin, near the AT-rich region where strand separation takes place during initiation of replication. The same binding sites seemed to be preferred irrespective of whether the origin was in the newly replicated (hemimethylated) state or not. In addition to binding specifically to groups of GATC sites, the SeqA protein was capable of interacting non-specifically with negatively supercoiled DNA, restraining the supercoils in a fashion similar to that seen with histone-like protein HU. The restraint of supercoils by SeqA was, in contrast to that of HU, cooperative.

Statistical molecular design of building blocks for combinatorial chemistry.

The reduction of the size of a combinatorial library can be made in two ways, either base the selection on the building blocks (BB's) or base it on the full set of virtually constructed products. In this paper we have investigated the effects of applying statistical designs to BB sets compared to selections based on the final products. The two sets of BB's and the virtually constructed library were described by structural parameters, and the correlation between the two characterizations was investigated. Three different selection approaches were used both for the BB sets and for the products. In the first two the selection algorithms were applied directly to the data sets (D-optimal design and space-filling design), while for the third a cluster analysis preceded the selection (cluster-based design). The selections were compared using visual inspection, the Tanimoto coefficient, the Euclidean distance, the condition number, and the determinant of the resulting data matrix. No difference in efficiency was found between selections made in the BB space and in the product space. However, it is of critical importance to investigate the BB space carefully and to select an appropriate number of BB's to result in an adequate diversity. An example from the pharmaceutical industry is then presented, where selection via BB's was made using a cluster-based design.

New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids.

In this study 87 amino acids (AA.s) have been characterized by 26 physicochemical descriptor variables. These descriptor variables include experimentally determined retention values in seven thin-layer chromatography (TLC) systems, three nuclear magnetic resonance (NMR) shift variables, and 16 calculated variables, namely six semiempirical molecular orbital indices, total, polar, and nonpolar surface area, van der Waals volume of the side chain, log P, molecular weight, and four indicator variables describing hydrogen bond donor and acceptor properties, and side chain charge. In the present study, the data from a previous characterization of 55 AA.s from our laboratory have been extended with data for 32 additional AA.s and 14 new descriptor variables. The new 32 AA.s were selected to represent both intermediate and more extreme physicochemical properties, compared to the 20 coded AA.s. The new extended and updated principal property scales, the z-scales, were calculated and aligned to previously reported z(old)-scales. The appropriateness of the extended z-scales were validated by the use in quantitative sequence-activity modeling (QSAM) of 89 elastase substrate analogues and in a QSAM of 29 neurotensin analogues.

Effects of purified SeqA protein on oriC-dependent DNA replication in vitro.

In vivo studies suggest that the Escherichia coli SeqA protein modulates replication initiation in two ways: by delaying initiation and by sequestering newly replicated origins from undergoing re-replication. As a first approach towards understanding the biochemical bases for these effects, we have examined the effects of purified SeqA protein on replication reactions performed in vitro on an oriC plasmid. Our results demonstrate that SeqA directly affects the biochemical events occurring at oriC. First, SeqA inhibits formation of the pre-priming complex. Secondly, SeqA can inhibit replication from an established pre-priming complex, without disrupting the complex. Thirdly, SeqA alters the dependence of the replication system on DnaA protein concentration, stimulating replication at low concentrations of DnaA. Our data suggest that SeqA participates in the assembly of initiation-competent complexes at oriC and, at a later stage, influences the behaviour of these complexes.

Statistical molecular design of peptoid libraries.

Statistical experimental design provides an efficient approach for selecting the building blocks to span the structural space and increase the information content in a combinatorial library. A set of renin-inhibitors, hexapeptoids, is used to illustrate the approach. Multivariate quantitative structure-activity relationships (MQSARs) were developed relating renin inhibition to the peptoid sequences variation, parametrized by the z-scales. By using the information from the models, the number of building block sets could be reduced from six to three. Using a statistical molecular design (SMD) reduces the number of compounds from more than 100,000 down to 90. A second SMD was used for comparison, based on less prior knowledge. This gave a reduction from over 2 billion to 120 compounds.

Septic shock in pregnancy associated with legionella pneumonia: case report.

We report the first case of legionella infection in pregnancy complicated by sepsis and hemodynamic compromise. Legionnaires' disease is rarely found in pregnancy, possibly because subacute infections may often be overlooked and empiric therapy of pneumonia in pregnancy may be curative without definitive etiologic diagnosis.

Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA.

Three categories of molecular flexibility are defined. A novel method of aligning partly flexible molecules with each other is described. The binding mode of one of these molecules to its receptor site was already well known from previous crystallographic studies, and this known binding mode was used to predict the binding mode of the other molecules at their receptor. The predictions were checked by comparison with previous observations, and were correct. Two novel methods were combined in this research. It was necessary to take account of the conformational changes which occur when each ligand molecule binds to the protein, and a new release of programme Grid was used for this. It was also necessary to analyse the Grid results in order to distinguish the role of each chemical group at the receptor site. This was done by applying hierarchical principal component analysis (Hi-PCA) methods to the descriptors obtained from Grid.

The Escherichia coli Fis protein prevents initiation of DNA replication from oriC in vitro.

Fis protein participates in the normal control of chromosomal replication in Escherichia coli. However, the mechanism by which it executes its effect is largely unknown. We demonstrate an inhibitory influence of purified Fis protein on replication from oriC in vitro. Fis inhibits DNA synthesis equally well in replication systems either dependent upon or independent of RNA polymerase, even when the latter is stimulated by the presence of HU or IHF. The extent of inhibition by Fis is modulated by the concentrations of DnaA protein and RNA polymerase; the more limiting the amounts of these, the more severe the inhibition by Fis. Thus, the level of inhibition seems to depend on the ease with which the open complex can be formed. Fis-mediated inhibition of DNA replication does not depend on a functional primary Fis binding site between DnaA boxes R2 and R3 in oriC, as mutations that cause reduced binding of Fis to this site do not affect the degree of inhibition. The data presented suggest that Fis prevents formation of an initiation-proficient structure at oriC by forming an alternative, initiation-preventive complex. This indicates a negative role for Fis in the regulation of replication initiation.

The speed of the Escherichia coli fork in vivo depends on the DnaB:DnaC ratio.

The DnaC protein is required for loading the DnaB helicase at oriC. Thus DnaC promotes the formation of the pre-replication complex, but must leave the complex in order for the DnaB protein to function as a helicase. In vitro, a slight excess of DnaC inhibits the movement of replication forks by inhibiting DnaB helicase activity (Allen and Kornberg, 1991). Here we show that inhibition of DNA replication by excess DnaC also occurs in vivo. The rate of replication-fork movement was measured by flow cytometry. Initiation of replication was inhibited with rifampicin and the rate of fork movement monitored during replication runout by measuring the increase in the fraction of the cell population with fully replicated chromosomes. The replication rate was inversely related to the amount of excess DnaC protein. Initiation of replication was also inhibited. Co-overexpression of DnaB protein alleviated the inhibition of replication caused by moderate excess of DnaC. The results show that DnaC interacts with replication forks during elongation in vivo, probably by binding to DnaB and inhibiting its helicase activity. Therefore, the ratio of DnaC to DnaB and the affinity of DnaC for a helicase hexamer at an established replication fork are of great importance for the rate of replication fork movement also in vivo.

E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration.

The seqA gene negatively modulates replication initiation at the E. coli origin, oriC. seqA is also essential for sequestration, which acts at oriC and the dnaA promoter to ensure that replication initiation occurs exactly once per chromosome per cell cycle. Initiation is promoted by full methylation of GATC sites clustered in oriC; sequestration is specific to the hemimethylated forms generated by replication. SeqA protein purification and DNA binding are described. SeqA interacts with fully methylated oriC strongly and specifically. This reaction requires multiple molecules of SeqA and determinants throughout oriC, including segments involved in open complex formation. SeqA interacts more strongly with hemimethylated DNA; in this case, oriC and non-oriC sequences are bound similarly. Also, binding of hemimethylated oriC by membrane fractions is due to SeqA. Direct interaction of SeqA protein with the replication origin is likely to be involved in both replication initiation and sequestration.

The initiation mass for DNA replication in Escherichia coli K-12 is dependent on growth rate.

It is widely accepted that the initiation mass of Escherichia coli is constant and independent of growth rate, and therefore is an important parameter in the regulation of initiation of DNA replication. We have used flow cytometry to measure the initiation mass of E. coli K-12 cells as a function of growth rate. The average initiation mass was determined by two methods: (i) from a mathematical relationship between average cell mass, cell age at initiation and number of origins present in the cells, and (ii) directly from the cell mass distribution. The light scattering signal from individual cells and the protein content per cell were employed as measures of cell mass. The initiation mass was found to increase monotonically with decreasing growth rate, being 1.6 times higher (light scattering) or 2.1 times higher (protein content) at 0.3 than at 2.5 doublings per hour. We conclude that the initiation mass is dependent on growth rate. This finding indicates that the control for timing of initiation is not governed by a direct connection between mass accumulation and the molecule(s) determining initiation of replication.

In vivo therapeutic efficacy of cefdinir (FK482), a new oral cephalosporin, against Staphylococcus aureus and Haemophilus influenzae in mouse infection models.

Cefdinir (FK482), a new oral cephalosporin, displayed potent oral activity versus induced infections in mice. In studies using beta-lactamase-nonproducing (beta LAC-) and -producing (beta LAC+) Staphylococcus aureus strains, respective PD50s (in mg/kg) were 11 and 24 for preventing subcutaneous abscess and 2.7 and 2.3 for preventing lethal systemic infection. In studies using beta LAC- and beta LAC+ Haemophilus influenzae, respective PD50s were 5.8 and 3.1 for preventing lethal systemic infection. Time-kill studies versus H. influenzae showed that 6- to 12-mg/kg dosing was effective in reducing viable counts of these strains in blood by > or = 100-fold by 24 h after challenge. This in vivo performance was comparable to or exceeded values generated by cefaclor, cefpodoxime proxetil, and ampicillin.