Marine Life Science & Technology最新文献

{"title":"Current status of phylogenetic studies on ciliated protists (Alveolata, Protozoa, Ciliophora) by the OUC-group: advances, challenges and future perspectives.","authors":"Feng Gao, Yang Bai, Yong Chi, Xiaochen Feng, Chunyu Lian, Borong Lu, Xiaotian Luo, Mingzhen Ma, Congcong Wang, Yurui Wang, Zhe Wang, Gongaote Zhang, Saleh A Al-Farraj, Alan Warren, Weibo Song","doi":"10.1007/s42995-025-00326-5","DOIUrl":"10.1007/s42995-025-00326-5","url":null,"abstract":"<p><p>Ciliated protists (ciliates) represent a morphologically and genetically diverse group of single-celled eukaryotes, the phylogeny of which is critical for understanding eukaryotic evolution. Through international collaborations, the Laboratory of Protozoology at Ocean University of China (OUC-group) has conducted detailed research on ciliate phylogeny based on expanded taxonomic sampling, employing single gene as well as multi-gene markers, and phylogenomic datasets. We have systematically investigated > 1000 ciliate species spanning ~ 40 orders, sampled from diverse biotopes including marine environments in China seas and freshwater wetlands. This comprehensive sampling has generated three key datasets: (1) genomic DNA extracts from ~ 2600 strains, (2) ~ 2300 sequences of marker genes, and (3) single-cell genomic and/or transcriptomic datasets from ~ 120 species. Based on these datasets, the phylogenetic relationships covering all classes and most orders have been thoroughly reconstructed and investigated, resulting in the establishment of 93 new supraspecies taxa comprising two classes (Mesodiniea and Protocruziea), two subclasses (Protohypotrichia and Synhymenia), two orders (Wilbertomorphida and Lynnellida), 11 families, and 76 genera. Moreover, we have reconstructed a genome-scale tree of life for ciliates and provided an updated classification of the phylum Ciliophora. Furthermore, based on the robust phylogenetic tree of ciliates, we provide more reliable estimates for the origins and divergence times of the main ciliate groups. Future studies integrating advanced genomics, innovations in culturing and interdisciplinary applications will refine the ciliate tree of life, with broader impacts for our understanding of eukaryotic evolution and biodiversity.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"643-669"},"PeriodicalIF":5.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650088","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}

{"title":"Metamorphosis in <i>Aurelia aurita</i> from polyp to medusa: assessing composition and metabolism throughout development.","authors":"Vanesa Romero-Kutzner, Daniel R Bondyale-Juez, Ico Martínez, Alicia Herrera, Theodore T Packard, May Gómez","doi":"10.1007/s42995-025-00329-2","DOIUrl":"10.1007/s42995-025-00329-2","url":null,"abstract":"<p><p><i>Aurelia aurita</i> exhibits a triphasic life cycle involving metamorphosis, transitioning from sessile polyps to free-swimming ephyrae and eventually maturing into medusae. This metamorphic process is triggered by a reduction in temperature. In this investigation, we delve into the intricate changes in protein, lipid, and carbohydrate content, and examine alterations in respiratory and excretory metabolisms using both physiological and enzymatic methodologies. This study provides the first monitoring of these parameters. Observations at compositional and metabolic levels were conducted over 108 days in triplicate, with three simultaneous cultures maintained under identical conditions throughout the experiment. The findings reveal compositional changes, particularly in lipid content, one of the main sources of biological energy during metamorphosis. Additionally, a 20-day increase in water content from 89 to 99% occurred during the transition from strobila to metaephyra. Respiratory activity reduced by 76% during strobilation, due to the necessary temperature drop. Concurrently, excretory activity showed a more gradual increase in ammonium excretion during the planktonic stages once feeding resumed. These findings highlight the role of temperature-dependent triggers and metabolic shifts in facilitating energy storage among other functions. This knowledge may provide insights into the potential impacts of future environmental change on the entire lifecycle.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00329-2.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"742-756"},"PeriodicalIF":5.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650170","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}

{"title":"Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.","authors":"Heyu Lin, Xiao-Yu Zhu, Chun-Xu Xue, Peng Yao, Liang Fu, Zuosheng Yang, Xiao-Hua Zhang, John W Moreau","doi":"10.1007/s42995-025-00332-7","DOIUrl":"10.1007/s42995-025-00332-7","url":null,"abstract":"<p><p>Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair <i>hgcAB</i> encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. \"Blue holes\" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, <i>Nitrospina</i> and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00332-7.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"8 1","pages":"206-220"},"PeriodicalIF":5.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12953829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147357349","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}

{"title":"Multi-omics analysis guided discovery: hydroxyproline enhance muscle hardness of hybrid bream (BBTB, <i>Megalobrama amblycephala</i> ♀ × <i>Culter alburnus</i> ♂) via myofiber proliferation and collagen deposition.","authors":"Anli Zuo, Zhehua Xu, Yimiao He, Junchi Zhao, Qianting Zheng, Mingyu Zhang, Weiting Zhang, Jianzhou Tang, Shenping Cao, Qiong Zhao, Junyan Jin, Zhen Liu","doi":"10.1007/s42995-025-00331-8","DOIUrl":"https://doi.org/10.1007/s42995-025-00331-8","url":null,"abstract":"<p><p>Hardness is widely regarded as a critical factor influencing the whole texture of fish flesh. The objective of this study was to elucidate the regulatory mechanism underlying muscle hardness in hybrid bream (BBTB, <i>Megalobrama amblycephala</i> ♀ × <i>Culter alburnus</i> ♂). A comparison of the physiological features of high hardness (HH) and low hardness (LH) muscle revealed that the former had higher contents of collagen I and lower muscle fiber diameter. Transcriptomic data revealed that the myofiber assembly pathway and the HIF-1 signaling pathway were activated in HH muscle. At the metabolic level, the categories of amino acids and lipids were the principal differentially abundant metabolites between the HH and LH muscle. The detection of amino acid profiles further revealed significant differences in amino acid metabolism between the HH and LH muscles, with the HH muscle having higher levels of amino acids than the LH muscle, especially hydroxyproline (Hyp). Furthermore, through supplementation of Hyp in BBTB myoblasts, the results indicated that 0.8 mmol/L Hyp increased the proliferation, differentiation, migration, and collagen synthesis of myoblasts. Finally, BBTB was treated with Hyp intraperitoneally for 15 days. The results revealed that 0.1 g/kg Hyp significantly increased muscle hardness, myofiber density, myofibrillar protein synthesis, and HIF-1 protein content. The results obtained in this study indicated that Hyp supplementation promoted collagen synthesis and proliferation of myoblast and muscle fibers in the BBTB, which may be induced by activation of the transcription factor HIF1 and contributes to the impacts of Hyp on improvements in muscle hardness in the BBTB.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00331-8.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"962-977"},"PeriodicalIF":5.3,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145649802","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}

{"title":"The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.","authors":"Ruyi Dong, Yongqin Liu, Ninglian Wang, Kellynn K Y Tan, Mukan Ji","doi":"10.1007/s42995-025-00323-8","DOIUrl":"https://doi.org/10.1007/s42995-025-00323-8","url":null,"abstract":"<p><p>Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00323-8.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"978-988"},"PeriodicalIF":5.3,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650114","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}

{"title":"Integrative analysis of coral plasticity and adaptations reveals key proteins driving resilience to changes in ocean carbonate chemistry.","authors":"Xiangcheng Yuan, Ellias Y Feng, Jingtian Wang, Lei Jiang, Tao Yuan, Hui Huang, Weihua Zhou, Jack Chi-Ho Ip, Wei-Jun Cai, Senjie Lin","doi":"10.1007/s42995-025-00321-w","DOIUrl":"10.1007/s42995-025-00321-w","url":null,"abstract":"<p><p>Understanding how corals adapt to changes in seawater carbonate chemistry is crucial for developing effective coral conservation strategies. Research to date has mostly focused on short-term experiments, overlooking long-term evolutionary effects. Here, we investigated the link between short-term stress responses and long-term genetic adaptations in the coral species <i>Porites pukoensis</i> through experiments under varying CO₂ and alkalinity conditions. Our results showed that alkalinity enrichment significantly increased coral calcification rates by 35%-45% compared to high CO₂ treatment, highlighting the potential of alkalinity enrichment to mitigate acidification impacts. Corals modulated relative expression levels of basic and acidic proteins in response to changes in seawater carbonate chemistry in the stress experiments. Genomic data revealed that this mechanism has been evolutionarily fixed in various organisms adapting to seawater carbonate chemistry. Additionally, both experimental and genomic results showed that extracellular matrix proteins, like collagen with von Willebrand factor type A domain, were modified in response to distinct carbonate environments. Molecular dynamics simulations and in-vitro experiments demonstrated that the structural stability of these proteins contributes to coral resilience under acidified conditions. This study established an integrated framework combining stress experiments, multi-omics analyses, molecular simulations, and in-vitro validation to identify key proteins involved in coral adaptation to acidification.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00321-w.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"1008-1020"},"PeriodicalIF":5.3,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650037","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}

{"title":"Taurine alleviates endoplasmic reticulum stress, oxidative stress, apoptosis, and glycogen accumulation induced by high glucose in the muscle cells of golden pompano (<i>Trachinotus ovatus</i>).","authors":"Ming-Jian Liu, Lu-Ke Zhang, Ke-Cheng Zhu, Hua-Yang Guo, Teng-Fei Zhu, Bao-Suo Liu, Nan Zhang, Dian-Chang Zhang","doi":"10.1007/s42995-025-00324-7","DOIUrl":"10.1007/s42995-025-00324-7","url":null,"abstract":"<p><p>High-glucose environments induce cellular stress, particularly endoplasmic reticulum stress (ERS) and oxidative stress, in aquatic animals. Taurine, known for its cell-protective properties, has potential in mitigating such stress. This study investigated taurine's effects on ERS, oxidative stress, apoptosis, and glycogen accumulation in golden pompano (<i>Trachinotus ovatus</i>) muscle cells under high-glucose conditions. Cells were cultured with varying glucose concentrations and taurine supplementation. Techniques including Cell Counting Kit-8 (CCK-8) assay, Nile Red staining, periodic acid-Schiff (PAS) staining, and transmission electron microscopy (TEM) were used to assess cell viability, lipid deposition, glycogen accumulation, and ultrastructural changes, respectively. High glucose increased the ADP/ATP ratio, reactive oxygen species (ROS) levels, and reduced mitochondrial membrane potential (MMP), activating AMP-activated protein kinase (AMPK). This led to glycogen accumulation via increased glycogen synthase (<i>gysm</i>) expression and decreased glycogen phosphorylase (<i>pygm</i>) expression. Taurine supplementation restored glycogen balance, reduced glucose transporter 4 (GLUT4) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) protein levels, and alleviated ERS, as evidenced by reduced PKR-like ER kinase (<i>perk</i>) mRNA and glucose-regulated protein 78 (GRP78) protein expression. Also, taurine improved mitochondrial function, inhibiting apoptosis by reducing cytochrome C (CytC) release. In conclusion, taurine alleviated ERS, glycogen accumulation, apoptosis, and mitochondrial oxidative stress, providing new insights into taurine's mechanisms and supporting its potential use as a feed additive in aquaculture.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00324-7.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"820-835"},"PeriodicalIF":5.3,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145649981","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}

{"title":"Species-specific marker development for accurate identification of three red algae (<i>Grateloupia asiatica</i>, <i>Pachymeniopsis lanceolata</i> and <i>Polyopes affinis</i>) based on complete organelle genomes.","authors":"Yong Jin Lee, Yeon Mi Kim, Cheol Min Kim, Sung-Je Choi, Cheol Seong Jang","doi":"10.1007/s42995-025-00327-4","DOIUrl":"10.1007/s42995-025-00327-4","url":null,"abstract":"<p><p>Red alga species in the phylum Rhodophyta are ecologically and economically important, which are widely used as food and medicinal products because they are rich in bioactive compounds. Unfortunately, researchers often meet challenges in identifying red algal species and understanding the evolutionary relationship among them. Shooting away these limitations necessitates detailed genomic studies, including those of cellular organelles. In this study, we sequenced circular organelle genomes of three red macroalgal species, <i>Grateloupia asiatica</i>, <i>Pachymeniopsis lanceolata</i> and <i>Polyopes affinis</i>, yielding two complete chloroplast genomes of <i>P. lanceolata</i> and <i>P. affinis</i> and one mitochondrial genome of <i>P. affinis</i>. The average chloroplast and mitochondrial genome sizes were 192,724 bp and 29,699 bp, respectively, which encoded 202 and 25 proteins, respectively, on average. The short- and long-repeat sequences, gene rearrangements, the nucleotide diversity, and phylogenetic relationship among these three species were analyzed. Memo: revise conjunctions and prepositions to form a clearer list (A, B, C, and D). The 194 chloroplast and 23 mitochondrial protein-coding genes shared by the species belonging to Florideophyceae and Bangiophyceae were used to reconstruct a maximum-likelihood phylogenetic tree. In addition, we developed 15 species-specific PCR markers, five for each species, using single-nucleotide polymorphism information. Our results should aid in identifying these species and deciphering the evolutionary relationship among species in the phylum Rhodophyta.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00327-4.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"717-729"},"PeriodicalIF":5.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145649983","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}

{"title":"Antibacterial dimeric phenazine derivatives from a marine-derived <i>Streptomyces</i> sp. OUCMDZ-4923.","authors":"Dongyang Wang, Peipei Liu, Yuwei Xia, Liping Wang, Ning Li, Weiming Zhu","doi":"10.1007/s42995-025-00328-3","DOIUrl":"https://doi.org/10.1007/s42995-025-00328-3","url":null,"abstract":"<p><p>Phenazine derivatives, a class of naturally occurring antibiotics primarily produced by bacteria, are regarded as promising scaffolds for developing new antibiotics. In this study, eight new dimeric phenazine derivatives, phenazostains K‒R (<b>1</b>‒<b>8</b>), along with two reported dimeric analogues, phenazostains B (<b>9</b>) and C (<b>10</b>), were isolated from the fermentation broth of the marine-derived <i>Streptomyces</i> sp. OUCMDZ-4923. Their structures were elucidated through spectroscopic analysis, primarily using NMR and HRESIMS spectra, ECD calculations, and the modified Mosher's method. Compounds <b>1</b>‒<b>10</b> feature the 12-deoxysaphenate unit linked to various sites on methyl saphenate, phenazine, or methyl phenazine-1-carboxylate. Notably, compounds <b>1</b> and <b>2</b> represent the first dimeric phenazines linked by a 12,12'-oxy bridge. Our experimental results suggest that these dimers could be formed from methyl saphenate (<b>12</b>) through a nonenzymatic pathway. Moreover, the analysis of gene roles within their biosynthetic gene cluster revealed that phenazostains <b>1</b>‒<b>8</b> are formed through a nonenzymatic process. Additionally, all dimers were evaluated for their antibacterial activity; compounds <b>1</b>, <b>3</b>‒<b>5</b>, and <b>9</b> exhibited inhibitory activities against both <i>Staphylococcus aureus</i> and its methicillin-resistant strain (MRSA), with MIC values ranging from 1.56 to 25.0 μg/mL.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00328-3.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"925-936"},"PeriodicalIF":5.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650050","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}

{"title":"scITDG: a tool for identifying time-dependent genes in single-cell transcriptome sequencing data.","authors":"Yandong Zheng, Chengyu Liu, Weiqi Zhang, Jing Qu, Shuai Ma, Guang-Hui Liu","doi":"10.1007/s42995-025-00311-y","DOIUrl":"https://doi.org/10.1007/s42995-025-00311-y","url":null,"abstract":"<p><p>Our study introduces scITDG, a tool designed for the analysis of time-dependent gene expression in single-cell transcriptomic sequencing data, effectively filling a gap in current analytical resources. A key advantage of scITDG is its ability to identify dynamic gene expression patterns across multiple time points at single-cell resolution, which is pivotal for deciphering complex biological processes such as aging and tissue regeneration. The tool is compatible with widely used single-cell analysis platforms such as Seurat and Scanpy. By integrating natural cubic splines regression with bootstrapping resampling, scITDG enhances the functionality of these platforms and broadens their applicability. In this study, based on scITDG, we revealed intricate gene expression modules in mice aging and axolotl limb regeneration, providing valuable insights into cellular function and response mechanisms. The versatility of scITDG makes it applicable to a wide range of biological contexts, including development, circadian rhythms, disease progression, and therapeutic responses.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-025-00311-y.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"7 4","pages":"792-807"},"PeriodicalIF":5.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12662966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145649805","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}