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      Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents

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          Abstract

          Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems.

          This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

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          Most cited references184

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          U1 snRNP regulates cancer cell migration and invasion in vitro

          Stimulated cells and cancer cells have widespread shortening of mRNA 3’-untranslated regions (3’UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in introns and last exons. U1 snRNP (U1), vertebrates’ most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread premature transcription termination and mRNA shortening. Here we show that low U1 AMO doses increase cancer cells’ migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3’UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected role for U1 homeostasis (available U1 relative to transcription) in oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.
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            The biomass distribution on Earth

            Significance The composition of the biosphere is a fundamental question in biology, yet a global quantitative account of the biomass of each taxon is still lacking. We assemble a census of the biomass of all kingdoms of life. This analysis provides a holistic view of the composition of the biosphere and allows us to observe broad patterns over taxonomic categories, geographic locations, and trophic modes.
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              Antibiotic resistance: a rundown of a global crisis

              The advent of multidrug resistance among pathogenic bacteria is imperiling the worth of antibiotics, which have previously transformed medical sciences. The crisis of antimicrobial resistance has been ascribed to the misuse of these agents and due to unavailability of newer drugs attributable to exigent regulatory requirements and reduced financial inducements. Comprehensive efforts are needed to minimize the pace of resistance by studying emergent microorganisms, resistance mechanisms, and antimicrobial agents. Multidisciplinary approaches are required across health care settings as well as environment and agriculture sectors. Progressive alternate approaches including probiotics, antibodies, and vaccines have shown promising results in trials that suggest the role of these alternatives as preventive or adjunct therapies in future.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: Writing – review & editing
                Journal
                Philos Trans R Soc Lond B Biol Sci
                Philos Trans R Soc Lond B Biol Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                August 15, 2022
                June 27, 2022
                June 27, 2022
                : 377
                : 1857 , Theme issue ‘Ecological complexity and the biosphere: the next 30 years’ compiled and edited by Ricard Solé and Simon A. Levin
                : 20210395
                Affiliations
                Systems Biology Department, Centro Nacional de Biotecnología-CSIC, , Campus de Cantoblanco, Madrid 28049, Spain
                Author notes

                One contribution of 15 to a theme issue ‘ Ecological complexity and the biosphere: the next 30 years’.

                Author information
                http://orcid.org/0000-0002-6041-2731
                Article
                rstb20210395
                10.1098/rstb.2021.0395
                9234819
                35757882
                9ce20121-10d1-4bd5-8748-7b255eaf985f
                © 2022 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : January 9, 2022
                : Feburary 9, 2022
                Funding
                Funded by: Ministerio de Ciencia y Tecnología, http://dx.doi.org/10.13039/501100006280;
                Award ID: ERA-COBIOTECH 2018 - PCI2019-111859-2 of MCIN/AEI
                Award ID: RTI2018-095584-B-C42-MCIN/ AEI /10.13039/501100011
                Funded by: Horizon 2020 Framework Programme, http://dx.doi.org/10.13039/100010661;
                Award ID: H2020-FET-OPEN-RIA-2017-1-766975
                Award ID: H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650
                Award ID: MIX-UP H2020-BIO-CN-2019-870294
                Funded by: Consejería de Educación e Investigación, http://dx.doi.org/10.13039/501100010774;
                Award ID: S2017/BMD-3691
                Award ID: Y2020/TCS- 6555
                Categories
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                Custom metadata
                August 15, 2022

                Philosophy of science
                synthetic biology,chassis,horizontal gene transfer,pseudomonas,containment,digital twins

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