Expression of Toll-like receptors 2 and 4 and its association with matrix metalloproteinases in symptomatic and asymptomatic apical periodontitis.

To determine Toll-like receptors (TLR)2 and TLR4 expression levels and associate them with matrix metalloproteinases (MMPs) in asymptomatic apical periodontitis (AAP), symptomatic apical periodontitis (SAP), and healthy controls. Apical tissue/lesion samples were obtained from chronic AAP (n = 35) and SAP (n = 29), and healthy periodontal ligament (HPL, n = 10) with indication of tooth extraction, respectively. mRNA expression levels of TLR2, TLR4, MMP-1, MMP-2, MMP-8, and MMP-13 were determined by real-time reverse-transcription polymerase chain reaction. The data were analyzed with Kruskal-Wallis and Dunn's pot hoc test (p < 0.05). The correlation coefficient was obtained using the Spearman correlation (p < 0.05). TLR2, MMP-1, MMP-2, and MMP-13 mRNA levels were the highest in SAP followed by AAP and controls (p < 0.05). TLR4 and MMP-8 were over expressed in AAP and SAP compared to HPL (p < 0.05). TLR2 positively correlated with TLR4, MMP-1, MMP-8, and MMP-13 in SAP (p < 0.05). TLR2 and TLR4 are overexpressed in apical lesions versus healthy periodontal ligament and correlate with collagenolytic MMPs. Particularly, TLR2 is overexpressed in SAP in association with MMP-1, MMP-8, and MMP-13. Our results suggest that the activation of TLR2 along with MMP overexpression might contribute to SAP clinical presentation and progression. TLRs, MMPs, and their interaction can explain the clinical presentations and evolution of apical periodontitis and might represent key targets for new diagnostic and treatment approaches.

Report into a discordant result at D16S539 between SGM Plus® and PowerPlex® ESI 16 kits in a criminal case sample and implications for the UK National DNA Database upgrade.

Upon re-testing of a DNA extract as part of a defence examination, a discordant result was observed at D16S539. Further STR testing and DNA sequencing of the sample identified the cause as a primer binding site mutation which was shown to be a previously unreported SNP. The testing results obtained in this case are considered in light of the current ongoing Multiplex Upgrade Project in the UK and the likely increase in discordant results that may be observed once different next generation kits are introduced.

A common epigenetic clock from childhood to old age.

Forensic age estimation is a DNA intelligence tool that forms an important part of Forensic DNA Phenotyping. Criminal cases with no suspects or with unsuccessful matches in searches on DNA databases; human identification analyses in mass disasters; anthropological studies or legal disputes; all benefit from age estimation to gain investigative leads. Several age prediction models have been developed to date based on DNA methylation. Although different DNA methylation technologies as well as diverse statistical methods have been proposed, most of them are based on blood samples and mainly restricted to adult age ranges. In the current study, we present an extended age prediction model based on 895 evenly distributed Spanish DNA blood samples from 2 to 104 years old. DNA methylation levels were detected using Agena Bioscience EpiTYPER® technology for a total of seven CpG sites located at seven genomic regions: ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, MIR29B2CHG and chr16:85395429 (GRCh38). The accuracy of the age prediction system was tested by comparing three statistical methods: quantile regression (QR), quantile regression neural network (QRNN) and quantile regression support vector machine (QRSVM). The most accurate predictions were obtained when using QRNN or QRSVM (mean absolute prediction error, MAE of ± 3.36 and ± 3.41, respectively). Validation of the models with an independent Spanish testing set (N = 152) provided similar accuracies for both methods (MAE: ± 3.32 and ± 3.45, respectively). The main advantage of using quantile regression statistical tools lies in obtaining age-dependent prediction intervals, fitting the error to the estimated age. An additional analysis of dimensionality reduction shows a direct correlation of increased error and a reduction of correct classifications as the training sample size is reduced. Results indicated that a minimum sample size of six samples per year-of-age covered by the training set is recommended to efficiently capture the most inter-individual variability..

Characterization of the public transit air microbiome and resistome reveals geographical specificity.

BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.

The application of comprehensive two-dimensional gas chromatography to the analysis of wildfire debris for ignitable liquid residue.

Arsonous wildfires are complex investigations due to the high abundance of natural background compounds and subsequent pyrolysis by-products formed during combustion. These interfering compounds can be present in large concentrations and overwhelm the marker compounds used to identify ignitable liquid residue (ILR). Complex matrix effects often interfere with the identification of ILR, providing ambiguous results. The use of comprehensive two-dimensional gas chromatography with time of flight mass spectrometry (GC×GC-TOFMS) separates natural compounds from interfering with ILR compounds of interest. When compared to standard gas chromatography-mass spectrometry (GC-MS) analysis, GC×GC was able to reduce the number of tentative results by 20%. Certain compounds were determined to be unusable for the identification of ILR in wildfire debris samples, in particular the Three Musketeer Group (ethylbenzene, m,p-xylene, and o-xylene), which are ubiquitous in all samples, as well as long chain n-alkylbenzenes, which are formed in the pyrolysis of organic matter. Conversely, the presence of C1- and C2-alkylnaphthalenes were excellent indicators of the presence of gasoline-type ILR. A sizeable number of background samples were collected that helped to provide additional lines of evidence when classifying samples for ILR. Given the complicated matrices encountered in arsonous wildfires, it is evident that GC×GC provides better capabilities at identifying ILR than the standard GC-MS analytical technique.

A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies.

Individual age estimation can be applied to criminal, legal, and anthropological investigations. DNA methylation has been established as the biomarker of choice for age prediction, since it was observed that specific CpG positions in the genome show systematic changes during an individual's lifetime, with progressive increases or decreases in methylation levels. Subsequently, several forensic age prediction models have been reported, providing average age prediction error ranges of ±3-4 years, using a broad spectrum of technologies and underlying statistical analyses. DNA methylation assessment is not categorical but quantitative. Therefore, the detection platform used plays a pivotal role, since quantitative and semi-quantitative technologies could potentially result in differences in detected DNA methylation levels. In the present study, we analyzed as a shared sample pool, 84 blood-based DNA controls ranging from 18 to 99 years old using four different technologies: EpiTYPER®, pyrosequencing, MiSeq, and SNaPshotTM. The DNA methylation levels detected for CpG sites from ELOVL2, FHL2, and MIR29B2 with each system were compared. A restricted three CpG-site age prediction model was rebuilt for each system, as well as for a combination of technologies, based on previous training datasets, and age predictions were calculated accordingly for all the samples detected with the previous technologies. While the DNA methylation patterns and subsequent age predictions from EpiTYPER®, pyrosequencing, and MiSeq systems are largely comparable for the CpG sites studied, SNaPshotTM gives bigger differences reflected in higher predictive errors. However, these differences can be reduced by applying a z-score data transformation.

Functional importance of sequence in the stem-loop of a transcription terminator.

Intrinsic transcription terminators of prokaryotes are distinguished by a common RNA motif: a stem-loop structure high in guanine and cytosine content, followed by multiple uridine residues. Models explaining intrinsic terminators postulate that the stem-loop sequence is necessary only to form structure. In the tR2 terminator of coliphage lambda, single-nucleotide changes reducing potential RNA stem stability eliminated tR2 activity, and a compensatory change that restored the stem structure restored terminator activity. However, multiple changes in the stem sequence that should have either maintained or increased stability reduced terminator activity. These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure.

Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel.

Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.

Background levels of dioxin-like polychlorinated biphenyls (dlPCBs), polychlorinated, polybrominated and mixed halogenated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs, PBDD/Fs & PXDD/Fs) in sera of pregnant women in Accra, Ghana.

Human exposure data on dioxins and dioxin-like compounds (DLCs) in Ghana are limited. Based on health risks associated with dioxins and DLCs, the impact of maternal body burdens on foetal exposure is significant. This is the first study that assesses polychlorinated, polybrominated and mixed halogenated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs, PBDD/Fs and PXDD/Fs), and dioxin-like polychlorinated biphenyls (dlPCBs) in sera of primiparous Ghanaians. Our sample selection includes 34 participants from two municipalities (Accra and Tema), and explores contributions from environmental and dietary exposures using questionnaire data. Sample preparation involved C18 solid phase extraction, purification with acidified silica and lipid removal cartridges, and detection with gas chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry. The calculated average toxic equivalent concentration was 5.3 pg TEQ/g lw, with contributions from dlPCBs (1.25 pg TEQ/g lw), PCDD/Fs (3.10 pg TEQ/g lw), PBDD/Fs (0.49 pg TEQ/g lw) and PXDD/Fs (0.50 pg TEQ/g lw). The calculated total TEQ concentration was lower than background TEQ concentrations reported in sera of pregnant women globally. Positive correlations were obtained for total dioxins and DLC concentrations with age and Body Mass Index (BMI). Dietary intake of seafood and dairy products had a strong influence on PCDD/F and dlPCB concentrations. Statistically significant differences were observed for dioxins and DLCs in participants from Accra (in close proximity to Agbogbloshie e-waste site) and Tema. Given the significant TEQ contribution of PBDD/Fs and PXDD/Fs (~20%), it is essential to explore these classes of dioxins and DLCs in future biomonitoring studies as they may pose health risks, and add extra diagnostic information in source exposure investigations.

Effects of the S288c genetic background and common auxotrophic markers on mitochondrial DNA function in Saccharomyces cerevisiae.

Saccharomyces cerevisiae is a valuable model organism for the study of eukaryotic processes. Throughout its development as a research tool, several strain backgrounds have been utilized and different combinations of auxotrophic marker genes have been introduced into them, creating a useful but non-homogeneous set of strains. The ade2 allele was used as an auxotrophic marker, and for 'red-white' screening for respiratory competence. his3 alleles that influence the expression of MRM1 have been used as selectable markers, and the MIP1[S] allele, found in the commonly used S228c strain, is associated with mitochondrial DNA defects. The focus of the current work was to examine the effects of these alleles, singly and in combination, on the maintenance of mitochondrial function. The combination of the ade2 and MIP1[S] alleles is associated with a slight increase in point mutations in mitochondrial DNA. The deletion in the his3Delta200 allele, which removes the promoter for MRM1, is associated with loss of respiratory competence at 37 degrees C in the presence of either MIP1 allele. Thus, multiple factors can contribute to the maintenance of mitochondrial function, reinforcing the concept that strain background is an important consideration in both designing experiments and comparing results obtained by different research groups.

Forensic source attribution for toluene in environmental samples.

The formation of toluene by microbiological processes can confound environmental investigations relating to petroleum releases. This is because toluene is a constituent of petroleum and can move readily within wetland environments, and analysis for toluene in relation to a petroleum release can lead to incorrect assignment of detected biogenic toluene as related to the release. No legally defensible method of distinguishing biogenic and petrogenic origins of detectible concentrations of toluene have been demonstrated to date. Using example petrogenic samples and samples of peat from 2 wetland environments, a poor bog and a poor fen, the present study demonstrates the use of an established ASTM International analytical methodology that was originally designed for arson analysis for the determination of the origin of toluene. Environmental forensic data-interpretation methods such as chromatogram inspection and diagnostic ratios are shown to be capable of readily distinguishing biogenic and petrogenic origins of toluene. Environ Toxicol Chem 2018;37:729-737. © 2017 SETAC.

Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise.

In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols. The provided primer pools for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms included 33 and 29 body fluid specific targets, respectively, to identify blood, saliva, semen, vaginal secretion, menstrual blood and skin. The results demonstrated moderate to high count values in the body fluid or tissue of interest with little to no counts in non-target body fluids. There was some inter-laboratory variability in read counts, but overall the results of the laboratories were comparable in that highly expressed markers showed high read counts and less expressed markers showed lower counts. We performed a partial least squares (PLS) analysis on the data, where blood, menstrual blood, saliva and semen markers and samples clustered well. The results of this collaborative mRNA massively parallel sequencing (MPS) exercise support targeted mRNA sequencing as a reliable body fluid identification method that could be added to the repertoire of forensic MPS panels.

Role of the intermembrane-space domain of the preprotein receptor Tom22 in protein import into mitochondria.

Tom22 is an essential component of the protein translocation complex (Tom complex) of the mitochondrial outer membrane. The N-terminal domain of Tom22 functions as a preprotein receptor in cooperation with Tom20. The role of the C-terminal domain of Tom22, which is exposed to the intermembrane space (IMS), in its own assembly into the Tom complex and in the import of other preproteins was investigated. The C-terminal domain of Tom22 is not essential for the targeting and assembly of this protein, as constructs lacking part or all of the IMS domain became imported into mitochondria and assembled into the Tom complex. Mutant strains of Neurospora expressing the truncated Tom22 proteins were generated by a novel procedure. These mutants displayed wild-type growth rates, in contrast to cells lacking Tom22, which are not viable. The import of proteins into the outer membrane and the IMS of isolated mutant mitochondria was not affected. Some but not all preproteins destined for the matrix and inner membrane were imported less efficiently. The reduced import was not due to impaired interaction of presequences with their specific binding site on the trans side of the outer membrane. Rather, the IMS domain of Tom22 appears to slightly enhance the efficiency of the transfer of these preproteins to the import machinery of the inner membrane.

A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing.

A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment. The samples had a variable complexity and comprised straightforward single-source samples, samples with dropout or altered peak sizing, a point heteroplasmy and two-component mixtures resulting in one to five bi-allelic calls. The overall success rate in obtaining useful results was high (97.6%) given that some of the participating laboratories had no previous experience with the typing technology and/or mtDNA analysis. The majority of the participants proceeded to haplotype inference to assess the feasibility of assigning a haplogroup and checking phylogenetic consistency when only 18 SNPs are typed. To mimic casework procedures, the participants compared the SNP typing data of all 13 samples to a set of eight mtDNA reference profiles that were described according to standard nomenclature (Parson et al., 2014) [2], and indicated whether these references matched each sample or not. Incorrect scorings were obtained for 2% of the comparisons and derived from a subset of the participants, indicating a need for training and guidelines regarding mini-mtSNaPshot data interpretation.

Reactivation of 2 genetically distinct varicella-zoster viruses in the same individual.

Varicella-zoster viruses recovered from 2 episodes of herpes zoster in an immunocompetent man were found to be different genotypes. The fact that the 2 isolates came from the same individual was confirmed by DNA fingerprinting. Immunity following chickenpox may not always protect against systemic reinfection. This finding raises questions about varicella-zoster virus pathogenesis and may have an impact on public health policy.

Bacteriophage lambda: alive and well and still doing its thing.

The lambda (lambda) family of bacteriophages continues to provide significant insights into the understanding of basic biological processes, as well as useful technological innovations. Areas in which recent advances have occurred include transcription elongation, repressor interactions, genomics and post-transcriptional regulation. The homologous lambda recombination functions have been exploited as an efficient in vivo recombinant engineering system for functional genomic studies. The virulence of some pathogenic strains of Escherichia coli is enhanced by the expression of Shiga toxin (stx) genes encoded on a resident lambdoid prophage. Recent work suggests that the phage regulatory network may be a significant contributor to toxin production and release by these pathogenic E. coli.

Y chromosome STR haplotype data for an Irish population.

Y chromosome haplotype data was collected for 155 Irish males residing in the Republic of Ireland. Eleven short tandem repeat (STR) markers: DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were analysed and the allele and haplotype frequencies calculated. This Irish data is presented here and was found to be less diverse when compared with the neighbouring UK population.

Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise.

Recently, there has been much debate about what kinds of genetic markers should be implemented as new core loci that constitute national DNA databases. The choices lie between conventional STRs, ranging in size from 100 to 450 bp; mini-STRs, with amplicon sizes less than 200 bp; and single nucleotide polymorphisms (SNPs). There is general agreement by the European DNA Profiling Group (EDNAP) and the European Network of Forensic Science Institutes (ENFSI) that the reason to implement new markers is to increase the chance of amplifying highly degraded DNA rather than to increase the discriminating power of the current techniques. A collaborative study between nine European and US laboratories was organised under the auspices of EDNAP. Each laboratory was supplied with a SNP multiplex kit (Foren-SNPs) provided by the Forensic Science Service, two mini-STR kits provided by the National Institute of Standards and Technology (NIST) and a set of degraded DNA stains (blood and saliva). Laboratories tested all three multiplex kits, along with their own existing DNA profiling technique, on the same sets of degraded samples. Results were collated and analysed and, in general, mini-STR systems were shown to be the most effective. Accordingly, the EDNAP and ENFSI working groups have recommended that existing STR loci are reengineered to provide smaller amplicons, and the adoption of three new European core loci has been agreed.