With the development of liquid biopsy technology, plasma cell-free DNA (cfDNA) becomes one of the research hotspots. Whole-genome bisulfite sequencing of plasma cell-free DNA has shown great potential medical applications such as cancer detection. However, the practical stability evaluation is still lacking. In this study, plasma cell-free DNA samples from two volunteers at different time were collected and prepared for sequencing in multiple laboratories. The library preparation strategies include pre-bisulfite, post-bisulfite and regular whole-genome sequencing. We established a set of quality control references for plasma cell-free DNA sequencing data and evaluated practical stability of blood collection, DNA extraction, and library preparation and sequencing depth. This work provided a technical practice guide for the application of plasma cfDNA methylation sequencing for clinical applications.
Cell-Free Nucleic Acids ; DNA Methylation ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; Sulfites ; Whole Genome Sequencing

Studies on the characteristic chemical markers of sulfur fumigation have become an effective auxiliary way for quality control of traditional Chinese medicine. This study established a quantitative analysis method for the determination of -hydroxybenzyl hydrogen sulfite (-HS) in Gastrodiae Rhizoma (GR) based on UPLC-MS/MS. Then, 37 batches of GR were screened, and the results showed that 27 batches of them were sulfur-fumigated. Especially, the GR samples in Yunnan producing areas were sulfur-fumigated more seriously. Based on the stability of -HS after different storage time and heat treatment methods, it was found that the content of -HS was stable and reliable in the storage period of 8 months and under normal heat treatment (50, 60, 70, 80 °C) conditions. In conclusion, this study shows a high sensitivity, good selectivity and good stability of -HS, which can provide reference for the quality control and sulfur fumigation screening of GR.
China ; Chromatography, Liquid ; Drugs, Chinese Herbal ; chemistry ; standards ; Fumigation ; Gastrodia ; chemistry ; Quality Control ; Rhizome ; chemistry ; Sulfites ; analysis ; Sulfur ; Tandem Mass Spectrometry

As an important part of epigenetic marker, DNA methylation involves in the gene regulation and attracts a wide spread attention in biological auxology, geratology and oncology fields. In forensic science, because of the relative stable, heritable, abundant, and age-related characteristics, DNA methylation is considered to be a useful complement to the classic genetic markers for age-prediction, tissue-identification, and monozygotic twins' discrimination. Various methods for DNA methylation detection have been validated based on methylation sensitive restriction endonuclease, bisulfite modification and methylation-CpG binding protein. In recent years, it is reported that the third generation sequencing method can be used to detect DNA methylation. This paper aims to make a review on the detection method of DNA methylation and its applications in forensic science.
CpG Islands ; DNA Methylation/genetics* ; Epigenesis, Genetic ; Epigenomics ; Forensic Genetics/trends* ; Genetic Markers/genetics* ; Humans ; Sulfites ; Twins, Monozygotic/genetics*

OBJECTIVETo establish a rapid and convenient method of DNA modification by bisulfite sodium for the detection of DNA methylation.

METHODSThrough increasing the bisulfite sodium concentration and the temperature of treatment, cutting down the modification time, besides using glassmilk to adsorb the DNA in the purification and recovery, to improve the methods of DNA modification. Efficiency of cytosine converted to thymine in MAGE-A3 gene and DAP-K gene fragments were analyzed by bisulfite sequencing PCR in order to evaluate the DNA modification effect among the improved method, traditional method and kit method.

RESULTSThe operating time of test was shortened to about 3 hours by the improved method; conversion rate of unmethylated cytosine to thymine was over 99%; compared with the traditional method and kit method, there was no significant difference (χ(2) = 0.0564, P > 0.05); the improved method was only for the unmethylated cytosine conversion modification, and there was no significant difference in process of methylated cytosine converted to thymine comparing with the traditional method (χ(2) = 0.0149, P > 0.05).

CONCLUSIONThe improved method has high efficiency of DNA modification and has no significant effect on excessive modification;meanwhile, it has many advantages such as time-saving and easy to operate etc.

Cytosine ; chemistry ; DNA ; chemistry ; DNA Methylation ; Polymerase Chain Reaction ; Sulfites ; chemistry ; Thymine ; chemistry

To conduct a kinetic study of paraquat (PQ), we investigated 9 patients with acute PQ intoxication. All of them ingested more than 20 ml of undiluted PQ herbicide to commit suicide and arrived at our hospital early, not later than 7 h after PQ ingestion. The urine dithionite test for PQ in all of the nine patients was strongly positive at emergency room. Blood samples were obtained every 30 min for the first 2~3 h and then every 1 or 2 h, as long as the clinical progression was stable among the patients for 30 h after PQ ingestion. The area under the plasma concentration-time curve (AUCinf), which was extrapolated to infinity, was calculated using the trapezoidal rule. Toxicokinetic parameters, such as the terminal elimination half-life, apparent oral clearance, and apparent volume of distribution (Vd/F) were calculated. The maximum PQ concentration (Cmax) and the time to reach maximum PQ concentration (Tmax) were also obtained. Plasma PQ concentrations in nine patients were well described by a bi-exponential curve with a mean terminal elimination half-life of 13.1+/-6.8 h. Cmax and AUCinf were 20.8+/-25.7 mg/l and 172.5+/-160.3 h.mg/l, respectively. Apparent volume of distribution and apparent oral clearance were 50.9+/-61.3 l/kg and 173.4+/-111.2 l/h, respectively. There were a significant correlation (r =0.84; p<0.05) between the PQ amount ingested and Cmax. AUCinf also showed a significant correlation (r =0.83; p<0.05) with the PQ amount ingested. These correlations provide evidence that PQ has dose-linear toxicokinetic characteristics.
Dithionite ; Eating ; Emergency Service, Hospital ; Half-Life ; Humans ; Paraquat* ; Pharmacokinetics* ; Plasma ; Poisoning* ; Suicide

Sodium houttuyfonate (SH) is a derivative of effective component of a Chinese material medica, Houttuynia cordata, which is applied in anti-infection of microorganism. But, the antimicrobial mechanisms of SH still remain unclear. Here, we firstly discovered that SH effectively inhibits the three types of virulence related motility of.Pseudomonas aeruginosa, i.e., swimming, twitching and swarming. The plate assay results showed that the inhibitory action of SH against swimming and twitching in 24 h and swarming in 48 h is dose-dependent; and bacteria nearly lost all of the motile activities under the concentration of 1 x minimum inhibitory concentration (MIC) (512 mg x L(-1) same as azithromycin positive group (1 x MIC, 16 mg x L(-1)). Furthermore, we found that the expression of structural gene flgB and pilG is down-regulated by SH, which implies that inhibitory mechanism of SH against motility of P. aeruginosa may be due to the inhibition of flagella and pili bioformation of P. aeruginosa by SR Therefore, our presented results firstly demonstrate that SH effectively inhibits the motility activities of P. aeruginosa, and suggest that SH could be a promising antipseudomonas agents in clinic.
Alkanes ; pharmacology ; Anti-Bacterial Agents ; pharmacology ; Bacterial Proteins ; genetics ; metabolism ; Biofilms ; drug effects ; Drugs, Chinese Herbal ; pharmacology ; Fimbriae, Bacterial ; drug effects ; genetics ; metabolism ; Houttuynia ; chemistry ; Pseudomonas aeruginosa ; cytology ; drug effects ; genetics ; pathogenicity ; Sulfites ; pharmacology ; Virulence ; drug effects

OBJECTIVETo investigate the resistant effect of houttuyfonate sodium (SH) combined with imipenem (IMP) against Pseudomonas aeruginosa (Pa) biofilms.

METHODThe two-fold dilution method was used to examine the minimum inhibitory concentration (MIC) of the tested drug. The crystal violet staining was applied to detect the effect of the combination of 1/2MIC, 1MIC, 2MIC of SH, single IMP, 1/2MIC of SH and IMP of various concentrations on the clearance rate of adherent bacteria, growth of biofilms and alginate production. Fluorescein diacetate (FDA)-propidium iodide (PI) doubling staining assay was employed to observe the bacterial viability and morphological changes after membrane dispersion of each drug group.

RESULTSodium houttuyfonate could enhance the effect of IMP against pseudomonas aeruginosa biofilms. Particularly, the combination group with the concentration of 2MIC showed the highest effect, with P < 0.001 compared with the negative control group. The above results were proved by the bacterial viability and biofilm morphology under fluorescence microscope.

CONCLUSIONAfter being combined with imipenem, sodium houttuyfonate shows a higher effect against biofilms. It is expected that the combination of the two drugs could improve the clinical efficacy of associated infections.

Alkanes ; pharmacology ; Biofilms ; drug effects ; growth & development ; Drug Synergism ; Imipenem ; pharmacology ; Microbial Sensitivity Tests ; Microbial Viability ; drug effects ; Pseudomonas aeruginosa ; drug effects ; physiology ; Sulfites ; pharmacology

This study was to analyze the risk of sulfites in food consumed by the Chinese people and assess the health protection capability of maximum-permitted level (MPL) of sulfites in GB 2760-2011. Sulfites as food additives are overused or abused in many food categories. When the MPL in GB 2760-2011 was used as sulfites content in food, the intake of sulfites in most surveyed populations was lower than the acceptable daily intake (ADI). Excess intake of sulfites was found in all the surveyed groups when a high percentile of sulfites in food was in taken. Moreover, children aged 1-6 years are at a high risk to intake excess sulfites. The primary cause for the excess intake of sulfites in Chinese people is the overuse and abuse of sulfites by the food industry. The current MPL of sulfites in GB 2760-2011 protects the health of most populations.
Adolescent ; Adult ; Child ; Child, Preschool ; China ; Female ; Food Additives ; adverse effects ; standards ; Humans ; Infant ; Male ; Risk Assessment ; Sulfites ; adverse effects ; Young Adult

BACKGROUNDBoth in vitro and in vivo data have demonstrated the TGFBI gene functions as a putative tumor suppressor and is frequently downregulated in human tumors of different histological types. The hypermethylation of the TGFBI promoter, as one of the main regulatory mechanisms, is associated with TGFBI silencing. In this study, we used a methylation-specific PCR (MSP) method to evaluate the methylation status of the TGFBI promoter in human leukemias.

METHODSReal-time RT-PCR and methylation-specific PCR approaches were performed to define the TGFBI expression and promoter methylation in human leukemia cell lines and clinical samples. Genomic DNA was isolated from peripheral blood mononuclear cells from leukemia patients, bisulfite-converted, and analyzed by the MSP method.

RESULTSHypermethylation of the TGFBI promoter occurred in leukemia cell lines and demethylation treatment reexpressed TGFBI at a substantially increased level in most of leukemia cell lines tested. Furthermore, a much higher level of CpG island methylation and a significantly lower TGFBI expression were also identified in clinical leukemia samples.

CONCLUSIONThe results suggest an important role of promoter methylation in regulating TGFBI expression in leukemia, which provides a useful diagnostic marker for clinical management of human leukemias.

Cell Line, Tumor ; CpG Islands ; genetics ; DNA Methylation ; drug effects ; genetics ; Epigenesis, Genetic ; drug effects ; genetics ; Extracellular Matrix Proteins ; genetics ; Humans ; Leukemia ; epidemiology ; Promoter Regions, Genetic ; genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sulfites ; pharmacology ; Transforming Growth Factor beta ; genetics

As the International Human Epigenome Consortium (IHEC) launched officially at the 2010 Washington meeting, a giant step toward the conquest of unexplored regions of the human genome has begun. IHEC aims at the production of 1,000 reference epigenomes to the international scientific community for next 7-10 years. Seven member institutions, including South Korea, Korea National Institute of Health (KNIH), will produce 25-200 reference epigenomes individually, and the produced data will be publically available by using a data center. Epigenome data will cover from whole genome bisulfite sequencing, histone modification, and chromatin access information to miRNA-seq. The final goal of IHEC is the production of reference maps of human epigenomes for key cellular status relevant to health and disease.
Chromatin ; Genome ; Genome, Human ; Histones ; Humans ; Korea ; MicroRNAs ; Republic of Korea ; Sulfites ; Washington