• Clinical and Experimental Reproductive Medicine
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• v.46 no.4
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• pp.147-151
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• 2019

Objective: The aim of this study was to investigate DNA fragmentation status in human spermatozoa according to specific tail swelling patterns determined via hypo-osmotic swelling test (HOST). Methods: Frozen semen samples from 21 healthy donors were thawed and prepared by the swim-up technique for use in intracytoplasmic sperm injection. The semen samples were treated for 5 minutes as part of the HOST procedure and then underwent the sperm chromatin dispersion test using a Halosperm kit. DNA fragmentation status (large halo, medium halo, small halo, no halo, or degraded) and the specific tail swelling pattern ("a"-"g") were assessed at the level of a single spermatozoon. A total of 42,000 spermatozoa were analyzed, and the percentage of spermatozoa without DNA fragmentation (as evidenced by a large or medium halo) was assessed according to the specific tail swelling patterns observed. Results: The HOST examinations showed that > 93% of spermatozoa across all types displayed no DNA fragmentation. The percentage of spermatozoa without DNA fragmentation was 100% in type "d", 98.67% in type "g", and 98.17% in type "f" spermatozoa. Conclusion: We found that the type "d" spermatozoa displayed no DNA fragmentation, but the other types of spermatozoa also displayed very low rates of DNA fragmentation. This result may be associated with the processing of the spermatozoa by density gradient centrifugation and the swim-up technique.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8059-8065
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• 2016

Nasopharyngeal carcinoma (NPC) is a common tumor in southern China and south-eastern Asia. Effective strategies for the prevention or screening of NPC are limited. Exploring effective biomarkers for the early diagnosis and prognosis of NPC continues to be a rigorous challenge. Evidence is accumulating that DNA methylation alterations are involved in the initiation and progression of NPC. Over the past few decades, aberrant DNA methylation in single or multiple tumor suppressor genes (TSGs) in various biologic samples have been described in NPC, which potentially represents useful biomarkers. Recently, large-scale DNA methylation analysis by genome-wide methylation platform provides a new way to identify candidate DNA methylated markers of NPC. This review summarizes the published research on the diagnostic and prognostic potential biomarkers of DNA methylation for NPC and discusses the current knowledge on DNA methylation as a biomarker for the early detection and monitoring of progression of NPC.

• Genomics & Informatics
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• v.9 no.2
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• pp.89-91
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• 2011

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.

• Molecular & Cellular Toxicology
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• v.1 no.2
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• pp.92-98
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• 2005

DNA microarray analysis of gene expression in toxicogenomics typically requires relatively large amounts of total RNA. This limits the use of DNA microarray when the sample available is small. To confront this limitation, different methods of linear RNA amplification that generate antisense RNA (aRNA) have been optimized for microarray use. The target preparation strategy using amplified RNA in DNA microarray protocol can be divided into direct-incorporation labeling which resulted in cDNA targets (Cy-dye labeled cDNA from aRNA) and indirect-labeling which resulted in cRNA targets (i.e. Cy-dye labeled aRNA), respectively. However, despite the common use of amplified targets (cDNA or cRNA) from aRNAs, no systemic assessment for the use of amplified targets and bias in terms of hybridization performance has been reported. In this investigation, we have compared the hybridization performance of cRNA targets with cDNA targets from aRNA on a 10 K cDNA microarrays. Under optimized hybridization conditions, we found that 43% of outliers from cDNA technique and 86% from the outlier genes were reproducibly detected by both targets hybridization onto cDNA microarray. This suggests that the cRNA labeling method may have a reduced capacity for detecting the differential gene expression when compared to the cDNA target preparation. However, further validation of this discordant result should be pursued to determine which techniques possesses better accuracy in identifying truly differential genes.

• Molecules and Cells
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• v.23 no.2
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• pp.239-245
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• 2007

DnaK is a major antigen in Streptococcus pneumoniae, and is induced by a minor shift in temperature (30 to $37^{\circ}C$) but not by ethanol shock. Although HrcA in the presence of $Ca^{{+}{+}}$ represses the expression of both groEL and hrcA, the control of transcription of the dnaK operon is not completely understood. In this study, the dnaK operon of S. pneumoniae (5' hrcA-grpE-dnaK-dnaJ) was cloned and analyzed. It contains large intergenic regions in grpE/dnaK and dnaK/dnaJ. Pulse labeling with [$^{35}S$]-methionine and immunoblot analyses revealed the presence of higher levels of DnaK than of HrcA even in the presence of $Ca^{{+}{+}}$ after heat shock suggesting that $Ca^{{+}{+}}$ differentially regulates the heat shock responses of hrcA and dnaK. By blocking de novo mRNA synthesis with rifampin it was shown that neither the hrcA nor the groEL transcripts were stabilized by heat shock even though dnaK transcripts were stabilized. We conclude that S. pneumoniae uses fine regulation of the transcription of the individual genes of the tetracistronic dnaK operon to cope with the various stresses experienced during infections.

• ALGAE
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• v.22 no.2
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• pp.57-67
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• 2007

We analyzed the nuclear-encoded large subunit ribosomal RNA gene (LSU rDNA) sequences of 19 dinoflagellates occurring in costal waters off Korea and reconstructed a phylogenetic tree containing 74 representative species from 37 distinct genera. Of these, the LSU rDNA sequences of Amylax triacantha (Jörgensen) Sournia, Gonyaulax verior Sournia (= Amylax diacantha Meunier), Gyrodinium fissum (Levander) Kofoid et Swezy, Katodinium glaucum (Lebour) Lebour III, Noctiluca scintillans (Macartney) Kofoid et Swezy, Oxyphysis oxytoxoides Kofoid, and Pyrophacus steinii (Schiller) Wall et Dale are reported for the first time. Our LSU rDNA tree consistently placed Oxyrrhis marina Dujardin and N. scintillans at the most primitive positions, giving rise to a strongly supported monophyletic group of typical dinoflagellate species belonging to the Dinophyceae. The phylogenetic relationships among the typical dinoflagellates, however, were not resolved in the higher taxonomic levels in general. Only genera at terminal branches were usually supported with high confidence. The Dinophysiales, represented by Dinophysis species and O. oxytoxoides, formed a strongly supported monophyletic assemblage. The Gymnodiniales and Peridiniales were recovered as polyphyletic groupings. Members of the Gonyaulacales were consistently grouped together, but lacked statistical support. Within this order, the Ceratiaceae and Goniodomataceae each formed a monophyletic group, but the Gonyaulacaceae was polyphyletic. The phylogenetic relationships of the Gonyaulacaceae were generally congruent with differences in the combinations of the apical pore complex, hypothecal organization and thecal formula.

• The Korean Journal of Mycology
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• v.48 no.3
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• pp.217-228
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• 2020

Endophytic fungi were isolated from the leaves of plants inhabiting the Hansando Island in Korea. We identified the fungal strains based on their morphological characteristics and on the phylogenetic analysis using DNA sequences of the internal transcribed spacer, small subunit rDNA, large subunit rDNA, and translation elongation factor 1- α regions. In this study, we isolated five endophytic fungi that have not been recorded in Korea, Arthrinium camelliaesinensis, Beltraniella humicola, B. portoricensis, Microxiphium theae, and Piceomphale pinicola. Their morphological characteristics as well as the results of molecular phylogenetic analysis are reported here.

• The Korean Journal of Mycology
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• v.48 no.4
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• pp.415-421
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• 2020

We isolated endophytic fungi from the leaves of woody plants inhabiting the Ulleungdo Island and Yeosu in South Korea. The fungal strains were identified based on their morphological characteristics in conjunction with phylogenetic analysis, which was performed using sequences of the internal transcribed spacer, large subunit rDNA, and β-tubulin DNA. We confirmed the presence of Neofusicoccum mangiferae and Thyronectria cucurbitula, two endophytic fungal species that had not been previously recorded in Korea. In this report, we describe the morphological characteristics of these fungal strains and results of the DNA-based phylogenetic analysis.

• Parasites, Hosts and Diseases
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• v.56 no.5
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• pp.453-461
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• 2018

The aim of this study is to delineate 'admixed hybrid' and 'introgressive' Fasciola genotypes present in the Fasciola population in Vietnam. Adult liver flukes collected from ruminants in 18 Provinces were morphologically sorted out by naked eyes for small (S), medium (M) and large (L) body shapes; and human samples (n=14) from patients. Nuclear ribosomal (rDNA) ITS1 and ITS2, and mitochondrial (mtDNA) nad1 markers were used for determination of their genetic status. Total 4,725 worm samples of ruminants were tentatively classified by their size: 6% (n=284) small (S)-, 13% (n=614) medium (M)-, and 81% (n=3,827) large (L)-forms. All the representative (n=120, as 40 each group) and 14 human specimens, possessed maternal mtDNA of only F. gigantica and none of F. hepatica. Paternally, all (100%) of the L-(n=40) and 77.5% (n=31) of the M-flukes had single F. gigantica rDNA indicating 'pure' F. gigantica. A majority (90%, n=36) of the S- and 15% (n=6) of the M-worms had single F. hepatica rDNA, indicating their introgressive; the rest (10%, n=4) of the S- and 7.5% (n=3) of the M-flukes had mixture of both F. gigantica and F. hepatica rDNAs, confirming their admixed hybrid genetic status. Fourteen human samples revealed 9 (64%) of pure F. gigantica, 3 (22%) of introgressive and 2 (14%) of admixed hybrid Fasciola spp. By the present study, it was confirmed that the small worms, which are morphologically identical with F. hepatica, are admixed and/or introgressive hybrids of Fasciola spp., and able to be the pathogens of human fascioliasis.

• Journal of Microbiology and Biotechnology
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• v.27 no.6
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• pp.1098-1105
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• 2017

Vesicular stomatitis virus G glycoprotein (VSV-G) has been widely used for pseudotyping retroviral, lentiviral, and artificial viral vectors. The objective of this study was to establish a potential approach for large-scale production of VSV-G. To this end, VSV-G was cloned with an N-terminal His-tag into Pichia pastoris expression vector pPIC3.5K. Three clones ($Mut^s$) containing the VSV-G expression cassette were identified by PCR. All clones proliferated normally in expansion medium, whereas the proliferation was reduced significantly under induction conditions. VSV-G protein was detected in cell lysates by western blot analysis, and the highest expression level was observed at 96 h post induction. VSV-G could also be obtained from the condition medium of yeast protoplasts. Furthermore, VSV-G could be incorporated into Ad293 cells and was able to induce cell fusion, leading to the transfer of cytoplasmic protein. Finally, VSV-G-mediated DNA transfection was assayed by flow cytometry and luciferase measurement. Incubation of VSV-G lysate with the pGL3-control DNA complex increased the luciferase activity in Ad293 and HeLa cells by about 3-fold. Likewise, incubation of VSV-G lysate with the pCMV-DsRed DNA complex improved the transfection efficiency into Ad293 by 10% and into HeLa cells by about 1-fold. In conclusion, these results demonstrate that VSV-G could be produced from P. pastoris with biofunctionalities, demonstrating that large-scale production of the viral glycoprotein is feasible.