Methods in molecular biology
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Immunohistochemistry is the identification of a cell protein by a specific antibody targeting that protein. It is the most common ancillary test to study the pathology of cancer. Immunohistochemical protein markers are used to differentiate poorly differentiated squamous cell carcinoma from poorly differentiated adenocarcinoma or neuroendocrine carcinomas. ⋯ Successful application of the immunochemistry depends on understanding the mechanisms and principles as well as the limitations of the procedure. Automation of the procedure by different models of automatic stainers is widely used in diagnostic laboratories. The use of autostainers streamlines the workflows and certainly reduces the labor, time, and cost of using immunohistochemistry in clinical and research settings.
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Methylation of cytosines in DNA is the most stable type of epigenetic modification that is established and maintained by different enzymes. In plants, DNA methylation is inherited from one generation to another leaving an epigenetic mark as a memory of previous state, which may include encounter with stress or pathogen. ⋯ Though the sequencing technologies have evolved drastically, analysis of WGBS data still remains challenging. Here, we provide a methodology for performing WGBS data analysis along with critical steps for identification of methylation marks in plant genomes including legumes.
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Cryptosporidium has historically been a difficult organism to work with, and molecular genomic data for this important pathogen have typically lagged behind other prominent protist pathogens. CryptoDB ( http://cryptodb.org/ ) was launched in 2004 following the appearance of draft genome sequences for both C. parvum and C. hominis. CryptoDB merged with the EuPathDB Bioinformatics Resource Center family of databases ( https://eupathdb.org ) and has been maintained and updated regularly since its establishment. ⋯ Recent years have seen several new genome sequences for both existing and new Cryptosporidium species as well as transcriptomics, proteomics, SNP, and isolate population surveys. This chapter introduces the extensive data mining and visualization capabilities of the EuPathDB software platform and introduces the data types and tools that are currently available for Cryptosporidium. Key features are demonstrated with Cryptosporidium-relevant examples and explanations.
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Esophageal squamous cell carcinoma (ESCC) is an aggressive disease. Many patients have locally advanced disease or already have distant metastasis at presentation. ⋯ Definitive radiotherapy (RT) with or without chemotherapy is used in patients who decline surgery or are medically inoperable. Palliative radiotherapy using external beam radiotherapy or intraluminal brachytherapy is effective for dysphagia and pain control.d.
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Early detection of cancer and the monitoring of cancer recurrence in treated patients are significant challenges in esophageal squamous cell carcinoma (ESCC). Liquid biopsy is the identification of tumor biomarkers from minimally invasive samples of biological fluids, including urine, blood, stool, saliva, or cerebrospinal fluid. ⋯ These sources of information have the potential to significantly improve the management of patients with ESCC. In this chapter, we detail a method for the isolation of cell-free DNA from blood plasma and DNA associated with exosomes in blood from patients with esophageal squamous cell carcinomas.