• Analytical Science and Technology
• /
• v.31 no.2
• /
• pp.65-70
• /
• 2018

This study compared two methods for preparing ancient DNA (aDNA) for the construction of successful shotgun libraries that may be applied to massive parallel sequencing. For the comparative analysis, the DNA of prehistoric rib samples from Hungary was extracted using either a manually prepared silica suspension or the Amicon Ultracel-15 10K ultracentrifugal device (Millipore). After the extraction of the same amount of bone powder (about 150 mg) from three samples by each method, the amount of extracted double-stranded DNA and the subsequent degree of construction of the shotgun library were analyzed. The Amicon device method was rapid and easier to perform and resulted in an approximately 11-fold higher DNA recovery than that obtained using the silica suspension. The shotgun library constructed using DNA templates prepared by the Amicon device was more successful than that constructed from templates isolated using the silica suspension. The comparative study of these two aDNA extraction methods showed that the Amicon device has the advantages of saving time, process simplicity, and high efficiency.

• Parasites, Hosts and Diseases
• /
• v.57 no.6
• /
• pp.567-573
• /
• 2019

An archaeoparasitological analysis of the soil samples from Nadym Gorodok site of Western Siberia has been carried out in this study. The archaeological site was dated as the 13 to 18th century, being characterized as permafrost region ensuring good preservation of ancient parasite eggs. Parasite eggs as Opisthorchis felineus, Alaria alata, and Diphyllobothrium sp. were found in the archaeological soil samples, which made clear about the detailed aspects of Nadym Gorodok people's life. We found the Diphyllobothrium sp. eggs throughout the 14 to 18th century specimens, allowing us to presume that raw or undercooked fish might have been commonly used for the foods of Nadym Gorodok inhabitants and their dogs for at least the past 400 years. Our study on Nadym Gorodok specimens also demonstrate that there might have been migratory interactions and strong economic ties between the people and society in Western Siberia, based on archaeoparasitological results of Opisthorchis felineus in Western Siberia.

• Clinical and Experimental Reproductive Medicine
• /
• v.44 no.2
• /
• pp.63-72
• /
• 2017

Objective: Hyperstimulation methods are broadly used for in vitro fertilization (IVF) in patients with infertility; however, the side effects associated with these therapies, such as ovarian hyperstimulation syndrome (OHSS), have not been well studied. N-glycoproteomes are subproteomes used for the remote sensing of ovarian stimulation in follicular growth. Glycoproteomic variation in human follicular fluid (hFF) has not been evaluated. In this study, we aimed to identify and quantify the glycoproteomes and N-glycoproteins (N-GPs) in natural and stimulated hFF using label-free nano-liquid chromatography/electrospray ionization-quad time-of-flight mass spectrometry. Methods: For profiling of the total proteome and glycoproteome, pooled protein samples from natural and stimulated hFF samples were selectively isolated using hydrazide chemistry to obtain the total proteomes and glycoproteomes. N-GPs were validated by the consensus sequence N-X-S/T (92.2% specificity for the N-glycomotif at p<0.05). All data were compared between natural versus hyperstimulated hFF samples. Results: We detected 41 and 44 N-GPs in the natural and stimulated hFF samples, respectively. Importantly, we identified 11 N-GPs with greater than two-fold upregulation in stimulated hFF samples compared to natural hFF samples. We also validated the novel N-GPs thyroxine-binding globulin, vitamin D-binding protein, and complement proteins C3 and C9. Conclusion: We identified and classified N-GPs in hFF to improve our understanding of follicular physiology in patients requiring assisted reproduction. Our results provided important insights into the prevention of hyperstimulation side effects, such as OHSS.

• Journal of the Korea Institute of Military Science and Technology
• /
• v.27 no.4
• /
• pp.507-515
• /
• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.10
• /
• pp.1616-1621
• /
• 2007

We have established a SYBR Green-based realtime PCR method using AnyDirect solution, which enhances PCR from whole blood, for direct amplification of the virA gene of Shigella flexneri and the invA gene of Salmonella typhimurium from human feces without prior DNA purification. When we compared the efficiency of conventional or realtime PCR amplification of the virA and invA genes from the supernatant of boiled feces supplemented with S. flexneri and S. typhimurium in the presence or absence of AnyDirect solution, amplification products were detected only in reactions to which AnyDirect solution had been added. The detection limit of real-time PCR was $1{\times}10^4\;CFU/g$ feces for S. flexneri and $2{\times}10^4\;CFU/g$ feces for S. typhimurium; this sensitivity level was comparable to other studies. Our real-time PCR assay with AnyDirect solution is simple, rapid, sensitive, and specific, and allows simultaneous detection of S. flexneri and S. typhimurium directly from fecal samples without prior DNA purification.

• Toxicological Research
• /
• v.24 no.4
• /
• pp.297-305
• /
• 2008

This study was carried out to measure the concentration of heavy metals (Pb, Mn, Cr, Cd, Ni, Zn, and Cu) in water and Bolti fish (Tilapia nilotica) samples collected from Rasheed branch of River Nile, north of El-Giza Governorate, Egypt by atomic absorption spectrophotometry. The investigated districts through which the branch passes include El-Manashi, Gezzaya, El Katta, Abo Ghaleb and Wardan. Based on WHO and FAO safety reference standards, the results of the current study showed that water and fish tissues were found to contain heavy metals at significantly variable concentration levels among the investigated districts. They were polluted with respect to all the metals tested at Gezzaya district. However, the levels of analyzed metals in water and fish tissues were found lower than legal limits in other districts. The heavy metals showed differential bioaccumulation in fish tissues of the different districts as the accumulation pattern (as total heavy metal residues) was district dependant as follow: Gezzaya > Wardan > El Katta > Abo Ghaleb > El Manashi.

• Parasites, Hosts and Diseases
• /
• v.52 no.3
• /
• pp.235-242
• /
• 2014

Paleoparasitology is the application of conventional or molecular investigative techniques to archeological samples in order to reveal parasitic infection patterns among past populations. Although pioneering studies already have reported key paleoparasitological findings around the world, the same sorts of studies had not, until very recently, been conducted in sufficient numbers in Korea. Mummified remains of individuals dating to the Korean Joseon Dynasty actually have proved very meaningful to concerned researchers, owing particularly to their superb preservation status, which makes them ideal subjects for paleoparasitological studies. Over the past several years, our study series on Korean mummies has yielded very pertinent data on parasitic infection patterns prevailing among certain Joseon Dynasty populations. In this short review, we summarized the findings and achievements of our recent paleoparasitological examinations of Joseon mummies and discussed about the prospects for future research in this vein.

• Communications for Statistical Applications and Methods
• /
• v.26 no.1
• /
• pp.1-9
• /
• 2019

Various probabilistic methods have been proposed for using interpopulation allele frequency differences to infer the ethnic group of a DNA specimen. The selection of the statistical method is critical because the accuracy of the statistical classification results vary. For the ancestry classification, we proposed a new ancestry evaluation method that estimate the combined ethnicity index as well as compared its performance with various classical classification methods using two real data sets. We selected 13 SNPs that are useful for the inference of ethnic origin. These single nucleotide polymorphisms (SNPs) were analyzed by restriction fragment mass polymorphism assay and followed by classification among ethnic groups. We genotyped 400 individuals from four ethnic groups (100 African-American, 100 Caucasian, 100 Korean, and 100 Mexican-American) for 13 SNPs and allele frequencies that differed among the four ethnic groups. Additionally, we applied our new method to HapMap SNP genotypes for 1,011 samples from 4 populations (African, European, East Asian, and Central-South Asian). Our proposed method yielded the highest accuracy among statistical classification methods. Our ethnic group classification system based on the analysis of ancestry informative SNP markers can provide a useful statistical tool to identify ethnic groups.

• Parasites, Hosts and Diseases
• /
• v.61 no.1
• /
• pp.89-93
• /
• 2023

Parasite infection rates estimated by examining ancient coprolites can provide insights into parasitism in Joseon society. Using newly discovered Joseon period cases is essential to regularly update the parasite infection rates and reinforce the reliability of our previous estimations. In the present study, we investigated parasite infections in Joseon coprolites newly isolated from the cities of Euijeongbu, Gumi, and Wonju. We then updated the overall parasite infection rates of Joseon period samples (n= 30) as follows: 86.7% (26/30) for Trichuris trichiura, 56.7% (17/30) for Ascaris lumbricoides, 30.0% (9/30) for Clonorchis sinensis, and 30.0% (9/30) for Paragonimus westermani. The parasite infection rates in the Joseon society, estimated through coprolite examination, were very similar to those determined previously despite the addition of new cases to the existing data pool.

• Safety and Health at Work
• /
• v.13 no.4
• /
• pp.507-511
• /
• 2022

Law enforcement officers (LEOs) often encounter rapidly changing and uncontrolled situations that expose them to various hazards. A law enforcement agency requested an evaluation by the National Institute for Occupational Safety and Health (NIOSH) when multiple LEOs reported illness after executing a search warrant and taking a suspect into custody. NIOSH investigators interviewed LEOs and reviewed medical records, forensic laboratory results for collected evidence, and environmental testing results of samples taken after the operation. Two-thirds (25 of 38) of LEOs who participated in the operation reported ≥1 symptom. Eleven LEOs met a case definition for influenza-like illness (ILI). Members of one unit were more likely to have ILI than non-members (prevalence ratio (PR), 4.1; 95% confidence interval (CI): 1.3-13.0; p = 0.01). Influenza vaccination was associated with a lower prevalence of ILI (PR, 0.2; 95% CI, 0.1-0.9; p = 0.02). Preventing employees from working while ill and annual influenza vaccination might prevent similar occurrences.