Cold Spring Harbor perspectives in biology最新文献_第6页

Multiple Sclerosis and Other Acquired Demyelinating Diseases of the Central Nervous System. 多发性硬化症和其他后天性中枢神经系统脱髓鞘疾病。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-28 DOI: 10.1101/cshperspect.a041374

Michael D Kornberg, Peter A Calabresi

引用次数: 0

Physical Forces in Regeneration of Cells and Tissues. 细胞和组织再生中的物理力

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-28 DOI: 10.1101/cshperspect.a041527

Sindy K Y Tang, Wallace F Marshall

引用次数: 0

Satellite Glial Cells: No Longer the Most Overlooked Glia. 卫星胶质细胞：卫星胶质细胞：不再是最被忽视的胶质细胞

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-20 DOI: 10.1101/cshperspect.a041367

Susan J Birren, Lisa V Goodrich, Rosalind A Segal

引用次数: 0

Understanding the Influence of Host Radiation on Symbiont Speciation through Parasites of Species Flocks. 通过种群寄生虫了解宿主辐射对共生体物种变异的影响

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-20 DOI: 10.1101/cshperspect.a041450

Maarten P M Vanhove, Nikol Kmentová, Christel Faes, Jorge M O Fernandes, Christoph Hahn, Niel Hens, Antoine Pariselle, Stephan Koblmüller

引用次数: 0

Coevolutionary Interactions between Sexual and Habitat Isolation during Reinforcement. 强化过程中性隔离与生境隔离之间的共同进化相互作用

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041431

Roman Yukilevich, Fumio Aoki, Scott Egan, Linyi Zhang

{"title":"Coevolutionary Interactions between Sexual and Habitat Isolation during Reinforcement.","authors":"Roman Yukilevich, Fumio Aoki, Scott Egan, Linyi Zhang","doi":"10.1101/cshperspect.a041431","DOIUrl":"10.1101/cshperspect.a041431","url":null,"abstract":"Speciation often involves the evolution of multiple genetic-based barriers to gene flow (i.e., \"coupling\"). However, barriers may exhibit a diversity of evolutionary interactions during speciation. These dynamics are important in reinforcement, where selection may favor different prezygotic isolating barriers to avoid maladaptive hybridization. Here we study the interaction between evolution of sexual and habitat isolation. We first review the empirical literature where both barriers were explicitly considered, and then develop a population genetic model of reinforcement. Most studies of both sexual and habitat isolation were found in phytophagous insect systems. In 76% of these studies, both barriers coevolved; the remaining cases either showed only habitat isolation (21%) or only sexual isolation (3%). Our two-allele genetic mechanism model of each barrier also found that these often coevolved, but habitat isolation was generally more effective during reinforcement. Depending on the fitness of hybrids (e.g., Dobzhansky-Muller incompatibilities) and initial migration rate, these barriers could either facilitate, curtail, or have no effect on each other. This indicates that basic parameters will alter the underlying evolutionary dynamics, and thus the nature of \"speciation coupling\" will be highly variable in natural systems. Finally, we studied initially asymmetrical migration rates and found that populations with higher initial emigration evolved stronger habitat isolation, while populations that initially received more immigrants exhibited stronger sexual isolation. These results are in line with observations in some empirical studies, but more data is needed to test their generality.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Petabase-Scale Homology Search for Structure Prediction. 用于结构预测的 Petabase 级同源搜索。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041465

Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger

{"title":"Petabase-Scale Homology Search for Structure Prediction.","authors":"Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger","doi":"10.1101/cshperspect.a041465","DOIUrl":"10.1101/cshperspect.a041465","url":null,"abstract":"The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2-based prediction methods. To push the boundaries of MSA utilization, we conducted a petabase-scale search of the Sequence Read Archive (SRA), resulting in gigabytes of aligned homologs for CASP15 targets. These were merged with default MSAs produced by ColabFold-search and provided to ColabFold-predict. By using SRA data, we achieved highly accurate predictions (GDT_TS > 70) for 66% of the non-easy targets, whereas using ColabFold-search default MSAs scored highly in only 52%. Next, we tested the effect of deep homology search and ColabFold's advanced features, such as more recycles, on prediction accuracy. While SRA homologs were most significant for improving ColabFold's CASP15 ranking from 11th to 3rd place, other strategies contributed too. We analyze these in the context of existing strategies to improve prediction.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Cell Adhesion Molecule Signaling at the Synapse: Beyond the Scaffold. 突触中的细胞粘附分子信号：超越支架。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041501

Ben Verpoort, Joris de Wit

引用次数: 0

Microbial Catalysis for CO₂ Sequestration: A Geobiological Approach. 微生物催化CO2封存：一种地球生物学方法。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041673

Martin Van Den Berghe, Nathan G Walworth, Neil C Dalvie, Chris L Dupont, Michael Springer, M Grace Andrews, Stephen J Romaniello, David A Hutchins, Francesc Montserrat, Pamela A Silver, Kenneth H Nealson

{"title":"Microbial Catalysis for CO2 Sequestration: A Geobiological Approach.","authors":"Martin Van Den Berghe, Nathan G Walworth, Neil C Dalvie, Chris L Dupont, Michael Springer, M Grace Andrews, Stephen J Romaniello, David A Hutchins, Francesc Montserrat, Pamela A Silver, Kenneth H Nealson","doi":"10.1101/cshperspect.a041673","DOIUrl":"10.1101/cshperspect.a041673","url":null,"abstract":"One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is not enough. Carbon dioxide removal (CDR) will also be needed to avoid the catastrophic effects of global warming. Although the drawdown and storage of CO2 occur naturally via the coupling of the silicate and carbonate cycles, they operate over geological timescales (thousands of years). Here, we suggest that microbes can be used to accelerate this process, perhaps by orders of magnitude, while simultaneously producing potentially valuable by-products. This could provide both a sustainable pathway for global drawdown of CO2 and an environmentally benign biosynthesis of materials. We discuss several different approaches, all of which involve enhancing the rate of silicate weathering. We use the silicate mineral olivine as a case study because of its favorable weathering properties, global abundance, and growing interest in CDR applications. Extensive research is needed to determine both the upper limit of the rate of silicate dissolution and its potential to economically scale to draw down significant amounts (Mt/Gt) of CO2 Other industrial processes have successfully cultivated microbial consortia to provide valuable services at scale (e.g., wastewater treatment, anaerobic digestion, fermentation), and we argue that similar economies of scale could be achieved from this research.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":7.2,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41112380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Peripheral Nervous System (PNS) Myelin Diseases. 周围神经系统 (PNS) 髓鞘疾病。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041376

Steven S Scherer, John Svaren

引用次数: 0

Drivers of Morphogenesis: Curvature Sensor Self-Assembly at the Membrane 形态发生的驱动因素：膜曲率传感器的自组装

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-05-02 DOI: 10.1101/cshperspect.a041528

Brandy N. Curtis, Amy S. Gladfelter

{"title":"Drivers of Morphogenesis: Curvature Sensor Self-Assembly at the Membrane","authors":"Brandy N. Curtis, Amy S. Gladfelter","doi":"10.1101/cshperspect.a041528","DOIUrl":"https://doi.org/10.1101/cshperspect.a041528","url":null,"abstract":"This review examines the relationships between membrane chemistry, curvature-sensing proteins, and cellular morphogenesis. Curvature-sensing proteins are often orders of magnitude smaller than the membrane curvatures they localize to. How are nanometer-scale proteins used to sense micrometer-scale membrane features? Here, we trace the journey of curvature-sensing proteins as they engage with lipid membranes through a combination of electrostatic and hydrophobic interactions. We discuss how curvature sensing hinges on membrane features like lipid charge, packing, and the directionality of membrane curvature. Once bound to the membrane, many curvature sensors undergo self-assembly (i.e., they oligomerize or form higher-order assemblies that are key for initiating and regulating cell shape transformations). Central to these discussions are the micrometer-scale curvature-sensing proteins’ septins. By discussing recent literature surrounding septin membrane association, assembly, and their many functions in morphogenesis with support from other well-studied curvature sensors, we aim to synthesize possible mechanisms underlining cell shape sensing.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":7.2,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140833415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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