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Related Concept Videos

Sampling Methods: Sample Types01:18

Sampling Methods: Sample Types

274
Sampling materials are classified into three main types: solid, liquid, and gas.
Solid samples include a variety of substances, such as sediments from water bodies, soil, metals, and biological tissues. Two standard methods for extracting sediments from water bodies are grab sampling and piston coring. Grab sampling involves using a device to collect a discrete sediment sample from the bottom of a water body with minimal disturbance. Grab samples do not always represent the entire area due to...
274
Upper GI Series: Barium Swallow01:24

Upper GI Series: Barium Swallow

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The Barium Swallow Study, or a Barium Esophagogram, is a diagnostic imaging method used to visualize the upper gastrointestinal (GI) tract, including the esophagus, stomach, and small intestine. It employs barium sulfate, a radiopaque contrast material, to provide clear images of the upper digestive system, helping to identify abnormalities, diseases, or structural issues.
Purpose and Procedure
Patients undergoing this procedure ingest a liquid containing barium sulfate with a chalky...
484
Assessment of the Gastrointestinal System I: Subjective Data01:17

Assessment of the Gastrointestinal System I: Subjective Data

225
Assessing the gastrointestinal (GI) system is a complex process that begins with collecting subjective data. This data, collected through patient interviews, provides crucial insights into the patient's health history, perception patterns, and lifestyle habits, all contributing significantly to GI health.
Health History
The initial step in assessing the GI system is obtaining a comprehensive health history. This includes inquiring about the patient's history or presence of problems...
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Peptic Ulcer Disease III: Clinical Manifestations and Diagnostic Studies01:28

Peptic Ulcer Disease III: Clinical Manifestations and Diagnostic Studies

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Peptic ulcer disease (PUD) presents with diverse symptoms depending on the location and severity of the ulcer. Clinical manifestations of peptic ulcer include dull pain and a burning sensation in the mid-epigastric region.
Few clinical manifestations differentiate gastric ulcers from duodenal ulcers. Distinctions in the location, timing, and pain relief are crucial for healthcare providers in differentiating between gastric and duodenal ulcers during clinical assessments.
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Methods for Studying Drug Absorption: In situ01:09

Methods for Studying Drug Absorption: In situ

266
In situ experiments, such as the Doluisio method and Single-Pass Perfusion technique, provide critical insights into drug uptake by simulating in vivo conditions for drug absorption.
The Doluisio method involves perfusing a prepared segment of a rat's small intestine with a solution of radiolabeled drug and a non-absorbable marker. This helps to differentiate between absorbed and non-absorbed drug concentrations. The intestinal segment is connected at both ends using tubing and syringes,...
266
Endoscopic Procedures I: Esophagogastroduodenoscopy01:29

Endoscopic Procedures I: Esophagogastroduodenoscopy

176
An Esophagogastroduodenoscopy (EGD) is a diagnostic procedure in which an endoscopist uses a flexible, lighted endoscope to visualize the upper gastrointestinal (GI) tract. The procedure includes visualizing the oropharynx, esophagus, stomach, and the first part of the small intestine, the duodenum.
During an EGD, the endoscope can be used to:
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Related Experiment Video

Updated: Jul 19, 2025

Gastric Mucosa Quantitative Polymerase Chain Reaction Analysis for Detecting Helicobacter pylori and Antibiotic Resistance
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Sample Collection Methods in Upper Gastrointestinal Research.

Hyo-Joon Yang1, Seung In Seo2, Jin Lee3

  • 1Division of Gastroenterology, Department of Internal Medicine and Gastrointestinal Cancer Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea.

Journal of Korean Medical Science
|August 15, 2023
PubMed
Summary
This summary is machine-generated.

This review proposes an endoscopic biopsy protocol for upper gastrointestinal research. It details optimal sample collection for microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid cultures.

Keywords:
BiopsyEndoscopySampleTranslational Research

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Area of Science:

  • Gastroenterology
  • Translational Research
  • Biopsy Techniques

Background:

  • Translational research in upper gastrointestinal (GI) studies has advanced significantly.
  • Endoscopic biopsy is a low-risk method for obtaining upper GI tissue, applicable even in unresectable gastric cancer.
  • Standardized protocols for endoscopic biopsy sample acquisition and storage are lacking but crucial for research integrity.

Purpose of the Study:

  • To propose a comprehensive protocol for collecting upper GI tissue samples from endoscopic biopsies.
  • To guide researchers on optimal sample collection for various analyses, including microbiome, molecular, and organoid studies.
  • To address the need for standardized methods in upper GI endoscopic biopsy research.

Main Methods:

  • A comprehensive literature review was conducted to identify existing methods and best practices for endoscopic biopsy sample collection.
  • The review synthesized information on sample requirements for diverse research applications.
  • A protocol was developed based on the literature review findings.

Main Results:

  • For microbiome analysis, 1-2 biopsy tissues, 5 mL gastric fluid, and 3-4 mL saliva are recommended.
  • DNA/RNA analyses require at least one biopsy tissue; proteomics requires 2-3 tissues.
  • Single-cell RNA sequencing needs 3-5 tissues, with additional samples preferred; organoid culture necessitates multiple samples for quality.

Conclusions:

  • A standardized protocol for endoscopic biopsy sample collection is essential for reliable upper GI research.
  • Specific sample quantities are recommended for microbiome, molecular analyses, and organoid culture.
  • This protocol aims to enhance the quality and reproducibility of translational research in the upper GI field.