• Parasites, Hosts and Diseases
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• v.48 no.1
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• pp.57-59
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• 2010

A 59-year-old Korean man complained of a painless scrotal hard nodule and weak urine stream. The ultrasound scan revealed a 2.2-cm sized round heteroechogenic nodule located in the extratesticular area. Microscopic hematuria was detected in routine laboratory examinations. On scrotal exploration, multiple spargana were incidentally found in the mass and along the left spermatic cord. On cystoscopy, a 10-mm sized mucosal elevation was found in the right side of the bladder dome. After transurethral resection of the covered mucosa, larval tapeworms were removed from inside of the nodule by forceps. Plerocercoids of Spirometra erinacei was confirmed morphologically and also by PCR-sequencing analysis from the extracted tissue of the urinary bladder. So far as the literature is concerned, this is the first worm (PCR)-proven case of sparganosis in the urinary bladder.

• Biomedical Science Letters
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• v.21 no.4
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• pp.233-240
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• 2015

Some virulence proteins of Helicobacter pylori, such as vacuolating cytotoxic protein A (VacA) and cytotoxin-associated gene protein A (CagA) have been reported to be causative agents of various gastric diseases including chronic gastritis, gastric ulcer or gastric adenocarcinoma. The expression level of these virulence proteins can be regulated when H. pylori is exposed to the antibacterial agent, cyanidin 3-O-glucoside (C3G) as previously reported. In this study, we analyzed the quantitative change of various virulence proteins including CagA and VacA by C3G treatment. We used 2-dimensional electrophoresis (2-DE) to analyze the quantitative change of representative ten proteome components of H. pylori 60190 ($VacA^+/CagA^+$; standard strain of Eastern type). After 2-DE analysis, spot intensities were analyzed using ImageMaster$^{TM}$ 2-DE Platinum software then each spot was identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) or peptide sequencing using Finnigan LCQ ion trap mass spectrometer (LC-MS/MS). Next, we selected major virulence proteins of H. pylori among quantitatively meaningful ten spots and confirmed the 2-DE results by Western blot analysis. These results suggest that cyanidin 3-O-glucoside can modulate a variety of H. pylori pathogenic determinants.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.45 no.4
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• pp.358-366
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• 2012

A novel neuropeptide was isolated from the skin of the conger eel Conger myriaster using hagfish Eptatretus burgeri intestine as a bioassay system. The sequence of the purified peptide was analyzed using automated amino acid sequencing and MALDI-TOF mass spectrophotometry. The molecular ion peak in the MALDI-TOF mass spectrum of the peptide was at m/z 962.89 $(M+H)^+$. The sequence of the peptide was determined to be L-P-M-L-E-T-Q-M, and was tentatively named comyrin. To investigate the complete primary structure of comyrin, comyrin-OH and comyrin-$NH_2$ were synthesized and the chemical and pharmacological properties of the synthetic peptides were compared with those of the native peptide. However, the elution time of synthetic peptides did not match that of the native peptide on the reverse-phase HPLC chromatogram. In addition, the synthetic peptides did not cause contractile activity in the intestinal smooth muscle of the hagfish. Based on these results, one possible reason for this disagreement may be the presence of a D-amino acid in comyrin.

• Genomics & Informatics
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• v.12 no.4
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• ALGAE
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• v.28 no.2
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• pp.131-147
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• 2013

Major progress has been made in the past decade towards understanding of the biosynthesis of red carotenoid astaxanthin and its roles in stress response while exploiting microalgae-based astaxanthin as a potent antioxidant for human health and as a coloring agent for aquaculture applications. In this review, astaxanthin-producing green microalgae are briefly summarized with Haematococcus pluvialis and Chlorella zofingiensis recognized to be the most popular astaxanthin-producers. Two distinct pathways for astaxanthin synthesis along with associated cellular, physiological, and biochemical changes are elucidated using H. pluvialis and C. zofingiensis as the model systems. Interactions between astaxanthin biosynthesis and photosynthesis, fatty acid biosynthesis and enzymatic defense systems are described in the context of multiple lines of defense mechanisms working in concert against photooxidative stress. Major pros and cons of mass cultivation of H. pluvialis and C. zofingiensis in phototrophic, heterotrophic, and mixotrophic culture modes are analyzed. Recent progress in genetic engineering of plants and microalgae for astaxanthin production is presented. Future advancement in microalgal astaxanthin research will depend largely on genome sequencing of H. pluvialis and C. zofingiensis and genetic toolbox development. Continuous effort along the heterotrophic-phototrophic culture mode could lead to major expansion of the microalgal astaxanthin industry.

• Mass Spectrometry Letters
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• v.12 no.3
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• pp.60-65
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• 2021

As a part of the Chromosome-centric Human Proteome Project (C-HPP), we have developed a few algorithms for accurate identification of missing proteins, alternative splicing variants, single amino acid variants, and characterization of function unannotated proteins. We have found missing proteins, novel and known ASVs, and SAAVs using LC-MS/MS data from human brain and olfactory epithelial tissue, where we validated their existence using synthetic peptides. According to the neXtProt database, the number of missing proteins in chromosome 11 shows a decreasing pattern. The development of genomic and transcriptomic sequencing techniques make the number of protein variants in chromosome 11 tremendously increase. We developed a web solution named as SAAvpedia for identification and function annotation of SAAVs, and the SAAV information is automatically transformed into the neXtProt web page using REST API service. For the 73 uPE1 in chromosome 11, we have studied the function annotaion of CCDC90B (NX_Q9GZT6), SMAP (NX_O00193), and C11orf52 (NX_Q96A22).

• Parasites, Hosts and Diseases
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• v.58 no.5
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• pp.577-581
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• 2020

A 22-year-old Thai man from the Northeast region presented with acute eye swelling, itching, and discharge on his left eye. He was suspected of having gnathostomiasis and treated with albendazole and prednisolone for 3 weeks. Nine months later, he was treated with high-dose oral prednisolone for the preliminary and differential diagnoses with thyroid-associated orbitopathy and lymphoma. He had been administered prednisolone intermittently over a few years. Then he developed a painless movable mass at the left upper eyelid and recurrent pseudotumor oculi was suspected. The surgical removal of the mass was performed. A white pseudosegmented worm revealed a definite diagnosis of ocular sparganosis by a plerocercoid larva. Molecular diagnosis of the causative species was made based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Proper technique of extraction and amplification of short fragments DNA from formalin-fixed paraffin-embedded tissue successfully identified parasite species. The result from the sequencing of the PCR-amplified cox1 fragments in this study showed 99.0% sequence homology to Spirometra ranarum. This is the first report of S. ranarum in Thailand.

• 한국생물공학회:학술대회논문집
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• 2000.04a
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• pp.527-530
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• 2000

A kiwi fruit ,called as the Chinese gooseberry, is originated from the Yangtze River Valley of Northern China and Zhejiang Province on the cost of Eastern China. Around 1950, a large mass production began at New Zealand with an Improved breeding. Plant origin actinidin from kiwi fruit belongs to the papain family of cysteine proteinase, which in plants includes papain from papaya, bromelain from pineapple, Cl4 protease from tomato and aleurain from barley. Actinidin is involved in the ripening-related gene family. In this study, protease gene of chinese wild kiwi fruit was isolated and characterized. 1.2kb PCR-amplified fragment was obtained from the total RNA using RT-PCR. pWACT-1 was obtained by subcloning of amplified fragment into pGEM-T Easy cloning vector and analyzed nucleotide sequence by DNA sequencing and amino acid sequence. In Result, high levels of homology between wild kiwi and New Zealand cultured-kiwi was obtained.

• BMB Reports
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• v.37 no.1
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• pp.133-138
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• 2004

Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular proteomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).

• Journal of Computing Science and Engineering
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• v.10 no.1
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• pp.21-31
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• 2016

With the application and development of biomedical techniques such as next-generation sequencing, mass spectrometry, and medical imaging, the amount of biomedical data have been growing explosively. In terms of processing such data, we face the problems surrounding big data, highly intensive computation, and high dimensionality data. Fortunately, cloud computing represents significant advantages of resource allocation, data storage, computation, and sharing and offers a solution to solve big data problems of biomedical research. In order to improve the efficiency of resource management in cloud computing, this paper proposes a clustering method and adopts Radial Basis Function in order to compress comprehensive data sets found in biology and medicine in high quality, and stores these data with resource management in cloud computing. Experiments have validated that with such a data-compression-based resource management in cloud computing, one can store large data sets from biology and medicine in fewer capacities. Furthermore, with reverse operation of the Radial Basis Function, these compressed data can be reconstructed with high accuracy.