Abstract:This study was to develop anovel and efficient method using endonuclease (benzonase) to preparedecellularized lamellar porcine corneal stroma (DLPCS). The DLPCS was preparedfrom native lamellar porcine corneal stroma (NLPCS) and was treated with 1000 U/ml benzonase for 5hours. We conducted the following measurements and animal transplantation tocompare DLPCS and NLPCS. The residual DNA was decreased significantly from 367.13 ± 19.96 ng/mg to 15.41 ± 0.65 ng/mg after treatment of benzonase by the detection of f… Show more
“…Benzonase endonuclease is often used as the main decellularizing agent in a detergent-free approach, based on its ability to quickly infiltrate the corneal stroma, combined with its easy removal by repeated washes. This approach minimizes the destruction of the ECM, with minimal loss of optical transparency and proper results in animal transplantation assays [186].…”
The extracellular matrix (ECM) is a complex network with multiple functions, including specific functions during tissue regeneration. Precisely, the properties of the ECM have been thoroughly used in tissue engineering and regenerative medicine research, aiming to restore the function of damaged or dysfunctional tissues. Tissue decellularization is gaining momentum as a technique to obtain potentially implantable decellularized extracellular matrix (dECM) with well-preserved key components. Interestingly, the tissue-specific dECM is becoming a feasible option to carry out regenerative medicine research, with multiple advantages compared to other approaches. This review provides an overview of the most common methods used to obtain the dECM and summarizes the strategies adopted to decellularize specific tissues, aiming to provide a helpful guide for future research development.
“…Benzonase endonuclease is often used as the main decellularizing agent in a detergent-free approach, based on its ability to quickly infiltrate the corneal stroma, combined with its easy removal by repeated washes. This approach minimizes the destruction of the ECM, with minimal loss of optical transparency and proper results in animal transplantation assays [186].…”
The extracellular matrix (ECM) is a complex network with multiple functions, including specific functions during tissue regeneration. Precisely, the properties of the ECM have been thoroughly used in tissue engineering and regenerative medicine research, aiming to restore the function of damaged or dysfunctional tissues. Tissue decellularization is gaining momentum as a technique to obtain potentially implantable decellularized extracellular matrix (dECM) with well-preserved key components. Interestingly, the tissue-specific dECM is becoming a feasible option to carry out regenerative medicine research, with multiple advantages compared to other approaches. This review provides an overview of the most common methods used to obtain the dECM and summarizes the strategies adopted to decellularize specific tissues, aiming to provide a helpful guide for future research development.
“… 39 Benzonase, while also unable to act as a principal decellularizing agent, is compatible for use with several detergent-free decellularization protocols. 173 – 175 DNase can be used as a replacement for TNBP, which similarly works to reduce negative impacts caused by chemical agents, as DNase achieves similar results with shorter protocols and higher mechanical stability and GAG content. 39 ECM treated with DNase or RNase must be put through numerous rinse cycles, as they are immunogenic compounds that can hinder recellularization attempts.…”
Decellularization of natural tissues to produce extracellular matrix is a promising method for three-dimensional scaffolding and for understanding microenvironment of the tissue of interest. Due to the lack of a universal standard protocol for tissue decellularization, recent investigations seek to develop novel methods for whole or partial organ decellularization capable of supporting cell differentiation and implantation towards appropriate tissue regeneration. This review provides a comprehensive and updated perspective on the most recent advances in decellularization strategies for a variety of organs and tissues, highlighting techniques of chemical, physical, biological, enzymatic, or combinative-based methods to remove cellular contents from tissues. In addition, the review presents modernized approaches for improving standard decellularization protocols for numerous organ types.
“…Benzonase breaks down both ssDNA, dsDNA, RNA and DNA:RNA hybrids, while DNase targets primarily dsDNA with reduced specificity for ssDNA and DNA:RNA hybrids. Benzonase is thus an ideal candidate for extracellular DNA depletion that may provide a more efficient solution than the more frequently used DNase (Sutton et al ., 1997; Liu et al ., 2019; Amar et al ., 2021).…”
Section: Introductionmentioning
confidence: 99%
“…This is congruent with previous studies where the application of a saline wash or treatment with the MolYsis kit (Molzym, Germany), reduced contaminating DNA(Votintseva et al, 2015;Votintseva et al, 2017).The benzonase treatment protocol demonstrated a significant enrichment effect. We initially hypothesized that benzonase was superior to a simple wash or DNase treatment because it more effectively removes extracellular contaminating ssDNA in addition to dsDNA, RNA and DNA:RNA hybrids, while DNase targets only dsDNA(Sutton et al, 1997;Liu et al, 2019;Amar et al, 2021). However, there was only a small difference in total DNA by the Qubit ssDNA between the DNase and benzonase treated samples (0,55 ± 0,302 ng/µl and 0,51 ± 0,213 ng/µl respectively), arguing that more effective ssDNA degradation is not the only reason for the benzonase effect.…”
Background: Whole Genome Sequencing (WGS) can detect within-host Mycobacterium tuberculosis (Mtb) genetic diversity, resulting from either mixed infection or within host microevolution of a single infecting strain. Within-host diversity may signal impending resistance or treatment failure and is best captured through sequencing directly from sputum. Here we sought to compare three sample preprocessing steps that aim to remove contaminating non-Mtb DNA and yield of a new custom target enrichment protocol for optimal WGS from direct patient samples. Design/Methods: Mtb positive NALC - NaOH decontaminated patient sputum sediments were pooled, and heat inactivated. The pooled sample was split in replicates, pelleted, and then washed with Tris-EDTA buffer, and treated by either an additional wash, DNase I or Benzonase digestion, to remove contaminating extracellular DNA. Levels of contaminating host DNA and target Mtb DNA was assessed by Quantitative PCR (qPCR), followed by WGS with and without custom target enrichment. Results: Quantitative PCR results initially indicated a high host to target ratio (6 168 +/- 1 638 host copies/ng to 212,3 +/- 59,4 Mtb copies/ng) which decreased in response to an additional wash and both nuclease treatment procedures. The benzonase treated group demonstrated a 100-fold significant enrichment of Mtb DNA (3 422 +/- 2 162 host copies/ng to 11 721 +/- 7 096 Mtb copies/ng) when compared to the control. We assessed the performance of novel Twist DNA probe panel for the enrichment of Mtb from direct sputum sediment samples, by applying it to a H37Rv limit of detection as well as direct sputum sediments. The Twist kit managed to successfully prepare enriched libraries from as little as 0,000 452 ng of Mtb DNA (equivalent to a 100 genome copies). Applied to direct sputum sediments and comparing the benzonase treated sputum to a directly sequenced counterpart, revealed that the target enrichment panel increased the percent of sequencing reads mapping to the Mtb reference from 1,18 % to 90,95%. Conclusion: Current results indicate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction has a positive effect on enrichment of Mtb DNA in decontaminated sediments but is not adequate to allow sequencing without target capture. Additionally, the study also highlights the first application of a novel cost competitive DNA probe panel for target capture and enrichment of Mtb from direct sputum specimens.
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