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Astrobiology Jul 2018Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly...
Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly different on other planets and moons, particularly as we expand our efforts to explore ocean worlds like Europa and Enceladus. We propose a new concept for life detection that harnesses the power of DNA sequencing to yield intricate informatics fingerprints, even for life that is not nucleic acid-based. The concept is based on the fact that folded nucleic acid structures (aptamers) have been shown to be capable of binding a wide variety of compounds, whether inorganic, organic, or polymeric, and irrespective of being from a biotic or abiotic source. Each nucleic acid sequence can be thought of as a code, and a combination of codes as a "fingerprint." Over multiple analytes, the "fingerprint" of a non-terran sample can be analyzed by chemometric protocols to provide a classifier of molecular patterns and complexity. Ultimately the chemometric fingerprints of living systems, which may differ significantly from nonliving systems, could provide an empirical, agnostic means of detecting life. Because nucleic acids are exponentially amplified by the polymerase chain reaction, even very small input signals could be translated into a robust readable output. The derived sequences could be identified by a small, portable sequencing device or by capture and optical imaging on a DNA microarray. Without presupposing any particular molecular framework, this agnostic approach to life detection could be used from Mars to the far reaches of the Solar System, all within the framework of an instrument drawing little heat and power. Key Words: Agnostic biosignatures-Astrobiology-Chemometrics-DNA sequencing-Life detection-Proximity ligation assay. Astrobiology 18, 915-922.
Topics: DNA; DNA Fingerprinting; Exobiology; Extraterrestrial Environment; Life; Planets; Sequence Analysis, DNA
PubMed: 29634318
DOI: 10.1089/ast.2017.1712 -
Forensic Science International. Genetics Sep 2022The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed...
The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed software solutions for automated DNA profile analysis, contamination check, major donor inference, DNA database (DDB) comparison and reporting of the conclusions. This represents the Fast DNA IDentification Line (FIDL) and this study describes its development, validation and implementation in criminal casework at the authors' institute. This first implementation regards single donor profiles and major contributors to mixtures. The validation included testing of the software components on their own and examination of the performance of different DDB search strategies. Furthermore, end-to-end testing was performed under three conditions: (1) testing of scenarios that can occur in DNA casework practice, (2) tests using three months of previous casework data, and (3) testing in a casework production environment in parallel to standard casework practices. The same DNA database candidates were retrieved by this automated line as by the manual workflow. The data flow was correct, results were reproducible and robust, results requiring manual analysis were correctly flagged, and reported results were as expected. Overall, we found FIDL valid for use in casework practice in our institute. The results from FIDL are automatically reported within three working days from receiving the trace sample. This includes the time needed for registration of the case, DNA extraction, quantification, polymerase chain reaction and capillary electrophoresis. FIDL itself takes less than two hours from intake of the raw CE data to reporting. Reported conclusions are one of five options: (1) candidate retrieved from DDB, (2) no candidate retrieved from DDB, (3) high evidential value with regards to reference within the case, (4) results require examination of expert, or (5) insufficient amount of DNA obtained to generate a DNA profile. In our current process, the automated report is sent within three working days and a complete report, with confirmation of the FIDL results, and signed by a reporting officer is sent at a later time. The signed report may include additional analyses regarding e.g. minor contributors. The automated report with first case results is quickly available to the police enabling them to act upon the DNA results prior to receiving the full DNA report. This line enables a uniform and efficient manner of handling large numbers of traces and cases and provides high value investigative leads in the early stages of the investigation.
Topics: DNA; DNA Fingerprinting; Electrophoresis, Capillary; Humans; Polymerase Chain Reaction; Software
PubMed: 35691141
DOI: 10.1016/j.fsigen.2022.102738 -
Forensic Science, Medicine, and... Mar 2023Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess...
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
Topics: Humans; DNA; DNA Damage; DNA Degradation, Necrotic; DNA Fingerprinting; Microsatellite Repeats; Real-Time Polymerase Chain Reaction; Blood Specimen Collection
PubMed: 36355320
DOI: 10.1007/s12024-022-00549-3 -
Methods in Molecular Biology (Clifton,... 2023In the field of forensic science, the DNA extraction of bone is utilized in investigations involving mass disasters, unidentified remains, and missing persons. However,...
In the field of forensic science, the DNA extraction of bone is utilized in investigations involving mass disasters, unidentified remains, and missing persons. However, bone samples can be challenging samples due to their exposure to extreme environmental conditions over long periods of time. The use of an effective DNA extraction method to properly isolate and purify the DNA is essential for bone samples. This chapter describes the DNA extraction of bone samples through a total demineralization protocol, which aims to entirely dissolve the bone matrix in order to access the DNA molecules.
Topics: DNA Fingerprinting; Microsatellite Repeats; Bone and Bones; DNA; Bone Matrix
PubMed: 37439977
DOI: 10.1007/978-1-0716-3295-6_6 -
International Journal of Legal Medicine Sep 2022The choice of skeletal element types and their intra-bone parts is important because of differences in DNA preservation, and this must be considered when sampling bones...
The choice of skeletal element types and their intra-bone parts is important because of differences in DNA preservation, and this must be considered when sampling bones for DNA testing. When incomplete skeletons are found, ribs and vertebrae have been shown to be the most suitable for genetic identification of bones from the torso. This study compares the preservation of DNA between 12th thoracic vertebrae and first ribs to determine which bone type is more suitable for genetic typing. The study analyzed 35 12th thoracic vertebrae and 29 first ribs from one mass grave from the Second World War with commingled skeletal remains excavated. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation and through short tandem repeat (STR) typing success. Previous studies performed on aged skeletal remains have shown that the DNA content of the first ribs and 12th thoracic vertebrae has high intra-bone variability, and this was considered when sampling the bones. After full demineralization extraction, the PowerQuant System (Promega) was used to measure the quantity and quality of DNA, and the GlobalFiler kit (Applied Biosystems) was used for STR typing. The results showed that DNA yield and degradation and STR typing success exhibited no statistically significant difference between first ribs and 12th thoracic vertebrae, and there was no intra-individual difference when comparing only paired bones from the same individuals. Consequently, with intra-bone DNA variability considered, the first ribs or the 12th thoracic vertebrae can be selected when sampling to genetically identify the skeletal remains of highly degraded torsos. HIGHLIGHTS: The first ribs and thoracic vertebrae are the most suitable bones for sampling from the torso. The proximal part of first rib and posterior vertebral column of the 12th thoracic vertebrae yielded the most DNA. The first ribs were compared with the 12th thoracic vertebrae, and the sampling process considered intra-bone DNA variability. The quality and quantity of nuclear DNA and success of STR typing were measured. The first ribs yielded the same DNA yields as well as STR typing success as the 12th thoracic vertebrae. When only the torso is present, it is not of high importance whether the first ribs or the 12th thoracic vertebrae are collected.
Topics: Aged; Body Remains; DNA; DNA Fingerprinting; Humans; Microsatellite Repeats; Ribs; Spine; Thoracic Vertebrae
PubMed: 35729437
DOI: 10.1007/s00414-022-02860-8 -
Yakugaku Zasshi : Journal of the... 2019As criminal cases have become more complicated, Japan's law enforcement officials are promoting the use of more sophisticated technologies, such as DNA analysis, in the... (Review)
Review
As criminal cases have become more complicated, Japan's law enforcement officials are promoting the use of more sophisticated technologies, such as DNA analysis, in the course of criminal investigations in order to verify facts with objective evidence. The primary DNA analysis method employed by law enforcement officials is short tandem repeat (STR) analysis, a method for identifying individuals utilizing individual differences in the number of repeat units of characteristic DNA sequences. Presently, STR analysis can discriminate between individuals with the probability of one in approximately 4.7 trillion, even when the DNA profile is the most common type among the Japanese population. In every prefectural police department, members of criminal investigation laboratories, who were trained and certified by the Training Center of Forensic Science at the National Research Institute of Police Science, perform STR analysis. Forensic DNA analysis plays an important role not only in criminal investigations but also following large-scale disasters, to aid in individual identification. The accuracy of DNA typing is increasing with the availability of STR typing kits that can examine more loci than conventional kits. However, it remains difficult for DNA analysis to identify individuals with only small amounts of samples, old samples, or mixed samples. New methods for handling these problematic samples are required. Here, we review current investigative techniques and challenges of DNA analysis, and focus on the latest research for solutions to these challenges.
Topics: Crime; DNA Fingerprinting; Forensic Anthropology; Humans; Japan; Microsatellite Repeats; Sequence Analysis, DNA
PubMed: 31061341
DOI: 10.1248/yakushi.18-00166-6 -
Journal of Forensic Sciences May 2023Forensic "touch" DNA samples are low-quantity samples that are recovered from surfaces that have been touched by single or multiple individuals. These samples can...
Forensic "touch" DNA samples are low-quantity samples that are recovered from surfaces that have been touched by single or multiple individuals. These samples can include DNA from primary contributors who directly touched the surface, as well as secondary contributors whose DNA was transferred to the surface through an intermediary. It is difficult to determine the type of transfer, or how often and under what conditions DNA transfer occurs. In this paper, we present an innovative protocol that combines (1) a paired male and female transfer DNA experimental design in which the presence of male DNA indicates secondary transfer and (2) a cost-effective quantitative PCR (qPCR) assay of a sex-specific region in the Amelogenin gene to detect male and female DNA. We evaluate the ability of the Amelogenin qPCR assay to detect low concentrations of male and female DNA in mixed samples. We also test experimental DNA samples using our transfer DNA protocol to differentiate primary and secondary DNA transfer. Male DNA was detected in the majority of known mixed samples, even in samples with 4× more female DNA-this result demonstrates the ability to detect low concentrations of male DNA and the presence of secondary transfer DNA in our experimental design. Primary DNA transfer was detected in 100% of our experimental trials and secondary DNA transfer was detected in 37.5% of trials. Our innovative protocol mimics realistic case scenarios to establish rates of primary and secondary DNA transfer in an inexpensive and simplified manner.
Topics: Humans; Male; Female; Pilot Projects; Research Design; Amelogenin; Polymerase Chain Reaction; DNA; DNA Fingerprinting
PubMed: 36975017
DOI: 10.1111/1556-4029.15243 -
GigaScience 2015Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the... (Review)
Review
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants. Direct use of optical mapping to study population-level genetic diversity is currently limited to microbial strain typing and human diversity studies. Nonetheless, optical mapping shows great promise in the study of plant trait development, domestication and polyploid evolution. Here we review the current applications and future prospects of optical mapping in the field of plant comparative genomics.
Topics: Chromosome Mapping; Chromosomes, Plant; DNA Fingerprinting; Genome, Plant; Plants; Sequence Analysis, DNA
PubMed: 25699175
DOI: 10.1186/s13742-015-0044-y -
Science & Justice : Journal of the... Mar 2022Successful DNA typing of forensically relevant evidence is reliant on both the quality and quantity of biological material recovered from a crime scene. In geographical...
Successful DNA typing of forensically relevant evidence is reliant on both the quality and quantity of biological material recovered from a crime scene. In geographical areas of the world exposed to cold climates, it is not uncommon for biological evidence to encounter a diversity of challenging surfaces and environments, including snowy surfaces. Currently, there is no standard protocol for recovery of bloodstain evidence in snow and very few publications exploring adequate methods of recovering biological evidence from snowy surfaces. In this study, three common substrates (e.g., cotton swabs, FTA paper, and untreated filter paper) utilized by investigators for evidence recovery were evaluated for their ability to recover human blood (DNA) evidence from snow that would be viable for traditional forensic DNA typing. Each biological sample was extracted and quantified to evaluate the quality and quantity of DNA recovered. All samples yielded sufficient non-degraded DNA to proceed with DNA profiling, where complete DNA profiles were generated from each collection substrate. The experimental findings presented herein demonstrate that the ability to recover viable DNA from human blood collected on surface snow is possible using all three collection methods tested.
Topics: DNA; DNA Fingerprinting; Humans; Microsatellite Repeats; Snow; Specimen Handling
PubMed: 35277228
DOI: 10.1016/j.scijus.2022.01.001 -
Genes Mar 2024The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The... (Review)
Review
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
Topics: Humans; Polymerase Chain Reaction; Forensic Sciences; DNA Fingerprinting; DNA; Forensic Genetics
PubMed: 38674373
DOI: 10.3390/genes15040438