BMC Biology最新文献

筛选
英文 中文
Receptor deorphanization in starfish reveals the evolution of relaxin signaling as a regulator of reproduction. 海星受体去孤儿化揭示了松弛素信号作为生殖调节因子的进化。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-25 DOI: 10.1186/s12915-025-02158-2
Yuling Feng, Nayeli Escudero Castelán, Mohammed Akhter Hossain, Hongkang Wu, Hidekazu Katayama, Stuart J Smith, Scott F Cummins, Masatoshi Mita, Ross A D Bathgate, Maurice R Elphick
{"title":"Receptor deorphanization in starfish reveals the evolution of relaxin signaling as a regulator of reproduction.","authors":"Yuling Feng, Nayeli Escudero Castelán, Mohammed Akhter Hossain, Hongkang Wu, Hidekazu Katayama, Stuart J Smith, Scott F Cummins, Masatoshi Mita, Ross A D Bathgate, Maurice R Elphick","doi":"10.1186/s12915-025-02158-2","DOIUrl":"10.1186/s12915-025-02158-2","url":null,"abstract":"<p><strong>Background: </strong>Relaxins are a family of peptides that regulate reproductive physiology in vertebrates. Evidence that this is an evolutionarily ancient role of relaxins has been provided by the discovery of two relaxin-like gonad-stimulating peptides (RGP1 and RGP2) that trigger spawning in starfish. The main aim of this study was to identify the receptor(s) that mediate(s) the effects of RGP1 and RGP2 in starfish.</p><p><strong>Results: </strong>Here we show that RGP1 and RGP2 belong to a family of peptides that include vertebrate relaxins, Drosophila insulin-like peptide 8 (Dilp8), and other relaxin-like peptides in several protostome taxa. An ortholog of the human relaxin receptors RXFP1 and RXFP2 and the Drosophila receptor LGR3 was identified in starfish (RXFP/LGR3). In Drosophila, but not in humans and other vertebrates, there is a paralog of LGR3 known as LGR4, and here an LGR4-type receptor was also identified in starfish. In vitro pharmacological experiments revealed that both RGP1 and RGP2 act as ligands for RXFP/LGR3 in the starfish Acanthaster cf. solaris and Asterias rubens, but neither peptide acts as a ligand for LGR4 in these species.</p><p><strong>Conclusions: </strong>Discovery of the RXFP/LGR3-type receptor for RGP1 and RGP2 in starfish provides a new insight into the evolution of relaxin-type signaling as a regulator of reproductive processes. Furthermore, our findings indicate that RXFP/LGR3-type receptors have been lost in several phyla, including urochordates, mollusks, bryozoans, platyhelminthes, and nematodes.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"59"},"PeriodicalIF":4.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Harnessing ferroptosis for precision oncology: challenges and prospects. 利用铁下垂进行精确肿瘤学:挑战和前景。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-24 DOI: 10.1186/s12915-025-02154-6
Roberto Fernández-Acosta, Iuliana Vintea, Ine Koeken, Behrouz Hassannia, Tom Vanden Berghe
{"title":"Harnessing ferroptosis for precision oncology: challenges and prospects.","authors":"Roberto Fernández-Acosta, Iuliana Vintea, Ine Koeken, Behrouz Hassannia, Tom Vanden Berghe","doi":"10.1186/s12915-025-02154-6","DOIUrl":"10.1186/s12915-025-02154-6","url":null,"abstract":"<p><p>The discovery of diverse molecular mechanisms of regulated cell death has opened new avenues for cancer therapy. Ferroptosis, a unique form of cell death driven by iron-catalyzed peroxidation of membrane phospholipids, holds particular promise for targeting resistant cancer types. This review critically examines current literature on ferroptosis, focusing on its defining features and therapeutic potential. We discuss how molecular profiling of tumors and liquid biopsies can generate extensive multi-omics datasets, which can be leveraged through machine learning-based analytical approaches for patient stratification. Addressing these challenges is essential for advancing the clinical integration of ferroptosis-driven treatments in cancer care.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"57"},"PeriodicalIF":4.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11849278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Unveiling the thermotolerance mechanism of Pichia kudriavzevii LC375240 through transcriptomic and genetic analyses. 通过转录组学和遗传分析揭示毕赤酵母LC375240的耐热性机制。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-23 DOI: 10.1186/s12915-025-02159-1
Yanhua Qi, Qijian Qin, Jiayin Ma, Bin Wang, Cheng Jin, Wenxia Fang
{"title":"Unveiling the thermotolerance mechanism of Pichia kudriavzevii LC375240 through transcriptomic and genetic analyses.","authors":"Yanhua Qi, Qijian Qin, Jiayin Ma, Bin Wang, Cheng Jin, Wenxia Fang","doi":"10.1186/s12915-025-02159-1","DOIUrl":"10.1186/s12915-025-02159-1","url":null,"abstract":"<p><strong>Background: </strong>Thermotolerance is a critical trait for yeasts employed in industrial settings, and the utilization of unconventional yeasts has gained notable attention in recent years. However, the mechanisms underlying thermotolerance in unconventional yeasts, particularly Pichia spp., remain insufficiently elucidated.</p><p><strong>Results: </strong>This study focuses on the thermotolerance of a non-traditional yeast strain Pichia kudriavzevii LC375240, renowned for its remarkable thermotolerance. Through transcriptomic analysis of both short-term and long-term heat shock exposures, we uncovered an intricate regulatory response in P. kudriavzevii. During long-term heat treatment, the yeast exhibited elevated expression of genes involved in the tricarboxylic acid (TCA) cycle and suppressed expression of genes in the pentose phosphate pathway (PPP). Additionally, long-term heat treatment led to an upregulation of heat shock proteins (HSPs) and an increase in trehalose, glutathione (GSH), and superoxide dismutase (SOD) levels, along with a reduction in the intracellular NADPH/NADP<sup>+</sup> ratio and pyruvate content. These changes collectively contribute to the thermotolerance of P. kudriavzevii. CRISPR-Cas9-mediated knockout experiments further highlighted the critical roles of HSPs, antioxidases, and the trehalose metabolic pathway in the yeast's response to high temperatures.</p><p><strong>Conclusions: </strong>Taken together, this study demonstrates that P. kudriavzevii adapts to thermal stress through a combination of enhanced TCA cycle, reduced PPP, increased HSPs, trehalose, GSH, and SOD levels. These findings provide a comprehensive understanding of the molecular mechanisms underlying thermotolerance in P. kudriavzevii.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"55"},"PeriodicalIF":4.4,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11849260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Expression of a pheromone binding protein affected by timeless gene governs female mating behavior in Bactrocera dorsalis. 受时间基因影响的信息素结合蛋白的表达支配着背小实蝇雌性交配行为。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-23 DOI: 10.1186/s12915-025-02164-4
Yuting Jiao, Guohong Luo, Yongyue Lu, Daifeng Cheng
{"title":"Expression of a pheromone binding protein affected by timeless gene governs female mating behavior in Bactrocera dorsalis.","authors":"Yuting Jiao, Guohong Luo, Yongyue Lu, Daifeng Cheng","doi":"10.1186/s12915-025-02164-4","DOIUrl":"10.1186/s12915-025-02164-4","url":null,"abstract":"<p><strong>Background: </strong>The rhythmic mating behavior of insects has been extensively documented, yet the regulation of this behavior through sex pheromone sensing olfactory genes affected by the clock genes in the rhythm pathway remains unclear.</p><p><strong>Results: </strong>In this study, we investigated the impact of circadian rhythm on female recognition of male rectal Bacillus-produced sex pheromone in B. dorsolis. Behavioral and electrophysiological assays revealed a peak in both mating behavior and response to sex pheromones in the evening in females. Comparative transcriptome analysis of female heads demonstrated rhythmic expression of the Timeless gene-Tim and odorant binding protein gene-Pbp5, with the highest expression levels occurring in the evening. Protein structural modeling, tissue expression patterns, RNAi treatment, and physiological/behavioral studies supported Pbp5 as a sex pheromone binding protein whose expression is affected by Tim. Furthermore, manipulation of the female circadian rhythm resulted in increased morning mating activity, accompanied by consistent peak expression of Tim and Pbp5 during this time period. These findings provide evidence that insect mating behavior can be modulated by clock genes through their effects on sex pheromone sensing processes.</p><p><strong>Conclusions: </strong>Our results also contribute to a better understanding of the molecular mechanisms underlying rhythmic insect mating behavior.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"56"},"PeriodicalIF":4.4,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11849186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons. 转座子介导的鲶鱼性染色体的起源、进化和易位。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02160-8
Shuqing Zheng, Hongyan Tao, Yuheng Song, Mao Li, Haowen Yang, Jianzhen Li, Hongwei Yan, Bakhtiyor Sheraliev, Wenjing Tao, Zuogang Peng, Yaoguang Zhang, Deshou Wang
{"title":"The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons.","authors":"Shuqing Zheng, Hongyan Tao, Yuheng Song, Mao Li, Haowen Yang, Jianzhen Li, Hongwei Yan, Bakhtiyor Sheraliev, Wenjing Tao, Zuogang Peng, Yaoguang Zhang, Deshou Wang","doi":"10.1186/s12915-025-02160-8","DOIUrl":"10.1186/s12915-025-02160-8","url":null,"abstract":"<p><strong>Background: </strong>Sex chromosome (SC) evolution is a longstanding topic of focus in evolutionary biology. Teleosts often exhibit rapid turnover of SCs and sex-determining (SD) genes, alongside a diverse range of SC differentiation mechanisms.</p><p><strong>Results: </strong>On the basis of new chromosome-scale assemblies of three Silurus species (S. microdorsalis, S. glanis, and S. lanzhouensis) and two outgroup species (Pterocryptis cochinchinensis and Kryptopterus bicirrhis), along with our previous assemblies of S. meridionalis and S. asotus, we traced the evolution of SC in the Silurus genus (Siluriformes), following the fate of the known SD gene amhr2y. Phylogenetic analysis showed that amhr2y occurred at least before the divergence of Pterocryptis, Kryptopterus, and Silurus and lost in P. cochinchinensis and K. bicirrhis. Chr24 has become the SC in the ancestor of five Silurus species due to the duplication-and-translocation of amhr2 mediated by LTR transposon. Then, a proto Y was formed and maintained with a shared 60 kb male-specific region of the Y chromosome (MSY) by transposable elements (TEs) expansion and gene gathering. Due to the continuous TEs accumulation, genes other than amhr2y in MSYs have degenerated or been lost, while non-recombinant regions continue to expend, forming MSYs of different sizes in different Silurus species (from 320 to 550 kb). Two turnover events, one homologous (from the left arm to the right arm of Chr24) and one nonhomologous (from Chr24 to Chr5), occurring among five Silurus species were possibly mediated by hAT and Helitron transposons.</p><p><strong>Conclusions: </strong>Our results on the dynamic evolutionary trajectory of SD gene amhr2y, MSYs, and SCs in Silurus catfish indicated the variability and diversity of fish SCs and confirmed that frequent turnover is an important way to maintain the homology and low differentiation of fish SCs.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"54"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
A whole-body atlas of BMP signaling activity in an adult sea anemone. 成体海葵BMP信号活动的全身图谱。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02150-w
Paul Knabl, David Mörsdorf, Grigory Genikhovich
{"title":"A whole-body atlas of BMP signaling activity in an adult sea anemone.","authors":"Paul Knabl, David Mörsdorf, Grigory Genikhovich","doi":"10.1186/s12915-025-02150-w","DOIUrl":"10.1186/s12915-025-02150-w","url":null,"abstract":"<p><strong>Background: </strong>BMP signaling is responsible for the second body axis patterning in Bilateria and in the bilaterally symmetric members of the bilaterian sister clade Cnidaria-corals and sea anemones. However, medusozoan cnidarians (jellyfish, hydroids) are radially symmetric, and yet their genomes contain BMP signaling components. This evolutionary conservation suggests that BMP signaling must have other functions not related to axial patterning, which keeps BMP signaling components under selective pressure.</p><p><strong>Results: </strong>To find out what these functions might be, we generated a detailed whole-body atlas of BMP activity in the sea anemone Nematostella. In the adult polyp, we discover an unexpected diversity of domains with BMP signaling activity, which is especially prominent in the head, as well as across the neuro-muscular and reproductive parts of the gastrodermis. In accordance, analysis of two medusozoan species, the true jellyfish Aurelia and the box jellyfish Tripedalia, revealed similarly broad and diverse BMP activity.</p><p><strong>Conclusions: </strong>Our study reveals multiple, distinct domains of BMP signaling in Anthozoa and Medusozoa, supporting the versatile nature of the BMP pathway across Cnidaria. Most prominently, BMP signaling appears to be involved in tentacle formation, neuronal development, and gameto- or gonadogenesis.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"49"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Functional characterization and evolution of olfactory responses in coeloconic sensilla of the global fruit pest Drosophila suzukii. 全球水果害虫铃木果蝇(Drosophila suzuki)听觉感受器嗅觉反应的功能特征与进化。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02151-9
Qi Xue, Kazi Sifat Hasan, Omar Dweck, Shimaa A M Ebrahim, Hany K M Dweck
{"title":"Functional characterization and evolution of olfactory responses in coeloconic sensilla of the global fruit pest Drosophila suzukii.","authors":"Qi Xue, Kazi Sifat Hasan, Omar Dweck, Shimaa A M Ebrahim, Hany K M Dweck","doi":"10.1186/s12915-025-02151-9","DOIUrl":"10.1186/s12915-025-02151-9","url":null,"abstract":"<p><strong>Background: </strong>When a species changes its host preference, it often requires modifications in its sensory systems. Many of these changes remain largely uninvestigated in the global fruit pest Drosophila suzukii (also known as spotted wing Drosophila, SWD). This species, which shares a last common ancestor with the model organism D. melanogaster-a species that prefers overripe fruits- ~ 15 million years ago, has shifted its preference from overripe to ripe, soft-skinned fruits, causing significant damage to fruit industries worldwide.</p><p><strong>Results: </strong>Here, we functionally characterized the coeloconic sensilla in D. suzukii and compared their responses to those of its close relatives, D. biarmipes and D. melanogaster. We find that D. suzukii's responses are grouped into four functional types. These responses are consistent across sexes and reproductive status. The odorant receptor co-receptor Orco is required for certain responses. Comparative analysis across these species revealed evolutionary changes in physiological and behavioral responses to specific odorants, such as acetic acid, a key indicator of microbial fermentation, and phenylacetaldehyde, an aromatic compound found in a diverse range of fruits. Phenylacetaldehyde produced lower electrophysiological responses in D. suzukii compared to D. melanogaster and elicited strong attraction in D. suzukii but not in any of the other tested species.</p><p><strong>Conclusions: </strong>The olfactory changes identified in this study likely play a significant role in the novel behavior of D. suzukii. This work also identifies phenylacetaldehyde as a potent attractant for D. suzukii, which can be used to develop targeted management strategies to mitigate the serious impact of this pest.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"50"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Rapid and high-throughput screening of proteolysis targeting chimeras using a dual-reporter system expressing fluorescence protein and luciferase. 利用表达荧光蛋白和荧光素酶的双报告系统快速高通量筛选蛋白水解靶向嵌合体。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02153-7
Shuai Meng, Yuan Meng, Xuena Yang, Wenwen Yu, Bole Li, Tianjun Liu, Jie Zhang, Xiubao Ren, Lin Zhang
{"title":"Rapid and high-throughput screening of proteolysis targeting chimeras using a dual-reporter system expressing fluorescence protein and luciferase.","authors":"Shuai Meng, Yuan Meng, Xuena Yang, Wenwen Yu, Bole Li, Tianjun Liu, Jie Zhang, Xiubao Ren, Lin Zhang","doi":"10.1186/s12915-025-02153-7","DOIUrl":"10.1186/s12915-025-02153-7","url":null,"abstract":"<p><strong>Background: </strong>Proteolysis targeting chimera (PROTAC), a novel drug discovery strategy, utilizes the ubiquitin-proteasome system to degrade target proteins in cells. While Western blotting, mass spectrometry, and Lumit Immunoassay have been instrumental in determining protein levels, the rapid screening of PROTACs continues to pose challenges, necessitating the development of alternative methodologies.</p><p><strong>Results: </strong>We herein reported an alternative high-throughput method for screening PROTACs using a dual-reporter system expressing a Renilla luciferase (RLUC)-fused target protein and enhanced green fluorescent protein (EGFP). EGFP served as an internal reference and RLUC as an indicated target protein degradation. Rapid measurement of EGFP or RLUC light signals was achieved using a fluorescence/luminescence plate-based reader in the endpoint mode. The feasibility of the screening model was tested using ARV110, a clinical trial-stage PROTAC targeting the androgen receptor (AR). In EGFP/RLUC-tAR-expressing modal cells treated with varying concentrations of ARV110, normalized RLUC luminescence decreased dose-dependently, as confirmed via western blotting detection of AR expression. Then the platform was used to practically screen Sirtuin 2 (SIRT2) degraders from a small group of PROTACs that we built. Normalized RLUC luminescence changes in model cells expressing EGFP/RLUC-SIRT2 reflected the degradation efficiencies of PROTACs. Compounds 128 and 129 exhibited the highest degradation efficacies, leading to dose-dependent degradation of endogenous SIRT2 protein in the MCF-7 cell line and inducing cell growth arrest.</p><p><strong>Conclusions: </strong>The dual-reporter system using both fluorescence and chemiluminescence was successfully constructed. Using this method, we identified effective candidate PROTACs against SIRT2. The dual-reporter system may accelerate drug discovery during PROTAC development.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"51"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
An ensemble deep learning framework for multi-class LncRNA subcellular localization with innovative encoding strategy. 基于创新编码策略的多类LncRNA亚细胞定位集成深度学习框架。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02148-4
Wenxing Hu, Yan Yue, Ruomei Yan, Lixin Guan, Mengshan Li
{"title":"An ensemble deep learning framework for multi-class LncRNA subcellular localization with innovative encoding strategy.","authors":"Wenxing Hu, Yan Yue, Ruomei Yan, Lixin Guan, Mengshan Li","doi":"10.1186/s12915-025-02148-4","DOIUrl":"10.1186/s12915-025-02148-4","url":null,"abstract":"<p><strong>Background: </strong>Long non-coding RNA (LncRNA) play pivotal roles in various cellular processes, and elucidating their subcellular localization can offer crucial insights into their functional significance. Accurate prediction of lncRNA subcellular localization is of paramount importance. Despite numerous computational methods developed for this purpose, existing approaches still encounter challenges stemming from the complexity of data representation and the difficulty in capturing nucleotide distribution information within sequences.</p><p><strong>Results: </strong>In this study, we propose a novel deep learning-based model, termed MGBLncLoc, which incorporates a unique multi-class encoding technique known as generalized encoding based on the Distribution Density of Multi-Class Nucleotide Groups (MCD-ND). This encoding approach enables more precise reflection of nucleotide distributions, distinguishing between constant and discriminative regions within sequences, thereby enhancing prediction performance. Additionally, our deep learning model integrates advanced neural network modules, including Multi-Dconv Head Transposed Attention, Gated-Dconv Feed-forward Network, Convolutional Neural Network, and Bidirectional Gated Recurrent Unit, to comprehensively exploit sequence features of lncRNA.</p><p><strong>Conclusions: </strong>Comparative analysis against commonly used sequence feature encoding methods and existing prediction models validates the effectiveness of MGBLncLoc, demonstrating superior performance. This research offers novel insights and effective solutions for predicting lncRNA subcellular localization, thereby providing valuable support for related biological investigations.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"47"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Proteomics revealed novel functions and drought tolerance of Arabidopsis thaliana protein kinase ATG1. 蛋白质组学揭示了拟南芥蛋白激酶ATG1的新功能和耐旱性。
IF 4.4 1区 生物学
BMC Biology Pub Date : 2025-02-21 DOI: 10.1186/s12915-025-02149-3
Shan Cheng, Siqi Fan, Chao Yang, Weiming Hu, Fen Liu
{"title":"Proteomics revealed novel functions and drought tolerance of Arabidopsis thaliana protein kinase ATG1.","authors":"Shan Cheng, Siqi Fan, Chao Yang, Weiming Hu, Fen Liu","doi":"10.1186/s12915-025-02149-3","DOIUrl":"10.1186/s12915-025-02149-3","url":null,"abstract":"<p><p>ATG1 stimulates autophagy biogenesis and serves as a gatekeeper for classical autophagy. To obtain insight into the control of autophagy by ATG1 and determine whether ATG1 has broader processes, we performed a thorough proteomics analysis on the Col-0 wild-type and atg1abct mutant in Arabidopsis thaliana. Proteomic data analysis pointed out that ATG1 has an unidentified function within the inositol trisphosphate and fatty acid metabolism. We also discovered ATG1-dependent autophagy has an emerging connection with ER homeostasis and ABA biosynthesis. Moreover, Gene Ontology terms for abiotic and biotic stress were strongly enriched in differentially abundant proteins, consistent with the reported role of canonical autophagy in these processes. Additional physiological and biochemical analysis revealed that atg1abct exhibited stronger drought resistance under both PEG-simulated drought treatment and natural drought stress. Results from DAB staining also indicated that atg1abct accumulation fewer ROS than Col-0 following drought treatment. As a result, these results illuminate previously unknown functions for ATG1 and offers novel perspectives into the underlying processes of autophagy function.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"48"},"PeriodicalIF":4.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信