Journal of Molecular Evolution最新文献_第3页

EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids. EasyDIVER +：用于分析核酸或氨基酸体外进化的高通量测序数据的先进工具。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-04-01 Epub Date: 2025-04-05 DOI: 10.1007/s00239-025-10244-w

Celia Blanco, Allison Tee, Pramesh Sharma, Matilda S Newton, Kun-Hwa Lee, Samuel E Erickson, Burckhard Seelig, Irene A Chen

{"title":"EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids.","authors":"Celia Blanco, Allison Tee, Pramesh Sharma, Matilda S Newton, Kun-Hwa Lee, Samuel E Erickson, Burckhard Seelig, Irene A Chen","doi":"10.1007/s00239-025-10244-w","DOIUrl":"10.1007/s00239-025-10244-w","url":null,"abstract":"In vitro evolution is a powerful technique for identifying functional nucleic acids and peptides, but the analysis of the resulting high-throughput sequencing data poses significant challenges, particularly in peptide selections. Existing bioinformatics tools often lack the specificity needed for this task, leaving researchers to navigate complex datasets with inadequate resources. To address these challenges, we present EasyDIVER + , an enhanced pipeline building on the foundation of the original EasyDIVER tool, which was designed for pre-processing sequencing data. EasyDIVER + not only processes raw, paired-end, demultiplexed Illumina read files but also introduces advanced analytical capabilities, including the calculation of enrichment values for each unique sequence across consecutive selection rounds. Furthermore, EasyDIVER + offers a highly flexible and customizable visualization platform, enabling detailed graphical representations of sequence metrics. These new features mark a significant advance in bioinformatics for peptide and protein data, providing researchers with intuitive tools for comprehensive data analysis and interpretation.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"229-237"},"PeriodicalIF":2.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12006205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788530","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

nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models. nT4X和nT4M：新的时间不可逆混合物氨基酸取代模型。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-20 DOI: 10.1007/s00239-024-10230-8

Nguyen Huy Tinh, Cuong Cao Dang, Le Sy Vinh

{"title":"nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.","authors":"Nguyen Huy Tinh, Cuong Cao Dang, Le Sy Vinh","doi":"10.1007/s00239-024-10230-8","DOIUrl":"10.1007/s00239-024-10230-8","url":null,"abstract":"One of the most important and difficult challenges in the research of molecular evolution is modeling the process of amino acid substitutions. Although single-matrix models, such as the LG model, are popular, their capability to properly capture the heterogeneity of the substitution process across sites is still questioned. Several mixture models with multiple matrices have been introduced and shown to offer advantages over single-matrix models. Current general mixture models assume the reversibility of the evolutionary process, implying that substitution rates between any two amino acids are equal in both forward and backward directions. This assumption is not based on biological properties but rather on computational simplicity. The well-known hypothesis is that more realistic models can yield more accurate evolutionary inferences; therefore, our aim is to estimate more biologically realistic models. To this end, we relax the assumption of reversibility and introduce two new general non-reversible 4-matrix mixture models, called nT4M and nT4X. Using alignments from HSSP and TreeBASE databases as data, our newly estimated models outperformed all single-matrix models and almost all reversible mixture models. Moreover, the new non-reversible mixture models enable us to infer rooted trees.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"136-148"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006938","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

Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning. 更正：分子进化原理：多层学习理论的非平衡热力学概念。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 DOI: 10.1007/s00239-024-10228-2

Jens Smiatek

引用次数: 0

Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms. Fox基因家族在扁虫体内多个独立扩展的证据。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-18 DOI: 10.1007/s00239-024-10226-4

Ludwik Gąsiorowski

{"title":"Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms.","authors":"Ludwik Gąsiorowski","doi":"10.1007/s00239-024-10226-4","DOIUrl":"10.1007/s00239-024-10226-4","url":null,"abstract":"Expansion and losses of gene families are important drivers of molecular evolution. A recent survey of Fox genes in flatworms revealed that this superfamily of multifunctional transcription factors, present in all animals, underwent extensive losses and expansions during platyhelminth evolution. In this paper, I analyzed Fox gene complement in four additional species of platyhelminths, that represent early-branching lineages in the flatworm phylogeny: catenulids (Stenostomum brevipharyngium and Stenostomum leucops) and macrostomorphs (Macrostomum hystrix and Macrostomum cliftonense). Phylogenetic analysis of Fox genes from this expanded set of species provided evidence for multiple independent expansions of Fox gene families within flatworms. Notably, FoxG, a panbilaterian brain-patterning gene, appears to be the least susceptible to duplication, while FoxJ1, a conserved ciliogenesis factor, has undergone extensive expansion in various flatworm lineages. Analysis of the single-cell atlas of S. brevipharyngium, combined with RNA in situ hybridization, elucidated the tissue-specific expression of the selected Fox genes: FoxG is expressed in the brain, three of the Fox genes (FoxN2/3-2, FoxO4 and FoxP1) are expressed in the pharyngeal cells of likely glandular function, while one of the FoxQD paralogs is specifically expressed in the protonephridium. Overall, the evolution of Fox genes in flatworms appears to be characterized by an early contraction of the gene complement, followed by lineage-specific expansions that have enabled the co-option of newly evolved paralogs into novel physiological and developmental functions.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"124-135"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006923","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 Amphibian Major Histocompatibility Complex-A Review and Future Outlook. 两栖动物主要组织相容性复合体——综述与展望。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-07 DOI: 10.1007/s00239-024-10223-7

Joana Sabino-Pinto, Martine E Maan

{"title":"The Amphibian Major Histocompatibility Complex-A Review and Future Outlook.","authors":"Joana Sabino-Pinto, Martine E Maan","doi":"10.1007/s00239-024-10223-7","DOIUrl":"10.1007/s00239-024-10223-7","url":null,"abstract":"The major histocompatibility complex (MHC) is a cluster of functionally related genes encoding proteins which, among other functions, mediate immune system activation. While the MHC of many vertebrates has been extensively studied, less is known about the amphibian MHC. This represents an important knowledge gap because amphibians mark the evolutionary transition from an aquatic to a terrestrial lifestyle and often maintain a biphasic lifestyle. Hence, they tend to be exposed to both aquatic and terrestrial pathogen communities, providing opportunities to gain fundamental insights into how the immune system responds to different environmental challenges. Moreover, amphibians are globally threatened by invasive pathogens and the MHC may play a role in combating population decline. In this review, we summarize the current state of knowledge regarding the amphibian MHC and identify the major differences with other vertebrates. We also review how the number of MHC gene copies varies across amphibian groups and how MHC-based variation relates to amphibian ontogeny, behaviour, disease, and phylogeography. We conclude by identifying knowledge gaps and proposing priorities for future research.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"38-61"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950109","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

The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported. 两个大脑基因在人类谱系中的从头出现似乎是不支持的。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-27 DOI: 10.1007/s00239-024-10227-3

Joseph Hannon Bozorgmehr

引用次数: 0

Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes. 人类pirna及其在蛋白质编码基因中的潜在靶点之间的进化非独立性。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-02 DOI: 10.1007/s00239-024-10220-w

Chong He, Hao Zhu

{"title":"Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes.","authors":"Chong He, Hao Zhu","doi":"10.1007/s00239-024-10220-w","DOIUrl":"10.1007/s00239-024-10220-w","url":null,"abstract":"PIWI-interacting RNAs (piRNAs) are the most diverse small RNAs in animals. These small RNAs have been known to play an important role in the suppression of transposable elements (TEs). Protein-coding genes (PCGs) are the most well-recognized functional genes in genomes. In the present study, we designed and performed a set of statistics-based evolutionary analyses to reveal nonrandom phenomena in the evolution of human piRNA-PCG targeting relationships. Through analyzing the occurrence of single nucleotide variants (SNVs) in potential piRNA target sites in human PCGs, we provide evidence that there exists a mutational force biased to strengthen piRNA-PCG targeting relationships. Through analyzing the allele frequencies of SNVs in potential piRNA target sites in human PCGs, we provide evidence that there exists a piRNA-dependent selective force acting on potential piRNA target sites in human PCGs. Because of these nonrandom evolutionary forces, human piRNAs and their potential target sites in PCGs are not independent in evolution. Additionally, we found evidence that potential piRNA target sites in human PCGs are particularly likely to be present in regions derived from Alu elements. This finding suggests that the aforementioned evolutionary forces acting on piRNA-PCG targeting relationships could be particularly prone to affect Alu-derived regions in human PCGs. Collectively, our findings provide new insights into the evolutionary interplay between piRNAs, PCGs, and Alu elements in the evolution of the human genome.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"83-99"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769745","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

Human Riboviruses: A Comprehensive Study. 人类核病毒：一项综合研究。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2024-12-31 DOI: 10.1007/s00239-024-10221-9

Gauravya Mohan, Akangkha Choudhury, Jeevika Bhat, Rajendra Phartyal, Rup Lal, Mansi Verma

{"title":"Human Riboviruses: A Comprehensive Study.","authors":"Gauravya Mohan, Akangkha Choudhury, Jeevika Bhat, Rajendra Phartyal, Rup Lal, Mansi Verma","doi":"10.1007/s00239-024-10221-9","DOIUrl":"10.1007/s00239-024-10221-9","url":null,"abstract":"The urgency to understand the complex interactions between viruses, their animal reservoirs, and human populations has been necessitated by the continuous spread of zoonotic viral diseases as evidenced in epidemics and pandemics throughout human history. Riboviruses are involved in some of the most prevalent human diseases, responsible for causing epidemics and pandemics. These viruses have an animal origin and have been known to cross the inter-species barrier time and time again, eventually infecting human beings. Their evolution has been a long road to harbour important adaptations for increasing fitness, mutability and virulence; a result of natural selection and mutation pressure, making these viruses highly infectious and difficult to counter. Accumulating favourable mutations in the course, they imitate the GC content and codon usage patterns of the host for maximising the chances of infection. A myriad of viral and host factors determine the fate of specific viral infections, which may include virus protein and host receptor compatibility, host restriction factors and others. Thus, understanding the biology, transmission and molecular mechanisms of Riboviruses is essential for the development of effective antiviral treatments, vaccine development and strategies to prevent and control viral infections. Keeping these aspects in mind, this review aims to provide a holistic approach towards understanding Riboviruses.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"11-37"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909758","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

Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates. 修正：脊椎动物性别决定的随机表观遗传修饰和进化。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 DOI: 10.1007/s00239-024-10229-1

Sergio Branciamore, Andrei S Rodin, Arthur D Riggs

引用次数: 0

Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria. 细菌丝氨酸消旋酶同源物的进化和功能多样化。

IF 2.1 3区生物学

Journal of Molecular Evolution Pub Date : 2025-02-01 Epub Date: 2025-01-17 DOI: 10.1007/s00239-024-10231-7

Kouji Uda, Rie Nishimura, Yuexuan Li, Eisaku Shimoda, Tetsuya Miyamoto, Luke A Moe

{"title":"Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria.","authors":"Kouji Uda, Rie Nishimura, Yuexuan Li, Eisaku Shimoda, Tetsuya Miyamoto, Luke A Moe","doi":"10.1007/s00239-024-10231-7","DOIUrl":"10.1007/s00239-024-10231-7","url":null,"abstract":"Amino acid racemases catalyze the interconversion of L- and D-amino acids, maintaining intracellular levels of both D- and L-amino acids. While alanine and glutamate racemases are widespread in bacteria, serine racemase (SerR) is predominantly found in animals. Recently, homologs of animal SerR were reported in some bacterial genomes, but their evolutionary distribution and functional roles remain poorly understood. In this study, we cloned and expressed 20 SerR homologous genes from 13 bacterial species spanning five phyla and characterized their enzymatic activity. Six homologs exhibited serine dehydratase activity, while the remaining showed racemase activity with serine, aspartate, asparagine, or arginine. Notably, the SerR homologs from Parafannyhessea umbonata (Actinomycetota), Clostridium aceticum, Anaerovirgula multivorans, Alkaliphilus oremlandii (Bacillota), Acetomicrobium mobile, and Thermovirga lienii (Synergistota) demonstrated strong arginine racemase activity, with Km values ranging from 0.167 to 0.885 mM and kcat values ranging from 5.86 to 61.5 s-1 for L-arginine. Phylogenetic analysis revealed that bacterial and eukaryotic SerR homologs share a common ancestral gene, and substrate specificity has independently changed multiple times during evolution. Amino acid sequence alignment and analysis of site-directed mutants revealed that residues at positions 146 to 148 and surrounding regions, located near the substrate-binding site, play a crucial role in substrate specificity and/or catalytic activity. These results highlight the evolutionary processes that drive functional diversification in serine racemase homologs.","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":" ","pages":"149-162"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006926","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