Quantitative DNA Analysis Research Articles

Impact of bariatric surgery on gut microbiota composition in obese patients compared to healthy controls

Bariatric surgery is vital for sustainable weight loss and metabolic improvement in obese individuals, but its effects on gut microbiota and their role in these benefits require further investigation. Investigate the temporal changes in gut microbiota in obese patients undergoing bariatric surgery (gastric sleeve gastrectomy or Roux-en-Y Gastric Bypass (RYGB)) compared to healthy controls, aiming to understand their role in weight loss and metabolic health improvement. A case-control study included 30 obese patients aged 65–95 undergoing bariatric surgery, and 18 matched healthy controls. Selection criteria were based on age, race, BMI, history of antibiotics, probiotics, and prebiotics usage. Stool samples were collected at baseline, three months, and six months post-surgery for DNA extraction and quantitative real-time PCR analysis to assess gut microbiota changes. Physical activity and dietary intake were evaluated using standardized questionnaires. Statistical analyses were performed using R. Post-surgery, patients showed significant reductions in weight and BMI, with changes in dietary habits and physical activity. Quantitative real-time PCR analysis revealed substantial alterations in bacterial groups such as Bacteroides and Fusobacterium. However, some groups showed no significant changes, indicating a complex interaction between gut microbiota and bariatric surgery. Notable correlations were found between body weight, BMI, and specific bacterial groups like the C. cluster IV and Lactobacillus, particularly in RYGB patients. Bariatric surgery significantly alters gut microbiota, aiding weight loss and metabolic regulation in obese patients. Understanding these changes is crucial for developing effective obesity management strategies, requiring further research to optimize outcomes.

Dammed coastal waterways are less diverse, more homogenous, and dominated by non-native species: Comprehensive insights from quantitative analysis of environmental DNA

Small dams are commonplace worldwide and impact local and regional aquatic diversity by altering habitats and disrupting dispersal networks. Quantifying the local and regional impacts of dams requires nearly comprehensive species occurrence data. We used environmental DNA (eDNA) metabarcoding to test theoretical predictions about the impacts of dams on local and regional bony fish diversity within the Chesapeake Bay Watershed, USA. We analyzed eDNA from 465 sampling points within 34 waterbodies documenting the distributions of 61 species. On average, dammed waterbodies had approximately half (48 %) as many species per site as undammed (lower alpha diversity) and more homogenous species composition (lower beta diversity). Native migratory species were less than one tenth (0.08) as likely to be detected at dammed sites than undammed sites, native resident (non-migratory) species were one third (0.34) as likely, whereas introduced species were 2.6 times more likely to be detected. Our sampling and bioinformatics methods were validated by a diverse mock community control. Our results suggest that dams in coastal waterways homogenize fish metacommunities, reduce local biodiversity through dispersal limitation and habitat alteration, and favor the dominance of lentic-adapted introduced species while potentially restricting the spread of introduced catfish. Decisions to construct or decommission dams should consider local and regional impacts on biodiversity.

ISOLATION AND ANALYSIS OF NATIVE DNA AND RNA FROM ROOTS OF RUBBER-PRODUCING SPECIES SCORZONERA TAU-SAGHYZ LIPSCH. ET G.G. BOSSE

Scorzonera tau-saghyz Lipsch. et G.G.Bosse, is endemic species, growing in South Kazakhstan and alternative (to Hevea brasilians) source of natural rubber, related to the Asteraceae Family. Natural rubber (NR) is an indispensable raw material for the production of different products for medicine, automotive and aviation industries. The introduction of tau-saghyz into the culture will make it possible to obtain NC not only in Kazakhstan, but also on the territory of the countries of the Northern latitudes. At the growing phases of ontogenesis of tau-saghyz (April-June) latex is actively synthesized in the leaves and transported to the roots. In our experiments it was necessary to conduct molecular genetic studies of the selected forms of tau-saghyz with high rubber concentration. In this regard, it became necessary to isolate and analyze native DNA and RNA from dry roots. Samples with the highest rubber content were used for DNA extraction. The main problem in the isolation of DNA from the dry roots of tau-saghyz is the significant content of natural rubber. In this research the following commercial kits were used: 1) DNeasy Plant Mini Kit (Qiagene); 2) GenElute Plant Genomic DNA Miniprep Kit (Sigma); 3) NucleoSpin® Plant II / Midi / Maxi kit (Macherey-Nagel). Further DNA isolation was carried out in accordance with the kit manufacturer's protocol. Quantitative DNA analysis was performed using both UV spectrophotometry (Nanodrop) and fluorometric analysis (Qubit) method. DNA extracted by the 2 kit (Sigma) was further purified by precipitation with ethanol and demonstrates satisfactory quality. Functional analysis of isolated DNA samples was performed both by restriction analysis and by DNA amplification. It is worth to mention that for reaction primers that are characteristic of gene AACT (ACETOACETYL-COA TRANSFERASE) Cucumis melo were used. This enzyme catalyzes the first reaction of biosynthesis in the mevalonate pathway, which the final product is IDP (isopentenyl diphosphate). The cis-prenyltransferase (CPT) enzyme catalyzes the biosynthesis of rubber by the sequential addition of IDP to the terminal group of the initiating allylic pyrophosphate (APP). As a result of PCR analysis a putative 1200 bp AAST gene for tau-saghyz was identified. In this study two methods of RNA isolation were chosen: 1. A method widely used for plants of the Cucurbitaceae family; 2. A method approved for plants with a high content of polyphenols. The RNA isolation was carried out as described in the relevant protocols with minor modifications (Verwoerd TC, Dekker BMM, Hoekema A (1989) A small-scale procedure for the rapid isolation of plant RNAs. Nucleic Acids Res 17:2362). The final precipitates were dissolved in 50 µl of water pretreated with diethylpyrocarbonate. Quantitative analysis of RNA was carried out using UV spectrophotometry (Nanodrop). Functional analysis of extracted RNA samples was conducted by cDNA synthesis with usage of reverse transcriptase Superscript IV with the following amplification in PCR. In this reaction the primers specific for CPT gene of Taraxacum kok-saghyz were used. The prospective CPT gene was excised from the gel, purified and cloned into the pJET vector. In the further research it is planned to perform its sequencing and comparison with the CPT gene of Taraxacum kok-saghyz and Hevea brasiliensis.

Label-Free Detection of DNA Base Mutation and Hybridized DNA by an Electrostatically Modified 3D Plasmonic Array.

Surface-enhanced Raman scattering (SERS) represents a promising avenue for DNA detection as it offers intrinsic chemical insights with high sensitivity compared to conventional methods. However, label-free and quantitative detection of unmodified DNA by SERS remains a major challenge in DNA analysis. To overcome this challenge, we propose a positively charged plasmonic nanosurface for DNA capture and quantitative analysis. Highly sensitive and uniform SERS enhancement was realized by a three-dimensional plasmonic array supporting well-designed hybrid plasmonic modes. Subsequently, the plasmonic array was modified with an electrostatically functionalized PDDA (poly(diene-dimethylammonium-chloride)) self-assembled monolayer in a single step. The effectiveness of the resulting PDDA-SERS substrate was demonstrated by the label-free and quantitative detection of base content and base mutation in hybridized DNA. The PDDA-SERS substrate provides a robust platform for SERS analysis not only of DNA but also of other electronegative analytes.

Cell-Free DNA Analysis for the Determination of Fetal Red Blood Cell Antigen Genotype in Individuals With Alloimmunized Pregnancies.

To evaluate the accuracy of next-generation sequencing-based quantitative cell-free DNA analysis for fetal antigen genotyping in individuals with alloimmunized pregnancies undergoing clinical testing in practices across the United States as early as 10 weeks of gestation, with the objective of identifying individuals with pregnancies at risk for hemolytic disease of the fetus and newborn and guiding management. This prospective cohort study included patients with alloimmunized pregnancies undergoing clinical fetal antigen cell-free DNA analysis between 10 0/7 and 37 0/7 weeks of gestation at 120 clinical sites. Both the pregnant person with the alloimmunized pregnancy and the neonates resulting from the pregnancies were included. The laboratory issued the cell-free DNA results prospectively as a part of clinical care. After delivery, neonatal buccal swabs collected between 0 and 270 days of life were sent to an outside independent laboratory for antigen genotyping. The outside laboratory was blinded to the fetal cell-free DNA results, and the results were compared. Concordance was reported for the fetal antigen cell-free DNA analysis for antigens to which the pregnant person was alloimmunized and for all antigens for which the pregnant person was genotype negative. A total of 156 pregnant people who received clinically ordered cell-free DNA fetal antigen testing provided neonatal buccal swabs for genotyping after delivery. Overall, 15.4% of participants were Hispanic, 9.0% were non-Hispanic Black, 65.4% were non-Hispanic White, 4.5% were Asian, 1.3% were more than one race or ethnicity, and 4.5% were unknown. The median gestational age at the time of testing was 16.4 weeks with a median fetal fraction of 11.1%. Concordance between cell-free DNA analysis results and neonatal genotype was determined for 465 antigen calls for the following antigens: K1 (n=143), E (124), C (60), Fya (50), c (47), and D(RhD) (41). These 465 calls included 145 in which the fetus was antigen positive and 320 in which the fetus was antigen negative. We observed complete concordance between prenatal fetal antigen cell-free DNA analysis results and neonatal genotypes for the 465 calls, resulting in 100% sensitivity, specificity, and accuracy. In a diverse multicenter cohort, cell-free DNA analysis was highly sensitive and specific for determining fetal antigen genotype as early as 10 weeks of gestation in individuals with alloimmunized pregnancies. Taken together with previously published evidence, this study supports the implementation of cell-free DNA testing to manage individuals with alloimmunized pregnancies in the United States.

Evaluation of Nanonanoliposomal Curcumin on Cutaneous Leishmaniasis Skin Lesions Caused by Leishmania major in BALB/c Mice.

Curcumin is an extract of rhizome turmeric (diferuloylmethane), with antioxidant, anti-inflammatory, antimicrobial, and anti-parasitic properties, which making it a potential candidate for the treatment of leishmaniasis. The aim of the presented study was to evaluate curcumin as possible candidate for treatment of cutaneous leishmaniasis. We investigated the physicochemical properties and anti-leishmanial effects of nanoliposomal curcumin (40, 80, and 120 μM) in Leishmania major (MRHO/IR/75/ER) infected BALB/c mice at the faculty of Veterinary Medicinem University of Tehran, Iran. For this aim, L. major promastigotes (MHROM/IR/75/ER) at stationary phase (2×106) were inoculated sub-cutaneously into the upper area of the tail in BALB/c mice (six groups, n= 10 per group). For evaluation of nanoliposomal curcumin, the zeta potential, particle size and stability of nanoliposomal curcumin was determined. Furthermore, the anti-leishmanial effects of nanoliposomal curcumin formulation on the lesion sizes was determined and the parasite burden in the leishmania induced lesion was performed using semi quantitative PCR. Treatment of L. major infected BALB/c mice with nanoliposomal curcumin led to a reduction in the kinetic of the skin lesion size development. The semi quantitative PCR analysis of DNA extracted from the lesions showed reduction of parasite burden. The most effective treatment could be found in 80 μM nanoliposomal curcumin. Treatment with Glucantime, as a positive control, also showed a nearly similar effect compared to the effect of 80 μM nanoliposomal curcumin. Nanoliposomal curcumin could be considered as a potential drug against cutaneous leishmaniasis caused by L. major in susceptible animal models.

An intra-stimuli resonance energy transfer-based electrochemiluminescence biosensor for DNA methylation detection

Aberrant DNA methylation, as one of the promising biomarkers, is intimately connected to a variety of genetic and tumor diseases. Herein, we constructed an innovative intra-stimuli electrochemiluminescence resonance energy transfer (ECL-RET) biosensor for methylated DNA detection with high sensitivity and accuracy. Glucose oxidase (GOD) was modified at the terminal of assist DNA as functional conjugation (assist DNA-GOD), which then hybridized with methylated target DNA and hairpin DNA to form Y-shaped DNA ternary conjugate. Ru(bpy)32+ encapsulated silica nanospheres (RuSiO2 NPs) were uniformly coated with silver nanoparticles (Ag NPs) and the formed RuSiO2@Ag nanocomposites were introduced to the terminal of hairpin DNA via amide bond. The combination of the ECL donor (RuSiO2 NPs) and acceptor (Ag NPs) on one nanostructure yielded an intra-molecular ECL-RET. Afterward, the presence of H2O2 as the product of GOD catalyzing glucose induced the etching of Ag NPs and subsequent recovery of ECL signal from RuSiO2 NPs. Thus, due to the dependence of the ECL enhancement on the target concentration, this method achieved the quantitative analysis of methylated target DNA with good selectivity, repeatability, and practical utility.

3D Bioprinting-Based Dopamine-Coupled Flexible Material for Nasal Cartilage Repair.

Since 3D printing can be used to design implants according to the specific conditions of patients, it has become an emerging technology in tissue engineering and regenerative medicine. How to improve the mechanical, elastic and adhesion properties of 3D-printed photocrosslinked hydrogels is the focus of cartilage tissue repair and reconstruction research. We established a strategy for toughening hydrogels by mixing GelMA-DOPA (GD), which is prepared by coupling dopamine (DA) with GelMA, with HAMA, bacterial cellulose (BC) to produce composite hydrogels (HB-GD). HB-GD hydrogel scaffolds were characterized in vitro by scanning electron microscopy (SEM), Young's modulus, swelling property and rheological property tests. And biocompatibility and chondrogenic ability were tested by live/dead staining, DNA quantitative analysis and immunofluorescence staining. Combined with 3D bioprinting technology, mouse chondrocytes (ADTC5) were added to form a biological chain to construct an in vitro model, and the feasibility of the model for nasal cartilage regeneration was verified by cytology evaluation. With the increase of GD concentration, the toughness of the composite hydrogel increased (47.0 ± 2.7 kPa (HB-5GD)-158 ± 3.2 kPa (HB-20GD)), and it had excellent swelling properties, rheological properties and printing properties. The HB-GD composite hydrogel promoted the proliferation and differentiation of ATDC5. Cells in 3D printed scaffolds had higher survival rates (> 95%) and better protein expression than the encapsulated cultures. The HB-10GD hydrogel can be made into a porous scaffold with precise shape, good internal pore structure, high mechanical strength and good swelling rate through extrusion 3D printing. This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

A highly integrated digital PCR system with on-chip heating for accurate DNA quantitative analysis

Digital polymerase chain reaction (dPCR) is extensively used for highly sensitive disease diagnosis due to its single-molecule detection ability. However, current dPCR systems require intricate DNA sample distribution, rely on cumbersome external heaters, and exhibit sluggish thermal cycling, hampering efficiency and speed of the dPCR process. Herein, we presented the development of a microwell array based dPCR system featuring an integrated self-heating dPCR chip. By utilizing hydrodynamic and electrothermal simulations, the chip's structure is optimized, resulting in improved partitioning within microwells and uniform thermal distribution. Through strategic hydrophilic/hydrophobic modifications on the chip's surface, we effectively secured the compartmentalization of sample within the microwells by employing an overlaying oil phase, which renders homogeneity and independence of samples in the microwells. To achieve precise, stable, uniform, and rapid self-heating of the chip, the ITO heating layer and the temperature control algorithm are deliberately designed. With a capacity of 22,500 microwells that can be easily expanded, the system successfully quantified EGFR plasmid solutions, exhibiting a dynamic linear range of 105 and a detection limit of 10 copies per reaction. To further validate its performance, we employed the dPCR platform for quantitative detection of BCR-ABL1 mutation gene fragments, where its performance was compared against the QuantStudio 3D, and the self-heating dPCR system demonstrated similar analytical accuracy to the commercial dPCR system. Notably, the individual chip is produced on a semiconductor manufacturing line, benefiting from mass production capabilities, so the chips are cost-effective and conducive to widespread adoption and accessibility.

Conjugated Oligoelectrolyte with DNA Affinity for Enhanced Nuclear Imaging and Precise DNA Quantification.

Precise DNA quantification and nuclear imaging are pivotal for clinical testing, pathological diagnosis, and drug development. The detection and localization of mitochondrial DNA serve as crucial indicators of cellular health. We introduce a novel conjugated oligoelectrolyte (COE) molecule, COE-S3, featuring a planar backbone composed of three benzene rings and terminal side chains. This unique amphiphilic structure endows COE-S3 with exceptional water solubility, a high quantum yield of 0.79, and a significant fluorescence Stokes shift (λex = 366 nm, λem = 476 nm), alongside a specific fluorescence response to DNA. The fluorescence intensity correlates proportionally with DNA concentration. COE-S3 interacts with double-stranded DNA (dsDNA) through an intercalation binding mode, exhibiting a binding constant (K) of 1.32 × 106 M-1. Its amphiphilic nature and strong DNA affinity facilitate its localization within mitochondria in living cells and nuclei in apoptotic cells. Remarkably, within 30 min of COE-S3 staining, cell vitality can be discerned through real-time nuclear fluorescence imaging of apoptotic cells. COE-S3's high DNA selectivity enables quantitative intracellular DNA analysis, providing insights into cell proliferation, differentiation, and growth. Our findings underscore COE-S3, with its strategically designed, shortened planar backbone, as a promising intercalative probe for DNA quantification and nuclear imaging.

Capillary force-driven microfluidic device for quantitative analysis of single-molecule DNA

Capillary force-driven microfluidic device for quantitative analysis of single-molecule DNA

An eco-friendly and ultrasensitive micro-orifice resistance assay for the detection of Listeria monocytogenes based on calcium carbonate signal probes harvested from discarded eggshells

The development of eco-friendly analytical methods for the detection of foodborne pathogens is of great importance for protecting human health and alleviating environmental pressure. Here, we demonstrate that a material (CaCO3 microparticles) prepared from discarded eggshells can be used as signal probes for micro-orifice resistance assay (MORA) and can be combined with ligation-mediated branching hybridization chain reaction (LB-HCR)-based signal-amplification technique (e-LMORA) for high sensitivity detection of Listeria monocytogenes. This strategy used LB-HCR-induced aggregation of streptavidin-modified CaCO3 microparticles, which were recognized by the particle counter for quantitative analysis of the target DNA. Compared with traditional MORA using polystyrene microspheres as signal probes, CaCO3 microparticles prepared from waste eggshells are more environmentally friendly. The combination of DNA-recognition probe, signal probes, and enzyme-free signal-amplification strategy not only reduces the cost synergistically, but also enables the biosensor to attain high sensitivity (limit of detection = 21 CFU/mL) due to its efficient signal amplification.

Genetic Diversity Analysis of Exon-2 Growth Hormone (GH) Gene in Crossbred Chicken (Sentul X Arab) using PCR-RFLP Technique

The research aims to analyze the genetic diversity of the GH gene using the PCR-RFLP technique. Fifty blood samples were collected from crossed Sentul and Arab Chickens aged three months. DNA was extracted from whole blood samples, and its quantity was evaluated by bio-drop technique. Extracted DNA was amplified for gene GH using a PCR machine. The PCR product was restricted by MspI (C↓CGG) and Hae-III (GG↓CC) enzymes for identifying the fragment length diversity. The variables observed in this study were DNA quantitative analysis, the genotype, and alleles of the obtained genotype. The result shows the extracted DNA is of good quality because it has values >1.8 and <2.0, which means there’s no contamination in the DNA. GH gene was amplified with primers of 519 bp and showed that a DNA band matched the target in the specified primer design. Analysis of Genetic Diversity shows the monomorphic GH gene in this research. The genotype obtained at the GH-HaeIII locus is AA, and at the GH-MspI locus is TT. Both enzymes weren’t restricted to these amplification design sites.

The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma.

Low-grade gliomas (LGGs) represent children's most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples. We examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants. Our findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9ng). While CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.

A CRISPR/Cas12a-powered gold/nickel foam surface-enhanced Raman spectroscopy biosensor for nucleic acid specific detection in foods.

Food is a necessary source of energy, but it also serves as a pathway for transmitting infectious pathogens, making food safety a matter of great concern. Rapid, accurate, and specific detection methods for foodborne viruses are crucial. Surface-Enhanced Raman Scattering (SERS), due to its superior sensitivity and characteristic fingerprint spectra, holds enormous potential. However, due to the limitations of SERS, it requires specific conditions to achieve specificity. In order to enhance the specificity and accuracy of nucleic acid detection based on SERS, we have developed a CRISPR-Cas12a-mediated SERS technique to identify target DNA, harnessing the targeting recognition capability of CRISPR-Cas12a and ultra-sensitive SERS tags and successfully addressing SERS' lack of specific detection capability. This system includes a gold/nickel foam substrate (Au-NFs) and a reporter (ssDNA-ROX). The phenomenon of colloidal gold/silver nano-aggregation due to magnesium ions, which is commonly encountered in CRISPR-SERS, was simultaneously solved using AuNFs. The qualitative and quantitative analysis of target DNA in drinking water was performed by monitoring the intensity change of ROX Raman reporter molecules. The results showed that the sensor detected DNA within 30 min and the limit of detection (LOD) was 8.23 fM. This is expected to become one of the alternative methods for nucleic acid detection for its rapid detection and high specificity.

Tendon stem/progenitor cells are promising reparative cell sources for multiple musculoskeletal injuries of concomitant articular cartilage lesions associated with ligament injuries

BackgroundTrauma-related articular cartilage lesions usually occur in conjunction with ligament injuries. Torn ligaments are frequently reconstructed with tendon autograft and has been proven to achieve satisfactory clinical outcomes. However, treatments for the concomitant articular cartilage lesions are still very insufficient. The current study was aimed to evaluate whether stem cells derived from tendon tissue can be considered as an alternative reparative cell source for cartilage repair.MethodsPrimary human tendon stem/progenitor cells (hTSPCs) were isolated from 4 male patients (32 ± 8 years) who underwent ACL reconstruction surgery with autologous semitendinosus and gracilis tendons. The excessive tendon tissue after graft preparation was processed for primary cell isolation with an enzyme digestion protocol. Decellularization cartilage matrix (DCM) was used to provide a chondrogenic microenvironment for hTSPCs. Cell viability, cell morphology on the DCM, as well as their chondrogenic differentiation were evaluated.ResultsDAPI staining and DNA quantitative analysis (61.47 μg per mg dry weight before and 2.64 μg/mg after decellularization) showed that most of the cells in the cartilage lacuna were removed after decellularization process. Whilst, the basic structure of the cartilage tissue was preserved and the main ECM components, collagen type II and sGAG were retained after decellularization, which were revealed by DMMB assay and histology. Live/dead staining and proliferative assay demonstrated that DCM supported attachment, survival and proliferation of hTSPCs with an excellent biocompatibility. Furthermore, gene expression analysis indicated that chondrogenic differentiation of hTSPC was induced by the DCM microenvironment, with upregulation of chondrogenesis-related marker genes, COL 2 and SOX9, without the use of exogenous growth factors.ConclusionDCM supported hTSPCs attachment and proliferation with high biocompatibility. Moreover, TSPCs underwent a distinct chondrogenesis after the induction of a chondrogenic microenvironment provided by DCM. These results indicated that TSPCs are promising reparative cell sources for promoting cartilage repair. Particularly, in the cohort that articular cartilage lesions occur in conjunction with ligament injuries, autologous TSPCs can be isolated from a portion of the tendon autograph harvested for ligaments reconstruction. In future clinical practice, combined ligament reconstruction with TSPCs- based therapy for articular cartilage repair can to be considered to achieve superior repair of these associated injuries, in which autologous TSPCs can be isolated from a portion of the tendon autograph harvested for ligaments reconstruction.

TB-ISATEST: a Diagnostic LAMP Assay for Differentiation of &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt;

Consumption, white plague, tuberculosis… Only relatively recently, this disease has ceased to be an absolutely death sentence for infected people, but problems of the spread and diagnosis of the disease are still relevant. This paper presents results of the development of a new loop isothermal amplification (LAMP) assay, named TB-ISATEST, which targeting the species-specific gene rv2341 for the differentiation of Mycobacterium tuberculosis from non-tuberculosis mycobacteria. The assay is applicable for quantitative analysis of genomic DNA and allows detecting tenfold difference in concentration. The results of amplification optimization using a unique two-stage protocol based on the method of orthogonal Taguchi matrices are presented for the first time. A theoretical interpretation of the high amplification efficiency values observed in the LAMP reaction is proposed. Limit of detection of the developed assay is 40 copies of genomic DNA per reaction and amplification requires 15 min. In terms of the combination of characteristics, the TB-ISATEST assay surpasses all the known ways for identifying M. tuberculosis by the LAMP method.

Chip-based digital PCR as a direct quantification method for residual DNA in mRNA drugs

Residual exogenous DNA, as common contaminants in biological products, must be monitored and removed to ensure safety. Digital PCR (dPCR) technology is widely applied in DNA quantitative analysis due to high specificity, sensitivity, absolute quantification, etc. Data support is relatively lacking in deciphering the dPCR technology application in residual DNA of mRNA drugs. The current study helped establish the dPCR methods corresponding to two different mRNA vaccines to detect the residual DNA template. The established dPCR methods have a wide linear range, good precision, accuracy, and specificity without being interfered with by encapsulating and demulsifying reagents. The method is simple, rapid, and sensitive which demonstrates that dPCR can directly quantitate other types of risky DNA in mRNA drugs accurately as well.

Quantitative analysis of mitochondrial DNA in porcine-mouse cloned embryos.

The aim of the research is to identify that porcine oocytes can function as recipients for interspecies cloning and have the ability to develop to blastocysts. Furthermore each mitochondrial DNA (mtDNA) in interspecises cloned embryos was analyzed. For the study, mouse-porcine and porcine-porcine cloned embryos were produced with mouse fetal fibroblasts (MFF) and porcine fetal fibroblasts (PFF), respectively, introduced as donor cells into enucleated porcine oocytes. The developmental rate and cell numbers of blastocysts between intraspecies porcine-porcine and interspecies mouse-porcine cloned embryos were compared and real-time polymerase chain reaction (PCR) was performed for the estimate of mouse and porcine mtDNA copy number in mouse-porcine cloned embryos at different stages.There was no significant difference in the developmental rate or total blastocyst number between mouse-porcine cloned embryos and porcine-porcine cloned embryos (11.1 ± 0.9%, 25 ± 3.5 vs. 10.1 ± 1.2%, 24 ± 6.3). In mouse-porcine reconstructed embryos, the copy numbers of mouse somatic cell-derived mtDNA decreased between the 1-cell and blastocyst stages, whereas the copy number of porcine oocyte-derived mtDNA significantly increased during this period, as assessed by real-time PCR analysis. In our real-time PCR analysis, we improved the standard curve construction-based method to analyze the level of mtDNA between mouse donor cells and porcine oocytes using the copy number of mouse beta-actin DNA as a standard. Our findings suggest that mouse-porcine cloned embryos have the ability to develop to blastocysts in vitro and exhibit mitochondrial heteroplasmy from the 1-cell to blastocyst stages and the mouse-derived mitochondria can be gradually replaced with those of the porcine oocyte in the early developmental stages of mouse-porcine cloned embryos.

Biomechanical properties of derma materials for hernioplasty

The most common problem in the surgical treatment of hernias using tension herni-oplasty is a strong tension in the suture area, which can lead to wound dehiscence, de-formation of the hernia area, fistulas and recurrence. Therefore, at present, the technique of tension-free hernioplasty using both synthetic and natural materials is increasingly being used. Natural materials are more reliable due to biocompatibility, lack of cytotoxicity and minimal biodegradation. However, not all biomaterials have the necessary mechani-cal characteristics, such as elasticity and strength. The main goal of this study was a comparative assessment of the biomechanical properties of the acellular dermal matrix, bioplastic material obtained by the methods of detergent-enzymatic and chemical decellu-larization, respectively, and the surgical implant Permacol™. All materials were subjected to histological analysis and quantitative DNA analysis. Strength studies (stress, strain at break and initial modulus of elasticity) were carried out using an Instron 1122 universal tensile testing machine. BIoplastic material showed significantly lower values of defor-mation-strength properties and modulus of elasticity. The obtained results showed that the acellular dermal matrix and the commercial Permacol™ implant are the closest to the native dermis in strength characteristics, however, the histological structure of the acellu-lar dermal matrix is closest to the histological features of the organization of the porcine dermis, which makes this material promising for further research.