BioEssays最新文献_第5页

From the Selfish Gene to the “We”: Cooperation Often Needs Suppressors 从自私基因到“我们”：合作往往需要抑制者。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-07-08 DOI: 10.1002/bies.70161

Michel Salzet

{"title":"From the Selfish Gene to the “We”: Cooperation Often Needs Suppressors","authors":"Michel Salzet","doi":"10.1002/bies.70161","DOIUrl":"10.1002/bies.70161","url":null,"abstract":"<div>\u0000 \u0000 <p>Human cooperation is often explained through motivations and values, but it is also a strategic and evolutionary problem: locally advantageous behavior can erode the collective arrangements on which everyone depends. Dawkins’ gene-centered view remains useful here, not as a moral theory of selfish people, but as a way to track how lower-level selection can destabilize higher-level organization. I argue, however, that cooperation is stabilized by a broader repertoire than external punishment alone. Repeated interaction, partner choice, aligned incentives, and architectural constraints can all make cheating unattractive; in many settings, additional suppressors then make defection costly or unprofitable. On this view, game theory and a multilevel evolutionary lens are complementary. The Folk Theorem shows how cooperative outcomes can be sustained endogenously under patience and monitoring, while biology shows how the informational and structural conditions for such equilibria are themselves produced or maintained. The point is diagnostic rather than fatalistic: cooperation is typically conditional, costly to sustain, and shaped by trade-offs, but humans can redesign incentives and institutions, especially in digital environments where misinformation and attention now propagate with unusual speed and fidelity.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 7","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148410683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Issue Information: BioEssays 7/2026 期刊信息：BioEssays 7/2026

IF 3.3 3区生物学

BioEssays Pub Date : 2026-07-02 DOI: 10.1002/bies.70162

引用次数: 0

AI in Genomics: From Variant Calling to Multi-Omics Integration 基因组学中的人工智能：从变体呼唤到多组学整合

IF 3.3 3区生物学

BioEssays Pub Date : 2026-07-02 DOI: 10.1002/bies.70160

Hina Sultana, Sabyasachi Mohanty, Abhishikt David Solomon, Mohammad Yamaan Iqbal, Atif Khurshid Wani, Vinay Kumar, Arun Khattri

{"title":"AI in Genomics: From Variant Calling to Multi-Omics Integration","authors":"Hina Sultana, Sabyasachi Mohanty, Abhishikt David Solomon, Mohammad Yamaan Iqbal, Atif Khurshid Wani, Vinay Kumar, Arun Khattri","doi":"10.1002/bies.70160","DOIUrl":"https://doi.org/10.1002/bies.70160","url":null,"abstract":"<div>\u0000 \u0000 <p>Artificial intelligence (AI) strategies are revolutionizing genomics by extracting complex patterns that traditional statistical pipelines are likely to miss. This mini-review aims to provide a concise overview of how AI is transforming major genomic technologies including variant calling, gene expression analysis, single-cell transcriptomics, CRISPR-Cas9 optimization, and multi-omics integration. In genome sequencing, machine learning variant callers greatly improve the accuracy and the rate at which single nucleotide and structural variants are called. In bulk RNA-Seq, AI augmented quantification, denoising, and differential expression modules complement the highly established STAR-featureCounts-DESeq2 pipeline, revealing subtle signals in big data sets. In single cell transcriptomics, deep learning approaches enhance batch correction, automate cell type annotation, and track developmental trajectories, hence clarifying cellular heterogeneity. AI-assisted guide RNA design, outcome prediction, and nuclease engineering enable more efficient CRISPR-Cas9 editing, reducing experimental cycles, and off-target effects. Finally, integrated platforms that combine genomic, transcriptomic, epigenomic, proteomic, and metabolomic layers provide an integrative view of cellular regulation and disease mechanisms. The review also covers current limitations, sparsity of data, model bias, privacy, and the need for standardized benchmarks and offers future directions in the form of interpretable models, collaborative learning, and open science practices. Together, these developments render AI an indispensable partner to unravel genomic complexity and accelerate precision medicine applications.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 7","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148358235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Temporal Architecture of Human Cells: Organelle Clocks and Distributed Circadian Time 人类细胞的时间结构：细胞器时钟和分布的昼夜时间。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-06-29 DOI: 10.1002/bies.70157

Jhommara Bautista, Andrés López-Cortés

{"title":"The Temporal Architecture of Human Cells: Organelle Clocks and Distributed Circadian Time","authors":"Jhommara Bautista, Andrés López-Cortés","doi":"10.1002/bies.70157","DOIUrl":"10.1002/bies.70157","url":null,"abstract":"<div>\u0000 \u0000 <p>For decades, eukaryotic circadian timing has been framed mainly through nuclear transcription–translation feedback loops (TTFLs). Here, we synthesize evidence supporting a broader organelle-centered model in which cellular time emerges from dynamic coupling between TTFL clocks, post-translational feedback loop (PTFL) oscillators, and entrained rhythmic modules across mitochondria, endoplasmic reticulum, lysosomes, peroxisomes, Golgi apparatus, plasma membrane, and cytoskeleton. Metabolic flux, redox cycling, proteostasis, ion handling, membrane excitability, trafficking, and mechanotransduction act as temporal currencies that either sustain selected transcription-independent rhythms or transmit phase information within a TTFL-coordinated network. In this layered architecture, the TTFL remains a central integrator that stabilizes inter-organelle phase relationships, aligns intracellular rhythms with environmental Zeitgebers, and links biochemical state to epigenetic and RNA-based regulation. We propose that circadian dysfunction reflects progressive intracellular desynchronization rather than isolated clock-gene failure, opening diagnostic and therapeutic opportunities aimed at restoring subcellular temporal coherence.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 6","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Opposing Activity at the Apical Surface: An Antagonistic Collaboration Between Crumbs and Myosin II Determines Organ Shape 顶端表面的对立活动：碎屑和肌球蛋白II之间的拮抗合作决定了器官形状。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-06-29 DOI: 10.1002/bies.70154

Ji Hoon Kim, Deborah J. Andrew

{"title":"Opposing Activity at the Apical Surface: An Antagonistic Collaboration Between Crumbs and Myosin II Determines Organ Shape","authors":"Ji Hoon Kim, Deborah J. Andrew","doi":"10.1002/bies.70154","DOIUrl":"10.1002/bies.70154","url":null,"abstract":"<p>Morphogenesis, the sculpting of tissues into functional architectures, requires precise orchestration of cell shape changes and rearrangements. In the <i>Drosophila</i> salivary gland (SG), recent studies reveal that Crumbs (Crb) and non-muscle Myosin II (MyoII) act as collaborative antagonists to drive SG internalization. Crb, a conserved type I transmembrane protein best known as a master regulator of apical-basal polarity, stabilizes attachments by forming homophilic extracellular bridges between neighboring cells and restricting the distribution of junctional MyoII. Conversely, MyoII is a highly conserved motor protein that drives apical constriction and junctional shrinkage by generating contractile forces on apicomedial and cortical actin and promoting apical membrane removal. During SG invagination, these opposing activities are exquisitely tuned, with Crb-mediated stabilization balancing MyoII-mediated destabilization to facilitate apical constriction for internalization and neighbor exchange for tube elongation. The conserved interplay between Crb and MyoII goes beyond the shaping of organs, serving as a critical mechanism for cell extrusion and EMT-like processes in animal development.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 6","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rethinking One Health: Microbial Foundations for Ecological Governance 重新思考同一个健康：生态治理的微生物基础。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-06-29 DOI: 10.1002/bies.70155

Andrea Fernandez Diaz, Frédéric Keck, Melissa K. Melby, Vinh-Kim Nguyen, Louis-Patrick Haraoui

{"title":"Rethinking One Health: Microbial Foundations for Ecological Governance","authors":"Andrea Fernandez Diaz, Frédéric Keck, Melissa K. Melby, Vinh-Kim Nguyen, Louis-Patrick Haraoui","doi":"10.1002/bies.70155","DOIUrl":"10.1002/bies.70155","url":null,"abstract":"<p>The One Health (OH) framework has gained prominence in recent years, promoting an approach integrating the health of humans, animals, and the environment. However, its implementation as it pertains to the microbial world has largely prioritized zoonotic diseases, antimicrobial resistance, as well as pandemic preparedness and management, narrowing its ecological scope and confining microorganisms to the realm of pathogens. We explore the historical development of OH to identify key gaps and limitations and argue for the integration of microorganisms as ecologically constitutive, critical to sustain life processes and ecosystem functioning. We provide actionable recommendations, beginning with a shift in how microorganisms are conceptualized, extending to the development of microbial metrics and culminating in proposals for microbial governance to address current shortcomings and inform future policymaking. Collectively, these measures aim to strengthen the OH framework in confronting global challenges, including biodiversity loss and climate change, while aligning with its broader commitments to health and sustainable development.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 6","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biobanked Liver Organoids: A Roadmap for Precision Hepatology 生物库肝类器官：精确肝病学的路线图。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-06-29 DOI: 10.1002/bies.70156

Elisa J. Cabré, Silvia Cobo-González, Luis Sánchez Valle, Sonia Martínez, María Del Pilar Ramos-Álvarez, Yanira Sáez-Álvarez

{"title":"Biobanked Liver Organoids: A Roadmap for Precision Hepatology","authors":"Elisa J. Cabré, Silvia Cobo-González, Luis Sánchez Valle, Sonia Martínez, María Del Pilar Ramos-Álvarez, Yanira Sáez-Álvarez","doi":"10.1002/bies.70156","DOIUrl":"10.1002/bies.70156","url":null,"abstract":"<p>Cryopreservation-enabled workflows decouple tissue acquisition from organoid generation, allowing archived biopsies and surgical explants to be revisited as renewable experimental models. This shift expands access to patient-specific material, reduces the logistical and batch variability inherent in fresh-tissue pipelines, and enables retrospective and longitudinal studies anchored in real-world clinical cohorts. Proof-of-concept studies show that liver organoids can be derived from cryopreserved human tissues that retain viability and disease-relevant phenotypes, but performance remains sensitive to the source material, culture lines, and protocol details. The field remains fragmented, lacking broadly adopted standard operating procedures, shared post-thaw quality benchmarks, and interoperable data infrastructures linking organoid biobanks to clinical metadata.</p><p>In this work, we argue that cryopreservation-enabled organoid biobanking should be treated as foundational infrastructure for precision hepatology, and we outline a pragmatic roadmap for coordinated implementation over the next decade.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 6","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70156","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hidden Fungal DNA Structures May Shape Sequencing Outcomes 隐藏的真菌DNA结构可能影响测序结果。

IF 3.3 3区生物学

BioEssays Pub Date : 2026-06-15 DOI: 10.1002/bies.70153

Paul W. Thomas

引用次数: 0

An Engineering Perspective on the Importance of Obtaining Operational Stability in Graduate School 从工程角度看研究生院获得运行稳定性的重要性。

IF 2.7 3区生物学

BioEssays Pub Date : 2026-06-09 DOI: 10.1002/bies.70149

Ashton F. Oliver, Frank L. Douglas, Ravirajsinh N. Jadeja, Merry L. Lindsey, Amadou Gaye, Pamela M. Martin

{"title":"An Engineering Perspective on the Importance of Obtaining Operational Stability in Graduate School","authors":"Ashton F. Oliver, Frank L. Douglas, Ravirajsinh N. Jadeja, Merry L. Lindsey, Amadou Gaye, Pamela M. Martin","doi":"10.1002/bies.70149","DOIUrl":"10.1002/bies.70149","url":null,"abstract":"<p>Student navigation through a PhD Program is marked by intellectual challenges, emotional fluctuations, and personal growth. Students develop excellence by absorbing and adjusting, recovering, and improving in response to challenges. The ability to bounce back is termed elasticity, an engineering principle where systems are designed to withstand stress, recover from disruptions, and maintain functionality. Students can proceed from elasticity (resilience) to then develop antifragility, the ability to become better from an experience. It occurred to the first author (a PhD graduate student in biomedical sciences) that developing antifragility is conceptually easier to understand by applying basic engineering concepts. We examine five thematic categories that connect engineering concepts with practical realities of graduate study: (1) load and stress management; (2) redundancy and backup systems; (3) setback modes and recovery; (4) adaptive capacity and flexibility; and (5) sustainability and long-term performance. By understanding how to gain antifragility, one can navigate demands more effectively.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148204262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biomolecular Condensates at the Crossroads of HIV Infection and Immune Evasion 生物分子凝聚物在HIV感染和免疫逃避的十字路口。

IF 2.7 3区生物学

BioEssays Pub Date : 2026-06-03 DOI: 10.1002/bies.70152

Selen Ay, Antonio Marino Cerrato, Francesca Di Nunzio

引用次数: 0