DNA Quantification Assays Research Articles

Developmental validation of a multiplex qPCR assay for simultaneous quantification of nuclear and mitochondrial DNA

Quantification of human DNA is key in forensic genetics. A more accurate estimate of the amount of DNA is essential for planning and optimising genotyping assays, as is evaluating the presence of PCR inhibitory substances and DNA degradation status. Multiplex qPCR assays are helpful in forensics because they can quantify different targets simultaneously, thus saving valuable samples, time, and labour. The aim of this study was to highlight the challenges in the developmental validation of a multiplex real-time PCR assay and the drawbacks encountered in translating a previously described and validated assay (SD quants) to a different technology by modifying the dye probes and reagent mix to be used in a different instrument. We developed a TaqMan probe-based multiplex qPCR using reagents and fluorescent probes adapted for the Rotor-Gene 6000 instrument (QIAGEN, Hilden, Germany). The initial assay combined two mitochondrial DNA (mtDNA) and two nuclear DNA (nDNA) targets, with amplification products of different sizes (mtDNA = 69 and 143bp; nDNA = 71 and 181bp), to estimate the DNA degradation status and an internal positive control (IPC) to detect potential inhibitors. During the initial testing of the assay, we observed an interaction between the 69bp mtDNA target and the 71bp nDNA target probe, and experiments were conducted to resolve this issue without success. We removed the small nDNA target (71bp) and changed from a 5-plex to a 4-plex qPCR assay (qMIND). The final tetraplex assay was tested on 105 forensic samples and/or small amounts of degraded DNA, such as bones, teeth, fingernails, formalin-fixed paraffin-embedded tissues (FFPE), and hair shaft samples. The quantification results were compared with data acquired from the same samples using another commercially available quantification system commonly used in forensic laboratories. In addition, the short tandem repeat (STR) profiles were investigated to determine their correlation with the quantitative values obtained. Overall, the qPCR assay was robust and reliable for DNA quantification in samples commonly used in forensic practice.

Comprehensive Study of Thiazole‐Orange‐Based DNA Dyes

AbstractThe rapid advancement of biotechnology over the recent decades has amplified the importance of DNA detection and quantification assays. Many of these assays, such as gel electrophoresis, microscopy, flow cytometry, and the detection of amplification in quantitative polymerase chain reaction (qPCR), rely on the use of DNA‐binding fluorescent dyes. This article presents a comprehensive study of six Thiazole‐Orange‐based fluorescent DNA‐binding dyes: SYBR Safe, SYBR Green, Pico Green, SYTO‐16, SYTO‐9, and the benzothiazole‐based analogue (TOPhBu) of the latter. The selected DNA markers were synthesized at a 10‐milligram scale and characterised spectroscopically to quantify their fluorescence enhancement upon binding to double‐stranded DNA. The ability of the dyes to detect DNA at low concentrations was evaluated using two new metrics, absolute fluorescence enhancement (AFE) and relative fluorescence enhancement (RFE). Quantum chemical calculations shed new light on the mechanism of their fluorogenicity through modelling the excited state behaviour and DNA binding of the dyes. Their analytical performance was further tested in qPCR experiments. The experimental results of this work highlight some important differences in the sensitivity and qPCR efficiency of the studied DNA‐binding dyes which will facilitate the DNA marker selection for analytical purposes and the future development of novel DNA sensors.

Biomimetic pulp scaffolds prepared from extracellular matrix derived from stem cells from human exfoliated deciduous teeth promote pulp-dentine complex regeneration.

To evaluate the role of biomimetic pulp scaffolds derived from the extracellular matrix derived of stem cells from human exfoliated deciduous teeth (SHED-ECM-PS) in promoting pulp-dentine complex regeneration. SHED-ECM-PS was prepared through cell aggregation and decellularization techniques. Histological and immunofluorescence analyses, scanning electron microscopy, and DNA quantification assays were used to characterize the SHED-ECM-PS. Additionally, a tooth slice implantation model was established to evaluate the effects of SHED-ECM-PS on regeneration of the pulp-dentine complex invivo. Extraction medium for SHED-ECM-PS was prepared, and its effect on bone marrow mesenchymal stem cells (BMMSCs) was assessed invitro. Cell counting kit-8 and Ki-67 staining assays were performed to determine cell proliferation. The rate of apoptosis was evaluated by flow cytometry. Wound healing and transwell assays were conducted to evaluate cell migration. Alizarin red S staining was performed to examine mineralized nodule formation. Western blotting was used to detect the expression of osteogenic and odontogenic markers. The results were analysed using an independent two-tailed Student's t-test. p < .05 was considered statistically significant. SHED-ECM-PS was successfully constructed, exhibiting a striped dental pulp-like shape devoid of nuclear structures or DNA components, and rich in fibronectin, collagen I, DMP1 and DSPP. Notably, SHED-ECM-PS showed no impact on the proliferation or apoptosis of BMMSCs. Histological analysis revealed that dental pulp fibroblasts formed an interwoven mesh in the root canal, and angiogenesis was observed in the SHED-ECM-PS group. Moreover, a continuous, newly formed tubular dentine layer with polarized odontoblast-like cells was observed along the inner wall of the root canal. SHED-ECM-PS promoted the migration, polar alignment and mineralized nodule formation of BMMSCs and specifically elevated the expression levels of odontogenic markers, but not osteogenic markers, compared with the control group invitro. SHED-ECM-PS exhibited no cytotoxicity and promoted pulp-dentine complex regeneration invivo as well as cell migration and odontogenic differentiation of BMMSCs invitro. These findings provide evidence that SHED-ECM-PS, as a novel biological scaffold, has the potential to improve the outcomes of REPs.

Evaluation of an automated real-time transcription-mediated amplification (TMA) assay for detection and quantification of cytomegalovirus DNA in different clinical specimens

BackgroundReliable and fast detection and quantification of human cytomegalovirus (CMV) DNA in various diagnostic specimens is essential for care of immunocompromised or congenitally infected individuals. ObjectivesTo evaluate the analytical and clinical performance of the Panther Aptima® CMV (Hologic) quantitative real-time transcription mediated amplification (TMA) assay. Study designPerformance of the TMA assay run on the Hologic Panther Fusion was analysed for 32 proficiency testing samples and 21 quantitative reproducibility panel samples; additionally, we compared results of TMA assay and routine quantitative real-time PCR assays ("PCR-A"= Biomérieux CMV R-gene® or "PCR-B"= Laboratory-developed CMV-PCR) in 518 diagnostic specimens (254 plasma, 120 EDTA whole blood, 43 urine, 45 amniotic fluid and 56 breast milk) at two university hospital laboratories. ResultsAll proficiency panel samples were correctly identified and quantified by the TMA assay; replicate testing of the reproducibility panel samples showed good reproducibility within and between the two laboratories. Sensitivity in plasma and WB was higher for the TMA assay detecting low-level CMV-DNAemia in samples tested negative by routine PCR. Quantitative CMV-DNAemia values correlated well between TMA and real-time PCR. Similarly, urine, AF and BM specimens showed a high rate of concordant results (91%, 98% and 98%, respectively) among TMA and PCR with good correlation of quantitative values. ConclusionThe performance of the Aptima® CMV TMA assay for viral blood load testing compared well to established real-time PCRs. In addition, it can be useful for diagnostics in urine, amniotic fluid and breast milk specimens.

Human neutrophil extracellular traps do not impair in vitro Toxoplasma gondii infection.

Toxoplasma gondii, responsible for causing toxoplasmosis, is a prevalent food and waterborne pathogen worldwide. It commonly infects warm-blooded animals and affects more than a third of the global human population. Once ingested, the parasite enters the host's small intestine and rapidly disseminates throughout the body via the bloodstream, infiltrating various tissues. Leukocyte-driven responses are vital against T. gondii, with neutrophils playing a dual role: swiftly recruited to infection sites, releasing inflammatory mediators, and serving as a replication hub and Trojan horses, aiding parasite spread. Neutrophils from various hosts release extracellular traps (NETs) against the protozoan. However, gaps persist regarding the mechanisms of NETs production to parasite and their significance in infection control. This study investigates the interplay between human neutrophils and T. gondii, exploring dynamics, key molecules, and signaling pathways involved in NETs production upon protozoan challenge. Using confocal and electron microscopy, live cell imaging, pharmacological inhibitors, and DNA quantification assays, we find that human neutrophils promptly release both classical and rapid NETs upon pathogen stimulation. The NETs structure exhibits diverse phenotypes over time and is consistently associated with microorganisms. Mechanisms involve neutrophil elastase and peptidylarginine deiminase, along with intracellular calcium signaling and the PI3K pathway. Unexpectedly, human traps do not diminish viability or infectivity, but potentially aid in capturing parasites for subsequent neutrophil phagocytosis and elimination. By revealing NETs formation mechanisms and their nuanced impact on T. gondii infection dynamics, our findings contribute to broader insights into host-pathogen relationships.

Cell cycle status of male and female gametes during Arabidopsis reproduction.

Fertilization in Arabidopsis (Arabidopsis thaliana) is a highly coordinated process that begins with a pollen tube delivering the 2 sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization remains elusive as DNA quantification and DNA replication assays have given conflicting results. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all phases of the cell cycle. We show that male and female Arabidopsis gametes are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.

Evaluation of miRNA Expression in 3D In Vitro Scaffold-Based Cancer Models.

Accumulating experimental evidence suggests that 3D in vitro cancer models strengthen our understanding of vital processes in the tumor microenvironment (TME) and accelerate the drug discovery pipeline. Previous studies examining the effects of specific miRNAs on cancer cells in vitro have involved ectopic expression of miRNA mimics in 2D in vitro culture. Assessment of cell viability and gene expression ensures that upregulation of the chosen miRNA and repression of its target genes have been achieved. However, this 2D culture is overly simplified and lacks the complex cell to extracellular matrix (ECM) interactions observed in the native TME, yielding results often not reproduced when progressed to in vivo studies. Hence, this chapter describes a novel method of overexpressing the miRNA mimic in cells cultured on 3D collagen-based scaffolds adapted from tissue engineering techniques. Cell growth on scaffolds is sequentially monitored via a DNA quantification assay, and overexpression of the miRNA mimic and repression of its target gene is assessed via reverse transcription quantitative PCR (RT-qPCR).

Preparation of hybrid meniscal constructs using hydrogels and acellular matrices

To search for a suitable meniscus repair material, acellular hybrid scaffolds consisting of in situ cross-linkable 3-D interpenetrating network structures were obtained by decellularization of the meniscus tissues followed by integration of the gel system. Decellularization efficiency was confirmed using a DNA quantification assay (82% decrease in DNA content) and histological stainings. In the second part of the study, the gelatin molecule was functionalized by adding methacrylic anhydride and the degree of functionalization was found to be 75% by (Proton-Nuclear Magnetic Resonance) 1H-NMR. Using this, a series of hybrid constructs named GelMA-Hybrid (G-Hybrid), GELMA/PEGDMA-Hybrid (PG-Hybrid), and GelMA/PEGDMA/HAMA-Hybrid (PGH-Hybrid) were prepared by cross-linking with UVA. Changes in the chemical structure were determined with Fourier Transform Infrared Spectrophotometer (FTIR). Water uptake capacities of cross-linked hybrid structures were measured in swelling studies, and it was found that hybrid scaffolds showed similar swelling properties compared to native counterparts. By compressive mechanical tests, enhanced mechanical properties were revealed in cross-linked scaffolds with PGH-Hybrid having the highest cross-link density. Protein denaturation and decomposition transition temperatures were improved by adding hydrogels to acellular scaffolds according to thermal gravimetric analyses (TGA). Cross-linked acellular scaffolds have exhibited a behavior close to native tissues with below 25% mass loss in phosphate buffer saline (PBS) and enzymatic solution. Cell viability was examined through Alamar Blue on the first day and cell viability in hybrid constructs was found to be above 80% while it was closer to the control group on the 7th day. It was concluded that the developed biomaterials could be used in meniscus tissue engineering with their tunable physicochemical and mechanical properties.

Evaluation of Hepatitis B viral Serological Patterns and HBV DNA levels in Hepatitis B subjects at Nauth Nnewi, Southeastern Nigeria

Nigeria is one of the countries with the highest incidence of Hepatitis B Virus (HBV) infection worldwide. The inaccessibility and unaffordability of HBV DNA quantification (viral load) assay which is the key laboratory test for therapy initiation, and monitoring is a challenge to HBV management. This study aimed at evaluating the HBV DNA viral load differences across the serological markers of HBV in order to develop a more cost-effective diagnostic algorithm for Hepatitis B management. Cross sectional study design was used with a total of 264 subjects comprising of 88 HBsAg seropositive treatment naïve subjects, 88 HBsAg seropositive subjects on antiviral therapy as case subjects and 88 age-matched apparently healthy HBsAg seronegative individuals were recruited as control subjects. Hepatitis B Virus DNA assay was performed using real time PCR technique, Hepatitis B core Antibody Immunoglobulin M and Hepatitis D Virus Immunoglobulin G assay. Immunochromatography was used for HBV Panel, Hepatitis C Virus assay and Human Immunodeficiency Virus testing. The non-treatment group has higher viral load (M=805.50 IU/ml) compared with treatment group (M = 65.50 IU/ml) (p&lt;0.001). There was a significant difference in the HBV DNA levels of the four serological patterns observed in the study (P&lt; 0.001). Among the four serological patterns observed, the second pattern with positive surface antibody, positive envelope antigen and negative envelope antibody showed highest viral load (M= 46850189.50 IU/ml) followed by the third pattern with negative surface antibody, negative envelope antigen, and negative envelope antibody (M=46555 IU/ml). The first pattern which has negative surface antibody, negative envelope antigen and positive envelope antibody has the lowest viral load (M=21.00 IU/ml) followed by the fourth pattern with positive surface antibody, negative envelope antigen and positive envelope antibody (M=493.00 IU/ml). This study showed that HBV serological markers can predict viral load and should be used as its alternative in resource poor settings.

The development of a 3D printable chitosan-based copolymer with tunable properties for dentoalveolar regeneration

Dentoalveolar tissue engineering is an emerging yet challenging field, considering the lack of suitable materials and difficulty to produce patient-specific hydrogel scaffolds. The present paper aims to produce a 3D printable and tuneable biomaterial by copolymerizing a synthesized water-soluble chitosan derivative called maleic anhydride grafted chitosan (MA-C) with gelatin using genipin, a natural crosslinking agent. Development and testing of this material for 3D printing, degradation, and swelling demonstrated the ability to fabricate scaffolds with controlled physical properties based on pre-determined designs. The MA-C-gelatin copolymer demonstrated excellent biocompatibility, which was verified by analyzing the viability, growth and proliferation of human dental pulp stem cells seeded on MA-C-gelatin constructs through live/dead, alamar blue and DNA quantification assays. Based on the present findings, the proposed material might be a suitable candidate for dentoalveolar tissue engineering, while further research is required to achieve this goal.

Nanohydroxyapatite-Protein Interface in Composite Sintered Scaffold Influences Bone Regeneration in Rabbit Ulnar Segmental Defect

The healing physiology of bone repair and remodeling that occurs after normal fracture is well orchestrated. However, it fails in complex clinical conditions and hence requires augmentation by grafts. In this study, composite nanohydroxyapatite (nHA), poly(hydroxybutyrate) (PHB) and poly(ɛ-caprolactone) (PCL) constituted microspheres sintered three-dimensional scaffold were evaluated in rabbit ulnar segmental defect. A composite scaffold using PHB-PCL-nHA microspheres was developed with protein interface by solvent/non-solvent sintering to provide multiple cues such as biocomposition, cancellous bone equivalent meso-micro multi-scale porosity, and compressive strength. In vitro DNA quantification and alkaline phosphatase (ALP) assays revealed that the protein interfaced composite scaffolds supported osteoblast proliferation and mineralization significantly higher than scaffolds without protein and TCPS (p < 0.05). Scanning electron micrographs of osteoblasts cultured scaffolds demonstrated cell-matrix interaction, cell spreading, colonization and filopodial extension across the porous voids. Cylindrical scaffolds (5 × 10 mm) were implanted following segmental defect (10 mm) in rabbit ulnar bone and compared with untreated control. Radiography (4, 8 and 12 weeks) and µ-computed tomography (12 weeks) analysis showed directional bone tissue formation by bridging defective site in both scaffolds with and without protein interface. Whereas, undesired sclerotic-like tissue formation was observed in control groups from 8 weeks. Histology by hot Stevenel’s blue and van Gieson’s picrofuchsin staining has confirmed enhanced bone maturation in scaffold groups while presence of osteoids was observed in control after 12 weeks. Thus, the developed composite matrices exhibits osteoinductive, osteoconductive properties and demonstrates its bone regenerative potential owing to its compositional, micro & macro structural and mechanical properties.Graphical abstract

Development of a Droplet Digital™ PCR DNA methylation detection and quantification assay of prenatal tobacco exposure.

DNA methylation is a labile modification associated with gene expression control and environmental adaptations. High throughput, scalable and quantitative assessments of specific DNA methylation modifications in complex genomic regions for use in large population studies are needed. The performance of Droplet Digital™ PCR (ddPCR™) was investigatedfor DNA methylation detection against next-generation bisulfite sequencing (NGS) to demonstrate the ability of ddPCRto detect and validate DNA methylation levels and complex patterns among neighboring CpGs in regions associated with prenatal tobacco exposure. While both techniques are reproducible, ddPCRdemonstrates a unique advantage for high-throughput DNA methylation analysis in large-scale population studies and provides the specificity to accurately measure DNA methylation of target CpGs in complex regions.

External quality assessment of HIV-1 DNA quantification assays used in the clinical setting in Italy

Total cell-associated HIV-1 DNA is a surrogate marker of the HIV-1 reservoir, however, certified systems for its quantification are not available. The Italian HIV DNA Network was launched to validate HIV-1 DNA quantification methods in use at University and Hospital labs. A quality control panel including HIV-1 DNA standards, reconstructed blood samples (RBSs) and DNA from different HIV-1 subtypes was blindly tested by 12 participating labs by quantitative real-time PCR (n = 6), droplet digital PCR (n = 3) or both (n = 3). The median 95% hit rate was 4.6 (3.7–5.5) copies per test and linearity in the tested range was excellent (R2 = 1.000 [1.000–1.000]). The median values obtained across labs were 3,370 (2,287–4,245), 445 (299–498), 59 (40–81) and 7 (6–11) HIV-1 DNA copies, for the 3,584, 448, 56 and 7-copy standards, respectively. With RBSs, measured values were within twofold with respect to the median in two thirds of cases. HIV-1 subtypes were missed (CRF01_AE by 3 labs) or underestimated by > 1 log (subtypes A, C, D, F by one lab; CRF01_AE by one lab; CRF02_AG by one lab). The overall performance was excellent with HIV-1 DNA standards, however detection of different HIV-1 subtypes must be improved.

Thiolene- and Polycaprolactone Methacrylate-Based Polymerized High Internal Phase Emulsion (PolyHIPE) Scaffolds for Tissue Engineering.

Highly porous emulsion templated polymers (PolyHIPEs) provide a number of potential advantages in the fabrication of scaffolds for tissue engineering and regenerative medicine. Porosity enables cell ingrowth and nutrient diffusion within, as well as waste removal from, the scaffold. The properties offered by emulsion templating alone include the provision of high interconnected porosity, and, in combination with additive manufacturing, the opportunity to introduce controlled multiscale porosity to complex or custom structures. However, the majority of monomer systems reported for PolyHIPE preparation are unsuitable for clinical applications as they are nondegradable. Thiol-ene chemistry is a promising route to produce biodegradable photocurable PolyHIPEs for the fabrication of scaffolds using conventional or additive manufacturing methods; however, relatively little research has been reported on this approach. This study reports the groundwork to fabricate thiol- and polycaprolactone (PCL)-based PolyHIPE materials via a photoinitiated thiolene click reaction. Two different formulations, either three-arm PCL methacrylate (3PCLMA) or four-arm PCL methacrylate (4PCLMA) moieties, were used in the PolyHIPE formulation. Biocompatibility of the PolyHIPEs was investigated using human dermal fibroblasts (HDFs) and human osteosarcoma cell line (MG-63) by DNA quantification assay, and developed PolyHIPEs were shown to be capable of supporting cell attachment and viability.

Enhanced osteoinductive capacity of poly(lactic-co-glycolic) acid and biphasic ceramic scaffolds by embedding simvastatin.

This study evaluated the effect of embedding simvastatin (SIM) on the osteoinductive capacity of PLGA + HA/βTCP scaffolds in stem cells from human exfoliated deciduous teeth (SHED). Scaffolds were produced by PLGA solvent dissolution, addition of HA/βTCP, solvent evaporation, and leaching of sucrose particles to impart porosity. Biphasic ceramic particles (70% HA/30% βTCP) were added to the PLGA in a 1:1 (w:w) ratio. Scaffolds with SIM received 1% (w:w) of this medication. Scaffolds were synthesized in a disc-shape and sterilized by ethylene oxide. The experimental groups were (G1) PLGA + HA/βTCP and (G2) PLGA + HA/βTCP + SIM in non-osteogenic culture medium, while (G3) SHED and (G4) MC3T3-E1 in osteogenic culture medium were the positive control groups. The release profile of SIM from scaffolds was evaluated. DNA quantification assay, alkaline phosphatase activity, osteocalcin and osteonectin proteins, extracellular calcium detection, von Kossa staining, and X-ray microtomography were performed to assess the capacity of scaffolds to induce the osteogenic differentiation of SHED. The release profile of SIM followed a non-liner sustained-release rate, reaching about 40% of drug release at day 28. Additionally, G2 promoted the highest osteogenic differentiation of SHED, even when compared to the positive control groups. In summary, the osteoinductive capacity of poly(lactic-co-glycolic) acid and biphasic ceramic scaffolds was expressively enhanced by embedding simvastatin. Bone regeneration is still a limiting factor in the success of several approaches to oral and maxillofacial surgeries, though tissue engineering using mesenchymal stem cells, scaffolds, and osteoinductive mediators might collaborate to this topic.

Tissue Engineering the Pinna: Comparison and Characterization of Human Decellularized Auricular Biological Scaffolds.

Decellularization is one of the promising techniques in tissue engineering used to create a biological scaffold for subsequent repopulation with the patient’s own cells. This study aims to compare two different decellularization protocols to optimize the process of auricle decellularization by assessing and characterizing the decellularization effects on human auricular cartilage. Herein, 12 pairs (8 females, 4 males) of freshly frozen adult human cadaveric auricles were de-epithelialized and defatted leaving only the cartilaginous framework. An auricle from each pair was randomly assigned to either protocol A (latrunculin B-based decellularization) or protocol B (trypsin-based decellularization). Gross examination of the generated scaffolds demonstrated preservation of the auricles’ contours and a change in color from pinkish-white to yellowish-white. Hematoxylin and eosin staining demonstrated empty cartilaginous lacunae in both study groups, which confirms the depletion of cells. However, there was greater preservation of the extracellular matrix in auricles decellularized with protocol A as compared to protocol B. Comparing protocol A to protocol B, Masson’s trichrome and Safranin-O stains also demonstrated noticeable preservation of collagen and proteoglycans, respectively. Additionally, scanning electron micrographs demonstrated preservation of the cartilaginous microtopography in both study groups. Biomechanical testing demonstrated a substantial decrease in Young’s modulus after decellularization using protocol B (1.3 MPa), albeit not significant (P-value > 0.05) when compared to Young’s modulus prior to decellularization (2.6 MPa) or after decellularization with protocol A (2.7 MPa). A DNA quantification assay demonstrated a significant drop (P-value < 0.05) in the DNA content after decellularization with protocol A (111.0 ng/mg) and protocol B (127.6 ng/mg) in comparison to before decellularization (865.3 ng/mg). Overall, this study demonstrated effective decellularization of human auricular cartilage, and it is concluded that protocol A provided greater preservation of the extracellular matrix and biomechanical characteristics. These findings warrant proceeding with the assessment of inflammation and cell migration in a decellularized scaffold using an animal model.

Decellularization of kidney tissue: comparison of sodium lauryl ether sulfate and sodium dodecyl sulfate for allotransplantation in rat.

An automatic decellularization device was developed to perfuse and decellularize male rats' kidneys using both sodium lauryl ether sulfate (SLES) and sodium dodecyl sulfate (SDS) and to compare their efficacy in kidney decellularization and post-transplantation angiogenesis. Kidneys were perfused with either 1% SDS solution for 4h or 1% SLES solution for 6h. The decellularized scaffolds were stained with hematoxylin and eosin, periodic acid Schiff, Masson's trichrome, and Alcian blue to determine cell removal and glycogen, collagen, and glycosaminoglycan contents, respectively. Moreover, scanning electron microscopy was performed to evaluate the cell removal and preservation of microarchitecture of both SDS and SLES scaffolds. Additionally, DNA quantification assay was applied for all groups in order to measure residual DNA in the scaffolds and normal kidney. In order to demonstrate biocompatibility of the decellularized scaffolds, human umbilical cord mesenchymal stromal/stem cells (hUC-MSCs) were seeded on the scaffolds. In addition, the allotransplantation was performed in back muscle and angiogenesis was evaluated. Complete cell removal in both SLES and SDS groups was observed in scanning electron microscopy and DNA quantification assays. Moreover, the extracellular matrix (ECM) architecture of rat kidney in the SLES group was significantly preserved better than the SDS group. The hUC-MSCs were successfully migrated from the cell culture plate surface into the SDS and SLES decellularized scaffolds. The formation of blood vessels was observed in the kidney in both SLES and SDS decellularized kidneys. The better preservation of ECM than SDS introduces SLES as the solvent of choice for kidney decellularization.

Verification of performance of a direct fluorescent assay for cell-free DNA quantification, stability according to pre-analytical storage conditions, and the effect of freeze-thawing.

A simple fluorescence-based cell-free DNA (CFD) assay has been previously developed that can directly measure nucleic acids without prior DNA extraction and amplification. However, studies on fluorescence-based CFD are lacking. In particular, there is no known information regarding the stability with regard to pre-analytical storage conditions in relation to time and temperature, or on the influence of freeze-thawing. Plasma was directly assayed to measure CFD using PicoGreen™ reagent. Standard linearity and accuracy were confirmed using salmon sperm DNA. Whole blood was left at room temperature (RT) and at 4˚C, and then plasma was separated. The CFD was also measured using thawed plasma after 1 week of freezing. As a correlation with a sperm DNA concentration, CFD demonstrated linearity over a wide range of concentrations, with a 0.998 correlation coefficient. The CFD level showed a change of up to 2.5 µg/ml according to pre-analytical storage time, and the changes were not consistent over time. The CFD values at RT after 1 h were similar to the baseline values, and the relative standard deviation was lowest under this condition. The CFD values between 4˚C and RT were similar over all time periods assessed. After freeze-thawing, the change in CFD value was reduced compared to that before freezing. The present study showed that CFD measurements using plasma processed within 1 h were optimal. Additionally, the effects of substantial changes according to storage conditions were reduced after freeze-thawing, and thus studies using stored samples is viable and relevant.

Discovery of Novel Pyrimidine-Based Capsid Assembly Modulators as Potent Anti-HBV Agents.

Core assembly modulators of viral capsid proteins have been developed as an effective treatment of chronic hepatitis B virus (HBV) infection. In this study, we synthesized novel potent pyrimidine derivatives as core assembly modulators, and their antiviral effects were evaluated in in vitro and in vivo biological experiments. One of the synthesized derivatives, compound 23h (R1 = MeSO2, R2 = 1-piperidin-4-amine, R3 = 3-Cl-4-F-aniline) displayed potent inhibitory effects in the in vitro assays (52% inhibition in the protein-based assay at 100 nM and an IC50 value of 181 nM in the serum HBV DNA quantification assay). Moreover, treatment with compound 23h for 5 weeks significantly decreased serum levels of HBV DNA levels (3.35 log reduction) in a human liver-chimeric uPA/SCID mouse model, and these effects were significantly increased when 23h was combined with tenofovir, a nucleotide analogue inhibitor of reverse transcriptase used for the treatment of HBV infection.

Pore geometry influences growth and cell adhesion of infrapatellar mesenchymal stem cells in biofabricated 3D thermoplastic scaffolds useful for cartilage tissue engineering

The most pressing need in cartilage tissue engineering (CTE) is the creation of a biomaterial capable to tailor the complex extracellular matrix of the tissue. Despite the standardized used of polycaprolactone (PCL) for osteochondral scaffolds, the pronounced stiffness mismatch between PCL scaffold and the tissue it replaces remarks the biomechanical incompatibility as main limitation. To overcome it, the present work was focused in the design and analysis of several geometries and pore sizes and how they affect cell adhesion and proliferation of infrapatellar fat pad-derived mesenchymal stem cells (IPFP-MSCs) loaded in biofabricated 3D thermoplastic scaffolds. A novel biomaterial for CTE, the 1,4-butanediol thermoplastic polyurethane (b-TPUe) together PCL were studied to compare their mechanical properties. Three different geometrical patterns were included: hexagonal (H), square (S), and, triangular (T); each one was printed with three different pore sizes (PS): 1, 1.5 and 2 mm. Results showed differences in cell adhesion, cell proliferation and mechanical properties depending on the geometry, porosity and type of biomaterial used. Finally, the microstructure of the two optimal geometries (T1.5 and T2) was deeply analyzed using multiaxial mechanical tests, with and without perimeters, μCT for microstructure analysis, DNA quantification and degradation assays. In conclusion, our results evidenced that IPFP-MSCs-loaded b-TPUe scaffolds had higher similarity with cartilage mechanics and T1.5 was the best adapted morphology for CTE.