Design, synthesis and biological evaluation of potent NAD+-dependent DNA ligase inhibitors as potential antibacterial agents. Part 2: 4-amino-pyrido[2,3-d]pyrimidin-5(8H)-ones

A series of 4-amino-pyrido[2,3-d]pyrimidin-5(8H)-ones were designed and synthesized as a novel class of inhibitors of NAD(+)-dependent DNA ligase that possess potency against Gram-positive bacteria.     

The Biophysical Properties of Basal Lamina Gels Depend on the Biochemical Composition of the Gel

The migration of cells within a three-dimensional extracellular matrix (ECM) depends sensitively on the biochemical and biophysical properties of the matrix. An example for a biological ECM is given by reconstituted basal lamina gels purified from the Engelbreth-Holm-Swarm sarcoma of mice. Here, we compare four different commercial variants of this ECM, which have all been purified according to the same protocol. Nevertheless, in those gels, we detect strong differences in the migration behavior of leukocyte cells as well as in the Brownian motion of nanoparticles. We show that these differences correlate with the mechanical properties and the microarchitecture of the gels which in turn arise from small variations in their biochemical composition.     

Selection-dominant and nonaccessible epitopes on cell-surface receptors revealed by cell-panning with a large phage antibody library.

To generate antibodies to defined cell-surface antigens, we used a large phage antibody fragment library to select on cell transfectants expressing one of three chosen receptors. First, in vitro panning procedures and phage antibody screening ELISAs were developed using whole live cells stably expressing the antigen of interest. When these methodologies were applied to Chinese hamster ovary (CHO) cells expressing one of the receptors for a neuropeptide, somatostatin, using either direct cell panning or a strategy of depletion or ligand-directed elution, many different pan-CHO-cell binders were selected, but none was receptor specific. However, when using direct panning on CHO-cells expressing the human membrane protein CD36, an extraordinary high frequency of antigen-specific phage antibodies was found. Panning on myoblasts expressing the rat homologue of CD36 revealed a similar selection dominance for anti-(CD36). Binding of all selected 20 different anti-(CD36) phage was surprisingly inhibited by one anti-(CD36) mAb CLB-IVC7, which recognizes a functional epitope that is also immunodominant in vivo. Similar inhibition was found for seven anti-(rat) CD36 that cross-reacted with human CD36. Our results show that, although cells can be used as antigen carriers to select and screen phage antibodies, the nature of the antigen target has a profound effect on the outcome of the selection.     

Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line

In our previous research, QTL analysis in an F₂ cross between the inbred New Hampshire (NHI) and White Leghorn (WL77) lines revealed a growth QTL in the distal part of chromosome 4. To physically reduce the chromosomal interval and the number of potential candidate genes, we performed fine mapping using individuals of generations F₁₀, F₁₁ and F₁₂ in an advanced intercross line that had been established from the initial F₂ mapping population. Using nine single nucleotide polymorphism (SNP) markers within the QTL region for an association analysis with several growth traits from hatch to 20 weeks and body composition traits at 20 weeks, we could reduce the confidence interval from 26.9 to 3.4 Mb. Within the fine mapped region, markers rs14490774, rs314961352 and rs318175270 were in full linkage disequilibrium (D′ = 1.0) and showed the strongest effect on growth and muscle mass (LOD ≥ 4.00). This reduced region contains 30 genes, compared to 292 genes in the original region. Chicken 60 K and 600 K SNP chips combined with DNA sequencing of the parental lines were used to call mutations in the reduced region. In the narrowed‐down region, 489 sequence variants were detected between NHI and WL77. The most deleterious variants are a missense variant in ADGRA3 (SIFT = 0.02) and a frameshift deletion in the functional unknown gene ENSGALG00000014401 in NHI chicken. In addition, five synonymous variants were discovered in genes PPARGC1A, ADGRA3, PACRGL, SLIT2 and FAM184B. In our study, the confidence interval and the number of potential genes could be reduced 8‐ and 10‐ fold respectively. Further research will focus on functional effects of mutant genes.     

The Escherichia coli Cell Division Protein and Model Tat Substrate SufI (FtsP) Localizes to the Septal Ring and Has a Multicopper Oxidase-Like Structure

The Escherichia coli protein SufI (FtsP) has recently been proposed to be a component of the cell division apparatus. The SufI protein is also in widespread experimental use as a model substrate in studies of the Tat (twin arginine translocation) protein transport system. We have used SufI-GFP (green fluorescent protein) fusions to show that SufI localizes to the septal ring in the dividing cell. We have also determined the structure of SufI by X-ray crystallography to a resolution of 1.9 Å. SufI is structurally related to the multicopper oxidase superfamily but lacks metal cofactors. The structure of SufI suggests it serves a scaffolding rather than an enzymatic role in the septal ring and reveals regions of the protein likely to be involved in the protein-protein interactions required to assemble SufI at the septal ring.     

Preparation and use of cross-linked enzyme aggregates (CLEAs) of laccases

Cross-linked enzyme aggregates (CLEA^®) were prepared from laccases from three different sources: Trametes versicolor, Trametes villosa and Agaricus bisporus. The effect of the various parameters – nature of the precipitant, pH, temperature, glutaraldehyde concentration and cross-linking time – on the activity recovery and storage and operational stability of the resulting CLEAs was different. The laccase CLEAs exhibited the expected increased stability compared to the free enzyme but there was no direct correlation with the number of surface lysine residues in the latter. It is clearly not the only parameter influencing the properties of the CLEA. Co-aggregation with albumin did not improve the stability. The laccase CLEAs, in combination with the stable N-oxy radical, TEMPO, were shown to be active and stable catalysts for the aerobic oxidation of linear C₅–C₁₀ aliphatic alcohols, to the corresponding aldehydes, in aqueous buffer (pH 4). Rates were an order of magnitude higher than those observed with the corresponding free enzyme and the CLEAs could be recycled several times without appreciable loss of activity. The addition of water immiscible or water miscible solvents showed no further improvement in rate compared with reactions in aqueous buffer alone.     

Kinetics of adhesion of the oral bacterium Streptococcus sanguis CH3 to polymers with different surface free energies.

The kinetics of adhesion of Streptococcus sanguis CH3 from suspension to polymers with different surface free energies were studied by using three bacterial concentrations (2.5 X 10(7), 2.5 X 10(8), and 2.5 X 10(9) cells per ml-1). Substratum surface free energies (gamma s) ranged from 18 to 120 erg cm-2. The kinetics of bacterial adhesion to these surfaces showed a typical two-step adhesion process, indicating an equilibrium in both steps. In the initial adhesion step (step 1), low equilibrium numbers of adhering bacteria were counted on substrata with surface free energies lower than 55 erg cm-2. A maximal number adhered on substrata with higher surface free energies. At the lowest bacterial concentration tested, the highest number of bacteria were found on substrata with a surface free energy around 55 erg cm-2. For each substratum, step 2 started after a characteristic time interval tau, being short (30 min) for gamma s less than 50 and long (120 min) for gamma s greater than 50 erg cm-2. The relationship between the substratum surface free energy and the number of bacteria adhering at equilibrium after step 2 was similar to, although less distinct than, that during step 1 with a slight indication of a bioadhesive minimum around gamma s = 35 erg cm-2. The results are indicative of a two-step adhesion model, in which step 1 is controlled by macroscopic substratum properties.     

Fine needle aspiration cytology of inflammatory pseudotumor of the lung (plasma cell granuloma). Report of four cases

The fine needle aspiration (FNA) cytologic findings in four cases of inflammatory pseudotumor of the lung are described. Histologic material was available for comparison in three of the four cases. FNA of these lesions usually yielded moderately to poorly cellular smears. The smears showed a mixture of chronic inflammatory cells and tissue fragments, without a predominance of plasma cells. Characteristic cytologic findings were not observed. The cytologic findings can be distinguished from those of other circumscribed benign and malignant lesions, however. The diagnosis of an inflammatory pseudotumor of the lung may be suggested by a combination of roentgenographic (a localized density) and FNA findings, which may justify a more conservative surgical approach.     

Surface free energies of oral streptococci

Abstract The surface free energies ( γ _b) of a variety of oral streptococci were determined from contact angle measurements on bacterial deposits, using the concept of dispersion and polar components. At least four strains of each species were tested. Strains of Streptococcus mutans, S. sanguis and S. salivarius possessed relatively high surface free energies (103 ± 12 mJ · m⁻²) and at the species level no significant difference was found. In contrast, the strains of S. mitis had remarkably low surface free energies (45 ± 14 mJ · m⁻²). S. milleri appeared to be a heterogeneous species, showing surface free energies over a range of 32–119 mJ · m⁻². No significant differences were observed between laboratory strains and strains freshly isolated from the oral cavity.