• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.30-30
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• 2022

Philippines is the second world supplier of coconut by-products. As its first major genomics project, the Philippine Genome Center program for Agriculture (PGC-Agriculture) took the challenge to sequence and assemble the whole coconut genome. The project aims to provide advance genetics tools for our collaborating coconut researchers while taking the opportunity to initiate local capacity. Combination of different NGS platforms was explored and the Philippine 'Catigan Green Dwarf' (CATD) variety was selected with the breeders to be the crop's reference genome. A high quality genome assembly of CATD was generated and used to characterize important genes of coconut towards the development of resilient and outstanding varieties especially for added high-value traits. The talk will present the significant results of the project as published in various papers including the first report of whole genome sequence of a dwarf coconut variety. Updates will include the challenges hurdled and specific applications such as gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties). Genome-wide DNA markers as published and genes related to coconut oil qualitative/quantitative traits will also be presented, including initial molecular/biochemical studies that support nutritional and medicinal claims. A web-based genome database is currently built for ease access and wider utility of these genomics tools. Indeed, a major milestone accomplished by the coconut genomics research team, which was facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with advance research institutes.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.24 no.1
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• pp.17-25
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• 2024

Fabry disease (FD) is an X-linked lysosomal storage disorder. It is caused by mutations in the α-galactosidase A gene, which results in deficient or absent activity of α-galactosidase A (α-Gal A). This leads to a progressive accumulation of globotriaosylceramide (Gb3) in various tissues. Manifestations of Fabry disease include serious and progressive impairment of renal and cardiac function. In addition, patients experience pain, gastrointestinal disturbance, transient ischaemic attacks, and strokes. Additional effects on the skin, eyes, ears, lungs, and bones are often seen. Reduced life expectancy and deadly consequences are being caused by cardiac involvement. Chaperone therapy or enzyme replacement therapy (ERT) are two disease-specific treatments for FD. Thus, early detection of FD is critical for decreasing morbidity and mortality. Globotriaosysphingosine (lyso-Gb3) for identifying atypical FD variants and highly sensitive troponin T (hsTNT) for detecting cardiac involvement are both significant diagnostic indicators. This review aimed to offer a basic resource for the early diagnosis and update on the diagnosis of having FD. We will also provide a general diagnostic algorithm and information on ERT and its accompanying treatments.

• Horticultural Science & Technology
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• v.30 no.1
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• pp.64-72
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• 2012

Phytophthora root rot has been causing a serious yield loss in pepper production. Since 2004, the year in which commercial cultivars resistant to the disease were firstly commercialized, it has been necessary to introduce the resistance into domestic pepper cultivars for dried red pepper. Therefore, developing molecular markers linked to the resistance is required for an accurate selection of resistant plants and increasing breeding efficiency. Until now, several markers associated with the major dominant gene resistant to Phytophthora root rot have been reported but they have some serious limitations for their usage. In this study, we aimed to develop molecular markers linked to the major dominant gene that can be used for almost of all genetic resources resistant to Phytophthora root rot. Two segregating $F_2$ populations derived from a 'Subicho' ${\times}$ 'CM334' combination and a commercial cultivar 'Dokyacheongcheong' were used to develop molecular markers associated with the resistance. After screening 1,024 AFLP primer combinations with bulked segregant analysis, three AFLP (AFLP1, AFLP2, and AFLP3) markers were identified and converted into three CAPS markers (M1-CAPS, M2-CAPS, and M3-CAPS), respectively. Among them, M3-CAPS marker was further studied in ten resistants, fourteen susceptibles, five hybrids and 53 commercial cultivars. As a result, M3-CAPS marker was more fitted to identify Phytophthora resistance than previously reported P5-SNAP and Phyto5.2-SCAR markers. The result indicated that the M3-CAPS marker will be useful for resistance breeding to Phytophthora root rot in chili pepper.

• KSBB Journal
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• v.23 no.3
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• pp.231-238
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• 2008

The second family member of tissue inhibitors of matrix metalloproteinases, TIMP-2, is a 21kDa protein which inhibits matrix metalloproteinases 2 (MMP-2). Expression of mammalian proteins in E. coli often forms inclusion bodies that are made up of mis-folded or insoluble protein aggregates. The requirement for the formation of 6 disulfide bonds in the process of the TIMP-2 folding is likely to be incompatible with the reducing environment of E. coli. However, this incompatibility can be often overcome by introducing a mutagenesis that could lead to enhancement of the protein solubility. In this reason, we have attempted to express the soluble TIMP-2 in E. coli by applying a modified staggered extension process (StEP), one of the in vitro PCR-based recombinant mutagenesis methods, and error-prone PCR. C-terminally located CAT fusion protein with respect to mutated TIMP-2 proteins enables us to differentiate the soluble TIMP-2 from the insoluble in E. coli by virtue of chloramphenicol resistance. According to this scheme, E. coli harboring properly-folded CAT fused to TIMP-2 protein was selected, and some of the resulting colonies exhibited an enhanced, soluble expression of TIMP-2 compared to the wild type, implying (i) the StEP technique is successfully employed to enhance the proper folding thereby increasing the solubility of TIMP-2, and (ii) the CAT dependent screening may be a simple and effective method to differentiate the soluble protein expression in E. coli.

• Korean Journal of Food Science and Technology
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• v.42 no.3
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• pp.355-360
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• 2010

Vibrio parahaemolyticus (V. parahaemolyticus), which is commonly found in raw seafood, causes gastroenteritis in humans. Rapid and effective methods have been developed as culture methods require up to 5-7 days. In this study, real-time PCR was compared with the standard culture method for detecting V. parahaemolyticus in seafood and radish sprout samples. Five hundred grams of the samples were artificially contaminated with V. parahaemolyticus then divided into 20 samples. The samples were incubated in alkaline peptone water and then streaked onto thiosulfate-citrate-bile saltssucrose agar. Biochemical tests for suspicious colonies were performed using the API 20NE strip. In parallel, real-time PCR was performed targeting the toxR gene using the enrichment broth. The real-time PCR was sensitive in discriminating V. parahaemolyticus from other foodborne pathogens. The detection limit of the real-time PCR was $10^3\;CFU/mL$ in phosphate-buffered saline. Although the real-time PCR detected more positive samples (76 out of 180, 42%) than the culture method (66 out of 180, 37%), there was no significant statistical difference (p>0.05) between the two methods. In conclusion, real-time PCR assays could be an alternative to the standard culture method for detecting V. parahaemolyticus in seafood and radish sprouts, which has many advantages in terms of detection time, labor, and sensitivity.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.16 no.1
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• pp.34-41
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• 2016

Adult-onset type II citrullinemia (CTLN2) is characterized by episodes of neurologic symptoms associated with hyperammonemia leading to disorientation, irritability, seizures, and coma. CTLN2 is distinct from classical citrullinemia, which is caused by a mutation of the argininosuccinic acid synthetase (ASS) gene. The serum citrulline level is elevated, while the activity of ASS in liver tissue is decreased. CTLN2 is known to have a poor prognosis if the proper treatment is not taken. We reported a female aged 37 years who developed recurrent attacks of altered consciousness, aberrant behavior, and vomiting. We initially suspected the patient had CTLN2 because of the signs of hyperammonemic encephalopathy, such as altered mentality, memory disturbance, and aberrant behaviors provoked by exercise-induced stress and excessive intravenous amino acid administration. Through her peculiar diet preferences and laboratory findings that included hyperammonemia and citrullinemia, we diagnosed the patient as CTLN2, and SLC25A13 sequencing revealed known compound heterozygous mutations (IVS11+1G>A, c.674C> A). Her parents were heterozygous carriers, and we identified that her older sister had the same mutations. The older sister had not experienced any episodes of hyperammonemia, but she had peculiar diet preferences. The patient and her sister have been well with conservative management. When considering the clinical course of CTLN2, it was meaningful that the older sister could be diagnosed early in an asymptomatic period and that preemptive treatment was employed. Through this case, CTLN2 should be considered in adults who present symptoms of hyperammonemic encephalopathy without a definite etiology. Because of its rare incidence and similar clinical features, CTLN2 is frequently misdiagnosed as hepatic encephalopathy, and it shows a poor prognosis due to the lack of early diagnosis and proper treatment. A high-carbohydrate diet, which is usually used to treat other urea cycle defects, can also exaggerate the clinical course of CTLN2, so proper metabolic screening tests and genetic studies should be performed.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.415-422
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• 2005

library of the mutants was prepared by transposon mutagenesis of the Mycobacterium bovis BCG. We screened this library for the resistance to an anti-tuberculosis antibiotic, PA-824. Most of the mutants resistant to the PA-824 were not able to synthesize the coenzyme $F_{420}$ which is normally produced by the wild type M. bovis BCG strains. HPLC analysis of the cellular extract showed that one of those mutants which lost the ability to synthesize $F_{420}$ still produced F0. The insertion site of the transposon in this mutant was determined by an inverse PCR and the transposon was found to be inserted in the Rv2435c open reading frame (ORF). Rv2435c ORF is predicted to encode an 80.3 kDa protein. Rv2435c protein appears to be bound to the cytoplasmic membrane, its N-terminal present in the periplasm and C-terminal in the cytoplasm. The C-terminal portion of this protein is highly homologous with the adenylyl cyclases of both prokaryotes and eukaryotes. There are 15 ORFs which have homology with the class III AC proteins in the genome of the M. tuberculosis and M. bovis. Two of those, Rv1625c and Rv2435c, are highly homologous with the mammalian ACs. We cloned the cytoplasmic domain of the Rv2435c ORF and expressed it with six histidine residues attached on its C-terminal in Escherichia coli to find out if this protein is a genuine AC. Production of that protein in E. coli was proved by purifying the histidine-tagged protein by using the Ni-NTA resin. This protein, however, failed to complement the cya mutation in E. coli, indicating that this protein lacks the AC activity. All of the further attempts to convert this protein to a functional AC by a mutagenesis with UV or hydroxylamine, or construction of several different fusion proteins with Rv1625c failed. It is, therefore, possible that Rv2435c protein might affect the conversion of F0 to $F_{420}$ not by synthesizing cAMP but by some other way.

• Tuberculosis and Respiratory Diseases
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• v.58 no.4
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• pp.352-358
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• 2005

Microsatellites are short tandem repeated nucleotide sequences that are present throughout the human genome. Variations in the repeat number or a loss of heterozygosity around the microsatellites have been termed a microsatellite alteration (MA). A MA reflects the genetic instability caused by an impairment in the DNA mismatch repair system and is suggested to be a novel tumorigenic mechanism. A number of studies have reported that MA in the DNA extracted from the plasma occurs at varying frequencies among patients with a non-small cell lung carcinoma (NSCLC). The genomic DNA from 9 subjects with a non-small cell lung cancer (squamous cell cancer 6, adenocarcinoma 2, non-small cell lung cancer1) and 9 age matched non-cancer control subjects (AMC: tuberculosis 3, other inflammatory lung disease 6) and 12 normal control subjects (NC) were extracted from the peripheral blood leukocytes and plasma. Three microsatellite loci were amplified with the primers targeting the Gene Bank sequence D21S1245, D3S1300, and D3S1234. MA in the form of an allelic loss or a band shift was examined with 6% polyacrylamide gel electrophoresis and silver staining. None (0/12) of the NC subjects less than 40 years of age showed a MA in any of the three markers, while 88.9%(8/9) of the AMC above 40 showed a MA in at least one of the three markers (p<0.05). Sixty percent(6/10) of the control subjects with a smoking history showed a MA in one of the three markers, while 9.1%(1/11) of the control subjects without smoking history showed a MA (p<0.05). However, not only did 66.7%(6/9) of lung cancer patients show a MA in at least one of the three markers but so did 88.9%(8/21) of the AMC patients (p>0.05). In conclusion, a MA in the D21S1245, D3S1300, and D3S1234 loci using DNA extracted from the plasma was detected in 66.7% of lung cancer while no MA was found in the young non-smoking control subjects. However, many of the non-cancer control subjects (aged smokers) also showed a MA, which compromised the specificity of the MA analysis as a screening test. Therefore, a further study with a larger sample size will be needed.

• Korean Journal of Breeding Science
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• v.41 no.3
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• pp.292-298
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• 2009

A new rice cultivar "Keumo 3" was developed for adopting under double cropping system with after or before cash crop cultivation. It was selected from the cross-combination between YR17202 $F_2$/Shinkeumobyeo//YR15727-B-B-B-102. The parent, YR17202 $F_2$ individual plant, was used for tolerance to lodging, it derived from a cross between Nonganbyeo/Shinkeumobyeo. Nonganbyeo is well known to lodging tolerance cultivar, as well as biotic stress, because it was developed by crossing with Tongil type. And the YR15727-B-B-B-102 line used as another parent with short growth duration, likewise highly resistance to rice blast disease. The pedigree derived from the cross-combination YR17202 $F_2$/Shinkeumobyeo//YR15727-B-B-B-102 were generated to $F_7$, and a best line among them named as Milyang 201. After a series of yield trials, including local adaptability test conducted throughout the peninsular of Korea, Milyang 201 was registered with the name of "Keumo 3" in 2005. The cultivar belongs to a early maturing group and heads 4 days earlier than Keumobyeo, a standard cultivar. It has short culm, and less spikelet number per panicle than Keumobyeo. However, its milled rice yield grown under extremely late transplanting time, 10. July, over the 3 local sites for 2003-2005 years, averaged 4,48 MT/ha, which is 6% higher than the standard, Keumobyeo. "Keumo 3" has showed a durable resistance to leaf blast disease during fourteen blast nurseries screening covered from south to north in Korea for 2003-2007 years. And it was confirmed harbours pi-zt, a durable blast resistance gene. Moreover it was incompatible with 19 blast isolates under artificial inoculation, except one isolate, K1101. Additionally, "Keumo 3" exhibits resistance to $K_1$, $K_2$ and $K_3$ of bacterial blight pathogen, as well as strip virus disease resistance, and moderate resistance to dwarf virus disease. Consequently, the new rice cultivar "Keumo 3" would be well adopted where a bio stress makes a big problem annually.

• Korean Journal of Soil Science and Fertilizer
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• v.40 no.6
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• pp.447-453
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• 2007

With a broad objective for the development of microbial based fertilizers, a total of 373 strains were isolated from rhizoplane and rhizosphere of pepper, tomato, lettuce, pasture, and grass. The efficacy of the isolates to augument overall plant growth was evaluated. After screening for their plant growth promotion and antagonistic properties in vitro efficient strains were further selected. The most efficient strains was characterized by 16S rRNA gene sequences and biochemical techniques and was designated as Bacillus subtilis S37-2. The strains facilitated plant growth and inhibited the plant phathogenic fungi such as Fusarium oxysporum (KACC 40037, Rhizoctonia solani (KACC 40140), and Sclerotinia sclerotiorum (KACC 40457). Pot based bioassay using lettuce as test plant was conducted by inoculating suspension ($10^5$ to $10^8cells\;mL^{-1}$) of B. subtilis S37-2 to the rhizosphere of lettuce cultivated in soil pots. Compared with non-inoculated pots, marked increase in leaf (42.3%) and root mass (48.7%) was observed in the inoculation group where the 50ml of cell mixture ($8.7{\times}10^8cells\;ml^{-1}$) was applied to the rhizosphere of letuce either once or twice. Antagonistic effects of B. subtilis S37-2 strain on S. sclerotiorum (KACC 40457) were tested. All the tested lettuce plants perished after 9 days in treatment containing only S. sclerotiorum, but only 17% of lettuce was perished in the inoculation plot. B. subtilis grew well in the TSB culture medium. The isolates grew better in yeast extracts than peptone and tryptone as nitrogen source. The growth rate was 2~4 times greater at $37^{\circ}C$ as compared with $30^{\circ}C$ incubation temperature. B. subitlis S37-2 produced $0.1{\mu}g\;ml^{-1}$ of IAA (indole 3-acetic acid) in the TSB medium containing L-tryptophan($20mg\;L^{-1}$) in 24 hours.