Evaluation of five DNA extraction methods for purification of DNA from atherosclerotic tissue and estimation of prevalence of Chlamydia pneumoniae in tissue from a Danish population undergoing vascular repair

Artificial Intelligence in Forensic Sciences: A Systematic Review of Past and Current Applications and Future Perspectives

The aim of this study is to review the available knowledge concerning the use of artificial Intelligence (AI) in general in different areas of Forensic Sciences from human identification to postmortem interval estimation and the estimation of different causes of death. This paper aims to emphasize the different uses of AI, especially in Forensic Medicine, and elucidate its technical part. This will be achieved through an explanation of different technologies that have been so far employed and through new ideas that may contribute as a first step to the adoption of new practices and to the development of new technologies. A systematic literature search was performed in accordance with the Preferred Reported Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines in the PubMed Database and Cochrane Central Library. Neither time nor regional constrictions were adopted, and all the included papers were written in English. Terms used were MACHINE AND LEARNING AND FORENSIC AND PATHOLOGY and ARTIFICIAL AND INTELIGENCE AND FORENSIC AND PATHOLOGY. Quality control was performed using the Joanna Briggs Institute critical appraisal tools. A search of 224 articles was performed. Seven more articles were extracted from the references of the initial selection. After excluding all non-relevant articles, the remaining 45 articles were thoroughly reviewed through the whole text. A final number of 33 papers were identified as relevant to the subject, in accordance with the criteria previously established. It must be clear that AI is not meant to replace forensic experts but to assist them in their everyday work life.

Rapid, equipment-free extraction of DNA from skin biopsies for point-of-care diagnostics

Kaposi's sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi's sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process. In this study, a simplified, POC-compatible alkaline DNA extraction, ColdSHOT, was optimized for 0.75 mm human skin punch biopsies. The optimized ColdSHOT extraction consistently produced 40,000+ copies of DNA per 5 µl reaction from 3 mg samples-a yield comparable to standard spin column extractions-within 1 h without significant equipment. The DNA yield was estimated sufficient for KSHV detection from KS-positive patient biopsies, and the LAMP assay was not affected by non-target tissue in the unpurified samples. Furthermore, the yields achieved via ColdSHOT were robust to sample storage in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer prior to DNA extraction, and the DNA sample was stable after extraction. The results presented in this study indicate that the ColdSHOT DNA extraction could be implemented to simplify and accelerate the LAMP-based diagnosis of Kaposi's sarcoma using submillimeter biopsy samples.

Applications of artificial intelligence in forensic sciences: Current potential benefits, limitations and perspectives

In recent years, new studies based on artificial intelligence (AI) have been conducted in the forensic field, posing new challenges and demonstrating the advantages and disadvantages of using AI methodologies to solve forensic well-known problems. Specifically, AI technology has tried to overcome the human subjective bias limitations of the traditional approach of the forensic sciences, which include sex prediction and age estimation from morphometric measurements in forensic anthropology or evaluating the third molar stage of development in forensic odontology. Likewise, AI has been studied as an assisting tool in forensic pathology for a quick and easy identification of the taxonomy of diatoms. The present systematic review follows the PRISMA 2020 statements and aims to explore an emerging topic that has been poorly analyzed in the forensic literature. Benefits, limitations, and forensic implications concerning AI are therefore highlighted, by providing an extensive critical review of its current applications on forensic sciences as well as its future directions. Results are divided into 5 subsections which included forensic anthropology, forensic odontology, forensic pathology, forensic genetics, and other forensic branches. The discussion offers a useful instrument to investigate the potential benefits of AI in the forensic fields as well as to point out the existing open questions and issues concerning its application on real-life scenarios. Procedural notes and technical aspects are also provided to the readers.

A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic

Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l^-1) followed by the canyon head (1,065 μg l^-1) and lowest at the canyon flank (494 μg l^-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.

Optimization of Brucella abortus Protocols for Downstream Molecular Applications

We compared the performances of various DNA extraction kits for their ability to recover Brucella abortus strain 19 inoculated into Brucella-free bovine tissues. Tissues were homogenized in a FastPrep bead homogenizer and extracted in triplicate by using one of five kits (Qiagen DNeasy, GE Illustra, Omega Bio-tek E.Z.N.A., Quanta Extracta, and IBI Science DNA Tissue kit). Whole blood was also taken from animals prior to chemical euthanasia, aliquoted, and then fractioned into buffy coat, red blood cells, and plasma. DNA was extracted from whole blood, buffy coat, and plasma by using four kits (Qiagen DNeasy, Omega Bio-tek E.Z.N.A., IBI Science DNA Blood kit, and 5PRIME PerfectPure). Previously reported primers targeting strain 19 were used to amplify extracted DNA and identify the optimal extraction kit. Real-time PCR was performed, and kits were compared for statistical differences by using quantification cycles as an outcome measure. Omega Bio-tek E.Z.N.A. was superior (P < 0.0068) in its lower quantification cycle values across all tissue kits. The IBI Science DNA Blood kit was superior to Qiagen DNeasy, 5PRIME PerfectPure, and Quanta Extracta (P < 0.0001, P = 0.0004, and P = 0.0013, respectively) but was not different from Omega Bio-tek E.Z.N.A. (P = 1.0). In summary, the optimal extraction kit for B. abortus strain 19 for tissues is Omega Bio-tek E.Z.N.A., and that for blood and its fractions is the IBI Science Mini Genomic DNA kit. Eluted DNA was also concentrated by using the Zymo Research DNA Clean & Concentrator-25 kit. Concentrated eluted DNA with the target was superior (P = <0.0001) to unconcentrated eluted DNA.

Nucleic Acid Extraction and Enrichment

Nucleic acid extraction is the first step of any amplification experiment no matter what kind of amplification is used to detect a specific pathogen. Efficient nucleic acid extraction is essential to obtain good results using any molecular test. The optimal extraction method should fulfill the following conditions: speed, short working time, cost-effectiveness, high sensitivity and specificity, good reproducibility, and safety. The methods can be divided into solution or column based according to differences of their principles. The automated extraction instruments have many advantages, and these have proven to be very useful. Moreover, in recent years, fully automated instruments combining NA extraction and amplification have been commercially available. However, the method itself does not provide assurance, and the DNA recovery can be different among various kits or instruments that use the similar principles. Therefore, it is important to carefully evaluate the performance of any extraction method used in the clinical microbiology laboratory even though manufacturers may have reported good validation results with specific organisms.

Chlamydia Pneumoniae in PBMC: Reproducibility of the OMPA Nested Touchdown PCR

The aim of our study was to evaluate whether the replicate PCR testing may provide more accurate estimates of C. pneumoniae DNA prevalence in PBMC of patients undergoing carotid endarterectomy. Clinical sensitivity and reproducibility of ompA nested touchdown PCR was also performed. Clinical sensitivity and reproducibility was examined by testing C. pneumoniae-negative PBMC spiked with serial dilutions of semipurified C. pneumoniae elementary bodies (from 8 to 0.002 IFU/ml). Detection of C. pneumoniae DNA was performed by ompA nested touchdown PCR. Each clinical and spiked PBMC DNA specimen was analyzed in replicates of 1,3,5 and 10. PCR results of serial dilutions of C. pneumoniae DNA performed in replicates of 10 were analysed by probit analysis.

C. pneumoniae DNA was detected in 14 of the 30 (46.7%) PBMC clinical specimens examined when 10 replicates were tested. When we analyzed 1, 3 and 5 replicates, 4 (13.3%), 7(23.3%), 12(40%) of the 30 specimens were positive, respectively. The limit of detection of ompA nested PCR touchdown was 0.008 IFU/ml when 10 replicates were tested. The ompA nested PCR had reproducibility scores of 10 for 10 from 8 to 4 IFU/ml concentration, but scores decreased for smaller numbers of IFU/ml. Our results showed that repeat testing of the same specimen increased clinical sensitivity as well as reproducibility of the ompA nested touchdown PCR. In conclusion the replicate PCR testing improves the performance of ompA nested touchdown PCR and provides a more accurate estimates of the prevalence of C. pneumoniae in PBMC of patients with atherosclerotic cardiovascular disease.

Development of a novel DNA extraction method for identification and quantification of Mycobacterium avium subsp. paratuberculosis from tissue samples by real-time PCR

Mycobacterium avium subsp. paratuberculosis (Map) is the causative agent of Johne's disease in ruminants and possibly associated with human Crohn's disease. One impediment in furthering our understanding of this potential association has been the lack of an accurate method for detection of Map in affected tissues. Real time polymerase chain reaction (RT-PCR) methods have been reported to have different sensitivities in detection of Map. This is in part attributable to the difficulties of extracting Map DNA and removing PCR inhibitors from the clinical specimens. The maximum efficiency of RT-PCR can only be achieved by using high quality DNA samples. In this study, we present a novel pre-treatment method which significantly increases Map DNA recovery and decreases PCR inhibitors (p<0.05). When the pre-treatment method was combined with the DNeasy Blood and Tissue kit (Qiagen), PCR inhibition was not detected in any of three different RT-PCR methods tested in this study. The results obtained with the IS900 probe showed an excellent Kappa value (0.849) and a high correlation coefficient r (0.940) compared to the results of culture method. When used to examine unknown field samples (n=15), more positive tissues were identified with DNA extracts prepared with pre-treatment method than without (5 vs 3). This improved Map DNA extraction method from tissue samples will make RT-PCR a more powerful tool for a wide range of applications for Map identification and quantification.

Comparison of six simple methods for extracting ribosomal and mitochondrial DNA from Toxocara and Toxascaris nematodes

Six simple methods for extraction of ribosomal and mitochondrial DNA from Toxocara canis, Toxocara cati and Toxascaris leonina were compared by evaluating the presence, appearance and intensity of PCR products visualized on agarose gels and amplified from DNA extracted by each of the methods. For each species, two isolates were obtained from the intestines of their respective hosts: T. canis and T. leonina from dogs, and T. cati from cats. For all isolates, total DNA was extracted using six different methods, including grinding, boiling, crushing, beating, freeze-thawing and the use of a commercial kit. To evaluate the efficacy of each method, the internal transcribed spacer (ITS) region and the cytochrome c oxidase subunit 1 (cox1) gene were chosen as representative markers for ribosomal and mitochondrial DNA, respectively. Among the six DNA extraction methods, the beating method was the most cost effective for all three species, followed by the commercial kit. Both methods produced high intensity bands on agarose gels and were characterized by no or minimal smear formation, depending on gene target; however, beating was less expensive. We therefore recommend the beating method for studies where costs need to be kept at low levels.

Nucleic Acid Extraction Techniques

Since thermostable Taq DNA polymerase was discovered in 1987, nucleic acid amplification techniques have made great strides and contributed greatly to progress in the life sciences. These techniques were introduced into the clinical laboratory and have produced great changes in diagnostic tools and tests. In particular, there have been many innovative molecular testing developments in the field of diagnostic microbiology.

Evaluation of an automated extraction method for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Cobas Amplicor PCR from different sample materials

A commercially available automated device (MagNA Pure LC) was adapted for nucleic acid extraction of urogenital specimen for subsequent PCR detection of Chlamydia trachomatis and Neisseria gonorrhoeae in a clinical laboratory. Results were compared to the standard manual extraction procedure and showed excellent correlation, with even slightly increased sensitivity.

Measurement of Chlamydia pneumoniae bacterial load in peripheral blood mononuclear cells may be helpful to assess the state of chlamydial infection in patients with carotid atherosclerotic disease

BACKGROUND

Chlamydia pneumoniae has been repeatedly associated with atherosclerotic cardiovascular diseases. We investigated the pattern of distribution of C. pneumoniae among patients with carotid atherosclerotic disease evaluating chlamydial load in carotid plaque, peripheral blood mononuclear cells (PBMC) and lymph node from same patient.

METHODS AND RESULTS

Thirty carotid plaques, 30 PBMC and 30 lymph nodes were examined by real-time PCR assay. C. pneumoniae DNA was detected, in carotid plaques, PBMC and lymph nodes in 11 patients; in carotid plaques and PBMC in five patients; in PBMC and lymph nodes in four patients; in lymph nodes in two patients; and in PBMC only in one patient. C. pneumoniae DNA in PBMC significantly coincided with the presence of the respective DNA in carotid plaque (p=0.0001) and lymph node (p=0.02). A higher chlamydial load was detected in PBMC than in lymph nodes and carotid plaques. More than 90% of patients with carotid plaques, PBMC and lymph nodes positive to C. pneumoniae were symptomatic, smokers, hypertensives, dyslipidemics and showed carotid plaques with rupture on the surface, hemorrhage and thrombosis.

CONCLUSION

The measurement of chlamydial load in PBMC may be helpful in the future to assess the state of C. pneumoniae infection and the risk of developing sequelae.

Mycoplasma genitalium, Chlamydia trachomatis, and tubal factor infertility--a prospective study

OBJECTIVE

To determine the presence of M. genitalium and C. trachomatis in women attending fertility clinics and to follow these women for the effects of previous infections or tubal damage on pregnancy rate and outcome.

DESIGN

Prospective study.

SETTING

Fertility clinics and university.

PATIENT(S)

Two hundred twelve couples attending fertility clinics.

INTERVENTION(S)

Blood and cervical swab samples from the women. Tubal status was assessed by culdoscopy and/or laparoscopy.

MAIN OUTCOME MEASURE(S)

Presence of M. genitalium and C. trachomatis was determined by polymerase chain reaction. Serum samples were tested for antibodies against M. genitalium and C. trachomatis.

RESULT(S)

One swap sample was positive to C. trachomatis and none positive to M. genitalium. Thirty of the 194 women had tubal factor infertility (TFI); 23% and 17% of women with TFI had antibodies to C. trachomatis and M. genitalium, respectively, compared with 15% and 4%, respectively, of women with normal tubes; 36% and 14% of women with a self-reported history of pelvic inflammatory disease (PID) were seropositive to C. trachomatis and M. genitalium, respectively, compared with 10% and 6%, respectively, of women without past PID.

CONCLUSION(S)

A strong antibody response against M. genitalium or C. trachomatis but no sign of current or chronic infection was found in women with TFI, indicating that previous infections caused by these microorganisms may have resulted in permanent damage and occlusion of the fallopian tubes.

Real-time PCR method with statistical analysis to compare the potential of DNA isolation methods to remove PCR inhibitors from samples for diagnostic PCR

A real-time PCR method for fast comparison of different DNA isolation methods to remove PCR inhibitors from samples is presented. A fixed amount of target-200 copies of a 79-bp region of the COCH gene of the zebrafish (Danio rerio)-was added to each PCR reaction together with isolated DNA from different types of samples including chicken feces. Four commercial DNA isolation kits and a chelex-based technique were compared using this method. The copy numbers calculated and the endpoint fluorescence were statistically compared to the values of 22 control samples containing the control target and water instead of isolated DNA, processed together in the same PCR run. The level of the endpoint fluorescence was more often negatively influenced by inhibitors than the copy number calculated, suggesting a more pronounced effect on the plateau phase of the reaction by limiting one or more compounds in the PCR reaction.

Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies

Prochlorococcus is a marine cyanobacterium which is found at high abundances in world's tropical and subtropical oligotrophic oceans. The genus Prochlorococcus can be divided into two major groups based on light physiology. Both of these groups can be further subdivided into genetically distinct lineages, or ecotypes. Real-time polymerase chain reaction (PCR) assays based on sequence differences in the 16S-23S rDNA internal transcribed spacer or the 23S rDNA were developed to examine the distribution of each ecotype in the field. The real-time PCR assays enabled linear quantification of concentrations ranging from 10 to 4 x 10(5) cells ml(-1). These assays were applied to a stratified water column in the Sargasso Sea. The majority of Prochlorococcus cells above 110 m belonged to the one of the low chlorophyll b/a ratio (high-light adapted) ecotypes, while two types of high chlorophyll b/a ratio (low-light adapted) cells dominated below 110 m. The other three types were found at significantly lower numbers or not detected at all. Differences in the abundance of ecotypes within the major light physiology groupings suggest that other factors, such as nutrient utilization and differential mortality, are driving their relative distributions. Real-time PCR assays will enable further exploration of these factors and temporal and geographic variability in ecotype abundance.

Current and developing technologies for monitoring agents of bioterrorism and biowarfare

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.

Application of the BioRobot EZ1 in a forensic laboratory

In a forensic laboratory, the routine application of an automated DNA extraction and purification robot has to fulfil several conditions, like producing reproducible DNA's of sufficient quantity and quality from all the different forensic biological stains relevant to various carrier materials. In this study, the suitability of the BioRobot EZ1 system from QIAGEN (Hilden, Germany), which offers fully automated extraction and purification of nucleic acids using magnetic bead technology, was tested. In summary, the DNA's obtained from the BioRobot EZ1 for different forensic relevant biological materials showed a quantity and quality comparable to those of the forensic standard protocols normally used in our laboratory. The system saves time, because there is no need of any further purification or concentration step after the automated DNA extraction. It can also be used as a replacement for time consuming organic extractions. A disadvantage of the system was the unsteady quality of the chemical regencies used by the robot. Nineteen different lots were tested with a self designed test system.

Ion-exchange chromatography method for the purification of genomic DNA fraction from Mycobacterium bovis Bacillus Calmette-Guérin

The goal of this study was to provide practical strategies for purifying genomic DNA fraction from Mycobacterium bovis Bacillus Calmette-Guérin (BCG-DNA) by ion-exchange chromatography. A multistep process was developed to purify BCG-DNA. The process consisted of sonication, heating, trypsin digestion, ion-exchange chromatography, gel-filter chromatography, and lyophilization. After ion-exchange chromatography, BCG-DNA was highly purified and possessed potent biological effects. The methods described were efficient and had good reproducibility. Further, this was the first reported chromatography method to purify BCG-DNA.

Enhanced anaerobic biodegradation of benzene-toluene-ethylbenzene-xylene-ethanol mixtures in bioaugmented aquifer columns

Methanogenic flowthrough aquifer columns were used to investigate the potential of bioaugmentation to enhance anaerobic benzene-toluene-ethylbenzene-xylene (BTEX) degradation in groundwater contaminated with ethanol-blended gasoline. Two different methanogenic consortia (enriched with benzene or toluene and o-xylene) were used as inocula. Toluene was the only hydrocarbon degraded within 3 years in columns that were not bioaugmented, although anaerobic toluene degradation was observed after only 2 years of acclimation. Significant benzene biodegradation (up to 88%) was observed only in a column bioaugmented with the benzene-enriched methanogenic consortium, and this removal efficiency was sustained for 1 year with no significant decrease in permeability due to bioaugmentation. Benzene removal was hindered by the presence of toluene, which is a more labile substrate under anaerobic conditions. Real-time quantitative PCR analysis showed that the highest numbers of bssA gene copies (coding for benzylsuccinate synthase) occurred in aquifer samples exhibiting the highest rate of toluene degradation, which suggests that this gene could be a useful biomarker for environmental forensic analysis of anaerobic toluene bioremediation potential. bssA continued to be detected in the columns 1 year after column feeding ceased, indicating the robustness of the added catabolic potential. Overall, these results suggest that anaerobic bioaugmentation might enhance the natural attenuation of BTEX in groundwater contaminated with ethanol-blended gasoline, although field trials would be needed to demonstrate its feasibility. This approach may be especially attractive for removing benzene, which is the most toxic and commonly the most persistent BTEX compound under anaerobic conditions.

Immunohistostaining assays for detection of Chlamydia pneumoniae in atherosclerotic arteries indicate cross-reactions with nonchlamydial plaque constituents

Detection of Chlamydia pneumoniae antigens in PCR-negative atheromata by immunohistochemistry assays has given rise to controversies regarding a link between the bacterium and atherosclerosis. One hundred ninety-seven human arterial segments removed surgically were examined for C. pneumoniae DNA by conventional PCR with three different primer pairs and by real-time PCR in two different laboratories. No C. pneumoniae DNA was detected. Eighty atherosclerotic lesions were studied by immunohistochemistry assays. Immunoreactivity for C. pneumoniae was frequently present but was not related to the extent of atherosclerosis. Mammary arteries showed immunoreactivity. Serial sections of 17 atheromata were analyzed by Western blotting, histological staining, and UV fluorescence microscopy. Chlamydial proteins were not detected. The sites with positive results by C. pneumoniae immunohistostaining assays precisely matched the sites with autofluorescent ceroid deposits. Immunoblotting and antigenic staining for C. pneumoniae were negative in tests with fetal aortas. The absence of C. pneumoniae DNA in human atherosclerotic lesions, together with negative results for C. pneumoniae proteins by Western blotting analysis, and the perfect matching of C. pneumoniae immunoreactive sites with sites with autofluorescent ceroid deposits suggest a nonspecific reactivity of antichlamydial antibodies with plaque constituents. On the basis of the results of the present study, there are no arguments for an etiologic role of C. pneumoniae in atherosclerosis.