• Communications for Statistical Applications and Methods
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• v.29 no.6
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• pp.655-664
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• 2022

On the motivation by an integrative study of multi-omics data, we are interested in estimating the structure of the sparse cross correlation matrix of two high-dimensional random vectors. We rewrite the problem as a multiple testing problem and propose a new method to estimate the sparse structure of the cross correlation matrix. To do so, we test the correlation coefficients simultaneously and threshold the correlation coefficients by controlling FRD at a predetermined level α. Further, we apply the proposed method and an alternative adaptive thresholding procedure by Cai and Liu (2016) to the integrative analysis of the protein expression data (X) and the mRNA expression data (Y) in TCGA breast cancer cohort. By varying the FDR level α, we show that the new procedure is consistently more efficient in estimating the sparse structure of cross correlation matrix than the alternative one.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.1
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• pp.42-47
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• 2005

The possibility of using Moringa oleifera as a ruminant protein supplement was investigated by comparison between nutritive and anti-nutritive value of its different morphological parts with that of conventionally used Leucaena leucocephala leaf meal (LL). Parameters determined were chemical composition, rumen degradable protein (RDP), acid detergent insoluble protein (ADIP), pepsin soluble protein (PESP), non-protein nitrogen (NPN) total soluble protein (TSP) and protein potentially digested in the intestine (PDI). Total phenols (TP) and total extractable tannins (TET) were also evaluated as anti-nutritive factors. In vitro gas production characteristics were measured and organic matter digestibility (OMD) was estimated basing on 24 h-gas production. Crude protein content ranged from 265-308 g/kg DM in M. oleifera leaves (MOL) and seed cake (MOC) respectively. Leucaena leucocephala and Moringa oleifera soft twigs and leaves (MOLSTL) had CP content of 236 and 195 g/kg DM while Moringa oleifera soft twigs alone (MOST) and Moringa oleifera bucks (MOB) had 160, 114 and 69.3 g/kg DM respectively. RDP was highest in (MOC) (181 g/kg DM) followed by (MOL) (177 g/kg DM) and was lowest in MOB (40 g/kg DM). The proportion of the protein that was not available to the animal (ADIP) was (p<0.05) higher in MOL and MOC (72 and 73 g/kg DM) respectively and lowest in LL (29 g/kg DM). The PDI was high in LL (74 g/kg DM) followed by MOC (55 g/kg DM) then MOL (16 g/kg DM). PESP was highest (p<0.05) in MOC followed by MOL then LL (273, 200 and 163 g/kg DM respectively). MOC exhibited highest NPN content (116 g/kg DM) and was lowest in MOB (18 g/kg DM) (p<0.05). Highly (p<0.05) TSP was observed in MOC and MOL (308 and 265 g/kg DM respectively) followed by LL (236 g/kg DM). MOL had negligible TET (20 g/kg DM) when compared with about 70 g/kg DM in LL. Highly (p<0.05) b and a+b values were observed for MOLSTL (602 and 691 g/kg DM respectively) followed by MOL (490 and 538 g/kg DM). Highest c value was observed in MOSTL followed by MOC and MOL (0.064, 0.056 and 0.053 rate/hour) respectively. OMD was highest (p<0.05) for MOSTL followed by MOC and then MOL (579, 579 and 562 g/kg DM respectively). LL exhibited lower (p<0.05) OMD (467 g/kg DM). It was concluded from this study that the high crude protein content in MOL and MOLST could be well utilized by ruminant animals and increase animal performance however, high proportion of unavailable protein to the lower gut of animals and high rumen degradable protein due to negligible tannin content render it a relatively poor protein supplement for ruminants. MOC can be a best alternative protein supplement to leaves and leaves and soft twigs for ruminants.

• Journal of Embryo Transfer
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• v.26 no.4
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• pp.237-244
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• 2011

Ski protein is implicated in proliferation/differentiation in a variety of cells. We had previously reported that Ski protein is present in granulosa cells of atretic follicles, but not in preovulatory follicles, suggesting that Ski has a role in apoptosis of granulosa cells. The alternative fate of granulosa cells other than apoptosis is to differentiate to luteal cells, however, it is unknown whether Ski is expressed and has a role in granulosa cells undergoing luteinization. Thus, the aim of the present study was to examine whether the initiation of luteinization with luteinizing hormone (LH) directly regulates expression of Ski in the luteinized granulosa and luteal cells after ovulation by in vitro models. RT-PCR and real time PCR analysis respectively revealed that LH had no effect on c-Ski mRNA expression in the cultured granulosa cells regardless of LH treatment. Though Ski protein is absent in granulosa cells of preovulatory follicle, its mRNA (c-Ski) was expressed and the level was unchanged even after LH surge. Taken together, these results demonstrated that Ski protein expression is induced in granulosa cells upon luteinization, and suggested that its expression is regulated post-transcriptionally. Moreover, expression of mRNA of Arkadia, an E3 ubiquitin ligases, in luteinizing granulosa cells in vivo was assessed by realtime-PCR. The levels of Arkadia mRNA expression were unchanged during follicular growth and postovulatory luteinization. These findings suggest that Ski protein level may be regulated during luteinization at translational and/or post-translational level but not by Arkadia.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.56-58
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• 2000

Post-genomics may be defined in different ways depending on how one views the challenges after the genome. A popular view is to follow the concept of the central dogma in molecular biology, namely from genome to transcriptome to proteome. Projects are going on to analyze gene expression profiles both at the mRNA and protein levels and to catalog protein 3D structure families, which will no doubt help the understanding of information in the genome. However complete, such catalogs of genes, RNAs, and proteins only tell us about the building blocks of life. They do not tell us much about the wiring (interaction) of building blocks, which is essential for uncovering systemic functional behaviors of the cell or the organism. Thus, an alternative view of post-genomics is to go up from the molecular level to the cellular level, and to understand, what I call, the "interactome"or a complete picture of molecular interactions in the cell. KEGG (http://www.genome.ad.jp/kegg/) is our attempt to computerize current knowledge on various cellular processes as a collection of "generalized"protein-protein interaction networks, to develop new graph-based algorithms for predicting such networks from the genome information, and to actually reconstruct the interactomes for all the completely sequenced genomes and some partial genomes. During the reconstruction process, it becomes readily apparent that certain pathways and molecular complexes are present or absent in each organism, indicating modular structures of the interactome. In addition, the reconstruction uncovers missing components in an otherwise complete pathway or complex, which may result from misannotation of the genome or misrepresentation of the KEGG pathway. When combined with additional experimental data on protein-protein interactions, such as by yeast two-hybrid systems, the reconstruction possibly uncovers unknown partners for a particular pathway or complex. Thus, the reconstruction is tightly coupled with the annotation of individual genes, which is maintained in the GENES database in KEGG. We are also trying to expand our literature surrey to include in the GENES database most up-to-date information about gene functions.

• Fisheries and Aquatic Sciences
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• v.23 no.8
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• pp.22.1-22.8
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• 2020

Background: High demand and low supply of fishmeal due to overexploitation of fisheries resources have resulted in a dramatic increase in the price of this ingredient. Olive flounder (Paralichthys olivaceus) commercial feed contains approximately 60% fishmeal and limited success has been achieved in identifying sustainable alternative protein sources for this species. Methods: An on-farm feeding trial was conducted to compare a basal diet containing 65% as the control (CONT) with two experimental diets replacing 10% of fishmeal by animal protein (AP₁₀) or 20% of fishmeal by animal and plant protein (APP₂₀). Sub-adult olive flounder averaging 327 ± 9.3 g (mean±SD) were fed one of the three diets in triplicate groups for 16 weeks. Results: Weight gain, specific growth rate, feed efficiency, protein efficiency ratio, and survival were not significantly different among fish fed all the experimental diets (P > 0.05). Also, non-specific immune responses (superoxide dismutase and lysozyme activity), serum biochemical parameters, and intestinal villi length were not significantly different among fish fed all the experimental diets (P > 0.05). Conclusions: Therefore, based on growth performance, non-specific immune responses, serum biochemical parameters, and intestinal histology, dietary animal and plant protein mixtures could replace up to 20% of fishmeal in the diet of sub-adult olive flounder.

• Preventive Nutrition and Food Science
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• v.16 no.3
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• pp.248-252
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• 2011

Soy protein based formula (SPF) has been developed for infants who are at a high risk for atopic dermatitis (AD) and cow's milk protein allergy (CMA). We performed this study to evaluate the therapeutic efficacy and safety of SPF compared to conventional hydrolyzed cow's milk formula (hCMF) in the feeding of infants with AD and CMA. 38 infants (12 to 24 months of age) diagnosed with CMA and AD were randomized to receive either SPF or hCMF for 12 weeks. Follow-up was conducted at 4, 8 and 12 weeks. Growth parameters of the infants were evaluated during each visit. Clinical evaluations, including AD severity scores, pruritus, specific immunoglobulin E (IgE) (cow's milk protein and soy protein) levels of peripheral blood, were made at enrollment and week 12. Analysis was performed on the 32 infants (SPF: n=16, hCMF: n=16) who completed the 12-week intervention. Eczema area and severity index (EASI) scores, a measure of the severity of AD, and pruritus were significantly reduced after 12 weeks compared to enrollment in the both groups; however, the median changes for EASI scores and pruritus were not statistically different between the two groups. The growth parameters did not differ significantly between both groups at any assessed time point. This study suggests that SPF could be useful in decreasing the severity of AD without affecting infant growth status. Therefore SPF could provide an adequate and safe alternative to hCMF in treating infants with AD and CMA during the first 12 to 24 months of their life.

• Korean Chemical Engineering Research
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• v.57 no.1
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• pp.85-89
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• 2019

Cell-free protein synthesis utilizes the translational machinery in a cell extract. Unlike the conventional cell-based expression methods, not being affected by the conditions for cell growth, cell-free protein synthesis enables flexible manipulation of individual factors affecting the efficiency protein biosynthesis. However, the high cost and low stability of the energy sources to regenerate ATP have limited the use of cell-free synthesis for large-scale production of recombinant proteins. One of the approaches to address this problem is to use glucose as an alternative energy source to regenerate ATP through the glucose-metabolizing pathways in a cell extract. In this study, in an attempt to improve the efficiency of ATP regeneration by reinforcing oxidative phosphorylation process, we supplemented with cellular lipids to a glucose-fueled reaction mixture for cell-free protein synthesis. As a result of the lipid supplementation, the productivity of chloramphenicol acetyltransferase in a cell-free synthesis system using glucose increased more than 6 fold compared to when the lipid was not supplemented.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.265-273
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• 2019

Objective: Terminalia arjuna plant, specially its leaves, bark, and roots, are widely used in traditional herbal medicine due to presence of bioactive components and being a rich source of natural antioxidants. But its fruit has not been used for any such purposes despite its potential to retard oxidation. Hence, the antioxidant potential of Arjuna fruit extract (AFE) in retarding lipid and protein oxidation of raw ground pork was evaluated during refrigerated storage for 9 days. Methods: The AFEs were prepared using different solvents viz. ethanol (EH), water, ethanol: water (60:40) and methanol:hot water (60:40). The AFEs were analysed for total phenolic content (TPC), 2, 2-diphenyl-1-picrylhydrazyl radical scavenging activity and reducing power. Water extract (WE) and ethanol-water extract (EH-WE) were selected and incorporated at 1.0% into freshly minced pork meat and compared with a synthetic antioxidant, in retarding lipid and protein oxidation during storage. Results: The TPC in AFEs using different solvents ranged from 11.04 to 16.53 mg gallic acid equivalents/g and extracts exhibited appreciable scavenging activity ranging from 50.02% to 58.62%. Arjuna extracts significantly (p<0.05) improved the colour score of meat samples by reducing the formation of metmyoglobin during storage. Both the AFEs (WE and EH-WE) significantly (p<0.05) lowered the thiobarbituric acid reactive substances value, peroxide formation and formation of protein carbonyls in raw pork than control sample during storage. Upon sensory evaluation of all samples, it was found that AFE treatment could prolong the storage period of meat samples, without influencing the colour and odour score, up to 6 days. Conclusion: AFEs used at 1% improved the oxidative stability, colour and odour score and prolonged the refrigerated shelf life of ground pork up 6 days. Therefore, AFE could be explored as an alternative natural antioxidant in retarding lipid and protein oxidation in meat products.

• Food Science of Animal Resources
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• v.43 no.3
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• pp.428-440
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• 2023

Global meat consumption is increasing worldwide, however, supply remains lacking. Several alternative protein sources, such as cultured meat, plant-based protein production, and edible insects, have been proposed to overcome this shortage. Interestingly, edible insects are characterized by superior digestive and absorptive qualities that make them the ideal replacement for traditional protein production. This study aims to further the processing ability of insect protein by investigating the effects of various pre-treatment methods, such as blanching (HB), roasting (HR), and superheated steam (HS), on the nutritional properties and physicochemical characteristics of proteins extracted from Hermetia illucens larvae. The drying rate, pH value, color analysis, amino and fatty acid profile, as well as bulk density, shear force, and rehydration ratios of the above pre-treatment methods, were explored. HS was found to have the highest drying rate and pH value analysis showed that HB and HS samples have significantly higher values compared to the other modalities. Raw edible insects had the highest value in the sum of essential amino acid (EAA) and EAA index when compared to EAAs. HB and HS showed significantly lower bulk density results, and HS showed the highest shear force and the highest value in rehydration ratio, regardless of immersion time. Therefore, taking the above results together, it was found that blanching and superheated steam blanching pre-treatment were the most effective methods to improve the processing properties of H. illucens after hot-air drying.

• Journal of Apiculture
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• v.34 no.2
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• pp.161-167
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• 2019

There is an urgent need for novel protein sources as an alternative to meat production. Insects, such as honeybees, hold potential as a safe, nutritious and reliable protein source for the future. In the present study, we established optimal powder preprocessing conditions of drone pupae (Apis mellifera L.) for use as a novel food. The content of moisture, crude protein, crude fat, crude ash, carbohydrate and crude fiber in drone pupae(Apis mellifera L.) were analyzed. The crude protein content ranged from 48.5 to 51.8% was found in both freeze-dried and hot-air powdered drone pupae. However, the protein content in the freeze-dried powder was higher than that in the hot-air powder by 3.3%. According to the Korean Food Standard Codex test method, coliforms, Salmonella spp. Staphylcoccus aureus, and Enterohamorrhagice Escherichia coli were not detected in both freeze-dried and hot-air powder. Therefore, we suggest that the high protein content of the powdered drone pupae prepared in this study can serve as a novel food.