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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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.
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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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Biobanking is important and fundamental for research and personalized medicine in patients with esophageal squamous cell carcinoma. The process often involves prospective collection of surgically obtained tissues (tissue banking) as well as serial blood samples (liquid biopsies) from the patients with esophageal squamous cell carcinoma. Apart from frozen tissues, formalin-fixed paraffin-embedded tissues are important sources of translational research. ⋯ The success and sustainability of the process needs proper infrastructure, advanced planning, funding, and multidisciplinary collaborations. The understanding of the principles and issues are detrimental for the success of biobanking. The technical procedures involved are standardized, complex, and time-consuming and needs coordinated taskforce.
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Endoscopic resection is commonly used for superficial squamous cell carcinoma or high-grade dysplasia of esophageal squamous cell carcinoma. The depth of invasion, clearance from resection margins, and other pathological parameters are important parameters to be examined. The depth of invasion by carcinoma is associated with the risk of lymph node metastases. In endoscopic resection of superficial squamous malignancies of the esophagus, proper pathological examination of the resected specimen could guide the management of the patients in terms of the need for additional treatment, including lymph node dissection, chemotherapy, and radiation therapies.