• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.459-466
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• 2013

The lactic acid bacterium Streptococcus thermophilus is widely used as a starter culture for the production of dairy products. Whole-genome sequencing is expected to utilize the genetic basis behind the metabolic functioning of lactic acid bacterium (LAB), for development of their use in biotechnological and probiotic applications. We sequenced the whole genome of Streptococcus thermophilus MTCC 5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion Torrent PGM. We performed comparative genome analysis using the local BLAST and RDP for 16S rDNA comparison and by the RAST server for functional comparison against the published genome sequence of Streptococcus thermophilus CNRZ 1066. The whole genome size of S. thermophilus MTCC 5461 is of 1.73Mb size with a GC content of 39.3%. Streptococcal virulence-related genes are either inactivated or absent in the strain. The genome possesses coding sequences for features important for a probiotic organism such as adhesion, acid tolerance, bacteriocin production, and lactose utilization, which was found to be conserved among the strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of 17 sugars by the bacterium, where the presence of genes encoding enzymes involved in metabolism for 16 of these 17 sugars were confirmed in the genome. This study supports the facts that the strain MTCC 5461 is nonpathogenic and harbors essential features that can be exploited for its probiotic potential.

• Journal of Microbiology and Biotechnology
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• v.23 no.2
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• pp.137-143
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• 2013

The diversity and distribution of methanogenic archaea in a four-compartment anaerobic baffled reactor (ABR) treating sugar refinery wastewater were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At an organic loading rate of 5.33 kg $COD/m^3{\cdot}day$, the ABR could perform steadily with the mean chemical oxygen demand (COD) removal of 94.8% and the specific $CH_4$ yield of 0.21 l/g $COD_{removed}$. The $CH_4$ content in the biogas was increased along the compartments, whereas the percentage of $H_2$ was decreased, indicating the distribution characteristics of the methanogens occurred longitudinally down the ABR. A high phylogenetic and ecological diversity of methanogens was found in the ABR, and all the detected methanogens were classified into six groups, including Methanomicrobiales, Methanosarcinales, Methanobacteriales, Crenarchaeota, Arc I, and Unidentified. Among the methanogenic population, the acid-tolerant hydrogenotrophic methanogens including Methanoregula and Methanosphaerula dominated the first two compartments. In the last two compartments, the dominant methanogenic population was Methanosaeta, which was the major acetate oxidizer under methanogenic conditions and could promote the formation of granular sludge. The distribution of the hydrogenotrophic (acid-tolerant) and acetotrophic methanogens in sequence along the compartments allowed the ABR to perform more efficiently and steadily.

• Fisheries and Aquatic Sciences
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• v.21 no.3
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• pp.5.1-5.8
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• 2018

Stimulator of interferon gene (STING) is induced by various inflammatory agents, such as lipopolysaccharide and microbial pathogens, including virus and bacteria. In this study, we obtained a full-length cDNA of a STING homolog from olive flounder using rapid amplification of cDNA ends PCR technique. The full-length cDNA of Paralichthys olivaceus STING (PoSTING) was 1442 bp in length and contained a 1209-bp open reading frame that translated into 402 amino acids. The theoretical molecular mass of the predicted protein sequence was 45.09 kDa. In the PoSTING protein, three transmembrane domains and the STING superfamily domain were identified as characteristic features. Quantitative real-time PCR revealed that PoSTING expressed in all the tissues analyzed, but showed the highest level in the spleen. Temporal expression analysis examined the significantly upregulated expression of PoSTING mRNA after viral hemorrhagic septicemia virus (VHSV) stimulation. In contrast, no significant changes in the PoSTING expression were detected in Edwardsiella tarda-challenged group compared to the un-injected control. The expression of P. olivaceus type I interferon (PoIFN-I) was also highly upregulated upon VHSV challenge. These results suggest that STING might be involved in the essential immune defense against viral infection together with the activation of IFN-I in olive flounder.

• IMMUNE NETWORK
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• v.11 no.1
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• pp.50-58
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• 2011

Background: Epstein-Barr virus associated gastric lymphoepithelioma-like carcinoma (LELC) is characterized by the intensive infiltration of lymphoid cells, the presence of EBV, and the better prognosis over typical adenocarcinoma. Thus, it was assumable that viral latent proteins may be responsible for the recruitment of a certain T cell repertoire to EBV-associated gastric carcinoma. Methods: To examine above possibility, EBV gene expression in gastric carcinoma tissues and usage of TCR among the tumor infiltrating lymphocytes were analyzed. Results: EBV specific DNA and EBERs RNA were detected in 4 out of 30 patients. RT-PCR analysis revealed that all 4 of EBV-positive tumor tissues expressed EBNA1 mRNA and BARTs and LMP2a was detected only one sample out of 4. However, the EBNA2 and LMP-1 transcripts were not detected in these tissues. $CD8^+$ T cells were the predominant population of infiltrating lymphocytes in the EBV-positive gastric carcinoma. According to spectra type analysis of infiltrating T cells, 10 predominant bands were detected by TCR $V{\beta}$ CDR3 specific RT-PCR from 4 EBV-positive tumor tissues. Sequence analysis of these bands revealed oligoclonal expansion of T cells. Conclusion: These findings suggest that clonally expanded T cells in vivo might be a population of cytotoxic T cells reactive to EBV-associated gastric carcinoma.

• Advances in pediatric surgery
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• v.6 no.1
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• pp.10-18
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• 2000

Multisystem organ failure resulting from gram negative bacterial sepsis is associated with high morbidity and mortality in surgical neonates. There are differences in the clinical characteristics of organ failure in neonates and adults. The purpose of this study is to identify the differences and determine the order of organ failure between baby rats and adult rats after induction of gram negative sepsis. Fifty baby rats less than 30-day-old and another 50 adult rats more than 2-month-old were divided into control group (G1) and experimental group (G2). The G1 consisted of 10 baby- and 10 adult-rats, and the G2 consisted of 40 babies and 40 adults. E. coli ($10^8/mL$ per 100g of body weight) were injected into the peritoneal cavity in G2 and same amount of saline was injected in G 1. Blood samples were obtained before injection, 24 hour, 48 hour, 72 hour and after death. WEC, platelet, $PaO_2$, $PaCO_2$, total bilirubin, BUN, creatinine, albumin and abdominal wall thickness were measured to evaluate the sequence of organ failure. The mortality was 55.0 % in G2-babies and 32.5 % in G2-adults. In baby rats, microvascular, hematologic and renal failure appeared within 24 hours after injection and pulmonary failure followed. Pulmonary, renal and liver failure developed within 24-48 hours in adult rats; however, microvascular failure did not appear until they were moribund. Thrombocytopenia, hypoalbuminemia, increased BUN and generalized edema was the earlist sign of sepsis in baby rats.

• Genomics & Informatics
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• v.3 no.4
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• pp.133-141
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• 2005

Most of the endogenous retroviral genes integrated into the primate genome after the split of New World monkeys in the Oligocene era, approximately 33 million years ago. Because they can change the structure of adjacent genes and move between and within chromosomes they may play important roles in evolutionas well as in many kinds of disease and the creation of genetic polymorphism. Comparative analysis of HERVs (human endogenous retroviruses) and their LTR (long terminal repeat) elements in the primate genomes will help us to understand the possible impact of HERV elements in the evolution and phylogeny of primates. For example, HERV-K LTR and SINE-R elements have been identified that have been subject to recent change in the course of primate evolution. They are specific elements to the human genome and could be related to biological function. The HERV-M element is related to the superfamily of HERV-K and is integrated into the periphilin gene as the truncated form, 5'LTR-gag-pol-3'LTR. PCR and RT-PCR approaches indicated that the insertion of various retrotransposable elements in a common ancestor genome may make different transcript variants in different primate species. Examination of the HERV-W elementrevealed that env fragments were detected on human chromosomes 1, 3-7, 12, 14, 17, 20, and X, whilst the pol fragments were detected on human chromosomes 2-8, 10-15, 20, 21, X, and Y. Bioinformatic blast search showed that almost full-length of the HERV-W family was identified on human chromosomes 1-8, 11-15, 17, 18, 21, and X. Expression analysis of HERV-W genes (gag, pol, and env) in human tissues by RT-PCR indicated that gag and pol were expressed in specific tissues, whilst env was constituitively expressed in all tissues examined. DNA sequence based phylogenetic analysis indicated that the gag, pol and env genes have evolved independently during primate evolution. It will thus be of considerable interest to expand the current HERV gene information of various primates and disease tissues.

• BMB Reports
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• v.38 no.3
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• pp.320-327
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• 2005

Five ripening-related ACC synthase cDNA isoforms were cloned from 80% ripe papaya cv. 'Sinta' by reverse transcription-PCR using gene-specific primers. Clone 2 had the longest transcript and contained all common exons and three alternative exons. Clones 3 and 4 contained common exons and one alternative exon each, while clone 1, the most common transcript, contained only the common exons. Clone 5 could be due to cloning artifacts and might not be a unique cDNA fragment. Thus, there are only four isoforms of ACC synthase mRNA. Southern blot analysis indicates that all five clones came from only one gene existing as a single copy in the 'Sinta' papaya genome. Multiple sequence alignment indicates that the four isoforms arise from a single gene, possibly through alternative splicing mechanisms. All the putative alternative exons were present at the 5'-end of the gene comprising the N-terminal region of the protein. 'Sinta' ACC synthase cDNAs were of the capacs 1 type and are most closely related to a 1.4 kb capacs 1-type DNA(AJ277160) from Eksotika papaya. No capacs 2-type cDNAs were cloned from 'Sinta' by RT-PCR. This is the first report of possible alternative splicing mechanism in ripening-related ACC synthase genes in hybrid papaya, possibly to modulate or fine-tune gene expression relevant to fruit ripening.

• Journal of the Korean Society of Costume
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• v.58 no.9
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• pp.29-37
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• 2008

The purpose of this study was to investigate insulation of thermal clothing under still and dynamic air conditions(with 2.1m/sec air velocity) and decrease of insulation in both conditions, to analyze correlations among them, and to estimate insulation and decrease of insulation using factors, such as fabric insulation, fabric weight, clothing weight, air permeability, and water vapor resistance. A total of 25 kinds of clothing were tested(9 types for suits, 6 types of jacket, 5 types for shirts, and 5 types for trousers). The results of this study were as follows; Thermal resistance of clothing under the dynamic air condition decreased comparing to that of clothing under still air condition in all types of clothing. Decrease in shirts was the biggest(47.5%), followed by suits(39.51%), trousers(37.48%), and jackets(34.49%) in sequence. Thermal resistance of clothing under dynamic air condition showed very high correlation(0.98, p<0.01) with that of clothing under still air condition, followed by thermal resistance of fabric(0.86, p<0.01). Decrease in thermal resistance of clothing showed the highest correlation with air permeability. It didn't show correlation with other factors. Regression analysis showed that fabric thickness would be useful factor for estimating thermal resistance of clothing and air permeability also would be useful factor for estimating decrease in thermal resistance of clothing.

• The Korean Journal of Malacology
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• v.32 no.4
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• pp.241-247
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• 2016

Macrophage Migration Inhibitory Factor (MIF) are well-defined role as unique cytokine and critical mediator in acute and chronic inflammatory diseases, autoimmune diseases. In this study, we isolated and characterized a full-length of MIF cDNA from the abalone (Haliotis discus hannai). The full-length cDNA of abMIF was of 1264 bp, consisting of a 5'-terminal UTR of 143 bp, an open reading frame of 360 bp and a 3-terminal UTR of 761 bp. The abalone MIF cDNA encodes a 119-amino acid polypeptide with a calculated molecular mass of 13.4 kDa and isoelectric point of 9.07. Multiple alignments and phylogenetic analysis with the deduced abalone MIF protein and showed strong homology with disk abalone (Haliotis discusdiscus). The deduced amino acid sequence of abMIF exhibited homology with other reported MIFs, such as 80%, with that of other disk abalone H. discus discus MIF gene. Quantitative real-time PCR (qRT-PCR) analysis indicated that abMIF was highly expression observed in hapatopacreas, intestine, foot, and gonad of normal conditioned abalone. Even though AbMIF mRNA level in hemocytes was low under the normal condition, it was sharply up-regulated and reached the maximum at 6 h post-infection with Vibrio parahaemolyticus, and then decreased at 24 h post-infection. This result indicates that abMIF plays an important role in responding in the innate immune system.

• Biomaterials and Biomechanics in Bioengineering
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• v.2 no.1
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• pp.47-59
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• 2015

A bioactive and multifunctional elastin-like polymer (ELP) was produced by genetic engineering techniques to develop new artificial matrices with the ability to mimic the extracellular matrix (ECM). The basic composition of this ELP is a thermo- and pH-sensitive elastin pentapeptide which has been enriched with RGD-containing domains, the RGD loop of fibronectin, for recognition by integrin receptors on their sequence to promote efficient cell attachment. Hydrogels of this RGD-containing polymer were obtained by crosslinking with hexamethylene diisocyanate, a lysine-targeted crosslinker. These materials retain the "smart" nature and temperature-responsive character, and the desired mechanical behavior of the elastin-like polymer family. The influence of the degree of crosslinking on the morphology and properties of the matrices were tested by calorimetric techniques and scanning electron microscopy (SEM). Their mechanical behavior was studied by dynamical mechanical analysis (DMA). These results show the potential of these materials in biomedical applications, especially in the development of smart systems for tissue engineering.