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International Journal of Molecular... Dec 2022Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although... (Review)
Review
Collection and interpretation of "touch DNA" from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were "single-swab", "double-swab", and "other methods" (i.e., cutting out, adhesive tape, FTA paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool's probative value.
Topics: Touch; DNA Fingerprinting; DNA; Specimen Handling
PubMed: 36555182
DOI: 10.3390/ijms232415541 -
Forensic Science International. Genetics Mar 2023DNA identification of human remains has a valuable role in the field of forensic science and wider. Although DNA is vital in identification of unknown human remains,... (Meta-Analysis)
Meta-Analysis Review
DNA identification of human remains has a valuable role in the field of forensic science and wider. Although DNA is vital in identification of unknown human remains, post-mortem environmental factors can lead to poor molecular preservation. In this respect, focus has been placed on DNA extraction methodologies for hard tissue samples, as these are the longest surviving. Despite decades of research being conducted on DNA extraction methods for bone and teeth, little consensus has been reached as to the best performing. Therefore, the aim of this study was to conduct a thorough systematic literature review to identify potential DNA extraction technique(s) which perform optimally for forensic DNA profiling from hard tissue samples. PRISMA guidelines were used, by which a search strategy was developed. This included identifying databases and discipline specific journals, keywords, and exclusion and inclusion criteria. In total, 175 articles were identified that detailed over 50 different DNA extraction methodologies. Results of the meta-analysis conducted on 41 articles - meeting further inclusion criteria - showed that statistically significant higher DNA profiling success was associated with solid-phase magnetic bead/resin methods. In addition, incorporating a demineralisation pre-step resulted in significantly higher profiling successes. For hard tissue type, bone outperformed teeth, and even though dense cortical femur samples were more frequently used across the studies, profiling success was comparable, and in some cases, higher in cancellous bone samples. Notably, incomplete data sharing resulted in many studies being excluded, thus an emphasis for minimum reporting standards is made. In conclusion, this study identifies strategies that may improve success rates of forensic DNA profiling from hard tissue samples. Finally, continued improvements to current methods can ensure faster times to resolution and restoring the identity of those who died in obscurity.
Topics: Humans; Body Remains; DNA; Tooth; DNA Fingerprinting; Bone and Bones
PubMed: 36502616
DOI: 10.1016/j.fsigen.2022.102818 -
Forensic Science International Aug 2019Different stakeholders use forensic DNA databases for different purposes; for example, law enforcement agencies use them as an investigative tool to identify suspects,...
Different stakeholders use forensic DNA databases for different purposes; for example, law enforcement agencies use them as an investigative tool to identify suspects, and criminologists use them to study the offending patterns of unidentified suspects. A number of researchers have already studied their effectiveness, but none has performed an overview of the relevant literature. Such an overview could help future researchers and policymakers by evaluating their creation, use and expansion. Using a systematic review, this article synthesizes the most relevant research into the effectiveness of forensic DNA databases published between January 1985 and March 2018. We report the results of the selected studies and look deeper into the evidence by evaluating the relationship between the purpose, content, and effectiveness of DNA databases, three inseparable elements in this type of research. We classify the studies by purposes: (i) detection and clearance; (ii) deterrence; and (iii) criminological scientific knowledge. Each category uses different measurements to evaluate effectiveness. The majority of these studies report positive results, supporting the assumption that DNA databases are an effective tool for the police, society, and criminologists.
Topics: Criminal Law; DNA Fingerprinting; Databases, Nucleic Acid; Humans
PubMed: 31212144
DOI: 10.1016/j.forsciint.2019.05.052 -
Sensors (Basel, Switzerland) Jan 2023This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of... (Review)
Review
This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of aspects, such as performance, time-to-result, ease-of-use, portability, and costs (per analysis run) of these three (modified) rapid DNA analysis systems, are considered. Despite their advantages and developmental progress, major steps still have to be made before rapid systems can be broadly applied at crime scenes for full DNA profiling. Aspects in particular that need (further) improvement are portability, performance, the possibility to analyze a (wider) variety of (complex) forensic samples, and (cartridge) costs. Moreover, steps forward regarding ease-of-use and time-to-result will benefit the broader use of commercial rapid DNA systems. In fact, it would be a profit if rapid DNA systems could be used for full DNA profile generation as well as indicative analyses that can give direction to forensic investigators which will speed up investigations.
Topics: Forensic Genetics; Microsatellite Repeats; Polymerase Chain Reaction; DNA Fingerprinting; DNA
PubMed: 36772114
DOI: 10.3390/s23031075 -
Phytomedicine : International Journal... Jul 2024It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for...
BACKGROUND
It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.
PURPOSE
To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.
METHODS/RESULTS
this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.
CONCLUSION
This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.
Topics: Drugs, Chinese Herbal; Drug Contamination; Quality Control; Chromatography, High Pressure Liquid; DNA Barcoding, Taxonomic
PubMed: 38728918
DOI: 10.1016/j.phymed.2024.155667 -
Water Research Nov 2014Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning... (Review)
Review
Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes.
Topics: Bacteria; DNA, Bacterial; Denitrification; Environmental Microbiology; In Situ Hybridization, Fluorescence; Nitrogen; Sewage; Waste Disposal, Fluid
PubMed: 25078442
DOI: 10.1016/j.watres.2014.06.042 -
PloS One 2014We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if... (Meta-Analysis)
Meta-Analysis Review
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
Topics: Adolescent; Adult; Cluster Analysis; Female; Humans; Microbial Consortia; Microbiota; Pregnancy; Vagina; Vaginosis, Bacterial
PubMed: 25148517
DOI: 10.1371/journal.pone.0105998 -
Frontiers in Pharmacology 2022Botanical drug products consist of complex phytochemical constituents that vary based on various factors that substantially produce different pharmacological activities...
Botanical drug products consist of complex phytochemical constituents that vary based on various factors that substantially produce different pharmacological activities and possible side effects. (Blume) Kuntze (Primulaceae) is one of the most popular Malay traditional botanical drugs and widely recognized for its medicinal use. Many studies have been conducted focusing on the identification of bioactive substances, pharmacological and toxicological activities in its specific varieties but less comprehensive study on authentication. Lack of quality control (QC) measurement assessment may cause different quality issues on containing products like adulteration by pharmaceutical substances, substitution, contamination, misidentification with toxic plant species, which may be detrimental to consumers' health and safety. This systematic literature review aims to provide an overview of the current scenario on the quality control of botanical drug products as determined by pharmacopoeia requirements specifically for authentication or identification. A systematic search for peer-reviewed publications to document literature search for authentication was performed using four electronic databases: Web of Science, PubMed, Scopus and ScienceDirect for related studies from January 2010 to December 2021. The research studies published in English and related articles for identification or authentication of were the main inclusion criteria in this review. A total 122 articles were identified, whereby 33 articles met the inclusion criteria. Macroscopy, microscopy, chemical fingerprinting techniques using chromatography, spectroscopy and hyphenated techniques, and genetic-based fingerprinting using DNA barcoding method have been used to identify and to distinguish between different varieties and plant parts. The study concluded that a combination of approaches is necessary for authenticating botanical drug substances and products containing to assure the quality, safety, and efficacy of marketed botanical drug products, particularly those with therapeutic claims.
PubMed: 35754509
DOI: 10.3389/fphar.2022.855384 -
BMC Research Notes Nov 2014Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454... (Review)
Review
BACKGROUND
Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software.
FINDINGS
Seven software packages met our inclusion criteria of being cost free and publically available, offering analysis functions from platform sequencing to results presentation, and included documentation and data security. We installed and executed each of the software packages and describe the installation, documentation, features, and functions of each.
CONCLUSIONS
For the user, pipeline choices may be limited because some packages only run on select operating systems. Users should be aware of the availability of features and functions of each package. Of utmost importance is that the user must be aware of the default settings and underlying assumptions of each function. All packages are lacking sufficient methods for longitudinal analysis.Researchers can do well using any one of these seven packages. However, two packages are outstanding; mothur and QIIME, due not only to the comprehensive suite of functions and procedures incorporated into the pipelines but also because of the accompanying documentation.
Topics: Animals; DNA Contamination; Humans; Sequence Analysis, DNA; Software
PubMed: 25421430
DOI: 10.1186/1756-0500-7-830 -
Tropical Medicine & International... Aug 2009The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
The proportion of tuberculosis cases in a population that are clustered (i.e. share identical strains of Mycobacterium tuberculosis) reflects ongoing M. tuberculosis transmission. It varies markedly, but it is unclear how much of this variation reflects measurable differences in study design, setting and the patient population. We aimed to assess the relative impact of these factors and develop a tool to improve interpretation of the proportion clustered from an individual study.
METHODS
We systematically reviewed all population-based TB clustering studies that used IS6110 RFLP as their main DNA fingerprinting technique. Meta-regression was used to see how much of the variation in the proportion clustered between studies could be explained by variables describing study design, setting and population. We compared expected clustering, based on study design and setting, with that observed.
RESULTS
Forty-six studies were included. Just four factors related to study design and setting-study duration, sampling fraction, handling of low band strains and tuberculosis incidence-explained 28% of the variation in the proportion clustered. Additionally including average patient age and proportion foreign born explained 60% of the variation in clustering for industrialized countries. Comparison of expected and observed proportions showed that for some studies the expected proportion clustered differed strongly from that observed.
CONCLUSIONS
We were able to account for much of the variation in the proportion clustered. The comparison of expected and observed clustering allows for a more valid comparison of studies and provides a tool for identifying outliers that warrant further investigation.
Topics: Adult; Aged; Analysis of Variance; DNA Fingerprinting; DNA, Bacterial; Epidemiologic Studies; Female; Humans; Male; Middle Aged; Mycobacterium tuberculosis; Tuberculosis
PubMed: 19702595
DOI: 10.1111/j.1365-3156.2009.02316.x