• ALGAE
• /
• v.34 no.1
• /
• pp.57-70
• /
• 2019

DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

• Korean Journal of Biological Psychiatry
• /
• v.11 no.1
• /
• pp.33-39
• /
• 2004

Objective:Nitric oxide(NO) has been known to be associated with tolerance and preference to alcohol. It has also been known to affect various alcohol drinking behavior, alcohol withdrawal symptoms and alcohol- induced brain damage. The purpose of this study was to determine the difference, among alcohol dependence group, alcohol drinking group and abstinence group, in serum concentration of nitrite, a stable metabolite of NO, and it's relationship to clinical and biochemical markers of alcoholism. Methods:Forty subjects diagnosed as alcohol dependence according to DSM-IV diagnostic criteria were evaluated for the clinical characteristics and biochemical markers of alcohol dependence including nitrite with their CIWA-Ar scores checked just after admission. Thirty-nine healthy controls were also evaluated, divided into twenty-three alcohol drinking group and sixteen abstinence group. Clinical characteristics were evaluated by CIWA-Ar, CAGE and AUDIT questionnaires. Aspartate aminotransferase(AST), alanine aminotransferase (ALT), gamma glutamyltransferase(GGT) and mean corpuscular volume(MCV) were used as the biochemical markers of alcohol dependence. Serum nitrite concentrations were measured by Griess reaction. Results:1) The concentrations of nitrite in alcohol dependence patients were not different from those in the control subjects. 2) There were no significant association between the nitrite concentrations and the CIWA-Ar scores in alcohol dependence patients. 3) Nitrites are significantly increased in alcohol dependence group and alcohol drinking group compared with abstinence group. Conclusions:These findings suggest that serum nitrite concentration has no relation with alcohol withdrawal symptoms, but alcohol drinking increases serum nitrite concentration influenced by general condition of the body.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.5
• /
• pp.1727-1735
• /
• 2012

Regardless of advances in treatment modalities with the invention of newer therapies, breast cancer remains a major health problem with respect to its diagnosis, treatment and management. This female malignancy with its tremendous heterogeneous nature is linked to high incidence and mortality rates, especially in developing region of the world. It is the malignancy composed of distinct biological subtypes with diverse clinical, pathological, molecular and genetic features as well as different therapeutic responsiveness and outcomes. This inconsistency can be partially overcome by finding novel molecular markers with biological significance. In recent years, newer technologies help us to indentify distinct biomarkers and increase our understanding of the molecular basis of breast cancer. However, certain issues need to be resolved that limit the application of gene expression profiling to current clinical practice. Despite the complex nature of gene expression patterns of cDNAs in microarrays, there are some innovative regulatory molecules and functional pathways that allow us to predict breast cancer behavior in the clinic and provide new targets for breast cancer treatment. This review describes the landscape of different molecular markers with particular spotlight on vitamin D signaling pathway and apoptotic specific protein of p53 (ASPP) family members in breast cancer.

• Korean Journal of Biological Psychiatry
• /
• v.5 no.2
• /
• pp.235-242
• /
• 1998

Objectives : Alcohol-induced oxidative stress has been known to injure various tissues or organs. This stress is related with free radicals which are produced as the result of long-term alcohol consumption. Malonyldialdehyde(MDA) is produced by the interaction of free radicals and cell membrane lipids, and indicates the degree of lipid peroxidation indirectly. The purpose of this study was to investigate the relationship between red blood cell(RBC) membrane lipid peroxidation by free radicals, and associated hepatic injuries and hematologic changes. Methods : Thirty-three subjects diagnosed as alcohol dependence according to DSM-IV diagnostic criteria were evaluated within 72 hours after discontinuing alcohol drinking. Clinical characteristics were evaluated by CAGE questionnaire and Korean Michigan Alcoholism Screening Test(MAST). RBC membrane MDA level was measured as the marker of RBC membrane lipid peroxidation. Aspartate aminotransferase(AST), alanine aminotransferase(ALT) and gamma-glutamyltransferase(GGT) were used as the biochemical markers of liver damage due to alcohol ingestion. The alcohol-induced hematologic change was assessed by mean corpuscular volume(MCV). Results : The results were as follows. Clinical characteristics were not different between two groups having normal and abnormal levels of AST, ALT, GGT or MCV. The levels of MDA were not correlated with the clinical characteristics and serum levels of AST, ALT and GGT. However, there was a significant correlation between the levels of MDA and the value of MCV(p=0.017). Conclusions : These findings suggest that oxidative stress in alcohol dependence may not be reflected in liver enzyme markers such as AST, ALT and GGT, but may be reflected in MCV.

• Korean Journal of Biological Psychiatry
• /
• v.12 no.1
• /
• pp.3-12
• /
• 2005

Most suicides(about 90%) occur in the context of psychiatric disorders. Prediction of suicide risk in patients with mental illness is very important in preventing suicide attempts. However, current approaches to predict suicidality are based on clinical history and have low specificity and biological markers are not yet included. Many studies have explored the association between different biological parameters and suicidality. Studies of cerebro-spinal fluid(CSF) demonstrated that 5-HIAA and HVA levels were lower in patients with a history of suicide. Platelet serotonin transporter and the 5-HT2 serotonin receptor have also been studied in relation to violence and suicide. Depressive patients with greater suicidal tendency had significantly lower cholesterol concentrations but some researchers failed to find the correlation. DST non-supression is reported to predict suicidality in major depression. Several studies demonstrated a relationship between intron 7 polymorphism of tryptophan hydroxylase and suicidal behavior. Since suicide is not occurred in a single disease, the systematic and comprehensive study in large samples with various diagnoses is necessary to find the biological and genetic predictors of suicidal behavior.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
• /
• v.31 no.3
• /
• pp.154-160
• /
• 2020

Objectives: It remains unclear whether methylphenidate (MPH) has yadverse effects on growth in children. This study aimed to investigate the association of MPH with serum biological markers of growth in children with attention-deficit/hyperactivity disorder (ADHD). Methods: The present study included 103 children with ADHD (64 drug-naive children, 39 MPH-treated children) and 112 control subjects. Children with ADHD were diagnosed on the basis of a semi-structured interview. Levels of biochemical markers of growth, including insulin-like growth factor-I, thyroid stimulating hormone (TSH), free T₄, calcium, phosphorus, alkaline phosphatase, vitamin D, hemoglobin, total protein, albumin, total cholesterol, and hematocrit were measured in these individuals. Results: Except in case of TSH, no intergroup differences were found in the levels of the growth markers. The levels of TSH were found to be lower in the MPH-treated boys with ADHD than in the drug-naive and control groups (p<0.05), although the levels of TSH in all the groups were within normal limits. Conclusion: In this cross-sectional study, no significant association was found between MPH and growth markers. This calls for the need to carry out prospective longitudinal research studies in the future that investigate the effect of MPH on the growth trajectory in children.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• v.38 no.4
• /
• pp.204-211
• /
• 2012

Objectives: Dental implants installation in patients with diabetes remains controversial as altered bone healing around implants has been reported. And little is known about the biological factors involved in bone healing around implants. The present study aimed to investigate the biological markers around immediately placed implants in rats with controlled and uncontrolled diabetes. Materials and Methods: Twenty rats (40 sites) were divided into the control, insulin-treated and diabetic groups. The rats received streptozotocin (60 mg/kg) to induce diabetes; animals in the insulin-treated group also received three units of subcutaneous slow-release insulin. Two threaded titanium alloy implant ($1.2{\times}3mm$) were placed in the extraction socket of the both maxillary first molars and allowed for healing. Bone blocks including implant were harvested at 3 days, 1, 2 and 4 weeks. The levels of bone morphogenetic protein (BMP)-4, transforming growth factor (TGF)-${\beta}1$, osteocalcin (OC) and osteonectin (ON) were measured in the peri-implant osseous samples by RT-PCR. Results: The BMP-4 level increased immediately in all groups by day 3, then decreased abruptly in the control and the insulin-treated groups. However, by week 4, all groups showed mostly the same amount of BMP-4 expression. The level of TGF-${\beta}1$ also instantly increased by day 3 in the insulin-treated group. This level elevated again reaching the same values as the control group by week 4, but was not as high as the diabetic group. In addition, the expression of OC and ON in the control and insulin-treated groups was higher than that of the diabetic group at 2 weeks and 4 weeks, indicating active bone formation in these groups. Conclusion: The immediate placement of titanium implants in the maxilla of diabetic rat led to an unwanted bone healing response. Conclusively, the results of this study suggest that immediate implant insertion in patients with poorly controlled diabetes might be contraindicated.

• Korean Journal of Plant Taxonomy
• /
• v.41 no.4
• /
• pp.299-314
• /
• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.

• Animal cells and systems
• /
• v.13 no.3
• /
• pp.305-314
• /
• 2009

The control region of mitochondrial DNA (13516-14619) is located between srRNA and $tRNA^{lle}$ gene in swimming crab, Portunus trituberculatus. The present study was investigated the genetic polymorph isms of the control region in samples of P. trituberculatus collected at coastal waters of the Yellow Sea in Korea. A total of 300 substitution and indel polymorphic sites were identified. In addition to SNPs and indel variation, a hypervariable microsatellite motif was also identified at position from 14358 to 14391, which exhibited 10 alleles including 53 different suballeles. When the hypervariable microsatellite motif was removed from the alignment, 95 haplotypes were identified (93 unique haplotypes). The nucleotide and haplotype diversities were ranged from 0.024 to 0.028 and from 0.952 to 1.000, respectively. The statistically significant evidence for geographical structure was not detected from the analyses of neighbor-joining tree and minimum-spanning network, neither. This result suggest that population of P. trituberculatus are capable of extensive gene flow among populations. We believed that the polymorph isms of the control region will be used for informative markers to study phylogenetic relationships of P. trituberculatus.

• Journal of the Korean Society of Tobacco Science
• /
• v.30 no.2
• /
• pp.85-93
• /
• 2008

This report describes a set of seven informative single-nucleotide polymorphisms (SNPs) and one insertion-deletion (INDEL) distributed over 24 cultivars that can be used for tobacco (Nicotiana tabacum L.) cultivar identification. We analyzed 163,000 genomic DNA sequences downloaded from Tobacco Genome Initiative database and assembled 31,370 contigs and 60,000 singletons. Using relatively long contigs, we designed primer sets for PCR amplification. We amplified 61 loci from 24 cultivars and sequenced the PCR products. We found seven significant SNPs and one INDEL among the sequences and we classified the 24 cultivars into 10 groups. SNP frequency of tobacco, 1/8,380 bp, was very low in comparison with those of other plant species, between 1/46 bp and 1/336 bp. For exact identification of tobacco cultivars, many more SNP markers should be developed. This study is the first attempt to identify tobacco cultivars using SNP markers.