[ { "id": "https://authors.library.caltech.edu/records/41wsf-mr159", "eprint_id": 82309, "eprint_status": "archive", "datestamp": "2023-08-19 04:55:22", "lastmod": "2023-10-17 22:11:07", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "DePas-W", "name": { "family": "DePas", "given": "W." } }, { "id": "Bergkessel-M", "name": { "family": "Bergkessel", "given": "M." }, "orcid": "0000-0002-4530-1224" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "D. K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Aggregation of Nontuberculous Mycobacteria in Vitro and in Situ", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2017 Wiley Periodicals, Inc. \n\nIssue online: 19 September 2017; Version of record online: 19 September 2017.", "abstract": "The incidence of nontuberculous mycobacterial (NTM) infections in cystic fibrosis (CF) patients is increasing, with some CF clinics in the US reporting NTM prevalence upwards of 25%. In addition, the current treatment\nregimen for NTM involves long courses of antibiotic cocktails that demonstrate limited efficacy and cause frequent and serious side effects.\nMycobacterium abscessus, in particular, is difficult to treat and correlates with a more rapid decline in lung function compared to Mycobacterium avium complex. Studies with zebrafish and human cell cultures have demonstrated that M. abscessus is more virulent when aggregated into cord-like biofilms, in part because of the decreased ability of phagocytes to efficiently engulf and kill corded M. abscessus compared to diffuse M. abscessus cells. Translating these findings into useful clinical strategies\nfor treating NTM infections will be greatly aided by 1.) A thorough understanding of the environmental conditions and genetic networks that control NTM aggregation, and 2.) Information about the in vivo aggregation state of NTM during infection. To address item 1, we developed an in\nvitro aggregation assay in which NTM such as M. abscessus and the model strain Mycobacterium smegmatis aggregate and disperse regularly in liquid culture. We found that M. smegmatis aggregation was dependent on carbon source type and availability. In particular, glycerol catabolism induces\naggregation while pyruvate or amino acid catabolism leads to growth as dispersed cells. In contrast, oxygen availability does not induce changes in aggregation state. Currently, we are performing experiments in order to elucidate the genetic regulators that trigger aggregation in response to glycerol catabolism.", "date": "2017-09", "date_type": "published", "publisher": "Wiley", "id_number": "CaltechAUTHORS:20171012-103413414", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171012-103413414", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1002/ppul.23840", "resource_type": "conference_item", "pub_year": "2017", "author_list": "DePas, W.; Bergkessel, M.; et el." }, { "id": "https://authors.library.caltech.edu/records/xd2v1-pe260", "eprint_id": 82310, "eprint_status": "archive", "datestamp": "2023-08-22 01:38:41", "lastmod": "2023-10-17 22:11:12", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jorth-P", "name": { "family": "Jorth", "given": "P." }, "orcid": "0000-0002-0981-740X" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "D. K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Clarifying the Intracellular and Extracellular Lifestyles of CF Microbes in Three Dimensions", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2017 Wiley Periodicals, Inc. \n\nIssue online: 19 September 2017; Version of record online: 19 September 2017.", "abstract": "Imaging of sputum smears and thin sections have suggested that P. aeruginosa persists as extracellular bacterial aggregates, or biofilms, during chronic CF infections. However, emerging evidence indicates that host cells may also provide a protective reservoir for P. aeruginosa\nduring infection. While phagocytes that flood the CF airways normally kill infecting bacteria, CFTR-deficient murine macrophages fail to kill P. aeruginosa,\nraising the possibility that CF macrophages could house viable bacteria. Epithelial cells may also provide an intracellular home for P. aeruginosa, since P. aeruginosa can invade epithelial cells in tissue culture systems. Together, these results have led to our hypothesis that the intracellular environment is a protective reservoir for P. aeruginosa during chronic CF infections. We are using a state-of-the-art imaging technique termed MiPACT to study\nhow bacteria are spatially organized and functioning in CF sputum in relation to host cells. MiPACT was previously developed for the characterization of growth rates and spatial organization of microbes in millimeter thick\nthree-dimensional CF sputum specimens. A major advantage to MiPACT is that the sputum specimens are embedded in a hydrogel and passively cleared with a detergent, which renders the sputum optically transparent and maintains the original biogeography of the specimens. This represents\na substantial advance over traditional techniques like smears and thin sections, which were essentially limited to analyses in two dimensions. In this study, we have further advanced MiPACT in two ways to study how P. aeruginosa interacts with host cells. First, we can now detect bacterial gene expression in situ with fluorescent nucleic acid probes, which will allow us to determine whether specific genes are expressed when bacteria associate\nwith host cells. Second, we have combined MiPACT with immunofluorescence to label bacteria and host cell proteins with fluorescent antibodies. In these preliminary studies, we have developed probes to detect P. aeruginosa\nalginate gene expression in vitro and successfully used immunofluorescence to label neutrophils, macrophages, and P. aeruginosa in CF sputum in situ. The immunofluorescence revealed that P. aeruginosa can be detected as extracellular and intracellular aggregates in sputum. Ongoing work is being performed to determine which host cells are housing intracellular P. aeruginosa and whether intracellular bacteria are viable or in the process\nof being killed. These new methods will shed important light on how P. aeruginosa persists in the CF airways.", "date": "2017-09", "date_type": "published", "publisher": "Wiley", "id_number": "CaltechAUTHORS:20171012-103857991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171012-103857991", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1002/ppul.23840", "resource_type": "conference_item", "pub_year": "2017", "author_list": "Jorth, P. and Newman, D. K." }, { "id": "https://authors.library.caltech.edu/records/edrvt-vx355", "eprint_id": 57209, "eprint_status": "archive", "datestamp": "2023-08-22 14:23:30", "lastmod": "2023-10-23 17:09:43", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mariita-R-M", "name": { "family": "Mariita", "given": "R. M." } }, { "id": "Bhatnagar-S", "name": { "family": "Bhatnagar", "given": "S." } }, { "id": "Hanselmann-K", "name": { "family": "Hanselmann", "given": "K." } }, { "id": "Hossain-Mohammad-J", "name": { "family": "Hossain", "given": "M." }, "orcid": "0000-0003-3848-9035" }, { "id": "Liles-M", "name": { "family": "Liles", "given": "M." } }, { "id": "Moss-A-G", "name": { "family": "Moss", "given": "A. G." } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "J. R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "D. K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Characterization, Comparative Genomics and Genome Mining for Antibiotics and Secondary Metabolite of two Actinomycetales isolates", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2014 American Society for Cell Biology. TUESDAY-POSTER PRESENTATION.\n\n2014 Microbial Diversity, Marine Biological Laboratory. Pacific Biotechnology. RMM support:\nAU-CMB Peaks of Excellence summer graduate research award, Selman A. Waksman Endowed Scholarship in Microbial Diversity, Bernard Davis Endowed Scholarship (47802012050), Auburn Graduate School, and the AU-DBS Farrington Fund. We are grateful to Scott Dawson, George OToole, Alison\nBulter, Emil Ruff, Arpita Bose and Suzanne Kern for their assistance.\n\n
Published - Mariita_2014pP2378.pdf
", "abstract": "Actinomycetes are ubiquitous Gram (+) bacteria commonly found to have high G+C content and best\nknown for their metabolic by-products and novel enzymes [1]. Isolates CCMMD2014 & MRMD2014\nwere co-cultured from soil impacted by a rusty fire hydrant in Woods Hole, MA. The Streptomyces sp.\nand Curtobacterium sp. isolates were identified by marker genes for 16S rRNA, rpoB, xylose isomerase,\ntryptophan synthase beta chain and Cytochrome P450 monooxygenase. Both isolates showed lactic acid\nfermentation and urease activity. The co-isolates were separated by selective culturing with antibiotics.\nIn addition, whole genome sequencing revealed distinct inherent metabolic pathways in each culture\nthat allowed for mutually exclusive selective culture conditions. Assembly was done using HGAP3 with\nCelera8 assembler using SMRT portal [2,3]. Annotation was done using the RAST server [4], with 7540\nand 3969 CDS for Streptomyces sp. and Curtobacterium sp. respectively being revealed by AMIGene and\nBASys [5,6]. Subsequently, antiSMASH [7], was used to predict 52 and 26 secondary metabolite\nbiosynthetic clusters that included genes for lantipeptides, terpenes, siderophores, polyketide synthases\ntype I and II, bacteriocin and nonribosomal peptide synthase genes for Streptomyces sp. and\nCurtobacterium sp. respectively. The isolates have genes of potentially beneficial traits that could help\nstudy, among others, the role of fimbrial adhesins and iron in biofilm formation and investigation on\nnatural products.", "date": "2014-12", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20150504-143203439", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150504-143203439", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "AU-CMB Peaks of Excellence summer graduate research award" }, { "agency": "Selman A. Waksman Endowed Scholarship in Microbial Diversity" }, { "agency": "Auburn Graduate School, Bernard Davis Endowed Scholarship", "grant_number": "47802012050" }, { "agency": "AU-DBS Farrington Fund" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "contributors": { "items": [ { "id": "Lippincott-Schwartz-J", "name": { "family": "Lippincott-Schwartz", "given": "Jennifer" } }, { "id": "Marshall-W", "name": { "family": "Marshall", "given": "Wallace" } }, { "id": "Marks-M", "name": { "family": "Marks", "given": "Michael" } } ] }, "primary_object": { "basename": "Mariita_2014pP2378.pdf", "url": "https://authors.library.caltech.edu/records/edrvt-vx355/files/Mariita_2014pP2378.pdf" }, "resource_type": "conference_item", "pub_year": "2014", "author_list": "Mariita, R. M.; Bhatnagar, S.; et el." } ]