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A multi-kingdom genetic barcoding system for precise clone isolation

Nature Biotechnology 2025年 1-14页

作者： Soh Ishiguro Rina C. Sakata Ren Takimoto Rina Yogo Yusuke Kijima Samuel King Omar Bashth Nanami Masuyama Arman Adel Nika Shakiba Nozomu Yachie Kana Ishida Minori Ichiraku Takuya Yamamoto Yasuhiro Takashima Hideto Mori Mamoru Tanaka Hiromi Toyoshima Motoaki Seki Hiroyuki Aburatani Shoko Tarumoto Taro Tsujimura Ju Hee Oh Anne-Sophie Archambault Akihiko Kondo Ramon I. Klein Geltink Keiji Nishida Satoru Kuhara School of Biomedical Engineering Faculty of Applied Science and Faculty of Medicine The University of British Columbia Vancouver British Columbia Canada Institute for Advanced Biosciences Keio University Tsuruoka Japan Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe) The University of Osaka Osaka Japan Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Spiber Inc Tsuruoka Japan Center for iPS Cell Research and Application Kyoto University Kyoto Japan Institute for the Advanced Study of Human Biology (WPI-ASHBi) Kyoto University Kyoto Japan BC Children’s Hospital Research Institute Department of Pathology and Laboratory Medicine The University of British Columbia Vancouver British Columbia Canada Engineering Biology Research Center Kobe University Kobe Japan Graduate School of Science Technology and Innovation Kobe University Kobe Japan Department of Chemical Science and Engineering Graduate School of Engineering Kobe University Kobe Japan Graduate School of Bioresource and Bioenvironmental Sciences Faculty of Agriculture Kyushu University Fukuoka Japan

Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.

关键词： Genes

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Machine Learning for Prediction of Adverse Drug Reactions: Application to Neonatal Intensive Care Units

SSRN

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SSRN 2023年

作者： do Nascimento, Amanda Roseane Farias Greati, Victor Rodrigues Leopoldino, Ramon Weyler Duarte Martins, Rand Randall Barbosa, Euzebio Guimarães Graduate Program in Pharmaceutical Sciences Health Sciences Center Federal University of Rio Grande do Norte Rio Grande do Norte Natal Brazil Graduate Program in Systems and Computing Department of Informatics and Applied Mathematics Federal University of Rio Grande do Norte Rio Grande do Norte Natal Brazil

Introduction: The intensive care of neonates is associated with the entry of a large volume of data in their medical records. The treatment of this data can be done through Machine Learning: a tool capable of assisting in the detection and decision-making of a wide range of medical conditions, including adverse drug reactions (ADR). Objective: To train a prediction model to assist in the detection of adverse drug reactions in neonates admitted to an ICU. Methodology: observational study developed in the Neonatal Intensive Care Unit of a teaching hospital in Brazil. Clinical data were collected from daily pharmacotherapeutic follow-up, processed and analyzed by machine learning through libraries written in Python language. Results: Eight hundred and three neonates were included in the study, with a mean gestational age of 32.2 ± 4.2 weeks and mean birth weight of 1807.2 ± 936.6g. The incidence of ADR was 10.8%. Antimicrobials, especially aminoglycosides, were the most prescribed drugs for this population. An algorithm was trained and tested to predict ADR in the NICU, in which the metrics were precision (0.35) and recall (0.823), with specificity (80%) and sensitivity (67%). Conclusion: There is a high potential in the machine learning method to predict ADR in neonates admitted to an ICU. © 2023, The Authors. All rights reserved.

关键词： Forecasting

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A Systematic Review of the Potential Effects of Propolis Extracts on Experimentally-induced Diabetes

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Planta Medica 2022年第3期89卷 236-244页

作者： Gustavo Aparecido da Cunha Paulo Fernando Carlstrom Marcelo Franchin Severino Matias Alencar Masaharu Ikegaki Pedro Luiz Rosalen Biological Sciences Graduate Program Federal University of Alfenas Alfenas MG Brazil Biosciences and Biotechnology Applied to Pharmacy Graduate Program São Paulo State University Araraquara SP Brazil Faculty of Dentistry Federal University of Alfenas Alfenas MG Brazil Department of Agri-Food Industry Food and Nutrition Luiz de Queiroz College of Agriculture University of São Paulo Piracicaba SP Brazil Faculty of Pharmaceutical Science Federal University of Alfenas Alfenas MG Brazil

Oxidative stress (OS) is involved in the development of diabetes mellitus (DM) and its complications. Thus, OS reduction may be an important strategy for DM therapy. Propolis is bee resins with high antioxidant activity and is used in the treatment of different diseases, including DM. Therefore, in this systematic review, we evaluated the impact of propolis administration in diabetic animals. We used the PRISMA strategy to collect preclinical studies published in English up to November 2021 in three databases (PubMed/Medline, Scopus, and Web of Science). We used the SYRCLE tool to analyze the risk of methodological bias. Our primary search returned 198 studies, of which 14 were considered eligible to be included in this review. The administration of propolis induced a hypoglycemic effect in the treated animals, which is probably due to the reduction of OS. The animals showed restoration of endogenous antioxidant defenses and reduced levels of markers for OS. The administration of propolis resulted in improvement in the lipid profile of treated animals. Our risk of bias assessment showed a methodological quality score of less than 30% due to a lack of randomization, blinding, and proper allocation of animals. Heterogeneity in treatments, lack of results, and use of non-standard extracts are limitations in our data analysis. Despite these limitations, propolis induced a significant hypoglycemic effect in diabetic animals when compared to untreated controls. This effect was associated with a reduction in OS, a process mediated by ROS neutralization and restoration of endogenous antioxidant defenses.

关键词： propolis flavonoids diabetes bee glue

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Fungal impacts on Earth’s ecosystems

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Nature 2025年第8049期638卷 49-57页

作者： Case, Nicola T. Gurr, Sarah J. Fisher, Matthew C. Blehert, David S. Boone, Charles Casadevall, Arturo Chowdhary, Anuradha Cuomo, Christina A. Currie, Cameron R. Denning, David W. Ene, Iuliana V. Fritz-Laylin, Lillian K. Gerstein, Aleeza C. Gow, Neil A. R. Gusa, Asiya Iliev, Iliyan D. James, Timothy Y. Jin, Hailing Kahmann, Regine Klein, Bruce S. Kronstad, James W. Ost, Kyla S. Peay, Kabir G. Shapiro, Rebecca S. Sheppard, Donald C. Shlezinger, Neta Stajich, Jason E. Stukenbrock, Eva H. Taylor, John W. Wright, Gerard D. Cowen, Leah E. Heitman, Joseph Segre, Julia A. Department of Molecular Genetics University of Toronto Toronto ON Canada Biosciences University of Exeter Exeter United Kingdom University of Utrecht Utrecht Netherlands MRC Center for Global Infectious Disease Analysis Imperial College London London United Kingdom National Wildlife Health Center U.S. Geological Survey Madison WI United States Donnelly Centre University of Toronto Toronto ON Canada RIKEN Center for Sustainable Resource Science Wako Japan Department of Molecular Microbiology and Immunology Johns Hopkins University Baltimore MD United States Medical Mycology Unit Department of Microbiology Vallabhbhai Patel Chest Institute University of Delhi Delhi India National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens Vallabhbhai Patel Chest Institute University of Delhi Delhi India Department of Molecular Microbiology and Immunology Brown University Providence RI United States Department of Biochemistry and Biomedical Sciences McMaster University Hamilton ON Canada Department of Bacteriology University of Wisconsin–Madison Madison WI United States Manchester Fungal Infection Group Faculty of Biology Medicine and Health Manchester Academic Health Science Centre University of Manchester Manchester United Kingdom Fungal Heterogeneity Group Institut Pasteur Université Paris Cité Paris France Department of Biology University of Massachusetts Amherst MA United States Department of Microbiology University of Manitoba Winnipeg MB Canada Department of Statistics University of Manitoba Winnipeg MB Canada Medical Research Council Centre for Medical Mycology University of Exeter Exeter United Kingdom Department of Molecular Genetics and Microbiology Duke University Durham NC United States Joan and Sanford I. Weill Department of Medicine Weill Cornell Medicine Cornell University New York NY United States Jill Roberts Institute for Research in Inflammatory Bowel Disease Weill Cornell Medicine New York NY United St

Over the past billion years, the fungal kingdom has diversified to more than two million species, with over 95% still undescribed. Beyond the well-known macroscopic mushrooms and microscopic yeast, fungi are heterotrophs that feed on almost any organic carbon, recycling nutrients through the decay of dead plants and animals and sequestering carbon into Earth’s ecosystems. Human-directed applications of fungi extend from leavened bread, alcoholic beverages and biofuels to pharmaceuticals, including antibiotics and psychoactive compounds. Conversely, fungal infections pose risks to ecosystems ranging from crops to wildlife to humans;these risks are driven, in part, by human and animal movement, and might be accelerating with climate change. Genomic surveys are expanding our knowledge of the true biodiversity of the fungal kingdom, and genome-editing tools make it possible to imagine harnessing these organisms to fuel the bioeconomy. Here, we examine the fungal threats facing civilization and investigate opportunities to use fungi to combat these threats. © This is a U.S. Government work and not under copyright protection in the US;foreign copyright protection may apply 2025.

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Self-Compassion Around the World: Measurement Invariance of the Short Form of the Self-Compassion Scale (SCS-SF) Across 65 Nations, 40 Languages, Gender Identities, and Age Groups

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Mindfulness 2025年 1-28页

作者： Swami, Viren Tran, Ulrich S. Voracek, Martin Aavik, Toivo Ranjbar, Hamed Abdollahpour Adebayo, Sulaiman Olanrewaju Afhami, Reza Ahmed, Oli Aimé, Annie Akel, Marwan Al Halbusi, Hussam Alexias, George Ali, Khawla F. Alp-Dal, Nursel Alsalhani, Anas B. Álvarez-Solas, Sara Amaral, Ana Carolina Soares Andrianto, Sonny Aspden, Trefor Argyrides, Marios Aruta, John Jamir Benzon R. Atkin, Stephen Ayandele, Olusola Baceviciene, Migle Bahbouh, Radvan Ballesio, Andrea Barron, David Bellard, Ashleigh Bender, Sóley Sesselja Beydaǧ, Kerime Derya Birovljević, Gorana Blackburn, Marie-Ève Borja-Alvarez, Teresita Borowiec, Joanna Bozogáňová, Miroslava Bratland-Sanda, Solfrid Browning, Matthew H. E. M. Brytek-Matera, Anna Burakova, Marina Çakır-Koçak, Yeliz Camacho, Pablo Camilleri, Vittorio Emanuele Cazzato, Valentina Cerea, Silvia Chaiwutikornwanich, Apitchaya Chaleeraktrakoon, Trawin Chambers, Tim Chen, Qing-Wei Chen, Xin Chien, Chin-Lung Chobthamkit, Phatthanakit Choompunuch, Bovornpot Compte, Emilio J. Corrigan, Jennifer Cosmas, Getrude Cowden, Richard G. Czepczor-Bernat, Kamila Czub, Marcin da Silva, Wanderson Roberto Dadfar, Mahboubeh Dalley, Simon E. Dany, Lionel Datu, Jesus Alfonso D. de Carvalho, Pedro Henrique Berbert de Holanda Coelho, Gabriel Lins De Jesus, Avila Odia S. Debbabi, Sonia Harzallah Dhakal, Sandesh Di Bernardo, Francesca Dimitrova, Donka D. Dion, Jacinthe Dixson, Barnaby Donofrio, Stacey M. Drysch, Marius Du, Hongfei Dzhambov, Angel M. El-Jor, Claire Enea, Violeta Eskin, Mehmet Farbod, Farinaz Farrugia, Lorleen Fian, Leonie Fisher, Maryanne L. Folwarczny, Michał Frederick, David A. Fuller-Tyszkiewicz, Matthew Furnham, Adrian García, Antonio Alías Geller, Shulamit Ghisi, Marta Ghorbani, Alireza Martinez, Maria Angeles Gomez Gradidge, Sarah Graf, Sylvie Grano, Caterina Gyene, Gyöngyvér Hallit, Souheil Hamdan, Motasem Handelzalts, Jonathan E. Hanel, Paul H. P. Hawks, Steven R. Hekmati, Issa Helmy, Mai Hill, Tetiana Hina, Farah Holenweger, Geraldine Hřebíčková, Martina Ijabadeniyi, Olasupo Augustine Imam, Asma İ School of Psychology and Sport Science Anglia Ruskin University Cambridge United Kingdom Centre for Psychological Medicine Perdana University Kuala Lumpur Malaysia Department of Cognition Emotion and Methods in Psychology Faculty of Psychology University of Vienna Vienna Austria Institute of Psychology University of Tartu Tartu Estonia Department of Psychology Istinye University Istanbul Turkey Department of Psychology and Behavioural Studies Ekiti State University Ado-Ekiti Nigeria Department of Art Studies Tarbiat Modares University Tehran Iran Department of Psychology University of Chittagong Chattogram Bangladesh Department of Psychoeducation and Psychology Université du Québec en Outaouais Saint-Jérôme Canada INSPECT-LB: National Institute of Public Health Clinical Epidemiology and Toxicology Beirut Lebanon School of Pharmacy Lebanese International University Beirut Lebanon Department of Management Ahmed Bin Mohammad Military College Doha Qatar Faculty of Psychology Panteion University of Social and Political Sciences Athens Greece Royal College of Surgeons Ireland-Bahrain Adliya Bahrain Department of Midwifery Faculty of Health Sciences Munzur University Tunceli Turkey Department of Oral Medicine and Diagnostic Sciences Vision College of Dentistry and Nursing Vision Colleges Riyadh Saudi Arabia Facultad de Salud Universidad Internacional de La Rioja Logroño Spain Science and Technology of Southeast Minas Gerais Federal Institute of Education Barbacena Brazil Department of Psychology Universitas Islam Indonesia Yogyakarta Indonesia Department of Psychology Aberystwyth University Ceredigion United Kingdom Department of Psychology Neapolis University Pafos Paphos Cyprus Department of Psychology De La Salle University Manila Philippines Department of General Studies The Polytechnic Ibadan Nigeria Department of Psychology University of Ibadan Ibadan Nigeria Health Research and Innovation Science Centre Faculty of Health Sciences Klai

Objectives: The 12-item Self-Compassion Scale–Short Form (SCS–SF) is a widely used instrument for the assessment of self-compassion. To date, there have been few examinations of this instrument’s psychometric properties, particularly across nations and languages. Therefore, we used data from the Body Image in Nature Survey (BINS) to assess measurement invariance of the SCS–SF across nations, languages, gender identities, and age groups. Methods: Participants (N = 56,968) from 65 nations completed the SCS–SF in 40 languages. Using these data, we tested various hypothesised models of the SCS–SF in the total sample and, using multi-group confirmatory factor analysis, tested for invariance of the optimal model across national groups, languages, gender identities, and age groups. Results: In the total dataset, we found that an 11-item, 2-factor model (i.e., SCS-11) provided best fit to the data, with the two factors tapping distinct constructs of compassionate and uncompassionate self-responding. The SCS-11 was found to be partially scalar invariant across national groups and languages, and fully scalar invariant across gender identities and age groups. There was wide variation in latent means for the two factors, particularly across national groups and languages. Further analyses showed negligible associations between the two factors and sociodemographic variables, including marital status, financial security, and urbanicity. Conclusions: Our results suggest that it may be possible to derive a stable 2-factor model of the SCS–SF for use in cross-cultural research, but also highlight the likelihood of cross-national and cross-linguistic variations in the way that self-compassion is understood. © The Author(s) 2025.

关键词： Cross-cultural Measurement invariance Multi-group confirmatory factor analysis (MG-CFA) Self-Compassion Scale Short Form

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Endophytic fungi of Brunfelsia uniflora: Isolation, cryopreservation, and determination of enzymatic and antioxidant activity

Research Square

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Research Square 2021年

作者： Marsola, Sara Jane Jorge, Lais Freitas Meniqueti, Adriano Borges Bertéli, Miria Benetati Delgado de Lima, Thaís Emanuelle Feijó Bezerra, José Luiz Lopes, Ana Daniela Gazim, Zilda Cristiani do Valle, Juliana Silveira Colauto, Nelson Barros Linde, Giani Andrea Universidade Paranaense Graduate Program of Biotechnology Applied to Agriculture Umuarama87502-210 Brazil Universidade Federal do Recôncavo da Bahia Cruz das Almas44380-00 Brazil Federal University of Bahia Ondina Campus Graduate Program in Food Science - Faculty of Pharmacy Salvador40110-115 Brazil Federal University of Bahia Canela Campus Graduate Program in Food Nutrition and Health - School of Nutrition Salvador40110-907 Brazil

Brunfelsia uniflora (Pohl.) D. Don (Solanaceae), commonly known as manacá-de-cheiro, is widely distributed in Brazil and used by local indigenous peoples as an antirheumatic, antisyphilitic, depurative, emetic, vermifuge, and purgative agent. Several studies have examined the biological activities and phytochemical profile of Brunfelsia;however, few have focused on the diversity of endophytic microorganisms that colonize members of the genus. This study aimed to isolate and cryopreserve endophytic fungi from B. uniflora and determine their cellulase, laccase, and antioxidant activities. Endophytic fungi were isolated from B. uniflora stems, cultured on wheat grains, immersed in a 150 g·L-1 aqueous sucrose solution, and cryopreserved at −80°C for 1 and 6 months. Cellulase activity was determined by a qualitative test using carboxymethylcellulose medium and laccase activity by a quantitative test based on the oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate). Prior to antioxidant activity assays, fungi were grown in malt extract broth for production of mycelial biomass. A methanolic extract was prepared for evaluation of DPPH• scavenging activity, FRAP activity, and total phenolic content. A total of 46 endophytic fungal isolates were obtained from B. uniflora stems and classified into 24 groups according to morphological similarities. B. uniflora was shown to harbor a great diversity of endophytic fungi. Mycelial viability was observed after 1 and 6 months of cryopreservation at −80 °C. Fungi exhibited cellulase and laccase activities. Isolate CE23 had the highest laccase activity after 7 days of cultivation. Twelve isolates were found to have low total phenolic contents and DPPH• and FRAP activities. © 2021, CC BY.

关键词： Enzymes

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Neuromotor and Functional Adaptations in Schoolchildren Practicing Exergames

Neuromotor and Functional Adaptations in Schoolchildren Prac...

引用

Technology Innovations for healthcare (ICTIH), International Conference on

作者： Estelio Henrique Martin Dantas Karollyni Bastos Andrade Madson Rodrigo Silva Bezerra Renato Ramos Coelho Estevão Scudese Eric Marcos Nunes Calvacante João Wolney Teles Soares Thigna De Carvalho Batista Roberto Jerônimo Dos Santos Silva Master and Doctor's Degree Program in Health and Environment - PSA Tiradentes University - UNIT Doctor's Degree Program in Nursing and Biosciences - PPgEnfBio Federal University of the State of Rio de Janeiro UNIRIO Rio de Janeiro Brazil Aracaju Brazil Master and Doctor's Degree Program in Health and Environment PSA Tiradentes University (UNIT) Aracaju Brazil Post graduate Program in Biotechnology of RENORBIO Aracaju Brazil Nomus Consultoria Belo Horizonte Brazil Doctor's Degree Program in Nursing and Biosciences - PPgEnfBio Federal University of the State of Rio de Janeiro - UNIRIO Rio de Janeiro Brazil Unama (Universidade da Amazônia) Belém Brazil Universidade Tiradentes Aracaju Brazil Post graduate Program in Physical Education Federal University of Sergipe São Cristóvão Brazil

Exergames can become an alternative tool for enhancing neuromotor capacity from routines and systematization. Thirty-two students (age group: 8 - 10 years) were evaluated and divided into two random groups, the control group - CG (n = 10) and the exergame group - EG (n = 22). Flexibility capacity and abdominal and upper limbs resistance were evaluated before and after 16 weeks. A 2x2 factorial ANOVA, Post-Hoc Bonferroni, and the effect size was calculated using SPSS for Windows v.23. Significant changes in flexibility were observed, which F (1.30) = 7.683; p < 0.01; r = 0.45; EG presented significant alteration F (1.30) = 15.1; p < 0.01; r = 0.57, however, CG showed no significant changes F (1.30) = 0.52; p = 0.47; r = 0.13. For the upper limbs strength analysis, only EG presented significant adaptation F (1.30) = 5.01; p < 0.05; r = 0.37. Finally, there were no significant changes in the variable abdominal strength.

关键词： Resistance Technological innovation Medical services Analysis of variance

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Bioindustry ethics /

引用

2005年

作者： David L. Finegold ... [et al.].

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N-ACT: An Interpretable Deep Learning Model for Automatic Cell Type and Salient Gene Identification

arXiv

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arXiv 2022年

作者： Ali Heydari, A. Davalos, Oscar A. Hoyer, Katrina K. Sindi, Suzanne S. Department of Applied Mathematics University of California United States Health Sciences Research Institute Quantitative and Systems Biology Graduate Program Department of Molecular and Cell Biology University of California Merced United States

Single-cell RNA sequencing (scRNAseq) is rapidly advancing our understanding of cellular composition within complex tissues and organisms. A major limitation in most scRNAseq analysis pipelines is the reliance on manual annotations to determine cell identities, which are time consuming, subjective, and require expertise. Given the surge in cell sequencing, supervised methods–especially deep learning models–have been developed for automatic cell type identification (ACTI), which achieve high accuracy and scalability. However, all existing deep learning frameworks for ACTI lack interpretability and are used as "black-box" models. We present N-ACT (Neural-Attention for Cell Type identification): the first-of-its-kind interpretable deep neural network for ACTI utilizing neural attention to detect salient genes for use in cell-types identification. We compare N-ACT to conventional annotation methods on two previously manually annotated data sets, demonstrating that N-ACT accurately identifies marker genes and cell types in an unsupervised manner, while performing comparably on multiple data sets to current state-of-the-art model in traditional supervised ACTI. © 2022, CC BY.

关键词： Genes

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Glyphosate-Residues in Roundup-Ready Soybean Impair Daphnia magna Life-Cycle

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Journal of Agricultural Chemistry and Environment 2015年第1期4卷 24-36页

作者： Marek Cuhra Terje Traavik Mickael Dando Raul Primicerio Daniel Ferreira Holderbaum Thomas Bohn Faculty of Health Sciences The Arctic University of NorwayTromsoNorway GenOk—Centre for Biosafety The Science ParkTromsoNorway Faculty of Biosciences Fisheries and EconomicsThe Arctic University of NorwayTromsoNorway Graduate Program in Plant Genetic Resources Federal University of Santa Catarina(UFSC)FlorianópolisBrazil

Herbicide tolerant plants such as Roundup-Ready soybean contain residues of glyphosate herbicide. These residues are considered safe and previous animal-feeding-studies have failed to find negative effects related to such chemical residues. The present study tests 8 experimental soy- meal diets as feed in groups (each containing 20 individuals) of test-animals (D. magna). The diets have different levels of glyphosate residues and we show that animal growth, reproductive maturity and number of offspring are correlated with these chemicals. The tested soybeans are from ordinary agriculture in Iowa USA and the residues are below the regulatory limits. Despite this, clear negative effects are seen in life-long feeding. The work enhances the need for including analysis of herbicide residues in future assessment of GMO.

关键词： Transgenic GTS 40-3-2 Roundup-Ready Soybean Glyphosate Residues Life-Long Animal Feeding Study GMO Risk-Assessment Herbicide-Tolerant Cultivar Quality Aquatic Invertebrate Ecotoxicology

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