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A Mycobacterial Systems Resource for the Research Community.

ABSTRACT: Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulcerans IMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.

SUBMITTER: Judd JA

PROVIDER: S-EPMC8092266 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectiveThe Learning Health Systems Rehabilitation Research Network (LeaRRn), an NIH-funded rehabilitation research resource center, aims to advance the research capacity of learning health systems (LHSs) within the rehabilitation community. A needs assessment survey was administered to inform development of educational resources.MethodsThe online survey included 55 items addressing interest in and knowledge of 33 LHS research core competencies in 7 domains and additional items on respondent characteristics. Recruitment targeting rehabilitation researchers and health system collaborators was conducted by LeaRRn, LeaRRn health system partners, rehabilitation professional organizations, and research university program directors using email, listservs, and social media announcements.ResultsOf the 650 people who initiated the survey, 410 respondents constituted the study sample. Respondents indicated interest in LHS research and responded to at least 1 competency item and/or demographic question. Two-thirds of the study sample had doctoral research degrees, and one-third reported research as their profession. The most common clinical disciplines were physical therapy (38%), communication sciences and disorders (22%), and occupational therapy (10%). Across all 55 competency items, 95% of respondents expressed "a lot" or "some" interest in learning more, but only 19% reported "a lot" of knowledge. Respondents reported "a lot" of interest in a range of topics, including selecting outcome measures that are meaningful to patients (78%) and implementing research evidence in health systems (75%). "None" or "some" knowledge was reported most often in Systems Science areas such as understanding the interrelationships between financing, organization, delivery, and rehabilitation outcomes (93%) and assessing the extent to which research activities will improve the equity of health systems (93%).ConclusionResults from this large survey of the rehabilitation research community indicate strong interest in LHS research competencies and opportunities to advance skills and training.ImpactCompetencies where respondents indicated high interest and limited knowledge can inform development of LHS educational content that is most needed.

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A Mycobacterial Systems Resource for the Research Community.

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