Gustavo B. Paterno, Fabian Brambach, Nathaly Guerrero-Ramírez, Delphine Clara Zemp, Aiza F. Cantillo, Nicolò Camarretta, Carina C. M. Moura, Oliver Gailing, Johannes Ballauff, Andrea Polle, Michael Schlund, Stefan Erasmi, Najeeb A. Iddris, Watit Khokthong, Leti Sundawati, Bambang Irawan, Dirk Hölscher, Holger Kreft
In monoculture-dominated landscapes, recovering biodiversity is a priority, but effective restoration strategies have yet to be identified. In this study, we experimentally tested passive and active restoration strategies to recover taxonomic, phylogenetic, and functional diversity of woody plants within 52 tree islands established in an oil palm landscape. Large tree islands and higher initial planted diversity catalyzed diversity recovery, particularly functional diversity at the landscape level. At the local scale, results demonstrated that greater initial planting diversity begets greater diversity of native recruits, overcoming limitations of natural recruitment in highly modified landscapes. Establishing large and diverse tree islands is crucial for safeguarding rare, endemic, and forest-associated species in oil palm landscapes.
{"title":"Diverse and larger tree islands promote native tree diversity in oil palm landscapes","authors":"Gustavo B. Paterno, Fabian Brambach, Nathaly Guerrero-Ramírez, Delphine Clara Zemp, Aiza F. Cantillo, Nicolò Camarretta, Carina C. M. Moura, Oliver Gailing, Johannes Ballauff, Andrea Polle, Michael Schlund, Stefan Erasmi, Najeeb A. Iddris, Watit Khokthong, Leti Sundawati, Bambang Irawan, Dirk Hölscher, Holger Kreft","doi":"10.1126/science.ado1629","DOIUrl":"10.1126/science.ado1629","url":null,"abstract":"<div >In monoculture-dominated landscapes, recovering biodiversity is a priority, but effective restoration strategies have yet to be identified. In this study, we experimentally tested passive and active restoration strategies to recover taxonomic, phylogenetic, and functional diversity of woody plants within 52 tree islands established in an oil palm landscape. Large tree islands and higher initial planted diversity catalyzed diversity recovery, particularly functional diversity at the landscape level. At the local scale, results demonstrated that greater initial planting diversity begets greater diversity of native recruits, overcoming limitations of natural recruitment in highly modified landscapes. Establishing large and diverse tree islands is crucial for safeguarding rare, endemic, and forest-associated species in oil palm landscapes.</div>","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6723","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"To target, to escape, perchance to cure: Borrowing a page from cancer’s playbook, scientists learn to evade their own therapies","authors":"Gabriele Casirati","doi":"10.1126/science.adt9029","DOIUrl":"10.1126/science.adt9029","url":null,"abstract":"","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6723","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.science.org/doi/reader/10.1126/science.adt9029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142627551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
With a vocabulary of just four nucleotides, the language of DNA encodes the fundamental information needed to orchestrate all layers of regulation in a cell, from DNA to RNA and proteins. These instructions direct the function of each cell and transmit information between generations. Changes in the genomic sequence drive evolution, enabling organisms to adapt to their environments through natural selection of advantageous DNA sequences. Therefore, comparing DNA sequences across evolutionarily diverse genomes could enable a large language model to learn the grammar of DNA, which has eluded models trained on single genomes (1). On page 746 of this issue, Nguyen et al. (2) present Evo, a foundation model trained on 2.7 million evolutionarily diverse prokaryotic and phage genomes. Having learned genomic logic, Evo can decode natural genomes; enable predictions and design tasks across DNA, RNA, and proteins; and generate DNA at the whole-genome scale.
基因组基础模型可广泛用于序列建模、预测和设计。
{"title":"Learning the language of DNA","authors":"Christina V. Theodoris","doi":"10.1126/science.adt3007","DOIUrl":"10.1126/science.adt3007","url":null,"abstract":"<div >With a vocabulary of just four nucleotides, the language of DNA encodes the fundamental information needed to orchestrate all layers of regulation in a cell, from DNA to RNA and proteins. These instructions direct the function of each cell and transmit information between generations. Changes in the genomic sequence drive evolution, enabling organisms to adapt to their environments through natural selection of advantageous DNA sequences. Therefore, comparing DNA sequences across evolutionarily diverse genomes could enable a large language model to learn the grammar of DNA, which has eluded models trained on single genomes (<i>1</i>). On page 746 of this issue, Nguyen <i>et al</i>. (<i>2</i>) present Evo, a foundation model trained on 2.7 million evolutionarily diverse prokaryotic and phage genomes. Having learned genomic logic, Evo can decode natural genomes; enable predictions and design tasks across DNA, RNA, and proteins; and generate DNA at the whole-genome scale.</div>","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6723","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142627542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Quantum computing can handle complex calculations that are otherwise infeasible for classical computers, which use binary logic (a bit, or digital information, is a 0 or 1). However, a quantum bit (qubit) often has a short life span, or coherence time, which is not sufficient to process a multitude of problems. Mechanical systems such as resonators can provide long lifetimes compared with quantum systems that are used for qubits. Resonators change shape in response to perturbations and can be coupled with a variety of external signals to create devices such as sensors and transducers, but at the quantum level, their direct manipulation is challenging. On page 783 of this issue, Yang et al. (1) report a bulk acoustic resonator coupled with a superconducting qubit that can be directly manipulated. This allows a mechanical resonator to store quantum information.
可以直接操纵声共振来存储量子信息。
{"title":"The journey to a mechanical qubit","authors":"Fabio Pistolesi","doi":"10.1126/science.adt2497","DOIUrl":"10.1126/science.adt2497","url":null,"abstract":"<div >Quantum computing can handle complex calculations that are otherwise infeasible for classical computers, which use binary logic (a bit, or digital information, is a 0 or 1). However, a quantum bit (qubit) often has a short life span, or coherence time, which is not sufficient to process a multitude of problems. Mechanical systems such as resonators can provide long lifetimes compared with quantum systems that are used for qubits. Resonators change shape in response to perturbations and can be coupled with a variety of external signals to create devices such as sensors and transducers, but at the quantum level, their direct manipulation is challenging. On page 783 of this issue, Yang <i>et al</i>. (<i>1</i>) report a bulk acoustic resonator coupled with a superconducting qubit that can be directly manipulated. This allows a mechanical resonator to store quantum information.</div>","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6723","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142627550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cristian Prieto-Garcia, Vigor Matkovic, Thorsten Mosler, Congxin Li, Jie Liang, James A. Oo, Felix Haidle, Igor Mačinković, Alfredo Cabrera-Orefice, Rayene Berkane, Giulio Giuliani, Fenfen Xu, Anne-Claire Jacomin, Ines Tomaskovic, Marion Basoglu, Marina E. Hoffmann, Rajeshwari Rathore, Ronay Cetin, Doha Boutguetait, Süleyman Bozkurt, María Clara Hernández Cañás, Mario Keller, Jonas Busam, Varun Jayeshkumar Shah, Ilka Wittig, Manuel Kaulich, Petra Beli, Wojciech P. Galej, Ingo Ebersberger, Likun Wang, Christian Münch, Alexandra Stolz, Ralf P. Brandes, William Ka Fai Tse, Stefan Eimer, Didier Y. R. Stainier, Stefan Legewie, Kathi Zarnack, Michaela Müller-McNicoll, Ivan Dikic
RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanisms and cellular responses remain poorly understood. In this work, we report that deficiency of ubiquitin-specific protease 39 (USP39) in human cell lines, zebrafish larvae, and mice led to impaired spliceosome assembly and a cytotoxic splicing profile characterized by the use of cryptic 5′ splice sites. Disruptive cryptic variants evaded messenger RNA (mRNA) surveillance pathways and were translated into misfolded proteins, which caused proteotoxic aggregates, endoplasmic reticulum (ER) stress, and, ultimately, cell death. The detrimental consequence of splicing-induced proteotoxicity could be mitigated by up-regulating the ubiquitin-proteasome system and selective autophagy. Our findings provide insight into the molecular pathogenesis of spliceosome-associated diseases.
{"title":"Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy","authors":"Cristian Prieto-Garcia, Vigor Matkovic, Thorsten Mosler, Congxin Li, Jie Liang, James A. Oo, Felix Haidle, Igor Mačinković, Alfredo Cabrera-Orefice, Rayene Berkane, Giulio Giuliani, Fenfen Xu, Anne-Claire Jacomin, Ines Tomaskovic, Marion Basoglu, Marina E. Hoffmann, Rajeshwari Rathore, Ronay Cetin, Doha Boutguetait, Süleyman Bozkurt, María Clara Hernández Cañás, Mario Keller, Jonas Busam, Varun Jayeshkumar Shah, Ilka Wittig, Manuel Kaulich, Petra Beli, Wojciech P. Galej, Ingo Ebersberger, Likun Wang, Christian Münch, Alexandra Stolz, Ralf P. Brandes, William Ka Fai Tse, Stefan Eimer, Didier Y. R. Stainier, Stefan Legewie, Kathi Zarnack, Michaela Müller-McNicoll, Ivan Dikic","doi":"10.1126/science.adi5295","DOIUrl":"10.1126/science.adi5295","url":null,"abstract":"<div >RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanisms and cellular responses remain poorly understood. In this work, we report that deficiency of ubiquitin-specific protease 39 (USP39) in human cell lines, zebrafish larvae, and mice led to impaired spliceosome assembly and a cytotoxic splicing profile characterized by the use of cryptic 5′ splice sites. Disruptive cryptic variants evaded messenger RNA (mRNA) surveillance pathways and were translated into misfolded proteins, which caused proteotoxic aggregates, endoplasmic reticulum (ER) stress, and, ultimately, cell death. The detrimental consequence of splicing-induced proteotoxicity could be mitigated by up-regulating the ubiquitin-proteasome system and selective autophagy. Our findings provide insight into the molecular pathogenesis of spliceosome-associated diseases.</div>","PeriodicalId":21678,"journal":{"name":"Science","volume":"386 6723","pages":""},"PeriodicalIF":44.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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