BioEssays最新文献

{"title":"Safeguarding Scientific Accuracy in a Rapidly Changing World","authors":"Dave Speijer","doi":"10.1002/bies.202500016","DOIUrl":"10.1002/bies.202500016","url":null,"abstract":"<p>Recently, I have become more aware of the fact that scientific mores are changing when it comes to publishing results or theories. After a period of increased rigor (no more “unpublished results” in papers, please), the rules seem to be relaxing somewhat. One example: referring to papers that have not undergone peer review (yet). Preprint repositories, such as bioRxiv, were around from the nineties but they really multiplied and got intensely used from about 2010 onward. To be honest, I have one manuscript, reflecting unfinished business, in such a repository myself. It has been there since 2013 and was, to my surprise, quoted on several occasions. I would still hesitate to do so myself and I will explain why.</p><p>Current Biology is an excellent journal with, for example, high-quality reviews that are a joy to read. Recently, I encountered a great paper about the evolutionary arms race with defense systems and anti-defense systems constantly evolving in prokaryotes on the one hand and phages and plasmids on the other [<span>1</span>]. While perusing it, I stumbled upon a surprising fact: more than 5% (6 out of 103) of the references were to non-peer reviewed manuscripts on bioRxiv (deposited in 2023 and 2024). This example illustrates a pronounced development over the last decade: the use of preprints in such manner is now widely accepted [<span>2</span>]. The positive aspects seem clear. Researchers can get rapid feedback and community review, as well as hasten dissemination, and all this in open access form. In mathematics, meeting abstracts and preprints are even standard and encouraged by major journals (the actual publication process is almost an afterthought). On the minus side stands the possible loss of one of the safeguards of scientific quality: peer review. However, on balance, the fact that the preprint is publicly available and is clearly identified as still having to undergo peer scrutiny, does help in neutralizing the potential harm of sub-standard research.</p><p>Indeed, the quality of the process of peer review itself could be under pressure. At the risk of anecdotal misrepresentation, I have the strong impression of seeing more mistakes in published articles nowadays as compared to a few decades before. This could just reflect a greater “publish or perish” pressure, as well as ever more complicated techniques and algorithms associated with massively increased datasets. However, rapidly evolving new areas of expertise, time pressures, and the “courtesy” basis of relatively unrewarded reviewing seem to be taking their toll. I will give just one example of an error that should have been spotted before publication, having to do with one of my own hobbyhorses, the mitochondrial electron transport chain (ETC). A highly interesting PNAS perspective looks at how modern-day ETCs could tell us something about how the earliest stages of evolution might have harnessed the potential available in electrochemical gradients [<span>3</span>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202500016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381585","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}

{"title":"Selective Diversity in RNA Viruses: Do They Know How to Evolve? A Hypothesis","authors":"Lev G. Nemchinov","doi":"10.1002/bies.202400281","DOIUrl":"10.1002/bies.202400281","url":null,"abstract":"<p>Genetic diversity of viral populations is almost unanimously attributed to the build-up of random mutations along with accidental recombination events. This passive role of viruses in the selection of viable genotypes is widely acknowledged. According to the hypothesis presented here, populations of steady-state error copies of a master viral sequence would have a dominant mutant rather than a random pool of heterogeneous viral genomes with changes scattered uniformly without any preferential distribution. It would let viruses face the selection stage of host surveillance having a preceding set of potential survivors or “guard” genomes among an ordinary cloud of random quasispecies.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363664","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}

{"title":"Unlocking Disease-Modifying Treatments for TDP-43-Mediated Neurodegeneration","authors":"Rebecca San Gil,&nbsp;Adam K. Walker","doi":"10.1002/bies.202400257","DOIUrl":"10.1002/bies.202400257","url":null,"abstract":"<p>Neurons degenerate in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), causing progressive and inevitably fatal neurological decline. The best therapeutic strategies target underlying disease mediators, but after decades of intensive research, the causes of these neurodegenerative diseases remain elusive. Recently, coordinated activities of large consortia, increasing open access to large datasets, new methods such as cryo-transmission electron microscopy, and advancements in high-resolution omics technologies have offered new insights into the biology of disease that bring us closer to understanding mechanisms of neurodegeneration. In particular, improved understanding of the roles of the key pathological protein TAR DNA binding protein 43 (TDP-43) in disease has revealed intriguing new opportunities that provide hope for better diagnostic tools and effective treatments for ALS and FTD.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400257","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122172","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}

{"title":"Issue Information: BioEssays 2/2025","authors":"","doi":"10.1002/bies.202570002","DOIUrl":"https://doi.org/10.1002/bies.202570002","url":null,"abstract":"","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202570002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143118287","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}

{"title":"Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes","authors":"Francisco Rodriguez-Algarra,&nbsp;Elliott Whittaker,&nbsp;Sandra del Castillo del Rio,&nbsp;Vardhman K. Rakyan","doi":"10.1002/bies.202400232","DOIUrl":"10.1002/bies.202400232","url":null,"abstract":"<p>Although genome-scale analyses have provided insights into the connection between genetic variability and complex human phenotypes, much trait variation is still not fully understood. Genetic variation within repetitive elements, such as the multi-copy, multi-locus ribosomal DNA (rDNA), has emerged as a potential contributor to trait variation. Whereas rDNA was long believed to be largely uniform within a species, recent studies have revealed substantial variability in the locus, both within and across individuals. This variation, which takes the form of copy number, structural arrangement, and sequence differences, has been found to be associated with human phenotypes. This review summarizes what is currently known about human rDNA variation, its causes, and its association with phenotypic outcomes, highlighting the technical challenges the field faces and the solutions proposed to address them. Finally, we suggest experimental approaches that can help clarify the elusive mechanisms underlying the phenotypic consequences of rDNA variation.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000411","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}

{"title":"Mechanisms of Lipid-Associated Macrophage Accrual in Metabolically Stressed Adipose Tissue","authors":"Isabel Reinisch,&nbsp;Sarah Enzenhofer,&nbsp;Andreas Prokesch","doi":"10.1002/bies.202400203","DOIUrl":"10.1002/bies.202400203","url":null,"abstract":"<p>Adipose tissue (AT) inflammation, a hallmark of the metabolic syndrome, is triggered by overburdened adipocytes sending out immune cell recruitment signals during obesity development. An AT immune landscape persistent throughout weight loss and regain constitutes an immune-obesogenic memory that hinders long-term weight loss management. Lipid-associated macrophages (LAMs) are emerging as major players in diseased, inflamed metabolic tissues and may be key contributors to an obesogenic memory in AT. Our previous study found that LAM abundance increases with weight loss via intermittent fasting (IF) in obese mice, which is driven by adipocyte p53 signalling. However, the specific signals causing LAM accumulation in AT under IF remain unknown. In this piece, we hypothesise on a range of adipocyte-secreted signals that can harbor immune-attractive features upon fasting/refeeding cycles. We highlight possible mechanisms including cell death signalling, matrikines, and other damage-associated molecular patterns (DAMPs), as well as adipo(-cyto)kines, lipid mediators, metabolites, extracellular vesicles, and epigenetic rewiring. Finally, we consider how advances in mechanisms of AT LAM recruitment gleaned from preclinical models might be translatable to long-term weight management in humans. Thus, we provide vantage points to study signals driving monocyte recruitment, polarisation towards LAMs, and LAM retention, to harness the therapeutic potential of modulating AT LAM levels by impacting the immune-obesogenic memory in metabolic disease.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400203","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000413","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}

{"title":"Nucleic Acid Aptamer-Based Sensors for Bacteria Detection: A Review","authors":"Yalan Tang,&nbsp;Yun Li,&nbsp;Ping Chen,&nbsp;Shian Zhong,&nbsp;Yanjing Yang","doi":"10.1002/bies.202400111","DOIUrl":"10.1002/bies.202400111","url":null,"abstract":"<div>\u0000 \u0000 <p>Bacteria have a significant impact on human production and life, endangering human life and health, so rapid detection of infectious agents is essential to improve human health. Aptamers, which are pieces of oligonucleotides (DNA or RNA) have been applied to biosensors for bacteria detection due to their high affinity, selectivity, robust chemical stability, and their compatibility with various signal amplification and signal transduction mechanisms. In this review, we summarize the different bacterial aptamers selected in recent years using SELEX technology and discuss the differences in optical and electrochemical bacterial aptamer sensors. In addition the technological developments and innovations in bacterial aptamer sensor technology are introduced. Combining new materials and methods, the efficiency and stability of the sensors have also been improved. This review summarizes the progress of current bacterial aptamer sensors based on their practical application status and provides an outlook on their future development.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000414","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}

{"title":"Metabolic Dysregulation as a Central Mechanism in 16p11.2 Deletion Syndrome: A Multigenic Perspective on Clinical Variability and Therapeutic Opportunities","authors":"Rana Fetit","doi":"10.1002/bies.202400299","DOIUrl":"10.1002/bies.202400299","url":null,"abstract":"","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982849","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}

{"title":"Epithelial Polarity Loss and Multilayer Formation: Insights Into Tumor Growth and Regulatory Mechanisms","authors":"Jie Sun,&nbsp;Md Biplob Hosen,&nbsp;Wu-Min Deng,&nbsp;Aiguo Tian","doi":"10.1002/bies.202400189","DOIUrl":"10.1002/bies.202400189","url":null,"abstract":"<div>\u0000 \u0000 <p>Epithelial tissues serve as critical barriers in metazoan organisms, maintaining structural integrity and facilitating essential physiological functions. Epithelial cell polarity regulates mechanical properties, signaling, and transport, ensuring tissue organization and homeostasis. However, the barrier function is challenged by cell turnover during development and maintenance. To preserve tissue integrity while removing dying or unwanted cells, epithelial tissues employ cell extrusion. This process removes both dead and live cells from the epithelial layer, typically causing detached cells to undergo apoptosis. Transformed cells, however, often resist apoptosis, leading to multilayered structures and early carcinogenesis. Malignant cells may invade neighboring tissues. Loss of cell polarity can lead to multilayer formation, cell extrusion, and invasion. Recent studies indicate that multilayer formation in epithelial cells with polarity loss involves a mixture of wild-type and mutant cells, leading to apical or basal accumulation. The directionality of accumulation is regulated by mutations in polarity complex genes. This phenomenon, distinct from traditional apical or basal extrusion, exhibits similarities to the endophytic or exophytic growth observed in human tumors. This review explores the regulation and implications of these phenomena for tissue biology and disease pathology.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906623","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}

{"title":"Vascular-Associated Mononuclear Phagocytes: First-Line Soldiers Ambushing Metastasis","authors":"Han-ying Huang,&nbsp;Xin-nan Zheng,&nbsp;Lin Tian","doi":"10.1002/bies.202400261","DOIUrl":"https://doi.org/10.1002/bies.202400261","url":null,"abstract":"<div>\u0000 \u0000 <p>Mononuclear phagocytes (MPs), which consist of dendritic cells, monocytes, and macrophages, are distributed throughout the body and actively eliminate invading microorganisms and abnormal cells. Depending on the local microenvironment, MPs manifest considerably various lifespans and phenotypes to maintain tissue homeostasis. Vascular-associated mononuclear phagocytes (VaMPs) are the special subsets of MPs that are localized either within the lumen side or on the apical surface of vessels, acting as the critical sentinels to recognize and defend against disseminated tumor cells. In this review, we introduce three major types of VaMPs, patrolling monocytes, Kupffer cells, and perivascular macrophages, and discuss their emerging roles in immunosurveillance during incipient metastasis. We also explore the roles of lineage-determining transcription factors and cell surface receptors that endow VaMPs with potent anti-tumor activity. Finally, we highlight the molecular and cellular mechanisms that drive the phenotypic plasticity of VaMPs and summarize combinatory strategies for targeting VaMPs in overt metastasis.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143475849","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}