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  1. Article ; Online: Modified in-vitro AATCC-100 procedure to measure viable bacteria from wound dressings.

    Lee, Sang Hyuk / Glover, Thomas / Lavey, Nathan / Fu, Xiao / Donohue, Marc / Karunasena, Enusha

    PloS one

    2024  Volume 19, Issue 3, Page(s) e0298829

    Abstract: ... 100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P ...

    Abstract Chronic wounds are reoccurring healthcare problems in the United States and cost up to $50 billion annually. Improper wound care results in complications such as wound debridement, surgical amputation, and increased morbidity/ mortality due to opportunistic infections. To eliminate wound infections, many antimicrobial dressings are developed and submitted to FDA for evaluation. AATCC-100 is a standard method widely used to evaluate cloth wound dressings. This method, requires enrichment, followed by culturing to measure the concentration of culturable organisms; a caveat to this method could result in neglected viable but nonculturable (VBNC) bacteria and overestimate the antimicrobial properties of wound dressings. Therefore, the objectives of this study were to assess this accepted protocol with quantitative real-time polymerase chain reaction (qRT-PCR), to measure time dependent antimicrobial efficacy of wound dressing, and to examine for potential viable bacteria but non-culturable as compared with traditional plating methods. The test organisms included opportunistic pathogens: Pseudomonas aeruginosa (ATCC 15692) and Staphylococcus aureus (ATCC 43300). To mimic a wound dressing environment, samples of commercially available wound dressings (McKesson Inc.) with silver ion (positive control) and dressings without silver ion (positive control) were assessed under sterile conditions. All samples were examined by the original protocol (the extended AATCC-100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P. aeruginosa and 16s rRNA for S. aureus). Based on these tests, log reduction of experimental conditions was compared to identify time dependent and precise antimicrobial properties from wound dressing samples. These results showed antimicrobial properties of wound dressings diminished as incubation days are increased for both methods from day 1 PCR result of 4.31 ± 0.54 and day 1 plating result of 6.31 ± 3.04 to day 3 PCR result of 1.22 ± 0.97 and day 3 plating result of 5.89 ± 2.41. These results show that data from qRT-PCR generally produced lower standard deviation than that of culture methods, hence shown to be more precise. Complementary parallel analysis of samples using both methods better characterized antimicrobial properties of the tested samples.
    MeSH term(s) Humans ; Silver ; Staphylococcus aureus ; RNA, Ribosomal, 16S ; Bandages ; Anti-Infective Agents/pharmacology ; Wound Infection/microbiology ; Pseudomonas aeruginosa
    Chemical Substances Silver (3M4G523W1G) ; RNA, Ribosomal, 16S ; Anti-Infective Agents
    Language English
    Publishing date 2024-03-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0298829
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Identification of ClpP Dual Isoform Disruption as an Antisporulation Strategy for Clostridioides difficile.

    Bishop, Catherine E / Shadid, Tyler M / Lavey, Nathan P / Kempher, Megan L / Ballard, Jimmy D / Duerfeldt, Adam S

    Journal of bacteriology

    2021  Volume 204, Issue 2, Page(s) e0041121

    Abstract: The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and ... ...

    Abstract The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. By extension, the identification of druggable targets that significantly attenuate sporulation would have a significant impact on thwarting C. difficile infection. By use of a new CRISPR-Cas9 nickase genome editing methodology, stop codons were inserted early in the coding sequence for
    MeSH term(s) Bacterial Proteins/antagonists & inhibitors ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bortezomib/pharmacology ; Clostridioides difficile/chemistry ; Clostridioides difficile/drug effects ; Clostridioides difficile/genetics ; Clostridioides difficile/metabolism ; Clostridium Infections/microbiology ; Gene Editing/methods ; Gene Expression Regulation, Bacterial ; Humans ; Mutation ; Phenotype ; Protein Isoforms/genetics ; Spores, Bacterial/genetics ; Spores, Bacterial/metabolism ; Virulence
    Chemical Substances Bacterial Proteins ; Protein Isoforms ; Bortezomib (69G8BD63PP)
    Language English
    Publishing date 2021-11-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00411-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Clostridium difficile ClpP Homologues are Capable of Uncoupled Activity and Exhibit Different Levels of Susceptibility to Acyldepsipeptide Modulation.

    Lavey, Nathan P / Shadid, Tyler / Ballard, Jimmy D / Duerfeldt, Adam S

    ACS infectious diseases

    2018  Volume 5, Issue 1, Page(s) 79–89

    Abstract: Caseinolytic protease P (ClpP) has emerged as a promising new target for antibacterial development ...

    Abstract Caseinolytic protease P (ClpP) has emerged as a promising new target for antibacterial development. While ClpPs from single isoform expressing bacteria have been studied in detail, the function and regulation of systems with more than one ClpP homologue are still poorly understood. Herein, we present fundamental studies toward understanding the ClpP system in C. difficile, an anaerobic spore-forming pathogen that contains two chromosomally distant isoforms of ClpP. Examination of proteomic and genomic data suggest that ClpP1 is the primary isoform responsible for normal growth and virulence, but little is known about the function of ClpP2 or the context required for the formation of functional proteases. For the first time in a pathogenic bacterium, we demonstrate that both isoforms are capable of forming operative proteases. Interestingly, ClpP1 is the only homologue that possesses characteristic response to small molecule acyldepsipeptide activation. On the contrary, both ClpP1 and ClpP2 respond to cochaperone activation to degrade an ssrA-tagged substrate. These observations indicate that ClpP2 is less susceptible to acyldepsipeptide activation but retains the ability to interact with a known cochaperone. Homology models reveal no obvious characteristics that would allow one to predict less efficient acyldepsipeptide binding. The reported findings establish the uniqueness of the ClpP system in C. difficile, open new avenues of inquiry, and highlight the importance of more detailed structural, genetic, and biological characterization of the ClpP system in C. difficile.
    MeSH term(s) Clostridium difficile/drug effects ; Clostridium difficile/enzymology ; Clostridium difficile/genetics ; Depsipeptides/chemistry ; Depsipeptides/pharmacokinetics ; Endopeptidase Clp/chemistry ; Endopeptidase Clp/genetics ; Gene Expression Regulation, Bacterial ; Isoenzymes/genetics ; Proteolysis ; Proteomics ; Sequence Homology, Amino Acid ; Virulence
    Chemical Substances Depsipeptides ; Isoenzymes ; Endopeptidase Clp (EC 3.4.21.92)
    Language English
    Publishing date 2018-11-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2373-8227
    ISSN (online) 2373-8227
    DOI 10.1021/acsinfecdis.8b00199
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Sclerotiamide: The First Non-Peptide-Based Natural Product Activator of Bacterial Caseinolytic Protease P.

    Lavey, Nathan P / Coker, Jesse A / Ruben, Eliza A / Duerfeldt, Adam S

    Journal of natural products

    2016  Volume 79, Issue 4, Page(s) 1193–1197

    Abstract: Caseinolytic protease P (ClpP) maintains essential roles in bacterial homeostasis ...

    Abstract Caseinolytic protease P (ClpP) maintains essential roles in bacterial homeostasis. As such, both the inhibition and activation of this enzyme result in bactericidal activity, making ClpP a promising target for antibacterial drug development. Herein, we report the results of a fluorescence-based screen of ∼450 structurally diverse fungal and bacterial secondary metabolites. Sclerotiamide (1), a paraherquamide-related indolinone, was identified as the first non-peptide-based natural product activator of ClpP. Structure-activity relationships arising from the initial screen, preliminary biochemical evaluation of 1, and rationale for the exploitation of this chemotype to develop novel ClpP activators are presented.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Biological Products/chemistry ; Biological Products/pharmacology ; Catalysis ; Endopeptidases/metabolism ; Indolizines/chemistry ; Indolizines/pharmacology ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Spiro Compounds/chemistry ; Spiro Compounds/pharmacology ; Structure-Activity Relationship
    Chemical Substances Anti-Bacterial Agents ; Biological Products ; Indolizines ; Spiro Compounds ; sclerotiamide ; Endopeptidases (EC 3.4.-) ; paraherquamide (R72VB4E4KC)
    Language English
    Publishing date 2016-03-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 304325-3
    ISSN 1520-6025 ; 0163-3864
    ISSN (online) 1520-6025
    ISSN 0163-3864
    DOI 10.1021/acs.jnatprod.5b01091
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Sclerotiamide: The First Non-Peptide-Based Natural Product Activator of Bacterial Caseinolytic Protease P

    Lavey, Nathan P / Coker Jesse A / Duerfeldt Adam S / Ruben Eliza A

    Journal of natural products. 2016 Apr. 22, v. 79, no. 4

    2016  

    Abstract: Caseinolytic protease P (ClpP) maintains essential roles in bacterial homeostasis ...

    Abstract Caseinolytic protease P (ClpP) maintains essential roles in bacterial homeostasis. As such, both the inhibition and activation of this enzyme result in bactericidal activity, making ClpP a promising target for antibacterial drug development. Herein, we report the results of a fluorescence-based screen of ∼450 structurally diverse fungal and bacterial secondary metabolites. Sclerotiamide (1), a paraherquamide-related indolinone, was identified as the first non-peptide-based natural product activator of ClpP. Structure-activity relationships arising from the initial screen, preliminary biochemical evaluation of 1, and rationale for the exploitation of this chemotype to develop novel ClpP activators are presented.
    Keywords antibacterial properties ; antibiotics ; chemotypes ; fungi ; homeostasis ; proteinases ; secondary metabolites ; structure-activity relationships
    Language English
    Dates of publication 2016-0422
    Size p. 1193-1197.
    Publishing place American Chemical Society and American Society of Pharmacognosy
    Document type Article
    ZDB-ID 304325-3
    ISSN 1520-6025 ; 0163-3864
    ISSN (online) 1520-6025
    ISSN 0163-3864
    DOI 10.1021%2Facs.jnatprod.5b01091
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Consequences of Depsipeptide Substitution on the ClpP Activation Activity of Antibacterial Acyldepsipeptides.

    Li, Yangxiong / Lavey, Nathan P / Coker, Jesse A / Knobbe, Jessica E / Truong, Dat C / Yu, Hongtao / Lin, Yu-Shan / Nimmo, Susan L / Duerfeldt, Adam S

    ACS medicinal chemistry letters

    2017  Volume 8, Issue 11, Page(s) 1171–1176

    Abstract: The acyldepsipeptide (ADEP) antibiotics operate through a clinically unexploited mechanism of action and thus have attracted attention from several antibacterial development groups. The ADEP scaffold is synthetically tractable, and deep-seated ... ...

    Abstract The acyldepsipeptide (ADEP) antibiotics operate through a clinically unexploited mechanism of action and thus have attracted attention from several antibacterial development groups. The ADEP scaffold is synthetically tractable, and deep-seated modifications have produced extremely potent antibacterial leads against Gram-positive pathogens. Although newly identified ADEP analogs demonstrate remarkable antibacterial activity against bacterial isolates and in mouse models of bacterial infections, stability issues pertaining to the depsipeptide core remain. To date, no study has been reported on the natural ADEP scaffold that evaluates the sole importance of the macrocyclic linkage on target engagement, molecular conformation, and bioactivity. To address this gap in ADEP structure-activity relationships, we synthesized three ADEP analogs that only differ in the linkage motif (i.e., ester, amide, and
    Language English
    Publishing date 2017-10-19
    Publishing country United States
    Document type Journal Article
    ISSN 1948-5875
    ISSN 1948-5875
    DOI 10.1021/acsmedchemlett.7b00320
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: The role of Indigenous peoples and local communities in effective and equitable conservation

    Neil M. Dawson / Brendan Coolsaet / Eleanor J. Sterling / Robin Loveridge / Nicole D, . Gross-Camp / Supin Wongbusarakum / Kamaljit K. Sangha / Lea M. Scherl / Hao Phuong. Phan / Noelia Zafra-Calvo / Warren G. Lavey / Patrick Byakagaba / C. Julián Idrobo / Aude Chenet / Nathan J. Bennett / Stephanie Mansourian / Francisco J. Rosado-May

    Ecology and Society, Vol 26, Iss 3, p

    2021  Volume 19

    Abstract: Debate about what proportion of the Earth to protect often overshadows the question of how nature should be conserved and by whom. We present a systematic review and narrative synthesis of 169 publications investigating how different forms of governance ... ...

    Abstract Debate about what proportion of the Earth to protect often overshadows the question of how nature should be conserved and by whom. We present a systematic review and narrative synthesis of 169 publications investigating how different forms of governance influence conservation outcomes, paying particular attention to the role played by Indigenous peoples and local communities. We find a stark contrast between the outcomes produced by externally controlled conservation, and those produced by locally controlled efforts. Crucially, most studies presenting positive outcomes for both well-being and conservation come from cases where Indigenous peoples and local communities play a central role, such as when they have substantial influence over decision making or when local institutions regulating tenure form a recognized part of governance. In contrast, when interventions are controlled by external organizations and involve strategies to change local practices and supersede customary institutions, they tend to result in relatively ineffective conservation at the same time as producing negative social outcomes. Our findings suggest that equitable conservation, which empowers and supports the environmental stewardship of Indigenous peoples and local communities represents the primary pathway to effective long-term conservation of biodiversity, particularly when upheld in wider law and policy. Whether for protected areas in biodiversity hotspots or restoration of highly modified ecosystems, whether involving highly traditional or diverse and dynamic local communities, conservation can become more effective through an increased focus on governance type and quality, and fostering solutions that reinforce the role, capacity, and rights of Indigenous peoples and local communities. We detail how to enact progressive governance transitions through recommendations for conservation policy, with immediate relevance for how to achieve the next decade's conservation targets under the UN Convention on Biological Diversity.
    Keywords biodiversity conservation ; customary tenure ; environmental justice ; environmental stewardship ; equity ; governance ; human rights ; institutions ; iplc ; protected areas ; tenure security ; traditional ecological knowledge ; well-being ; Biology (General) ; QH301-705.5 ; Ecology ; QH540-549.5
    Subject code 333
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Resilience Alliance
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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