• Journal of The Korean Society of Inherited Metabolic disease
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• v.20 no.2
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• pp.55-62
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• 2020

A 22-month-old girl who had taken iron supplements due to iron deficiency anemia, presented bloody mucoid stool for one month. She had a bruise at the right periorbital area due to minor trauma and hepatosplenomegaly. Laboratory studies showed anemia, thrombocytopenia, elevated alkaline phosphatase (ALP), hypophosphatemia, decreased haptoglobin, hypocomplementemia, negative direct/indirect Coomb's test, normal vitamin D3 level and high PTHi. Wrist x-ray showed no signs of rickets. The abdominal ultrasound showed only accessory spleen. Tandem mass spectrometry was normal. During follow up, bloody stool regressed after seven days of withdrawal of iron supplement and cow milk, and the total CO2 level had been within 15-20 mEq/L with normal anion gap. NGS (next generation sequencing) panel test for evaluation of renal tubular acidosis showed negative results. After low dose steroid and vitamin D supplements under the impression of hypocomplementemic vasculitis, thrombocytopenia, C3/C4, decreased haptoglobin, and elevated ALP level became normal. At 57 months of age, laboratory findings showed elevated liver enzyme, ALP and gamma-glutamyl transferase again. And liver cirrhosis with splenomegaly and diffuse renal disease were reported with abdomen CT scan. Liver biopsy reported macro- and micronodular cirrhosis. Urine organic acid profile showed elevated succinylacetone level. Whole exome sequencing revealed novel compound heterozygous mutations (NM_00137.2:c.107T>C, NM_00137, 2:c.614T>C) in FAH gene and confirmed by Sanger sequencing. Consequently, the patient was diagnosed as chronic hereditary tyrosinemia type I. She started low phenylalanine/tyrosine diet and nitisinone treatment. Our case had presented symptoms very slowly, which is the first case of chronic tyrosinemia type I in South Korea.

• Journal of the Korean Recycled Construction Resources Institute
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• v.8 no.1
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• pp.97-104
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• 2020

The present study conducted mock-up tests under the simulated sewage environments to examine the practical significance and limitation of coating materials that were previously developed on the basis of the bacterial glycocalix as a protection of concrete structures exposed to microbiological and sulphate attacks. The variations of the compressive strength and mass of the concrete due to the sulphate attack were measured using cylinder specimens. The bacteria growth and glycocalix formulation were calculated from the samples extracted from the sewage pipes. The next generation sequencing analysis was also conducted for environmental damage assessment due to the use of Rhodobacter capsulatus in the simulated sewage environments. The mock-up tests revealed that the developed coating materials have a good potential in resisting the sulphate attack, indicating no reduction on compressive strength and mass of the coated concrete under the sewage environment. At the age of 91 days, the concentrations of viable bacteria and glycocalix measured from the hardened coating materials were 1.4×10⁴cell/mL and 67.5mg/㎤, respectively. Moreover, harmful strains were not observed in the sewage water including glycocalix-coated concrete pipes. This implies that Rhodobacter capsulatus used in the coating materials does not influence negatively the microorganism cluster in the sewage environments.

• Korean Journal of Environmental Agriculture
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• v.37 no.2
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• pp.135-140
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• 2018

BACKGROUND: The Asian hornet (Vespa velutina nigrithorax), a wasp species, has attacked honey bee populations and affected the beekeeping industry in Korea over the past 15 years. However, little research has been done with this invasive species. In this study, we investigated the intestine bacterial microbiota of Asian hornets and honey bees to design an attractive trap for Asian hornets. METHODS AND RESULTS: Genomic DNAs isolated from the intestine microorganisms of Asian hornets and honey bees were utilized to amplify bacterial 16S rDNA for the comparative sequence analysis. The next generation sequencing analysis identified that the orders Flavobacteriales as the most abundant intestinal microorganisms in Asian hornets, showing a clear difference compared to honey bees in which Aeromonadales are dominant. We also report five newly identified 16S rDNA sequences of Asian hornet intestinal bacteria. According to the sequence blast search, these five bacteria belong to the genera Thalassomonas, Caedobacter, Vampirovibrio, Alkaliphilus and Calothrix. CONCLUSION: While Asian hornets and honey bees show similar intestine bacterial diversity, the relative ratio of bacterial populations is different. providing useful information to design pest control agents specifically targeting Asian hornets.

• Genomics & Informatics
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• v.18 no.1
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• pp.8.1-8.10
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• 2020

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.386-398
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• 2020

Wheat is one of the world's top three crops and is an important staple crop, accounting for 20% of the nutrient calories consumed by the world's population. However, due to its complex heterogeneous hexaploid chromosomes and vast genome of approximately 16 Gb, compared to those of other crops, molecular biology and biotechnology studies on wheat are lacking. In recent years, wheat genome analysis has been performed using the latest next-generation sequencing technology so that useful genes can be easily obtained, and wheat biotechnology research is accelerating in various fields. In this review, wheat transformation, an indispensable technique for developing new functional biotech wheat by revealing the function of wheat genes, is described in detail. In addition, the latest research results for overcoming plant diseases, abiotic stresses, and wheat-related diseases that are difficult to solve by classical breeding through wheat transformation and biotechnology are described.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.312-325
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• 2015

In this review, we summarized the trends of genomics and transcriptomics research on peach, a model species of Rosaceae. Peach genome maps have been developed from various progeny groups with many next-generation sequencing (NGS) based single nucleotide polymorphism markers. Molecular markers of qualitative traits and quantitative trait loci (QTL) such as fruit characteristics, blooming date, and disease resistance have been analyzed. Among many characteristics, markers related to flesh softening and flesh adhesion are useful for marker assisted selection. Through comparative genomics, peach genome has been compared to the genome of Arabidopsis, Populus, Malus, and Fragaria species. Through transcriptomics and proteomics, fruit growth and development, and flavonoid synthesis, postharvest related transcriptomes and disease resistance related proteins have been reported. Recently, development of NGS based markers, construction of core collection of germplasm, and genotyping of various progenies have been preceded. In the near future, accurate QTL analysis and identification of useful genes are expected to establish a foundation for effective molecular breeding.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.372-378
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• 2017

For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.131-140
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• 2020

Solanum stoloniferum, one of the wild tetraploid Solanum species belonging to the Solanaceae family, is an excellent resource for potato breeding owing to its resistance to several important pathogens. However, the sexual hybridization of S. stoloniferum with S. tuberosum (potato) is hampered due to the sexual incompatibility between the two species. To overcome this and introgress the various novel traits of S. stoloniferum in cultivated potatoes, cell fusion can be performed. The identification of the fusion products is crucial and can be achieved with the aid of molecular markers. In this study, the chloroplast genome sequence of S. stoloniferum was obtained by next-generation sequencing technology, and compared with that of six other Solanum species to identify S. stoloniferum-specific molecular markers. The length of the complete chloroplast genome of S. stoloniferum was found to be 155,567 bp. The structural organization of the chloroplast genome of S. stoloniferum was similar to that of the six other Solanum species studied. Phylogenetic analysis of S. stoloniferum with nine other Solanaceae family members revealed that S. stoloniferum was most closely related to S. berthaultii. Additional comparison of the complete chloroplast genome sequence of S. stoloniferum with that of five Solanum species revealed the presence of six InDels and 39 SNPs specific to S. stoloniferum. Based on these InDels and SNPs, four PCR-based markers were developed to differentiate S. stoloniferum from other Solanum species. These markers will facilitate the selection of fusion products and accelerate potato breeding using S. stoloniferum.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.141-149
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• 2020

Solanum hougasii, one of the wild Solanum species, has been widely used in potato breeding since it exhibits excellent resistance to diverse important pathogens. S. hougasii can be directly crossed with the cultivated tetraploid potato (S. tuberosum) owing to its EBN (Endosperm Balanced Number) value of 4, which is same as that of S. tuberosum although it is an allohexaploid. In this study, the complete chloroplast genome sequence of S. hougasii was obtained by next-generation sequencing technology, and compared with that of the chloroplast genome of seven other Solanum species to identify S. hougasii-specific PCR markers. The length of the complete chloroplast genome of S. hougasii was 155,549 bp. The structural organization of the chloroplast genome in S. hougasii was found to be similar to that of seven other Solanum species studied. Phylogenetic analysis of S. hougasii with ten other Solanaceae family members revealed that S. hougasii was most closely related to S. stoloniferum, followed by S. berthaultii, and S. tuberosum. Additional comparison of the chloroplast genome sequence with that of five other Solanum species revealed five InDels and 43 SNPs specific to S. hougasii. Based on these SNPs, four PCR-based markers were developed for the differentiation of S. hougasii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary and breeding aspects of Solanum species.

• Journal of Microbiology and Biotechnology
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• v.30 no.10
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• pp.1467-1479
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• 2020

Profiling the transcriptome changes involved in xylose metabolism by the fungus Trichoderma reesei allows for the identification of potential targets for ethanol production processing. In the present study, the transcriptome of T. reesei HJ-48 grown on xylose versus glucose was analyzed using next-generation sequencing technology. During xylose fermentation, numerous genes related to central metabolic pathways, including xylose reductase (XR) and xylitol dehydrogenase (XDH), were expressed at higher levels in T. reesei HJ-48. Notably, growth on xylose did not fully repress the genes encoding enzymes of the tricarboxylic acid and respiratory pathways. In addition, increased expression of several sugar transporters was observed during xylose fermentation. This study provides a valuable dataset for further investigation of xylose fermentation and provides a deeper insight into the various genes involved in this process.