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      DNA Repair Biosensor-Identified DNA Damage Activities of Endophyte Extracts from Garcinia cowa

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          Abstract

          Recent developments in chemotherapy focus on target-specific mechanisms, which occur only in cancer cells and minimize the effects on normal cells. DNA damage and repair pathways are a promising target in the treatment of cancer. In order to identify novel compounds targeting DNA repair pathways, two key proteins, 53BP1 and RAD54L, were tagged with fluorescent proteins as indicators for two major double strand break (DSB) repair pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). The engineered biosensor cells exhibited the same DNA repair properties as the wild type. The biosensor cells were further used to investigate the DNA repair activities of natural biological compounds. An extract from Phyllosticta sp., the endophyte isolated from the medicinal plant Garcinia cowa Roxb. ex Choisy, was tested. The results showed that the crude extract induced DSB, as demonstrated by the increase in the DNA DSB marker γH2AX. The damaged DNA appeared to be repaired through NHEJ, as the 53BP1 focus formation in the treated fraction was higher than in the control group. In conclusion, DNA repair-based biosensors are useful for the preliminary screening of crude extracts and biological compounds for the identification of potential targeted therapeutic drugs.

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          ImageJ2: ImageJ for the next generation of scientific image data

          Curtis Rueden, Johannes Schindelin, Mark C Hiner … (2018)
          Background ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. Results We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Conclusions Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1934-z) contains supplementary material, which is available to authorized users.
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            Non-homologous DNA end joining and alternative pathways to double-strand break repair

            Howard H. Y. Chang, Nicholas Pannunzio, Noritaka Adachi … (2017)
            In mammalian cells, DNA double-strand breaks (DSBs) are repaired predominantly by the non-homologous end joining (NHEJ) pathway, which includes subpathways that can repair different DNA-end configurations. Furthermore, the repair of some DNA-end configurations can be shunted to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA).
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              Natural products from endophytic microorganisms.

              Gary Strobel, Bryn Daisy, Uvidelio Castillo … (2004)
              Endophytic microorganisms are to be found in virtually every plant on earth. These organisms reside in the living tissues of the host plant and do so in a variety of relationships ranging from symbiotic to pathogenic. Endophytes may contribute to their host plant by producing a plethora of substances that provide protection and ultimately survival value to the plant. Ultimately, these compounds, once isolated and characterized, may also have potential for use in modern medicine, agriculture, and industry. Novel antibiotics, antimycotics, immunosuppressants, and anticancer compounds are only a few examples of what has been found after the isolation and culturing of individual endophytes followed by purification and characterization of some of their natural products. The prospects of finding new drugs that may be effective candidates for treating newly developing diseases in humans, plants, and animals are great. Other applications in industry and agriculture may also be discovered among the novel products produced by endophytic microbes.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Biomolecules
                Journal ID (iso-abbrev): Biomolecules
                Journal ID (publisher-id): biomolecules
                Title: Biomolecules
                Publisher: MDPI
                ISSN (Electronic): 2218-273X
                Publication date (Electronic): 16 December 2020
                Publication date Collection: December 2020
                Volume: 10
                Issue: 12
                Electronic Location Identifier: 1680
                Affiliations
                [1 ]Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; tassanee.ler@ 123456mahidol.ac.th (T.L.); sermsiri.chi@ 123456mahidol.ac.th (S.C.); wasana.sti@ 123456mahidol.ac.th (W.S.)
                [2 ]Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; wiki.rakkreat@ 123456gmail.com
                [3 ]Siriraj Center of Research for Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; somponnat.sam@ 123456mahidol.ac.th (S.S.); siwanon.jir@ 123456mahidol.ac.th (S.J.)
                [4 ]Center of Excellent in Research for Agricultural Biotechnology and Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
                Author notes
                Author information
                https://orcid.org/0000-0001-9526-951X
                https://orcid.org/0000-0002-1582-9378
                https://orcid.org/0000-0001-8367-9415
                Article
                Publisher ID: biomolecules-10-01680
                DOI: 10.3390/biom10121680
                PMC ID: 7765599
                PubMed ID: 33339185
                SO-VID: 74b69bd0-8f9c-4818-b63e-07809dc147f2
                Copyright © © 2020 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 02 October 2020
                Date accepted : 10 December 2020
                Categories
                Subject: Article

                Keywords: garcinia cowa roxb. ex choisy,endophyte,dna damage and repair,cancer,biosensor
                Data availability:
                Keywords: garcinia cowa roxb. ex choisy, endophyte, dna damage and repair, cancer, biosensor

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