• Animal Systematics, Evolution and Diversity
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• v.28 no.4
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• pp.269-278
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• 2012

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.2051-2055
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• 2012

Background: The cell cycle checkpoint kinase 2 (CHEK2) gene I157T variant may be associated with an increased risk of colorectal cancer, but it is unclear whether the evidence is sufficient to recommend testing for the mutation in clinical practice. Materials and Methods: We systematically searched PubMed, EMBASES, Elsevier and Springer for relevant articles before Apr 2012. Summary odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using a fixed-effects or random-effects models with Review Manager 5.0 software. Results: A total of seven studies including 4,029 cases and 13,844 controls based on the search criteria were included for analysis. A significant association of the CHEK2 I157T C variant with unselected CRC was found (OR = 1.61, 95% CI = 1.40-1.87, P < 0.001). We also found a significant association with sporadic CRC (OR = 1.48, 95% CI = 1.23-1.77, P < 0.001) and separately with familial CRC (OR = 1.97, 95% CI = 1.41-2.74, P < 0.001). Conclusion: This meta-analysis demonstrates that the CHEK2 I157T variant may be another important CRC-predisposing gene, which increases CRC risk, especially in familial CRC.

• Korean Journal of Biological Psychiatry
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• v.16 no.2
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• pp.121-126
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• 2009

Objectives : The serotonin transporter gene(SLC6A4) is one of the most widely studied candidate genes in autism spectrum disorder(ASD), but there have been conflicting results from studies into the association between SLC6A4 and ASD. The aim of this study was to evaluate the association between single nucleotide polymorphisms(SNPs) in the SLC6A4 gene and ASD in the Korean population. Methods : We selected 12 SNPs in SLC6A4 and observed the genotype of 151 Korean ASD trios. We tested the family-based association for each individual polymorphism and haplotype by using the standard TDT method in Haploview(http://www.broad.mit.edu/mpg/haploview/). Results : Through transmission-disequilibrium testing and haplotype analysis, we could not find any statistically significant transmitted allele or haplotype. In addition, a case-control association test with Korean HapMap data did not reveal any statistical significance. Conclusion : Although serotonin-related genes must be considered candidate genes for ASD, we suggest that common SNPs of SLC6A4 are not important markers for associations with Korean ASD.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.22 no.5
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• pp.479-486
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• 2019

Progressive familial intrahepatic cholestasis (PFIC) is a group of severe genetic disorders, inherited in an autosomal recessive manner, causing cholestasis of hepatocellular origin, later progressing to biliary cirrhosis and liver failure. This is the first report of PFIC type 1 with novel compound heterozygous mutations in Korea. The patient was presented with intrahepatic cholestasis, a normal level of serum ${\gamma}-glutamyl$ transferase, steatorrhea, and growth failure. Genetic testing of this patient revealed novel compound heterozygous mutations (p.Glu585Ter and p.Leu749Pro) in the ATP8B1 gene. After a liver transplantation at age 19 months, the patient developed severe post-transplant steatohepatitis.

• Journal of Genetic Medicine
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• v.18 no.2
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• pp.121-126
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• 2021

Chronic progressive external ophthalmoplegia (CPEO) is a complex slowly progressive mitochondrial disorder characterized by extraocular muscle weakness with or without multisystem involvement. The mainstay of therapy in a patient with CPEO is supportive. However, in moderate cases, surgery might be indicated including surgeries for ptosis and strabismus. In this article, we report a Saudi patient with CPEO due to compound heterozygous variants in the DNA polymerase gamma (POLG) gene c.2246T>C p.(Phe749Ser) and c.1735C>T p.(Arg579Trp), which are classified as pathogenic. Proper diagnosis with genetic testing confirmation is important to guide the management and counsel the patient about the prognosis and the management options. The patient was successfully managed with bilateral frontalis sling and illustrates the importance of surgical intervention to improve vision and cosmetic appearance in patients with CPEO. We emphasize the importance of multidisciplinary care in the management of cases of mitochondriopathy, especially CPEO.

• Computers and Concrete
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• v.28 no.5
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• pp.451-463
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• 2021

Inorganic basalt fiber (BF) is a novel sort of commercial concrete fiber which is made with basalt rocks. Previous studies have not sufficiently handled the behavior of self-compacted concrete, at elevated temperature, containing basalt fiber. Present endeavor covers experimental work to examine the characteristics of this material at high temperature considering different fiber content and applied temperature. Different tests were carried out to measure the mechanical properties such as compressive strength (fc), modulus of elasticity (E), Poisson's ratio, splitting tensile strength (fsplit), flexural strength (fflex), and slant shear strength (fslant) of HSC and hybrid concrete. Gene expression programming (GEP) was employed to propose new constitutive relationships depending on experimental data. It was noticed from the testing records that there is no remarkable effect of BF on the Poisson's ratio and modulus of elasticity of self-compacted concrete. The flexural strength of basalt fiber self-compacted concrete was not sensitive to temperature in comparison to other mechanical properties of concrete. Fiber volume fraction of 0.25% was found to be the optimum to some extend according to degradation of strength. The proposed GEP models were in good matching with the experimental results.

• Geomechanics and Engineering
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• v.33 no.3
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• pp.231-242
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• 2023

This paper represents a comparative study in which Gene Expression Programming (GEP), Group Method of Data Handling (GMDH), and multiple linear regressions (MLR) were utilized to derive new equations for the prediction of time-dependent bearing capacity of pile foundations driven in cohesive soil, technically called pile set-up. This term means that many piles which are installed in cohesive soil experience a noticeable increase in bearing capacity after a specific time. Results of researches indicate that side resistance encounters more increase than toe resistance. The main reason leading to pile setup in saturated soil has been found to be the dissipation of excess pore water pressure generated in the process of pile installation, while in unsaturated conditions aging is the major justification. In this study, a comprehensive dataset containing information about 169 test piles was obtained from literature reviews used to develop the models. to prepare the data for further developments using intelligent algorithms, Data mining techniques were performed as a fundamental stage of the study. To verify the models, the data were randomly divided into training and testing datasets. The most striking difference between this study and the previous researches is that the dataset used in this study includes different piles driven in soil with varied geotechnical characterization; therefore, the proposed equations are more generalizable. According to the evaluation criteria, GEP was found to be the most effective method to predict set-up among the other approaches developed earlier for the pertinent research.

• Journal of Microbiology and Biotechnology
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• v.34 no.3
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• pp.681-688
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• 2024

The accurate and rapid detection of methicillin-resistance of Staphylococcus aureus (SA) holds significant clinical importance. However, the methicillin-resistance detection strategies commonly require complicated cell lysis and gene extraction. Herein, we devised a novel colorimetric approach for the sensitive and accurate identification of methicillin-resistance of SA by combining allosteric probe-based target recognition with self-primer elongation-based target recycling. The PBP2a aptamer in the allosteric probe successfully identified the target MRSA, leading to the initiation of self-primer elongation based-cascade signal amplification. The peroxidase-like hemin/G-quadruplex undergo an isothermal autonomous process that effectively catalyzes the oxidation of ABTS2- and produces a distinct blue color, enabling the visual identification of MRSA at low concentrations. The method offers a shorter duration for bacteria cultivation compared to traditional susceptibility testing methods, as well as simplified manual procedures for gene analysis. The overall amplification time for this test is 60 min, and it has a detection limit of 3 CFU/ml. In addition, the approach has exceptional selectivity and reproducibility, demonstrating commendable performance when tested with real samples. Due to its advantages, this colorimetric assay exhibits considerable potential for integration into a sensor kit, thereby offering a viable and convenient alternative for the prompt and on-site detection of MRSA in patients with skin and soft tissue infections.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1394-1406
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• 2015

The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.

• Clinical and Experimental Reproductive Medicine
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• v.28 no.3
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• pp.183-190
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• 2001

Objective: Recently, microdissection of tissue sections has been used increasingly for the isolation of morphologically identified homogeneous cell populations, thus overcoming the obstacle of tissue complexity for the analysis cell-specific expression of macromolecules. The aim of the present study was to establish the minimal conditions required for the RNA extraction and amplification from the cells captured by the laser captured microdissection. Methods : Mouse ovaries were fixed and cut into serial sections (7 im thickness). Oocytes were captured by laser captured microdissection (LCM) method by using PixCell $II^{TM}$ system. The frozen sections were fixed in 70% ethanol and stained with hematoxylin and eosin, while the paraffin sections were stained with Multiple stain. Sections were dehydrated in graded alcohols followed by xylene and air-dried for 20 min prior to LCM. All reactions were performed in ribonuclease free solutions to prevent RNA degradation. After LCM, total RNA extraction from the captured oocytes was performed using the guanidinium isothiocyanate (GITC) solution, and subsequently evaluated by reverse transcriptase-polymerase chain reaction (RT-PCR) for glyceraldehyde-3-phosphate-dehydrogenase (GAPDH). Results: With the frozen sections, detection of the GAPDH mRNA expression in the number of captured 25 oocytes were not repeatable, but the expression was always detectable from 50 oocytes. With 25 oocytes, at least 27 PCR cycles were required, whereas with 50 oocytes, 21 cycles were enough to detect GA PDH expression. Amount of the primary cDNA required for RT-PCR was reduced down to at least 0.25 $\grave{i}$ l with 50 oocytes, thus the resting 19.75 il cDNA can be used for the testing other interested gene expression. Tissue-to-slide, tissue-to-tissue forces were very high in the paraffin sections, thus the greater number of cell procurement was required than the frozen sections. Conclusion: We have described a method for analyzing gene expression at the RNA level with the homogeneously microdissected cells from the small amount of tissues with complexity. We found that LCM coupled with RT-PCR could detect housekeeping gene expression in 50 oocytes captured. This technique can be easily applied for the study of gene expression with the small amount of tissues.