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Watrous J.D.,University of California at San Diego | Phelan V.V.,University of California at San Diego | Hsu C.-C.,University of California at San Diego | Moree W.J.,University of California at San Diego | And 5 more authors.
ISME Journal | Year: 2013

Mono-and multispecies microbial populations alter the chemistry of their surrounding environments during colony development thereby influencing multicellular behavior and interspecies interactions of neighboring microbes. Here we present a methodology that enables the creation of three-dimensional (3D) models of a microbial chemotype that can be correlated to the colony phenotype through multimodal imaging analysis. These models are generated by performing matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) imaging mass spectrometry (IMS) on serial cross-sections of microbial colonies grown on 8 mm deep agar, registering data sets of each serial section in MATLAB to create a model, and then superimposing the model with a photograph of the colonies themselves. As proof-of-principle, 3D models were used to visualize metabolic exchange during microbial interactions between Bacillus subtilis and Streptomyces coelicolor, as well as, Candida albicans and Pseudomonas aeruginosa. The resulting models were able to capture the depth profile of secreted metabolites within the agar medium and revealed properties of certain mass signals that were previously not observable using two-dimensional MALDI-TOF IMS. Most significantly, the 3D models were capable of mapping previously unobserved chemical distributions within the array of sub-surface hyphae of C. albicans and how this chemistry is altered by the presence of P. aeruginosa, an opportunistic pathogen known to alter virulence of C. albicans. It was determined that the presence of C. albicans triggered increased rhamnolipid production by P. aeruginosa, which in turn was capable of inhibiting embedded hyphal growth produced beneath the C. albicans colony at ambient temperature. © 2013 International Society for Microbial Ecology All rights reserved. Source


Su L.Y.,San Diego State University | Su L.Y.,San Diego Biotechnology | Willner D.L.,San Diego State University | Segall A.M.,San Diego State University
Antimicrobial Agents and Chemotherapy | Year: 2010

The hexapeptide WRWYCR was previously identified on the basis of its ability to inhibit bacteriophage lambda integrase-mediated recombination by trapping and preventing resolution of the Holliday junction intermediate. This peptide inhibits several unrelated DNA repair enzymes that bind to and process Holliday junctions and branched DNA substrates. WRWYCR and its D stereoisomer, wrwycr, are bactericidal against both Gram-positive and Gram-negative bacteria, causing the accumulation of DNA breaks, chromosome segregation defects, and the filamentation of cells. DNA repair is a novel target of antibiotics. In the present study, we examined the ability of the peptides to inhibit the growth of Salmonella in mammalian cells. J774A.1 macrophage-like cells and murine peritoneal macrophages were infected with Salmonella enterica serovar Typhimurium and grown in the presence or absence of peptide. We found that peptide wrwycr reduced the number of Salmonella cells recovered after 24 h growth in J774A.1 cells by 100 to 1,000 times, depending on the multiplicity of infection. The peptide also inhibited Salmonella growth in peritoneal macrophages, and although higher doses were required, these were not toxic to the host cells. The apparent lower level of potency of the peptide paralleled the lower level of replication of Salmonella and the lower level of permeation of the peptide in the peritoneal macrophages than in the J774.1 cells. Treatment with peptide wrwycr elicited the SOS response in a significant fraction of the intracellular bacteria, as would be expected if the mechanism of bacterial killing was the same in pure culture and in host cells. These results represent a proof of principle of the antimicrobial activities of compounds that target DNA repair. Copyright © 2010, American Society for Microbiology. All Rights Reserved. Source


Ethell D.W.,Western University of Health Sciences | Ethell D.W.,San Diego Biotechnology
Journal of Alzheimer's Disease | Year: 2014

Plaques and tangles may be manifestations of a more substantial underlying cause of Alzheimer's disease (AD). Disease-related changes in the clearance of amyloid-β (Aβ) and other metabolites suggest this cause may involve cerebrospinal fluid (CSF) flow through the interstitial spaces of the brain, including an archaic route through the olfactory system that predates neocortical expansion by three hundred million years. This olfactory CSF conduit (OCC) runs from the medial temporal lobe (MTL) along the lateral olfactory stria, through the olfactory trigone, and down the olfactory tract to the olfactory bulb, where CSF seeps through the cribriform plate to the nasal submucosa. Olfactory dysfunction is common in AD and could be related to alterations in CSF flow along the OCC. Further, reductions in OCC flow may impact CSF hydrodynamics upstream in the MTL and basal forebrain, resulting in less efficient Aβ removal from those areas - among the first affected by neuritic plaques in AD. Factors that reduce CSF drainage across the cribriform plate and slow the clearance of metabolite-laden CSF could include aging-related bone changes, head trauma, inflammation of the nasal epithelium, and toxins that affect olfactory neuron survival and renewal, as well as vascular effects related to diabetes, obesity, and atherosclerosis - all of which have been linked to AD risk. Problems with CSF-mediated clearance could also provide a link between these seemingly disparate factors and familial AD mutations that induce plaque and tangle formation. I hypothesize that disruptions of CSF flow across the cribriform plate are important early events in AD, and I propose that restoring this flow will enhance the drainage of Aβ oligomers and other metabolites from the MTL. © 2014 - IOS Press and the authors. All rights reserved. Source


Sule S.V.,Rensselaer Polytechnic Institute | Dickinson C.D.,San Diego Biotechnology | Lu J.,Eli Lilly and Company | Chow C.-K.,Eli Lilly and Company | Tessier P.M.,Rensselaer Polytechnic Institute
Molecular Pharmaceutics | Year: 2013

A key challenge in developing therapeutic antibodies is their highly variable propensities to self-associate at high antibody concentrations (>50 mg/mL) required for subcutaneous delivery. Identification of monoclonal antibodies (mAbs) in the initial discovery process that not only have high binding affinity but also have high solubility and low viscosity would simplify the development of safe and effective antibody therapeutics. Unfortunately, the low purities, small quantities and large numbers of antibody candidates during the early discovery process are incompatible with current methods of measuring antibody self-association. We report a method (affinity-capture self-interaction nanoparticle spectroscopy, AC-SINS) capable of identifying mAbs with low self-association propensity that is robust even at low mAb concentrations (5-50 μg/mL) and in the presence of cell culture media. Gold nanoparticles are coated with polyclonal antibodies specific for human antibodies, and then human mAbs are captured from dilute antibody solutions. We find that the wavelength of maximum absorbance (plasmon wavelength) of antibody-gold conjugates - which red-shifts as the distance between particles is reduced due to attractive mAb self-interactions - is well correlated with light scattering measurements conducted at several orders of magnitude higher antibody concentrations. The generality of AC-SINS makes it well suited for use in diverse settings ranging from antibody discovery to formulation development. © 2013 American Chemical Society. Source


Watrous J.D.,University of California at San Diego | Alexandrov T.,University of Bremen | Dorrestein P.C.,University of California at San Diego | Dorrestein P.C.,San Diego Biotechnology
Journal of Mass Spectrometry | Year: 2011

Within the past decade, imaging mass spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution and current state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research. © 2011 John Wiley & Sons, Ltd. Source

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