IF 4.2 3区生物学

Methods Pub Date : 2025-04-04 DOI: 10.1016/j.ymeth.2025.03.014

Fanyu Kong , Han Liu , Xiaoqi Liu , Lei Shi

{"title":"Predicting genes associated with ossification of the posterior longitudinal ligament using graph attention network","authors":"Fanyu Kong , Han Liu , Xiaoqi Liu , Lei Shi","doi":"10.1016/j.ymeth.2025.03.014","DOIUrl":"10.1016/j.ymeth.2025.03.014","url":null,"abstract":"<div><div>Ossification of the posterior longitudinal ligament is a degenerative disease that severely impacts the spine, with a complex pathogenesis involving the interplay of multiple genes. This study utilizes a combination of graph neural networks and deep neural networks to systematically analyze genes associated with OPLL, leveraging genomics and bioinformatics techniques. By integrating gene data from the DisGeNET and HumanNetV2 databases, we constructed a GNN model to identify potential pathogenic genes for OPLL and validated the expression characteristics and mechanisms of these genes in different cell types. The findings indicate that the GNN model achieves remarkable accuracy and reliability in predicting genes associated with OPLL. Additionally, cellular trajectory analysis and immune cell infiltration studies uncovered distinct cellular environments and immune features in OPLL patients, emphasizing the significant roles of fibroblasts and mesenchymal stem cells in the disease's progression. Drug sensitivity analysis also sheds light on future personalized treatment options. This study not only enhances the understanding of OPLL's molecular mechanisms but also suggests new avenues for diagnostic and targeted therapy development.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"240 ","pages":"Pages 47-53"},"PeriodicalIF":4.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794190","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

Optimized toolkit for the manipulation of immortalized axolotl fibroblasts 永生化蝾螈成纤维细胞的优化工具箱。

IF 4.2 3区生物学

Methods Pub Date : 2025-04-03 DOI: 10.1016/j.ymeth.2025.03.019

Benjamin J. Tajer , Glory Kalu , Sarah Jay , Eric Wynn , Antoine Decaux , Paul Gilbert , Hani D. Singer , Maddeline D. Kidd , Jeffery A. Nelson , Noora Harake , Noah J. Lopez , Nathan R. Souchet , Anna G. Luong , Aaron M. Savage , Sangwon Min , Alparslan Karabacak , Sebastian Böhm , Ryan T. Kim , Tim Froitzheim , Konstantinos Sousounis , Jessica L. Whited

{"title":"Optimized toolkit for the manipulation of immortalized axolotl fibroblasts","authors":"Benjamin J. Tajer , Glory Kalu , Sarah Jay , Eric Wynn , Antoine Decaux , Paul Gilbert , Hani D. Singer , Maddeline D. Kidd , Jeffery A. Nelson , Noora Harake , Noah J. Lopez , Nathan R. Souchet , Anna G. Luong , Aaron M. Savage , Sangwon Min , Alparslan Karabacak , Sebastian Böhm , Ryan T. Kim , Tim Froitzheim , Konstantinos Sousounis , Jessica L. Whited","doi":"10.1016/j.ymeth.2025.03.019","DOIUrl":"10.1016/j.ymeth.2025.03.019","url":null,"abstract":"<div><div>The axolotl salamander model has broad utility for regeneration studies, but this model is limited by a lack of efficient cell-culture-based tools. The Axolotl Limb-1 (AL-1) fibroblast line, the only available immortalized axolotl cell line, was first published over 20 years ago, but many established molecular biology techniques, such as lipofectamine transfection, CRISPR-Cas9 mutagenesis, and antibiotic selection, work poorly or remain untested in AL-1 cells. Innovating technologies to manipulate AL-1 cells in culture and study their behavior following transplantation into the axolotl will complement <em>in-vivo</em> studies, decrease the number of animals used, and enable the faster, more streamlined investigation of regenerative biology questions. Here, we establish transfection, mutagenesis, antibiotic selection, and <em>in-vivo</em> transplantation techniques in axolotl AL-1 cells. These techniques will enable efficient culture with AL-1 cells and guide future tool development for the culture and manipulation of other salamander cell lines.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"240 ","pages":"Pages 21-34"},"PeriodicalIF":4.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787640","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

3D printing of calcium doped Isomalt via custom-made Extruder: Facile approach for creating blood vascular like networks within tissue mimicking hydrogel matrix 通过定制挤出机三维打印掺钙异麦芽酮：在组织模拟水凝胶基质中创建类似血管网络的简便方法。

IF 4.2 3区生物学

Methods Pub Date : 2025-04-02 DOI: 10.1016/j.ymeth.2025.03.018

Amar Dhwaj , Nimisha Roy , Amit Prabhakar , Deepti Verma

{"title":"3D printing of calcium doped Isomalt via custom-made Extruder: Facile approach for creating blood vascular like networks within tissue mimicking hydrogel matrix","authors":"Amar Dhwaj , Nimisha Roy , Amit Prabhakar , Deepti Verma","doi":"10.1016/j.ymeth.2025.03.018","DOIUrl":"10.1016/j.ymeth.2025.03.018","url":null,"abstract":"<div><div>3D printing domain has witnessed rapid advancements with immense applications in various fields ranging from aerospace to 3D printed organs. This study describes a facile biofabrication approach for creating an Artificial blood vascular network inside the Hydrogel matrix by using Isomalt sugar (Sugar Alcohol) as a sacrificial component inside a composite-Hydrogel matrix. Conventional 3D-printers have extruder and hot-end assembly, whereas Bioprinters use pneumatic-piston, and piezoelectric-driven extrusion mechanisms. In this study, we describe the design and operation of a custom-made miniature precision lead screw-based syringe-pump extruder mechanism with integrated temperature-controlled heat-block. We are currently using this integrated setup for melt Isomalt-based 3D printing, which can be easily mounted over the Z-axis and is driven using a geared stepper motor with high torque, providing controlled extrusion of highly viscous polymers where sugar structures are used as sacrificial materials for making Artificial blood vascular like networks in the microfluidics domain within the composite Hydrogel matrix. Computational studies using COMSOL Multiphysics were performed to predict the diffusion pattern of the DMEM culture medium to estimate the rate of mass flow through a porous media. Furthermore, Cell based testing is performed using Human Adipose Derived Mesenchymal Stem Cells (HAD-MSC’s) which were cultured over the vascular Hydrogel matrix perfused with culture media with defined flowrates to mimic the natural function of the Nutrient and gaseous exchange inside human tissues. The proposed can be used to produce equivalent Tissue models which could be potentially used in On-chip drug testing platforms, drug discovery and regenerative medicine domains.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 72-84"},"PeriodicalIF":4.2,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787637","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

Multi-Omics clustering by integrating clinical features from large language model 整合大型语言模型临床特征的多组学聚类

IF 4.2 3区生物学

Methods Pub Date : 2025-04-01 DOI: 10.1016/j.ymeth.2025.03.017

Xiucai Ye, Tianyi Shi, Dong Huang, Tetsuya Sakurai

{"title":"Multi-Omics clustering by integrating clinical features from large language model","authors":"Xiucai Ye, Tianyi Shi, Dong Huang, Tetsuya Sakurai","doi":"10.1016/j.ymeth.2025.03.017","DOIUrl":"10.1016/j.ymeth.2025.03.017","url":null,"abstract":"<div><div>Multi-omics clustering has emerged as a powerful approach for understanding complex biological systems and enabling cancer subtyping by integrating diverse omics data. Existing methods primarily focus on the integration of different types of omics data, often overlooking the value of clinical context. In this study, we propose a novel framework that incorporates clinical features extracted from large language model (LLM) to enhance multi-omics clustering. Leveraging clinical data extracted from pathology reports using a BERT-based model, our framework converts unstructured medical text into structured clinical features. These features are integrated with omics data through an autoencoder, enriching the information content of each omics layer to improve feature extraction. The extracted features are then projected into a latent subspace using singular value decomposition (SVD), followed by spectral clustering to obtain the final clustering result. We evaluate the proposed framework on six cancer datasets on three omics levels, comparing it with several state-of-the-art methods. The experimental results demonstrate that the proposed framework outperforms existing methods in multi-omics clustering for cancer subtyping. Moreover, the results highlight the efficacy of integrating clinical features derived from LLM, significantly enhancing clustering performance. This work underscores the importance of clinical context in multi-omics analysis and showcases the transformative potential of LLM in advancing precision medicine.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 64-71"},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143769113","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

Strategies for ocular drug delivery 眼部给药策略。

IF 4.2 3区生物学

Methods Pub Date : 2025-03-28 DOI: 10.1016/j.ymeth.2025.03.020

Silvia L. Fialho (Guest editor)

引用次数: 0

Corrigendum to “Production of AFM wedged cantilevers for stress-relaxation experiments: Uniaxial loading of soft, spherical cells” [Methods 236 (2025) 1–9] “用于应力松弛实验的AFM楔形悬臂梁的生产：软球形单元的单轴加载”的勘误表[方法236 (2025)1-9]

IF 4.2 3区生物学

Methods Pub Date : 2025-03-28 DOI: 10.1016/j.ymeth.2025.03.013

Riccardo Campanile , Jonne Helenius , Cristina Scielzo , Lydia Scarfò , Domenico Salerno , Mario Bossi , Marta Falappi , Alessia Saponara , Daniel J. Müller , Francesco Mantegazza , Valeria Cassina

引用次数: 0

A methodological comparison of synthesizing heavy metal substituted bioapatite 合成重金属取代生物磷灰石的方法比较

IF 4.2 3区生物学

Methods Pub Date : 2025-03-25 DOI: 10.1016/j.ymeth.2025.03.016

Kennedy A. Drake, Tyler A. Grubelich, Stephanie Wong, Alix C. Deymier

{"title":"A methodological comparison of synthesizing heavy metal substituted bioapatite","authors":"Kennedy A. Drake, Tyler A. Grubelich, Stephanie Wong, Alix C. Deymier","doi":"10.1016/j.ymeth.2025.03.016","DOIUrl":"10.1016/j.ymeth.2025.03.016","url":null,"abstract":"<div><div>This study evaluates two methods—maturation and direct precipitation—for synthesizing heavy metal substituted biomimetic hydroxyapatite (HA), focusing on their efficacy in mimicking human bone composition and crystallinity. Cobalt (Co) and chromium (Cr) substitutions were investigated due to their relevance to metal-on-metal implant degradation and the potential integration of these ions into bone mineral. The maturation method involves prolonged incubation, producing amorphous and bioresorbable apatites, while the direct precipitation (DP) method achieves rapid synthesis of highly crystalline apatites through controlled titration. Both approaches were characterized using X-ray diffraction (XRD), Raman spectroscopy, and Fourier Transform Infrared (FTIR) spectroscopy, confirming the apatitic nature of the samples and lattice strain induced by metal ion substitution. This study highlights the maturation method’s adaptability for long-term biological interactions and the DP method’s mechanical stability for load-bearing applications. Comparison of the structural and chemical properties of substituted HA from each method provides insights into optimizing synthesis techniques for diverse biomedical applications, such as bone tissue engineering and mitigating the effects of heavy metal ion release on bone health. These findings contribute to advancing hydroxyapatite-based biomaterials tailored for therapeutic and regenerative medicine needs.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 42-48"},"PeriodicalIF":4.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143714607","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

An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models 细胞外场电位概述：不同的增强和可测量成分，解释和海马突触活动模型。

IF 4.2 3区生物学

Methods Pub Date : 2025-03-25 DOI: 10.1016/j.ymeth.2025.03.015

Maryam Radahmadi , Alireza Halabian , Arshia Halabian

{"title":"An overview of extracellular field potentials: Different potentiation and measurable components, interpretations, and hippocampal synaptic activity models","authors":"Maryam Radahmadi , Alireza Halabian , Arshia Halabian","doi":"10.1016/j.ymeth.2025.03.015","DOIUrl":"10.1016/j.ymeth.2025.03.015","url":null,"abstract":"<div><div>The hippocampus and some other brain regions are critically involved in synaptic plasticity. Electrophysiological recordings using extracellular field potentials (EFPs) reveal diverse synaptic activity within the hippocampus, including input/output functions (reflecting neural excitability), paired-pulse responses (reflecting short-term plasticity), and long-term potentiation (reflecting long-term plasticity). EFP techniques offer various measurable components for assessing multiple neural functions. These include fEPSP slope, amplitude, and area under curve (AUC), as well as latency (fEPSP onset or peak after stimulation), width at half amplitude, fiber volley, decay time, time-course (fEPSP rise and decay time constants; tau), initial slope/initial area and −/late area derived from a fEPSP waveform sample. Each of these parameters is separately evaluated and provides distinct electrophysiological interpretations. Despite the rich data offered by EFP techniques, many studies adopt a limited approach, focusing solely on fEPSP slope, amplitude, and occasionally AUC, thereby neglecting the potential insights provided by other parameters. Given the inherent variability of fEPSP components within a single recording and timeframe, a comprehensive analysis of synaptic activity within a specific hippocampal region is necessary for obtaining the full spectrum of fEPSP-related data. Researchers should consider the potential influence of additional factors contributing to the variability of synaptic activity magnitude. A detailed analysis considering different parts of extracellular fEPSP recordings and their properties is crucial for a deeper understanding of synaptic activity changes within the brain. Therefore, this review aims to provide a comprehensive overview of diverse forms of hippocampal synaptic activity, measurable components of EFP recordings, and their corresponding interpretations.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 50-63"},"PeriodicalIF":4.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727501","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

A synergistic strategy for E2E+ESM2-driven protein a design and wet lab validation E2E+ esm2驱动蛋白的协同策略的设计和湿实验室验证

IF 4.2 3区生物学

Methods Pub Date : 2025-03-20 DOI: 10.1016/j.ymeth.2025.03.008

Huijia Song, Shibo Zhang, Qiang He, Huainian Zhang, Chun Fang, Xiaozhu Lin

{"title":"A synergistic strategy for E2E+ESM2-driven protein a design and wet lab validation","authors":"Huijia Song, Shibo Zhang, Qiang He, Huainian Zhang, Chun Fang, Xiaozhu Lin","doi":"10.1016/j.ymeth.2025.03.008","DOIUrl":"10.1016/j.ymeth.2025.03.008","url":null,"abstract":"<div><div>Protein A is widely used in the biopharmaceutical field, playing a key role in antibody purification. It also serves as an important tool for the research of other biomolecules. Therefore, Protein A design is critical for bioengineering and drug development. Although computational protein design has made progress in model building and functional prediction, current methods still face the following limitations: (1) the predictive accuracy of generative models needs improvement, particularly in matching structural and functional features; (2) the multidimensional screening process for generated proteins requires further optimization. To address these issues, a synergistic strategy for Protein A design and wet-lab validation based on E2E+ESM2 is proposed. In the multidimensional screening process, this research introduces the innovative concept of feature distance. First, multiple Protein A-like sequences are synthesized using a generative model, and their tertiary structures are predicted using AlphaFold. Then, feature distances are calculated based on the ESM2 model, and multidimensional screening is performed by combining parameters such as skeleton distance and solubility. Finally, the functional performance of the selected synthetic proteins is validated through affinity testing. The experimental results show that the synthetic protein V2 exhibits excellent binding kinetics, with a <span><math><msub><mrow><mi>K</mi></mrow><mrow><mi>D</mi></mrow></msub></math></span> value of 3.81±0.17E-10 M, close to the target Protein A. The balance between the association and dissociation rates indicates strong binding performance. This method improves the functional consistency and application potential of the generated proteins, providing a promising solution for protein design.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 30-41"},"PeriodicalIF":4.2,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143681301","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

Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context 预测非编码 RNA 与疾病关联的多任务学习模型：结合本地和全球背景。

IF 4.2 3区生物学

Methods Pub Date : 2025-03-18 DOI: 10.1016/j.ymeth.2025.03.009

Xiaohan Li, Guohua Wang, Dan Li, Yang Li

{"title":"Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context","authors":"Xiaohan Li, Guohua Wang, Dan Li, Yang Li","doi":"10.1016/j.ymeth.2025.03.009","DOIUrl":"10.1016/j.ymeth.2025.03.009","url":null,"abstract":"<div><div>Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are crucial non-coding RNAs involved in various diseases. Understanding these interactions is vital for advancing diagnostic, preventive, and therapeutic strategies. Existing computational methods often address lncRNA-miRNA-disease associations as isolated tasks, resulting in sparse connections and limited generalizability. Additionally, these ncRNA-disease relationships involve higher-order topological information that is frequently overlooked. To address these challenges, we propose the MTL-NRDA model, which employs a multi-task learning framework to simultaneously predict lncRNA-disease associations, miRNA-disease associations, and lncRNA-miRNA interactions. The model integrates multi-source information through a heterogeneous network encompassing lncRNAs, miRNAs, and disease association networks as well as various similarity networks. Node embeddings are optimized by combining local and global contexts, and local features are aggregated using higher-order graph convolutional networks (HOGCN) to capture ncRNA-disease associations, while global features are extracted via a transformer encoder, effectively handling long-range dependencies. MTL-NRDA uses independent bilinear output layers for each task and dynamically adjusts the loss weights to calculate task-specific association probabilities. Experiments on two independent datasets show that MTL-NRDA outperforms existing models. Ablation studies confirmed the effectiveness of the model components and multi-task strategy, whereas hyperparameter tuning further improved the performance. Case studies on breast and liver cancers demonstrated the practical applicability of the model.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"239 ","pages":"Pages 10-21"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668683","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

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