Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging.

A more complete and holistic view on host-microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Salmonella Typhimurium infection in the liver of a mouse model using the S. Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. IMC revealed a marked increase in immune cell markers and localization in immune aggregates in infected tissues. A correlative computational method (network analysis) was deployed to find metabolic features associated with infection and revealed metabolic clusters of acetyl carnitines, as well as phosphatidylcholine and phosphatidylethanolamine plasmalogen species, which could be associated with pro-inflammatory immune cell types. By developing an IMC marker for the detection of Salmonella LPS, we were further able to identify and characterize those cell types which contained S. Typhimurium.

Protective Effect of Nigella sativa and Nigella damascena Fixed Oils Against Aflatoxin Induced Mutagenicity in the Classical and Modified Ames Test.

The antioxidant and mutagenic/antimutagenic activities of the fixed oils from Nigella sativa (NSO) and Nigella damascena (NDO) seeds, obtained by cold press-extraction from the cultivar samples, were comparatively investigated for the first time. The antimutagenicity test was carried out using classical and modified Ames tests. The fatty acid composition of the fixed oils was characterized by gas chromatography-mass spectrometry (GC-MS) while the quantification of thymoquinone in the fixed oils was determined by UPC2 . The main components of the NSO and NDO were found to be linoleic acid, oleic acid, and palmitic acid. The results of the Ames test confirmed the safety of NSO and NDO from the viewpoint of mutagenicity. The results of the three antioxidant test methods were correlated with each other, indicating NDO as having a superior antioxidant activity, when compared to the NSO. Both NSO and NDO exhibited a significant protective effect against the mutagenicity induced by aflatoxin B1 in Salmonella typhimurium TA98 and TA100 strains. When microsomal metabolism was terminated after metabolic activation of the mycotoxin, a significant increase in antimutagenic activity was observed, suggesting that the degradation of aflatoxin B1 epoxides by these oils may be a possible antimutagenic mechanism. It is worthy to note that this is the first study to assess the mutagenicity of NSO and NDO according to the OECD 471 guideline and to investigate antimutagenicity of NDO in comparison to NSO against aflatoxin.

Monitoring of volatile and non-volatile urban air genotoxins using bacteria, human cells and plants.

Urban air contains many mutagenic pollutants. This research aimed to investigate the presence of mutagens in the air by short-term mutagenicity tests using bacteria, human cells and plants. Inflorescences of Tradescantia were exposed to air in situ for 6h, once a month from January to May, to monitor volatile compounds and micronuclei frequency was computed. On the same days PM10 was collected continuously for 24h. Half of each filter was extracted with organic solvents and studied by means of the Ames test, using Salmonella typhimurium TA98 and TA100 strains, and the comet assay on human leukocytes. A quarter of each filter was extracted with distilled water in which Tradescantia was exposed. PM10 concentration was particularly high in the winter season (> 50 µg/m(3)). In situ exposure of inflorescences to urban air induced a significant increase in micronuclei frequency at all the sites considered, but only in January (p < 0.01). Aqueous extracts collected in January and February induced genotoxic effects in Tradescantia exposed in the laboratory (p < 0.01). Ames test showed that organic extracts of winter urban air were able to induce genetic mutations in S. typhimurium TA98 strain (± S9), but not in TA100 strain, with a revertants/plate number nine times higher than the negative control. Comet assay showed that winter extracts were more toxic and genotoxic than spring extracts. All the mutagenicity tests performed confirmed that urban air in North Italy in winter contains both volatile and non-volatile genotoxic substances able to induce genetic damage in bacteria, human cells and plants.

Assessment of mutagenic effect of G. acerosa and S. wightii in S. typhimurium (TA 98, TA 100, and TA 1538 strains) and evaluation of their cytotoxic and genotoxic effect in human mononuclear cells: a non-clinical study.

The marine red algae (Gelidiella acerosa and Sargassum wightii) possessing excellent antioxidant and anticholinesterase activity were subjected to toxicity evaluation for a deeper understanding of other bioprotective properties of seaweeds. Cytotoxic evaluation was done by trypan blue exclusion, and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays using human PBMC (peripheral blood mononuclear cells) and RBC (red blood cells) lysis assay using human erythrocytes. Mutagenicity of the seaweeds was analyzed by Ames salmonella mutagenicity test with the histidine dependent mutant strains TA 98, TA100 and TA 1538. Genotoxic activity was verified in PBMC by comet assay. The results suggest that benzene extract of G. acerosa (BEGA) and dichloromethane extract of S. wightii (DMESW) did not show cytotoxic effect both in PBMC and erythrocytes. Evaluation of mutagenic activity suggests that the seaweeds did not cause any mutagenic effects both in the absence and the presence of S9 microsomal fraction in all the three Salmonella mutant strains. Results of genotoxic study showed that PBMC treated with seaweed extracts (1 mg/mL) exhibit less or no damage to cells, thus proving the non-genotoxic effect of the extract. Since these in vitro non-clinical studies clearly demonstrate the non-toxic nature of the seaweeds, they could be exploited for further characterization, which would result in development of novel and safe therapeutic entities.

Chemical rescue of the post-translationally carboxylated lysine mutant of allantoinase and dihydroorotase by metal ions and short-chain carboxylic acids.

Bacterial allantoinase (ALLase) and dihydroorotase (DHOase) are members of the cyclic amidohydrolase family. ALLase and DHOase possess similar binuclear metal centers in the active site in which two metals are bridged by a post-translationally carboxylated lysine. In this study, we determined the effects of carboxylated lysine and metal binding on the activities of ALLase and DHOase. Although DHOase is a metalloenzyme, purified DHOase showed high activity without additional metal supplementation in a reaction mixture or bacterial culture. However, unlike DHOase, ALLase had no activity unless some specific metal ions were added to the reaction mixture or culture. Substituting the metal binding sites H59, H61, K146, H186, H242, or D315 with alanine completely abolished the activity of ALLase. However, the K146C, K146D and K146E mutants of ALLase were still active with about 1-6% activity of the wild-type enzyme. These ALLase K146 mutants were found to have 1.4-1.7 mol metal per mole enzyme subunit, which may indicate that they still contained the binuclear metal center in the active site. The activity of the K146A mutant of the ALLase and the K103A mutant of DHOase can be chemically rescued by short-chain carboxylic acids, such as acetic, propionic, and butyric acids, but not by ethanol, propan-1-ol, and imidazole, in the presence of Co2+ or Mn2+ ions. However, the activity was still ~10-fold less than that of wild-type ALLase. Overall, these results indicated that the 20 natural basic amino acid residues were not sufficiently able to play the role of lysine. Accordingly, we proposed that during evolution, the post-translational modification of carboxylated lysine in the cyclic amidohydrolase family was selected for promoting binuclear metal center self-assembly and increasing the nucleophilicity of the hydroxide at the active site for enzyme catalysis. This kind of chemical rescue combined with site-directed mutagenesis may also be used to identify a binuclear metal center in the active site for other metalloenzymes.

Engineered socket study of signaling through a four-helix bundle: evidence for a yin-yang mechanism in the kinase control module of the aspartate receptor.

The chemoreceptors of Escherichia coli and Salmonella typhimurium form stable oligomers that associate with the coupling protein CheW and the histidine kinase CheA to form an ultrasensitive, ultrastable signaling lattice. Attractant binding to the periplasmic domain of a given receptor dimer triggers a transmembrane conformational change transmitted through the receptor to its cytoplasmic kinase control module, a long four-helix bundle that binds and regulates CheA kinase. The kinase control module comprises three functional regions: the adaptation region possessing the receptor adaptation sites, a coupling region that transmits signals between other regions, and the protein interaction region possessing contact sites for receptor oligomerization and for CheA-CheW binding. On the basis of the spatial clustering of known signal locking Cys substitutions and engineered disulfide bonds, this study develops the yin-yang hypothesis for signal transmission through the kinase control module. This hypothesis proposes that signals are transmitted through the four-helix bundle via changes in helix-helix packing and that the helix packing changes in the adaptation and protein interaction regions are tightly and antisymmetrically coupled. Specifically, strong helix packing in the adaptation region stabilizes the receptor on state, while strong helix packing in the protein interaction region stabilizes the off state. To test the yin-yang hypothesis, conserved sockets likely to strengthen specific helix-helix contacts via knob-in-hole packing interactions were identified in the adaptation, coupling, and protein interaction regions. For 32 sockets, the knob side chain was truncated to Ala to weaken the knob-in-hole packing and thereby destabilize the local helix-helix interaction provided by that socket. We term this approach a "knob truncation scan". Of the 32 knob truncations, 28 yielded stable receptors. Functional analysis of the signaling state of these receptors revealed seven lock-off knob truncations, all located in the adaptation region, that trap the receptor in its "off" signaling state (low kinase activity, high methylation activity). Also revealed were five lock-on knob truncations, all located in the protein interaction region, that trap the "on" state (high kinase activity, low methylation activity). These findings provide strong evidence that a yin-yang coupling mechanism generates concerted, antisymmetric helix-helix packing changes within the adaptation and protein interaction regions during receptor on-off switching. Conserved sockets that stabilize local helix-helix interactions play a central role in this mechanism: in the on state, sockets are formed in the adaptation region and disrupted in the protein interaction region, while the opposite is true in the off state.

A multi-step NMR screen for the identification and evaluation of chemical leads for drug discovery.

A multi-step NMR based screening assay is described for identifying and evaluating chemical leads for their ability to bind a target protein. The multi-step NMR assay provides structure-related information while being an integral part of a structure based drug discovery and design program. The fundamental principle of the multi-step NMR assay is to combine distinct 1D and 2D NMR techniques, in such a manner, that the inherent strengths and weakness associated with each technique is complementary to each other in the screen. By taking advantage of the combined strengths of 1D and 2D NMR experiments, it is possible to minimize protein requirements and experiment time and differentiate between non-specific and stoichiometric binders while being able to verify ligand binding, determine a semi-quantitative dissociation constant, identify the ligand binding site and rapidly determine a protein-ligand co-structure. Furthermore, the quality and physical behavior of the ligand is readily evaluated to determine its appropriateness as a chemical lead. The utility of the multi-step NMR assay is demonstrated with the use of PrgI from Salmonella typhimurium and human serum albumin (HSA) as target proteins.

Phytomodulatory potentials of Aloe vera against Salmonella OmpR-mediated inflammation.

Mediators released during inflammatory response play an essential role in eliminating microbes or microbial products. However, the uncontrolled release of cytotoxic substances characterized by extensive inflammation may adversely affect normal tissues. Under such conditions it is important to manage the hyperinflammation in order to change the clinical manifestations of the disease. Accordingly, the present study was designed to evaluate the modulation of Salmonella OmpR mediated inflammation by Aloe vera, a plant known to contain antiinflammatory ingredients. It was observed that outer-membrane proteins (OMPs) extracted from the wild type strain of S. typhimurium caused inflammation of greater magnitude compared with the OMPs extracted from its mutant construct as evident from the oedema test as well as the hyperalgesic (flicking) response of the animals under experimental conditions. However, Aloe vera applied topically, administered intraperitoneally or in combination modulated the inflammatory response. The maximum effect was observed with the combined formulation indicating modulation at local as well as systemic levels. The results reveal that this modulation could be due to the potential of Aloe vera to decrease peroxidative damage via a decrease in the levels of monokines (TNF-alpha, IL-1 and IL-6) and an increase in the level of superoxide dismutase (SOD). Moreover, the presence of SOD in Aloe vera itself might be responsible for enhancing its levels in the macrophages. On the other hand, no significant change in the catalase activity was observed by Aloe vera treatment. The use of Aloe vera, therefore, seems to have a promising role in the modulation of Salmonella OmpR mediated inflammation.

Surface-enhanced Raman spectroscopy of bacteria and pollen.

A technique for distinguishing biological material based on surface-enhanced Raman scattering (SERS) is reported in this work. Of particular interest is biological material that can be airborne. Silver colloidal particles with diameters in the range 10 to 20 nm and with a characteristic ultraviolet-visible (UV-VIS) absorption band at 400 nm were used to obtain SERS spectra of Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhimurium bacteria and a number of tree and grass pollens (Cupressus arizonica (cypress), Sequoia sempervirens (redwood), Populus deltoides (cottonwood), Poa pratensis (Kentucky bluegrass), and Anthoxanthum odoratum (sweet vernal grass)). While differences in the SERS spectra among the bacteria were small, we found that the pollen spectra we analyzed could readily be distinguished from the bacteria spectra, and there were significant differences between pollen from different families. In order to obtain reproducible results, we studied the parameters controlling the interaction between the analyte and the nanoscale metallic surface. Our results show that the volume ratio of analyte to colloidal particles must be within a narrow range of values to optimize the signal-to-noise ratio of the SERS spectra and minimize the fluorescence from the analyte. Also, we found that the time-dependent behavior of colloidal/bacterial suspensions (or adsorption rate of the silver colloid particles on the bacteria) is strongly dependent on pH, density of bacteria in solution, and even, to some extent, the type of bacteria.

Lectin and carbohydrate affinity capture surfaces for mass spectrometric analysis of microorganisms.

In a preliminary report (Bundy, J. L.; Fenselau, C. Anal. Chem 1999, 71, 1460-1463), we demonstrated the use of lectin-derivatized surfaces to capture and concentrate complex carbohydrates as well as microorganisms from sample matrixes unamenable to direct MALDI mass spectrometry. Here, we extend the work to include samples representative of a wider variety of microorganisms of importance to human health and of enveloped viruses. In this study, lectins were immobilized directly to a membrane surface via primary amines. A complementary approach was also explored, using immobilized carbohydrates to capture bacteria via microbial lectins expressed on their surfaces. The carbohydrate-based surfaces were constructed by first immobilizing streptavidin to the membrane, followed by attachment of a commercially produced biotin/carbohydrate polymer. Acid treatment of the sample prior to mass spectrometric analysis permits the observation of protein biomarkers from the captured microbial samples in the 5-20 kDa mass range. Bacteria samples were detected from physiological buffers, urine, milk, and processed chicken samples using the biocapture probes. Viral samples were detected from culture based on glycoprotein moieties desorbed directly from the surface. The carbohydrate-based system provided greater sensitivity than the lectin system, possibly due to the larger number of accessible saccharide ligands on the polymer.

Modulatory effects of a tannin fraction isolated from Terminalia arjuna on the genotoxicity of mutagens in Salmonella typhimurium.

A fraction isolated from Terminalia arjuna was studied for its antimutagenic effect against 4-nitro-o-phenylenediamine (NPD) in TA98, sodium azide in TA100 and 2-aminofluorene (2AF, S9-dependent), a promutagen, in both TA98 and TA 100 tester strains of Salmonella typhimurium using the Ames assay. The fraction inhibited the mutagenicity of 2AF very significantly in both strains while the revertant colonies induced by NPD and sodium azide were reduced moderately. 1H-NMR, 13C-NMR, IR and UV-spectroscopic data of the fraction revealed it to be tannin in nature.

The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.

BACKGROUND: The periplasmic oligopeptide-binding protein OppA has a remarkably broad substrate specificity, binding peptides of two or five amino-acid residues with high affinity, but little regard to sequence. It is therefore an ideal system for studying how different chemical groups can be accommodated in a protein interior. The ability of the protein to bind peptides of different lengths has been studied by co-crystallising it with different ligands. RESULTS: Crystals of OppA from Salmonella typhimurium complexed with the peptides Lys-Lys-Lys (KKK) and Lys-Lys-Lys-Ala (KKKA) have been grown in the presence of uranyl ions which form important crystal contacts. These structures have been refined to 1.4 A and 2.1 A, respectively. The ligands are completely enclosed, their side chains pointing into large hydrated cavities and making few strong interactions with the protein. CONCLUSIONS: Tight peptide binding by OppA arises from strong hydrogen bonding and electrostatic interactions between the protein and the main chain of the ligand. Different basic side chains on the protein form salt bridges with the C terminus of peptide ligands of different lengths.