scholarly journals Comparison Between Currently Used Blood Samples And New Saliva Dna Collection Method For Quality Of Genomic Dna And Genotyping

2012 ◽  
Vol 18 (1) ◽  
pp. 19-23
Author(s):  
Loredana Mariana Aftenie ◽  
Irina Franciuc ◽  
Alina Martinescu ◽  
Adina Honcea
Keyword(s):  
Genomic Dna ◽  
Response Rate ◽  
Saliva Sample ◽  
Pcr Amplification ◽  
Good Alternative ◽  
Pcr Analysis ◽  
Blood Samples ◽  
Biospecimen Collection ◽  
Whole Saliva

AbstractObtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of two different methods for collecting samples: whole blood and whole saliva samples used further for DNA extraction and HLA genotyping in immunogenic disease on a group of patients registered at our Molecular Genetics Laboratory Faculty of Medicine “Ovidius” University Constanţa. Our data show that only 81% of the requested participants delivered a blood sample, whereas 19% delivered a saliva sample because they refuse the first sampling method. Analysis of purified genomic DNA by Nano Photometer and agarose gel electrophoresis revealed that blood and saliva samples resulted in DNA with the best quality. PCR analysis showed that DNA from 100% of the blood samples and 93% of the saliva samples could be subsequently amplified. Our study shows that the response rate of self-collection saliva samples had to be considering for the patients that have a low response rate of blood sampling. The quality of genomic DNA from saliva samples was comparable with blood samples as assessed by purity, concentration, yield and PCR amplification. We conclude that the use of saliva samples is a good alternative to blood samples to obtain genomic DNA of high quality and it will considerably increase the participant’s response rate for genetic studies.

DNA barcoding detects floral origin of Indian honey samples

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 341-348 ◽  
Author(s):  
Mohanasundaram Saravanan ◽  
Gunasekaran Mohanapriya ◽  
Ramachandra Laha ◽  
Ramalingam Sathishkumar
Keyword(s):  
Chemical Composition ◽  
Dna Barcoding ◽  
Plant Species ◽  
Genomic Dna ◽  
Pcr Amplification ◽  
Pollen Grains ◽  
The State ◽  
Nutritional Properties ◽  
Commercial Value

The unique medicinal and nutritional properties of honey are determined by its chemical composition. To evaluate the quality of honey, it is essential to study the surrounding vegetation where honeybees forage. In this study we used conventional melissopalynological and DNA barcoding techniques to determine the floral source of honey samples collected from different districts of the state of Mizoram, India. Pollen grains were isolated and genomic DNA was extracted from the honey samples. PCR amplification was carried out using universal barcode candidates ITS2 and rbcL to identify the plant species. Furthermore, TA cloning was carried out to screen the PCR amplicon libraries to identify the presence of multiple plant species. Results from both the melissopalynological and DNA barcoding analyses identified almost exactly the same 22 species, suggesting that both methods are suitable for analysis. However, DNA barcoding is easier and widely practiced. Hence, it can be concluded that DNA barcoding is a useful tool in determining the medicinal and commercial value of honey.

scholarly journals Genomic DNA PCR analysis to assess xenograft development in mouse mammary gland

BioTechniques ◽  
2020 ◽  
Vol 68 (4) ◽  
pp. 219-222
Author(s):  
Etienne Aujean ◽  
Johann Laubier ◽  
Nicolas Brun ◽  
Laurence Finot ◽  
Eric Chanat ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Pcr Amplification ◽  
Mouse Mammary Gland ◽  
Pcr Analysis ◽  
Mammary Fat Pad ◽  
Mammary Stem ◽  
Droplet Pcr ◽  
Functional Capacities ◽  
Dna Pcr ◽  
Transplantation Model

The mouse transplantation model remains the most relevant methodology to assess the functional capacities of mammary cells and is particularly appropriate for investigations regarding mammary stem cells, whatever the species studied. Following xenotransplantation in mice mammary fat pad, the development of the xenograft is commonly evaluated by immunohistology. Here, we present a simple and rapid method to control the species specificity of a xenograft based on genomic DNA PCR amplification. DNA is extracted from the fixed samples intended for histology, thus allowing the reuse of precious samples. Standard and digital droplet PCR (requiring low DNA quantities) methods have been used to make the present method suitable for the analysis of xenotransplanted samples.

scholarly journals Analisis Perbandingan Kualitas Produk Amplikon Gen PMSA2 Antara Spesimen Spot Darah Kering dan Vena

2020 ◽  
Vol 12 (1) ◽  
pp. 10-18
Author(s):  
Arsyam Mawardi ◽  
Hendra K. Maury ◽  
Yustinus Maladan
Keyword(s):  
Genomic Dna ◽  
Venous Blood ◽  
Dried Blood Spot ◽  
Laboratory Research ◽  
Blood Samples ◽  
Storage Method ◽  
Vacuum Tubes ◽  
Blood Specimens ◽  
Blood Spot

This study is aimed to analyze the comparative quality of PMSA2 gene amplicon product stability from two different specimen sources, spot specimens of dried blood and venous blood, as well as selecting the best storage method for specimens of blood samples. This research uses descriptive laboratory research methods. The research began with the process of sample preparation for dried blood spot and venous blood, each using Whatman 903 paper and vacuum tubes containing EDTA, isolating genomic DNA using KIT Zymo Research, amplification of PMSA-2 genes with PCR, detection of PCR products through electrophoresis, measurement of DNA concentration and absorbance, and data analysis. The results of this study are expected to be a source of information about the advantages of two specimen storage methods for clinical blood samples, as well as providing a clear description of the quality of each specimen storage method based on the quality of its amplicon products. The results showed that a total of ten medical samples of dried blood spot and ten venous blood were isolated from the genomic DNA of ten and nine, respectively. PMSA2 gene amplicons detected were seven in venous blood and six in dried blood spot. Venous blood specimens have sensitivity in detecting PMSA genes in samples with the highest value of 554 ng / μL and purity of 2,007 (WB7), and concentration of 550.2 and highest purity of 2,076 (WB10). Venous blood storage techniques using categorized vacuum tubes are effective in the detection of PMSA2 genes and have time efficiency in the process. From these results it was also concluded that the comparison analysis of amplicon products between venous blood specimens was better, more stable and efficient than dry blood spot specimens, thus recommending storage of venous blood specimens using vacuum tubes as the best storage method of blood sample specimens.

Detection of Clonal IGH Gene Rearrangements: Summary of Molecular Oncology Surveys of the College of American Pathologists

2007 ◽  
Vol 131 (2) ◽  
pp. 185-189
Author(s):  
Marina N. Nikiforova ◽  
Eric D. Hsi ◽  
Rita M. Braziel ◽  
Margaret L. Gulley ◽  
Debra G. B. Leonard ◽  
...  
Keyword(s):  
Southern Blot ◽  
Blot Analysis ◽  
Southern Blot Analysis ◽  
Response Rate ◽  
Pcr Amplification ◽  
Pcr Analysis ◽  
Gene Rearrangements ◽  
Laboratory Practice ◽  
Molecular Oncology ◽  
Fresh Frozen

Abstract Context.—The diagnosis of B-cell lymphoid malignancy can frequently be substantiated by detecting clonal immunoglobulin heavy chain (IGH) gene rearrangements, which is typically done by polymerase chain reaction (PCR) amplification and/or Southern blot analysis. Objective.—To characterize current laboratory practice for the assessment of IGH rearrangements and to identify opportunities for improvement. Design.—The data from the Molecular Oncology Proficiency Survey distributed to participating laboratories by the Molecular Pathology Committee of the College of American Pathologists from 1998 through 2003 were analyzed. Results.—Thirty-nine proficiency survey specimens (29 positive and 10 negative for clonal IGH rearrangements) were distributed. For Southern blot analysis, 944 results were reported, with a successful response rate of 95%. For PCR detection, 2349 results were reported, with a successful response rate of 72%. A higher rate of successful responses by PCR was achieved using framework 3 primers in combination with other frameworks (82%) compared with framework 3 primers only (76%) and when fresh/ frozen (72%) compared with paraffin-embedded (65%) tissues were analyzed. Conclusions.—The performance of the participating laboratories was very good, by both Southern blot and PCR analysis. As expected, Southern blot analysis consistently detects a higher proportion of IGH rearrangements than PCR analysis. Further improvement and standardization of the IGH PCR assay is important if it is to replace Southern blot analysis as the standard method. Participation in this survey is a valuable tool for assessing laboratory performance and it directs our attention to areas where we may improve laboratory practice.

scholarly journals Selection of the most suitable method for the extraction of DNA from foods and feeds for species identification

2010 ◽  
Vol 58 (2) ◽  
pp. 169-174
Author(s):  
Michaela Nesvadbová ◽  
Aleš Knoll ◽  
Anna Vašátková
Keyword(s):  
Species Identification ◽  
Genomic Dna ◽  
Pcr Amplification ◽  
Degraded Dna ◽  
Dna Purification ◽  
Pcr Analysis ◽  
Isolation System ◽  
Dna Yield ◽  
Pcr Products ◽  
Food And Feed

High quality and purity of DNA isolated from food and feed is essential for species identification and has unpredictable influences an effect of analysis. In this study, the efficiency of eight different methods for DNA isolation was investigated. For DNA extraction, the raw chicken meet, ham, sausages, tinned lunch meat, pate, tinned feeds for dogs, complete granulated feeds for dogs and chicken flour were used. Kits of several different producers, i.e.: NucleoSpin Food (Marchery-Nagel), Wizard Genomic DNA Purification Kit (Promega), Invisorb Spin Food Kit I (Invitek), Wizard SV Genomic DNA Purification System (Promega), JetQuick Tissue DNA Spin Kit (Genomed), RNA Blue (Top-Bio), JetQuick Blood & Cell Culture Kit (Genomed), QIAamp DNA Mini Kit and QIAamp DNA Blood Mini Kit (Qiagen) were employed in the study. Gel agarose electrophoresis for primary verification of DNA quality was performed. The isolates were subsequently assessed for quantity and quality using by spectrophotometer Nanodrop 2000 (Thermo Scientific). To verify of template usability and quality of isolated DNA, the polymerase chain reaction (PCR) was used.Differences between isolated DNA from tinned products and meat, ham, sausage, granulated dog feed and chicken flour were found. In tinned food and feed, the DNA was more degraded, DNA content and DNA purity was lower and also PCR amplification was the most difficult. Overall DNA yield and quality have important influence on PCR products amplification. The best results were obtained with NucleoSpin Food and JetQuick Tissue DNA Spin Kit. DNA extracted by these methods proved highest yields, purity and template quality in all foods and feeds and the results of PCR analysis are excellent reproducible. Analyses showed that results depended on different food or feed using and dif­fe­rent isolation system.The results of this work will be utilized to choose the suitable isolating kit for educational course, which is designed for students and also for following research and analyses.

Treatment of painful bone metastases in prostate and breast cancer patients with the therapeutic radiopharmaceutical rhenium-188-HEDP

2016 ◽  
Vol 55 (05) ◽  
pp. 188-195 ◽  
Author(s):  
Floor Overbeek ◽  
John de Klerk ◽  
Pieternel Pasker-de Jong ◽  
Alexandra van den Berk ◽  
Rob ter Heine ◽  
...  
Keyword(s):  
Bone Metastases ◽  
Clinical Benefit ◽  
Response Rate ◽  
Clinical Care ◽  
Pain Response ◽  
Pain Palliation ◽  
Breast Cancer Patients ◽  
Routine Clinical Care ◽  
Painful Bone Metastases

Summary Aim: Rhenium-188-HEDP (188Re-HEDP) is an effective radiopharmaceutical for the palliative treatment of osteoblastic bone metastases. However, only limited data on its routine use are available and its effect on quality of life (QoL) has not been studied. Therefore, we evaluated the clinical benefit of 188Re-HEDP in routine clinical care. Patients and methods: Prostate or breast cancer patients with painful bone metastases receiving 188Re-HEDP as a routine clinical procedure were eligible for evaluation. Clinical benefit was assessed in terms of efficacy and toxicity. Pain palliation and QoL were monitored using the visual analogue scale (VAS), corrected for opioid intake, and the EORTC QLQ-C30 Global health status/QoL-scale. Thrombocyte and leukocyte nadirs were used to assess haematological toxicity. Results: 45 and 47 patients were evaluable for pain palliation and QoL, respectively. After a single injection of 188Re-HEDP, the overall pain response rate was 69% and mean VAS-scores decreased relevantly and significantly (p < 0.05). Repeated treatment resulted in similar pain response. The overall QoL response rate was 68% and mean Global health status/QoL-scores increased relevantly and significantly. Haematological side effects were mild and transient. Conclusion: The clinically relevant response on pain and quality of life and the limited adverse events prove clinical benefit of treatment with 188Re-HEDP and support its use in routine clinical care. Its effectiveness appears comparable to that of external beam radiotherapy.

scholarly journals DMSO Improves the Ski-Slope Effect in Direct PCR

2021 ◽  
Vol 11 (4) ◽  
pp. 1943
Author(s):  
Joo-Young Kim ◽  
Ju Yeon Jung ◽  
Da-Hye Kim ◽  
Seohyun Moon ◽  
Won-Hae Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Pcr Amplification ◽  
Analytical Techniques ◽  
Direct Pcr ◽  
Dna Profile ◽  
Novel Technologies ◽  
Specific Amplification ◽  
Polymerase Chain ◽  
Dna Profiles

Analytical techniques such as DNA profiling are widely used in various fields, including forensic science, and novel technologies such as direct polymerase chain reaction (PCR) amplification are continuously being developed in order to acquire DNA profiles efficiently. However, non-specific amplification may occur depending on the quality of the crime scene evidence and amplification methods employed. In particular, the ski-slope effect observed in direct PCR amplification has led to inaccurate interpretations of the DNA profile results. In this study, we aimed to reduce the ski-slope effect by using dimethyl sulfoxide (DMSO) in direct PCR. We confirmed that DMSO (3.75%, v/v) increased the amplification yield of large-sized DNA sequences more than that of small-sized ones. Using 50 Korean buccal samples, we further demonstrated that DMSO reduced the ski-slope effect in direct PCR. These results suggest that the experimental method developed in this study is suitable for direct PCR and may help to successfully obtain DNA profiles from various types of evidence at crime scenes.

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