AI Article Synopsis
- Extracting DNA from formalin-fixed paraffin-embedded (FFPE) samples is challenging, with low success rates in PCR processes.
- A new simple protocol using molecular biology-grade mineral oil for deparaffinization and Qiagen FFPE kit for extraction was tested on 12 bone marrow biopsy samples, showing better results than traditional methods like xylene or Hemo-D.
- The mineral oil method not only provided higher quality DNA but also saved time and reduced manual labor compared to conventional extraction techniques.
Article Abstract
Extracting DNA from formalin-fixed paraffin-embedded (FFPE) archival samples remains difficult. Successful polymerase chain reactions (PCR) with DNA extracted from FFPE samples is still very low. We extracted DNA from 12 recent and old archival FFPE bone marrow trephine biopsies by use of a simple protocol on the basis of deparaffinization with molecular biology-grade mineral oil followed by DNA extraction with the Qiagen FFPE kit. Comparison of this deparaffinization method with standard protocols, for example, xylene or Hemo-D with subsequent rehydration using graded ethanols, was investigated. The quality and quantity of extracted DNA were tested by a combination of ultraviolet spectroscopy, analysis on a Caliper LabChip GX, and real-time PCR combined with high-resolution melt analysis. Highest quality PCR-amplifiable DNA was obtained by deparaffinization with mineral oil, whereas more variable results were obtained for the other 2 deparaffinization procedures. This result was confirmed by real-time PCR and high-resolution melt analysis. Besides improvements in the quality of extracted DNA, use of mineral oil for deparaffinization has the added benefit of decreased time (20 vs. 75 min) and a significant reduction of hands-on labor (1 step vs. multiple hands-on centrifugation and decanting steps).
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1097/PAI.0b013e3182a77bfe | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Illite Dissolution under Sodium Hydroxide Solution: Insights from Reactive Molecular Dynamics.
ACS Omega
December 2024
Key Laboratory for Enhanced Oil & Gas Recovery of the Ministry of Education, Northeast Petroleum University, Daqing 163318, Heilongjiang, China.
In alkali/surfactant/polymer (ASP) flooding systems, alkalis react with clay minerals such as Illite, montmorillonite, and kaolinite, leading to reservoir damage and impacting oil recovery rates. Therefore, studying the dissolution effects of strong alkalis on clay minerals is crucial for improving oil recovery. This study uses Illite as a representative clay mineral and employs the ReaxFF reactive force field and molecular dynamics simulations to model its dissolution in NaOH solution.
View Article and Find Full Text PDFCold-active lipase from Psychrobacter alimentarius ILMKVIT and its application in selective enrichment of ω-3 polyunsaturated fatty acids in flax seed oil.
Bioprocess Biosyst Eng
December 2024
School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
Lipases are one of the ubiquitous enzymes that belong to the hydrolases family and have a wide variety of applications. Cold-active lipases are of major attraction as they can act in lower temperatures and low water conditions because of their inherent greater flexibility. One of the novel applications of lipase is the enrichment of ω-3 polyunsaturated fatty acids (PUFA) in plant and fish oils.
View Article and Find Full Text PDFFish Oil Consumption: Its Effects on Bone and Blood Parameters of the Ovariectomized Rat Model of Osteopenia.
Nutrients
November 2024
Laboratory for Research of the Musculoskeletal System "Th. Garofalides", School of Medicine, National & Kapodistrian University of Athens, KAT Hospital, 14561 Athens, Greece.
: The beneficial effects of ω-3 fatty acids on the cardiovascular system have been observed in many epidemiological studies; however, their effects on the skeleton and in particular on postmenopausal bone loss appear to vary. The present study's purpose was to investigate the effects of oral fish oil (rich in ω-3 fatty acids) consumption on bone, plasma, and inflammation parameters in the ovariectomized (Ovx) rat model of osteopenia. : Four Groups of ten rats each were separated into Non-Ovx receiving fish oil (2.
View Article and Find Full Text PDFObjectives: The aim of the study was to investigate the caries-preventive effect of fluoride-free toothpastes, containing either herbal agents or (nano-)hydroxyapatite.
Methods: Bovine dentin specimens each having a sound [ST], and a demineralized area [DT]) were prepared and randomly allocated to eleven groups (n=187). Treatments during pH-cycling (28 days;6x120min demineralization/day) were brushing 2x/day with: 0ppm F- [NaF0], 500ppm F- [NaF500], 1,100ppm F- [NaF1100], grape seed extract [GSE], (nano-)hydroxyapatite [nHA, HA], melaleuca oil [MO1, MO2, MO-CU] and propolis + myrrh [PM1, PM2] containing dentifrices.
Ensuring the sustainability of energy is pivotal for achieving a harmonious balance between environmental conservation and economic growth. The mechanical behavior of deep shale reservoir rocks is intricate, presenting challenges in ascertaining their brittleness characteristics. To address this, the study employed a suite of evaluation techniques, encompassing analyses of stress-strain curve attributes, energy dissipation patterns, and mineral composition profiles.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!