Methods in molecular biology最新文献_第6页

Molegro Virtual Docker for Docking Screens. Molegro虚拟码头对接屏幕。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4949-7_10

Josimary Morais Vasconcelos Oliveira, Amauri Duarte da Silva, Alexandra Martins Dos Santos Soares, Walter Filgueira de Azevedo

引用次数: 0

Molegro Data Modeller for Machine Learning. Molegro机器学习数据建模器。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4949-7_11

Amauri Duarte da Silva, Nelson José Freitas da Silveira, Patrícia Rufino Oliveira, Walter Filgueira de Azevedo

引用次数: 0

ADAR1 RNA-Editing Enzyme Regulates Telomeric R-Loop Formation. ADAR1 rna编辑酶调控端粒r环形成

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4670-0_6

Eito Ichihashi, Mai Kubota, Yusuke Shiromoto, Masayuki Sakurai

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A Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Epidemiological Investigations of Cryptosporidium parvum. 小隐孢子虫流行病学调查的多位点可变数串联重复分析（MLVA）方案。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4824-7_8

Harriet Risby, Guy Robinson, Rachel M Chalmers

引用次数: 0

Optimized Genome Assembly Protocol for Cryptosporidium. 隐孢子虫基因组组装方案优化。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4824-7_9

Wanyi Huang, Lihua Xiao

引用次数: 0

Genomic Characterization of Cryptosporidium spp. via iNextEra Library Preparation and Hybridization Bait Capture. 利用iNextEra文库制备和杂交诱饵捕获技术对隐孢子虫进行基因组鉴定。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4824-7_4

Mohammad Imtiaj Uddin Bhuiyan, Fiifi Agyabeng-Dadzie, Amanda H Sullivan, Megan S Beaudry, Kelly N Petersen, Piotr T Tuczapski, Michael E Grigg, Jessica C Kissinger, Travis C Glenn

{"title":"Genomic Characterization of Cryptosporidium spp. via iNextEra Library Preparation and Hybridization Bait Capture.","authors":"Mohammad Imtiaj Uddin Bhuiyan, Fiifi Agyabeng-Dadzie, Amanda H Sullivan, Megan S Beaudry, Kelly N Petersen, Piotr T Tuczapski, Michael E Grigg, Jessica C Kissinger, Travis C Glenn","doi":"10.1007/978-1-0716-4824-7_4","DOIUrl":"10.1007/978-1-0716-4824-7_4","url":null,"abstract":"Next-generation DNA sequencing (NGS) is used to study the genome sequences of Cryptosporidium spp., but NGS is challenging when pure Cryptosporidium oocysts are limited in number or not available. Varying levels of parasites present in fecal samples, combined with the abundance of host cells, bacterial and other microbial cells, and undigested food particles, often result in fecal DNA samples with ~0.1% Cryptosporidium DNA, making genome-scale sequencing of Cryptosporidium from such samples cost-prohibitive. DNA extractions from fecal samples are, however, widely available and commonly used for polymerase chain reaction (PCR)-based diagnostics which can detect fg levels of Cryptosporidium DNA in complex DNA mixtures. Here, we describe an Illumina NGS sample preparation protocol (iNextEra) that can generate libraries from a wide range of DNA input (<1 ng to >60 ng). We then use those libraries within a modified myBaits capture hybridization protocol using CryptoCap_100K baits to enrich Cryptosporidium genomic DNA from a complex DNA background to increase the percentage of generated sequence reads that map to target Cryptosporidium reference genome sequences. Thus, iNextEra libraries and capture hybridization facilitate genome-level sequencing of this critical pathogen from widely available samples with less cost, thereby opening new opportunities to understand the complex biology of this important pathogen.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2978 ","pages":"41-64"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145378061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Method for the Dissection of Genomic Loci Associated with Chickpea Root Penetration Traits in Compact Soil. 鹰嘴豆根系渗透性状基因组位点的解剖方法。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4820-9_9

Jahanvi Ganotra, Mandavi Pandey, Ravindra Donde, Jitender Giri

{"title":"Method for the Dissection of Genomic Loci Associated with Chickpea Root Penetration Traits in Compact Soil.","authors":"Jahanvi Ganotra, Mandavi Pandey, Ravindra Donde, Jitender Giri","doi":"10.1007/978-1-0716-4820-9_9","DOIUrl":"10.1007/978-1-0716-4820-9_9","url":null,"abstract":"Mechanical impedance in agricultural land is a significant constraint in modern agriculture. It dramatically affects seed germination, plant growth, development, and grain yield. Soil compaction hinders root growth and the ability to access deeper nutrients and water resources, impacting climate resilience, crop productivity, and global food security. Crops display variations in root system architecture (RSA) traits when grown in compacted soils. We can better understand the mechanisms behind soil compaction by examining root-related traits and their associated genes. Our recently published study investigated RSA traits across different soil compaction levels and identified significant genomic associations in chickpeas. We developed reliable methods for creating soils with varying bulk densities (i.e., compaction levels), growing chickpea seedlings, and harvesting the roots. We also conducted high-throughput phenotyping and screening of root-related traits using winRHIZO software. By integrating these phenotypic data with available genotypic data through Genome-Wide Association Studies (GWAS), we could identify genetic loci influencing root penetration in response to increasing soil compaction. These methods will help us identify key architectural traits of roots that can be targeted in crop breeding efforts to enhance resilience and productivity in compacted soils. By improving the root system and understanding the genes involved, we aim to develop plants more responsive to root penetration.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2977 ","pages":"119-133"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Host-Derived Molecules as Novel Chagas Disease Biomarkers: Hypercoagulability Markers and Extracellular Vesicles. 宿主衍生分子作为新的恰加斯病生物标志物：高凝性标志物和细胞外囊泡。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4848-3_19

Berta Barnadas-Carceller, Dolors Tàssies, Irene Losada Galván, Julio Alonso-Padilla, Joan Carles Reverter, Carmen Fernandez-Becerra, María-Jesús Pinazo

{"title":"Host-Derived Molecules as Novel Chagas Disease Biomarkers: Hypercoagulability Markers and Extracellular Vesicles.","authors":"Berta Barnadas-Carceller, Dolors Tàssies, Irene Losada Galván, Julio Alonso-Padilla, Joan Carles Reverter, Carmen Fernandez-Becerra, María-Jesús Pinazo","doi":"10.1007/978-1-0716-4848-3_19","DOIUrl":"10.1007/978-1-0716-4848-3_19","url":null,"abstract":"Diagnostic methods for Chagas disease rely primarily on serological and molecular tests to detect anti-T cruzi antibodies or parasite-derived DNA. However, these tests do not predict clinical outcomes or treatment responses, as serological results may take years to turn negative, making them impractical for monitoring treatment progress. Molecular tests, though highly sensitive, can identify parasites but cannot rule out the presence of dormant forms or low levels of parasitemia, which may later reactivate. Due to the lack of reliable biomarkers for disease prognosis and treatment monitoring, there has been growing interest in host-derived markers as alternatives. One area of focus is the hypercoagulability observed in T. cruzi-infected individuals, which increases the risk of thrombotic events due to factors like chronic inflammation, dysregulation of immunothrombosis, and vasculitis. In addition, extracellular vesicles (EVs), i.e., double-membrane-enclosed particles found in various biological fluids, have emerged as a potential source of biomarkers for disease detection, prognosis, and monitoring. EVs contain proteins, lipids, and nucleic acids that can provide valuable molecular information about a patient's condition. This chapter outlines procedures for detecting host-derived biomarkers of Chagas disease, particularly those related to hypercoagulability, such as F1 + 2 and endogenous thrombin potential assays, and the isolation and characterization of EVs as biomarkers for response to treatment and disease progression.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2982 ","pages":"285-307"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145438382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computer-Aided Discovery of Drugs Against Chagas Disease. 计算机辅助发现对抗恰加斯病的药物。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4848-3_1

Carolina L Bellera, Lucas N Alberca, Alan Talevi

{"title":"Computer-Aided Discovery of Drugs Against Chagas Disease.","authors":"Carolina L Bellera, Lucas N Alberca, Alan Talevi","doi":"10.1007/978-1-0716-4848-3_1","DOIUrl":"10.1007/978-1-0716-4848-3_1","url":null,"abstract":"Chagas disease affects around 6-8 million people worldwide. The available treatments have considerable limitations, including their uncertain efficacy in the chronic phase of the disease in adults, their unfavorable safety profile that usually compromises adherence to treatment, their long duration, and the emergence of resistant strains. All these considerations justify the continuous search for improved therapies.Informatics has been increasingly integrated into all levels of biomedical sciences, including the discovery and development of new drugs. In silico methods are relevant in all domains of therapeutics, but especially in the field of neglected diseases, in which their adoption can leverage the active participation of low- and middle-income countries (the ones historically affected by these diseases) in the development of new diagnostic and therapeutic options.This chapter describes the in silico methodologies that can be used to validate new pharmacological targets, compile data sets to train and/or validate computational models to apply in in silico screening campaigns, and implement retrospective and prospective in silico screening experiments.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2982 ","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145438417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Use of B-cell Tetramers for the Study of Trypanosoma cruzi-Specific B cells. B细胞四聚体在克氏锥虫特异性B细胞研究中的应用

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4848-3_17

Damián Pérez-Mazliah

引用次数: 0