• Journal of Information Technology Applications and Management
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• v.25 no.4
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• pp.145-156
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• 2018

This study proposes a content-based recommendation algorithm (NRA) for pet food. The proposed algorithm tries to recommend appropriate or inappropriate feed by using collective intelligence based on user experience and prior knowledge of experts. Based on the physical and health status of the dogs, this study suggests what kind of nutrients are necessary for the dogs and the most recommended pet food containing these nutrients. Performance evaluation was performed in terms of recall, precision, F1 and AUC. As a result of the performance evaluation, the AUC and F1 value of the proposed NRA was 15% and 42% higher than that of the baseline model, respectively. In addition, the performance of NRA is shown higher for recommendation of normal dogs than disease dogs.

• Mass Spectrometry Letters
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• v.4 no.1
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• pp.1-9
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• 2013

Fungal biotechnology has been well established in food and healthcare sector, and now being explored for lignocellulosic biorefinery due to their great potential to produce a wide array of extracellular enzymes for nutrient recycling. Due to global warming, environmental pollution, green house gases emission and depleting fossil fuel, fungal enzymes for lignocellulosic biomass refinery become a major focus for utilizing renewal bioresources. Proteomic technologies tender better biological understanding and exposition of cellular mechanism of cell or microbes under particular physiological condition and are very useful in characterizing fungal secretome. Hence, in addition to traditional colorimetric enzyme assay, mass-spectrometry-based quantification methods for profiling lignocellulolytic enzymes have gained increasing popularity over the past five years. Majority of these methods include two dimensional gel electrophoresis coupled to mass spectrometry, differential stable isotope labeling and label free quantitation. Therefore, in this review, we reviewed more commonly used different proteomic techniques for profiling fungal secretome with a major focus on two dimensional gel electrophoresis, liquid chromatography-based quantitative mass spectrometry for global protein identification and quantification. We also discussed weaknesses and strengths of these methodologies for comprehensive identification and quantification of extracellular proteome.

• Journal of Microbiology and Biotechnology
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• v.24 no.8
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• pp.1123-1132
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• 2014

This study evaluated the growth and nutrient removal ability of an indigenous algal consortium on real untreated municipal wastewater in a high rate algal pond (HRAP). The HRAP was operated semicontinuously under different hydraulic retention times (HRT: 2, 4, 6, and 8 days). The average removal efficiencies of chemical oxygen demand, and total nitrogen and phosphate of real municipal wastewater were maintained at $85.44{\pm}5.10%$, $92.74{\pm}5.82%$, and $82.85{\pm}8.63%$, respectively, in 2 day HRT. Algae dominated the consortium and showed high settling efficiency (99%), and biomass and lipid productivity of $0.50{\pm}0.03g/l/day$ and $0.103{\pm}0.0083g/l/day$ (2day HRT), respectively. Fatty acid methyl ester analysis revealed a predominance of palmitate (C16:0), palmitoleate (C16:1), linoleate (C18:2), and linolenate (C18:3). Microalgal diversity analyses determined the presence of Chlorella, Scenedesmus, and Stigeoclonium as the dominant microalgae. The algal consortium provides significant value not only in terms of energy savings and nutrient removal but also because of its bioenergy potential as indicated by the lipid content (20-23%) and FAME profiling.

• Journal of Nutrition and Health
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• v.35 no.10
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• pp.1053-1059
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• 2002

In post-genome period, the technique for identifying gene expression has been changed to high throughput screening. In the field of molecular nutrition, the need for this technique to clarify molecular function of the specific nutrient is essential. In this study, we have tested the zinc-regulated gene expression in zinc-deficient U937 cells, using cDNA microarray which is the cutting-edge technique to screen large numbers of gene expression simultaneously. The study result can be used for the preliminary gene screening data for clarifying, using monocyte U937 cell line, molecular Zn aspect in atherosclerosis. U937 cells were cultured in Zn-adequate (control, 12 $\mu$M Zn) or Zn-deficient (experimental, 0 $\mu$M Zn) ESMI media during 2 days, respectively. Cells were harvested and RNA was extracted. Total RNA was reverse-transcriptinized and synthesized cDNA probe labeled with Cy-3. fluorescent labeled cDNA probe was applied to microarray slide for hybridization slide, and after then, the slide was scanned using fluorescence scanner. ‘Highly expressed genes’ in Zn-deficient U937 cells, comparing to Zn-adequate group, are mainly about the genes for motility protein, immune system protein, oncogene and tumor suppressor and ‘Less highly expressed genes’ are about the genes for transcription, apoptosis associated protein, cell cycle, and several basic transcription factors. The results of this preliminary study imply the effectiveness of cDNA microarray for expression profiling of a singly nutrient deficiency, specially Zn. Furthur study, using tailored-cDNA array and capillary endothelial cell lines, would be beneficial to clarify molecular Zn function, more in detail.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1260-1269
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• 2024

The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.788-801
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• 2020

Objective: This study was conducted to evaluate the effects of diets containing different wet rice distillers' by-product (RDP) levels on growth performance, nutrient digestibility, blood profiles and gut microbiome of weaned piglets. Methods: A total of 48 weaned castrated male crossbred pigs, initial body weight 7.54±0.97 kg, and age about 4 wks, were used in this experiment. The piglets were randomly allocated into three iso-nitrogenous diet groups that were fed either a control diet, a diet with 15% RDP, or a diet with 30% RDP for a total of 35 days. Chromium oxide was used for apparent digestibility measurements. On d 14 and d 35, half of the piglets were randomly selected for hemato-biochemical and gut microbiota evaluations. Results: Increasing inclusion levels of RDP tended to linearly increase (p≤0.07) average daily gain on d 14 and d 35, and decreased (p = 0.08) feed conversion ratio on d 35. Empty stomach weight increased (p = 0.03) on d 35 while digestibility of diet components decreased. Serum globulin concentration decreased on d 14 (p = 0.003) and red blood cell count tended to decrease (p = 0.06) on d 35, parallel to increase RDP levels. Gene amplicon profiling of 16S rRNA revealed that the colonic microbiota composition of weaned pigs changed by inclusion of RDP over the period. On d 14, decreased proportions of Lachnospiraceae_ge, Ruminococcaceae_ge, Ruminococcaceae_UCG-005, and Bacteroidales_ge, and increased proportions of Prevotellaceae_ge, Prevotella_2, and Prevotella_9 were found with inclusion of RDP, whereas opposite effect was found on d 35. Additionally, the proportion of Lachnospiraceae_ge, Ruminococcaceae_ge, Ruminococcaceae_UCG-005, and Bacteroidales_ge in RDP diets decreased over periods in control diet but increased largely in diet with 30% RDP. Conclusion: These results indicate that RDP in a favorable way modulate gastrointestinal microbiota composition and improve piglet performance despite a negative impact on digestibility of lipids and gross energy.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.458-466
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• 2017

Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is a major threat to rice productivity. Here, we performed RNA-Seq based transcriptomic analysis of Xoo transcripts isolated under in planta growth (on both susceptible and resistant hosts) and in vitro culture conditions. Our in planta extraction method resulted in successful enrichment of Xoo cells and provided RNA samples of high quality. A total of 4,619 differentially expressed genes were identified between in planta and in vitro growth conditions. The majority of the differentially expressed genes identified under in planta growth conditions were related to the nutrient transport, protease activity, stress tolerance, and pathogenicity. Among them, over 1,300 differentially expressed genes were determined to be secretory, including 184 putative type III effectors that may be involved in Xoo pathogenicity. Expression pattern of some of these identified genes were further validated by semi-quantitative RT-PCR. Taken together, these results provide a transcriptome overview of Xoo under in planta and in vitro growth conditions with a focus on its pathogenic processes, deepening our understanding of the behavior and pathogenicity of Xoo.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1896-1907
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• 2018

Salmonellosis is commonly associated with meat and poultry products, but an increasing number of Salmonella outbreaks have been attributed to contaminated vegetables and fruits. Enteric pathogens including Salmonella enterica spp. can colonize diverse produce and persist for a long time. Considering that fresh vegetables and fruits are usually consumed raw without heat treatments, Salmonella contamination may subsequently lead to serious human infections. In order to understand the underlying mechanism of Salmonella adaptation to produce, we investigated the transcriptomics of Salmonella in contact with green vegetables, namely cabbage and napa cabbage. Interestingly, Salmonella pathogenicity island (SPI)-1 genes, which are required for Salmonella invasion into host cells, were up-regulated upon contact with vegetables, suggesting that SPI-1 may be implicated in Salmonella colonization of plant tissues as well as animal tissues. Furthermore, Salmonella transcriptomic profiling revealed several genetic loci that showed significant changes in their expression in response to vegetables and were associated with bacterial adaptation to unfavorable niches, including STM14_0818 and STM14_0817 (speF/potE), STM14_0880 (nadA), STM14_1894 to STM14_1892 (fdnGHI), STM14_2006 (ogt), STM14_2269, and STM14_2513 to STM14_2523 (cbi operon). Here, we show that nadA was required for bacterial growth under nutrient-restricted conditions, while the other genes were required for bacterial invasion into host cells. The transcriptomes of Salmonella in contact with cabbage and napa cabbage provided insights into the comprehensive bacterial transcriptional response to produce and also suggested diverse virulence determinants relevant to Salmonella survival and adaptation.

• ALGAE
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• v.33 no.2
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• pp.191-203
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• 2018

Fragilariopsis cylindrus is one of the most successful psychrophiles in the Southern Ocean. To investigate the molecular mechanism of biomineralization in this species, we attempted to synchronize F. cylindrus growth, since new cell wall formation is tightly coupled to the cell division process. Nutrient limitation analysis showed that F. cylindrus cultures rapidly stopped growing when deprived of silicate or light, while growth continued to a certain extent in the absence of nitrate. Flow cytometry analysis indicated that deprivation of either silicate or light could effectively arrest the cell cycle of this diatom species at the G1 phase, suggesting that synchrony can be established using either factor. Fluorescence labeling of new cell walls was faintly detectable as early as approximately 6 h after silicon repletion or light irradiation, and labeling was markedly intensified by 18 h. It is revealed that the synthesis of girdle bands begins before valve synthesis in this species, with active valve synthesis occurring during the G2 / M phase. Expression profiling revealed that selective member(s) of the F. cylindrus SIT genes (FcSIT) respond to silicate and light, with a different set of genes being responsive to each factor. The Si / light double depletion experiments demonstrated that expression of one FcSIT gene is possibly correlated to transition to G2 / M phase of the cell cycle, when the valve is actively formed.

• Journal of the Korean Society of Food Science and Nutrition
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• v.43 no.2
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• pp.179-186
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• 2014

Metabolomics is the study of changes in the metabolic status of an organism as a consequence of drug treatment, environmental influences, nutrition, lifestyle, genetic variations, toxic exposure, disease, stress, etc, through global or comprehensive identification and quantification of every single metabolite in a biological system. Since most chronic diseases have been demonstrated to be linked to nutrition, nutritional metabolomics has great potential for improving our understanding of the relationship between disease and nutritional status, nutrient, or diet intake by exploring the metabolic effects of a specific food challenge in a more global manner, and improving individual health. In particular, metabolite profiling of biofluids, such as blood, urine, or feces, together with multivariate statistical analysis provides an effective strategy for monitoring human metabolic responses to dietary interventions and lifestyle habits. Therefore, studies of nutritional metabolomics have recently been performed to investigate nutrition-related metabolic pathways and biomarkers, along with their interactions with several diseases, based on animal-, individual-, and population-based criteria with the goal of achieving personalized health care in the future. This article introduces analytical technologies and their application to determination of nutritional phenotypes and nutrition-related diseases in nutritional metabolomics.