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Urban river recovery: a systematic review on the effectiveness of water clean-up programs

Environmental Science and Pollution Research 2024年第18期31卷 26355-26377页

作者： Silva, Caroline Ferreira da Pereira, Elisabete Alves Carvalho, Mayara de Almeida Ribeiro Botero, Wander Gustavo de Oliveira, Luciana Camargo Federal University of São Carlos Sorocaba Campus Graduate Program in Biotechnology and Environmental Monitoring João Leme dos Santos Highway km 110 - SP-264 SP Sorocaba18052.780 Brazil Federal University of Alagoas Graduate Program in Chemistry and Biotechnology Alagoas Maceió57072-900 Brazil

Urban rivers are affected at different levels by the intensification of human activities, representing a serious threat to the maintenance of terrestrial life and sustainable urban development. Consequently, great efforts have been dedicated to the ecological restoration of urban rivers around the world, as a solution to recovering the environmental functionality of these environments. In this sense, the present work aimed to investigate the effectiveness of interventions carried out aimed at the recovery of urban rivers, through a systematic review of the literature between 2010 and 2022, using the search term "rivers recovery." The results showed that there have been notable advances in the implementation of river recovery programs in urban areas around the world between the years analyzed. The ecosystems studied were affected, for the most part, by the increase in the supply of nutrients from domestic and industrial effluents, in addition to having highly urbanized surroundings and with several changes in land use patterns. The preparation of this literature review made it possible to demonstrate that the effectiveness of river recovery is extremely complex, since river recovery projects are developed for different reasons, as well as being carried out in different ways according to the intended objective. Graphical abstract: (Figure presented.) © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

关键词： Water quality

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Arabidopsis mRNA decay landscape shaped by XRN 5′-3′ exoribonucleases

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Plant Journal 2023年第4期114卷 895-913页

作者： Han, Wan-Yin Hou, Bo-Han Lee, Wen-Chi Chan, Tze-Ching Lin, Tzu-Hsiang Chen, Ho-Ming Agricultural Biotechnology Research Center Academia Sinica Taipei11529 Taiwan Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program National Chung-Hsing University Taichung 40227 and Academia Sinica Taipei11529 Taiwan Graduate Institute of Biotechnology National Chung-Hsing University Taichung40227 Taiwan Biotechnology Center National Chung-Hsing University Taichung40227 Taiwan

5′-3′ exoribonucleases (XRNs) play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of Arabidopsis wild-type and mutant plants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 activity but not nuclear XRN2 activity greatly altered Arabidopsis mRNA decay profiles. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the unique function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that pre-mRNA 3′ end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wild-type plants include not only the primary substrates of XRN4 but also the products of XRN4-mediated cytoplasmic decay. An increase in decay intermediates with 5′ ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3′ untranslated regions of many Arabidopsis mRNAs. However, analysis of decay fragments in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence rarely result in major decay intermediates. Together, these findings reveal the major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data. © 2023 Society for Experimental Biology and John Wiley & Sons Ltd.

关键词： RNA

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Structure-Functional Activity of Pyrone Derivatives for Inhibition of Barnacle Settlement and Biofilm Formation

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Marine biotechnology 2024年第5期26卷 1000-1008页

作者： Khan, Mo Aqib Raza Wang, Bo-Wei Lin, Hsiu-Chin Yang, Yu-Liang Liaw, Chih-Chuang Department of Marine Biotechnology and Resources National Sun Yat-Sen University Kaohsiung80424 Taiwan Doctoral Degree Program in Marine Biotechnology National Sun Yat-Sen University Kaohsiung80424 Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei115 Taiwan Biotechnology Center in Southern Taiwan Academia Sinica Tainan711 Taiwan Graduate Institute of Natural Products Kaohsiung Medical University Kaohsiung807 Taiwan Graduate Institute of Pharmacognosy Taipei Medical University Taipei110 Taiwan

Naturally occurring 6-pentyl-2H-pyran-2-one and its synthetic analogues greatly inhibit the settlement of Amphibalanus amphitrite cyprids and the growth and biofilm formation of marine bacteria. To optimize the antifouling activities of pyrone derivatives, this study designed pyrone analogues by modifying functional groups, such as the benzyl group, cyclopentane, and halides, substituted on both sides of a pyrone. The antifouling effects of the synthesized pyrone derivatives were subsequently evaluated against five marine biofilm–forming bacteria, Loktanella hongkongensis, Staphylococcus cohnii, S. saprophyticus, Photobacterium angustum, and Alteromonas macleodii, along with barnacle cyprids of Amphibalanus amphitrite. Substituting nonpolar parts—such as the aliphatic, cyclopentyl, or phenyl moieties on C-5 or the furan moieties on C-3—not only increased antibacterial activity and inhibited biofilm formation but also inhibited barnacle cyprid settlement when compared to 6-pentyl-2H-pyran-2-one. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.

关键词： Bacteria

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TaxDiff: taxonomic-guided diffusion model for protein sequence generation

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Science China(Information Sciences) 2025年第4期68卷 385-386页

作者： Zongying LIN Hao LI Liuzhenghao LV Yu WANG Bin LIN Junwu ZHANG Zijun CHEN Calvin Yu-Chian CHEN Li YUAN Yonghong TIAN School of Electronic and Computer Engineering Peking University AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Peng Cheng Laboratory School of Chemical Biology and Biotechnology Peking University

Protein design aims to generate protein variants with targeted biological functions, which is significant in multiple biological areas, including enzyme reaction catalysis, vaccine design, and fluorescence intensity. Protein design contains two paradigms: sequence generation and structure generation. Recently, EvoDiff [1] proposed a universal designing paradigm, combining structure and sequence generation using the diffusion framework, which improves the protein design efficiency.

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Antcin A, a phytosterol regulates SARS-CoV-2 spike protein-mediated metabolic alteration in THP-1 cells explored by the ¹H-NMR-based metabolomics approach

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Phytotherapy Research 2023年第3期37卷 885-902页

作者： Dakpa, Gyaltsen Senthil Kumar, Kanthasamy Jayabal Tsao, Nai-Wen Wang, Sheng-Yang Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Graduate Institute of Biotechnology National Chung-Hsing University Taichung Taiwan Bachelor Program of Biotechnology National Chung Hsing University Taichung Taiwan Department of Forestry National Chung-Hsing University Taichung Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan

The mechanism of SARS-CoV-2 spike protein-mediated perturbations of metabolic pathways and modulation of antcin A, a steroid-like compound isolated from Taiwanofungus camphoratus, are not studied. Here, we investigated the metabolic alteration by SARS-CoV-2 spike protein and the regulatory effect of antcin A on SARS-CoV-2 spike protein-induced metabolic changes in the Phorbol 12-myristate 13-acetate (PMA)-induced human monocytes (THP-1) using proton nuclear magnetic resonance (¹H-NMR) and MetaboAnalyst 5.0 software. The cytotoxic potential of SARS-CoV-2 spike protein, antcin A, and dexamethasone was assessed by MTT assay. The metabolomic perturbations and their relation to human coronaviruses' receptors were evaluated by qPCR. This study indicated that the altered metabolites mediated by SARS-CoV-2 protein, such as methionine, phosphoenolpyruvic acid, canadine, glutamine, ethanolamine, and phenylalanine, were significantly reversed by antcin A. In addition, antcin A significantly inhibited SARS-CoV-2 spike protein-mediated up-regulation of TLR-4 and ACE2 receptors, while GRP78 inhibition was not statistically significant. This is the first study to use ¹H-NMR to investigate SARS-CoV-2 spike protein-induced metabolomic changes in PMA-induced THP-1 cells. Antcin A significantly reversed metabolomic alters while dexamethasone failed to fix them. Therefore, we believe that antcin A could be a potential candidate for therapeutic agents for viral infections related to a metabolic abnormality. © 2022 John Wiley & Sons Ltd.

关键词： 1H-NMR antcin A metabolomics SARS-CoV-2 spike protein Taiwanofungus camphoratus

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Rejuvenation of Meropenem by Conjugation with Tilapia Piscidin-4 Peptide Targeting NDM-1 Escherichia coli

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ACS Omega 2024年第27期9卷 29756-29764页

作者： Selvaraj, Sanjay Prasad Lin, Kuan-Hung Lin, Wen-Chun You, Ming-Feng Li, Tsung-Lin Chen, Jyh-Yih Molecular and Biological Agricultural Science Program Taiwan International Graduate Program Academia Sinica Graduate Institute of Biotechnology National Chung Hsing University Genomics Research Center Academia Sinica Marine Research Station Institute of Cellular and Organismic Biology Academia Sinica Biotechnology Center National Chung Hsing University The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine National Chung Hsing University

Gram-negative pathogens that produce β-lactamases pose a serious public health threat as they can render β-lactam antibiotics inactive via hydrolysis. This action contributes to the waning effectiveness of clinical antibiotics and creates an urgent need for new antimicrobials. Antimicrobial peptides (AMPs) exhibiting multimodal functions serve as a potential source in spite of a few limitations. Thus, the conjugation of conventional antibiotics with AMPs may be an effective strategy to leverage the advantages of each component. In this study, we conjugated meropenem to the AMP Tilapia piscidin 4 (TP4) using a typical coupling reaction. The conjugate was characterized by using HPLC-MS, HR-MS, and MS-MS fragmentation analysis. It was then evaluated in terms of antibacterial potency, hemolysis, and cytotoxicity toward RAW264.7 and CCD-966SK cell lines. The conjugation of meropenem with TP4 significantly reduced the cytotoxicity compared to TP4. Conjugation of unprotected TP4 with meropenem resulted in cross-linking at the N-terminal and lysine sites. The structural activity relationship of the two isomers of the TP4-meropenem conjugate was investigated. Both the isomers showed notable antibacterial activities against NDM-1 Escherichia coli and reduced red blood cell hemolysis as compared to TP4. Lysine conjugate (TP4-K-Mero) showed lesser hemolysis than the N-terminal conjugate (TP4-N-Mero). Molecular modeling further revealed that the conjugates can bind to lipopolysaccharides and inhibit NDM-1 β-lactamase. Together, these data show that conjugation of antibiotics with AMP can be a feasible approach to increase the therapeutic profile and effectively target multidrug-resistant pathogens. Furthermore, antibiotic conjugation at different AMP sites tends to show unique biological properties. © 2024 The Authors. Published by American Chemical Society.

关键词： Antimicrobial agents Show More

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Theoretical–experimental evaluation of the effects of Fe3+ ions in the disinfection of water supply by peracetic acid

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Discover Water 2024年第1期4卷 1-14页

作者： Souza, Aline Karla Nolberto Paggiaro, Juliana Martins, Warlyton Silva Pereira, Anna Karla Santos Pereira, Douglas Henrique Cavallini, Grasiele Soares Graduate Program in Chemistry Federal University of Tocantins Gurupi Brazil Graduate Program in Biotechnology Federal University of Tocantins Gurupi Brazil Graduate Program in Plant Production Federal University of Tocantins Gurupi Brazil

Peracetic acid (PAA) is efficient for disinfection processes in environmental sanitation and in the presence of transition metals its oxidative performance is enhanced. Thus, the present study aim evaluated the influence of Fe3+ ions during the inactivation process of Escherichia coli and Total Coliforms (TC). The process PAA + Fe3+ ions were also evaluated in relation to the disinfection kinetics, the participation of H2O2 and the influence of the organic load of the treated water. The tests showed an inactivation efficient of 0.5 to 0.9 log in relation to E. coli and 1.3 to 1.5 logs for TC in the concentrations evaluated and complete inactivation of E. coli was achieved within 15 min for both PAA and PAA/Fe3+ There is no damage to the disinfection process in the presence of Fe3+ ions, however, the decomposition of PAA is favored. In this sense, the formation of radicals can justify the maintenance of disinfection efficiency. The decay constants were close both microorganisms: for E. coli with PAA and PAA/Fe3+were 0.0323 and 0.0476 and for TC were 0.0637 and 0.0667. The values of R2 were above 0.95. Computer simulations of peptidoglycans that make up the bacterial cell wall showed that radicals preferentially attacked the carbons from the rings that composes the cell wall peptidoglycan of gram-negative bacteria allowing to break the structure during the disinfection process.

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Concerns about the application of resistance exercise with blood-flow restriction and thrombosis risk in hemodialysis patients

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Journal of Sport and Health Science 2024年第4期13卷 548-558,F0003页

作者： Hugo de Luca Correa Lysleine Alves Deus Dahan da Cunha Nascimento Nicholas Rolnick Rodrigo Vanerson Passos Neves Andrea Lucena Reis Thais Branquinho de Araujo Carmen Tzanno-Martins Fernanda Silveira Tavares Luiz Sinesio Silva Neto Claudio Avelino Rodrigues Santos Paolo Lucas Rodrigues-Silva Fernando Honorato Souza Vitoria Marra da Motta Vilalva Mestrinho Rafael Lavarini dos Santos Rosangela Vieira Andrade Jonato Prestes Thiago dos Santos Rosa Post-graduate Program of Physical Education Catholic University of BrasıliaBrasılia 71966-700Brazil The Human Performance Mechanic Lehman CollegeNew YorkNY 10011USA Clinical Group Home Dialysis Center and RenalClass Sao Paulo 01239-040Brazil Department of Medicine Catholic University of BrasıliaBrasılia 71966-700Brazil Faculty of Medicine Federal University of TocantinsTocantins 77001-090Brazil Embrapa Genetic Resources and Biotechnology Brasılia 70770-917Brazil Graduate Program of Genomic Sciences and Biotechnology Brasılia 71966-700Brazil

Background:Hemodialysis(HD) per se is a risk factor for *** the growing body of evidence on blood-flow restriction(BFR) exercise in HD patients,identification of possible risk factors related to the prothrombotic agent D-dimer is required for the safety and feasibility of this training *** aim of the present study was to identify risk factors associated with higher D-dimer levels and to determine the acute effect of resistance exercise(RE) with BFR on this ***:Two hundred and six HD patients volunteered for this study(all with a glomerular filtration rate of <15 mL/min/1.73 m2).The RE+BFR session consisted of 50% arterial occlusion pressure during 50 min sessions of HD(intradialytic exercise).RE repetitions included concentric and eccentric lifting phases(each lasting 2 s) and were supervised by a strength and conditioning ***:Several variables were associated with elevated levels of D-dimer,including higher blood glucose,citrate use,recent cardiovascular events,recent intercurrents,higher inflammatory status,catheter as vascular access,older patients(>70 years old),and HD ***,RE+BFR significantly increases D-dimer after 4 *** with borderline baseline D-dimer levels(400-490 ng/mL) displayed increased risk of elevating D-dimer over the normal range(≥500 ng/mL).Conclusion:These results identified factors associated with a heightened prothrombotic state and may assist in the screening process for HD patients who wish to undergo RE+BFR.D-dimer and/or other fibrinolysis factors should be assessed at baseline and throughout the protocol as a precautionary measure to maximize safety during RE+BFR.

关键词： Blood-flow restriction Chronic kidney disease Coagulation Hemodialysis Vascular occlusion exercises

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Neural regeneration research model to be explored:SH-SY5Y human neuroblastoma cells

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Neural Regeneration Research 2023年第6期18卷 1265-1266页

作者： Lavynia Ferreira Hoffmann Alexandre Martins Fernanda Majolo Verônica Contini Stefan Laufer Márcia Inês Goetiert Graduate Program in Biotechnology University of Vale do Taquari(Univates)LajeadoRio Grande do SulBrazil Graduate Program in Medical Sciences-PPGCM University of Vale do Taquari-UnivatesLajeado/RSBrazil Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery-TÜCADDEberhard Karls University TübingenTübingenGermany

In neuroscience research,neuronal models are crucial tools for elucidating the molecular and cellular processes involved in the disorders of the nervous *** easily and reproducibly executable studies,in vitro models,such as the SH-SY5Y cell line culture,help us explore the pathophysiological mechanisms of neurodegenerative diseases;they are also essential for the efficient screening of drugs for treating the diseases of the nervous system(Peng et al.,2021;Strother et al.,2021).

关键词： neuroblastoma diseases

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Cyto and genotoxicity induced by acute exposure to Novacron® Bold Deep Navy dye on Astyanax lacustris can be reduced after treatment through a vertical flow constructed wetland system

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Environmental Science and Pollution Research 2024年第59期31卷 66630-66642页

作者： da Silva, Josiane Rodrigues Rocha de Andrade, Camila Oliveira Ribeiro, Anna Carla Macruz, Paula Derksen Bergamasco, Rosângela Fernandes, Carlos Alexandre Graduate Program of Environmental Biotechnology Department of Biotechnology Genetics and Cell Biology State University of Maringá Paraná Maringá Brazil Department of Chemistry State University of Maringá Paraná Maringá Brazil Department of Chemical Engineering State University of Maringá Paraná Maringá Brazil Biological Sciences Center State University of Maringá Paraná Maringá Brazil Department of Biotechnology Genetics and Cell Biology State University of Maringá Avenida Colombo 5790 Paraná MaringáCEP 87020-900 Brazil

Reactive dyes used in the textile industry can be harmful to aquatic organisms. This study aimed to evaluate the potential cyto/genotoxic effects of the Novacron® Bold Deep Navy reactive dye on fish Astyanax lacustris before and after treatment through a vertical flow constructed wetland system (VFCW). Micronucleus test (MN), cellular morphological changes (CMC), and the comet assay were used to assess the effects of the dye in erythrocytes. During the experiment, A. lacustris specimens were exposed to sublethal concentrations (10, 20, 30, and 40 mg/L) of Novacron® Bold Deep Navy dye for 96 h. Results showed that the dye caused MN formation (27), DNA damage, and several types of CMC (3513) in all tested concentrations on A. lacustris. Notably, analyses were significant (p © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

关键词： Textile industry

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