Low DNA Content Research Articles

Molecular age prediction using skull bone samples from individuals with and without signs of decomposition: a multivariate approach combining analysis of posttranslational protein modifications and DNA methylation.

The prediction of the chronological age of a deceased individual at time of death can provide important information in case of unidentified bodies. The methodological possibilities in these cases depend on the availability of tissues, whereby bones are preserved for a long time due to their mineralization under normal environmental conditions. Age-dependent changes in DNA methylation (DNAm) as well as the accumulation of pentosidine (Pen) and D-aspartic acid (D-Asp) could be useful molecular markers for age prediction. A combination of such molecular clocks into one age prediction model seems favorable to minimize inter- and intra-individual variation. We therefore developed (I) age prediction models based on the three molecular clocks, (II) examined the improvement of age prediction by combination, and (III) investigated if samples with signs of decomposition can also be examined using these three molecular clocks. Skull bone from deceased individuals was collected to obtain a training dataset (n = 86), and two independent test sets (without signs of decomposition: n = 44, with signs of decomposition: n = 48). DNAm of 6 CpG sites in ELOVL2, KLF14, PDE4C, RPA2, TRIM59 and ZYG11A was analyzed using massive parallel sequencing (MPS). The D-Asp and Pen contents were analyzed by high performance liquid chromatography (HPLC). Age prediction models based on ridge regression were developed resulting in mean absolute errors (MAEs)/root mean square errors (RMSE) of 5.5years /6.6 years (DNAm), 7.7 years /9.3 years (Pen) and 11.7 years /14.6 years (D-Asp) in the test set. Unsurprisingly, a general lower accuracy for the DNAm, D-Asp, and Pen models was observed in samples from decomposed bodies (MAE: 7.4-11.8 years, RMSE: 10.4-15.4 years). This reduced accuracy could be caused by multiple factors with different impact on each molecular clock. To acknowledge general changes due to decomposition, a pilot model for a possible age prediction based on the decomposed samples as training set improved the accuracy evaluated by leave-one-out-cross validation (MAE: 6.6-12 years, RMSE: 8.1-15.9 years). The combination of all three molecular age clocks did reveal comparable MAE and RMSE results to the pure analysis of the DNA methylation for the test set without signs of decomposition. However, an improvement by the combination of all three clocks was possible for the decomposed samples, reducing especially the deviation in case of outliers in samples with very high decomposition and low DNA content. The results demonstrate the general potential in a combined analysis of different molecular clocks in specific cases.

Development of a microfluidic SNP assay for lineage discrimination in the endangered hazel dormouse

AbstractThe application of Genotyping-by-Sequencing (GBS) approaches is often restricted in wildlife monitoring and conservation genetics, as those fields often rely on noninvasively collected samples with low DNA content. Here we selected a subset of informative single-nucleotide polymorphisms (SNPs) from genome-wide data for lineage discrimination of a locally endangered Eurasian rodent, the hazel dormouse (Muscardinus avellanarius), and designed a microfluidic 96 SNP genotyping assay suitable for noninvasively collected samples. Analyses of 43 samples from different European countries confirmed successful discrimination of the Eastern and Western lineage and local substructure within those lineages, proving the suitability of the developed panel for identifying evolutionary significant units and conservation units. Application with 94 hair and scat samples collected in a recent monitoring study on the hazel dormouse in Southern Germany resulted in > 99.5% amplification success showing the applicability of the new tool in genetic wildlife monitoring and conservation studies.

O-278 The vaginal and endometrial microbiome: do they tell the same story?

Abstract Study question Is the composition of the endometrial microbiome comparable to that of the vagina and can vaginal sampling provide sufficient information to characterize the uterine microbiome? Summary answer The compositions of the endometrial and vaginal microbiome are largely comparable and therefore, in most cases, vaginal sampling is sufficient to characterize the uterine microbiome. What is known already A dysbiotic endometrial microbiome (i.e., a shift from a predominance of beneficial bacteria to less favourable species) has been reported in association with adverse pregnancy outcomes in assisted reproductive treatment (ART). If dysbiosis is detected, antibiotics or probiotics can be administered to restore an optimal microbiome. However, characterization of the endometrial microbiome is challenging, involving invasive sampling, and technical difficulties due to the low microbial mass in the endometrium. In contrast, vaginal sampling is considered minimally invasive and microbial analysis is technically less complex. It is important to clarify whether the microbiomes of the endometrium and the vagina are comparable. Study design, size, duration A prospective multi-centre study including 60 ART patients was conducted from June 2022 to August 2023. During the luteal phase (on average day-19), paired vaginal swabs and endometrial biopsies were collected sequentially and stored in a preservation medium for further analysis. Patients and physicians were also asked to complete a questionnaire to identify any lifestyle or medical factors that may have differentially affected the microbial composition of the vagina and endometrium. Participants/materials, setting, methods A carefully validated qPCR methodology was used to accurately assess the presence and relative abundance of the four major lactobacillus species associated with eubiosis (crispatus, gasseri, iners, and jensenii) and the 15 most common bacterial species implicated in dysbiosis. Additionally, the relative abundance of microbial and human DNA was examined. Of note, endometrial analysis required additional tissue lysis. Furthermore, due to the low microbial DNA content in endometrial samples, preamplification was necessary prior to qPCR. Main results and the role of chance The proportion of microbial versus human DNA was approximately 90 times higher in vaginal samples compared to endometrial samples (p < 0.0001). However, the microbial compositions of both the endometrium and the vagina showed remarkable similarities. Lactobacillus species were predominant at both sites, accounting for an average of 86% and 89% of the bacterial population in the vagina and endometrium, respectively (p = 0.6). Of the dysbiotic species, Gardnerella vaginalis was the most common, accounting for 8% (vagina) and 7% (endometrium) of the total bacterial population (p = 1). There was no difference in the average number of distinct microbial species between the two niches (1.8 vs. 2.1; p = 0.3). Direct comparison of paired samples highlighted the high similarity of microbial compositions between both sites and showed strong correlations of species abundances in individual patients (L.crispatus: r = 0.9, L.iners: r = 0.9, L.gasseri: r = 1, L.jensenii: r = 0.9, G.vaginalis: r = 0.7; p < 0.0001/all species). However, the microbial composition differed in four patients (6.6%), with three having a dysbiotic vaginal profile (≥50% dysbiotic species) but a eubiotic endometrial profile (≥50% lactobacillus species) and one showing the reverse pattern. The medical conditions of two patients, including chronic endometritis and use of antibiotics and probiotics in the preceding cycle, may account for the observed differences. Limitations, reasons for caution The species analysed were carefully selected to ensure a comprehensive analysis. Nevertheless, the potential presence of unevaluated species could impact the results. While the included patients displayed diversity in their reproductive histories, it is important to acknowledge that the observed results may still be influenced by underlying causes of infertility. Wider implications of the findings The close similarity between the microbiomes at the two sites investigated suggests that minimally invasive vaginal sampling may be sufficient to characterise the endometrial microbiome. The ease of vaginal sampling and processing is expected to improve patient recruitment in microbiome research and facilitate easier application of clinical microbiome tests. Trial registration number not applicable

Assessment of Commercial DNA Extraction Kits for Porcine Gelatin Detection Using RT-PCR and ddPCR

Gelatin is extensively applied in various industries, including food, beverages, cosmetics, and pharmaceuticals. Although the determination of gelatin species is essential for religious, health, and consumer preference reasons, a standardized analysis method is absent. The challenge in identifying gelatin through DNA-based methods arises from the low DNA content and extensive DNA denaturation in the gelatin matrix. This study assessed the efficacy of two commercial DNA extraction kits, namely the Processed Food DNA Extraction (PF kit) and the DNeasy Mericon Food Kit (DM kit), for extracting DNA from porcine gelatin powder and commercial products derived from gelatin. Additionally, we evaluate the amplification of the extracted porcine DNA using real time polymerase chain reaction (RT-PCR) and droplet digital polymerase chain reaction (ddPCR) techniques. The PF extraction kit demonstrated successful DNA extraction from porcine gelatin powder and commercial samples of porcine gelatin-based candies with a higher concentration (32.24-286.07 ng/uL) and purity (A260/A280 ratio of 1.82-2.33) compared to the DM kit (3.95-7.30 ng/uL and an A260/A280 ratio of 1.29-2.45). RT-PCR and ddPCR analyses yielded positive results for porcine DNA from gelatin powder for both PF and DM kits, albeit with differing Cq values and copy numbers. The choice of DNA extraction kit significantly impacted the amplification results when analyzing commercial samples of porcine gelatin-based candies. Using RT-PCR, all samples yielded negative results with the DM kit, while the PF kit detected one positive result for porcine DNA. Improved outcomes were observed with more sensitive analysis methods such as ddPCR, where the DM kit identified one positive result for porcine DNA while the PF kit detected positive results for all tested candies.

Tissue-engineered cellulose tubes for microvascular and lymphatic reconstruction: A translational and feasibility study

BackgroundLymphedema microsurgery is an emerging treatment modality, with dissimilar long-term outcomes. One of the main technical challenges in lymphatic microsurgery is the identification and availability of suitable donor vessels for anastomosis. Tissue engineering using biomaterials has shown promise in addressing vessel quality issues in other fields, but its application in microsurgery is still limited. MethodsDecellularized cellulose tubes were developed and bioengineered by decellularizing stems of Taraxacum-Ruderalia. The microscopic structure, mechanical properties, and remnant DNA content of the cellulose tubes were evaluated. Human and murine skin fibroblasts and dermal lymphatic endothelial cells were isolated and cultured for recellularization studies. Biocompatibility, proliferative capacity, and ex-vivo endothelialization of the cellulose tubes were assessed as potential interposition grafts. Finally, the engineered cellulose tubes were assessed as interposing xenografts for LVA in an ex-vivo swine limb model. ResultsThe decellularized cellulose tubes exhibited a suitable microscopic structure, mechanical properties, and low remnant DNA content. The tubes showed adequate biocompatibility, supported cell proliferation, and facilitated spontaneous ex-vivo endothelialization of lymphatic endothelial cells. In the swine limb model, LVA using the engineered cellulose tubes was successfully performed. ConclusionThis translational study presents the use of decellularized cellulose tubes as an adjunct for micro and supermicrosurgical reconstruction. The developed tubes demonstrated favorable structural, mechanical, and biocompatible properties, making them a potential candidate for improving long-term outcomes in lymphedema surgical treatment. The next translational step would be trialing the obtained tubes in a microsurgical in-vivo model.

An injectable dental pulp-derived decellularized matrix hydrogel promotes dentin repair through modulation of macrophage response

Maintaining the viability of damaged pulp is critical in clinical dentistry. Pulp capping, by placing dental material over the exposed pulp, is a main approach to promote pulp-dentin healing and mineralized tissue formation. The dental materials are desired to impact on intricate physiological mechanisms in the healing process, including early regulation of inflammation, immunity, and cellular events. In this study, we developed an injectable dental pulp-derived decellularized matrix (DPM) hydrogel to modulate macrophage responses and promote dentin repair. The DPM derived from porcine dental pulp has high collagen retention and low DNA content. The DPM was solubilized by pepsin digestion (named p-DPM) and subsequently injected through a 25G needle to form hydrogel facilely at 37 °C. In vitro results demonstrated that the p-DPM induced the M2-polarization of macrophages and the migration, proliferation, and dentin differentiation of human dental pulp stem cells from deciduous teeth (SHEDs). In a mouse subcutaneous injection test, the p-DPM hydrogel was found to facilitate cell recruitment and M2 polarization during the early phase of implantation. Additionally, the acute pulp restoration in rat models proved that injectable p-DPM hydrogel as a pulp-capping agent had excellent efficacy in dentin regeneration. This study demonstrates that the DPM promotes dentin repair by modulating macrophage responses, and has a potential for pulp-capping applications in dental practice.

Unveiling intra-skeletal variability in mature and immature human skeletal remains via ATR-FTIR spectroscopy

Molecular characteristics of skeletal remains were studied utilizing ATR-FTIR spectroscopy, focusing on comparisons between mature adult and immature non-adult skeletal elements. To cover the intra-skeletal variability, different types of bones were analysed. The objective was to identify significant differences between various skeletal elements of adults and non-adults. Additionally, the correlation between observed differences and DNA preservation was investigated. Despite exposure to taphonomic factors, findings indicate minimal diagenetic changes or a well-balanced alteration in mineral and collagen within bones. The identified differences primarily reflect functional and structural differences among various skeletal elements. Significant differences between adults and non-adults, or lack of it, is attributed to different paths of bone maturation from childhood to adulthood. High DNA preservation in non-adult petrous bones was attributed to the interplay between DNA and carbonates, both occupying hydroxyl sites in the lattice. Conversely, lower DNA content in other bones, especially non-adult bones, was correlated with high relative concentrations of collagen, in which DNA is less stable and more prone to degradation. This study highlights the importance of skeletal variation (inter, intra, developmental stage) when assessing the preservation state of the remains and choosing samples for further analyses such as DNA. For the first time, differences between mature adult and immature non-adult bones are included.

COULD A DECELLULARIZATION PROTOCOL BE VALIDATED WITHOUT TALKING ABOUT HUMAN LEUKOCYTE ANTIGEN?

Decellularization techniques have advanced to reduce the risk of immune rejection in transplantation. Validation of these protocols typically relies on Crapo's criteria1, which include the absence of visible nuclei and low DNA content. In our study, five decellularization protocols were compared to determine the optimal approach for human fascia lata (HFL) samples. However, our findings raised questions as to why recipients can still develop immunity despite meeting validation criteria.HFL samples were decellularized using four protocols with SDS-Triton X100-DNase (D1 to D4-HFL) and one protocol using solvent-detergent-based baths (D5-HFL). The decellularized samples (D-HFL) were compared to native samples (N-HFL) using histology, and DNA content was measured. The human leukocyte antigen (HLA) content within the matrix was assessed using western blot analysis. Both D-HFL and N-HFL samples, along with negative control patches, were implanted in the backs of 28 Wistar rats. Anti-human IgG serum levels were evaluated after one month.H&E and Hoechst staining revealed the absence of residual cells in all decellularization protocols. DNA content was consistently below the critical threshold (p<0.05). All implanted D-HFL samples resulted in significantly lower anti-human IgG levels compared to N-HFL (p<0.01). However, 2.5 out of 4 rats developed immunity after being implanted with D1 to D4-HFL, with varying levels of anti-human IgG. Only rats implanted with D5-HFL showed undetectable levels of IgG and were considered non-immunized. Western blot analysis indicated that only D5-HFL had a residual HLA content below 1%.The literature on decellularization has primarily relied on Crapo's criteria, which do not consider the role of HLA mismatch in acute immune rejection. Our results suggest that a residual HLA content below 1% should also be considered to prevent immunization, even if other validation criteria are met. Further research is needed to evaluate the impact of residual HLA levels on human allotransplantation outcomes.

Biomolecular composition of porcine ovarian follicles following in vitro treatment of vitamin D3 and insulin alone or in combination

The study aimed to analyze changes in biomolecular composition of granulosa and theca interna cells of porcine ovarian follicles following in vitro treatment of vitamin D3 and insulin alone or in combination. Medium antral follicles (n = 4/each group) were cultured alone (C; control) or in the presence of 1α,25(OH)2D3 (VD; 100 ng/mL) and insulin (I; 10 ng/mL) separately or in combination, VD and I (VD+I). Then paraplast-embedded ovarian follicles were used for Fourier Transform Infrared (FTIR) spectroscopy and respective histological stainings. FTIR analysis revealed changes in the content of fibrous proteins (mainly collagens) within theca interna following vitamin D3 and insulin co-administration that was verified by Masson’s trichrome staining. Treatment-dependent differences were also observed in the secondary structure of proteins, indicating enhanced conversion to α-helices in response to vitamin D3 and insulin action/interaction in both follicular compartments. In the granulosa and theca interna layers, tendency to lower DNA content in the VD+I group was noted and confirmed by Fulgen’s staining. Finally, altered monosaccharides production in both follicular layers was found. Based on FTIR results, it is possible to attribute the observed alterations to biological processes that could be regulated by vitamin D3 and insulin in the porcine ovarian follicles.

Seasonality Is the Main Determinant of Microbial Diversity Associated to Snow/Ice around Concordia Station on the Antarctic Polar Plateau.

The French-Italian Concordia Research Station, situated on the Antarctic Polar Plateau at an elevation of 3233 m above sea level, offers a unique opportunity to study the presence and variation of microbes introduced by abiotic or biotic vectors and, consequently, appraise the amplitude of human impact in such a pristine environment. This research built upon a previous work, which explored microbial diversity in the surface snow surrounding the Concordia Research Station. While that study successfully characterized the bacterial assemblage, detecting fungal diversity was hampered by the low DNA content. To address this knowledge gap, in the present study, we optimized the sampling by increasing ice/snow collected to leverage the final DNA yield. The V4 variable region of the 16S rDNA and Internal Transcribed Spacer (ITS1) rDNA was used to evaluate bacterial and fungal diversity. From the sequencing, we obtained 3,352,661 and 4,433,595 reads clustered in 930 and 3182 amplicon sequence variants (ASVs) for fungi and bacteria, respectively. Amplicon sequencing revealed a predominance of Basidiomycota (49%) and Ascomycota (42%) in the fungal component; Bacteroidota (65.8%) is the main representative among the bacterial phyla. Basidiomycetes are almost exclusively represented by yeast-like fungi. Our findings provide the first comprehensive overview of both fungal and bacterial diversity in the Antarctic Polar Plateau's surface snow/ice near Concordia Station and to identify seasonality as the main driver of microbial diversity; we also detected the most sensitive microorganisms to these factors, which could serve as indicators of human impact in this pristine environment and aid in planetary protection for future exploration missions.

Evaluation of low-cost bone and teeth processing methods for automated DNA extraction

Bone and teeth can often be the only, or the best, biological materials available as DNA sources for the identification of decomposed or skeletal human remains. While these hard tissues are resistant to decay and therefore offer endogenous DNA a certain protection from the environment, their mineral matrices make DNA extraction challenging, a problem compounded by the low DNA content and high degradation levels usually associated with these tissues. To help release DNA from the mineral matrix, they are generally ground into a powder to increase their surface area to the extraction reagents. Furthermore, it is now common to perform a demineralization to dissolve the powder and release DNA that remains trapped. A common pulverization method consists of the use of a cryogenic grinder, which prevents heating of the sample and avoids subjecting the DNA to heat damage, but this equipment is costly. That said, little is known about the effect of lower-cost alternatives to the expensive cryogenic grinder on the quality and quantity of DNA recovered. Thus, this study aimed to evaluate inexpensive grinding methods for their potential for use in a forensic laboratory setting. The methods deemed to be viable options for this purpose were investigated to determine their effects on the quantity and quality of extracted DNA. Bone samples were also subjected to freezing prior to pulverization to assess the possibility that a lower sample temperature could limit heat damage to the DNA during processing. Pig bone and tooth powders were extracted using an original and a modified PrepFiler BTA™ Kit protocol, with the latter featuring an added demineralization step. Out of the methods explored, a coffee grinder and mortar and pestle were determined to be the most suitable for bone and teeth processing in a forensic laboratory setting. No significant differences between the two methods were found regarding the quantity and quality of DNA recovered and the rate of powder recovery, although more powder loss occurred when teeth were crushed with the mortar and pestle. Likewise, freezing samples before grinding did not have a significant impact on DNA quality and quantity. Finally, the original DNA extraction protocol performed significantly better than the modified one for the quantity of DNA recovered from both bone and teeth, while the quality was only superior for the bone.

Increased genome size is caused by heterochromatin addition in two non-related bat species, Hesperoptenus doriae and Philetor brachypterus (Vespertilionidae, Chiroptera, Mammalia).

The average genome size (GS) of bats, which are the only mammals capable of powered flight, is approximately 18% smaller than that of closely related mammalian orders. The low nuclear DNA content of Chiroptera is comparable to that of birds, which are also characterized by a high metabolic rate. Only a few chiropteran taxa possess notable amounts of constitutive heterochromatin. Here, we studied the karyotypes of two non-related vesper bat species with unusually high amounts of constitutive heterochromatin: Hesperoptenus doriae and Philetor brachypterus. Conventional staining methods and whole-chromosome painting with probes derived from Myotismyotis (2n = 44), showing a karyotype close to that of the presumed ancestor of Vespertilionidae, revealed Robertsonian fusions as the main type of rearrangement leading to the exceptionally reduced diploid chromosome number of 2n = 26 in both species. Moreover, both karyotypes are characterized by large blocks of pericentromeric heterochromatin composed of CMA-positive and DA-DAPI-positive segments. In H. doriae, the heterochromatin accumulation has resulted in a genome size of 3.22pg (1C), which is 40% greater than the mean genome size for the family. For P. brachypterus, a genome size of 2.94pg was determined, representing an increase of about 28%. Most notably, in H. doriae, the presence of additional constitutive heterochromatin correlates with an extended mitotic cell cycle duration in vitro. A reduction in diploid chromosome number to 30 or lower is discussed as a possible cause of the accumulation of pericentromeric heterochromatin in Vespertilionidae.

2023 TERMIS – AMERICAS Conference & Exhibition Boston Marriott Copley Place April 11–14, 2023

2023 TERMIS – AMERICAS Conference & Exhibition Boston Marriott Copley Place April 11–14, 2023

Nested PCR Approach for petB Gene Metabarcoding of Marine Synechococcus Populations.

The molecular diversity of marine picocyanobacterial populations, an important component of phytoplankton communities, is better characterized using high-resolution marker genes than the 16S rRNA gene as they have greater sequence divergence to differentiate between closely related picocyanobacteria groups. Although specific ribosomal primers have been developed, another general disadvantage of bacterial ribosome-based diversity analyses is the variable number of rRNA gene copies. To overcome these issues, the single-copy petB gene, encoding the cytochrome b6 subunit of the cytochrome b6f complex, has been used as a high-resolution marker gene to characterize Synechococcus diversity. We have designed new primers targeting the petB gene and proposed a nested PCR method (termed Ong_2022) for metabarcoding of marine Synechococcus populations obtained by flow cytometry cell sorting. We evaluated the specificity and sensitivity of Ong_2022 against the standard amplification protocol (termed Mazard_2012) using filtered seawater samples. The Ong_2022 approach was also tested on flow cytometry-sorted Synechococcus populations. Samples (filtered and sorted) were obtained in the Southwest Pacific Ocean, from subtropical (ST) and subantarctic (SA) water masses. The two PCR approaches using filtered samples recovered the same dominant subclades, Ia, Ib, IVa, and IVb, with small differences in relative abundance across the distinct samples. For example, subclade IVa was dominant in ST samples with the Mazard_2012 approach, while the same samples processed with Ong_2022 showed similar contributions of subclades IVa and Ib to the total community. The Ong_2022 approach generally captured a higher genetic diversity of Synechococcus subcluster 5.1 than the Mazard_2012 approach while having a lower proportion of incorrectly assigned amplicon sequence variants (ASVs). All flow cytometry-sorted Synechococcus samples could be amplified only by our nested approach. The taxonomic diversity obtained with our primers on both sample types was in agreement with the clade distribution observed by previous studies that applied other marker genes or PCR-free metagenomic approaches under similar environmental conditions. IMPORTANCE The petB gene has been proposed as a high-resolution marker gene to access the diversity of marine Synechococcus populations. A systematic metabarcoding approach based on the petB gene would improve the characterization/assessment of the Synechococcus community structure in marine planktonic ecosystems. We have designed and tested specific primers to be applied in a nested PCR protocol (Ong_2022) for metabarcoding the petB gene. The Ong_2022 protocol can be applied to samples with low DNA content, such as those obtained by flow cytometry cell sorting, allowing the simultaneous assessment of the genetic diversity of Synechococcus populations and cellular properties and activities (e.g., nutrient cell ratios or carbon uptake rates). Our approach will allow future studies using flow cytometry to investigate the link between ecological traits and taxonomic diversity of marine Synechococcus.

Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples

Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts.

Integrated Approach from Sample-to-Answer for Grapevine Varietal Identification on a Portable Graphene Sensor Chip.

Identifying grape varieties in wine, related products, and raw materials is of great interest for enology and to ensure its authenticity. However, these matrices' complexity and low DNA content make this analysis particularly challenging. Integrating DNA analysis with 2D materials, such as graphene, offers an advantageous pathway toward ultrasensitive DNA detection. Here, we show that monolayer graphene provides an optimal test bed for nucleic acid detection with single-base resolution. Graphene's ultrathinness creates a large surface area with quantum confinement in the perpendicular direction that, upon functionalization, provides multiple sites for DNA immobilization and efficient detection. Its highly conjugated electronic structure, high carrier mobility, zero-energy band gap with the associated gating effect, and chemical inertness explain graphene's superior performance. For the first time, we present a DNA-based analytic tool for grapevine varietal discrimination using an integrated portable biosensor based on a monolayer graphene field-effect transistor array. The system comprises a wafer-scale fabricated graphene chip operated under liquid gating and connected to a miniaturized electronic readout. The platform can distinguish closely related grapevine varieties, thanks to specific DNA probes immobilized on the sensor, demonstrating high specificity even for discriminating single-nucleotide polymorphisms, which is hard to achieve with a classical end-point polymerase chain reaction or quantitative polymerase chain reaction. The sensor was operated in ultralow DNA concentrations, with a dynamic range of 1 aM to 0.1 nM and an attomolar detection limit of ∼0.19 aM. The reported biosensor provides a promising way toward developing decentralized analytical tools for tracking wine authenticity at different points of the food value chain, enabling data transmission and contributing to the digitalization of the agro-food industry.

Comparative study of Rapid DNA versus conventional methods on compromised bones

Equivalent amounts of compromised bones were used to directly compare STR success of conventional and Rapid DNA methods. Conventional DNA extraction methods, including manual full demineralization and semi-automated PrepFiler BTA/ AutoMate Express (ThermoFisher Scientific), provided insights regarding the DNA quantity and extent of degradation of each compromised bone analyzed with ANDE 6C (ANDE Corp) and RapidHIT ID (ThermoFisher Scientific) Rapid systems. Full demineralization provided higher DNA yields than extraction with the AutoMate Express for quality control (QC) and environmentally challenged bones. The degradation indices ranged from ∼1.8 to 73. Both demineralization and AutoMate Express extracts benefited from additional clean-up with NucleoSpin XS devices, which usually resulted in more alleles being detected than without further clean-up. Complete “CODIS 20″ profiles could be obtained with bone QC1 with all methods. However, among the 14 compromised bones with low DNA content, complete CODIS 20 profiles were detected for 7, 4, and 0 bones analyzed with demineralization, AutoMate Express and ANDE methods, respectively. The RapidHIT ID was the least sensitive method, providing the fewest detectable alleles for the bones tested. Whereas extracted DNA of approximately 0.1 ng can yield complete GlobalFiler STR profiles, at least 30 ng was required for complete FlexPlex 27 profiles using the ANDE 6C Rapid DNA system. In addition to being less sensitive than conventional methods, the tested Rapid DNA approaches were less predictable when attempting to improve STR success and proved to be less reliable in genotyping accuracy.

Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies.

Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness. Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.

Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities

Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.

Analysis of decellularized mouse liver fragment and its recellularization with human endometrial mesenchymal cells as a candidate for clinical usage.

Decellularized tissue has been used as a natural extracellular matrix (ECM) or bioactive biomaterial for tissue engineering. The present study aims to compare and analyze different decellularization protocols for mouse liver fragments and cell seeding and attachment in the created scaffold using human endometrial mesenchymal cells (hEMCs).After collecting and dissecting the mouse liver into small fragments, they were decellularized by Triton X-100 and six concentrations of sodium dodecyl sulfate (SDS; 0.025, 0.05, 0.1, 0.25, 0.5, and 1%) at different exposure times. The morphology and DNA content of decellularized tissues were studied, and the group with better morphology and lower DNA content was selected for additional assessments. Masson's tri-chrome and periodic acid Schiff staining were performed to evaluate ECM materials. Raman confocal spectroscopy analysis was used to quantify the amount of collagen type I, III and IV, glycosaminoglycans and elastin. Scanning electron microscopy and MTT assay were applied to assess the ultrastructure and porosity and cytotoxicity of decellularized scaffolds, respectively. In the final step, hEMCs were seeded on the decellularized scaffold and cultured for one week, and finally the cell attachment and homing were studied morphologically.The treated group with 0.1% SDS for 24h showed a well preserved ECM morphology similar to native control and showing the minimum level of DNA. Raman spectroscopy results demonstrated that the amount of collagen type I and IV was not significantly changed in this group compared to the control, but a significant reduction in collagen III and elastin protein levels was seen (P < 0.001). The micrographs showed a porous ECM in decellularized sample similar to the native control with the range of 2.25µm to 7.86µm. After cell seeding, the infiltration and migration of cells in different areas of the scaffold were seen. In conclusion, this combined protocol for mouse liver decellularization is effective and its recellularization with hEMCs could be suitable for clinical applications in the future.