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APTES: a high-throughput deep learning–based Arabidopsis phenotypic trait estimation system for individual leaves and siliques APTES:基于高通量深度学习的拟南芥叶片和叶片表型性状估计系统
IF 5 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-10-31 DOI: 10.1007/s42994-025-00239-y
Ruifang Zhai, Ning Tang, Zhi Liu, Sha Tao, Yupu Huang, Xue Jiang, Aobo Du, Jiashi Wang, Tao Luo, Jinbao Liu, Gina A. Garzon-Martınez, Fiona M. K. Corke, John H. Doonan, Wanneng Yang

High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation. To address this need, we developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs. The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN) achieved precision (measure of positive prediction accuracy), recall (sensitivity in detection), and F1 score values (harmonic mean of precision and recall) of 0.965, 0.958, and 0.961, respectively, for individual leaf segmentation. These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model. For silique segmentation, our enhanced DetectoRS model for silique segmentation attained precision, recall, and F1 scores of 0.954, 0.930, and 0.942, respectively. Notably, precision increased by 1%, while the F1 score improved by 2 percentage points. Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89% to 7.90%. We phenotyped 166 Arabidopsis accessions, using APTES, and subjected the resulting values to a genome-wide association study (GWAS), revealing 1,042 single-nucleotide polymorphisms (SNPs) as being significantly associated with 18 leaf and silique traits, and one significant SNP on chromosome 3 linked to silique number. Furthermore, we validated APTES across other public Arabidopsis databases and other plant species, with segmentation results demonstrating its applicability across diverse datasets. In conclusion, APTES is a valuable automated tool for leaf and silique segmentation and trait estimation, which should offer benefits to the broader plant science community.

模式植物拟南芥的生长动力学和器官大小的高通量表型分析需要快速和精确的性状估计方法。为了满足这一需求,我们开发了拟南芥表型性状估计系统(APTES),这是一个开放获取的高通量程序,使用计算机视觉和深度学习从照片中提取64个叶片性状和64个单株性状。增强分割模型Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN)对单叶分割的精度(正预测精度度量)、召回率(检测灵敏度)和F1评分值(精度和召回率的调和平均值)分别为0.965、0.958和0.961。这些指标显示了在基线模型上大约1个百分点的持续改进。对于单字分割,我们的增强检测器模型的单字分割精度、召回率和F1得分分别为0.954、0.930和0.942。值得注意的是,精确度提高了1%,F1分数提高了2个百分点。性状参数自动计算,叶片和单株性状的决定系数为0.776 ~ 0.976,平均绝对百分比误差为1.89% ~ 7.90%。我们利用APTES对166份拟南芥材料进行表型分析,并将结果值进行全基因组关联研究(GWAS),发现1042个单核苷酸多态性(SNP)与18个叶片和硅片性状显著相关,3号染色体上1个显著SNP与硅片数相关。此外,我们在其他公共拟南芥数据库和其他植物物种中验证了APTES,其分割结果表明其在不同数据集上的适用性。综上所述,APTES是一种有价值的叶片和硅片分割和性状估计的自动化工具,应该为更广泛的植物科学界带来好处。
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引用次数: 0
A near-complete genome assembly of cucumber line 6457 and identification of candidate gene controlling pedicel length. 黄瓜6457系近全基因组组装及花梗长度控制候选基因的鉴定。
IF 8.5 Q1 GENETICS & HEREDITY Pub Date : 2025-10-25 eCollection Date: 2025-11-01 DOI: 10.1093/hr/uhaf222
Yang Xie, Chenhao Zhang, Jiaojiao Zhang, Jianyu Zhao, Xiaofei Song, Xiaoxiao Lei, Lijin Fan, Xiaoli Li, Jianhua Jia, Chen Wang, Xiaolan Zhang, Liying Yan, Xiaoming Song
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引用次数: 0
Plant nitrate transport family NPF and its regulatory mechanism of protein modification. 植物硝酸盐转运家族NPF及其蛋白修饰调控机制。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.24-327
Yu-Chen Kou, Yi-Ning Xie, Yan-Hui Yuan, Xiao-Yi Shan, Xi Zhang

Nitrogen is an indispensable macronutrient for plant growth, and nitrate is the main source of nitrogen for plants. The relationship between supply and demand of nitrate has a decisive impact on plant development. The NRT1/PTR family (nitrate transporter 1/peptide transporter family, NPF) is a major nitrate transporter family, playing a key role in nitrate uptake. In plant research, this type of protein can regulate its function through post-translational modification, thereby regulating nitrate sense, uptake, and plant development. NRT1.1 (NPF6.3/CHL1), a key member of the NPF family, functions both as a nitrate transporter and a nitrate sensor. In this review, we elucidate the role of NPF nitrate transporter proteins in regulating nitrate uptake and utilization in Arabidopsis thaliana, Oryza sativa, and Zea mays, and summarize the effects of post-translational modification on nitrate transport and plant development. Finally, the prospect of related research in trees is discussed, in order to provide scientific basis and technical support for improving nitrogen fertilizer utilization efficiency, enhancing plant resistance to adverse conditions, and protecting ecological environment.

氮是植物生长不可缺少的大量营养元素,而硝酸盐是植物氮的主要来源。硝酸盐的供需关系对植物的发育具有决定性的影响。NRT1/PTR家族(硝酸盐转运蛋白1/肽转运蛋白家族,NPF)是一个主要的硝酸盐转运蛋白家族,在硝酸盐吸收中起关键作用。在植物研究中,这类蛋白可以通过翻译后修饰来调节其功能,从而调节硝酸盐的感知、吸收和植物的发育。NRT1.1 (NPF6.3/CHL1)是NPF家族的关键成员,同时具有硝酸盐转运蛋白和硝酸盐传感器的功能。本文综述了NPF硝酸盐转运蛋白在拟南芥、水稻和玉米中调控硝酸盐吸收和利用的作用,并对其翻译后修饰对硝酸盐转运和植物发育的影响进行了综述。最后,对树木相关研究前景进行了展望,以期为提高氮肥利用效率、增强植物抗逆性、保护生态环境提供科学依据和技术支持。
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引用次数: 0
Exploring the gene of "alcohol flush"--in-depth exploration and application of genetic experimental cases. 探究“酒精脸红”的基因——基因实验案例的深度探索与应用。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.25-002
Xue-Ying Zhao, You Li, Da-Ru Lu, Yan Pi

Genetic related technologies are increasingly influencing human health and life. From theory to practice, teaching through typical cases of disciplinary applications has become a popular new model in the field of genetics education. This experiment takes the phenotype case of "alcohol flush" as an example, organically integrating genetic knowledge from multiple perspectives and levels such as phenotypic analysis, population genetic analysis and pedigree analysis with experimental cases. In teaching practice, the "alcohol flush" case study can greatly stimulate students' interest in active learning, cultivate students' ability to connect theory with practice, discover and solve problems from practice, and further expand their learning of genetic testing related bioethics, genetic information protection, genetic resource protection, and other knowledge through personal practical teaching, thus cultivate students' scientific thinking ability and scientific literacy.

遗传相关技术对人类健康和生活的影响越来越大。从理论到实践,通过学科应用的典型案例教学已成为遗传学教育领域流行的一种新模式。本实验以“酒精脸红”表型病例为例,将表型分析、群体遗传分析、系谱分析等多角度、多层次的遗传知识与实验病例有机结合。在教学实践中,通过“酒红”案例学习,极大地激发了学生主动学习的兴趣,培养了学生理论联系实际、从实践中发现问题、解决问题的能力,并通过个人实践教学,进一步拓展了学生对基因检测相关生物伦理学、遗传信息保护、遗传资源保护等知识的学习,培养了学生的科学思维能力和科学素养。
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引用次数: 0
Progress on extracellular vesicles. 细胞外囊泡研究进展。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.yczz.24-371
Jia-Qiang Chen, Mei Ding

Extracellular vesicles are membrane-enclosed structures released by cells into the extracellular space, containing various biomolecules such as proteins, nucleic acids, and lipids. Extracellular vesicles exhibit broad cellular origins, diverse types, and high heterogeneity. They are involved in intercellular material transport, mediate intercellular communication, and play important roles in various cellular biological processes, including cell proliferation, apoptosis, and migration. This review summarizes recent advances in research on the isolation and identification, biogenesis mechanisms, and fate of extracellular vesicles, aiming to provide a reference for advancing research in this field.

细胞外囊泡是细胞释放到细胞外空间的膜封闭结构,含有多种生物分子,如蛋白质、核酸和脂质。细胞外囊泡具有广泛的细胞起源、多样的类型和高度的异质性。它们参与细胞间物质运输,介导细胞间通讯,并在细胞增殖、凋亡和迁移等多种细胞生物学过程中发挥重要作用。本文综述了近年来细胞外囊泡的分离鉴定、生物发生机制和命运等方面的研究进展,旨在为进一步开展这一领域的研究提供参考。
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引用次数: 0
Study on the microbial diversity and composition at different regions of stomach in adult pigs. 成年猪胃不同区域微生物多样性及组成的研究。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.25-027
Si-Yu Hu, Ruo-Han Yang, Zheng-Jiang Liu, Yi-Fei Cai, Juan Deng, Bo Zeng, Ming-Zhou Li, Fan-Li Kong

To investigate the microbial composition and diversity across distinct anatomical regions of the porcine stomach, this study took adult "Landrace×Yorkshire" hybrid pigs as the research subjects. Mucosal samples were collected from eight regions, including gastroesophageal groove, gastric fundus, lesser curvature of the gastric body, greater curvature of the gastric body, middle antrum of the gastric antrum, gastric diverticulum, round pillow of the pylorus, and pylorus, and subjected by high-throughput sequencing targeting the microbial 16S rRNA V3-V4 hypervariable regions. The results showed obvious difference in microbial diversity among the eight stomach regions. The gastric fundus and gastric body greater curvature exhibited higher microbial diversity and richness, while the esophageal groove, gastric body lesser curvature, gastric antrum middle section, gastric diverticulum, pyloric bulge, and pylorus showed lower diversity and richness. Firmicutes and Proteobacteria constituted the predominant phyla across all eight regions of the pig stomach. A` relatively high abundance of Cyanobacteria was also detected in the esophageal groove and gastric antrum middle section. However, the dominant genera varied substantially across regions. Lactobacillus predominated in the esophageal groove, fundus, lesser curvature, and greater curvature. Delftia and Chryseobacterium were dominant in the mid-antrum. Bacteroides dominated in the gastric diverticulum and pylorus. Proteus was the dominant genus in the pyloric torus. Further functional analysis of stomach microbiome indicated the regions with the most active metabolic processes and cellular activity within the stomach were the esophageal groove and lesser curvature of the gastric body. These findings provide valuable reference data for future research on the physiological structure and function of the stomach.

为了研究猪胃不同解剖区域的微生物组成和多样性,本研究以成年“Landrace×Yorkshire”杂交猪为研究对象。从胃食管沟、胃底、胃体小弯、胃体大弯、胃窦中腔、胃憩室、幽门圆枕、幽门8个区域采集粘膜标本,针对微生物16S rRNA V3-V4高变区进行高通量测序。结果表明,8个胃区微生物多样性差异明显。胃底和胃体大弯曲处微生物多样性和丰富度较高,而食管沟、胃体小弯曲、胃窦中段、胃憩室、幽门膨出和幽门处微生物多样性和丰富度较低。厚壁菌门和变形菌门构成了猪胃所有八个区域的优势门。在食管沟和胃窦中段也检测到相对较高丰度的蓝藻。然而,不同地区的优势属差异很大。乳杆菌主要分布在食管沟、眼底、小曲度和大曲度。Delftia和Chryseobacterium在中胃窦中占优势。胃憩室和幽门以拟杆菌为主。Proteus是幽门环部的优势属。进一步的胃微生物组功能分析表明,胃内代谢过程和细胞活动最活跃的区域是食管沟和胃小弯。这些发现为进一步研究胃的生理结构和功能提供了有价值的参考数据。
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引用次数: 0
Examining funding policies for postdoctoral researchers in life sciences: a case study of Shandong University. 生命科学博士后资助政策研究——以山东大学为例
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.25-178
Yan Zhou, Feng Liu

Postdoctoral researchers in life sciences confront distinct challenges, including extended training duration resulting from the inherently lengthy research cycles associated with their specialized research subjects and experimental materials. Based on national postdoctoral policies and comparison of funding policies between China and the United States, we focus on postdoctoral researchers in life sciences at the School of Life Sciences, Shandong University. Our analysis reveals how current university funding policies constrain the training process of postdoctoral researchers in this field. To address these limitations, we propose a coordinated reform strategy, including reinforcing ideological and political guidance, extending funding durations, establishing cost-sharing mechanisms, and implementing incentives for major achievements. These reforms aim to improve the quality of postdoctoral training and provide policy insights for optimizing the research talent development system in "Double First-Class" universities.

生命科学博士后研究人员面临着独特的挑战,包括由于其专业研究课题和实验材料固有的较长研究周期而导致的培训时间延长。基于国家博士后政策和中美两国资助政策的比较,我们重点招募山东大学生命科学学院生命科学领域的博士后。我们的分析揭示了当前的大学资助政策如何限制了这一领域博士后研究人员的培养过程。为了解决这些限制,我们提出了一个协调的改革战略,包括加强思想和政治指导,延长资助期限,建立成本分担机制,并对重大成就实施激励措施。这些改革旨在提高博士后培养质量,为优化“双一流”高校科研人才培养体系提供政策参考。
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引用次数: 0
The role and mechanism of cancer stem cells in breast carcinogenesis, progression and drug resistance. 肿瘤干细胞在乳腺癌发生、发展和耐药中的作用和机制。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.25-036
Hong-Bo Zhang, Feng-Gui Sun, Jian-Wei Sun, Qi Tang, Xu Zhang

Breast cancer stem cells (BCSCs) represent a distinctive subpopulation within breast cancer that exhibit stem cell-like characteristics, including self-renewal capability and multipotent differentiation. They are recognized as the central drivers of tumor initiation, progression, metastasis, and drug resistance. In-depth investigation of BCSCs represents a crucial avenue for overcoming the current therapeutic limitations in breast cancer. This review comprehensively summarizes recent advances in BCSCs-related research, focusing on key areas such as surface marker identification, mechanisms underlying tumor recurrence and metastasis, core regulatory signaling networks, and therapy resistance. Furthermore, it discusses potential clinical strategies targeting BCSCs, and explores future directions for precision medicine based on hetogeneity and dynamic regulation of BCSCs. These insights provide important theoretical foundations for the development of targeted therapies against breast cancer.

乳腺癌干细胞(BCSCs)是乳腺癌中一个独特的亚群,具有干细胞样特征,包括自我更新能力和多能分化。它们被认为是肿瘤发生、进展、转移和耐药的主要驱动因素。深入研究BCSCs是克服当前乳腺癌治疗局限性的重要途径。本文从表面标志物鉴定、肿瘤复发转移机制、核心调控信号网络、治疗耐药等方面综述了近年来bcscs相关研究进展。探讨了针对BCSCs的潜在临床策略,并探讨了基于BCSCs异质性和动态调控的精准医学未来发展方向。这些见解为开发针对乳腺癌的靶向治疗提供了重要的理论基础。
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引用次数: 0
Transcriptome analysis of postnatal mouse cardiac tissue growth and development. 出生后小鼠心脏组织生长发育的转录组分析。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.24-328
Xiao-Cong Zhu, Sheng-Nan Wang, Lin Jiang, Shu-Qin Liu

Postnatal cardiac function in mammals is closely associated with cardiomyocyte proliferation and hypertrophy. However, the molecular mechanisms regulating cardiomyocyte proliferation and hypertrophy have not yet been fully elucidated. Therefore, phenotypic measurements and transcriptomic sequencing were performed on myocardial tissues from 7-day-old (P7) and 3-month-old (3m) female C57BL/6 mice to investigate changes in cardiomyocytes during growth and development and to identify key genes regulating myocardial growth and development. In comparison to 7-day-old mice, 3-month-old mice exhibited a significant increase in heart weight (P<0.001) and the cross-sectional area of cardiomyocytes (P<0.001). Transcriptome sequencing identified 3,858 differentially expressed genes (DEGs), including 2,021 up-regulated and 1,837 down-regulated genes. Gene Ontology (GO) functional annotation analysis demonstrated that the differentially expressed genes were significantly enriched in biological processes including cell cycle, cell division, cardiac morphogenesis and cellular proliferation. Significantly enriched KEGG pathways were identified, including those for DNA replication, ECM-receptor interaction, the cell cycle, metabolic pathways, and other signaling pathways. Furthermore, key candidate genes associated with myocardial tissue growth and development in mice, including Hey2, Foxm1, Igf1, Xirp2, Sfrp2, Egf, Fgfr2, Tbx20, Fgf1 and Igf2 were identified through screening. qRT-PCR validation results demonstrated that the expression trends of the 10 candidate genes related to myocardial growth and development were consistent with the RNA-seq results, confirming the reliability of the sequencing data. The findings of this study provide new insights into the molecular mechanisms underlying the growth and development of mouse myocardial tissue.

哺乳动物出生后的心功能与心肌细胞增殖和肥厚密切相关。然而,调控心肌细胞增殖和肥厚的分子机制尚未完全阐明。因此,我们对7日龄(P7)和3月龄(3m)雌性C57BL/6小鼠心肌组织进行表型测定和转录组测序,以研究心肌细胞在生长发育过程中的变化,并鉴定调节心肌生长发育的关键基因。与7日龄小鼠相比,3月龄小鼠的心脏重量显著增加(通过筛选鉴定出PPHey2、Foxm1、Igf1、Xirp2、Sfrp2、Egf、Fgfr2、Tbx20、Fgf1和Igf2)。qRT-PCR验证结果表明,10个心肌生长发育相关候选基因的表达趋势与RNA-seq结果一致,证实了测序数据的可靠性。本研究结果为研究小鼠心肌组织生长发育的分子机制提供了新的思路。
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引用次数: 0
Geographical inference of dust from typical Chinese cities based on metagenomic shotgun sequencing. 基于宏基因组霰弹枪测序的中国典型城市尘埃地理推断。
Q3 Medicine Pub Date : 2025-10-20 DOI: 10.16288/j.yczz.25-009
Qi Yang, Ke-Lai Kang, Bo Zhao, Kai Feng, Yao-Sen Feng, Jian Ye, Ye Deng, Le Wang

Microbial profiles in dust are closely correlated with geographical locations and provide valuable clues for criminal investigation, demonstrating significant potential in forensic use. However, the feasibility of using microbial profiles from metagenomics datasets to infer the geographical locations remains underexplored. In this study, we collect 170 dust samples from resident communities in four cities across northern, eastern, southwestern, and northwestern China. All samples are subjected to shotgun metagenomic sequencing to reveal variations in microbial composition. In total, 41,029 species are annotated, including 93.39% bacteria, 6.37% eukaryotes, 0.21% viruses, and 0.03% archaea. Clear clustering patterns are observed among the four cities (R2=0.870, P<0.001). Further filtering of species with detection rates below 10% across all samples strengthens city-level clustering (R2=0.948, P<0.001). Additionally, 127 biomarkers are identified using linear discriminant analysis effect size (LEfSe) to distinguish between the cities. Each city harbors a distinct microbial community, with unique species and relatively abundant taxa that contribute to its differentiated microbial profile. All samples are randomly split into training and testing sets in a 7:3 ratio. Five machine learning models including SourceTracker, FEAST, LightGBM, Random Forest and Support Vector Machine are applied to 51 randomly sample data and achieve average accuracies of 88.89%, 92.16%, 98.04%, 99.35% and 69.28%, respectively. These results constitute a microbial genetic map of four cities in China that highlights distinct microbial taxonomic signatures and provides an approach for city-scale source tracking of dust samples.

粉尘中的微生物特征与地理位置密切相关,为刑事调查提供了有价值的线索,在法医鉴定中具有重要的应用潜力。然而,利用宏基因组数据集的微生物谱来推断地理位置的可行性仍未得到充分探索。在这项研究中,我们从中国北部、东部、西南部和西北部四个城市的居民社区收集了170份尘埃样本。所有样品都经过散弹枪宏基因组测序,以揭示微生物组成的变化。总共注释了41,029种,其中细菌93.39%,真核生物6.37%,病毒0.21%,古细菌0.03%。4个城市间存在明显的聚类模式(R2=0.870, P < R2=0.948, P < 0.05)
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引用次数: 0
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