Cold Spring Harbor perspectives in biology最新文献_第9页

Membrane Epilipidome-Lipid Modifications, Their Dynamics, and Functional Significance. 膜表脂体-脂质修饰、其动态变化和功能意义

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041417

Sider Penkov, Maria Fedorova

{"title":"Membrane Epilipidome-Lipid Modifications, Their Dynamics, and Functional Significance.","authors":"Sider Penkov, Maria Fedorova","doi":"10.1101/cshperspect.a041417","DOIUrl":"10.1101/cshperspect.a041417","url":null,"abstract":"Lipids are characterized by extremely high structural diversity translated into a wide range of physicochemical properties. As such, lipids are vital for many different functions including organization of cellular and organelle membranes, control of cellular and organismal energy metabolism, as well as mediating multiple signaling pathways. To maintain the lipid chemical diversity and to achieve rapid lipid remodeling required for the responsiveness and adaptability of cellular membranes, living systems make use of a network of chemical modifications of already existing lipids that complement the rather slow biosynthetic pathways. Similarly to biopolymers, which can be modified epigenetically and posttranscriptionally (for nucleic acids) or posttranslationally (for proteins), lipids can also undergo chemical alterations through oxygenation, nitration, phosphorylation, glycosylation, etc. In this way, an expanded collective of modified lipids that we term the \"epilipidome,\" provides the ultimate level of complexity to biological membranes and delivers a battery of active small-molecule compounds for numerous regulatory processes. As many lipid modifications are tightly controlled and often occur in response to extra- and intracellular stimuli at defined locations, the emergence of the epilipidome greatly contributes to the spatial and temporal compartmentalization of diverse cellular processes. Accordingly, epilipid modifications are observed in all living organisms and are among the most consistent prerequisites for complex life.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520207","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

Fisher's Geometric Model as a Tool to Study Speciation. 费雪几何模型作为研究物种的工具。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041442

Hilde Schneemann, Bianca De Sanctis, John J Welch

引用次数: 0

A History of Cancer Research: Oncogenic Transcription Factors. 癌症研究史：致癌转录因子。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-06-03 DOI: 10.1101/cshperspect.a035881

Joseph Lipsick

引用次数: 0

Predictability, an Orrery, and a Speciation Machine: Quest for a Standard Model of Speciation. 可预测性、奥里里和物种机器：探索物种繁衍的标准模型。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-06-03 DOI: 10.1101/cshperspect.a041456

Marius Roesti, Hannes Roesti, Ina Satokangas, Janette Boughman, Samridhi Chaturvedi, Jochen B W Wolf, R Brian Langerhans

{"title":"Predictability, an Orrery, and a Speciation Machine: Quest for a Standard Model of Speciation.","authors":"Marius Roesti, Hannes Roesti, Ina Satokangas, Janette Boughman, Samridhi Chaturvedi, Jochen B W Wolf, R Brian Langerhans","doi":"10.1101/cshperspect.a041456","DOIUrl":"10.1101/cshperspect.a041456","url":null,"abstract":"Accurate predictions are commonly taken as a hallmark of strong scientific understanding. Yet, we do not seem capable today of making many accurate predictions about biological speciation. Why? What limits predictability in general, what exactly is the function and value of predictions, and how might we go about predicting new species? Inspired by an orrery used to explain solar eclipses, we address these questions with a thought experiment in which we conceive an evolutionary speciation machine generating new species. This experiment highlights complexity, chance, and speciation pluralism as the three fundamental challenges for predicting speciation. It also illustrates the methodological value of predictions in testing and improving conceptual models. We then outline how we might move from the hypothetical speciation machine to a predictive standard model of speciation. Operationalizing, testing, and refining this model will require a concerted shift to large-scale, integrative, and interdisciplinary efforts across the tree of life. This endeavor, paired with technological advances, may reveal apparently stochastic processes to be deterministic, and promises to expand the breadth and depth of our understanding of speciation and more generally, of evolution.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":7.2,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11146309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139721956","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

Schwann Cells as Orchestrators of Nerve Repair: Implications for Tissue Regeneration and Pathologies. 作为神经修复协调者的许旺细胞：组织再生和病理学的意义

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-06-03 DOI: 10.1101/cshperspect.a041363

Ruth M Stassart, Jose A Gomez-Sanchez, Alison C Lloyd

引用次数: 0

Optimizing Crop Plant Stomatal Density to Mitigate and Adapt to Climate Change. 优化作物气孔密度以缓解和适应气候变化。

IF 7.2 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2024-06-03 DOI: 10.1101/cshperspect.a041672

Julie Gray, Jessica Dunn

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":" ","pages":""},"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":" ","pages":""},"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":" ","pages":""},"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