A Simple Method of DNA Extraction and STR Typing from Urine Samples Using a Commercially Available DNA/RNA Extraction Kit

2003 ◽  
Vol 48 (1) ◽  
pp. 2002184 ◽  
Author(s):  
Toshihiro Yasuda ◽  
Reiko Iida ◽  
Haruo Takeshita ◽  
Misuzu Ueki ◽  
Tamiko Nakajima ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Rna Extraction ◽  
Urine Samples ◽  
Str Typing ◽  
Simple Method

Hollow fiber supported liquid-phase microextraction combined with maltodextrin-modified capillary electrophoresis for the determination of citalopram enantiomers in urine samples

2015 ◽  
Vol 7 (5) ◽  
pp. 2012-2019 ◽  
Author(s):  
Jafar Abolhasani ◽  
Hamid Reza Jafariyan ◽  
Mohammad Mahdi khataei ◽  
Rahim Hosseinzadeh-khanmiri ◽  
Ebrahim Ghorbani-kalhor ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Liquid Phase ◽  
Hollow Fiber ◽  
Urine Samples ◽  
Simple Method ◽  
Liquid Phase Microextraction ◽  
Supported Liquid Phase

A simple method was developed for the separation and determination of citalopram enantiomers in urine samples.

scholarly journals A Rapid Bacteriophage DNA Extraction Method

2018 ◽  
Vol 1 (3) ◽  
pp. 27 ◽  
Author(s):  
Džiuginta Jakočiūnė ◽  
Arshnee Moodley
Keyword(s):  
Dna Extraction ◽  
Illumina Miseq ◽  
Extraction Methods ◽  
Resistant Bacteria ◽  
Simple Method ◽  
Antibiotic Resistant ◽  
Phage Dna ◽  
Specialized Equipment ◽  
Miseq Platform ◽  
Dna Extraction Methods

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understanding of phages and to determine if phages harbor putative virulence factors, whole genome sequencing is used, for which good quality phage DNA is needed. Traditional phage DNA extraction methods are tedious and time consuming, requiring specialized equipment e.g., an ultra-centrifuge. Here, we describe a quick and simple method (under four hours) to extract DNA from double stranded DNA (dsDNA) phages at titers above 1.0 × 1010 plaque-forming units (PFU)/mL. This DNA was suitable for library preparation using the Nextera XT kit and sequencing on the Illumina MiSeq platform.

scholarly journals Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

2019 ◽  
Author(s):  
Teresa L. Street ◽  
Leanne Barker ◽  
Nicholas D. Sanderson ◽  
James Kavanagh ◽  
Sarah Hoosdally ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Reference Genome ◽  
Extraction Methods ◽  
Urine Samples ◽  
Clinical Samples ◽  
Nanopore Sequencing ◽  
Human Dna ◽  
Whole Genomes ◽  
Dna Extraction Methods ◽  
Multiple Antibiotics

AbstractBackgroundEmpirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance.MethodsWe investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N. gonorrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA.ResultsIn simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections, but decreased yields in clinical samples. In ten urine samples from men with symptomatic urethral gonorrhoea, ≥87% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥92% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated Chlamydia co-infection.ConclusionUsing Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.

scholarly journals Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0240769
Author(s):  
Prasanna Channathodiyil ◽  
Jonathan Houseley
Keyword(s):  
Flow Cytometry ◽  
Transcriptome Analysis ◽  
Mammalian Cells ◽  
Single Cells ◽  
Rna Extraction ◽  
Cyclin B1 ◽  
Immunofluorescent Staining ◽  
Rna Seq ◽  
Simple Method ◽  
Staining Methods

A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal—a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.

A novel, 4-h DNA extraction method for STR typing of casework bone samples

2020 ◽  
Vol 134 (2) ◽  
pp. 461-471 ◽  
Author(s):  
Laila Hasap ◽  
Wilaiwan Chotigeat ◽  
Jintana Pradutkanchana ◽  
Uraporn Vongvatcharanon ◽  
Thitika Kitpipit ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Str Typing ◽  
Dna Extraction Method

Evaluation of three DNA extraction protocols for forensic STR typing after laser capture microdissection

2012 ◽  
Vol 6 (2) ◽  
pp. 258-262 ◽  
Author(s):  
Mado Vandewoestyne ◽  
Filip Van Nieuwerburgh ◽  
David Van Hoofstat ◽  
Dieter Deforce
Keyword(s):  
Dna Extraction ◽  
Laser Capture Microdissection ◽  
Str Typing ◽  
Laser Capture

STR typing from human faeces: a modified DNA extraction method

2003 ◽  
Vol 1239 ◽  
pp. 917-920 ◽  
Author(s):  
G. Iacovacci ◽  
M. Serafini ◽  
A. Berti ◽  
G. Lago
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Str Typing ◽  
Human Faeces ◽  
Dna Extraction Method ◽  
Modified Dna

scholarly journals Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR

2006 ◽  
Vol 55 (9) ◽  
pp. 1187-1191 ◽  
Author(s):  
Lisa J. Griffiths ◽  
Martin Anyim ◽  
Sarah R. Doffman ◽  
Mark Wilks ◽  
Michael R. Millar ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Extraction ◽  
Real Time Pcr ◽  
Diagnostic Technique ◽  
Extraction Methods ◽  
Simple Method ◽  
Bead Beating ◽  
Fungal Dna ◽  
Dna Extraction Methods ◽  
High Level

Newer methods such as PCR are being investigated in order to improve the diagnosis of invasive aspergillosis. One of the major obstacles to using PCR to diagnose aspergillosis is a reliable, simple method for extraction of the fungal DNA. The presence of a complex, sturdy cell wall that is resistant to lysis impairs extraction of the DNA by conventional methods employed for bacteria. Numerous fungal DNA extraction protocols have been described in the literature. However, these methods are time-consuming, require a high level of skill and may not be suitable for use as a routine diagnostic technique. Here, a number of extraction methods were compared: a freeze–thaw method, a freeze–boil method, enzyme extraction and a bead-beating method using Mini-BeadBeater-8. The quality and quantity of the DNA extracted was compared using real-time PCR. It was found that the use of a bead-beating method followed by extraction with AL buffer (Qiagen) was the most successful extraction technique, giving the greatest yield of DNA, and was also the least time-consuming method assessed.

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