• Asian-Australasian Journal of Animal Sciences
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• 제25권10호
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• pp.1481-1492
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• 2012

The interaction of the genes involved in intestinal development is the molecular basis of the regulatory mechanisms of intestinal development. The objective of this study was to identify the significant pathways and key genes that regulate intestinal development in Landrace piglets, and elucidate their rules of operation. The differential expression of genes related to intestinal development during suckling time was investigated using a porcine genome array. Time sequence profiles were analyzed for the differentially expressed genes to obtain significant expression profiles. Subsequently, the most significant profiles were assayed using Gene Ontology categories, pathway analysis, network analysis, and analysis of gene co-expression to unveil the main biological processes, the significant pathways, and the effective genes, respectively. In addition, quantitative real-time PCR was carried out to verify the reliability of the results of the analysis of the array. The results showed that more than 8000 differential expression transcripts were identified using microarray technology. Among the 30 significant obtained model profiles, profiles 66 and 13 were the most significant. Analysis of profiles 66 and 13 indicated that they were mainly involved in immunity, metabolism, and cell division or proliferation. Among the most effective genes in these two profiles, CN161469, which is similar to methylcrotonoyl-Coenzyme A carboxylase 2 (beta), and U89949.1, which encodes a folate binding protein, had a crucial influence on the co-expression network.

• Korean Journal of Radiology
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• 제22권2호
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• pp.233-242
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• 2021

Objective: To evaluate the association of MRI features with the major genomic profiles and prognosis of World Health Organization grade III (G3) gliomas compared with those of glioblastomas (GBMs). Materials and Methods: We enrolled 76 G3 glioma and 155 GBM patients with pathologically confirmed disease who had pretreatment brain MRI and major genetic information of tumors. Qualitative and quantitative imaging features, including volumetrics and histogram parameters, such as normalized cerebral blood volume (nCBV), cerebral blood flow (nCBF), and apparent diffusion coefficient (nADC) were evaluated. The G3 gliomas were divided into three groups for the analysis: with this isocitrate dehydrogenase (IDH)-mutation, IDH mutation and a chromosome arm 1p/19q-codeleted (IDHmut1p/19qdel), IDH mutation, 1p/19q-nondeleted (IDHmut1p/19qnondel), and IDH wildtype (IDHwt). A prediction model for the genetic profiles of G3 gliomas was developed and validated on a separate cohort. Both the quantitative and qualitative imaging parameters and progression-free survival (PFS) of G3 gliomas were compared and survival analysis was performed. Moreover, the imaging parameters and PFS between IDHwt G3 gliomas and GBMs were compared. Results: IDHmut G3 gliomas showed a larger volume (p = 0.017), lower nCBF (p = 0.048), and higher nADC (p = 0.007) than IDHwt. Between the IDHmut tumors, IDHmut1p/19qdel G3 gliomas had higher nCBV (p = 0.024) and lower nADC (p = 0.002) than IDHmut1p/19qnondel G3 gliomas. Moreover, IDHmut1p/19qdel tumors had the best prognosis and IDHwt tumors had the worst prognosis among G3 gliomas (p < 0.001). PFS was significantly associated with the 95th percentile values of nCBV and nCBF in G3 gliomas. There was no significant difference in neither PFS nor imaging features between IDHwt G3 gliomas and IDHwt GBMs. Conclusion: We found significant differences in MRI features, including volumetrics, CBV, and ADC, in G3 gliomas, according to IDH mutation and 1p/19q codeletion status, which can be utilized for the prediction of genomic profiles and the prognosis of G3 glioma patients. The MRI signatures and prognosis of IDHwt G3 gliomas tend to follow those of IDHwt GBMs.

• Genomics & Informatics
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• 제13권2호
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• pp.40-44
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• 2015

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.

• International Journal of Fluid Machinery and Systems
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• 제8권4호
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• pp.283-293
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• 2015

The effect of the inlet swirling flow in a hydraulic turbine draft tube is a very complex phenomenon, which has been extensively investigated both theoretically and experimentally. In fact, the finding of the optimal flow distribution at the draft tube inlet in order to get the best performance has remained a challenge. Thus, attempting to answer this question, it was assumed that through an automatic optimization process a Genetic Algorithm would be able to manage a parameterized inlet velocity profile in order to achieve the best flow field for a particular draft tube. As a result of the optimization process, it was possible to obtain different draft-tube flow structures generated by the automatic manipulation of parameterized inlet velocity profiles. Thus, this work develops a qualitative and quantitative analysis of these new draft tube flow field structures provoked by the redesigned inlet velocity profiles. The comparisons among the different flow fields obtained clearly illustrate the importance of the flow uniformity at the end of the conduit. Another important aspect has been the elimination of the re-circulating flow area which used to promote an adverse pressure gradient in the cone, deteriorating the pressure recovery effect. Thanks to the evolutionary optimization strategy, it has been possible to demonstrate that the optimized inlet velocity profile can suppress or mitigate, at least numerically, the undesirable draft tube flow characteristics. Finally, since there is only a single swirl number for which the objective function has been minimized, the energy loss factor might be slightly affected by the flow rate if the same relation of the axial-tangential velocity components is maintained, which makes it possible to scale the inlet velocity field to different operating points.

• Nutrition Research and Practice
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• 제14권1호
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• pp.32-44
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• 2020

BACKGROUND/OBJECTIVE: We have previously designed the anti-cancer food scoring model (ACFS) 1.0, an evidence-based quantitative tool analyzing the anti-cancer or carcinogenic potential of diets. Analysis was performed using simple quantitative indexes divided into 6 categories (S, A, B, C, D, and E). In this study, we applied this scoring model to wider recipes and evaluated its nutritional relevance. MATERIALS/METHODS: National or known regional databases were searched for recipes from 6 categories: Korean out-dining, Korean home-dining, Western, Chinese, Mediterranean, and vegetarian. These recipes were scored using the ACFS formula and the nutrition profiles were analyzed. RESULTS: Eighty-eight international recipes were analyzed. All S-graded recipes were from vegetarian or Mediterranean categories. The median code values of each category were B (Korean home-dining), C (Korean out-dining), B (Chinese), A (Mediterranean), S (vegetarian), and D (Western). The following profiles were correlated (P < 0.05) with ACFS grades in the univariate trend analysis: total calories, total fat, animal fat, animal protein, total protein, vitamin D, riboflavin, niacin, vitamin B₁₂, pantothenic acid, sodium, animal iron, zinc, selenium, and cholesterol (negative trends), and carbohydrate rate, fiber, water-soluble fiber, vitamin K, vitamin C, and plant calcium (positive trends). Multivariate analysis revealed that animal fat, animal iron, and niacin (negative trends) and animal protein, fiber, and vitamin C (positive trends) were statistically significant. Pantothenic acid and sodium showed non-significant negative trends (P < 0.1), and vitamin B₁₂ showed a non-significant positive trend. CONCLUSION: This study provided a nutritional basis and extended the utility of ACFS, which is a bridgehead for future cancer-preventive clinical trials using ACFS.

• Journal of Animal Science and Technology
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• 제56권5호
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• pp.16.1-16.9
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• 2014

Fatty acids (FA) have recently been used in several studies to infer the diet in a number of species. While these studies have been largely successful, most have dealt with predators that have a fairly specialized diet. In this paper, we used FA analysis as a tool to infer the diet of the nearctic river otter (Lontra canadensis). The river otter is an opportunistic predator known to subsist on a wide variety of prey including, fishes, crayfish, molluscs, reptiles and amphibians, among others. We analyzed the principle components of 60 FA from otters and 25 potential prey species in Illinois, USA. Prey species came from 4 major taxonomic divisions: fishes, crayfish, molluscs and amphibians. Within each division, most, but not all, species had significantly different profiles. Using quantitative FA signature analysis, our results suggest that, by mass, fish species are the most significant component of Illinois River otters' diet ($37.7{\pm}1.0%$). Molluscs ranked second ($32.0{\pm}0.8%$), followed by amphibians ($27.3{\pm}4.3%$), and finally, crayfish ($3.0{\pm}0.6%$). Our analysis indicates that molluscs make up a larger portion of the otter diet than previously reported. Throughout much of the Midwest there have been numerous otter reintroduction efforts, many of which appear to be successful. In regions where mollusc species are endangered, these data are essential for management agencies to better understand the potential impact of otters on these species. Our analysis further suggests that quantitative FA signature analysis can be used to infer diet even when prey species are diverse, to the extent that their FA profiles differ. Better understanding of the otter's metabolism of FA would improve inferences of diet from FA analysis.

• Journal of Microbiology and Biotechnology
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• 제18권4호
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• pp.648-657
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• 2008

In this study, we used functional genomic strategies, proteomics and quantitative real-time (qRT)-PCR, to advance our understanding of genes associated with fumonisin production in the fungus Fusarium verticillioides. Earlier studies have demonstrated that deletion of the FCC1 gene, which encodes a C-type cyclin, leads to a drastic reduction in fumonisin production and conidiation in the mutant strain (FT536). The premise of our research was that comparative analysis of F. verticillioides wild-type and FT536 proteomes will reveal putative proteins, and ultimately corresponding genes, that are important for fumonisin biosynthesis. We isolated proteins that were significantly upregulated in either the wild type or FT536 via two-dimensional polyacrylamide gel electrophoresis, and subsequently obtained sequences by mass spectrometry. Homologs of identified proteins, e.g., carboxypeptidase, laccase, and nitrogen metabolite repression protein, are known to have functions involved in fungal secondary metabolism and development. We also identified gene sequences corresponding to the selected proteins and investigated their transcriptional profiles via quantitative real-time (qRT)-PCR in order to identify genes that show concomitant expression patterns during fumonisin biosynthesis. These genes can be selected as targets for functional analysis to further verify their roles in $FB_1$ biosynthesis.

• The Korean Journal of Ceramics
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• 제1권1호
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• pp.7-12
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• 1995

When a $Ta_O_5$ dielectric film is deposited on a bare silicon, the growth of $SiO_2$ at the $Ta_O_5$/Si interface cannot be avoided. Even though the $SiO_2$ layer is ultrathin (a few nm), it has great effects on the electrical properties of the capacitor. The concentration depth profiles of the ultrathin interfacial $SiO_2$ and $SiO_2/Si_3N_4$ layers were obtained using an Auger electron spectroscopy (AES) equipped with a cylindrical mirror analyzer (CMA). These AES depth profiles were quantitatively analyzed by comparing with the theoretical depth profiles which were obtained by considering the inelastic mean free path of Auger electrons and the angular acceptance function of CMA. The direct measurement of the interfacial layer thicknesses by using a high resolution cross-sectional TEM confirmed the accuracy of the AES depth analysis. The $SiO_2/Si_3N_4$ double layers, which were not distinguishable from each other under the TEM observation, could be effectively analyzed by the AES depth profiling technique.

• 한국발생생물학회지:발생과생식
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• 제14권3호
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• pp.207-214
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• 2010

The tremendous changes of uterine endometrium are observed during early pregnancy and protease and their inhibitors are involved in regulation of cell proliferation and remodeling of the tissues through remodeling the extracellular matrix (ECM). Some of the proteases and protease inhibitors have been suspected to a factor in endometrial changes but many parts of their expression profiles and the physiological roles are not uncovered. To evaluate the functional roles of them, in this study the expression profiles of proteases and protease inhibitors were analyzed using real-time quantitative PCR analysis. Mmp9 (matrix metalloproteinase 9) mRNA levels peaked on day 4 at the time of implantation. On the other hand, Ela2 (neutrophil elastase, NE) mRNA levels were peaked on day 2 of pregnancy. Its expression were decreased until day 4 of pregnancy but increased rapidly until day 7 of pregnancy and decreased again. NE inhibitor Slpi (secretory leukocyte protease inhibitor, SLPI) mRNA levels were related with the implantation stage and with the levels of Ela2. At the time of implantation the expression levels of Slpi mRNA were about 5 times higher than the Ela2 mRNA in the uterus. In the implantation stage embryos, Mmp9 specific mRNA was only detected at the blastocyst. On the other hand, the expression level of SLPI was higher than that of the Ela2 mRNA at blastocyst and 4.5 day p.c. embryos. Based on these results it is suggested that MMP9, SLPI, and NE have important physiological role in embryo implantation both in uterus and embryos.

• 대한설비공학회:학술대회논문집
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• 대한설비공학회 2006년도 하계학술발표대회 논문집
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• pp.773-778
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• 2006

Velocity profiles inside a partially filled pipline have been investigated experimentally. To measure the velocity fields, a particle image velocimetry (PIV), which is a recent quantitative visualization technique, is applied. The velocity profile inside a circular pipe is well known, but if the pipe is partially filled, the problem is entirely different in the sense that the velocity distribution is significantly affected by the slope of pipe and filled water level, and so on. In order to calculate exact flow rate in the open channel or partially filled pipeline, three-dimensional velocity distributions at a given cross-sectional area are measured and compared the flow rates with the previously known empirical formula of Manning equation. The results show that the velocity profiles at center plane is considerably different from each other when the slope and water level change. Thus, The three-dimensional velocity profile can be the most plausible estimate for the exact flow rate.