A Simple Method for Storing Mosquito Bloodmeals for Human DNA Profiling

Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.

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Quantifiler Human DNA Quantification Kit (Applied Biosystems) as a screening kit for DNA profiling

Forensic Science International Genetics Supplement Series ◽

10.1016/j.fsigss.2009.08.040 ◽

2009 ◽

Vol 2 (1) ◽

pp. 106-107 ◽

Cited By ~ 5

Author(s):

A. Kremser ◽

B. Bayer ◽

S. Jung ◽

K. Anslinger

Keyword(s):

Dna Quantification ◽

Dna Profiling ◽

Human Dna

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Proposed Legislative: Human DNA Profiling Bill: Indian Scenario

Medico-Legal Update ◽

10.5958/0974-1283.2017.00045.7 ◽

2017 ◽

Vol 17 (1) ◽

pp. 209

Author(s):

Singh Sukhdeep ◽

B L Chaudhary ◽

Arvind Kumar ◽

G K Sharma

Keyword(s):

Dna Profiling ◽

Human Dna ◽

Indian Scenario

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Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

10.1101/2020.03.05.974907 ◽

2020 ◽

Author(s):

Tatiana R. Feuerborn ◽

Elle Palkopoulou ◽

Tom van der Valk ◽

Johanna von Seth ◽

Arielle R. Munters ◽

...

Keyword(s):

High Throughput ◽

Ancient Dna ◽

High Throughput Sequencing ◽

Cost Effective ◽

Simple Method ◽

Laboratory Methods ◽

Field Collection ◽

Human Dna ◽

Human Contamination ◽

Reference Genomes

AbstractBackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

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Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

BMC Genomics ◽

10.1186/s12864-020-07229-y ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Tatiana R. Feuerborn ◽

Eleftheria Palkopoulou ◽

Tom van der Valk ◽

Johanna von Seth ◽

Arielle R. Munters ◽

...

Keyword(s):

High Throughput ◽

Ancient Dna ◽

High Throughput Sequencing ◽

Cost Effective ◽

Simple Method ◽

Laboratory Methods ◽

Field Collection ◽

Human Dna ◽

Human Contamination ◽

Reference Genomes

Abstract Background After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Results Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. Conclusions We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

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Profil DNA Forensik pada Barang Bukti Dua Kasus Pembunuhan di Indonesia

Jurnal Sumberdaya Hayati ◽

10.29244/jsdh.4.2.48-56 ◽

2020 ◽

Vol 4 (2) ◽

pp. 48-56

Author(s):

PUJI RIANTI ◽

ELISA CRISTIN ◽

PUTUT TJAHJO WIDODO

Keyword(s):

Crime Scene ◽

Applied Science ◽

Dna Profiling ◽

International Standards ◽

Buccal Swab ◽

Blood Stains ◽

Str Markers ◽

Human Dna ◽

Dna Profiles ◽

National Police

DNA technology for profiling purposes has been used in many basic and applied science. One of the emerged applied science in genetics is it’s uses in solving crime cases. Homicide became one of highest crime cases in Indonesia. Solving its cases through DNA profiling technology using items of evidence as tool is needed. Here, we report the profiling of human DNA from several items of evidence available in the crime scene and the suspect. We used items of evidence from study cases no. 18098 and 18101, based on the legal permission of Indonesia’s National Police. We used 21 international standards of human STR markers, one sex-determining marker, one Y STR marker, and one independent Y marker to developed human alleles from tissue and blood stains left and/or shred on the victims, soap bottles, knifes, victim’s clothes and ropes as well as the buccal swab of the crime suspect. Our alleles identification matched between the victim and the crime suspect in both cases with the accuracy of DNA profiles compatibility at 99.99%. Detection of DNA profiling is depending on the evidence and time of storage which are influence by environment that can lead to the process of decayed and/or contaminated.

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A simple way for producing holographic filters suitable for image improvement

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100108271 ◽

1978 ◽

Vol 36 (1) ◽

pp. 226-227

Author(s):

K.-H. Herrmann ◽

E. Reuber ◽

P. Schiske

Keyword(s):

Transfer Functions ◽

Diffraction Order ◽

Lateral Position ◽

Simple Method ◽

Spatial Frequencies ◽

Resolution Electron ◽

Wiener Filters ◽

Image Improvement ◽

Optical Reconstruction ◽

Set Up

Aposteriori deblurring of high resolution electron micrographs of weak phase objects can be performed by holographic filters [1,2] which are arranged in the Fourier domain of a light-optical reconstruction set-up. According to the diffraction efficiency and the lateral position of the grating structure, the filters permit adjustment of the amplitudes and phases of the spatial frequencies in the image which is obtained in the first diffraction order.In the case of bright field imaging with axial illumination, the Contrast Transfer Functions (CTF) are oscillating, but real. For different imageforming conditions and several signal-to-noise ratios an extensive set of Wiener-filters should be available. A simple method of producing such filters by only photographic and mechanical means will be described here.A transparent master grating with 6.25 lines/mm and 160 mm diameter was produced by a high precision computer plotter. It is photographed through a rotating mask, plotted by a standard plotter.

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Rotary Beveling for In Situ Thin-Section Microscopy of Cell Cultures

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100099192 ◽

1981 ◽

Vol 39 ◽

pp. 550-551

Author(s):

Dean A. Handley ◽

Jack T. Alexander ◽

Shu Chien

Keyword(s):

Cell Growth ◽

Cell Cultures ◽

Molecular Interactions ◽

Convenient Method ◽

Petri Dish ◽

Simple Method ◽

Thin Section Microscopy ◽

Thin Sectioning ◽

Organic Fluids

In situ preparation of cell cultures for ultrastructural investigations is a convenient method by which fixation, dehydration and embedment are carried out in the culture petri dish. The in situ method offers the advantage of preserving the native orientation of cell-cell interactions, junctional regions and overlapping configurations. In order to section after embedment, the petri dish is usually separated from the polymerized resin by either differential cryo-contraction or solvation in organic fluids. The remaining resin block must be re-embedded before sectioning. Although removal of the petri dish may not disrupt the native cellular geometry, it does sacrifice what is now recognized as an important characteristic of cell growth: cell-substratum molecular interactions. To preserve the topographic cell-substratum relationship, we developed a simple method of tapered rotary beveling to reduce the petri dish thickness to a dimension suitable for direct thin sectioning.

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