scholarly journals Gleaning a Human DNA Profile from Trace Swabs Collected from Animal Hairs

2016 ◽  
Vol 66 (2) ◽  
pp. 187-202 ◽  
Author(s):  
Branimira Špoljarić ◽  
Maja Popović ◽  
Josip Crnjac ◽  
Zrinka Žderić Savatović ◽  
Martina Ratko ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Sample Collection ◽  
Dna Profile ◽  
Human Dna ◽  
Intraspecific Variations ◽  
Morphological Differences ◽  
Dna Profiles ◽  
Collection Methods

Abstract Animal hairs are an apt surface for retention of forensic trace epithelial samples. The aim of this study was threefold: to evaluate different methods of sample collection (moistened and dry swabs) and DNA extraction (Chelex® 100 method, Qiagen EZ1® DNA Investigator Kit), as well as to examine the morphological differences of hair fibres between two species (dog, sheep) and their ultimate impact on sample collection and processing. Our preliminary findings suggest that the use of EZ1® DNA Investigator Kit yields donor DNA profiles of higher quality. The results of different sample collection methods have shown intraspecific variations that require further investigation. The ability of retention and subsequent extraction of trace DNA appears to be similar between the two species, despite significant morphological differences between their coat hairs.

scholarly journals ‘Swabs’ then and now: cotton to flocked nylon

2010 ◽  
Vol 31 (3) ◽  
pp. 133 ◽  
Author(s):  
Joan Faoagali
Keyword(s):  
Molecular Detection ◽  
Detection Methods ◽  
Sample Collection ◽  
Forensic Dna ◽  
Microbial Detection ◽  
Human Dna ◽  
Pcr Inhibitor ◽  
Microbiological Sample ◽  
Polymerase Chain ◽  
Collection Methods

Microbiological sample collections using cotton-tipped swabs (with or without serum), Dacron?, rayon and calcium alginate, with shafts of wood, plastic and various thicknesses and types of metal have all been used over the years. The swabs have been contained in glass or plastic tubes with and without various types of transport media. Swabs are an easy and popular method of sample collection, although microbiology laboratories traditionally prefer tissue, body fluids or aspirates ahead of swabs. As microbiology laboratories increasingly adopt near patient testing and molecular detection methods to reduce test turnaround times, new sample collection methods are required to maximise the sensitivity of these expensive tests and reduce the possibility of failed tests due to sample inhibitors or poor collection techniques. Flocked nylon swabs have been developed by Copan in the last decade and are produced using a technique of spraying nylon fibres onto a rigid core. This has the effect of increasing the surface area for sample collection and also provides easy elution of the collected material. These swabs are polymerase chain reaction (PCR) inhibitor-free, RNase-negative and DNase-free and there is in addition a range of flocked swabs, specifically intended for forensic DNA investigations that are certified human DNA-free. The advantages, disadvantages and appropriate use of swab collections for microbial detection in the 21st century will be presented.

scholarly journals Comparing two automated methods of DNA extraction from degraded skeletal remains

2020 ◽  
Author(s):  
Linda Rubinstein
Keyword(s):  
Dna Extraction ◽  
Extraction Methods ◽  
Positive Control ◽  
Skeletal Remains ◽  
Variable Environment ◽  
Dna Profile ◽  
Preparation Step ◽  
Dna Profiles ◽  
Skeletal Samples ◽  
Automated Methods

AbstractDNA extraction from degraded skeletal samples is often particularly challenging. The difficulty derives from the fact that variable environment has significant effect on DNA preservation. During the years 2002-2015 unidentified degraded skeletal remains were accumulated at our institute, National Institute of Forensic Medicine (NIFM), most of them with none or partial DNA profile.As new methods rapidly emerge, we revisited the samples with partial DNA profiles. We have chosen to use these samples to compare two automated methods: Prepfiler Express BTA (Applied Biosystems) and QIAcube (Quiagen), in hope of acquiring a more complete DNA profile and eventually even make new identifications. In both methods a preparation step is required, after which the samples undergo automatic DNA extraction.The two protocols are based on different extraction methods. Fresh or non-problematic bone samples as the positive control gave the same results in both methods. In the degraded skeletal samples, the results were significantly better using the QIAcube method.

PREDIKSI PERINGKAT OBLIGASI SYARIAH DI INDONESIA

2014 ◽  
Vol 11 (3) ◽  
pp. 1-15
Author(s):  
Ike Arisanti ◽  
Isti Fadah ◽  
Novi Puspitasari
Keyword(s):  
Profit Sharing ◽  
Sample Collection ◽  
Purposive Sampling ◽  
Financial Factors ◽  
Financial Factor ◽  
Independent Variable ◽  
Rating Prediction ◽  
Collection Methods

This study purposes to analyze the influence of financial and non financial factors to prediction of the rating islamic bond in indonesia. The study used independent variable,that is financial factor (growth, size, profit sharing/fee, liquidity) and non financial factor ( secure and maturity) and dependent variable that is the rating of islamic bond. This study applied logistic regresion analysis with sample collection methods using purposive sampling. After selecting fixed criterias, there were 25 islamic bonds chosen with the numbers of 75 investigation from periods of 2010-2012. The result of this study showed that significantly effect the variable growth (X1) , size(X2), profit sharing/ fee (X3), liquidity (X4), secure (X5), maturity (X6) simultaneously to the rating prediction of islamic bond in indonesia. Partially, variable variables of growth (X1) , size (X2), profit sharing/ fee (X3) which referred not significant affecting to the rating prediction of islamic bond in indonesia. Meanwhile, variables of liquidity (X4), secure (X5), maturity ( X6) referred significant affecting to the rating prediction of islamic bond in indonesia.

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.

scholarly journals Autotetraploid Emergence via Somatic Embryogenesis in Vitis vinifera Induces Marked Morphological Changes in Shoots, Mature Leaves, and Stomata

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1336
Author(s):  
Caterina Catalano ◽  
Loredana Abbate ◽  
Antonio Motisi ◽  
Dalila Crucitti ◽  
Vincenzo Cangelosi ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Morphological Changes ◽  
Ploidy Levels ◽  
Dna Profile ◽  
Morphological Alterations ◽  
Cell Pair ◽  
Mature Leaves ◽  
Induction Process ◽  
Ploidy Changes ◽  
Dna Profiles

Polyploidy plays an important role in plant adaptation to biotic and abiotic stresses. Alterations of the ploidy in grapevine plants regenerated via somatic embryogenesis (SE) may provide a source of genetic variability useful for the improvement of agronomic characteristics of crops. In the grapevine, the SE induction process may cause ploidy changes without alterations in DNA profile. In the present research, tetraploid plants were observed for 9.3% of ‘Frappato’ grapevine somatic embryos regenerated in medium supplemented with the growth regulators β-naphthoxyacetic acid (10 µM) and N6-benzylaminopurine (4.4 µM). Autotetraploid plants regenerated via SE without detectable changes in the DNA profiles were transferred in field conditions to analyze the effect of polyploidization. Different ploidy levels induced several anatomical and morphological changes of the shoots and mature leaves. Alterations have been also observed in stomata. The length and width of stomata of tetraploid leaves were 39.9 and 18.6% higher than diploids, respectively. The chloroplast number per guard cell pair was higher (5.2%) in tetraploid leaves. On the contrary, the stomatal index was markedly decreased (12%) in tetraploid leaves. The observed morphological alterations might be useful traits for breeding of grapevine varieties in a changing environment.

scholarly journals Thyroglobulin measurement on fine-needle washout fluids: Influence of sample collection methods

2009 ◽  
Vol 37 (1) ◽  
pp. 42-44 ◽  
Author(s):  
Luca Giovanella ◽  
Luca Ceriani ◽  
Sergio Suriano ◽  
Stefano Crippa
Keyword(s):  
Sample Collection ◽  
Fine Needle ◽  
Collection Methods

Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies

2015 ◽  
Vol 10 (9) ◽  
pp. 1485-1504 ◽  
Author(s):  
Vincent Thomas ◽  
James Clark ◽  
Joël Doré
Keyword(s):  
Fecal Microbiota ◽  
Sample Collection ◽  
Microbiota Analysis ◽  
Collection Methods

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.

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