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Microbiome Analyses for Toxicological Studies 毒理学研究中的微生物组分析
Current protocols in toxicology Pub Date : 2018-07-25 DOI: 10.1002/cptx.53
Jacquelynn Benjamino, Lidia Beka, Joerg Graf
{"title":"Microbiome Analyses for Toxicological Studies","authors":"Jacquelynn Benjamino, Lidia Beka, Joerg Graf","doi":"10.1002/cptx.53","DOIUrl":"10.1002/cptx.53","url":null,"abstract":"Microbiomes can be thought of as the integration of biotic and abiotic factors, including the microbial communities and the distinct physio‐chemical properties that are present in a habitat. The microbes within a microbiome can influence the chemical environment by degrading medications inside patients or contaminants in the environment, such as hydrocarbons released after the Deepwater Horizon oil spill. Identifying and monitoring the relative abundance of microbes can help to elucidate variations in their response to toxins and should be considered as a variable in statistical analyses. In addition, the presence of pathogenic microbes or toxin‐producing species could affect the observed toxicity of an environment. The protocols in this unit begin with the collection of samples, proceeds to sequencing of the bacterial DNA, and ends with an analysis of the bacterial community in light of environmental metadata. © 2018 by John Wiley & Sons, Inc.","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.53","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36343099","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: 8
Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research 啮齿动物饮食选择和纤维类型对肠道微生物组和代谢疾病研究数据解释的影响
Current protocols in toxicology Pub Date : 2018-07-20 DOI: 10.1002/cptx.55
Michael A. Pellizzon, Matthew R. Ricci
{"title":"Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research","authors":"Michael A. Pellizzon,&nbsp;Matthew R. Ricci","doi":"10.1002/cptx.55","DOIUrl":"10.1002/cptx.55","url":null,"abstract":"<p>Poor diet reporting and improperly controlling laboratory animal diet continues to reduce our ability to interpret data effectively in animal studies. In order to make the best use of our resources and improve research transparency, proper reporting methods that include a diet design are essential to improving our understanding of the links between gut health and metabolic disease onset. This unit will focus on the importance of diet choice in laboratory animal studies, specifically as it relates to gut health, microbiome, and metabolic disease development. The two most commonly used diet types, grain-based (GB) diets, and purified ingredient diets, will each be described, with particular emphasis on their differences in dietary fiber. A further description of how these diet types and fiber can affect gut morphology and microbiota will be provided as well as how purified ingredient diets may be improved upon. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.55","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36331243","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: 23
Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions 产生无菌果蝇以研究肠道-微生物相互作用:在无菌条件下对后方果蝇的方案
Current protocols in toxicology Pub Date : 2018-06-22 DOI: 10.1002/cptx.52
Christa Kietz, Vilma Pollari, Annika Meinander
{"title":"Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions","authors":"Christa Kietz,&nbsp;Vilma Pollari,&nbsp;Annika Meinander","doi":"10.1002/cptx.52","DOIUrl":"10.1002/cptx.52","url":null,"abstract":"<p>As several diseases have been linked to dysbiosis of the human intestinal microflora, manipulation of the microbiota has emerged as an exciting new strategy for potentially treating and preventing diseases. However, the human microbiota consists of a plethora of different species, and distinguishing the impact of a specific bacterial species on human health is challenging. In tackling this challenge, the fruit fly <i>Drosophila melanogaster</i>, with its far simpler microbial composition, has emerged as a powerful model for unraveling host-microbe interactions. To study the interplay between the resident commensal microbiome and the host, flies can be made germ-free, or axenic. To elucidate the impact of specific bacteria, axenic flies can then be re-introduced to specific microbial species. In this unit, we provide a step-by-step protocol on how to rear <i>Drosophila melanogaster</i> under axenic conditions and confirm the axenity of flies. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.52","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36249614","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: 22
In Vitro Methods to Characterize the Effects of Tobacco and Nontobacco Products on Human Platelet Function 烟草和非烟草制品对人血小板功能影响的体外方法研究
Current protocols in toxicology Pub Date : 2018-05-24 DOI: 10.1002/cptx.46
Shannon G. Loelius, Sherry L. Spinelli, Katie L. Lannan, Richard P. Phipps
{"title":"In Vitro Methods to Characterize the Effects of Tobacco and Nontobacco Products on Human Platelet Function","authors":"Shannon G. Loelius,&nbsp;Sherry L. Spinelli,&nbsp;Katie L. Lannan,&nbsp;Richard P. Phipps","doi":"10.1002/cptx.46","DOIUrl":"10.1002/cptx.46","url":null,"abstract":"<p>In this document, we describe methods for the isolation, treatment, and functional testing of human blood platelets <i>in vitro</i>. Functional assays for inflammatory function include flow cytometry and immunoassays for platelet release of platelet factor 4, soluble CD40L, prostaglandin E<sub>2</sub>, and thromboxane. Assays for platelet hemostatic function described here examine platelet spreading, aggregation using platelet-rich plasma, and thromboelastography. Also described here are methods for testing cigarette smoke on primary human platelets <i>in vitro</i>, which our lab developed to address a major knowledge gap regarding how cigarette smoke dysregulates platelets and how this platelet dysregulation contributes to cardiovascular disease. Some of these protocols may be repurposed for investigation of the toxicity potential of other tobacco products and environmental insults. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.46","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36339621","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: 2
Newly Revised Quantitative PCR-Based Assay for Mitochondrial and Nuclear DNA Damage 新修订的基于定量pcr的线粒体和核DNA损伤检测方法
Current protocols in toxicology Pub Date : 2018-05-18 DOI: 10.1002/cptx.50
Laurie H. Sanders, Jeremy P. Rouanet, Evan H. Howlett, Tess C. Leuthner, John P. Rooney, J. Timothy Greenamyre, Joel N. Meyer
{"title":"Newly Revised Quantitative PCR-Based Assay for Mitochondrial and Nuclear DNA Damage","authors":"Laurie H. Sanders,&nbsp;Jeremy P. Rouanet,&nbsp;Evan H. Howlett,&nbsp;Tess C. Leuthner,&nbsp;John P. Rooney,&nbsp;J. Timothy Greenamyre,&nbsp;Joel N. Meyer","doi":"10.1002/cptx.50","DOIUrl":"10.1002/cptx.50","url":null,"abstract":"<p>Given the crucial role of DNA damage in human health and disease, it is important to be able to accurately measure both mitochondrial and nuclear DNA damage. This article describes a method based on a long-amplicon quantitative PCR–based assay that does not require a separate mitochondrial isolation step, which can often be labor-intensive and generate artifacts. The detailed basic protocol presented here is newly revised, with particular attention to application in <i>Homo sapiens</i>, <i>Rattus norvegicus</i>, and <i>Caenorhabditis elegans</i> resulting from changes in availability of PCR reagents. Optimized extraction support protocols are also described for high-quality DNA from multiple rat tissues for which these procedures had not previously been described. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.50","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10740322","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: 11
Determining Food Allergens by Skin Sensitization in Mice 小鼠皮肤致敏法测定食物过敏原
Current protocols in toxicology Pub Date : 2018-04-30 DOI: 10.1002/cptx.48
Norimasa Tamehiro, Reiko Adachi, Yoshie Kimura, Shinobu Sakai, Reiko Teshima, Kazunari Kondo
{"title":"Determining Food Allergens by Skin Sensitization in Mice","authors":"Norimasa Tamehiro,&nbsp;Reiko Adachi,&nbsp;Yoshie Kimura,&nbsp;Shinobu Sakai,&nbsp;Reiko Teshima,&nbsp;Kazunari Kondo","doi":"10.1002/cptx.48","DOIUrl":"10.1002/cptx.48","url":null,"abstract":"<p>A food allergy is a chronic inflammatory disease against dietary antigens with high prevalence in industrialized countries. Because there is currently no cure for food allergies, avoiding the allergen is crucial for the prevention of an allergic reaction. Therefore, a further understanding of the pathogenesis and risk factors that augment the sensitization to food allergens is required. We have previously developed a food allergy mouse model using transdermal sensitization, which influences the susceptibility to food allergies. In this model, mice sensitized with partially hydrolyzed wheat protein (HWP) successfully resembled the major features of HWP-sensitized and wheat allergy–induced patients. In this article, we describe transdermal sensitization of food allergens and induction of immediate-type food allergies in mice. The methodology detailed here was mainly adapted from an original work by Adachi and colleagues with some modifications to the dressing methods to reduce stress. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.48","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36339624","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: 3
An In Vitro Model of Hematotoxicity: Differentiation of Bone Marrow–Derived Stem/Progenitor Cells into Hematopoietic Lineages and Evaluation of Lineage-Specific Hematotoxicity 体外血液毒性模型:骨髓干细胞/祖细胞向造血谱系分化及谱系特异性血液毒性评价
Current protocols in toxicology Pub Date : 2018-04-30 DOI: 10.1002/cptx.45
Prathap Kumar Mahalingaiah, Tammy Palenski, Terry R. Van Vleet
{"title":"An In Vitro Model of Hematotoxicity: Differentiation of Bone Marrow–Derived Stem/Progenitor Cells into Hematopoietic Lineages and Evaluation of Lineage-Specific Hematotoxicity","authors":"Prathap Kumar Mahalingaiah,&nbsp;Tammy Palenski,&nbsp;Terry R. Van Vleet","doi":"10.1002/cptx.45","DOIUrl":"10.1002/cptx.45","url":null,"abstract":"<p>Hematotoxicity is a significant issue for drug safety and can result from direct cytotoxicity toward circulating mature blood cell types as well as targeting of immature blood-forming stem cells/progenitor cells in the bone marrow. In vitro models for understanding and investigating the hematotoxicity potential of new test items/drugs are critical in early preclinical drug development. The traditional method, colony forming unit (CFU) assay, is commonly used and has been validated as a method for hematotoxicity screening. The CFU assay has multiple limitations for its application in investigative work. In this paper, we describe a detailed protocol for a liquid-culture, microplate-based in vitro hematotoxicity assay to evaluate lineage-specific (myeloid, erythroid, and megakaryocytic) hematotoxicity at different stages of differentiation. This assay has multiple advantages over the traditional CFU assay, including being suitable for high-throughput screening and flexible enough to allow inclusion of additional endpoints for mechanistic studies. Therefore, it is an extremely useful tool for scientists in pharmaceutical discovery and development. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.45","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36339620","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: 7
Accidental and Programmed Cell Death in Investigative and Toxicologic Pathology 调查和毒理学病理学中的意外和程序性细胞死亡
Current protocols in toxicology Pub Date : 2018-04-30 DOI: 10.1002/cptx.51
Zaher A. Radi, Zachary S. Stewart, Shawn P. O'Neil
{"title":"Accidental and Programmed Cell Death in Investigative and Toxicologic Pathology","authors":"Zaher A. Radi,&nbsp;Zachary S. Stewart,&nbsp;Shawn P. O'Neil","doi":"10.1002/cptx.51","DOIUrl":"10.1002/cptx.51","url":null,"abstract":"<p>Cellular development and homeostasis are regulated via programmed cell death (PCD; apoptosis), which is a genetically regulated cellular process. Accidental cell death (ACD; necrosis) can be triggered by chemical, physical, or mechanical stress. Necrosis is the presence of dead tissues or cells in a living organism regardless of the initiating process and can be observed in infectious and non-infectious diseases and toxicities. This article describes tissue-based immunohistotechnical protocols used for assessing PCD and necrosis in formalin-fixed tissues obtained from preclinical species used in investigative and toxicologic pathology. Two commonly employed protocols for the identification of PCD and necrosis are described in this article: immunohistochemistry (IHC) for cleaved caspase 3, and terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL). TUNEL has been used to detect DNA fragmentation by labeling the terminal ends of nucleic acids in necrotic and apoptotic cells. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.51","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36338595","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: 10
Quantification of Serum Voriconazole, Isavuconazole, and Posaconazole by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) 液相色谱-串联质谱(LC-MS/MS)测定血清Voriconazole、Isavuconazole和Posaconazole
Current protocols in toxicology Pub Date : 2018-04-30 DOI: 10.1002/cptx.47
Andrew Smith, Justin Dowis, Deborah French
{"title":"Quantification of Serum Voriconazole, Isavuconazole, and Posaconazole by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS)","authors":"Andrew Smith,&nbsp;Justin Dowis,&nbsp;Deborah French","doi":"10.1002/cptx.47","DOIUrl":"10.1002/cptx.47","url":null,"abstract":"<p>Voriconazole, isavuconazole, and posaconazole are triazole anti-fungal drugs commonly used to treat invasive fungal infections. Therapeutic drug monitoring is commonly carried out when patients are prescribed these drugs to ensure that the serum concentrations are sufficiently high for efficacy, but do not reach toxic concentrations. Mass spectrometric (MS) assays have been successfully utilized to determine the serum concentrations of these drugs. This protocol describes a sample preparation procedure and a liquid chromatography-tandem mass spectrometry assay for quantifying serum voriconazole, isavuconazole, and posaconazole in a single method. © 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.47","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36336636","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: 10
Development of an In Vitro Method to Estimate the Sensitization Induction Level of Contact Allergens 一种评估接触过敏原致敏诱导水平的体外方法的建立
Current protocols in toxicology Pub Date : 2018-02-21 DOI: 10.1002/cptx.44
Valentina Galbiati, Sue Gibbs, Erwin Roggen, Emanuela Corsini
{"title":"Development of an In Vitro Method to Estimate the Sensitization Induction Level of Contact Allergens","authors":"Valentina Galbiati,&nbsp;Sue Gibbs,&nbsp;Erwin Roggen,&nbsp;Emanuela Corsini","doi":"10.1002/cptx.44","DOIUrl":"10.1002/cptx.44","url":null,"abstract":"<p>Recently, an in vitro procedure, which combines the epidermal equivalent potency assay with assessment of IL-18 to provide a single test for identification and classification of skin sensitizers, was developed and validated. This unit will describe a simple in vitro method for estimation of the expected sensitization induction level interpolating in vitro EC50 and IL-18 SI2 values to predict LLNA EC3 and/or human NOEL from standards curves generated using reference contact allergens, based on the use of Reconstituted human Epidermis (RhE).© 2018 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":72743,"journal":{"name":"Current protocols in toxicology","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cptx.44","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35891189","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: 16
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