15,989 results match your criteria dna quantification

Pristimerin synergistically sensitizes conditionally reprogrammed patient derived-primary hepatocellular carcinoma cells to sorafenib through endoplasmic reticulum stress and ROS generation by modulating Akt/FoxO1/p27 signaling pathway.

Phytomedicine 2021 Apr 4;86:153563. Epub 2021 Apr 4.

Department of Pharmacy, The First Affiliated Hospital, Sun Yat-sen University, 510080 Guangzhou, China. Electronic address:

Background: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. Sorafenib (SORA), as a first-line therapeutic drug, has been used to treat HCC, but resistance poses a major limitation on the efficacy of SORA chemotherapy. Pristimerin (PRIS), a natural bioactive component isolated from various plant species in the Celastraceae and Hippocrateaceae families, has been reported to exhibit outstanding antitumor effects in several types of cells in vitro. Read More

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Extraction and electrochemical detection for quantification of trace-level DNA.

Mikrochim Acta 2021 May 5;188(6):180. Epub 2021 May 5.

Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.

A novel strategy was developed to extract, detect, and quantify trace-level DNA. For the extraction step, a composite of methylene blue (MB), poly(acrylic acid) (PAA), and modified iron oxide magnetic nanoparticles (IOMNPs) (PAA/IOMNPs) was used to adsorb DNA from the sample. MB-PAA/IOMNPs with adsorbed DNA were then separated from the solution with an external magnet and MB-DNA was eluted from PAA/IOMNPs with acetic acid. Read More

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-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation.

Analyst 2021 May 5. Epub 2021 May 5.

Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia. and School of Environment and Science (ESC), Griffith University, Nathan Campus, QLD 4111, Australia.

The quantification of global 5-methylcytosine (5mC) content has emerged as a promising approach for the diagnosis and prognosis of cancers. However, conventional methods for the global 5mC analysis require large quantities of DNA and may not be useful for liquid biopsy applications, where the amount of DNA available is limited. Herein, we report magnetic nanoparticles-assisted methylated DNA immunoprecipitation (e-MagnetoMethyl IP) coupled with electrochemical quantification of global DNA methylation. Read More

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Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles.

Nanomaterials (Basel) 2021 Apr 29;11(5). Epub 2021 Apr 29.

Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave. 8, 630090 Novosibirsk, Russia.

Fluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in composition of ON-FDs) influenced the efficiency of their non-covalent associates' formation with GNPs (ON-FD/GNPs). Read More

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High-Throughput Detection of Multiple miRNAs and Methylated DNA by Droplet Digital PCR.

J Pers Med 2021 Apr 29;11(5). Epub 2021 Apr 29.

Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St., Baltimore, MD 21201, USA.

Altered miRNA expression and DNA methylation have highly active and diverse roles in carcinogenesis. Simultaneous detection of the molecular aberrations may have a synergistic effect on the diagnosis of malignancies. Herein, we develop a high-throughput assay for detecting multiple miRNAs and DNA methylation using droplet digital PCR (ddPCR) coupled with a 96-microwell plate. Read More

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Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands.

Nat Biotechnol 2021 May 3. Epub 2021 May 3.

Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Identification and quantification of low-frequency mutations remain challenging despite improvements in the baseline error rate of next-generation sequencing technologies. Here, we describe a method, termed SaferSeqS, that addresses these challenges by (1) efficiently introducing identical molecular barcodes in the Watson and Crick strands of template molecules and (2) enriching target sequences with strand-specific PCR. The method achieves high sensitivity and specificity and detects variants at frequencies below 1 in 100,000 DNA template molecules with a background mutation rate of <5 × 10 mutants per base pair (bp). Read More

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Parvovirus B19 DNA detectable in hearts of patients with dilated cardiomyopathy, but absent or inactive in blood.

ESC Heart Fail 2021 May 1. Epub 2021 May 1.

Department of Blood-borne Infections, Donor Medicine Research, Sanquin Blood Supply Foundation, Amsterdam, The Netherlands.

Aims: Parvovirus B19 (B19V) is often assumed to be a cause of dilated cardiomyopathy (DCM), based on the quantification of B19V DNA in endomyocardial biopsies (EMB). Whether the presence of B19V DNA correlates with active infection is still debated. Application of the enzyme endonuclease to blood samples results in degradation of B19V DNA remnants but leaves viral particles intact, which enables differentiation between active and past infection. Read More

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Detection of Dysbiosis and Increased Intestinal Permeability in Brazilian Patients with Relapsing-Remitting Multiple Sclerosis.

Int J Environ Res Public Health 2021 Apr 27;18(9). Epub 2021 Apr 27.

Microbiology Program, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, Sao Jose do Rio Preto 15054-000, Brazil.

Dysbiosis, associated with barrier disruption and altered gut-brain communications, has been associated with multiple sclerosis (MS). In this study, we evaluated the gut microbiota in relapsing-remitting patients (RRMS) receiving disease-modifying therapies (DMTs) and correlated these data with diet, cytokines levels, and zonulin concentrations. Stool samples were used for 16S sequencing and real-time PCR. Read More

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Droplet Digital PCR (ddPCR) Analysis for the Detection and Quantification of Cow DNA in Buffalo Mozzarella Cheese.

Animals (Basel) 2021 Apr 28;11(5). Epub 2021 Apr 28.

Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy.

Buffalo mozzarella cheese is one of the most appreciated traditional Italian products and it is certified as a Protected Designation of Origin (PDO) product under the European Commission Regulation No. 1151/2012. It is obtained exclusively from buffalo milk. Read More

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Accurate Quantification of AAV Vector Genomes by Quantitative PCR.

Genes (Basel) 2021 Apr 19;12(4). Epub 2021 Apr 19.

Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5&6, West Wing, Headley Way, Oxford OX3 9DU, UK.

The ability to accurately determine the dose of an adeno-associated viral (AAV) therapeutic vector is critical to the gene therapy process. Quantitative PCR (qPCR) is one of the common methods to quantify the AAV vector titre, but different variables can lead to inconsistent results. The aim of this study was to analyze the influence of the conformation of the DNA used as the standard control, and the enzymatic digestion was performed to release the viral genome from the protein capsid on the physical genome titration of a clinically relevant AAV8. Read More

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A Label-Free DNA-Immunosensor Based on Aminated rGO Electrode for the Quantification of DNA Methylation.

Nanomaterials (Basel) 2021 Apr 12;11(4). Epub 2021 Apr 12.

Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK.

In this work, we developed a sandwich DNA-immunosensor for quantification of the methylated tumour suppressor gene O-6-methylguanine-DNA methyltransferase (MGMT), which is a potential biomarker for brain tumours and breast cancer. The biosensor is based on aminated reduced graphene oxide electrode, which is achieved by ammonium hydroxide chemisorption and anti-5-methylcytosine (anti-5mC) as a methylation bioreceptor. The target single-strand (ss) MGMT oligonucleotide is first recognised by its hybridisation with complementary DNA to form double-stranded (ds) MGMT, which is then captured by anti-5mC on the electrode surface due to the presence of methylation. Read More

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Pregnancy-Related Extracellular Vesicles Revisited.

Int J Mol Sci 2021 Apr 9;22(8). Epub 2021 Apr 9.

Department of Surgical Oncology, Prof. Dr. Alexandru Trestioreanu Oncology Institute, Carol Davila University of Medicine and Pharmacy, 252 Fundeni Rd., 022328 Bucharest, Romania.

Extracellular vesicles (EVs) are small vesicles ranging from 20-200 nm to 10 μm in diameter that are discharged and taken in by many different types of cells. Depending on the nature and quantity of their content-which generally includes proteins, lipids as well as microRNAs (miRNAs), messenger-RNA (mRNA), and DNA-these particles can bring about functional modifications in the receiving cells. During pregnancy, placenta and/or fetal-derived EVs have recently been isolated, eliciting interest in discovering their clinical significance. Read More

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Effects of Human and Porcine Adipose Extracellular Matrices Decellularized by Enzymatic or Chemical Methods on Macrophage Polarization and Immunocompetence.

Int J Mol Sci 2021 Apr 8;22(8). Epub 2021 Apr 8.

Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain.

The decellularized extracellular matrix (ECM) obtained from human and porcine adipose tissue (AT) is currently used to prepare regenerative medicine bio-scaffolds. However, the influence of these natural biomaterials on host immune response is not yet deeply understood. Since macrophages play a key role in the inflammation/healing processes due to their high functional plasticity between M1 and M2 phenotypes, the evaluation of their response to decellularized ECM is mandatory. Read More

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Quantification of Circulating Cell Free Mitochondrial DNA in Extracellular Vesicles with PicoGreen™ in Liquid Biopsies: Fast Assessment of Disease/Trauma Severity.

Cells 2021 Apr 6;10(4). Epub 2021 Apr 6.

Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX 77555, USA.

The analysis of circulating cell free DNA (ccf-DNA) is an emerging diagnostic tool for the detection and monitoring of tissue injury, disease progression, and potential treatment effects. Currently, most of ccf-DNA in tissue and liquid biopsies is analysed with real-time quantitative PCR (qPCR) that is primer- and template-specific, labour intensive and cost-inefficient. In this report we directly compare the amounts of ccf-DNA in serum of healthy volunteers, and subjects presenting with various stages of lung adenocarcinoma, and survivors of traumatic brain injury using qPCR and quantitative PicoGreen™ fluorescence assay. Read More

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Acidified Nitrite Contributes to the Antitumor Effect of Cold Atmospheric Plasma on Melanoma Cells.

Int J Mol Sci 2021 Apr 4;22(7). Epub 2021 Apr 4.

Emil-Fischer-Center, Institute of Biochemistry, University of Erlangen-Nuernberg, 91054 Erlangen, Germany.

Cold atmospheric plasma (CAP) is partially ionized gas near room temperature with previously reported antitumor effects. Despite extensive research and growing interest in this technology, active components and molecular mechanisms of CAP are not fully understood to date. We used Raman spectroscopy and colorimetric assays to determine elevated nitrite and nitrate levels after treatment with a MiniFlatPlaster CAP device. Read More

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Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.

Microbiome 2021 04 29;9(1):95. Epub 2021 Apr 29.

Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan.

Background: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

Results: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. Read More

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Seminal plasma, and not sperm, induces time and concentration-dependent neutrophil extracellular trap release in donkeys.

Equine Vet J 2021 Apr 28. Epub 2021 Apr 28.

Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, E-17003, Girona, Spain.

Background:  In several mammalian species, acute endometritis driven by the recruitment of polymorphonuclear cells (PMN) occurs in response to semen. These PMNs release DNA to form neutrophil extracellular traps (NETs) in cattle, horse and human, leading to sperm entrapment. While there is no evidence of this phenomenon occurring in donkeys, artificial insemination (AI) with frozen-thawed semen, which results in very poor pregnancy rates, leads to a large PMN recruitment to the uterus. Read More

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Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer.

Nanomedicine 2021 Apr 24:102407. Epub 2021 Apr 24.

Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA; Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA. Electronic address:

5-hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Read More

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Argonaute integrated single-tube PCR system enables supersensitive detection of rare mutations.

Nucleic Acids Res 2021 Apr 27. Epub 2021 Apr 27.

State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Technological advances in rare DNA mutations detection have revolutionized the diagnosis and monitoring of tumors, but they are still limited by the lack of supersensitive and high-coverage procedures for identifying low-abundance mutations. Here, we describe a single-tube, multiplex PCR-based system, A-Star, that involves a hyperthermophilic Argonaute from Pyrococcus furiosus (PfAgo) for highly efficient detection of rare mutations beneficial from its compatibility with DNA polymerase. This novel technique uses a specific guide design strategy to allow PfAgo selective cleavage with single-nucleotide resolution at 94°C, thus mostly eliminating wild-type DNA in the denaturation step and efficiently amplifying rare mutant DNA during the PCR process. Read More

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Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay.

Sci Rep 2021 Apr 26;11(1):8945. Epub 2021 Apr 26.

Radioisotope Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.

Phosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. Read More

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Systematic STR analysis of old post-vasectomy seminal fluid stains to examine evidence stored for 16 years.

Sci Rep 2021 Apr 26;11(1):8918. Epub 2021 Apr 26.

Laboratório de Patologia Molecular, Departamento de Patologia - Escola Paulista de Medicina/Universidade Federal de São Paulo (EPM/UNIFESP), Rua Botucatu 740, Edifício Lemos Torres. Vila Clementino, São Paulo, SP, CEP 04023-62, Brazil.

To understand stored evidence and the insertion in genetic databases is important in forensic investigations. Blood, pre- and post-vasectomy semen from 90 fertile male individuals, aged 24 to 45, were donated for research after informed consent. The semen samples were stored in the form of 30 µL stains on cotton fabric, for 16 years at room temperature in the laboratory. Read More

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Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research.

Environ Microbiome 2020 Jul 28;15(1):14. Epub 2020 Jul 28.

Norwegian Defence Research Establishment FFI, P O Box 25, NO-2027, Kjeller, Norway.

Background: Reliable identification and quantification of bioaerosols is fundamental in aerosol microbiome research, highlighting the importance of using sampling equipment with well-defined performance characteristics. Following advances in sequencing technology, shotgun metagenomic sequencing (SMS) of environmental samples is now possible. However, SMS of air samples is challenging due to low biomass, but with the use of high-volume air samplers sufficient DNA yields can be obtained. Read More

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Current status of ctDNA in precision oncology for hepatocellular carcinoma.

J Exp Clin Cancer Res 2021 Apr 26;40(1):140. Epub 2021 Apr 26.

Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China.

The conventional method used to obtain a tumor biopsy for hepatocellular carcinoma (HCC) is invasive and does not evaluate dynamic cancer progression or assess tumor heterogeneity. It is thus imperative to create a novel non-invasive diagnostic technique for improvement in cancer screening, diagnosis, treatment selection, response assessment, and predicting prognosis for HCC. Circulating tumor DNA (ctDNA) is a non-invasive liquid biopsy method that reveals cancer-specific genetic and epigenetic aberrations. Read More

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Potential Functions of Histone H3.3 Lysine 56 Acetylation in Mammals.

Epigenetics 2021 Apr 26. Epub 2021 Apr 26.

Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA.

H3K56 acetylation (H3K56Ac) was first identified in yeast and has recently been reported to play important roles in maintaining genomic stability, chromatin assembly, DNA replication, cell cycle progression and DNA repair. Although H3.1K56Ac has been relatively well studied, the function of H3. Read More

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DNA methylation status of MutS genes in ameloblastoma.

Oral Dis 2021 Apr 26. Epub 2021 Apr 26.

Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil.

Objectives: Ameloblastoma is an odontogenic epithelial tumour with a low expression of mismatch repair system components. We aimed to investigate the methylation status of the genes MSH2, MSH3 and MSH6 (MutS group) in conventional ameloblastomas.

Materials And Methods: The ameloblastoma and dental follicle samples (n = 10 each) were collected from 20 different patients. Read More

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T cell immune discriminants of HIV reservoir size in a pediatric cohort of perinatally infected individuals.

PLoS Pathog 2021 Apr 26;17(4):e1009533. Epub 2021 Apr 26.

Bambino Gesu Children's Hospital, Rome, Italy.

The size of the latent HIV reservoir is associated with the timing of therapeutic interventions and overall health of the immune system. Here, we demonstrate that T cell phenotypic signatures associate with viral reservoir size in a cohort of HIV vertically infected children and young adults under durable viral control, and who initiated anti-retroviral therapy (ART) <2 years old. Flow cytometry was used to measure expression of immune activation (IA), immune checkpoint (ICP) markers, and intracellular cytokine production after stimulation with GAG peptides in CD4 and CD8 T cells from cross-sectional peripheral blood samples. Read More

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Utility of cell-free DNA concentrations and illness severity scores to predict survival in critically ill neonatal foals.

PLoS One 2021 26;16(4):e0242635. Epub 2021 Apr 26.

Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America.

Plasma cell-free DNA (cfDNA) levels have been associated with disease and survival status in septic humans and dogs. To date, studies investigating cfDNA levels in association with critical illness in foals are lacking. We hypothesized that cfDNA would be detectable in the plasma of foals, that septic and sick-nonseptic foals would have significantly higher cfDNA levels compared to healthy foals, and that increased cfDNA levels would be associated with non-survival. Read More

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Quantitative detection and monitoring of in rubber trees using real-time PCR.

Plant Dis 2021 Apr 26. Epub 2021 Apr 26.

Hainan University, 74629, College of Plant Protection, Haikou, Hainan, China;

is one of the most important pathogens of rubber trees in Asia. The proper detection and quantification of populations in rubber trees are of importance for monitoring the epidemics of the disease. In this study, we developed an ITS-based real-time PCR method to efficiently detect infecting rubber tree, which reliably detected as little as 100 fg genomic DNA, 100 copies of target DNA and 20 conidia. Read More

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A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquito : From genomic characterization to high-throughput field detection.

Evol Appl 2021 Apr 16;14(4):1009-1022. Epub 2021 Feb 16.

Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS - Université Grenoble-Alpes Grenoble France.

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterize a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito and to develop a molecular assay to monitor the associated resistance alleles in the field. Read More

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Efficient Transient Expression of Recombinant Proteins Using DNA Viral Vectors in Freshwater Microalgal Species.

Front Plant Sci 2021 7;12:650820. Epub 2021 Apr 7.

Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.

The increase in the world population, the advent of new infections and health issues, and the scarcity of natural biological products have spotlighted the importance of recombinant protein technology and its large-scale production in a cost-effective manner. Microalgae have become a significant promising platform with the potential to meet the increasing demand for recombinant proteins and other biologicals. Microalgae are safe organisms that can grow rapidly and are easily cultivated with basic nutrient requirements. Read More

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