• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1649-1659
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• 2012

Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.

• Fisheries and Aquatic Sciences
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• v.19 no.10
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• pp.40.1-40.14
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• 2016

Background: Due to the paucity of oceanic resources utilized in the preparation of diets for cultured fish, commercial feed producers have been trying to replace fishmeal (FM) using alternative protein sources such as vegetable protein meals (VMs). One of the main drawbacks of using VMs in fish feed is related to the presence of a variety of anti-nutritional factors, which could trigger an inflammation process in the distal intestine. This reduces the capacity of the enterocytes to absorb nutrients leading to reduced fish growth performances. Methods: We evaluated the mitigating effects of butyrate and taurine used as feed additives on the morphological abnormalities caused by a soybean meal (SBM)-based diet in the distal intestine of sea bass (Dicentrarchus labrax). We used three experimental diets, containing the same low percentage of FM and high percentage of SBM; two diets were supplemented with either 0.2% sodium butyrate or taurine. Histological changes in the intestine of fish were determined by light and transmission electron microscopy. Infiltration of $CD45^+$ leucocytes in the lamina propria and in the submucosa was assessed by immunohistochemistry. We also quantified by One-Step Taqman$^{(R)}$ real-time RT-PCR the messenger RNA (mRNA) abundance of a panel of genes involved in the intestinal mucosa inflammatory response such as $TNF{\alpha}$ (tumor necrosis factor alpha) and interleukins: IL-8, IL-$1{\beta}$, IL-10, and IL-6. Results: Fish that received for 2 months the diet with 30% soy protein (16.7% SBM and 12.8% full-fat soy) developed an inflammation in the distal intestine, as confirmed by histological and immunohistochemistry data. The expression of target genes in the intestine was deeply influenced by the type of fish diet. Fish fed with taurine-supplemented diet displayed the lowest number of mRNA copies of IL-$1{\beta}$, IL-8, and IL-10 genes in comparison to fish fed with control or butyrate-supplemented diets. Dietary butyrate caused an upregulation of the $TNF{\alpha}$ gene transcription. Among the quantified interleukins, IL-6 was the only one to be not influenced by the diet. Conclusions: Histological and gene expression data suggest that butyrate and taurine could have a role in normalizing the intestinal abnormalities caused by the SBM, but the underling mechanisms of action seem different.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.627-632
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• 2007

FoxO1, FoxO3a and FoxO4 belong to the FoxO gene family, which play important roles in the PI3K/PKB pathway. In this study, we cloned the porcine FoxO1, FoxO3a and FoxO4 sequences and assigned them to SSC11p11-15, SSC1p13 and SSC xq13 using somatic cell hybrid panel (SCHP) and radiation hybrid panel (IMpRH). RT-PCR results showed that these three genes are expressed in multiple tissues. Sequencing of PCR products from different breeds identified a synonymous T/C polymorphism in exon 2 of FoxO3a. This FoxO3a single nucleotide polymorphism (SNP) can be detected by AvaII restriction enzyme. The allele frequencies of this SNP were investigated in Dahuabai, Meishan, Tongcheng, Yushan, Large White, and Duroc pigs. Association of the genotypes with growth and carcass traits showed that different genotypes of FoxO3a were associated with carcass length and backfat thickness between 6th and 7th ribs (BTR) and drip loss (p<0.05).

• Journal of Animal Science and Technology
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• v.57 no.9
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• pp.31.1-31.11
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• 2015

Background: This study was conducted to investigate the potential association of variation in the insulin-like growth factor binding protein 2 (IGFBP2) gene with growth, carcass and meat quality traits in pigs. IGFBP2 is a member of the insulin-like growth factor binding protein family that is involved in regulating growth, and it maps to a region of pig chromosome 15 containing significant quantitative trait loci that affect economically important trait phenotypes. Results: An IGFBP2 polymorphism was identified in the Michigan State University (MSU) Duroc ${\times}$ Pietrain $F_2$ resource population (n = 408), and pigs were genotyped by MspI PCR-RFLP. Subsequently, a Duroc pig population from the National Swine Registry, USA, (n = 326) was genotyped using an Illumina Golden Gate assay. The IGFBP2 genotypic frequencies among the MSU resource population pigs were 3.43, 47.06 and 49.51 % for the AA, AB and BB genotypes, respectively. The genotypic frequencies for the Duroc pigs were 9.82, 47.85, and 42.33 % for the AA, AB and BB genotypes, respectively. Genotype effects (P < 0.05) were found in the MSU resource population for backfat thickness at $10^{th}$ rib and last rib as determined by ultrasound at 10, 13, 16 and 19 weeks of age, ADG from 10 to 22 weeks of age, and age to reach 105 kg. A genotype effect (P < 0.05) was also found for off test Longissimus muscle area in the Duroc population. Significant effects of IGFBP2 genotype (P < 0.05) were found for drip loss, 24 h postmortem pH, pH decline from 45 min to 24 h postmortem, subjective color score, CIE $L^*$ and $b^*$, Warner-Bratzler shear force, and sensory panel scores for juiciness, tenderness, connective tissue and overall tenderness in MSU resource population pigs. Genotype effects (P < 0.05) were found for 45-min pH, CIE $L^*$ and color score in the Duroc population. Conclusions: Results of this study revealed associations of the IGFBP2 genotypes with growth, carcass and meat quality traits in pigs. The results indicate IGFBP2 as a potential candidate gene for growth rate, backfat thickness, loin muscle area and some pork quality traits.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.4
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.18 no.1
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• pp.23-29
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• 2018

Carbamoyl phosphate synthetase 1 deficiency (CPS1D) is a rare autosomal recessive urea cycle disorder characterized by hyperammonemia. CPS1D is caused by mutations in the CPS1 gene on chromosome 2q35. Based on the age of onset, there are two phenotypes: the neonatal type and the delayed-onset type. The severity of clinical manifestation depends on the degree of CPS1 residual enzymatic activity, and can result in hyperammonemia and neurological dysfunction. We report a case of CPS1D in a neonate who developed vomiting, decreased consciousness and hyperammonemia at 25th day after birth. She showed excellent response to treatment including hydration, ammonia-lowering drugs and a low-protein diet without hemodialysis. Her growth, development and neurological outcomes were fair at the last follow-up at 17 months of age.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9915-9919
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• 2014

Lamellarin D (LamD) is a marine alkaloid with a pronounced cytotoxicity against a large panel of cancer cells, affecting cell growth and inducing apoptosis. However, the molecular mechanisms of action of this compound are poorly understood. In this study, the anticancer efficacy of LamD was investigated in human leukemia K562 cells. The results showed suppressed cell proliferation and induction of G0/G1-phase arrest,while expression of CDK1, and activity of smad3 and smad5 were reduced, but that of p27, p53 and STGC3 was increased. LamD induced cell apoptosis through activation of caspases-8/-3, inhibition of survivin and Bcl-2, suggesting that this compound may also act through a caspase-independent pathway. Moreover, LamD inhibited the secretion of TGF-${\beta}$, IL-$1{\beta}$, IL-6, IL-8 and other inflammatory cytokines and the transcriptional activity of transcription factor NF-${\kappa}B$ in human leukemia K562 cells.Taken together, our results suggest that LamD-mediated inhibition of leukemia cell proliferation may be related to the induction of apoptosis and the regulation of cell cycle, tumor-related gene expression and cytokine expression, which may provide a new way of thinking for the treatment leukemia.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.3223-3228
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• 2013

Gene expression profiling (GEP) has identified several molecular subtypes of breast cancer, with different clinico-pathologic features and exhibiting different responses to chemotherapy. However, GEP is expensive and not available in the developing countries where the majority of patients present at advanced stage. The St Gallen Consensus in 2011 proposed use of a simplified, four immunohistochemical (IHC) biomarker panel (ER, PR, HER2, Ki67/Tumor Grade) for molecular classification. The present study was conducted in 75 newly diagnosed patients of breast cancer with large (>5cm) tumors to evaluate the association of IHC surrogate molecular subtype with the clinical response to presurgical chemotherapy, evaluated by the WHO criteria, 3 weeks after the third cycle of 5 flourouracil, adriamycin, cyclophosphamide (FAC regimen). The subtypes of luminal, basal-like and HER2 enriched were found to account for 36.0 % (27/75), 34.7 % (26/75) and 29.3% (22/75) of patients respectively. Ten were luminal A and 14 luminal B (8 HER2 negative and 6HER2 positive). The triple negative breast cancer (TNBC) was most sensitive to chemotherapy with 19% achieving clinical-complete-response (cCR) followed by HER2 enriched (2/22 (9%) cCR), luminal B (1/6 (7%) cCR) and luminal A (0/10 (0%) cCR). Heterogeneity was observed within each subgroup, being most marked in the TNBC although the most responding tumors, 8% developing clinical-progressive-disease. The study supports association of molecular subtypes with response to chemotherapy in patients with advanced breast cancer and the existence of further heterogeneity within subtypes.

• Biomedical Science Letters
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• v.22 no.3
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• pp.83-97
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• 2016

The measurement of viral load in HIV-1 infected patients is essential for the establishment of a therapeutic strategy. Several commercial assays have shown shortcomings in quantifying rare genotypes of HIV-1 such as minor groups of N and O. In this study, the HIV-1 RT-qPCR assay was developed. The primers and probe of HIV-1 were designed to target the pol gene and to increase the detection efficiency of various subtypes including group N and O. The HIV-1 quantitative RT-qPCR assay was assessed for its analytical performance and clinical evaluation. The LoD was determined to 33.9 IU/ml. The LoD of several subtypes including A, C, D, CRF_01AE, F, CRF_02AG, G and H, were determined to less than 40 IU/ml. The HIV-1 quantitative RT-qPCR assay was evaluated using the China National Reference Panel of HIV-1 RNA to determine the analytical performance. The results were all within the acceptable range. The clinical evaluation was performed at Hunan CDC in China. The clinical evaluation results were compared with those of the China domestic commercial kit. A significant correlation (fresh samples; $R^2=0.84$, P<0.001, frozen samples; $R^2=0.76$, P<0.001) between the two systems was observed for 64 fresh samples and 76 frozen samples with viral loads, and the Bland-Altman plot showed good agreement (98.4%, 96.1%, respectively). In conclusion, the HIV-1 quantitative RT-qPCR assay had comparable analytical performance with several commercial kits. The study provides basic data for the research of HIV-1 diagnosis and the development of P < HIV-1 molecular diagnostic assay.

• Microbiology and Biotechnology Letters
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• v.49 no.2
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• pp.192-200
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• 2021

Kunun-zaki, produced by submerged fermentation of a combination of millet and sorghum, is a popular beverage in Northern Nigeria. Owing to the nature of the process involved in its production, kunun-zaki is highly susceptible to contamination by food spoilage microorganisms, leading to inconsistent quality and short shelf-life. In this study, we investigated various food spices, including cinnamon, garlic, and nutmeg, as potential preservatives that could be used to extend kunun-zaki shelf-life. Kunun-zaki varieties were fermented with each of these spices mentioned above and subjected to bacterial, nutritional, sensory, and quality maintenance assessments (using a twelve-member sensory panel to evaluate the organoleptic properties of kunun-zaki). Bacterial counts in the final products ranged between 10^5-7 CFU/ml. We identified two bacterial genera, Weissella and Enterococcus, based on partial 16S rRNA gene amplicon sequencing. Three amino acids, namely leucine, aspartate, and glutamate, were abundant in all kunun-zaki varieties, while the total essential amino acid content was above 39%, suggesting that kunun-zaki could potentially be considered as a protein-rich food source both for infants and adults. The kunun-zaki products were also rich in carbohydrates, crude proteins, ash, crude fiber, and fat, with contents estimated as 81-84, 8-11, 0.8-4.0, 2.9-3.58, and 5.1-6.3%, respectively. However, this nutritional content depreciated rapidly after 24 h of storage, except for kunun-zaki fermented with garlic, which its crude protein and fat content was maintained for up to 48 h. Our results revealed that organic spices increased the nutritional content of the kunun-zaki varieties and could be potentially be used as natural preservatives for enhancing the kunun-zaki shelf-life. However, garlic might be considered a better alternative based on our preliminary investigation. The presence of the isolated microorganisms in the analyzed kunun-zaki samples should be highlighted to raise awareness on the possible health hazards that could arise from poor handling and processing techniques.