• Journal of Biomedical and Translational Research
• /
• v.19 no.4
• /
• pp.116-124
• /
• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• Journal of Life Science
• /
• v.32 no.3
• /
• pp.249-255
• /
• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Proceedings of the KSAR Conference
• /
• 2001.03a
• /
• pp.56-56
• /
• 2001

The exogenous gene transfer by intracytoplasmic sperm injection (ICSI) procedure has been recently used to produce transgenic mice and pigs. Sperm-mediated DNA transfer has the potential to markedly simplify the generation of transgenic animals. This method may serve as an alternative to the pronucleus injection of DNA for the production of transgenic pigs. Therefore, in this study, we investigated the expression of transgene after co-injection of spermatozoon or sperm head with green fluorescent protein (GFP) gene into in vitro matured porcine oocytes. Spermatozoon and sperm head, that was obtained by sonication, were treated with 0.03% Triton X-100 to remove the membrane. They were preincubated with linearized pEGFP-N1 for 1 min, and then embryos cultured NCSU23 medium for 2.5 days after co-injected of sperm and DNA. We monitored expression of GFP in embryos under epifluorescent microscope. The remove of sperm membrane did not alter the developmental competence of embryos after ICSI. At 7 days following injection, the rates of blastocysts following injection of intact sperm (15.0%), and of sperm with disrupted membrane (14.2%) were higher than that following IVF (10.0%). Porcine oocytes injected with sperm which co-cultured with DNA concentration of 1, 0.1, and 0.01 ng were 60, 65.7 and 75% and 18.5, 37.4 and 22.2% for rates of cleavage and GFP expression, respectively. In vitro matured porcine oocytes injected with sperm and isolated sperm head resulted in 69 and 59.7% of cleavage rates, respectively The rates of embryo GFP expressed did not significantly different between sperm (20.4%) and sperm head (20.0%) injection. The transgenic embryos with the clusters of positive blastomeres were observed under fluorescent microscope. Most of embryos expressed GFP gene showed mosaicism. They showed GFP expression at 1/4, 2/4 and 3/4 of blastomeres at the 4-cell stage. Among these 4-cell embryos, the expression rate of 1/4 blastomere group (54.6%) was higher than the other groups (15.3-30.7%). These results indicate that membrane disrupted sperm could attach with exogenous DNA, and that this procedure may be useful to introduce foreign gene into porcine oocytes. Therefore, our data suggest that the ICSI car be a useful tool to efficiently produce transgenic pig as well as other mammals.

• Journal of the Korean Chemical Society
• /
• v.37 no.2
• /
• pp.191-198
• /
• 1993

The crystal structures of $Cd_{6-}A$ evacuated at $2{\times}10^{-6}$ torr and $750^{\circ}C$ (a = 12.204(1) $\AA$) and dehydrated $Cd_{6-}A$ reacted with 0.1 torr of Cs vapor at $250^{\circ}C$ for 12 hours (a = 12.279(1) $\AA$) have been determined by single crystal X-ray diffraction techniques in the cubic space group Pm3m at $21(1)^{\circ}C.$ Their structures were refined to final error indices, $R_1=$ 0.081 and $R_2=$ 0.091 with 151 reflections and $R_1=$ 0.095 and $R_2=$ 0.089 with 82 reflections, respectively, for which I > $3\sigma(I).$ In vacuum dehydrated $Cd_{6-}A$, six $Cd^{2+}$ ions occupy threefold-axis positions near 6-ring, recessed 0.460(3) $\AA$ into the sodalite cavity from the (111) plane at O(3) : Cd-O(3) = 2.18(2) $\AA$ and O(3)-Cd-O(3) = $115.7(4)^{\circ}.$ Upon treating it with 0.1 torr of Cs vapor at $250^{\circ}C$, all 6 $Cd^{2+}$ ions in dehydrated $Cd_{6-}A$ are reduced by Cs vapor and Cs species are found at 4 crystallographic sites : 3.0 $Cs^+$ ions lie at the centers of the 8-rings at sites of $D_{4h}$ symmetry; ca. 9.0 Cs+ ions lie on the threefold axes of unit cell, ca. 7 in the large cavity and ca. 2 in the sodalite cavity; ca. 0.5 $Cs^+$ ion is found near a 4-ring. In this structure, ca. 12.5 Cs species are found per unit cell, more than the twelve $Cs^+$ ions needed to balance the anionic charge of zeolite framework, indicating that sorption of Cs0 has occurred. The occupancies observed are simply explained by two unit cell arrangements, $Cs_{12}-A$ and $Cs_{13}-A$. About 50% of unit cells may have two $Cs^+$ ions in sodalite unit near opposite 6-rings, six in the large cavity near 6-ring and one in the large cavity near a 4-ring. The remaining 50% of unit cells may have two Cs species in the sodalite unit which are closely associated with two out of 8 $Cs^+$ ions in the large cavity to form linear $(Cs_4)^{3+}$ clusters. These clusters lie on threefold axes and extend through the centers of sodalite units. In all unit cells, three $Cs^+$ ions fill equipoints of symmetry $D_{4h}$ at the centers of 8-rings.

• Progress in Medical Physics
• /
• v.14 no.4
• /
• pp.211-217
• /
• 2003

The Principal component analysis (PCA) is a well-known data analysis method that is useful in linear feature extraction and data compression. The PCA is a linear transformation that applies an orthogonal rotation to the original data, so as to maximize the retained variance. PCA is a classical technique for obtaining an optimal overall mapping of linearly dependent patterns of correlation between variables (e.g. neurons). PCA provides, in the mean-squared error sense, an optimal linear mapping of the signals which are spread across a group of variables. These signals are concentrated into the first few components, while the noise, i.e. variance which is uncorrelated across variables, is sequestered in the remaining components. PCA has been used extensively to resolve temporal patterns in neurophysiological recordings. Because the retinal signal is stochastic process, PCA can be used to identify the retinal spikes. With excised rabbit eye, retina was isolated. A piece of retina was attached with the ganglion cell side to the surface of the microelectrode array (MEA). The MEA consisted of glass plate with 60 substrate integrated and insulated golden connection lanes terminating in an 8${\times}$8 array (spacing 200 $\mu$m, electrode diameter 30 $\mu$m) in the center of the plate. The MEA 60 system was used for the recording of retinal ganglion cell activity. The action potentials of each channel were sorted by off­line analysis tool. Spikes were detected with a threshold criterion and sorted according to their principal component composition. The first (PC1) and second principal component values (PC2) were calculated using all the waveforms of the each channel and all n time points in the waveform, where several clusters could be separated clearly in two dimension. We verified that PCA-based waveform detection was effective as an initial approach for spike sorting method.

• Journal of the Mineralogical Society of Korea
• /
• v.4 no.1
• /
• pp.22-31
• /
• 1991

Three crystal structures of dehydrated $Ag^+$-and $Ca^{2+}$- exchanged zeolite $A(Ag_4Ca_4-A,\;Ag_^Ca_3-A,\;and\;Ag_8Ca_2-A)$ treated at 250${\circ}C$ with 0.1 Torr of Rb vapor have been determined by single-crystal x-ray diffraction techniques in the cubic space group Pm3m at 21(1)${\circ}C$ (a=12,271(1)${\AA}$, 12.255(1)${\AA}$, and 12.339(1)${\AA}$, respectively). Their structures were refined to the final error indices. R(weighted) of 0.072 with 130 reflections, 0.050 with 110 reflections, and 0.083 with 86 reflections, respectively, for which $I>3{\rho}(I)$. In each structure, Rb species are found at three different crystallographic sites:3$Rb^+$+ions per unit cell are located at 8-ring centers, ca. 5.6 to 6.4 $Rb^+$ ions are found opposite 6-rings on threefold axes in the large cavity, and ca. 2.5 to 3.0 $Rb^+$ ions are found on threefold axes in the sodalite unit. Also, Ag species are found at two different crystallographic stites: ca. 0.7 to 2.1 $Ag^+$ lie opposite 4-rings and ca. 2.2 to 4.8 Ag atoms are located near the center of the large cavity. In these structures, the numbers of Ag atoms per unit cell are 2.2, 2.4, and 4.8, respectively, and these may form hexasilver clusters at the centers of the large cavities. The $Rb^+$ ions, by blocking 8-rings, may have prevented silver from migrating out of the structure. Each hexasilver cluster is stabilized by coordination to up to 13 $Rb^+$ions. An excess absorption of about 0.8 Rb atom per unit cell indicates that the presence of a triangular symmetric $(Rb_3)2^{+}$ cation in sodalite cavity. At least one large-cavity six-ring $Rb^+$ ion must necessarily approach this cluster and may be viewed as a member of it to give $(Rb)_4^{3+}$, $(Rb)_5^{4+}$ or $(Rb)_6^{5+}$.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
• /
• v.43 no.1
• /
• pp.29-36
• /
• 2017

Objectives: Acquired immunodeficiency syndrome (AIDS) is a disease of the human immune system caused by the human immunodeficiency virus (HIV). People with AIDS are much more vulnerable to infections, including opportunistic infections and tumors, than people with a healthy immune system. The objective of this study was to correlate oral lesions associated with HIV/AIDS and immunosuppression levels by measuring clusters of differentiation 4 (CD4) cell counts among patients living in the middle western regions of Ghana. Materials and Methods: A total of 120 patients who visited the HIV clinic at the Komfo Anokye Teaching Hospital and the Regional Hospital Sunyani of Ghana were consecutively enrolled in this prospective and cross-sectional study. Referred patients' baseline CD4 counts were obtained from medical records and each patient received an initial physician assessment. Intraoral diagnoses were based on the classification and diagnostic criteria of the EEC Clearinghouse, 1993. After the initial assessment, extra- and intraoral tissues from each enrolled patient were examined. Data analyses were carried out using simple proportions, frequencies and chi-square tests of significance. Results: Our study included 120 patients, and was comprised of 42 (35.0%) males and 78 (65.0%) females, ranging in age from 21 to 67 years with sex-specific mean ages of 39.31 years (males) and 39.28 years (females). Patient CD4 count values ranged from 3 to 985 cells/mL with a mean baseline CD4 count of 291.29 cells/mL for males and 325.92 cells/mL for females. The mean baseline CD4 count for the entire sample was 313.80 cells/mL. Of the 120 patients we examined, 99 (82.5%) were observed to have at least one HIV-associated intraoral lesion while 21 (17.5%) had no intraoral lesions. Oral candidiasis, periodontitis, melanotic hyperpigmentation, gingivitis and xerostomia were the most common oral lesions. Conclusion: From a total of nine oral lesions, six lesions that included oral candidiasis, periodontitis, melanotic hyperpigmentation, gingivitis, xerostomia and oral hairy leukoplakia were significantly correlated with declining CD4 counts.

• Horticultural Science & Technology
• /
• v.34 no.2
• /
• pp.324-330
• /
• 2016

To determine whether FT-IR spectral analysis based on multivariate analysis for whole cell extracts can be used to discriminate between artichoke (Cynara cardunculus var. scolymus L.) plants at the metabolic level, leaves of ten artichoke plants were subjected to Fourier transform infrared(FT-IR) spectroscopy. FT-IR spectral data from leaves were analyzed by principal component analysis (PCA), partial least square discriminant analysis (PLS-DA) and hierarchical clustering analysis (HCA). FT-IR spectra confirmed typical spectral differences between the frequency regions of 1,700-1,500, 1,500-1,300 and $1,100-950cm^{-1}$, respectively. These spectral regions reflect the quantitative and qualitative variations of amide I, II from amino acids and proteins ($1,700-1,500cm^{-1}$), phosphodiester groups from nucleic acid and phospholipid ($1,500-1,300cm^{-1}$) and carbohydrate compounds ($1,100-950cm^{-1}$). PCA revealed separate clusters that corresponded to their species relationship. Thus, PCA could be used to distinguish between artichoke species with different metabolite contents. PLS-DA showed similar species classification of artichoke. Furthermore these metabolic discrimination systems could be used for the rapid selection and classification of useful artichoke cultivars.

• Journal of Plant Biotechnology
• /
• v.32 no.4
• /
• pp.301-306
• /
• 2005

Conditions for efficient organogenesis and plant regeneration from Dianthus gratianopol suspension cultured cells were established. Shoot-forming calli of glossy surface, pale green and knobby type were selected from leaf explant-derived calli and were suspension-subcultured every week in CP liquid medium with 1.0 mg/L 2,4-D and 0.5 mg/L BAP. Combinations of 1.0 mg/L 2,4-D and 0.5 mg/L BAP, and 1.5 mg/L 2,4-D and 0.5 mg/L BAP were effective for the induction of regenerative callus from the suspension cultured cell clusters. Multiple shoot primordia were initiated from the green spots of these regenerative callus and formed shoots on MS medium with 1.0 mg/L TDZ and 0.5 mg/L PAA. Shoot regeneration frequency (calli regenerating at least one shoot) was about 87%. For plant regeneration, proliferated shoots were excised and transferred to MS medium with 0.1 mg/L NAA for root initiation after 9 weeks of culture. The regenerants were potted in soil and formed the flowering buds and petals. Also, adventitious shoots were formed from the excised green shoot primordia of regenerative callus and these shoots proliferated successfully and regenerated to whole plants.

• Journal of Plant Biotechnology
• /
• v.36 no.3
• /
• pp.281-288
• /
• 2009

Seed germination is the important stage to express many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mechanisms, we were analyzed the rice cDNA clones (Oryzasativa cultivar Ilpum) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,66 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as commonly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages. For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.