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1.
Forensic Sci Int Genet ; 70: 103027, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38422900

RESUMEN

Currently, the global elephant population has significantly declined due to the poaching of elephants for their ivory, and this is the reason why elephants are listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). However, Thailand allows the legal trade of ivory from registered, domesticated Asian elephants, leading to the smuggling of African elephant ivory, and passing them off as Asian elephant ivory. Therefore, this research aims to develop and validate a portable strip test to discriminate between Asian and African elephants DNA, using Recombinase Polymerase Amplification (RPA) and Lateral Flow Dipstick assay (LFD) according to international standards. The results showed that the strip test can be successfully developed with 100% accuracy (n = 105). This kit is specific to elephants, has a detection limit of 0.125 ng of DNA, and can effectively discriminate a variety of elephant ivory, including raw ivory, ivory products, and aged ivory over 25 years old, which had been damaged by fire, all with 100% accuracy (n = 117). Additionally, the developed strip test is designed to be portable and cost-effective. It does not require expensive laboratory equipment and provides a faster analysis process compared with conventional PCR-based methods. This will expedite the legal process and enforcement of laws related to elephant conservation, reducing the opportunities for illegal activities, and enabling timely prosecution under relevant wildlife conservation laws in Thailand and internationally.


Asunto(s)
Elefantes , Animales , Elefantes/genética , Conservación de los Recursos Naturales , Comercio , Internacionalidad , ADN/genética
2.
Int J Legal Med ; 136(5): 1237-1245, 2022 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-35715652

RESUMEN

Bloodstains on fabrics may be washed or cleaned to eliminate incriminating evidence. These actions reduce the chances of obtaining an interpretable DNA profile. Previous studies have shown that conventional short-tandem repeat (STR) typing is affected by various factors associated with washing or laundering of stains. Here, we aim to increase the chances of obtaining interpretable STR profiles from laundered bloodstains using direct PCR. Preliminary investigations showed direct STR typing resulted in more alleles compared to conventional STR typing. We then further investigated the following factors with direct STR typing: fabric type (cotton, polyester, and denim), washing method (hand-washing and machine-washing), type of detergents (powder and liquid), washing temperature (cold to 90 °C), pretreatment agents (sodium hypochlorite and hydrogen peroxide), and the number of washes (one, three, and five). Direct PCR could be successfully used for STR typing from laundered bloodstains with very high success rates. Among the three fabric types, only denim negatively affected direct STR typing, while laundering of bloodstains on cotton and polyester had a negligible effect as mostly full profiles were obtained. Multiple washes resulted in a decrease in both the numbers of alleles and peak heights. Surprisingly, washing method, type of detergent, washing temperature, and pretreatment agents only had minimal to no effect on STR profile quality. Due to the robustness and sensitivity of direct STR typing from laundered bloodstains, the method could be beneficial for violent crime investigations in forensic DNA laboratories worldwide.


Asunto(s)
Manchas de Sangre , Lavandería , ADN , Medicina Legal/métodos , Humanos , Poliésteres
3.
Forensic Sci Int ; 330: 111099, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34794063

RESUMEN

Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.


Asunto(s)
Dermatoglifia del ADN , Patologia Forense , Repeticiones de Microsatélite , ADN , Humanos , Rótula , Reacción en Cadena de la Polimerasa
4.
Mikrochim Acta ; 188(6): 180, 2021 05 05.
Artículo en Inglés | MEDLINE | ID: mdl-33950304

RESUMEN

A novel strategy was developed to extract, detect, and quantify trace-level DNA. For the extraction step, a composite of methylene blue (MB), poly(acrylic acid) (PAA), and modified iron oxide magnetic nanoparticles (IOMNPs) (PAA/IOMNPs) was used to adsorb DNA from the sample. MB-PAA/IOMNPs with adsorbed DNA were then separated from the solution with an external magnet and MB-DNA was eluted from PAA/IOMNPs with acetic acid. In the detection step, MB-DNA was adsorbed on the surface of 3-aminopropyltriethoxysilane (APTES)-modified glassy carbon electrode via electrostatic force. DNA was quantified by measuring the oxidation peak of MB at a potential -0.13 V vs. Ag/AgCl using differential pulse voltammetry. Under the optimal experimental conditions, the DNA sensor showed linear ranges from 0.001 to 0.005 pg µL-1, 0.005 to 0.070 pg µL-1, and 0.070 to 0.400 pg µL-1 and a limit of detection of 0.87 fg µL-1. The proposed sensor detected trace DNA in real samples with recoveries that ranged from 80.4 to 90.4%.


Asunto(s)
Fraccionamiento Químico/métodos , ADN/análisis , Técnicas Electroquímicas/métodos , Resinas Acrílicas/química , Adsorción , ADN/química , ADN/aislamiento & purificación , Técnicas Electroquímicas/instrumentación , Electrodos , Humanos , Límite de Detección , Nanopartículas Magnéticas de Óxido de Hierro/química , Azul de Metileno/química , Mucosa Bucal/química , Propilaminas/química , Reproducibilidad de los Resultados , Silanos/química
5.
Int J Legal Med ; 135(1): 107-115, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32975592

RESUMEN

BACKGROUND: Elephant populations have greatly reduced mainly due to illegal poaching for their ivory. The trade in elephant products is protected by national laws and CITES agreements to prevent them from further decline. For instance, in Thailand, it is illegal to trade ivory from African elephants; however, the law allows possession of ivory from Asian elephants if permission has been obtained from the authorities. As such, means of enforcement of legislation are needed to classify the legal status of seized ivory products. Many DNA-based techniques have been previously reported for this purpose, although all have a limit of detection not suitable for extremely degraded samples. AIM: We report an assay based on nested PCR followed by DGGE to confirm the legal or illegal status of seized ivory samples where it is assumed that the DNA will be highly degraded. METHOD AND RESULTS: The assay was tested on aged ivory from which the assay was tested for reproducibility, specificity, and, importantly, sensitivity. Blind testing showed 100% identification accuracy. Correct assignment in all 304 samples tested was achieved including confirmation of the legal status of 227 highly degraded, aged ivories, thus underlining the high sensitivity of the assay. CONCLUSION AND RECOMMENDATION: The research output will be beneficial to analyze ivory casework samples in wildlife forensic laboratories.


Asunto(s)
Degradación Necrótica del ADN , ADN/genética , Electroforesis en Gel de Gradiente Desnaturalizante , Elefantes/genética , Animales , Conservación de los Recursos Naturales , Crimen , Genética Forense/métodos , Reacción en Cadena de la Polimerasa , Reproducibilidad de los Resultados
6.
Int J Legal Med ; 134(2): 461-471, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31897668

RESUMEN

Bones are often found in mass grave crime scene. To increase DNA identification success rates, a highly efficient DNA extraction method should be selected. Several DNA extraction methods for human bones have been published yet never been systematically compared, and some are time-consuming or complex. As such, a quick and highly efficient DNA extraction method was developed and compared with three published methods (Hi-Flow silica-based, total demineralization (TD) and PrepFiler BTA) using 70 fresh and 22 casework bones from different body parts. The highest median DNA concentrations were obtained from developed method (135.85 ng/µL and 0.224 ng/µL for fresh and casework bones, respectively). For residual PCR inhibitors, the threshold cycle (Ct) of the internal positive control (IPC) showed that developed method and PrepFiler BTA removed most PCR inhibitors. Similarly, 95.45% of casework STR profiles obtained using the developed protocol meet the standard requirements for Australian National Criminal Investigative DNA Database (NCIDD) entry, followed by 86.35% using TD, 81.82% using PrepFiler BTA, and 45.45% using Hi-Flow. Additionally, DNA extracts from seven different bones revealed that the 1st distal phalange of the hand contained the highest DNA concentration of 338.43 ng/µL, which was three times higher than the tibia and femur. Our findings suggest that developed method was highly efficient for casework bone analysis. It significantly reduced the extraction processing time down to 4 h and is two to four times cheaper compared with other methods. In practice, both the extraction method and the bone sampling must be considered by a forensic DNA analyst to increase the chances of successful identification.


Asunto(s)
Huesos/química , Dermatoglifia del ADN/métodos , ADN/aislamiento & purificación , Genética Forense/métodos , Repeticiones de Microsatélite , Densidad Ósea , Fémur/química , Falanges de los Dedos de la Mano/química , Humanos , Tibia/química
7.
Forensic Sci Int Genet ; 41: 168-176, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31153002

RESUMEN

Bombing accounts for the largest share of terrorist incidents worldwide. Most involve an improvised explosive device (IED): a bomb made from household items. Touch DNA may be left on parts of an IED during assembly. However, an IED conflagration degrades DNA, and there has never been a way to locate where touch DNA may remain. To solve this problem, we combined the use of fluorescent dye to locate latent DNA and direct PCR to improve STR profiles of DNA obtained from IEDs. Six fluorescent DNA-binding dyes were evaluated at various concentrations for the purpose of staining latent DNA. SYBR® Green I and Diamond™ Nucleic Acid dye were able to visualize touch DNA on IED substrates. Inhibition studies with extracted DNA and touch DNA using both dyes revealed that Diamond™ dye inhibited direct STR amplification, while SYBR® Green I did not. Stability studies at three temperatures showed optimum performance of SYBR® Green I up to 24 h after formulation. As such, only SYBR® Green I was further used to develop a "visualized-direct PCR" method. Using the conventional approach and the novel "visualized-direct PCR" approach in a single-blind investigation of mock IED evidence, the "visualized-direct PCR" approach had a 98.6% chance of obtaining more alleles (95% highest density interval (HDI): 0.7 to 10.0 alleles). A decrease in non-donor's alleles (mixed profiles) was also observed. The developed approach has the potential to revolutionize the process of STR typing from touch DNA.


Asunto(s)
Bombas (Dispositivos Explosivos) , Dermatoglifia del ADN/métodos , Colorantes Fluorescentes , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa/métodos , Tacto , Alelos , Benzotiazoles , Diaminas , Humanos , Compuestos Orgánicos , Quinolinas
8.
Forensic Sci Int ; 301: 182-189, 2019 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-31174132

RESUMEN

Cartridges, bullets, and casings (CBCs) are commonly recovered after shooting incidents and could provide valuable DNA information from touch DNA that has been left behind during handling of bullets and loading of guns. Direct PCR, in which the DNA extraction and quantification steps are bypassed, has been shown to provide comparable and sometimes better results from touch DNA and trace DNA samples. Here, direct PCR was applied to touch DNA retrieved from bullet casings from three ammunition types and guns. The results were evaluated to determine whether the technique should be recommended as a standard operating protocol for forensic DNA analysts. Three experiments were carried out to investigate the following: the effect of firing bullets on DNA deposited on bullet casings; the effect of gun and ammunition types on short tandem repeat (STR) profile quality; and the feasibility of using direct PCR in real-world cases via typing of mock casework samples. DNA extraction resulted in a loss of about 40% of DNA originally deposited, and firing a bullet reduced the amount of DNA recovered by 27%. Using the direct PCR protocol, conventional extraction protocol, and dilution protocol on touch DNA from fired bullet casings, we recovered means (and 95% credible intervals), respectively, of 11.1 (7.9-13.9), 5.6 (3.0-7.7), and 2.3 (0.2-4.0) alleles. No statistical difference in alleles recovered was observed between different calibers of ammunition fired from three guns (9mm, 7.62mm, and 5.56mm from Glock Model 19, AK47, and Tavor T-21, respectively). As expected, mixed DNA profiles were observed in 40% of the mock casework samples, in which guns were shared between volunteers. This study showed that direct amplification of touch DNA from bullet casings improved STR profiles. As direct PCR is quicker, cheaper, and resulted in more alleles recovered, forensic DNA analysts may benefit from using direct PCR.

9.
Mol Ecol Resour ; 19(3): 691-701, 2019 May.
Artículo en Inglés | MEDLINE | ID: mdl-30758899

RESUMEN

Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.


Asunto(s)
Tampones (Química) , Código de Barras del ADN Taxonómico/métodos , ADN/aislamiento & purificación , Entomología/métodos , Insectos/clasificación , Insectos/genética , Reacción en Cadena de la Polimerasa/métodos , Animales , Costos y Análisis de Costo , ADN/genética , Código de Barras del ADN Taxonómico/economía , Entomología/economía , Reacción en Cadena de la Polimerasa/economía , Flujo de Trabajo
10.
Food Chem ; 271: 767-772, 2019 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-30236743

RESUMEN

A direct pentaplex PCR assay was developed for the identification of meat from sources other than those declared on the packaging. Species-specific primers were designed, based on the mitochondrial cytochrome oxidase I (COI) gene. The assay amplified specific DNA fragments from dog (230 bp), duck (283 bp), buffalo (363 bp), goat (396 bp), and sheep (477 bp). The proposed method is capable of identifying target species accurately and is reproducible, sensitive and robust for use with real-world foods and food products. In total, 26 of 117 meat and commercial food products tested were shown to contain DNA from species not declared on the label.


Asunto(s)
Productos de la Carne/análisis , Reacción en Cadena de la Polimerasa Multiplex/métodos , Animales , Búfalos/genética , Fragmentación del ADN , Cartilla de ADN , Perros/genética , Patos , Cabras , Carne , Ovinos/genética , Especificidad de la Especie
11.
Forensic Sci Int Genet ; 30: 1-9, 2017 09.
Artículo en Inglés | MEDLINE | ID: mdl-28605649

RESUMEN

Body fluids provide key pieces of information for a forensic investigation. However, sometimes only a small amount of body fluids is found and/or DNA are also degraded by environmental factors at the crime scene. In extreme cases, a forensic analyst may have to decide whether to perform a presumptive test on the stains or proceed straightaway to DNA profiling, which could be wasteful for non-biological stains. Additionally, due to the inefficient DNA extraction process, the amount of DNA may not be enough for STR typing, especially if parts of the evidence had been subjected to presumptive testing. To overcome these problems, we developed a direct PCR method for STR profiling of stains (blood, saliva, and semen) that had been subjected to presumptive tests and also those that had not undergone presumptive tests. Using the optimized protocols, 86 of 90 untreated samples (95.6%) resulted in a full DNA profile. For presumptively-tested samples, both the type of presumptive test used and the surfaces where the stains are deposited affected the quality of the STR profiles. With blood, we obtained full STR profiles from 88% of samples tested with luminol and 78% with Hemastix. The acid phosphatase test for semen and Phadebas test for saliva resulted in full STR profiles from 85% and 73% of samples, respectively. Different substrates also affected the resulting STR profiles, but there was no clear trend based on absorbency or texture. The interactions of types of body fluids, presumptive tests, and substrates must be considered together. Our direct PCR protocol can be used to detect DNA even with 6 months-old biological samples. The benefits of the developed protocol include increasing amount of DNA obtained from evidence, decreasing chances of DNA contamination from complex or lengthy extraction steps, using minimal sample amount for analysis, and most importantly, improving STR profiles. Also, the process could save analysis time and cost due to the omission of DNA extraction and quantification. Our developed method could be beneficial to cases with limited stains available, as forensic analysts can perform indirect presumptive testing on the suspected stains and direct PCR could be carried out from the filter paper used, thus leaving the original stain for subsequent DNA extraction or re-analysis.


Asunto(s)
Análisis Químico de la Sangre , Dermatoglifia del ADN/métodos , Repeticiones de Microsatélite , Saliva/química , Semen/química , Fosfatasa Ácida , Humanos , Luminol , Masculino , Reacción en Cadena de la Polimerasa , Tiras Reactivas
12.
Food Chem ; 233: 144-150, 2017 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-28530559

RESUMEN

We developed and validated the first direct multiplex real-time PCR assay with melt curve analysis for the identification of different types of meat. The assay detects six commonly eaten meat species and provides the following benefits: ease of use, shortened analysis time, and decreased analysis cost. Species-specific primers were designed from cytochrome b, cytochrome oxidase I, and 16S rRNA genes to generate PCR products with specific melting peaks that differentiate pork, beef, horsemeat, duck meat, ostrich meat, and chicken. Validation of the assay showed that it is robust, reproducible, specific, and sensitive down to 0.32ng of DNA template. It takes less than one hour from sample to result and costs less than one USD per sample. We also successfully amplified 92.5% of market samples, demonstrating the assay's robustness. The developed assay has the potential to be implemented in food testing laboratories worldwide.


Asunto(s)
Carne , Animales , Reacción en Cadena de la Polimerasa Multiplex , Reacción en Cadena de la Polimerasa , ARN Ribosómico 16S , Reacción en Cadena en Tiempo Real de la Polimerasa
13.
Sci Justice ; 56(6): 468-474, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27914554

RESUMEN

Many forensic STR kits are currently available in the market. The AmpFLSTR® Identifiler® Plus kit, which targets 15 STRs, is commonly used worldwide. The Thai forensic DNA community is built around it in terms of instrument, databases, and interpretation. QIAGEN's IDplex Plus kit targets the same loci, but the PCR cycling time is shorter by about 90min. A direct comparison that assesses forensic parameters and applicability to casework between the two kits has never been carried out. In this study, we performed a direct comparison between the two kits using serial dilutions of two control DNA samples and 60 randomly selected casework samples, including samples taken from improvised explosive devices and terrorist raids. We statistically compared the performance of the two kits in terms of peak height, number of allele detected (allelic drop-out), intra-locus balance, inter-locus balance, inhibitor tolerance, stutter ratio, concordance, and allelic drop-in. The results demonstrate that both kits are statistically similar in performance. IDplex Plus gave higher peak heights in sensitivity test and tolerated inhibitors better, but had slightly worse inter-locus balances and stutter ratios. However, these differences were not practically significant, as seen by the resulting profiles of the casework samples (p=0.601). The performance on low-template samples also was not different. In conclusion, laboratories looking to replace the aging Identifiler® Plus might consider the IDplex Plus as a faster, more robust alternative that fits right into their existing structure without further investment in instrument and DNA database. Having more kits available worldwide by different companies could help bring the technology to different forensic laboratories and the justice system as a whole.


Asunto(s)
Dermatoglifia del ADN/instrumentación , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa/instrumentación , Humanos
14.
Electrophoresis ; 37(23-24): 3068-3075, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27754560

RESUMEN

Despite continuous conservation efforts by national and international organizations, the populations of the three extant elephant species are still dramatically declining due to the illegal trade in ivory leading to the killing of elephants. A requirement to aid investigations and prosecutions is the accurate identification of the elephant species from which the ivory was removed. We report on the development of the first fully validated multiplex PCR-electrophoresis assay for ivory DNA analysis that can be used as a screening or confirmatory test. SNPs from the NADH dehydrogenase 5 and cytochrome b gene loci were identified and used in the development of the assay. The three extant elephant species could be identified based on three peaks/bands. Elephas maximus exhibited two distinct PCR fragments at approximate 129 and 381 bp; Loxodonta cyclotis showed two PCR fragments at 89 and 129 bp; and Loxodonta africana showed a single fragment of 129 bp. The assay correctly identified the elephant species using all 113 ivory and blood samples used in this report. We also report on the high sensitivity and specificity of the assay. All single-blinded samples were correctly classified, which demonstrated the assay's ability to be used for real casework. In addition, the assay could be used in conjunction with the technique of direct amplification. We propose that the test will benefit wildlife forensic laboratories and aid in the transition to the criminal justice system.


Asunto(s)
Estructuras Animales/química , Electroforesis Capilar/métodos , Elefantes/clasificación , Elefantes/genética , Reacción en Cadena de la Polimerasa Multiplex/métodos , Diente/química , Animales , Citocromos b/genética , Electroforesis en Gel de Agar , Elefantes/anatomía & histología , Límite de Detección , NADH Deshidrogenasa/genética , Reproducibilidad de los Resultados
15.
Forensic Sci Int ; 267: 210-217, 2016 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-27643759

RESUMEN

Demand for ivory and expansion of human settlements have resulted in a rapid decline in the number of elephants. Enforcement of local and international laws and regulations requires identification of the species from which any ivory, or ivory products, originated. Further geographical assignment of the dead elephant from which the ivory was taken can assist in forensic investigations. In this study, a real-time PCR assay using melt curve analysis was developed and fully validated for forensic use. The presence or absence of three Elephantidae-specific and elephant species-specific melting peaks was used to identify the elephant species. Using 141 blood and ivory samples from the three extant elephant species, the assay demonstrated very high reproducibility and accuracy. The limit of detection was as low as 0.031ng of input DNA for conventional amplification and 0.002ng for nested amplification. Both DNA concentrations are typically encountered in forensic casework, especially for degraded samples. No cross-reactivity was observed for non-target species. Evaluation of direct amplification and nested amplification demonstrated the assay's flexibility and capability of analyzing low-template DNA samples and aged samples. Additionally, blind trial testing showed the assay's suitability application in real casework. In conclusion, wildlife forensic laboratories could use this novel, quick, and low-cost assay to help combat the continuing poaching crises leading to the collapse of elephant numbers in the wild.


Asunto(s)
Conservación de los Recursos Naturales , Crimen , Dermatoglifia del ADN , Elefantes/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Animales , Polimorfismo de Nucleótido Simple , Reproducibilidad de los Resultados , Especificidad de la Especie , Temperatura de Transición
16.
Forensic Sci Int Genet ; 17: 53-60, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25828367

RESUMEN

Improvised explosive devices (IEDs) made from household items are encountered in terrorist attacks worldwide. Assembling an IED leaves trace DNA on its components, but deflagration degrades DNA. To maximize the amount of DNA recovered, a systematic evaluation of DNA collection methods was carried out and the most efficient methods were implemented with IED casework evidence as a validation exercise. Six swab types and six moistening agents were used to collect dried buffy coat stains on four common IED substrates. The most efficient swab/moistening agent combinations were then compared with tape-lifting using three brands of adhesive tape and also with direct DNA extraction from evidence. The most efficient collection methods for different IED substrates (post-study protocol) were then implemented for IED casework and compared with the pre-study protocol using 195 pieces of IED evidence. There was no single best swab type or moistening agent. Swab type had the largest effect on DNA recovery percentages, but moistening agents, substrates, and the interactions between factors all affected DNA recovery. The most efficient swab/moistening agent combinations performed equally well when compared with the best adhesive tape and direct extraction. The post-study protocol significantly improved STR profiles obtained from IED evidence. This paper outlines a comprehensive study of DNA collection methods for trace DNA and the validation of the most efficient collection methods with IED evidence. The findings from both parts of this study emphasize the need to continuously re-evaluate standard operating protocols with empirical studies.


Asunto(s)
Dermatoglifia del ADN/métodos , ADN/análisis , ADN/aislamiento & purificación , Sustancias Explosivas/química , Genética Forense/métodos , Manejo de Especímenes/métodos , ADN/genética , Humanos , Repeticiones de Microsatélite , Manejo de Especímenes/instrumentación
17.
J Hum Genet ; 59(12): 675-81, 2014 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-25339232

RESUMEN

Among the people living in the five deep Southern Thai provinces, Thai-Malay Muslims (MUS) constitute the majority, while the remaining are Thai Buddhists (BUD). Cultural, linguistic and religious differences between these two populations have been previously reported. However, their biological relationship has never been investigated. In this study, we aimed to reveal the genetic structure and genetic affinity between MUS and BUD by analyzing 15 autosomal short tandem repeats. Both distance and model-based clustering methods showed significant genetic homogeneity between these two populations, suggesting a common biological ancestry. After Islamization in this region during the fourteenth century AD, gradual albeit nonstatistically significant genetic changes occurred within these two populations. Cultural barriers possibly influenced these genetic changes. MUS have closer admixture to Malaysian-Malay Muslims than BUD countrywide. Admixture proportions also support certain degree of genetic dissimilarity between the two studied populations, as shown by the unequal genetic contribution from Malaysian-Malay Muslims. Cultural transformation and recent minor genetic admixture are the likely processes that shaped the genetic structure of both MUS and BUD.


Asunto(s)
Etnicidad/genética , Repeticiones de Microsatélite/genética , Humanos , Religión , Tailandia
18.
Food Chem ; 163: 77-82, 2014 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-24912698

RESUMEN

This is the first time that direct PCR - DNA amplification without prior DNA extraction - was successfully developed and fully validated for rapid and economical simultaneous identification of six commonly consumed meat species. To achieve this, six species-specific primers were selected from previous reports and newly designed from the mitochondrial cytochrome b (cyt b), cytochrome oxidase I (COI), and 12s rRNA gene. The assay generated PCR products of 100, 119, 133, 155, 253, and 311 bp for pork, lamb/mutton, chicken, ostrich meat, horsemeat and beef, respectively. Validation showed that the assay is robust, rapid, economical, reproducible, specific, and sensitive down to 12,500 mitochondrial copy (equating to seven fg). It could be used with a variety of raw meats and products, including highly degraded and processed food samples. This proposed method will be greatly beneficial to the consumers, food industry, and law enforcement.


Asunto(s)
Carne/análisis , Reacción en Cadena de la Polimerasa Multiplex/métodos , Animales , Bovinos/genética , Pollos/genética , Cartilla de ADN , ARN Ribosómico/genética , Ovinos/genética , Especificidad de la Especie , Porcinos/genética
19.
Forensic Sci Med Pathol ; 10(1): 29-38, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24435950

RESUMEN

Wildlife forensic DNA analysis by amplification of a mitochondrial locus followed by DNA sequencing is routine, yet suffers from being costly and time-consuming. To address these disadvantages we report on a low-cost two-step direct PCR assay to efficiently analyze 12 forensically relevant mammalian sample types without DNA extraction. A cytochrome oxidase I degenerate-universal primer pair was designed and validated for the developed assay. The 12 sample types, which included bone, horn, feces, and urine, were amplified successfully by the assay using a pre-direct PCR dilution protocol. The average amplification success rate was as high as 92.5 % (n = 350), with an average PCR product concentration of 220.71 ± 180.84 ng/µL. Differences in amplification success rate and PCR product quantity between sample types were observed; however, most samples provided high quality sequences, permitting a 100 % nucleotide similarity to their respective species via BLAST database queries. The combination of PBS and Phire(®) Hot Start II DNA polymerase gave comparable amplification success rate and amplicon quantity with the proprietary commercial kits (P > 0.05, n = 350) but at considerably lower cost. The stability of the assay was tested by successfully amplifying samples that had been stored for up to 12 months. Our data indicate that this low-cost two-step direct amplification assay has the potential to be a valuable tool for the forensic DNA community.


Asunto(s)
Animales Salvajes/genética , ADN/análisis , Complejo IV de Transporte de Electrones/genética , Genética Forense/métodos , Reacción en Cadena de la Polimerasa/veterinaria , Análisis de Secuencia de ADN , Animales , Crimen/prevención & control , Cartilla de ADN , Genética Forense/economía , Marcadores Genéticos , Humanos , Reacción en Cadena de la Polimerasa/economía , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN/economía
20.
Forensic Sci Int ; 233(1-3): 288-97, 2013 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-24314532

RESUMEN

Recent studies on bloodstains have focused on determining the time since deposition of bloodstains, which can provide useful temporal information to forensic investigations. This study is the first to use smartphone cameras in combination with a truly low-cost illumination system as a tool to estimate the age of bloodstains. Bloodstains were deposited on various substrates and photographed with a smartphone camera. Three smartphones (Samsung Galaxy S Plus, Apple iPhone 4, and Apple iPad 2) were compared. The environmental effects - temperature, humidity, light exposure, and anticoagulant - on the bloodstain age estimation process were explored. The color values from the digital images were extracted and correlated with time since deposition. Magenta had the highest correlation (R(2)=0.966) and was used in subsequent experiments. The Samsung Galaxy S Plus was the most suitable smartphone as its magenta decreased exponentially with increasing time and had highest repeatability (low variation within and between pictures). The quantifiable color change observed is consistent with well-established hemoglobin denaturation process. Using a statistical classification technique called Random Forests™, we could predict bloodstain age accurately up to 42 days with an error rate of 12%. Additionally, the age of forty blind stains were all correctly predicted, and 83% of mock casework samples were correctly classified. No within- and between-person variations were observed (p>0.05), while smartphone camera, temperature, humidity, and substrate color influenced the age determination process in different ways. Our technique provides a cheap, rapid, easy-to-use, and truly portable alternative to more complicated analysis using specialized equipment, e.g. spectroscopy and HPLC. No training is necessary with our method, and we envision a smartphone application that could take user inputs of environmental factors and provide an accurate estimate of bloodstain age.


Asunto(s)
Manchas de Sangre , Computadoras de Mano , Procesamiento de Imagen Asistido por Computador , Fotograbar/métodos , Algoritmos , Anticoagulantes , Color , Femenino , Medicina Legal/métodos , Humanos , Humedad , Luz , Modelos Lineales , Masculino , Temperatura , Factores de Tiempo , Adulto Joven
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