• Animal Bioscience
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• v.34 no.6
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• pp.941-948
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• 2021

Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan. Methods: Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences. Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1. Conclusion: The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.

• Parasites, Hosts and Diseases
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• v.59 no.2
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• pp.167-171
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• 2021

Haemonchosis remains a significant problem in small ruminants. In this study, the assay of recombinase polymerase amplification (RPA) combined with the lateral flow strip (LFS-RPA) was established for the rapid detection of Haemonchus contortus in goat feces. The assay used primers and a probe targeting a specific sequence in the ITS-2 gene. We compared the performance of the LFS-RPA assay to a PCR assay. The LFS-RPA had a detection limit of 10 fg DNA, which was 10 times less compared to the lowest detection limit obtained by PCR. Out of 24 goat fecal samples, LFS-RPA assay detected H. contortus DNA with 95.8% sensitivity, compared to PCR, 79.1% sensitivity. LFS-RPA assay did not detect DNA from other related helminth species and demonstrated an adequate tolerance to inhibitors present in the goat feces. Taken together, our results suggest that LFS-RPA assay had a high diagnostic accuracy for the rapid detection of H. contortus and merits further evaluation.

• Korean Journal of Veterinary Research
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• v.61 no.2
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• pp.13.1-13.8
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• 2021

Mammalian reovirus (MRV) causes respiratory and intestinal disease in mammals. Although MRV isolates have been reported to circulate in several animals, there are no reports on Korean MRV isolates from wildlife. We investigated the biological and molecular characteristics of Korean MRV isolates based on the nucleotide sequence of the segment 1 gene. In total, 144 swabs from wild animals were prepared for virus isolation. Based on virus isolation with specific cytopathic effects, indirect fluorescence assays, electron microscopy, and reverse transcription-polymerase chain reaction, only one isolate was confirmed to be MRV from a Korean roe deer (Capreolus pygargus). The isolate exhibited a hemagglutination activity level of 16 units with pig erythrocytes and had a maximum viral titer of 10^5.7 50% tissue culture infectious dose (TCID₅₀)/mL in Vero cells at 5 days after inoculation. The nucleotide and amino-acid sequences of the partial segment S1 of the MReo2045 isolate were determined and compared with those of other MRV strains. The MReo2045 isolate had nucleotide sequences similar to MRV-3 and was most similar (96.1%) to the T3/Bat/Germany/342/08 strain, which was isolated in Germany in 2008. The MReo2045 isolate will be useful as an antigen for sero-epidemiological studies and developing diagnostic tools.

• BMB Reports
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• v.55 no.7
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• pp.354-359
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• 2022

MitoNEET, a mitochondrial outer membrane protein containing the Asn-Glu-Glu-Thr (NEET) sequence, controls the formation of intermitochondrial junctions and confers autophagy resistance. Moreover, mitoNEET as a mitochondrial substrate undergoes ubiquitination by activated Parkin during the initiation of mitophagy. Therefore, mitoNEET is linked to the regulation of autophagy and mitophagy. Mitophagy is the selective removal of the damaged or unnecessary mitochondria, which is crucial to sustaining mitochondrial quality control. In numerous human diseases, the accumulation of damaged mitochondria by impaired mitophagy has been observed. However, the therapeutic strategy targeting of mitoNEET as a mitophagy-enhancing mediator requires further research. Herein, we confirmed that mitophagy is indeed activated by mitoNEET inhibition. CCCP (carbonyl cyanide m-chlorophenyl hydrazone), which leads to mitochondrial depolarization, induces mitochondrial dysfunction and superoxide production. This, in turn, contributes to the induction of mitophagy; mitoNEET protein levels were initially increased before an increase in LC3-II protein following CCCP treatment. Pharmacological inhibition of mitoNEET using mitoNEET Ligand-1 (NL-1) promoted accumulation of Pink1 and Parkin, which are mitophagy-associated proteins, and activation of mitochondria-lysosome crosstalk, in comparison to CCCP alone. Inhibition of mitoNEET using NL-1, or mitoNEET shRNA transfected into RAW264.7 cells, abrogated CCCP-induced ROS and mitochondrial cell death; additionally, it activated the expression of PGC-1α and SOD2, regulators of oxidative metabolism. In particular, the increase in PGC-1α, which is a major regulator of mitochondrial biogenesis, promotes mitochondrial quality control. These results indicated that mitoNEET is a potential therapeutic target in numerous human diseases to enhance mitophagy and protect cells by maintaining a network of healthy mitochondria.

• Genomics & Informatics
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• v.20 no.2
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• pp.18.1-18.7
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• 2022

According to long-term projections, by 2030, the world's population is predicted to reach 7.5 billion individuals, and there will be roughly 27 million new cancer cases diagnosed. The global burden of breast cancer (BC) is expected to rise. According to the Ministry of Health-Iraqi Cancer Registry, cancer is the second largest cause of death after cardiovascular disease. This study investigated the interleukin-18 (IL18) single-nucleotide polymorphisms (SNPs) -607C/A rs1946518 and -137G/C rs187238 using the sequence-specific amplification-polymerase chain reaction approach. Regarding the position -607C/A, there was a highly significant difference between the observed and expected frequencies in patients and controls (χ² = 3.16 and χ² = 16.5), respectively. The AA and CA genotypes were associated with significantly increased BC risk (odds ratio [OR], 3.68; p = 0.004 and OR, 2.83; p = 0.04, respectively). Women with the A allele had a 5.03-fold increased susceptibility to BC. The C allele may be a protective allele against BC (OR, 0.19). Although position -137G/C showed no significant differences in the CC genotype distribution (p = 0.18), the frequency of the CC genotype was significantly higher in patients than in controls. In contrast, patients had a significantly higher frequency of GC genotypes than controls (p = 0.04), which was associated with an increased risk of developing BC (OR, 2.63). The G allele frequency was significantly lower in patients than in controls (55.0% vs. 76.2%, respectively). This SNP may be considered a common genotype in the Iraqi population, with the wild-type G allele having a protective function (OR, 0.19) and the mutant C allele having an environmental effect (OR, 2.63).

• Genomics & Informatics
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• v.18 no.3
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• pp.28.1-28.9
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• 2020

Streptomyces coelicolor is a gram-positive soil bacterium which is well known for the production of several antibiotics used in various biotechnological applications. But numerous proteins from its genome are considered hypothetical proteins. Therefore, the present study aimed to reveal the functions of a hypothetical protein from the genome of S. coelicolor. Several bioinformatics tools were employed to predict the structure and function of this protein. Sequence similarity was searched through the available bioinformatics databases to find out the homologous protein. The secondary and tertiary structure were predicted and further validated with quality assessment tools. Furthermore, the active site and the interacting proteins were also explored with the utilization of CASTp and STRING server. The hypothetical protein showed the important biological activity having with two functional domain including POD-like_MBL-fold and rhodanese homology domain. The functional annotation exposed that the selected hypothetical protein could show the hydrolase activity. Furthermore, protein-protein interactions of selected hypothetical protein revealed several functional partners those have the significant role for the bacterial survival. At last, the current study depicts that the annotated hypothetical protein is linked with hydrolase activity which might be of great interest to the further research in bacterial genetics.

• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.65-74
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• 2021

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

• Geomechanics and Engineering
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• v.27 no.6
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• pp.561-571
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• 2021

Cofferdams made of teel sheet piles are commonly utilized as support structures for excavation of sea-crossing bridge foundations. As cofferdams are often subject to tide variation, it is imperative to consider potential effects of tide on stability and serviceability of sheet piles, particularly, ultralong steel sheet piles (USSPs). In this study, a real USSP cofferdam constructed using new construction technology in Nanxi River was reported. The design of key parts of USSP cofferdam in the presence of tidal action was first introduced followed by the description of entire construction technology and associated monitoring results. Subsequently, a three-dimensional finite-element model corresponding to all construction steps was established to back-analyze measured deflection of USSPs. Finally, a series of parametric studies was carried out to investigate effects of tide level, soil parameters, support stiffness and construction sequence on lateral deflection of USSPs. Monitoring results indicate that the maximum deflection during construction occurred near the riverbed. In addition, measured stress of USSPs showed that stability of USSP cofferdam strengthened as construction stages proceeded. Moreover, the numerical back-analysis demonstrated that the USSP cofferdam fulfilled the safety requirements for construction under tidal action. The maximum deflection of USSPs subject to high tide was only 13.57 mm at a depth of -4 m. Sensitivity analyses results showed that the design of USSP cofferdam system must be further improved for construction in cohesionless soils. Furthermore, the 5th strut level before concreting played an indispensable role in controlling lateral deflection of USSPs. It was also observed that pumping out water before concreting base slab could greatly simplify and benefit construction program. On the other hand, the simplification in construction procedures could induce seepage inside the cofferdam, which additionally increased the deflection of USSPs by 10 mm on average.

• Journal of Species Research
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• v.11 no.4
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• pp.266-277
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• 2022

The current surveys of Ulva in the subtidal area around Jeju Island give a chance to discover unrecorded green algal species of the Korean macroalgal flora. As a result of this investigation, we found Ulva adhaerens Matusmoto & Shimada, inhabiting the subtidal regions, up to 15 m deep, and conducted the DNA barcoding on plastid rbcL-3P and tufA regions with describing the morphological characteristics. Our specimens of U. adhaerens forms a monophyletic clade with the Japanese type specimen and U. piritoka Ngāti Kuri, Heesch & W.A. Nelson from New Zealand exhibiting each 0.3% sequence divergences, respectively, in the plastid rbcL-3P. The genetic variation of U. adhaerens clade is 1.0-3.9% in rbcL-3P and 4.8-9.8% in tufA to each Ulva species, including the generic type, U. lactuca Linneaus. The morphology of Korean U. adhaerens specimens is identical to the type specimens of U. adhaerens from Japan having the development of rhizoidal filaments from both of the cell layers of the distromatic blade and the extension of rhizoidal clumps with adhesive trait between blades by extended rhizoidal clumps at the basal blades. The thallus attachment to substrate is by numerous minute discoidal plates made up of rhizoids originating from the inner part of distromatic blades in basal. Although there are still some problems to resolve the relationship between U. adhaerens and U. piritoka in the rbcL dataset and the phylogenetic pattern of the Group II intron of rbcL, we propose the new record of U. adhaerens in Korean macroalgal flora based on the morphological characteristics of Korean specimens. Continued study of the genus Ulva by morphological and molecular assessment will delimit the species of Ulva, elucidate the relationships between them, and uncover the species diversity.

• Proceedings of the Korea Water Resources Association Conference
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• 1998.05b
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• pp.3-3
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• 1998

In this pressentation it is argued that the heterogeneity of a hydrologic attribute which may seem to be nonstationary at one scale, may become stationary at a larger scale. The fundamental reason for transformation from nonstationarity to stationarity whith the increase in scale is the phenomenon of coarse-graining of the hydrologic processes with increasing scale. Due to the phenomenon of aliasing, a particular scale hydrologic process heterogeneity which is observed as a nonstationary process at that scale, may be observed as a stationary process at a higher(larger) scale whose size is bigger than the stationary extent of the lower scale heterogeneity. As one goes through a hierarchical sequence of larger and larger scales for observations, one would eliminate nonstationarities which emerge at some lower scales at the expense of losing information on the high frequency fluctuations of the lower scale heterogeneities which will no longer be observed at the larger sampling scales. We call this phenimenon as the "coarse-graining in hydrologic observations". In this presentation, it is also argued that by the coarse-graining of hydrologic processes due to the averaging and aliasing operations at increasing scales, the conservation laws corresponging to these scales may still be quite parsimonious, and need not be more complicated as the scales get larger. It is shown that shen a higher(larger) scale process is formed by averaging a lower(smaller) scale process in time or space, the high frequency components of the lower scale process will be eliminated by the averaging operation. Thereby, the resuliiting average hydrologic dynamics, free from the effects of the high frequency components of the lower scale process, can still be quite simple in form. This is demonstrated by means of some recent upscaling work on the solute teansport conservation equation for hetergeneous aquifers. By means of this solute transport example, it is also shown that for the ensemble average form of a hydrologic conservation equation to be equivalent to its volume-average form at any scale, the parameter functions of that conservation equation at the immediately lower scale must be ergodic.