Biology Methods and Protocols最新文献_第8页

Multimodal pretraining for unsupervised protein representation learning. 用于无监督蛋白质表征学习的多模式预训练。

IF 2.5

Biology Methods and Protocols Pub Date : 2024-06-18 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae043

Viet Thanh Duy Nguyen, Truong Son Hy

{"title":"Multimodal pretraining for unsupervised protein representation learning.","authors":"Viet Thanh Duy Nguyen, Truong Son Hy","doi":"10.1093/biomethods/bpae043","DOIUrl":"10.1093/biomethods/bpae043","url":null,"abstract":"Proteins are complex biomolecules essential for numerous biological processes, making them crucial targets for advancements in molecular biology, medical research, and drug design. Understanding their intricate, hierarchical structures, and functions is vital for progress in these fields. To capture this complexity, we introduce Multimodal Protein Representation Learning (MPRL), a novel framework for symmetry-preserving multimodal pretraining that learns unified, unsupervised protein representations by integrating primary and tertiary structures. MPRL employs Evolutionary Scale Modeling (ESM-2) for sequence analysis, Variational Graph Auto-Encoders (VGAE) for residue-level graphs, and PointNet Autoencoder (PAE) for 3D point clouds of atoms, each designed to capture the spatial and evolutionary intricacies of proteins while preserving critical symmetries. By leveraging Auto-Fusion to synthesize joint representations from these pretrained models, MPRL ensures robust and comprehensive protein representations. Our extensive evaluation demonstrates that MPRL significantly enhances performance in various tasks such as protein-ligand binding affinity prediction, protein fold classification, enzyme activity identification, and mutation stability prediction. This framework advances the understanding of protein dynamics and facilitates future research in the field. Our source code is publicly available at https://github.com/HySonLab/Protein_Pretrain.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae043"},"PeriodicalIF":2.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11233121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141564683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Implementation of plate reader-based indooxine and Nessler protocols for monitoring L-asparaginase serum activity in childhood acute lymphoblastic leukaemia. 在儿童急性淋巴细胞白血病中采用基于平板阅读器的indooxine和Nessler方案监测L-天冬酰胺酶血清活性。

IF 2.5

Biology Methods and Protocols Pub Date : 2024-06-13 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae042

Bozhidar Vergov, Yordan Sbirkov, Danail Minchev, Tatyana Todorova, Alexandra Baldzhieva, Hasan Burnusuzov, Мariya I Spasova, Victoria Sarafian

{"title":"Implementation of plate reader-based indooxine and Nessler protocols for monitoring L-asparaginase serum activity in childhood acute lymphoblastic leukaemia.","authors":"Bozhidar Vergov, Yordan Sbirkov, Danail Minchev, Tatyana Todorova, Alexandra Baldzhieva, Hasan Burnusuzov, Мariya I Spasova, Victoria Sarafian","doi":"10.1093/biomethods/bpae042","DOIUrl":"10.1093/biomethods/bpae042","url":null,"abstract":"Monitoring the blood serum activity of L-asparaginase in children with acute lymphoblastic leukaemia (ALL) has been highly recommended to detect enzyme inactivation that can cause relapse and to avoid unwanted toxicity. Nevertheless, perhaps at least partially due to the lack of clinically approved commercially available kits or standardized and independently reproduced and validated in-house protocols, laboratory assay-based determination of the optimal doses of L-asparaginase is not carried out routinely. In this study, we adapted previously published protocols for two plate reader-based colorimetric methods, indooxine and Nessler, to measure asparaginase activity. Mock samples with dilutions of the enzyme for initial optimization steps, and patient samples were used as a proof of principle and to compare the two protocols. For the first time the indooxine and the Nessler methods are adapted for a plate reader and L-asparaginase serum activity levels are compared by both protocols. Passing-Bablok and Bland-Altman's statistical analyses found very little difference, strong correlation (r = 0.852), and bias of only 6% between the data from the two methods when used for fresh patient samples. Furthermore, we demonstrate that the Nessler method could also be applied for frozen sera as the results, compared to fresh samples, showed little difference, strong correlation (r = 0.817), and small bias (9%). We successfully adapted and validated two methods for measuring L-asparaginase activity in cALL and provided the most detailed description to date on how to reproduce and implement them in other clinical laboratories.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae042"},"PeriodicalIF":2.5,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11557903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142629633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. PROMER 技术：一种新的实时 PCR 工具，能够以高特异性和高灵敏度对点突变进行多重检测。

IF 2.5

Biology Methods and Protocols Pub Date : 2024-06-04 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae041

Hwanhee Nam, Esder Lee, Hichang Yang, Kyeyoon Lee, Taeho Kwak, Dain Kim, Hyemin Kim, Mihwa Yang, Younjoo Yang, Seungwan Son, Young-Hyean Nam, Il Minn

{"title":"PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity.","authors":"Hwanhee Nam, Esder Lee, Hichang Yang, Kyeyoon Lee, Taeho Kwak, Dain Kim, Hyemin Kim, Mihwa Yang, Younjoo Yang, Seungwan Son, Young-Hyean Nam, Il Minn","doi":"10.1093/biomethods/bpae041","DOIUrl":"https://doi.org/10.1093/biomethods/bpae041","url":null,"abstract":"Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae041"},"PeriodicalIF":2.5,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11208725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141471293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IntelliGenes: Interactive and user-friendly multimodal AI/ML application for biomarker discovery and predictive medicine. IntelliGenes：用于生物标记物发现和预测医学的交互式、用户友好型多模态人工智能/人工智能应用。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae040

Rishabh Narayanan, William DeGroat, Dinesh Mendhe, Habiba Abdelhalim, Zeeshan Ahmed

{"title":"IntelliGenes: Interactive and user-friendly multimodal AI/ML application for biomarker discovery and predictive medicine.","authors":"Rishabh Narayanan, William DeGroat, Dinesh Mendhe, Habiba Abdelhalim, Zeeshan Ahmed","doi":"10.1093/biomethods/bpae040","DOIUrl":"10.1093/biomethods/bpae040","url":null,"abstract":"Artificial intelligence (AI) and machine learning (ML) have advanced in several areas and fields of life; however, its progress in the field of multi-omics is not matching the levels others have attained. Challenges include but are not limited to the handling and analysis of high volumes of complex multi-omics data, and the expertise needed to implement and execute AI/ML approaches. In this article, we present IntelliGenes, an interactive, customizable, cross-platform, and user-friendly AI/ML application for multi-omics data exploration to discover novel biomarkers and predict rare, common, and complex diseases. The implemented methodology is based on a nexus of conventional statistical techniques and cutting-edge ML algorithms, which outperforms single algorithms and result in enhanced accuracy. The interactive and cross-platform graphical user interface of IntelliGenes is divided into three main sections: (i) Data Manager, (ii) AI/ML Analysis, and (iii) Visualization. Data Manager supports the user in loading and customizing the input data and list of existing biomarkers. AI/ML Analysis allows the user to apply default combinations of statistical and ML algorithms, as well as customize and create new AI/ML pipelines. Visualization provides options to interpret a diverse set of produced results, including performance metrics, disease predictions, and various charts. The performance of IntelliGenes has been successfully tested at variable in-house and peer-reviewed studies, and was able to correctly classify individuals as patients and predict disease with high accuracy. It stands apart primarily in its simplicity in use for nontechnical users and its emphasis on generating interpretable visualizations. We have designed and implemented IntelliGenes in a way that a user with or without computational background can apply AI/ML approaches to discover novel biomarkers and predict diseases.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae040"},"PeriodicalIF":3.6,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11176709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. 利用 HaloTag 富集质谱法绘制脂肪细胞相互作用组网络图。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae039

Junshi Yazaki, Takashi Yamanashi, Shino Nemoto, Atsuo Kobayashi, Yong-Woon Han, Tomoko Hasegawa, Akira Iwase, Masaki Ishikawa, Ryo Konno, Koshi Imami, Yusuke Kawashima, Jun Seita

{"title":"Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry.","authors":"Junshi Yazaki, Takashi Yamanashi, Shino Nemoto, Atsuo Kobayashi, Yong-Woon Han, Tomoko Hasegawa, Akira Iwase, Masaki Ishikawa, Ryo Konno, Koshi Imami, Yusuke Kawashima, Jun Seita","doi":"10.1093/biomethods/bpae039","DOIUrl":"10.1093/biomethods/bpae039","url":null,"abstract":"Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae039"},"PeriodicalIF":3.6,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Northern blotting of endogenous full-length human-specific LINE-1 RNA. 内源性全长人类特异性 LINE-1 RNA 的 Northern 印迹。

IF 2.5

Biology Methods and Protocols Pub Date : 2024-05-28 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae036

Maisa I Alkailani

引用次数: 0

An optimized ligation-mediated PCR method for chromosome walking and fusion gene chromosomal breakpoints identification. 用于染色体走行和融合基因染色体断点鉴定的优化连接介导 PCR 方法。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-05-25 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae037

Jrhau Lung, Ming-Szu Hung, Chao-Yu Chen, Tsung-Ming Yang, Chin-Kuo Lin, Yu-Hung Fang, Yuan-Yuan Jiang, Hui-Fen Liao, Yu-Ching Lin

引用次数: 0

Macro-based collagen quantification and segmentation in picrosirius red-stained heart sections using light microscopy. 使用光学显微镜对皮色红染色的心脏切片进行基于宏观的胶原蛋白定量和分割。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-04-27 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae027

Julian Kammerer, Alexandra Cirnu, Tatjana Williams, Melanie Hasselmeier, Mike Nörpel, Ruping Chen, Brenda Gerull

{"title":"Macro-based collagen quantification and segmentation in picrosirius red-stained heart sections using light microscopy.","authors":"Julian Kammerer, Alexandra Cirnu, Tatjana Williams, Melanie Hasselmeier, Mike Nörpel, Ruping Chen, Brenda Gerull","doi":"10.1093/biomethods/bpae027","DOIUrl":"10.1093/biomethods/bpae027","url":null,"abstract":"Picrosirius red staining constitutes an important and broadly used tool to visualize collagen and fibrosis in various tissues. Although multiple qualitative and quantitative analysis methods to evaluate fibrosis are available, many require specialized devices and software or lack objectivity and scalability. Here, we aimed to develop a versatile and powerful \"QuantSeg\" macro in the FIJI image processing software capable of automated, robust, and quick collagen quantification in cardiac tissue from light micrographs. To examine different patterns of fibrosis, an optional segmentation algorithm was implemented. To ensure the method's validity, we quantified the collagen content in a set of wild-type versus plakoglobin-knockout murine hearts exhibiting extensive fibrosis using both the macro and an established, fluorescence microscopy-based method, and compared results. To demonstrate the capabilities of the segmentation feature, rat hearts were examined post-myocardial infarction. We found the QuantSeg macro to robustly detect the differences in fibrosis between knockout and control hearts. In sections with low collagen content, the macro yielded more consistent results than using the fluorescence microscopy-based technique. With its wide range of output parameters, ease of use, cost effectiveness, and objectivity, the QuantSeg macro has the potential to become an established method for analysis of PSR-stained tissue. The novel segmentation feature allows for automated evaluation of different patterns of cardiac fibrosis for the first time.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae027"},"PeriodicalIF":3.6,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11116823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: An improved method for measuring catalase activity in biological samples. 更正：测量生物样本中过氧化氢酶活性的改进方法。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-04-26 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae025

引用次数: 0

Intra-arterial delivery of neurospheres into isolated perfused porcine colons: a proof of concept. 向离体灌注猪结肠动脉内输送神经球：概念验证。

IF 3.6

Biology Methods and Protocols Pub Date : 2024-04-02 eCollection Date: 2024-01-01 DOI: 10.1093/biomethods/bpae022

Richard D Martel, Nicolas A Hoyos, María Ángeles Tapia-Laliena, Irmgard Herrmann, Martin Herrmann, Rasul Khasanov, Karl-Herbert Schäfer

{"title":"Intra-arterial delivery of neurospheres into isolated perfused porcine colons: a proof of concept.","authors":"Richard D Martel, Nicolas A Hoyos, María Ángeles Tapia-Laliena, Irmgard Herrmann, Martin Herrmann, Rasul Khasanov, Karl-Herbert Schäfer","doi":"10.1093/biomethods/bpae022","DOIUrl":"https://doi.org/10.1093/biomethods/bpae022","url":null,"abstract":"Cell replacement in aganglionic intestines is a promising, yet merely experimental tool for the therapy of congenital dysganglionosis of the enteric nervous system like Hirschsprung disease. While the injection of single cells or neurospheres to a defined and very restricted location is trivial, the translation to the clinical application, where large aganglionic or hypoganglionic areas need to be colonized (hundreds of square centimetres), afford a homogeneous distribution of multiple neurospheres all over the affected tissue areas. Reaching the entire aganglionic area in vivo is critical for the restoration of peristaltic function. The latter mainly depends on an intact nervous system that extends throughout the organ. Intra-arterial injection is a common method in cell therapy and may be the key to delivering cells or neurospheres into the capillary bed of the colon with area-wide distribution. We describe an experimental method for monitoring the distribution of a defined number of neurospheres into porcine recta ex vivo, immediately after intra-arterial injection. We designed this method to localize grafting sites of single neurospheres in precise biopsies which can further be examined in explant cultures. The isolated perfused porcine rectum allowed us to continuously monitor the perfusion pressure. A blockage of too many capillaries would lead to an ischaemic situation and an increase of perfusion pressure. Since we could demonstrate that the area-wide delivery of neurospheres did not alter the overall vascular resistance, we showed that the delivery does not significantly impair the local circulation.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"9 1","pages":"bpae022"},"PeriodicalIF":3.6,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11018533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140862191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0