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The Plant Journal : For Cell and... Mar 2012One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring...
One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity--and therefore adaptation--relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology.
Topics: Arabidopsis; Cluster Analysis; Computational Biology; DNA Fingerprinting; DNA, Plant; Genetic Markers; Genome, Plant; Genotype; Genotyping Techniques; Internet; Polymorphism, Single Nucleotide; Selection, Genetic; User-Computer Interface
PubMed: 22077701
DOI: 10.1111/j.1365-313X.2011.04852.x -
Poultry Science Aug 1997The development of DNA-based markers has had a revolutionary impact on gene mapping and, more generally, on all of animal and plant genetics. With DNA-based markers, it... (Review)
Review
The development of DNA-based markers has had a revolutionary impact on gene mapping and, more generally, on all of animal and plant genetics. With DNA-based markers, it is theoretically possible to exploit the entire diversity in DNA sequence that exists in any cross. For this reason, high resolution genetic maps are being developed at an unprecedented speed. The most commonly used DNA-based markers include those based on a cloned and (usually) sequenced DNA fragment and other, more random, assays for genetic polymorphism that can be grouped under the heading of fingerprint markers. The advantages and disadvantages of the various marker types are discussed, along with their application to the reference chicken genetic linkage maps and to the search for quantitative trait loci (QTL). The prospects for the use of DNA-based markers in marker-assisted selection are considered, along with likely future trends in poultry gene mapping. Further development of both physical and linkage genome maps of the chicken will allow animal scientists to more efficiently detect and characterize QTL and will provide them access to the wealth of genetic information that is being generated about the human genome and the genomes of model species, such as the mouse and Drosophila.
Topics: Animals; Biotechnology; Chickens; Chromosome Mapping; Cloning, Molecular; DNA; DNA Fingerprinting; DNA, Satellite; Female; Genetic Markers; Male; Polymorphism, Restriction Fragment Length; Quantitative Trait, Heritable
PubMed: 9251136
DOI: 10.1093/ps/76.8.1108 -
Neuropsychopharmacology : Official... Jan 2020
Topics: Biomarkers; DNA Fingerprinting; Electroencephalography; Humans; Phenotype; Psychotic Disorders
PubMed: 31558770
DOI: 10.1038/s41386-019-0505-6 -
PCR Methods and Applications Aug 1994
Review
Topics: DNA Fingerprinting; DNA Primers; Polymerase Chain Reaction; Reproducibility of Results
PubMed: 9018327
DOI: 10.1101/gr.4.1.s59 -
Scientific Reports Mar 2021Forensic science has yet to take full advantage of single cell analysis. Its greatest benefit is the ability to alleviate the challenges associated with DNA mixture...
Forensic science has yet to take full advantage of single cell analysis. Its greatest benefit is the ability to alleviate the challenges associated with DNA mixture analysis, which remains a significant hurdle in forensic science. Many of the factors that cause complexity in mixture interpretation are absent in single cell analyses-multiple contributors, varied levels of contribution, and allele masking. This study revisits single cell analyses in the context of forensic identification, introducing previously unseen depth to the characterization of data generated from single cells using a novel pipeline that includes recovery of single cells using the DEPArray NxT and amplification using the PowerPlex Fusion 6c kit with varied PCR cycles (29, 30, and 31). The resulting allelic signal was assessed using analytical thresholds of 10, 100, and 150RFU. The mean peak heights across the sample sets generally increased as cycle number increased, 75.0 ± 85.3, 147.1 ± 172.6, and 226.1 ± 298.2 RFU, for 29, 30, and 31 cycles, respectively. The average proportion of allele/locus dropout was most significantly impacted by changes in the detection threshold, whereas increases in PCR cycle number had less impact. Overall data quality improved notably when increasing PCR from 29 to 30 cycles, less improvement and more volatility was introduced at 31 cycles. The average random match probabilities for the 29, 30, and 31 cycle sets at 150RFU are 1 in 2.4 × 10 ± 1.46 × 10, 1 in 1.49 × 10 ± 5.8 × 10, and 1 in 1.83 × 10 ± 8.09 × 10, respectively. This demonstrates the current power of single cell analysis in removing the need for complex mixture analysis.
Topics: Alleles; DNA Fingerprinting; Forensic Sciences; Humans; Polymerase Chain Reaction; Probability; Single-Cell Analysis
PubMed: 33782417
DOI: 10.1038/s41598-021-86271-6 -
Forensic Science International. Genetics Mar 2024Shedder status is defined as the propensity of an individual to leave DNA behind on touched items or surfaces and has been suggested as one of the major factors...
Shedder status is defined as the propensity of an individual to leave DNA behind on touched items or surfaces and has been suggested as one of the major factors influencing DNA transfer. However, little is known about whether shedder status is a constant property of an individual across multiple measurements or when the environmental conditions are changed. We have assessed DNA depositions of six males on 20 occasions to acquire a reference data set and to classify the participants into high, intermediate, or low shedders. This data set was also used to investigate how the probability of a correct shedder status classification changed when the number of DNA deposition measurements increased. Individual sweat rates were measured with a VapoMeter and data regarding hygiene routines were collected through a questionnaire on each sampling occasion. Next, we investigated how changes in the experimental conditions such as seasonal variation, hygiene routines, the temperature of the touched object, and repeated handling of an object influenced the DNA shedding. Additionally, we assessed DNA collected from the face and from T-shirts worn by the six participants to explore whether shedder status may be associated with the relative amount of DNA obtained from other body parts. Our results indicate that shedder status is a stable property across different seasons and different temperatures of handled objects. The relative DNA amounts obtained from repeatedly handled tubes, worn T-shirts, and from faces reflected the shedder status of the participants. We suggest that an individual's shedder status is highly influenced by the DNA levels on other body parts than hands, accumulating on the palms by frequently touching e.g., the face or previously handled items harboring self-DNA. Assessing physiological differences between the participants revealed that there were no associations between DNA shedding and individual sweat rates.
Topics: Male; Humans; Touch; DNA; Hand; Probability; DNA Fingerprinting
PubMed: 38176092
DOI: 10.1016/j.fsigen.2023.103002 -
Forensic Science, Medicine, and... Dec 2022Identifying charred human remains poses a challenge to forensic laboratories. High temperature completely incinerates the superficial tissues and partially destroys...
Identifying charred human remains poses a challenge to forensic laboratories. High temperature completely incinerates the superficial tissues and partially destroys bones, forcing the forensics to seek an alternative, for bones and teeth, forensic material that should quickly and cheaply deliver DNA of sufficient quantity and quality. We sought, other than rib cartilage, types of cartilages that could serve as a DNA source. DNA was isolated from the fibrous cartilage of a fibrous ring of intervertebral L1-L2 discs sampled from charred cadavers or charred body fragments: 5 victims of car fires, 1 victim of combustion during a residential house gas explosion, and 3 victims of nitroglycerin explosion. DNA was isolated by the column method. DNA quality and concentration were assessed by RT-PCR and multiplex PCR for 23 autosomal and 17 Y chromosome STR loci. STR polymorphism results obtained by capillary electrophoresis served for likelihood ratio (LR) calculations. DNA concentration in relation to the cadaver's age and post-mortem interval (PMI) were analyzed. All samples (n = 9) yielded good-quality DNA in quantities (0.57-17.51 ng/µL for T. Large autosomal sequence) suitable for STR-based amplification. The isolated DNA characterized a low degradation index (0.80-1.99), and we were able to obtain complete genetic profiles. In each of the nine cases, the genotyping results allowed identifying the victims based on comparative material from the immediate family. The results demonstrate the usefulness of human intervertebral disc fibrocartilage as an alternative DNA source for the genetic identification of charred bodies or charred torso fragments.
Topics: Humans; DNA Fingerprinting; Microsatellite Repeats; DNA; Cadaver; Fibrocartilage; Intervertebral Disc
PubMed: 36208368
DOI: 10.1007/s12024-022-00536-8 -
Forensic Science International. Genetics May 2023We present a novel rapid method for the recovery of cellular and free DNA from cotton swabs based on a simple elution buffer containing a high molecular weight polymer...
We present a novel rapid method for the recovery of cellular and free DNA from cotton swabs based on a simple elution buffer containing a high molecular weight polymer and detergent combined with a short proteinase K digestion to release cellular DNA. This method shows increased yields approaching 80% recovery of the input DNA compared to the QIAamp DNA Mini kit standard extraction protocol for swabs which has a recovery of 20-30%. The buffer components in the described method are compatible with direct PCR analysis of the isolated DNA without further purification. Recovery efficiencies were estimated by qPCR.
Topics: Humans; DNA; DNA Fingerprinting
PubMed: 36821959
DOI: 10.1016/j.fsigen.2023.102848 -
Journal of Forensic NursingHistorically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in...
Historically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in deoxyribonucleic acid (DNA) analysis methods, DNA profiles can be developed from touch DNA and applied to sexual assault cases. Following a literature review on factors affecting touch DNA transfer, a groping case study with innovative evidence collection is presented to support the expansion of touch DNA evidence collection in sexual assault cases. The groping case led to the development of a statewide sexual assault touch DNA form to guide evidence collection. DNA findings from additional groping sexual assault cases are reported to further show and justify the importance of evidence collection in groping cases. Implications on multidisciplinary practices are summarized to promote evidence collection and analysis in groping sexual assault cases. As forensic nurses are educated to accurately collect DNA evidence and provide trauma-informed, patient-centered care, they are best suited to provide nursing care for patients who have experienced groping sexual assaults. Optimal DNA findings in groping and sexual assault cases are best achieved through development of strong multidisciplinary, collaborative relationships between forensic nurses and forensic scientists.
Topics: Chromosomes, Human, Y; DNA; DNA Contamination; DNA Fingerprinting; Female; Forensic Nursing; Humans; Male; Sex Offenses; Specimen Handling; Touch
PubMed: 33843809
DOI: 10.1097/JFN.0000000000000324 -
Scientific Reports May 2019The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit...
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
Topics: DNA; DNA Fingerprinting; Equipment Design; Forensic Genetics; Humans; Lab-On-A-Chip Devices; Nucleic Acid Denaturation; Polymerase Chain Reaction; Silicon
PubMed: 31089203
DOI: 10.1038/s41598-019-43946-5