• Journal of Interdisciplinary Genomics
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• v.5 no.2
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• pp.18-23
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• 2023

Conventional evaluation method for identifying the organic cause of short stature has a low detection rate. If an infant who is small for gestational age manifests postnatal growth deterioration, triangular face, relative macrocephaly, and protruding forehead, a genetic testing of IGF2, H19, GRB10, MEST, CDKN1, CUL7, OBSL1, and CCDC9 should be considered to determine the presence of Silver-Russell syndrome and 3-M syndrome. If a short patient with prenatal growth failure also exhibits postnatal growth failure, microcephaly, low IGF-1 levels, sensorineural deafness, or impaired intellectual development, genetic testing of IGF1 and IGFALS should be conducted. Furthermore, genetic testing of GH1, GHRHR, HESX1, SOX3, PROP1, POU1F1, and LHX3 should be considered if patients with isolated growth hormone deficiency have short stature below -3 standard deviation score, barely detectable serum growth hormone concentration, and other deficiencies of anterior pituitary hormone. In short patients with height SDS <-3 and high growth hormone levels, genetic testing should be considered to identify GHR mutations. Lastly, when severe short patients (height z score <-3) exhibit high levels of prolactin and recurrent pulmonary infection, genetic testing should be conducted to identify STAT5B mutations.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.5
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• pp.686-690
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• 2015

The adrenergic receptor beta 2 (ADRB2) plays a role in various physiological responses of the muscle to exercise, such as contraction and relaxation. Given its important role in muscle function, we investigated the structure of the horse ADRB2 gene and its expression pattern after exercise to determine if it can serve as a putative biomarker for recovery. Evolutionary analyses using synonymous and non-synonymous mutation ratios, were compared with other species (human, chimpanzee, mouse, rat, cow, pig, chicken, dog, and cat), and revealed the occurrence of positive selection in the horse ADRB2 gene. In addition, expression analyses by quantitative polymerase chain reaction exhibited ubiquitous distribution of horse ADRB2 in various tissues including lung, skeletal muscle, kidney, thyroid, appendix, colon, spinal cord and heart, with the highest expression observed in the lung. The expression of ADRB2 in skeletal muscle was significantly up-regulated about four folds 30 minutes post-exercise compared to pre-exercise. The expression level of ADRB2 in leukocytes, which could be collected with convenience compared with other tissues in horse, increased until 60 min after exercise but decreased afterward until 120 min, suggesting the ADRB2 expression levels in leukocytes could be a useful biomarker to check the early recovery status of horse after exercise. In conclusion, we identified horse ADRB2 gene and analyzed expression profiles in various tissues. Additionally, analysis of ADBR2 gene expression in leukocytes could be a useful biomarker useful for evaluation of early recovery status after exercise in racing horses.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.4
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• pp.334-340
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• 2001

Two different types of molecular markers, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), were used to measure genetic diversity among five Korean, eight Thai, and three wild soybeans. For SSR analysis, a total of 20 markers were surveyed to detect polymorphisms. For SNP analysis, four primers were designed from consensus sequence regions on disease resistance protein homolog genes, and used to amplify the genomic region. The PCR products were sequenced. A number of polymorphic SSR and SNP bands were scored on all genotypes and their genetic similarity was measured. Clustering analysis was performed independently on both types of markers. Clustering based on SSR markers separated the genotypes into three main groups originated from Korea, Thailand, and wild soybeans. On the other hand, two main groups were classified using SNP analysis. It seemed that SSR was more informative than SNP in this study. This may be due to the fact that SNP was surveyed on the smaller genomic region than SSR. Grouping based on the combined data of both markers revealed similar results to that of SNP rather than that of SSR. This might be due to the fact that more loci from SNP were considered to measure genetic relatedness than those from the SSR.

• Genomics & Informatics
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• v.10 no.3
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• pp.167-174
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• 2012

AKT is a signal transduction protein that plays a central role in the tumorigenesis. There are 3 mammalian isoforms of this serine/threonine protein kinase-AKT1, AKT2, and AKT3-showing a broad tissue distribution. We first discovered 2 novel polymorphisms (AKT2 -9826 C/G and AKT3 -811 A/G), and we confirmed 6 known polymorphisms (AKT2 -9473 C/T, AKT2 -9151 C/T, AKT2 -9025 C/T, AKT2 -8618G/A, AKT3 -675 A/-, and AKT3 -244 C/T) of the AKT2 and AKT3 promoter region in 24 blood samples of Korean lung cancer patients using direct sequencing. To evaluate the role of AKT2 and AKT3 polymorphisms in the risk of Korean lung cancer, genotypes of the AKT2 and AKT3 polymorphisms (AKT2 -9826 C/G, AKT2 -9473 C/T, AKT2 -9151 C/T, AKT2 -9025 C/T, AKT2 -8618G/A, and AKT3 -675 A/-) were determined in 360 lung cancer patients and 360 normal controls. Statistical analyses revealed that the genotypes and haplotypes in the AKT2 and AKT3 promoter regions were not significantly associated with the risk of lung cancer in the Korean population. These results suggest that polymorphisms of the AKT2 and AKT3 promoter regions do not contribute to the genetic susceptibility to lung cancer in the Korean population.

• Clinical and Experimental Pediatrics
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• v.55 no.12
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• pp.487-490
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• 2012

We report a case of isodicentric chromosome 15 (idic(15) chromosome), the presence of which resulted in uncontrolled seizures, including epileptic spasms, tonic seizures, and global developmental delay. A 10-month-old female infant was referred to our pediatric neurology clinic because of uncontrolled seizures and global developmental delay. She had generalized tonic-clonic seizures since 7 months of age. At referral, she could not control her head and presented with generalized hypotonia. Her brain magnetic resonance imaging scans and metabolic evaluation results were normal. Routine karyotyping indicated the presence of a supernumerary marker chromosome of unknown origin (47, XX +mar). An array-comparative genomic hybridization (CGH) analysis revealed amplification from 15q11.1 to 15q13.1. Subsequent fluorescence in situ hybridization analysis confirmed a idic(15) chromosome. Array-CGH analysis has the advantage in determining the unknown origin of a supernumerary marker chromosome, and could be a useful method for the genetic diagnosis of epilepsy syndromes associated with various chromosomal aberrations.

• Journal of Microbiology and Biotechnology
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• v.27 no.9
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• pp.1649-1656
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• 2017

In simultaneous saccharification and fermentation (SSF) for production of cellulosic biofuels, engineered Saccharomyces cerevisiae capable of fermenting cellobiose has provided several benefits, such as lower enzyme costs and faster fermentation rate compared with wild-type S. cerevisiae fermenting glucose. In this study, the effects of an alternative intracellular cellobiose utilization pathway-a phosphorolytic pathway based on a mutant cellodextrin transporter (CDT-1 (F213L)) and cellobiose phosphorylase (SdCBP)-was investigated by comparing with a hydrolytic pathway based on the same transporter and an intracellular ${\beta}$-glucosidase (GH1-1) for their SSF performances under various conditions. Whereas the phosphorolytic and hydrolytic cellobiose-fermenting S. cerevisiae strains performed similarly under the anoxic SSF conditions, the hydrolytic S. cerevisiae performed slightly better than the phosphorolytic S. cerevisiae under the microaerobic SSF conditions. Nonetheless, the phosphorolytic S. cerevisiae expressing the mutant CDT-1 showed better ethanol production than the glucose-fermenting S. cerevisiae with an extracellular ${\beta}$-glucosidase, regardless of SSF conditions. These results clearly prove that introduction of the intracellular cellobiose metabolic pathway into yeast can be effective on cellulosic ethanol production in SSF. They also demonstrate that enhancement of cellobiose transport activity in engineered yeast is the most important factor affecting the efficiency of SSF of cellulose.

• Journal of Animal Science and Technology
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• v.65 no.2
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• pp.311-323
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• 2023

Beef consumers valued meat quality traits such as texture, tenderness, juiciness, flavor, and meat color that determining consumers' purchasing decision. Most research on meat quality has focused on marbling, a key characteristic related to meat eating quality. However, other important traits such as meat texture, tenderness, and color have not much studied in cattle. Among these traits, meat tenderness and texture of cattle are among the most important factors affecting quality evaluation of consumers. Collagen is the main component of connective tissues.It greatly affects meat tenderness. The objective of this study was to determine significant variants and candidate genes associated with collagen contents trait (total collagen) through genome-wide association studies (GWAS). Phenotypic and genomic data from 135 Hanwoo were used. The BLUPF90 family program and GRAMMAR method for GWAS were applied in this study. A total of 73 potential single nucleotide polymorphisms (SNPs) showed significant associations with collagen content. They were located in or near 108 candidate genes. TMEM135 and ME3 genes were identified to have the most significant SNPs associated with collagen contents trait. Data indicated that these genes were related to collagen. Biological processes and pathways for the prediction of biological functions of candidate genes were confirmed. We found that candidate genes were involved in positive regulation of CREB transcription factor activity and actin cytoskeleton related to tenderness and texture of beef. Three genes (CRTC3, MYO1C and MYLK4) belonging to these biological functions were related to tenderness. These results provide a basis for improving genomic characteristics of Hanwoo for the production of tender beef. Furthermore, they could be used they could be used as an index to select desired traits for consumers.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.403-415
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• 2023

This study aimed to isolate and identify L-(+)-lactic acid-producing bacteria from tree barks collected in Thailand and evaluate the potential strain as probiotics. Twelve strains were isolated and characterized phenotypically and genotypically. The strains exhibited a rod-shaped morphology, high-temperature tolerance, and the ability to ferment different sugars into lactic acid. Based on 16S rRNA gene analysis, all strains were identified as belonging to Weizmannia coagulans. Among the isolated strains, BKMTCR2-2 demonstrated exceptional lactic acid production, with 96.41% optical purity, 2.33 g/l of lactic acid production, 1.44 g/g of lactic acid yield (per gram of glucose consumption), and 0.0049 g/l/h of lactic acid productivity. This strain also displayed a wide range of pH tolerance, suggesting suitability for the human gastrointestinal tract and potential probiotic applications. The whole-genome sequence of BKMTCR2-2 was assembled using a hybridization approach that combined long and short reads. The genomic analysis confirmed its identification as W. coagulans and safety assessments revealed its non-pathogenic attribute compared to type strains and commercial probiotic strains. Furthermore, this strain exhibited resilience to acidic and bile conditions, along with the presence of potential probiotic-related genes and metabolic capabilities. These findings suggest that BKMTCR2-2 holds promise as a safe and effective probiotic strain with significant lactic acid production capabilities.

• Genomics & Informatics
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• v.18 no.1
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• pp.10.1-10.9
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• 2020

Advancements in next generation sequencing (NGS) technologies have significantly increased the translational use of genomics data in the medical field as well as the demand for computational infrastructure capable processing that data. To enhance the current understanding of software and hardware used to compute large scale human genomic datasets (NGS), the performance and accuracy of optimized versions of GATK algorithms, including Parabricks and Sentieon, were compared to the results of the original application (GATK V4.1.0, Intel x86 CPUs). Parabricks was able to process a 50× whole-genome sequencing library in under 3 h and Sentieon finished in under 8 h, whereas GATK v4.1.0 needed nearly 24 h. These results were achieved while maintaining greater than 99% accuracy and precision compared to stock GATK. Sentieon's somatic pipeline achieved similar results greater than 99%. Additionally, the IBM POWER9 CPU performed well on bioinformatic workloads when tested with 10 different tools for alignment/mapping.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.510-512
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• 2010

A series of thiobarbituric acid derivatives were constructed and evaluated for inhibitory activity on hepatitis C virus NS5B polymerase. In biochemical assays using purified viral polymerase and RNA template, the $IC_{50}$ value was improved to 0.41 ${\mu}M$ from the original compound's 1.7 ${\mu}M$ value. In HCV sub genomic replicon assay, the $EC_{50}$ value was improved to 3.7 ${\mu}M$ from the original compound's 12.3 ${\mu}M$ value. $CC_{50}$ was higher than 77 ${\mu}M$ for all compounds tested, suggesting that they are useful candidates for anti-HCV therapy.