Methods in molecular biology最新文献_第9页

Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations. 分析ChIP-Seq数据的指南：通过QC和分析考虑的过程。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4322-8_14

Bony De Kumar, Jaya Krishnan

引用次数: 0

Lineage Tracing by Light-Sheet Microscopy and Computational Reconstruction. 用薄层显微镜和计算重建进行谱系追踪。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4310-5_8

Maria Kalogeridi, Ioannis Liaskas, John Rallis, Anastasios Pavlopoulos

{"title":"Lineage Tracing by Light-Sheet Microscopy and Computational Reconstruction.","authors":"Maria Kalogeridi, Ioannis Liaskas, John Rallis, Anastasios Pavlopoulos","doi":"10.1007/978-1-0716-4310-5_8","DOIUrl":"https://doi.org/10.1007/978-1-0716-4310-5_8","url":null,"abstract":"Lineage tracing based on modern live imaging approaches enables to visualize, reconstruct, and analyze the developmental history, fate, and dynamic behaviors of cells in vivo in a direct, comprehensive, and quantitative manner. Light-sheet fluorescence microscopy (LSFM) has greatly boosted lineage tracing efforts, because fluorescently labeled specimens can be imaged in their entirety, over long periods of time, with high spatiotemporal resolution and minimal photodamage. In addition, an increasing arsenal of commercial and open-source software solutions for cell and nuclei segmentation and tracking can be employed to convert data from pixel-based to object-based representations, and to reconstruct the lineages of cells in their native context as they organize in tissues, organs, and whole organisms. This chapter describes the preparation of LSFM image datasets and the use of three freely available platforms, namely, the Fiji/ImageJ plugins Massive Multiview Tracker (MaMuT), Mastodon and TrackMate, for small-scale and large-scale lineage tracing purposes using manual, semi-automated, and fully automated pipelines for nuclei or cell tracking. Lineage tracing with these tools is described on LSFM image datasets of fluorescently labeled embryos from the crustacean model Parhyale hawaiensis that lends itself to multi-scale investigations of development and regeneration.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2886 ","pages":"153-176"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915408","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

In Vivo Investigation of Filovirus Glycoprotein-Mediated Infection in a BSL2 Setting. 在 BSL2 环境中对丝状病毒糖蛋白介导的体内感染进行研究。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4256-6_13

Paige T Richards, José Alberto Aguilar Briseño, Bethany A Brunton, Wendy Maury

引用次数: 0

Thyroid Hormones Determination in Euthyroid and LT4-Treated Patients During COVID-19 Hospitalization. 在 COVID-19 住院期间对甲状腺功能正常和接受过 LT4 治疗的患者进行甲状腺激素测定。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4252-8_16

Cristina Álvarez Castilla

{"title":"Thyroid Hormones Determination in Euthyroid and LT4-Treated Patients During COVID-19 Hospitalization.","authors":"Cristina Álvarez Castilla","doi":"10.1007/978-1-0716-4252-8_16","DOIUrl":"10.1007/978-1-0716-4252-8_16","url":null,"abstract":"The global impact of the novel coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was significant, including in Spain. The initial outbreak in late January 2020 prompted a frantic effort to comprehend the virus and contain its spread, given the limited knowledge available at the time. The study by Amich et al. (2022) in Frontiers in Endocrinology aimed to investigate the influence of thyroid hormone levels and age on the severity of COVID-19 in euthyroid and levothyroxine-treated patients. Although a direct correlation between thyroid hormone levels and the severity of COVID-19 has not been established, it is known that thyroid dysfunction affects immune function and general health, which may impact the outcomes of COVID-19. The research included patients from the Clinic San Carlos Hospital in Madrid, and a comprehensive range of data was collected from each patient, including demographic information, symptoms, comorbidities, and laboratory test results. This approach was employed in order to accurately match patients and identify factors that may influence the severity of COVID-19 outcomes. Blood samples were analyzed using chemiluminescence on a DXI-800® instrument, with the following hormones quantified: thyroid-stimulating hormone (TSH), free thyroxine (FT4), and free triiodothyronine (FT3). These insights contribute to an understanding of the interplay between thyroid function and the severity of COVID-19, highlighting the need for careful patient management in those with thyroid disorders during the pandemic.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2876 ","pages":"241-255"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695433","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

Molecular Dynamics Simulation for Membrane Fusion. 膜融合的分子动力学模拟。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4314-3_3

Owen Tyoe, Kai Zhang, Jiajie Diao

引用次数: 0

Tracking Abdominal-B Expression and Function in the Fly Internal Reproductive System by Explants Imaging. 利用外植体成像技术跟踪蝇体内生殖系统中腹部- b的表达和功能。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4322-8_3

David Foronda

引用次数: 0

CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression. 卡林：用于同时读取谱系历史和基因表达的小鼠系。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4310-5_14

Sarah Bowling, Fernando D Camargo

引用次数: 0

Advanced Method for the In Vivo Measurements of Lysophospholipid Translocation Across the Inner (Cytoplasmic) Membrane of Escherichia coli. 大肠杆菌内（胞质）膜溶血磷脂转运的先进体内测定方法

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4318-1_11

Yibin Lin, Lei Zheng, Mikhail Bogdanov

{"title":"Advanced Method for the In Vivo Measurements of Lysophospholipid Translocation Across the Inner (Cytoplasmic) Membrane of Escherichia coli.","authors":"Yibin Lin, Lei Zheng, Mikhail Bogdanov","doi":"10.1007/978-1-0716-4318-1_11","DOIUrl":"10.1007/978-1-0716-4318-1_11","url":null,"abstract":"Phospholipid translocation occurs ubiquitously in biological membranes and primarily is protein catalyzed. Lipid flippases mediate the net translocation of specific phospholipids from one leaflet of a membrane to the other. In the inner (cytoplasmic) membrane (IM) of Gram-negative bacteria, lysophospholipid translocase (LplT) and cytosolic bifunctional acyl-acyl carrier protein (ACP) synthetase/2-acylglycerolphosphoethanolamine acyltransferase (Aas) form a glycerophospholipid regeneration system, which is capable of facilitating rapid retrograde translocation of lyso forms of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin (CL) but not exogenous (host-derived) phosphatidylcholine (PC) across the IM of Gram-negative diderm (two-membraned) bacteria in consequential order lyso-PE = lyso-PG > > lysophosphatidic acid (lyso-PA) >> lyso-PC. Although several flippases that bind and move non-glycerophosphatidyl lipids across the IM are characterized in Gram-negative bacteria, LplT appears to be the first example of a bacterial protein capable of facilitating the rapid translocation of monoacylated glycerophospholipids. On the cytoplasmic surface, Aas restores the lysophospholipids to their diacyl forms with comparable efficiency but excludes any exogenous monoacylated lipid species. This coupled remodeling enzyme tandem provides an effective means to examine substrate specificity of lipid regeneration and lysophospholipid transport per se across the membrane. The current chapter describes two distinct but complementary methods for the measurement of lysophospholipid transport across membranes using Escherichia coli spheroplasts.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2888 ","pages":"147-165"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854697","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

A Protocol for GC-MS Profiling of Chiral Secondary Amino Acids. 手性二级氨基酸的气相色谱-质谱分析程序

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4334-1_11

Stanislav Opekar, Helena Zahradníčková, Petr Vodrážka, Lucie Řimnáčová, Martin Moos, Petr Šimek

{"title":"A Protocol for GC-MS Profiling of Chiral Secondary Amino Acids.","authors":"Stanislav Opekar, Helena Zahradníčková, Petr Vodrážka, Lucie Řimnáčová, Martin Moos, Petr Šimek","doi":"10.1007/978-1-0716-4334-1_11","DOIUrl":"https://doi.org/10.1007/978-1-0716-4334-1_11","url":null,"abstract":"A simple analytical workflow is described for gas chromatographic-mass spectrometric (GC-MS)-based chiral profiling of secondary amino acids (AAs) in biological matrices. The sample preparation is carried out directly in aqueous biological sample extracts and involves in situ heptafluorobutyl chloroformate (HFBCF) derivatization-liquid-liquid microextraction of nonpolar products into hexane phase followed by subsequent formation of the corresponding methylamides from the HFB esters by direct treatment with methylamine reagent solution. The (O, N) HFB-butoxycarbonyl-methylamide AA products (HFBOC-MA) are separated on a Chirasil-L-Val capillary column and quantitatively measured by GC-MS operated in selected ion monitoring (SIM) mode. The protocol includes 12 simple pipetting steps and covers the quantitative analysis of 8 L, D pairs of secondary amino acids, including proline, isomeric 3-, 4-hydroxyprolines, pipecolic acid, nipecotic acid, azetidine-2-carboxylic acid, and cis- and trans-5-hydroxy-L-pipecolic acid using 13C5 -L-proline as an internal standard. The individual analytical steps are commented on and explained, with emphasis on the chiral GC-MS analysis of secondary amino acids in human urine, serum, and peptide hydrolysate samples.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2891 ","pages":"205-219"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984009","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

Analysis of Urinary Metanephrines Using Liquid Chromatography Tandem Mass Spectrometry. 液相色谱串联质谱法分析尿中肾上腺素。

Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4334-1_14

Marlene N Thaitumu, Elizabeth L Frank

引用次数: 0