TY - JOUR
AU1 - Liu, Y.
AU2 - Song, M.
AU3 - Che, T. M.
AU4 - Bravo, D.
AU5 - Maddox, C. W.
AU6 - Pettigrew, J. E.
AB - Abstract This study was conducted to characterize the effects of feeding 3 plant extracts on gene expression in ileal mucosa of weaned pigs. Weaned pigs (n = 32, 6.3 ± 0.2 kg BW, and 21 d old) were housed in individual pens for 9 d and fed 4 different diets: a nursery basal diet as control diet, basal diet supplemented with 10 mg/kg of capsicum oleoresin, garlic botanical, or turmeric oleoresin. Results reported elsewhere showed that the plant extracts reduced diarrhea and increased growth rate of weaning pigs. Total RNA (4 pigs/treatment) was extracted from ileal mucosa of pigs at d 9. Double-stranded cDNA was amplified, labeled, and further hybridized to the microarray. Microarray data were analyzed in R using packages from the Bioconductor project. Differential gene expression was tested by fitting a mixed linear model equivalent to ANOVA using the limma package. Bioinformatics analysis was conducted by DAVID Bioinformatics Resources. Three pairwise comparisons were used to compare each plant extract diet with the control diet. Quantitative real time PCR was applied to verify the mRNA expression detected by microarray. Compared with the control diet, feeding capsicum oleoresin altered (P < 0.05) the expression of 490 genes (280 up, 210 down), and feeding garlic botanical altered (P < 0.05) the expression of 64 genes (33 up, 31 down), while feeding turmeric oleoresin altered (P < 0.05) the expression of 327 genes (232 up, 95 down). Compared with the control diet, feeding capsicum oleoresin and turmeric oleoresin increased [Expression Analysis Systematic Explorer (EASE) < 0.05] the expression of genes related to integrity of membranes and tight junctions, indicating enhanced gut mucosa health, but decreased (EASE < 0.05) the cell cycle pathway. Feeding each of the 3 plant extracts enhanced (EASE < 0.05) the expression of genes associated with immune responses, indicating that feeding these plant extracts may stimulate the immune responses of pigs in the normal conditions. In conclusion, plant extracts regulated the expression of genes in ileal mucosa of pigs, perhaps providing benefits by enhancing the gut mucosa health and stimulating the immune system. INTRODUCTION Plant extracts have been proposed and reviewed as feed additives in the pig industry (Windisch et al., 2008). The supplementation of plant extracts has produced variable responses in growth performance of newly weaned pigs. Simonson (2004) and Sads and Bilkei (2003) have found weaned pigs fed several plant extracts had greater growth performance and lower disease incidence, but other researchers found no beneficial effects of plant extracts on weaned pig performance (Neill et al., 2006; Nofrarías et al., 2006). Manzanilla et al. (2004) and Nofrarías et al. (2006) suggested that plant extracts might improve gut health by increasing stomach contents and percentage of DM. In addition, the supplementation of plant extracts reduced the number of intraepithelial lymphocytes and increased villus height/crypt depth in the distal small intestine (Manzanilla et al., 2006; Michiels et al., 2010). Our recent study has also shown that feeding plant extracts reduced diarrhea of pigs soon after weaning, reduced the recruitment of neutrophils and macrophages in the ileum, and increased the growth rate of weaned pigs (Liu et al., 2013). However, the mode of action is still speculative. Several mechanisms may be involved in the beneficial effects, such as direct suppression of the proliferation of pathogens, alteration of gut microbial populations, and enhancement of immune functions (Lee et al., 2004; Calsamiglia et al., 2007; Bakkali et al., 2008). The application of high-throughput genomics technology, a porcine genome array, may assist in understanding and providing novel information to investigate the molecular mechanisms of dietary modulation of host immunity, physiology, and metabolism. The objective of this study was to characterize gene expression of ileal mucosa of pigs fed different plant extracts using the porcine genome array and quantitative real-time reverse-transcription PCR (RT-PCR). MATERIALS AND METHODS The protocol for this experiment was reviewed and approved by the Institutional Animal Care and Use Committee at the University of Illinois at Urbana-Champaign. The experiment was conducted in the disease containment chambers of the Edward R. Madigan Laboratory at the University of Illinois at Urbana-Champaign. Animals, Housing, Experimental Design, and Diet A total of 32 weaned piglets (21 d old) with the same number of gilts and barrows (offspring of G-Performer boars and Fertilium 25 sows; Genetiporc Inc., Alexandria, MN) with average initial BW of 6.3 kg were selected from 12 sows at the Swine Research Center of the University of Illinois at Urbana-Champaign. The sows and piglets used in this experiment did not receive antibiotic injections or antibiotics in creep feed. At weaning, all pigs were transferred to the individual pens. All pigs were blocked by weight within sex and randomly assigned to 1 of 4 dietary treatments with the restriction that litters were balanced across treatments to the extent possible. There were 8 chambers and 4 pens per chamber. In each chamber, pigs were fed different diets. The individual pen measured 0.6 × 1.4 m in floor area and had a plastic-coated expanded-metal floor. Pens were adjustable to allow pigs to turn around comfortably as they grew bigger. There was a self-feeder and nipple waterer in each pen, and pigs had access to feed and water at all times. Pigs were housed in individual pens for 9 d after weaning. The 4 dietary treatments were the complex nursery basal diet (control) and the addition of 10 mg/kg capsicum oleoresin, 10 mg/kg garlic botanical, or 10 mg/kg turmeric oleoresin to the basal, respectively. There were 8 replicates per treatment. All 3 plant extracts were obtained from a commercial source (Pancosma S. A., Geneva, Switzerland). Capsicum and turmeric are extracted oleoresins, which were standardized to 6% capsaicin and dihydrocapsaicin and 98% curcuminoides, respectively. Garlic botanical is a botanical extract from garlic, standardized to 40% propyl thiosulfonates. The basal diet was formulated to meet or exceed the NRC (1998) estimates of nutrient requirements of weaned pigs (Table 1). Spray-dried plasma, antibiotics, or zinc oxide were not included in the basal diet. The same diets were fed throughout the experiment. Table 1. Composition of basal diet (as-fed basis) Item  Content  Ingredient, %        Corn, ground  41.54      Whey, dried  15.00      Soybean meal, dehulled  10.82      Fishmeal  10.00      Lactose  10.00      Soy protein concentrate  5.00      Poultry byproduct meal  4.27      Soybean oil  2.67      Mineral premix1  0.35      Vitamin premix2  0.20      L-Lys∙HCl  0.05      DL-Met  0.05      L-Thr  0.03      L-Trp  0.02      Total  100.00  Calculated energy and nutrients        ME, kcal/kg  3480      CP, %  22.67      Fat, %  6.34      Ca, %  0.80      P, %  0.72      Available P, %  0.49      Lys, %  1.50      Lactose, %  21.00  Item  Content  Ingredient, %        Corn, ground  41.54      Whey, dried  15.00      Soybean meal, dehulled  10.82      Fishmeal  10.00      Lactose  10.00      Soy protein concentrate  5.00      Poultry byproduct meal  4.27      Soybean oil  2.67      Mineral premix1  0.35      Vitamin premix2  0.20      L-Lys∙HCl  0.05      DL-Met  0.05      L-Thr  0.03      L-Trp  0.02      Total  100.00  Calculated energy and nutrients        ME, kcal/kg  3480      CP, %  22.67      Fat, %  6.34      Ca, %  0.80      P, %  0.72      Available P, %  0.49      Lys, %  1.50      Lactose, %  21.00  1Provided per kilogram of diet: 3000 mg of NaCl; 100 mg of Zn from zinc oxide; 90 mg of Fe from ferrous sulfate; 20 mg of Mn from manganese oxide; 8 mg of Cu from copper sulfate; 0.35 mg of I from calcium iodide; and 0.30 mg of Se from sodium selenite. 2Provided per kilogram of diet: 2273 μg of retinyl acetate; 17 μg of cholecalciferol; 88 mg of DL-α-tocopheryl acetate; 4 mg of menadione from menadione sodium bisulfite complex; 33 mg of niacin; 24 mg of D-Ca-pantothenate; 9 mg of riboflavin; 35 μg of vitamin B12; and 324 mg of choline chloride. View Large Table 1. Composition of basal diet (as-fed basis) Item  Content  Ingredient, %        Corn, ground  41.54      Whey, dried  15.00      Soybean meal, dehulled  10.82      Fishmeal  10.00      Lactose  10.00      Soy protein concentrate  5.00      Poultry byproduct meal  4.27      Soybean oil  2.67      Mineral premix1  0.35      Vitamin premix2  0.20      L-Lys∙HCl  0.05      DL-Met  0.05      L-Thr  0.03      L-Trp  0.02      Total  100.00  Calculated energy and nutrients        ME, kcal/kg  3480      CP, %  22.67      Fat, %  6.34      Ca, %  0.80      P, %  0.72      Available P, %  0.49      Lys, %  1.50      Lactose, %  21.00  Item  Content  Ingredient, %        Corn, ground  41.54      Whey, dried  15.00      Soybean meal, dehulled  10.82      Fishmeal  10.00      Lactose  10.00      Soy protein concentrate  5.00      Poultry byproduct meal  4.27      Soybean oil  2.67      Mineral premix1  0.35      Vitamin premix2  0.20      L-Lys∙HCl  0.05      DL-Met  0.05      L-Thr  0.03      L-Trp  0.02      Total  100.00  Calculated energy and nutrients        ME, kcal/kg  3480      CP, %  22.67      Fat, %  6.34      Ca, %  0.80      P, %  0.72      Available P, %  0.49      Lys, %  1.50      Lactose, %  21.00  1Provided per kilogram of diet: 3000 mg of NaCl; 100 mg of Zn from zinc oxide; 90 mg of Fe from ferrous sulfate; 20 mg of Mn from manganese oxide; 8 mg of Cu from copper sulfate; 0.35 mg of I from calcium iodide; and 0.30 mg of Se from sodium selenite. 2Provided per kilogram of diet: 2273 μg of retinyl acetate; 17 μg of cholecalciferol; 88 mg of DL-α-tocopheryl acetate; 4 mg of menadione from menadione sodium bisulfite complex; 33 mg of niacin; 24 mg of D-Ca-pantothenate; 9 mg of riboflavin; 35 μg of vitamin B12; and 324 mg of choline chloride. View Large Sample Collection All pigs used in this experiment were healthy throughout the experiment. Four pigs (2 barrows and 2 gilts) with similar BW from each treatment were euthanized on d 9. Before being euthanized, pigs were anesthetized by intramuscular injection of a 1-mL combination of telazol, ketamine, and xylazine (2:1:1) per 23 kg BW. The final mixture contained 100-mg telazol, 50 mg ketamine, and 50 mg xylazine in 1 mL (Fort Dodge Animal Health, Fort Dodge, IA). After anesthesia, pigs were euthanized by intracardiac injection with 78 mg sodium pentobarbital (Sleepaway; Vortech Pharmaceuticals, Ltd., Dearborn, MI) per 1 kg of BW. The 5-cm ileal samples (close to the ileocecal junction) were cut longitudinally and washed with ice-cold PBS. This specific ileal samples were collected because this part is identified by a continuous aggregate of lymphoid tissue as a bulky area of granular appearance, which is involved in the gastrointestinal mucosal immunity (Solano-Aguilar et al., 2000). In addition, the clinical responses reported elsewhere showed that plant extracts affected ileal structure and immunity of weaned pigs (Liu et al., 2013). The mucosal layer of the entire ileal samples from each pig was carefully scraped using a surgical scalpel and separately stored in liquid nitrogen immediately for further analysis. Total RNA Extraction and Gene Expression by Microarrays Total RNA (4 pigs/treatment) from ileal mucosa was extracted using a kit (PureLink RNA Mini Kit; Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. The RNA quality and quantity were assessed using an analyzer (Agilent 2100 Bioanalyzer; Agilent Technologies, Santa Clara, CA) and a spectrophotometer (ND-1000 Nanodrop Spectrophotometer; Thermo Scientific, Wilmington, DE), respectively. All samples used for further analysis had an OD260/OD280 ratio of 1.9 to 2.1, an OD260/OD230 ratio of > 1.8, and an RNA integrity number of ≥ 7.7. Double-stranded cDNA was first synthesized and employed as a template for in vitro amplification and labeling (GeneChip Expression 3'-Amplification IVT Labelling Kit; Affymetrix Inc., Santa Clara, CA). Then, cDNA was used to synthesize cRNA, which was hydrolyzed to produce fragmented cRNA in the 35 to 200 nucleotide size range for proper hybridization. The fragmented cRNA was labeled and further hybridized to a porcine genome array (Affymetrix GeneChip Porcine Genome Array; Affymetrix Inc.). Each array contained 23,937 probe sets to assess 23,256 transcripts in a pig, which represents 20,201 genes according to the manufacturer's instructions. Sixteen chips in total were used in this experiment. Analysis of Microarray Data All quality control assessments, data processing, and statistical analysis were done in R (R Development Core Team, 2008) using packages from the Bioconductor project (Gentleman et al., 2004). Quality control assessment (MacDonald, 2005) showed that all arrays were of acceptable quality. They were processed with the Guanine Cytosine Robust Multi-Array Analysis algorithm, which performs a GC-based background correction, does a quantile normalization between arrays, and summarizes the multiple probes into 1 probe set value using a median polish algorithm (Wu and Irizarry, 2005). Testing for differential gene expression was done by fitting a mixed linear model equivalent to ANOVA using the limma package (Che et al., 2011), which uses an empirical Bayes correction that helps to improve power by borrowing information across genes (Smyth, 2004). The statistical model included diet as a fixed effect and block as a random effect. The pig was the experimental unit. The appropriate pairwise comparisons were pulled as contrasts from the model: capsicum oleoresin vs. control, garlic botanical vs. control, and turmeric oleoresin vs. control. The limma model was fit and P-values were calculated using all 23,937 probe sets on the array. The modulated genes were defined by 1.5-fold difference and a cutoff of P < 0.05 by parameter tests. A total of 23,937 gene probe sets were included in the porcine array, but only 16,363 probe sets were detected in the ileal mucosa samples. Bioinformatics Analysis The DAVID Bioinformatics Resources (DAVID; http://david.abcc.ncifcrf.gov) consist of an integrated biological knowledgebase and analytic tools aiming at systematically extracting biological meaning from large gene lists (Huang et al., 2009). In brief, the analysis of selected genes in DAVID was as follows. First, all 16,363 probe sets in the porcine genome array were submitted to DAVID and 5,168 of them were mapped with identified gene function for 3,715 porcine genes. These 5,168 genes' Entrez IDs were uploaded as background for the analysis. Second, the modulated genes with 1.5-fold difference and a cutoff of P < 0.05 in each comparison were uploaded as the tested gene list. Third, the parameters and subparameters of interest in this experiment were established. In the present analysis, the main parameters in DAVID included Gene_Ontology and Pathways. The subparameters under the Gene_Ontology were GOTERN_BP_ALL (Gene_Ontology for biological process), GOTERN_CC_ALL (Gene_Ontology for cellular component), and GOTERN_MF_ALL (Gene_Ontology for molecular function), and the subparameter under Pathways was KEGG_PATHWAY (Kegg pathways). Finally, the functional annotation chart, which provided typical gene-term enrichment analysis, was run. The Expression Analysis Systematic Explorer (EASE) score, a modified Fisher Extract P-value, was used to examine the significance of gene-term enrichment with a modified Fisher's exact test. The EASE < 0.05 was considered as significantly affected. The fold enrichment score was used to measure the magnitude of enrichment for a functional category. For example, 5% of selected genes are kinases compared with 1% of genes in porcine genome (this is population background) that are kinases. Thus, the fold enrichment for this group of kinases is fivefold. Quantitative Real-Time RT-PCR The same total RNA (4 pigs/treatment) from ileal mucosa used to run the microarray was also used for real time RT-PCR. First-strand cDNA was produced from 1 μg of total RNA per sample (SuperScript III First-Strand Synthesis SuperMix for RT-PCR; Invitrogen) in a total volume of 20 μL. Total RNA was denatured at 65°C for 5 min and immediately annealed on ice for at least 1 min. Then, the reverse transcription reaction was performed at 50°C for 50 min, followed by heat inactivation at 85°C for 5 min. To verify the results from the microarray, quantitative analysis of IL1b, TNFa, TLR4, LBP, and MyD88 were assayed by RT-PCR. In addition, the mRNA expression levels of MUC2, NFkB, MAPK, CFTR, and COX2 in ileal mucosa were analyzed by RT-PCR. Data normalization was accomplished using β-actin as the housekeeping gene. Primers (Supplementary Table 1) were designed based on published sequences in pigs using the NCBI (Bethesda, MD) online primer design tool and published literature and were synthesized (Applied Biosystems, Foster, CA). One hundred nanograms of total RNA were assayed for each sample in triplicate. Each PCR reaction consisted of 5 μL of SYBR Green PCR Master Mix (Applied Biosystems), 0.4 μL of 10 μM forward primer, 0.4 μL of 10 μM reverse primer, 0.2 μL of DNase/RNase free water, and 4 μL of diluted cDNA. The real-time RT-PCR analysis was done using a sequence detection system (ABI PRISM 7900 Sequence Detection System; Applied Biosystems). Thermal cycling conditions were 50°C for 2 min and 95°C for 10 min, followed by 40 cycles with 15 s at 95°C and 1 min at 60°C. The dissociation cycle was 95°C for 15 s plus 65°C for 15 s. Standard curves were generated using serial dilutions of pooled cDNA from all samples. The arbitrary values were calculated based on the standard curve and normalized using the housekeeping genes. The fold changes were calculated based on the arbitrary values. RESULTS Gene Expression Profiles Induced by Plant Extracts A total of 23,362 gene probe sets were contained in the porcine array, but only 16,363 probe sets were detected in the ileal mucosa samples. Among these probe sets, 5,168 of them were mapped for 3,715 porcine genes with identified gene functions, and the other genes have not been identified. The supplementation of the 3 plant extracts displayed different effects on the gene expression in ileal mucosa of pigs (Table 2). Compared with the control and using a cutoff of 1.5-fold differential expression, a total of 490 genes were altered (P < 0.05) in pigs fed capsicum oleoresin (280 upregulated and 210 downregulated), and pigs fed turmeric oleoresin exhibited (P < 0.05) changes in 327 transcripts (232 upregulated and 95 downregulated), but pigs fed garlic botanical only displayed (P < 0.05) altered expression of 64 genes (33 upregulated and 31 downregulated). Table 2. Gene expression profiles in ileal mucosa induced by dietary supplementation of plant extracts to pigs1 Dietary supplement  Upregulated  Downregulated  Total  Capsicum oleoresin (10 mg/kg)  280  210  490  Garlic botanical (10 mg/kg)  33  31  64  Turmeric oleoresin (10 mg/kg)  232  95  327  Dietary supplement  Upregulated  Downregulated  Total  Capsicum oleoresin (10 mg/kg)  280  210  490  Garlic botanical (10 mg/kg)  33  31  64  Turmeric oleoresin (10 mg/kg)  232  95  327  1The gene expression changed by fold-change cutoff of 1.5 and P-value cutoff of 0.05. View Large Table 2. Gene expression profiles in ileal mucosa induced by dietary supplementation of plant extracts to pigs1 Dietary supplement  Upregulated  Downregulated  Total  Capsicum oleoresin (10 mg/kg)  280  210  490  Garlic botanical (10 mg/kg)  33  31  64  Turmeric oleoresin (10 mg/kg)  232  95  327  Dietary supplement  Upregulated  Downregulated  Total  Capsicum oleoresin (10 mg/kg)  280  210  490  Garlic botanical (10 mg/kg)  33  31  64  Turmeric oleoresin (10 mg/kg)  232  95  327  1The gene expression changed by fold-change cutoff of 1.5 and P-value cutoff of 0.05. View Large Gene Ontology Analysis Compared with the control diet, the administration of capsicum oleoresin upregulated (EASE < 0.05) the expression of genes related to the biological processes of ion transportation, activation of immune response, and positive regulation of transcription, but downregulated (EASE < 0.05) the mRNA expression of genes associated with the biological processes of RNA splicing, chromosome organization, multicellular organism reproduction, and nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process (Table 3; Supplemental Fig. 1). Feeding capsicum oleoresin altered (EASE < 0.05) the gene expression level of cellular components; it upregulated the cellular components integral to membranes and protein-lipid complexes, and downregulated the cellular components in microtubule, chromosome, and nucleus. For the molecular function, capsicum oleoresin increased (EASE < 0.05) antiporter activity, symporter activity, carbohydrate binding, lipid binding, and transporter activity, but decreased (EASE < 0.05) transferase activity and RNA binding. Table 3. Modulation of gene ontology by dietary supplementation of capsicum oleoresin to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Activation of immune response (biological Process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.94      C1qa  445461  Complement component 1, q subcomponent, A chain  1.74      C5  414437  Complement component 5  2.16      ccl25  448799  Chemokine (C-C motif) ligand 25  1.68      Cd46  396922  CD46 molecule, complement regulatory protein  1.95      CFB  100124383  B-factor, properdin  1.87      FCN2  396881  Ficolin  1.68      LOC733603  733603  Serum amyloid A2  1.54  Category 2: Positive regulation of transcription (biological process)      HNF1B  397002  HNF1 homeobox B  1.74      GATA-6  397600  Transcription factor GATA-6  2.01      myo6  397085  Myosin VI  1.57      PPARGC-1  397013  Peroxisome proliferator activated receptor gamma, coactivator 1 alpha  2.05  Category 3: Antiporter activity, Transporter activity, Symporter activity (molecular function)      Abcg2  100136901  ATP-binding cassette, sub-family G (WHITE), member 2  2.47      AECC  100127151  Epithelial chloride channel protein  2.23      APOA1  397477  Apolipoprotein A-I  1.56      APOC3  397200  Apolipoprotein C-III  2.83      APP  397085  Amyloid beta (A4) precursor protein  1.57      aqp1  100141400  Aquaporin 1  1.57      AQP3  397124  Aquaporin 3  1.67      atg4d  397113  ATG4 autophagy related 4 homolog D (S. cerevisiae)  1.67      ATP1A1  396898  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.56      Atp1b1  407773  ATPase, Na+/K+ transporting, beta 1 polypeptide  2.17      ATP9A  595106  ATPase, Class II, type 9A  2.11      CLC-5  100048996  Outwardly rectifying chloride channel  1.86      CTR1  100049680  High-affinity copper uptake protein  1.51      CYB561  397133  Cytochrome b-561  1.69      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DMBT1  397284  Deleted in malignant brain tumors 1  1.59      FABP2  100126235  Fatty acid binding protein 2, intestinal  2.35      FDX1  100156498  Ferredoxin  1.75      gltP  100037955  Glycolipid transfer protein  1.81      KCNN4  397421  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  1.47      LOC100037955  406187  Complement component C8G  1.84      LOC100127151  397056  Aquaporin 11  2.13      LOC100127152  397081  Aquaporin 8  1.60      LOC396873  751862  Haptocorrin  1.56      Mlph  397663  Melanophilin  1.65      myo6  397624  Myosin VI  2.86      PHEROC  407611  Pheromaxein C subunit  1.74      PKCNT1  100037973  Na/nucleoside cotransporter  1.74      PLIN3  100037972  Mannose-6-phosphate receptor binding protein 1  2.20      PLN  100144470  Phospholamban  1.94      rbp2  396765  Retinol binding protein 2, cellular  1.50      RBP4  553107  Retinol binding protein 4, plasma  1.62      RHBG  397263  Rh family, B glycoprotein  1.70      Sar1B  397376  SAR1 homolog B (S. cerevisiae)  1.90      SCAMP1  595103  Secretory carrier membrane protein 1  1.60      Slc15a1  414799  Solute carrier family 15 (oligopeptide transporter), member 1  1.81      SLC30A7  396873  Solute carrier family 30 (zinc transporter), member 7  1.64      SLC35A3  503546  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  3.16      SLC4A4  397186  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.21      SLC5A1  397073  Solute carrier family 5 (sodium/glucose cotransporter), member 1  2.32      SLC5A4  100101921  Solute carrier family 5 (low affinity glucose cotransporter), member 4  1.80      SLC7A7  397481  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.60      Slc7a9  397691  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.57      SLC9A2  494017  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.57  Category 4: Integral to membrane (cellular component)      Abcg2  404694  ATP-binding cassette, sub-family G (WHITE), member 2  1.71      adipor2  396919  Adiponectin receptor 2  1.64      ANPEP  553107  Alanyl (membrane) aminopeptidase  1.62      APP  445537  Amyloid beta (A4) precursor protein  10.32      aqp1  100135031  Aquaporin 1  2.29      AQP3  494013  Aquaporin 3  1.62      ATP1A1  414799  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.81      Atp1b1  397113  ATPase, Na+/K+ transporting, beta 1 polypeptide  1.67      ATP9A  397263  ATPase, Class II, type 9A  1.70      CAV1  396922  Caveolin 1  1.95      CAV2  397399  Caveolin 2  1.59      CCR9  397477  Chemokine (C-C motif) receptor 9  1.56      CD3D  397684  CD3d molecule, delta (CD3-TCR complex)  1.58      Cd3g  397081  CD3g molecule, gamma (CD3-TCR complex)  1.59      Cd46  431781  CD46 molecule, complement regulatory protein  2.20      CD9  397481  CD9 molecule  1.60      CLC-5  397624  Outwardly rectifying chloride channel  2.86      CLDN3  396661  Claudin 3  1.80      CTR1  100124377  High-affinity copper uptake protein  1.57      CYB561  397020  Cytochrome b-561  1.67      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DDR1  397492  Discoidin domain receptor tyrosine kinase 1  2.08      DGAT  396737  Diacylglycerol acyltransferase  2.27      DMBT1  397067  Deleted in malignant brain tumors 1  1.55      DPP4  397186  Dipeptidyl-peptidase 4  2.21      emp1  100144462  Epithelial membrane protein 1  1.95      ENPEP  397236  Glutamyl aminopeptidase (aminopeptidase A)  1.99      ENTPD1  414377  Ectonucleoside triphosphate diphosphohydrolase 1  1.80      Faah  396907  Fatty acid amide hydrolase  1.50      FCGR3B  396946  Fc fragment of IgG, low affinity IIIb, receptor (CD16b)  1.79      FCGRT  397663  Fc fragment of IgG, receptor, transporter, alpha  1.65      FGFR2  397298  Fibroblast growth factor receptor 2  1.55      ggt1  100125375  Gamma-glutamyltransferase 1  1.76      GUCY2C  396949  Guanylate cyclase 2C (heat stable enterotoxin receptor)  2.62      iyd  397193  Iodotyrosine dehalogenase 1  2.05      KCNN4  397073  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  2.32      KLRK1  414909  Killer cell lectin-like receptor subfamily K, member 1  1.90      LOC100127152  396898  Aquaporin 8  1.55      LPAR2  407773  Lysophosphatidic acid receptor 2  2.17      MAN1A1  100153386  Man9-mannosidase  1.78      MAOA  100048996  Monoamine oxidase A  1.86      MAOB  403124  Monoamine oxidase B  1.98      Ocln  733610  Occludin  1.65      PGRMC1  396623  Progesterone receptor membrane component 1  1.58      PKCNT1  397520  Na/nucleoside cotransporter  1.54      PLN  100136901  Phospholamban  2.47      Psen1  404693  Presenilin 1  1.63      RHBG  780411  Rh family, B glycoprotein  1.51      SCAMP1  100101477  Secretory carrier membrane protein 1  2.50      SLA-1  100037973  MHC class I antigen 1  1.74      SLA-2  503546  MHC class I antigen 2  3.16      SLA-DRB1  100101921  MHC class II histocompatibility antigen SLA-DRB1  1.80      Slc15a1  100037293  Solute carrier family 15 (oligopeptide transporter), member 1  2.48      SLC35A3  397200  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  2.83      SLC44A4  414424  Solute carrier family 44, member 4  2.46      SLC4A4  397056  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.13      SLC5A1  396762  Solute carrier family 5 (sodium/glucose cotransporter), member 1  1.59      SLC5A4  100126235  Solute carrier family 5 (low affinity glucose cotransporter), member 4  2.35      SLC7A7  397095  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.85      Slc7a9  397101  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.73      SLC9A2  397118  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.84      ST3GAL1  100038015  ST3 beta-galactoside alpha-2,3-sialyltransferase 1  1.64      tas1r3  100127440  Taste receptor, type 1, member 3  1.63      TLR2  397376  Toll-like receptor 2  1.90      tmbim6  397080  Transmembrane BAX inhibitor motif containing 6  1.62      tmem59  751862  Transmembrane protein 59  1.56      TNFRSF1A  100037972  Tumor necrosis factor receptor superfamily, member 1A  2.20      VIPR1  397421  Vasoactive intestinal peptide receptor  1.50  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      BAT1  396740  HLA-B associated transcript 1  -1.58      ATIC  100037949  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.58      dnmt1  448813  DNA (cytosine-5-)-methyltransferase 1  -1.59      GTF2H4  733590  General transcription factor IIH, polypeptide 4  -2.35      gucy1b3  100217383  Guanylate cyclase 1, soluble, beta 3  -1.51      LOC100038014  414912  Ribose 5-phosphate isomerase-like protein  -1.72      MEF2C  397583  Myocyte enhancer factor 2C  -2.34      NOR-1  100170844  Neuron-derived orphan receptor-1 alfa  -1.51      NR3C1  444999  Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -2.13      Oct2  396917  POU-domain protein  -1.75      pou2f1  606746  POU class 2 homeobox 1  -2.59      PRPF3  397501  PRP3 pre-mRNA processing factor 3 homolog  -1.66      Ptbp1  397461  Polypyrimidine tract binding protein 1  -1.51      QKI  414430  Quaking homolog, KH domain RNA binding (mouse)  -1.63      RAD18  100038014  RAD18 homolog (S. cerevisiae)  -2.16      SFRS1  654327  Splicing factor, arginine/serine-rich 1  -1.69      SFRS2  492277  Splicing factor, arginine/serine-rich 2  -1.58      SPI1  100152381  Transcription factor PU.1  -1.60  Category 6: Transferase activity (molecular function)      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      prmt5  100294711  Protein arginine methyltransferase 5  -1.62      EHMT2  100124382  Euchromatic histone-lysine N-methyltransferase 2  -1.53      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.54      QKI  492277  Quaking homolog, KH domain RNA binding (mouse)  -1.58  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Activation of immune response (biological Process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.94      C1qa  445461  Complement component 1, q subcomponent, A chain  1.74      C5  414437  Complement component 5  2.16      ccl25  448799  Chemokine (C-C motif) ligand 25  1.68      Cd46  396922  CD46 molecule, complement regulatory protein  1.95      CFB  100124383  B-factor, properdin  1.87      FCN2  396881  Ficolin  1.68      LOC733603  733603  Serum amyloid A2  1.54  Category 2: Positive regulation of transcription (biological process)      HNF1B  397002  HNF1 homeobox B  1.74      GATA-6  397600  Transcription factor GATA-6  2.01      myo6  397085  Myosin VI  1.57      PPARGC-1  397013  Peroxisome proliferator activated receptor gamma, coactivator 1 alpha  2.05  Category 3: Antiporter activity, Transporter activity, Symporter activity (molecular function)      Abcg2  100136901  ATP-binding cassette, sub-family G (WHITE), member 2  2.47      AECC  100127151  Epithelial chloride channel protein  2.23      APOA1  397477  Apolipoprotein A-I  1.56      APOC3  397200  Apolipoprotein C-III  2.83      APP  397085  Amyloid beta (A4) precursor protein  1.57      aqp1  100141400  Aquaporin 1  1.57      AQP3  397124  Aquaporin 3  1.67      atg4d  397113  ATG4 autophagy related 4 homolog D (S. cerevisiae)  1.67      ATP1A1  396898  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.56      Atp1b1  407773  ATPase, Na+/K+ transporting, beta 1 polypeptide  2.17      ATP9A  595106  ATPase, Class II, type 9A  2.11      CLC-5  100048996  Outwardly rectifying chloride channel  1.86      CTR1  100049680  High-affinity copper uptake protein  1.51      CYB561  397133  Cytochrome b-561  1.69      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DMBT1  397284  Deleted in malignant brain tumors 1  1.59      FABP2  100126235  Fatty acid binding protein 2, intestinal  2.35      FDX1  100156498  Ferredoxin  1.75      gltP  100037955  Glycolipid transfer protein  1.81      KCNN4  397421  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  1.47      LOC100037955  406187  Complement component C8G  1.84      LOC100127151  397056  Aquaporin 11  2.13      LOC100127152  397081  Aquaporin 8  1.60      LOC396873  751862  Haptocorrin  1.56      Mlph  397663  Melanophilin  1.65      myo6  397624  Myosin VI  2.86      PHEROC  407611  Pheromaxein C subunit  1.74      PKCNT1  100037973  Na/nucleoside cotransporter  1.74      PLIN3  100037972  Mannose-6-phosphate receptor binding protein 1  2.20      PLN  100144470  Phospholamban  1.94      rbp2  396765  Retinol binding protein 2, cellular  1.50      RBP4  553107  Retinol binding protein 4, plasma  1.62      RHBG  397263  Rh family, B glycoprotein  1.70      Sar1B  397376  SAR1 homolog B (S. cerevisiae)  1.90      SCAMP1  595103  Secretory carrier membrane protein 1  1.60      Slc15a1  414799  Solute carrier family 15 (oligopeptide transporter), member 1  1.81      SLC30A7  396873  Solute carrier family 30 (zinc transporter), member 7  1.64      SLC35A3  503546  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  3.16      SLC4A4  397186  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.21      SLC5A1  397073  Solute carrier family 5 (sodium/glucose cotransporter), member 1  2.32      SLC5A4  100101921  Solute carrier family 5 (low affinity glucose cotransporter), member 4  1.80      SLC7A7  397481  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.60      Slc7a9  397691  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.57      SLC9A2  494017  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.57  Category 4: Integral to membrane (cellular component)      Abcg2  404694  ATP-binding cassette, sub-family G (WHITE), member 2  1.71      adipor2  396919  Adiponectin receptor 2  1.64      ANPEP  553107  Alanyl (membrane) aminopeptidase  1.62      APP  445537  Amyloid beta (A4) precursor protein  10.32      aqp1  100135031  Aquaporin 1  2.29      AQP3  494013  Aquaporin 3  1.62      ATP1A1  414799  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.81      Atp1b1  397113  ATPase, Na+/K+ transporting, beta 1 polypeptide  1.67      ATP9A  397263  ATPase, Class II, type 9A  1.70      CAV1  396922  Caveolin 1  1.95      CAV2  397399  Caveolin 2  1.59      CCR9  397477  Chemokine (C-C motif) receptor 9  1.56      CD3D  397684  CD3d molecule, delta (CD3-TCR complex)  1.58      Cd3g  397081  CD3g molecule, gamma (CD3-TCR complex)  1.59      Cd46  431781  CD46 molecule, complement regulatory protein  2.20      CD9  397481  CD9 molecule  1.60      CLC-5  397624  Outwardly rectifying chloride channel  2.86      CLDN3  396661  Claudin 3  1.80      CTR1  100124377  High-affinity copper uptake protein  1.57      CYB561  397020  Cytochrome b-561  1.67      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DDR1  397492  Discoidin domain receptor tyrosine kinase 1  2.08      DGAT  396737  Diacylglycerol acyltransferase  2.27      DMBT1  397067  Deleted in malignant brain tumors 1  1.55      DPP4  397186  Dipeptidyl-peptidase 4  2.21      emp1  100144462  Epithelial membrane protein 1  1.95      ENPEP  397236  Glutamyl aminopeptidase (aminopeptidase A)  1.99      ENTPD1  414377  Ectonucleoside triphosphate diphosphohydrolase 1  1.80      Faah  396907  Fatty acid amide hydrolase  1.50      FCGR3B  396946  Fc fragment of IgG, low affinity IIIb, receptor (CD16b)  1.79      FCGRT  397663  Fc fragment of IgG, receptor, transporter, alpha  1.65      FGFR2  397298  Fibroblast growth factor receptor 2  1.55      ggt1  100125375  Gamma-glutamyltransferase 1  1.76      GUCY2C  396949  Guanylate cyclase 2C (heat stable enterotoxin receptor)  2.62      iyd  397193  Iodotyrosine dehalogenase 1  2.05      KCNN4  397073  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  2.32      KLRK1  414909  Killer cell lectin-like receptor subfamily K, member 1  1.90      LOC100127152  396898  Aquaporin 8  1.55      LPAR2  407773  Lysophosphatidic acid receptor 2  2.17      MAN1A1  100153386  Man9-mannosidase  1.78      MAOA  100048996  Monoamine oxidase A  1.86      MAOB  403124  Monoamine oxidase B  1.98      Ocln  733610  Occludin  1.65      PGRMC1  396623  Progesterone receptor membrane component 1  1.58      PKCNT1  397520  Na/nucleoside cotransporter  1.54      PLN  100136901  Phospholamban  2.47      Psen1  404693  Presenilin 1  1.63      RHBG  780411  Rh family, B glycoprotein  1.51      SCAMP1  100101477  Secretory carrier membrane protein 1  2.50      SLA-1  100037973  MHC class I antigen 1  1.74      SLA-2  503546  MHC class I antigen 2  3.16      SLA-DRB1  100101921  MHC class II histocompatibility antigen SLA-DRB1  1.80      Slc15a1  100037293  Solute carrier family 15 (oligopeptide transporter), member 1  2.48      SLC35A3  397200  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  2.83      SLC44A4  414424  Solute carrier family 44, member 4  2.46      SLC4A4  397056  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.13      SLC5A1  396762  Solute carrier family 5 (sodium/glucose cotransporter), member 1  1.59      SLC5A4  100126235  Solute carrier family 5 (low affinity glucose cotransporter), member 4  2.35      SLC7A7  397095  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.85      Slc7a9  397101  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.73      SLC9A2  397118  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.84      ST3GAL1  100038015  ST3 beta-galactoside alpha-2,3-sialyltransferase 1  1.64      tas1r3  100127440  Taste receptor, type 1, member 3  1.63      TLR2  397376  Toll-like receptor 2  1.90      tmbim6  397080  Transmembrane BAX inhibitor motif containing 6  1.62      tmem59  751862  Transmembrane protein 59  1.56      TNFRSF1A  100037972  Tumor necrosis factor receptor superfamily, member 1A  2.20      VIPR1  397421  Vasoactive intestinal peptide receptor  1.50  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      BAT1  396740  HLA-B associated transcript 1  -1.58      ATIC  100037949  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.58      dnmt1  448813  DNA (cytosine-5-)-methyltransferase 1  -1.59      GTF2H4  733590  General transcription factor IIH, polypeptide 4  -2.35      gucy1b3  100217383  Guanylate cyclase 1, soluble, beta 3  -1.51      LOC100038014  414912  Ribose 5-phosphate isomerase-like protein  -1.72      MEF2C  397583  Myocyte enhancer factor 2C  -2.34      NOR-1  100170844  Neuron-derived orphan receptor-1 alfa  -1.51      NR3C1  444999  Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -2.13      Oct2  396917  POU-domain protein  -1.75      pou2f1  606746  POU class 2 homeobox 1  -2.59      PRPF3  397501  PRP3 pre-mRNA processing factor 3 homolog  -1.66      Ptbp1  397461  Polypyrimidine tract binding protein 1  -1.51      QKI  414430  Quaking homolog, KH domain RNA binding (mouse)  -1.63      RAD18  100038014  RAD18 homolog (S. cerevisiae)  -2.16      SFRS1  654327  Splicing factor, arginine/serine-rich 1  -1.69      SFRS2  492277  Splicing factor, arginine/serine-rich 2  -1.58      SPI1  100152381  Transcription factor PU.1  -1.60  Category 6: Transferase activity (molecular function)      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      prmt5  100294711  Protein arginine methyltransferase 5  -1.62      EHMT2  100124382  Euchromatic histone-lysine N-methyltransferase 2  -1.53      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.54      QKI  492277  Quaking homolog, KH domain RNA binding (mouse)  -1.58  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large Table 3. Modulation of gene ontology by dietary supplementation of capsicum oleoresin to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Activation of immune response (biological Process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.94      C1qa  445461  Complement component 1, q subcomponent, A chain  1.74      C5  414437  Complement component 5  2.16      ccl25  448799  Chemokine (C-C motif) ligand 25  1.68      Cd46  396922  CD46 molecule, complement regulatory protein  1.95      CFB  100124383  B-factor, properdin  1.87      FCN2  396881  Ficolin  1.68      LOC733603  733603  Serum amyloid A2  1.54  Category 2: Positive regulation of transcription (biological process)      HNF1B  397002  HNF1 homeobox B  1.74      GATA-6  397600  Transcription factor GATA-6  2.01      myo6  397085  Myosin VI  1.57      PPARGC-1  397013  Peroxisome proliferator activated receptor gamma, coactivator 1 alpha  2.05  Category 3: Antiporter activity, Transporter activity, Symporter activity (molecular function)      Abcg2  100136901  ATP-binding cassette, sub-family G (WHITE), member 2  2.47      AECC  100127151  Epithelial chloride channel protein  2.23      APOA1  397477  Apolipoprotein A-I  1.56      APOC3  397200  Apolipoprotein C-III  2.83      APP  397085  Amyloid beta (A4) precursor protein  1.57      aqp1  100141400  Aquaporin 1  1.57      AQP3  397124  Aquaporin 3  1.67      atg4d  397113  ATG4 autophagy related 4 homolog D (S. cerevisiae)  1.67      ATP1A1  396898  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.56      Atp1b1  407773  ATPase, Na+/K+ transporting, beta 1 polypeptide  2.17      ATP9A  595106  ATPase, Class II, type 9A  2.11      CLC-5  100048996  Outwardly rectifying chloride channel  1.86      CTR1  100049680  High-affinity copper uptake protein  1.51      CYB561  397133  Cytochrome b-561  1.69      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DMBT1  397284  Deleted in malignant brain tumors 1  1.59      FABP2  100126235  Fatty acid binding protein 2, intestinal  2.35      FDX1  100156498  Ferredoxin  1.75      gltP  100037955  Glycolipid transfer protein  1.81      KCNN4  397421  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  1.47      LOC100037955  406187  Complement component C8G  1.84      LOC100127151  397056  Aquaporin 11  2.13      LOC100127152  397081  Aquaporin 8  1.60      LOC396873  751862  Haptocorrin  1.56      Mlph  397663  Melanophilin  1.65      myo6  397624  Myosin VI  2.86      PHEROC  407611  Pheromaxein C subunit  1.74      PKCNT1  100037973  Na/nucleoside cotransporter  1.74      PLIN3  100037972  Mannose-6-phosphate receptor binding protein 1  2.20      PLN  100144470  Phospholamban  1.94      rbp2  396765  Retinol binding protein 2, cellular  1.50      RBP4  553107  Retinol binding protein 4, plasma  1.62      RHBG  397263  Rh family, B glycoprotein  1.70      Sar1B  397376  SAR1 homolog B (S. cerevisiae)  1.90      SCAMP1  595103  Secretory carrier membrane protein 1  1.60      Slc15a1  414799  Solute carrier family 15 (oligopeptide transporter), member 1  1.81      SLC30A7  396873  Solute carrier family 30 (zinc transporter), member 7  1.64      SLC35A3  503546  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  3.16      SLC4A4  397186  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.21      SLC5A1  397073  Solute carrier family 5 (sodium/glucose cotransporter), member 1  2.32      SLC5A4  100101921  Solute carrier family 5 (low affinity glucose cotransporter), member 4  1.80      SLC7A7  397481  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.60      Slc7a9  397691  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.57      SLC9A2  494017  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.57  Category 4: Integral to membrane (cellular component)      Abcg2  404694  ATP-binding cassette, sub-family G (WHITE), member 2  1.71      adipor2  396919  Adiponectin receptor 2  1.64      ANPEP  553107  Alanyl (membrane) aminopeptidase  1.62      APP  445537  Amyloid beta (A4) precursor protein  10.32      aqp1  100135031  Aquaporin 1  2.29      AQP3  494013  Aquaporin 3  1.62      ATP1A1  414799  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.81      Atp1b1  397113  ATPase, Na+/K+ transporting, beta 1 polypeptide  1.67      ATP9A  397263  ATPase, Class II, type 9A  1.70      CAV1  396922  Caveolin 1  1.95      CAV2  397399  Caveolin 2  1.59      CCR9  397477  Chemokine (C-C motif) receptor 9  1.56      CD3D  397684  CD3d molecule, delta (CD3-TCR complex)  1.58      Cd3g  397081  CD3g molecule, gamma (CD3-TCR complex)  1.59      Cd46  431781  CD46 molecule, complement regulatory protein  2.20      CD9  397481  CD9 molecule  1.60      CLC-5  397624  Outwardly rectifying chloride channel  2.86      CLDN3  396661  Claudin 3  1.80      CTR1  100124377  High-affinity copper uptake protein  1.57      CYB561  397020  Cytochrome b-561  1.67      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DDR1  397492  Discoidin domain receptor tyrosine kinase 1  2.08      DGAT  396737  Diacylglycerol acyltransferase  2.27      DMBT1  397067  Deleted in malignant brain tumors 1  1.55      DPP4  397186  Dipeptidyl-peptidase 4  2.21      emp1  100144462  Epithelial membrane protein 1  1.95      ENPEP  397236  Glutamyl aminopeptidase (aminopeptidase A)  1.99      ENTPD1  414377  Ectonucleoside triphosphate diphosphohydrolase 1  1.80      Faah  396907  Fatty acid amide hydrolase  1.50      FCGR3B  396946  Fc fragment of IgG, low affinity IIIb, receptor (CD16b)  1.79      FCGRT  397663  Fc fragment of IgG, receptor, transporter, alpha  1.65      FGFR2  397298  Fibroblast growth factor receptor 2  1.55      ggt1  100125375  Gamma-glutamyltransferase 1  1.76      GUCY2C  396949  Guanylate cyclase 2C (heat stable enterotoxin receptor)  2.62      iyd  397193  Iodotyrosine dehalogenase 1  2.05      KCNN4  397073  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  2.32      KLRK1  414909  Killer cell lectin-like receptor subfamily K, member 1  1.90      LOC100127152  396898  Aquaporin 8  1.55      LPAR2  407773  Lysophosphatidic acid receptor 2  2.17      MAN1A1  100153386  Man9-mannosidase  1.78      MAOA  100048996  Monoamine oxidase A  1.86      MAOB  403124  Monoamine oxidase B  1.98      Ocln  733610  Occludin  1.65      PGRMC1  396623  Progesterone receptor membrane component 1  1.58      PKCNT1  397520  Na/nucleoside cotransporter  1.54      PLN  100136901  Phospholamban  2.47      Psen1  404693  Presenilin 1  1.63      RHBG  780411  Rh family, B glycoprotein  1.51      SCAMP1  100101477  Secretory carrier membrane protein 1  2.50      SLA-1  100037973  MHC class I antigen 1  1.74      SLA-2  503546  MHC class I antigen 2  3.16      SLA-DRB1  100101921  MHC class II histocompatibility antigen SLA-DRB1  1.80      Slc15a1  100037293  Solute carrier family 15 (oligopeptide transporter), member 1  2.48      SLC35A3  397200  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  2.83      SLC44A4  414424  Solute carrier family 44, member 4  2.46      SLC4A4  397056  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.13      SLC5A1  396762  Solute carrier family 5 (sodium/glucose cotransporter), member 1  1.59      SLC5A4  100126235  Solute carrier family 5 (low affinity glucose cotransporter), member 4  2.35      SLC7A7  397095  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.85      Slc7a9  397101  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.73      SLC9A2  397118  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.84      ST3GAL1  100038015  ST3 beta-galactoside alpha-2,3-sialyltransferase 1  1.64      tas1r3  100127440  Taste receptor, type 1, member 3  1.63      TLR2  397376  Toll-like receptor 2  1.90      tmbim6  397080  Transmembrane BAX inhibitor motif containing 6  1.62      tmem59  751862  Transmembrane protein 59  1.56      TNFRSF1A  100037972  Tumor necrosis factor receptor superfamily, member 1A  2.20      VIPR1  397421  Vasoactive intestinal peptide receptor  1.50  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      BAT1  396740  HLA-B associated transcript 1  -1.58      ATIC  100037949  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.58      dnmt1  448813  DNA (cytosine-5-)-methyltransferase 1  -1.59      GTF2H4  733590  General transcription factor IIH, polypeptide 4  -2.35      gucy1b3  100217383  Guanylate cyclase 1, soluble, beta 3  -1.51      LOC100038014  414912  Ribose 5-phosphate isomerase-like protein  -1.72      MEF2C  397583  Myocyte enhancer factor 2C  -2.34      NOR-1  100170844  Neuron-derived orphan receptor-1 alfa  -1.51      NR3C1  444999  Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -2.13      Oct2  396917  POU-domain protein  -1.75      pou2f1  606746  POU class 2 homeobox 1  -2.59      PRPF3  397501  PRP3 pre-mRNA processing factor 3 homolog  -1.66      Ptbp1  397461  Polypyrimidine tract binding protein 1  -1.51      QKI  414430  Quaking homolog, KH domain RNA binding (mouse)  -1.63      RAD18  100038014  RAD18 homolog (S. cerevisiae)  -2.16      SFRS1  654327  Splicing factor, arginine/serine-rich 1  -1.69      SFRS2  492277  Splicing factor, arginine/serine-rich 2  -1.58      SPI1  100152381  Transcription factor PU.1  -1.60  Category 6: Transferase activity (molecular function)      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      prmt5  100294711  Protein arginine methyltransferase 5  -1.62      EHMT2  100124382  Euchromatic histone-lysine N-methyltransferase 2  -1.53      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.54      QKI  492277  Quaking homolog, KH domain RNA binding (mouse)  -1.58  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Activation of immune response (biological Process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.94      C1qa  445461  Complement component 1, q subcomponent, A chain  1.74      C5  414437  Complement component 5  2.16      ccl25  448799  Chemokine (C-C motif) ligand 25  1.68      Cd46  396922  CD46 molecule, complement regulatory protein  1.95      CFB  100124383  B-factor, properdin  1.87      FCN2  396881  Ficolin  1.68      LOC733603  733603  Serum amyloid A2  1.54  Category 2: Positive regulation of transcription (biological process)      HNF1B  397002  HNF1 homeobox B  1.74      GATA-6  397600  Transcription factor GATA-6  2.01      myo6  397085  Myosin VI  1.57      PPARGC-1  397013  Peroxisome proliferator activated receptor gamma, coactivator 1 alpha  2.05  Category 3: Antiporter activity, Transporter activity, Symporter activity (molecular function)      Abcg2  100136901  ATP-binding cassette, sub-family G (WHITE), member 2  2.47      AECC  100127151  Epithelial chloride channel protein  2.23      APOA1  397477  Apolipoprotein A-I  1.56      APOC3  397200  Apolipoprotein C-III  2.83      APP  397085  Amyloid beta (A4) precursor protein  1.57      aqp1  100141400  Aquaporin 1  1.57      AQP3  397124  Aquaporin 3  1.67      atg4d  397113  ATG4 autophagy related 4 homolog D (S. cerevisiae)  1.67      ATP1A1  396898  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.56      Atp1b1  407773  ATPase, Na+/K+ transporting, beta 1 polypeptide  2.17      ATP9A  595106  ATPase, Class II, type 9A  2.11      CLC-5  100048996  Outwardly rectifying chloride channel  1.86      CTR1  100049680  High-affinity copper uptake protein  1.51      CYB561  397133  Cytochrome b-561  1.69      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DMBT1  397284  Deleted in malignant brain tumors 1  1.59      FABP2  100126235  Fatty acid binding protein 2, intestinal  2.35      FDX1  100156498  Ferredoxin  1.75      gltP  100037955  Glycolipid transfer protein  1.81      KCNN4  397421  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  1.47      LOC100037955  406187  Complement component C8G  1.84      LOC100127151  397056  Aquaporin 11  2.13      LOC100127152  397081  Aquaporin 8  1.60      LOC396873  751862  Haptocorrin  1.56      Mlph  397663  Melanophilin  1.65      myo6  397624  Myosin VI  2.86      PHEROC  407611  Pheromaxein C subunit  1.74      PKCNT1  100037973  Na/nucleoside cotransporter  1.74      PLIN3  100037972  Mannose-6-phosphate receptor binding protein 1  2.20      PLN  100144470  Phospholamban  1.94      rbp2  396765  Retinol binding protein 2, cellular  1.50      RBP4  553107  Retinol binding protein 4, plasma  1.62      RHBG  397263  Rh family, B glycoprotein  1.70      Sar1B  397376  SAR1 homolog B (S. cerevisiae)  1.90      SCAMP1  595103  Secretory carrier membrane protein 1  1.60      Slc15a1  414799  Solute carrier family 15 (oligopeptide transporter), member 1  1.81      SLC30A7  396873  Solute carrier family 30 (zinc transporter), member 7  1.64      SLC35A3  503546  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  3.16      SLC4A4  397186  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.21      SLC5A1  397073  Solute carrier family 5 (sodium/glucose cotransporter), member 1  2.32      SLC5A4  100101921  Solute carrier family 5 (low affinity glucose cotransporter), member 4  1.80      SLC7A7  397481  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.60      Slc7a9  397691  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.57      SLC9A2  494017  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.57  Category 4: Integral to membrane (cellular component)      Abcg2  404694  ATP-binding cassette, sub-family G (WHITE), member 2  1.71      adipor2  396919  Adiponectin receptor 2  1.64      ANPEP  553107  Alanyl (membrane) aminopeptidase  1.62      APP  445537  Amyloid beta (A4) precursor protein  10.32      aqp1  100135031  Aquaporin 1  2.29      AQP3  494013  Aquaporin 3  1.62      ATP1A1  414799  ATPase, Na+/K+ transporting, alpha 1 polypeptide  1.81      Atp1b1  397113  ATPase, Na+/K+ transporting, beta 1 polypeptide  1.67      ATP9A  397263  ATPase, Class II, type 9A  1.70      CAV1  396922  Caveolin 1  1.95      CAV2  397399  Caveolin 2  1.59      CCR9  397477  Chemokine (C-C motif) receptor 9  1.56      CD3D  397684  CD3d molecule, delta (CD3-TCR complex)  1.58      Cd3g  397081  CD3g molecule, gamma (CD3-TCR complex)  1.59      Cd46  431781  CD46 molecule, complement regulatory protein  2.20      CD9  397481  CD9 molecule  1.60      CLC-5  397624  Outwardly rectifying chloride channel  2.86      CLDN3  396661  Claudin 3  1.80      CTR1  100124377  High-affinity copper uptake protein  1.57      CYB561  397020  Cytochrome b-561  1.67      cyb5a  100127152  Cytochrome b5 type A (microsomal)  1.86      DDR1  397492  Discoidin domain receptor tyrosine kinase 1  2.08      DGAT  396737  Diacylglycerol acyltransferase  2.27      DMBT1  397067  Deleted in malignant brain tumors 1  1.55      DPP4  397186  Dipeptidyl-peptidase 4  2.21      emp1  100144462  Epithelial membrane protein 1  1.95      ENPEP  397236  Glutamyl aminopeptidase (aminopeptidase A)  1.99      ENTPD1  414377  Ectonucleoside triphosphate diphosphohydrolase 1  1.80      Faah  396907  Fatty acid amide hydrolase  1.50      FCGR3B  396946  Fc fragment of IgG, low affinity IIIb, receptor (CD16b)  1.79      FCGRT  397663  Fc fragment of IgG, receptor, transporter, alpha  1.65      FGFR2  397298  Fibroblast growth factor receptor 2  1.55      ggt1  100125375  Gamma-glutamyltransferase 1  1.76      GUCY2C  396949  Guanylate cyclase 2C (heat stable enterotoxin receptor)  2.62      iyd  397193  Iodotyrosine dehalogenase 1  2.05      KCNN4  397073  Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4  2.32      KLRK1  414909  Killer cell lectin-like receptor subfamily K, member 1  1.90      LOC100127152  396898  Aquaporin 8  1.55      LPAR2  407773  Lysophosphatidic acid receptor 2  2.17      MAN1A1  100153386  Man9-mannosidase  1.78      MAOA  100048996  Monoamine oxidase A  1.86      MAOB  403124  Monoamine oxidase B  1.98      Ocln  733610  Occludin  1.65      PGRMC1  396623  Progesterone receptor membrane component 1  1.58      PKCNT1  397520  Na/nucleoside cotransporter  1.54      PLN  100136901  Phospholamban  2.47      Psen1  404693  Presenilin 1  1.63      RHBG  780411  Rh family, B glycoprotein  1.51      SCAMP1  100101477  Secretory carrier membrane protein 1  2.50      SLA-1  100037973  MHC class I antigen 1  1.74      SLA-2  503546  MHC class I antigen 2  3.16      SLA-DRB1  100101921  MHC class II histocompatibility antigen SLA-DRB1  1.80      Slc15a1  100037293  Solute carrier family 15 (oligopeptide transporter), member 1  2.48      SLC35A3  397200  Solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3  2.83      SLC44A4  414424  Solute carrier family 44, member 4  2.46      SLC4A4  397056  Solute carrier family 4, sodium bicarbonate cotransporter, member 4  2.13      SLC5A1  396762  Solute carrier family 5 (sodium/glucose cotransporter), member 1  1.59      SLC5A4  100126235  Solute carrier family 5 (low affinity glucose cotransporter), member 4  2.35      SLC7A7  397095  Solute carrier family 7 (cationic AA transporter, y+ system), member 7  1.85      Slc7a9  397101  Solute carrier family 7 (cationic AA transporter, y+ system), member 9  1.73      SLC9A2  397118  Solute carrier family 9 (sodium/hydrogen exchanger), member 2  1.84      ST3GAL1  100038015  ST3 beta-galactoside alpha-2,3-sialyltransferase 1  1.64      tas1r3  100127440  Taste receptor, type 1, member 3  1.63      TLR2  397376  Toll-like receptor 2  1.90      tmbim6  397080  Transmembrane BAX inhibitor motif containing 6  1.62      tmem59  751862  Transmembrane protein 59  1.56      TNFRSF1A  100037972  Tumor necrosis factor receptor superfamily, member 1A  2.20      VIPR1  397421  Vasoactive intestinal peptide receptor  1.50  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      BAT1  396740  HLA-B associated transcript 1  -1.58      ATIC  100037949  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.58      dnmt1  448813  DNA (cytosine-5-)-methyltransferase 1  -1.59      GTF2H4  733590  General transcription factor IIH, polypeptide 4  -2.35      gucy1b3  100217383  Guanylate cyclase 1, soluble, beta 3  -1.51      LOC100038014  414912  Ribose 5-phosphate isomerase-like protein  -1.72      MEF2C  397583  Myocyte enhancer factor 2C  -2.34      NOR-1  100170844  Neuron-derived orphan receptor-1 alfa  -1.51      NR3C1  444999  Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -2.13      Oct2  396917  POU-domain protein  -1.75      pou2f1  606746  POU class 2 homeobox 1  -2.59      PRPF3  397501  PRP3 pre-mRNA processing factor 3 homolog  -1.66      Ptbp1  397461  Polypyrimidine tract binding protein 1  -1.51      QKI  414430  Quaking homolog, KH domain RNA binding (mouse)  -1.63      RAD18  100038014  RAD18 homolog (S. cerevisiae)  -2.16      SFRS1  654327  Splicing factor, arginine/serine-rich 1  -1.69      SFRS2  492277  Splicing factor, arginine/serine-rich 2  -1.58      SPI1  100152381  Transcription factor PU.1  -1.60  Category 6: Transferase activity (molecular function)      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      prmt5  100294711  Protein arginine methyltransferase 5  -1.62      EHMT2  100124382  Euchromatic histone-lysine N-methyltransferase 2  -1.53      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.54      QKI  492277  Quaking homolog, KH domain RNA binding (mouse)  -1.58  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large The supplementation of garlic botanical to pig diets increased (EASE < 0.05) the mRNA expression of genes involved in the biological processes of fatty acid biosynthetic process, defense response, and oxidation reduction, but decreased (EASE < 0.05) that related to the biological process of antigen processing and presentation and the molecular function associated with the iron ion binding (Table 4; Supplemental Fig. 2). Table 4. Modulation of gene ontology by dietary supplementation of garlic botanical to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Oxidation reduction (biological process)      AKR1C4  100144511  Aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)  1.67      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      ERO1L  100192435  ERO1-like (S. cerevisiae)  1.58      ME1  397538  Malic enzyme 1, NADP(+)-dependent, cytosolic  1.51      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 2: Defense response (biological process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.57      C5  414437  Complement component 5  1.74      CFB  100124383  B-factor, properdin  1.74      IRG6  396752  Inflammatory response protein 6  1.60      LOC780420  780420  SH21A  1.71      LYZ  100157211  Lysozyme (renal amyloidosis)  1.68  Category 3: Iron ion binding (biological process)      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  Cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 4: Fatty acid biosynthetic process (biological process)        ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      Prkaa2  397504  Protein kinase, AMP-activated, alpha 2 catalytic subunit  1.53      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55  Category 5: Antigen processing and presentation (biological process)      CD74  396660  CD74 antigen  -1.58      CREB1  397449  cAMP responsive element binding protein 1  -1.58      LOC100157996  100157996  Similar to MHC class II antigen  -1.55      lta  407742  Lymphotoxin alpha  -1.65      SLA-DRB1  100153386  MHC class II histocompatibility antigen SLA-DRB1  -1.76  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Oxidation reduction (biological process)      AKR1C4  100144511  Aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)  1.67      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      ERO1L  100192435  ERO1-like (S. cerevisiae)  1.58      ME1  397538  Malic enzyme 1, NADP(+)-dependent, cytosolic  1.51      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 2: Defense response (biological process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.57      C5  414437  Complement component 5  1.74      CFB  100124383  B-factor, properdin  1.74      IRG6  396752  Inflammatory response protein 6  1.60      LOC780420  780420  SH21A  1.71      LYZ  100157211  Lysozyme (renal amyloidosis)  1.68  Category 3: Iron ion binding (biological process)      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  Cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 4: Fatty acid biosynthetic process (biological process)        ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      Prkaa2  397504  Protein kinase, AMP-activated, alpha 2 catalytic subunit  1.53      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55  Category 5: Antigen processing and presentation (biological process)      CD74  396660  CD74 antigen  -1.58      CREB1  397449  cAMP responsive element binding protein 1  -1.58      LOC100157996  100157996  Similar to MHC class II antigen  -1.55      lta  407742  Lymphotoxin alpha  -1.65      SLA-DRB1  100153386  MHC class II histocompatibility antigen SLA-DRB1  -1.76  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large Table 4. Modulation of gene ontology by dietary supplementation of garlic botanical to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Oxidation reduction (biological process)      AKR1C4  100144511  Aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)  1.67      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      ERO1L  100192435  ERO1-like (S. cerevisiae)  1.58      ME1  397538  Malic enzyme 1, NADP(+)-dependent, cytosolic  1.51      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 2: Defense response (biological process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.57      C5  414437  Complement component 5  1.74      CFB  100124383  B-factor, properdin  1.74      IRG6  396752  Inflammatory response protein 6  1.60      LOC780420  780420  SH21A  1.71      LYZ  100157211  Lysozyme (renal amyloidosis)  1.68  Category 3: Iron ion binding (biological process)      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  Cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 4: Fatty acid biosynthetic process (biological process)        ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      Prkaa2  397504  Protein kinase, AMP-activated, alpha 2 catalytic subunit  1.53      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55  Category 5: Antigen processing and presentation (biological process)      CD74  396660  CD74 antigen  -1.58      CREB1  397449  cAMP responsive element binding protein 1  -1.58      LOC100157996  100157996  Similar to MHC class II antigen  -1.55      lta  407742  Lymphotoxin alpha  -1.65      SLA-DRB1  100153386  MHC class II histocompatibility antigen SLA-DRB1  -1.76  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Oxidation reduction (biological process)      AKR1C4  100144511  Aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)  1.67      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      ERO1L  100192435  ERO1-like (S. cerevisiae)  1.58      ME1  397538  Malic enzyme 1, NADP(+)-dependent, cytosolic  1.51      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 2: Defense response (biological process)      AMCF-II  396900  Alveolar macrophage-derived chemotactic factor-II  1.57      C5  414437  Complement component 5  1.74      CFB  100124383  B-factor, properdin  1.74      IRG6  396752  Inflammatory response protein 6  1.60      LOC780420  780420  SH21A  1.71      LYZ  100157211  Lysozyme (renal amyloidosis)  1.68  Category 3: Iron ion binding (biological process)      ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      CMAH  396918  Cytidine monophosphate-N-acetylneuraminic acid hydroxylase  1.64      CYP2C42  403111  Cytochrome P450 C42  2.12      Duox2  397060  Dual oxidase 2  1.58      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55      STEAP1  397573  Six transmembrane epithelial antigen of the prostate 1  1.77  Category 4: Fatty acid biosynthetic process (biological process)        ALOX12  396971  Arachidonate 15-lipoxygenase  2.01      Prkaa2  397504  Protein kinase, AMP-activated, alpha 2 catalytic subunit  1.53      SC4MOL  396590  Sterol-C4-methyl oxidase-like  1.55  Category 5: Antigen processing and presentation (biological process)      CD74  396660  CD74 antigen  -1.58      CREB1  397449  cAMP responsive element binding protein 1  -1.58      LOC100157996  100157996  Similar to MHC class II antigen  -1.55      lta  407742  Lymphotoxin alpha  -1.65      SLA-DRB1  100153386  MHC class II histocompatibility antigen SLA-DRB1  -1.76  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large Feeding turmeric oleoresin to pigs increased (EASE < 0.05) the expression levels of genes related to the biological processes of membrane recognition; small GTPase mediated signal transduction; metal ion transport and response to stress; the cellular components in apical junction complex, tight junction, cell-cell junction, and proteinaceous extracellular matrix; and the molecular function of antiporter activity, ATPase activity, carbohydrate binding, active transmembrane activity, and Ca ion binding (Table 5; Supplemental Fig. 3). However, the supplementation of turmeric oleoresin decreased (EASE < 0.05) the mRNA expression level of genes involved in the biological process of RNA splicing, mRNA processing, and others; the cellular components in MHC II protein complex and nucleus; and the molecular function of RNA binding. Table 5. Modulation of gene ontology by dietary supplementation of turmeric oleoresin to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Response to stress (biological process)      AMCF-II  396900  alveolar macrophage-derived chemotactic factor-II  1.66      B2M  397033  beta-2-microglobulin  2.21      C5  414437  complement component 5  1.82      ccl21  448797  chemokine (C-C motif) ligand 21  1.64      CCL28  554303  chemokine (C-C motif) ligand 28  2.51      CCL5  396613  chemokine (C-C motif) ligand 5  1.64      Cd46  396922  CD46 molecule, complement regulatory protein  1.66      CFB  100124383  B-factor, properdin  1.91      DDX58  396723  DEAD (Asp-Glu-Ala-Asp) box polypeptide 58  1.58      FCGRT  397399  Fc fragment of IgG, receptor, transporter, alpha  1.64      FCN2  396881  ficolin  1.72      IL15  397683  interleukin 15  1.67      Il7  397253  interleukin 7  1.57      IL8  396880  interleukin 8  1.65      IRG6  396752  inflammatory response protein 6  1.72      SLA-1  100037293  MHC class I antigen 1  3.43      TLR2  396623  toll-like receptor 2  1.68      TNFSF10  406191  tumor necrosis factor (ligand) superfamily, member 10  1.68  Category 2: Small GTPase mediated signal transduction (biological process)      arl1  595113  ADP-ribosylation factor-like 1  1.52      Arl3  595114  ADP-ribosylation factor-like protein 3  1.61      LOC595121  595121  ADP-ribosylation factor-like protein 4A  1.76      Rab11a  595117  Ras-related protein Rab-11A  1.58      RHOB  100144503  ras homolog gene family, member B  2.09      Rhof  100144500  ras homolog gene family, member F  1.75      rnd3  397559  Rho family GTPase 3  2.19  Category 3: Cell-cell junction (cellular component)      CLDN2  733684  Claudin 2  1.73      CLDN3  431781  Claudin 3  1.77      CLDN4  733578  Claudin 4  1.68      JUP  397592  Junction plakoglobin  2.34      Ocln  397236  Occludin  1.80      vcl  396974  Vinculin  1.53  Category 4: Carbohydrate binding (molecular function)      APP  397663  amyloid beta (A4) precursor protein  1.53      FCN2  396881  ficolin  1.72      galM  399536  galactose mutarotase  1.53      KLRK1  396737  killer cell lectin-like receptor subfamily K, member 1  1.82      LGALS1  414915  lectin, galactoside-binding, soluble, 1  1.50      LGALS8  100156193  lectin, galactoside-binding, soluble, 8  1.79      lgals9  396972  lectin, galactoside-binding, soluble, 9  2.00      Lpl  397537  lipoprotein lipase  1.60      PTF-BETA  397609  pleiotrophic factor beta  1.72      Sftpd  397198  surfactant protein D  2.15  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.56      BAT1  448813  HLA-B associated transcript 1  -1.51      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      gucy1b3  444999  guanylate cyclase 1, soluble, beta 3  -2.18      lipe  397583  lipase, hormone-sensitive  -1.54      LOC100038014  100038014  ribose 5-phosphate isomerase-like protein  -1.81      MED27  414430  mediator complex subunit 27  -1.53      MEF2C  733590  myocyte enhancer factor 2C  -2.33      NR3C1  396740  nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -1.77      pou2f1  397501  POU class 2 homeobox 1  -1.53      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      RAP80  100037949  retinoid x receptor interacting protein  -1.58      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      TFAM  397279  transcription factor A  -1.55      TOPOII  396917  topoisomersae II  -1.65  Category 6: RNA binding (molecular function)      BAT1  448813  HLA-B associated transcript 1  -1.51      lipe  397583  lipase, hormone-sensitive  -1.54      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      rps20  414395  ribosomal protein S20  -1.51      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      tlr9  397007  Toll-like receptor 9  -1.56  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Response to stress (biological process)      AMCF-II  396900  alveolar macrophage-derived chemotactic factor-II  1.66      B2M  397033  beta-2-microglobulin  2.21      C5  414437  complement component 5  1.82      ccl21  448797  chemokine (C-C motif) ligand 21  1.64      CCL28  554303  chemokine (C-C motif) ligand 28  2.51      CCL5  396613  chemokine (C-C motif) ligand 5  1.64      Cd46  396922  CD46 molecule, complement regulatory protein  1.66      CFB  100124383  B-factor, properdin  1.91      DDX58  396723  DEAD (Asp-Glu-Ala-Asp) box polypeptide 58  1.58      FCGRT  397399  Fc fragment of IgG, receptor, transporter, alpha  1.64      FCN2  396881  ficolin  1.72      IL15  397683  interleukin 15  1.67      Il7  397253  interleukin 7  1.57      IL8  396880  interleukin 8  1.65      IRG6  396752  inflammatory response protein 6  1.72      SLA-1  100037293  MHC class I antigen 1  3.43      TLR2  396623  toll-like receptor 2  1.68      TNFSF10  406191  tumor necrosis factor (ligand) superfamily, member 10  1.68  Category 2: Small GTPase mediated signal transduction (biological process)      arl1  595113  ADP-ribosylation factor-like 1  1.52      Arl3  595114  ADP-ribosylation factor-like protein 3  1.61      LOC595121  595121  ADP-ribosylation factor-like protein 4A  1.76      Rab11a  595117  Ras-related protein Rab-11A  1.58      RHOB  100144503  ras homolog gene family, member B  2.09      Rhof  100144500  ras homolog gene family, member F  1.75      rnd3  397559  Rho family GTPase 3  2.19  Category 3: Cell-cell junction (cellular component)      CLDN2  733684  Claudin 2  1.73      CLDN3  431781  Claudin 3  1.77      CLDN4  733578  Claudin 4  1.68      JUP  397592  Junction plakoglobin  2.34      Ocln  397236  Occludin  1.80      vcl  396974  Vinculin  1.53  Category 4: Carbohydrate binding (molecular function)      APP  397663  amyloid beta (A4) precursor protein  1.53      FCN2  396881  ficolin  1.72      galM  399536  galactose mutarotase  1.53      KLRK1  396737  killer cell lectin-like receptor subfamily K, member 1  1.82      LGALS1  414915  lectin, galactoside-binding, soluble, 1  1.50      LGALS8  100156193  lectin, galactoside-binding, soluble, 8  1.79      lgals9  396972  lectin, galactoside-binding, soluble, 9  2.00      Lpl  397537  lipoprotein lipase  1.60      PTF-BETA  397609  pleiotrophic factor beta  1.72      Sftpd  397198  surfactant protein D  2.15  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.56      BAT1  448813  HLA-B associated transcript 1  -1.51      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      gucy1b3  444999  guanylate cyclase 1, soluble, beta 3  -2.18      lipe  397583  lipase, hormone-sensitive  -1.54      LOC100038014  100038014  ribose 5-phosphate isomerase-like protein  -1.81      MED27  414430  mediator complex subunit 27  -1.53      MEF2C  733590  myocyte enhancer factor 2C  -2.33      NR3C1  396740  nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -1.77      pou2f1  397501  POU class 2 homeobox 1  -1.53      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      RAP80  100037949  retinoid x receptor interacting protein  -1.58      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      TFAM  397279  transcription factor A  -1.55      TOPOII  396917  topoisomersae II  -1.65  Category 6: RNA binding (molecular function)      BAT1  448813  HLA-B associated transcript 1  -1.51      lipe  397583  lipase, hormone-sensitive  -1.54      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      rps20  414395  ribosomal protein S20  -1.51      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      tlr9  397007  Toll-like receptor 9  -1.56  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large Table 5. Modulation of gene ontology by dietary supplementation of turmeric oleoresin to pig diets1 Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Response to stress (biological process)      AMCF-II  396900  alveolar macrophage-derived chemotactic factor-II  1.66      B2M  397033  beta-2-microglobulin  2.21      C5  414437  complement component 5  1.82      ccl21  448797  chemokine (C-C motif) ligand 21  1.64      CCL28  554303  chemokine (C-C motif) ligand 28  2.51      CCL5  396613  chemokine (C-C motif) ligand 5  1.64      Cd46  396922  CD46 molecule, complement regulatory protein  1.66      CFB  100124383  B-factor, properdin  1.91      DDX58  396723  DEAD (Asp-Glu-Ala-Asp) box polypeptide 58  1.58      FCGRT  397399  Fc fragment of IgG, receptor, transporter, alpha  1.64      FCN2  396881  ficolin  1.72      IL15  397683  interleukin 15  1.67      Il7  397253  interleukin 7  1.57      IL8  396880  interleukin 8  1.65      IRG6  396752  inflammatory response protein 6  1.72      SLA-1  100037293  MHC class I antigen 1  3.43      TLR2  396623  toll-like receptor 2  1.68      TNFSF10  406191  tumor necrosis factor (ligand) superfamily, member 10  1.68  Category 2: Small GTPase mediated signal transduction (biological process)      arl1  595113  ADP-ribosylation factor-like 1  1.52      Arl3  595114  ADP-ribosylation factor-like protein 3  1.61      LOC595121  595121  ADP-ribosylation factor-like protein 4A  1.76      Rab11a  595117  Ras-related protein Rab-11A  1.58      RHOB  100144503  ras homolog gene family, member B  2.09      Rhof  100144500  ras homolog gene family, member F  1.75      rnd3  397559  Rho family GTPase 3  2.19  Category 3: Cell-cell junction (cellular component)      CLDN2  733684  Claudin 2  1.73      CLDN3  431781  Claudin 3  1.77      CLDN4  733578  Claudin 4  1.68      JUP  397592  Junction plakoglobin  2.34      Ocln  397236  Occludin  1.80      vcl  396974  Vinculin  1.53  Category 4: Carbohydrate binding (molecular function)      APP  397663  amyloid beta (A4) precursor protein  1.53      FCN2  396881  ficolin  1.72      galM  399536  galactose mutarotase  1.53      KLRK1  396737  killer cell lectin-like receptor subfamily K, member 1  1.82      LGALS1  414915  lectin, galactoside-binding, soluble, 1  1.50      LGALS8  100156193  lectin, galactoside-binding, soluble, 8  1.79      lgals9  396972  lectin, galactoside-binding, soluble, 9  2.00      Lpl  397537  lipoprotein lipase  1.60      PTF-BETA  397609  pleiotrophic factor beta  1.72      Sftpd  397198  surfactant protein D  2.15  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.56      BAT1  448813  HLA-B associated transcript 1  -1.51      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      gucy1b3  444999  guanylate cyclase 1, soluble, beta 3  -2.18      lipe  397583  lipase, hormone-sensitive  -1.54      LOC100038014  100038014  ribose 5-phosphate isomerase-like protein  -1.81      MED27  414430  mediator complex subunit 27  -1.53      MEF2C  733590  myocyte enhancer factor 2C  -2.33      NR3C1  396740  nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -1.77      pou2f1  397501  POU class 2 homeobox 1  -1.53      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      RAP80  100037949  retinoid x receptor interacting protein  -1.58      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      TFAM  397279  transcription factor A  -1.55      TOPOII  396917  topoisomersae II  -1.65  Category 6: RNA binding (molecular function)      BAT1  448813  HLA-B associated transcript 1  -1.51      lipe  397583  lipase, hormone-sensitive  -1.54      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      rps20  414395  ribosomal protein S20  -1.51      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      tlr9  397007  Toll-like receptor 9  -1.56  Gene symbol  Gene ID NCBI  Gene name  Fold change2  Category 1: Response to stress (biological process)      AMCF-II  396900  alveolar macrophage-derived chemotactic factor-II  1.66      B2M  397033  beta-2-microglobulin  2.21      C5  414437  complement component 5  1.82      ccl21  448797  chemokine (C-C motif) ligand 21  1.64      CCL28  554303  chemokine (C-C motif) ligand 28  2.51      CCL5  396613  chemokine (C-C motif) ligand 5  1.64      Cd46  396922  CD46 molecule, complement regulatory protein  1.66      CFB  100124383  B-factor, properdin  1.91      DDX58  396723  DEAD (Asp-Glu-Ala-Asp) box polypeptide 58  1.58      FCGRT  397399  Fc fragment of IgG, receptor, transporter, alpha  1.64      FCN2  396881  ficolin  1.72      IL15  397683  interleukin 15  1.67      Il7  397253  interleukin 7  1.57      IL8  396880  interleukin 8  1.65      IRG6  396752  inflammatory response protein 6  1.72      SLA-1  100037293  MHC class I antigen 1  3.43      TLR2  396623  toll-like receptor 2  1.68      TNFSF10  406191  tumor necrosis factor (ligand) superfamily, member 10  1.68  Category 2: Small GTPase mediated signal transduction (biological process)      arl1  595113  ADP-ribosylation factor-like 1  1.52      Arl3  595114  ADP-ribosylation factor-like protein 3  1.61      LOC595121  595121  ADP-ribosylation factor-like protein 4A  1.76      Rab11a  595117  Ras-related protein Rab-11A  1.58      RHOB  100144503  ras homolog gene family, member B  2.09      Rhof  100144500  ras homolog gene family, member F  1.75      rnd3  397559  Rho family GTPase 3  2.19  Category 3: Cell-cell junction (cellular component)      CLDN2  733684  Claudin 2  1.73      CLDN3  431781  Claudin 3  1.77      CLDN4  733578  Claudin 4  1.68      JUP  397592  Junction plakoglobin  2.34      Ocln  397236  Occludin  1.80      vcl  396974  Vinculin  1.53  Category 4: Carbohydrate binding (molecular function)      APP  397663  amyloid beta (A4) precursor protein  1.53      FCN2  396881  ficolin  1.72      galM  399536  galactose mutarotase  1.53      KLRK1  396737  killer cell lectin-like receptor subfamily K, member 1  1.82      LGALS1  414915  lectin, galactoside-binding, soluble, 1  1.50      LGALS8  100156193  lectin, galactoside-binding, soluble, 8  1.79      lgals9  396972  lectin, galactoside-binding, soluble, 9  2.00      Lpl  397537  lipoprotein lipase  1.60      PTF-BETA  397609  pleiotrophic factor beta  1.72      Sftpd  397198  surfactant protein D  2.15  Category 5: Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (biological process)      ATIC  100170854  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase  -1.56      BAT1  448813  HLA-B associated transcript 1  -1.51      dnmt1  606746  DNA (cytosine-5-)-methyltransferase 1  -2.01      gucy1b3  444999  guanylate cyclase 1, soluble, beta 3  -2.18      lipe  397583  lipase, hormone-sensitive  -1.54      LOC100038014  100038014  ribose 5-phosphate isomerase-like protein  -1.81      MED27  414430  mediator complex subunit 27  -1.53      MEF2C  733590  myocyte enhancer factor 2C  -2.33      NR3C1  396740  nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)  -1.77      pou2f1  397501  POU class 2 homeobox 1  -1.53      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      RAP80  100037949  retinoid x receptor interacting protein  -1.58      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      TFAM  397279  transcription factor A  -1.55      TOPOII  396917  topoisomersae II  -1.65  Category 6: RNA binding (molecular function)      BAT1  448813  HLA-B associated transcript 1  -1.51      lipe  397583  lipase, hormone-sensitive  -1.54      Ptbp1  397461  polypyrimidine tract binding protein 1  -1.61      QKI  492277  quaking homolog, KH domain RNA binding (mouse)  -1.60      rps20  414395  ribosomal protein S20  -1.51      SFRS1  654327  splicing factor, arginine/serine-rich 1  -1.52      SPI1  414912  transcription factor PU.1  -1.68      tlr9  397007  Toll-like receptor 9  -1.56  1Gene ID NCBI = Gene identification number, NCBI (Bethesda MD). All data were analyzed by DAVID Bioinformatics Resources 6.7 [National Institute of Allergy and Infectious Diseases (NIH, Bethesda, MD)]. 2Negative value indicates reduction in gene expression. View Large Kegg Pathway Analysis Compared with the pigs fed control diet, feeding capsicum oleoresin upregulated (EASE < 0.05) the expression of genes related to drug metabolism, metabolism of xenobiotics by cytochrome P450, and AA metabolism, but downregulated (EASE < 0.05) the expression levels of genes associated with the cell cycle and B cell receptor signaling pathway (Fig. 1; Supplemental Table 2). The supplementation of garlic botanical increased (EASE < 0.05) the mRNA expression of genes involved in the complement and coagulation cascades, but decreased (EASE < 0.05) those genes in antigen processing and presentation and Fc γ R-mediated phagocytosis (Fig. 1; Supplemental Table 3). In addition, the addition of turmeric oleoresin in pig diets increased (EASE < 0.05) the expression of genes in drug metabolism, arachidonic acid metabolism, and tight junctions, but reduced (EASE < 0.05) the mRNA expression of genes related to cell cycle (Fig. 1; Supplemental Table 4). Fig. 1. View largeDownload slide Modulation of Kegg pathway by dietary supplementation of weanling pig diets with (A) capsicum oleoresin, (B) garlic botanical, or (C) turmeric oleoresin. The values in pie chart indicate the number of genes involved in each category. Positive value indicates upregulation in gene expression, whereas negative value indicates downregulation in gene expression. Fig. 1. View largeDownload slide Modulation of Kegg pathway by dietary supplementation of weanling pig diets with (A) capsicum oleoresin, (B) garlic botanical, or (C) turmeric oleoresin. The values in pie chart indicate the number of genes involved in each category. Positive value indicates upregulation in gene expression, whereas negative value indicates downregulation in gene expression. Quantitative RT-PCR Five genes were selected based on the microarray data and tested by quantitative RT-PCR to validate the microarray results. As shown in Table 6, the transcriptional changes in these genes as assessed by quantitative RT-PCR showed similar patterns when compared with the original microarray data. Table 6. Verification of gene expression in ileal mucosa by quantitative real-time reverse transcription PCR (RT-PCR)1   Fold change3    CAP vs. CON  GAR vs. CON  TUR vs. CON  Gene2  Microarray  RT-PCR  Microarray  RT-PCR  Microarray  RT-PCR  IL1B  -1.44  -3.17*  -1.01  -1.75*  -1.36  -2.87*  LBP  1.83  -1.05  1.61  1.47  2.50  1.16  MyD88  -1.07  -1.29*  -1.01  -1.17  -1.01  -1.12  TLR4  -1.04  -1.19  -1.24  -1.20  -1.11  -1.16  TNFa  -1.44  -1.58  -1.03  -1.30  -1.39  -1.39  CFTR  –  1.69*  –  1.16  –  1.37*  COX2  –  1.57  –  1.34  –  2.01*  MUC2  –  1.33*  –  1.26  –  1.16  p38 MAPK  –  1.21*  –  1.00  –  1.30*  p65 NFkB  –  -1.26*  –  -1.08  –  -1.15*    Fold change3    CAP vs. CON  GAR vs. CON  TUR vs. CON  Gene2  Microarray  RT-PCR  Microarray  RT-PCR  Microarray  RT-PCR  IL1B  -1.44  -3.17*  -1.01  -1.75*  -1.36  -2.87*  LBP  1.83  -1.05  1.61  1.47  2.50  1.16  MyD88  -1.07  -1.29*  -1.01  -1.17  -1.01  -1.12  TLR4  -1.04  -1.19  -1.24  -1.20  -1.11  -1.16  TNFa  -1.44  -1.58  -1.03  -1.30  -1.39  -1.39  CFTR  –  1.69*  –  1.16  –  1.37*  COX2  –  1.57  –  1.34  –  2.01*  MUC2  –  1.33*  –  1.26  –  1.16  p38 MAPK  –  1.21*  –  1.00  –  1.30*  p65 NFkB  –  -1.26*  –  -1.08  –  -1.15*  *The comparison was significant different (P < 0.05) in RT-PCR studies. 1CAP = uninfected pigs fed capsicum oleoresin; CON = uninfected pigs fed the control diet; GAR = uninfected pigs fed garlic botanical; and TUR = uninfected pigs fed turmeric oleoresin. The total RNA samples (4 pigs/treatment) that were used to run the porcine microarray (Affymetrix Inc., Santa Clara, CA) were employed for RT-PCR. 2The average threshold cycle values for IL-1B, lipopolysaccharide binding protein (LBP), myeloid differentiation primary response gene 88 (MyD88), toll-like receptor 4 (TLR4), tumor necrosis factor alpha (TNFa), cystic fibrosis transmembrane conductance regulator (CFTR), cyclooxygenase 2 (COX2), mucin 2 (MUC2), p38 mitogen-activated protein kinases (p38 MAPK), p65 nuclear factor kappa-light-chain-enhancer of activated B cells (p65 NFkB) were 28.7, 30.2, 22.6, 24.6, 27.3, 25.1, 23.2, 23.2, 17.4, 22.0, respectively; and β-actin (ACTB) and GAPDH were used as endogenous controls for RT-PCR. 3Negative value indicates reduction in gene expression. View Large Table 6. Verification of gene expression in ileal mucosa by quantitative real-time reverse transcription PCR (RT-PCR)1   Fold change3    CAP vs. CON  GAR vs. CON  TUR vs. CON  Gene2  Microarray  RT-PCR  Microarray  RT-PCR  Microarray  RT-PCR  IL1B  -1.44  -3.17*  -1.01  -1.75*  -1.36  -2.87*  LBP  1.83  -1.05  1.61  1.47  2.50  1.16  MyD88  -1.07  -1.29*  -1.01  -1.17  -1.01  -1.12  TLR4  -1.04  -1.19  -1.24  -1.20  -1.11  -1.16  TNFa  -1.44  -1.58  -1.03  -1.30  -1.39  -1.39  CFTR  –  1.69*  –  1.16  –  1.37*  COX2  –  1.57  –  1.34  –  2.01*  MUC2  –  1.33*  –  1.26  –  1.16  p38 MAPK  –  1.21*  –  1.00  –  1.30*  p65 NFkB  –  -1.26*  –  -1.08  –  -1.15*    Fold change3    CAP vs. CON  GAR vs. CON  TUR vs. CON  Gene2  Microarray  RT-PCR  Microarray  RT-PCR  Microarray  RT-PCR  IL1B  -1.44  -3.17*  -1.01  -1.75*  -1.36  -2.87*  LBP  1.83  -1.05  1.61  1.47  2.50  1.16  MyD88  -1.07  -1.29*  -1.01  -1.17  -1.01  -1.12  TLR4  -1.04  -1.19  -1.24  -1.20  -1.11  -1.16  TNFa  -1.44  -1.58  -1.03  -1.30  -1.39  -1.39  CFTR  –  1.69*  –  1.16  –  1.37*  COX2  –  1.57  –  1.34  –  2.01*  MUC2  –  1.33*  –  1.26  –  1.16  p38 MAPK  –  1.21*  –  1.00  –  1.30*  p65 NFkB  –  -1.26*  –  -1.08  –  -1.15*  *The comparison was significant different (P < 0.05) in RT-PCR studies. 1CAP = uninfected pigs fed capsicum oleoresin; CON = uninfected pigs fed the control diet; GAR = uninfected pigs fed garlic botanical; and TUR = uninfected pigs fed turmeric oleoresin. The total RNA samples (4 pigs/treatment) that were used to run the porcine microarray (Affymetrix Inc., Santa Clara, CA) were employed for RT-PCR. 2The average threshold cycle values for IL-1B, lipopolysaccharide binding protein (LBP), myeloid differentiation primary response gene 88 (MyD88), toll-like receptor 4 (TLR4), tumor necrosis factor alpha (TNFa), cystic fibrosis transmembrane conductance regulator (CFTR), cyclooxygenase 2 (COX2), mucin 2 (MUC2), p38 mitogen-activated protein kinases (p38 MAPK), p65 nuclear factor kappa-light-chain-enhancer of activated B cells (p65 NFkB) were 28.7, 30.2, 22.6, 24.6, 27.3, 25.1, 23.2, 23.2, 17.4, 22.0, respectively; and β-actin (ACTB) and GAPDH were used as endogenous controls for RT-PCR. 3Negative value indicates reduction in gene expression. View Large Another 5 genes not included in the microarray, CFTR, COX2, MUC2, p38 MAPK, and p65 NFkB, were tested by RT-PCR. Compared with the control diet, feeding capsicum oleoresin upregulated (P < 0.05) CFTR, MUC2, and p38 MAPK expression, but downregulated (P < 0.05) p65 NFkB expression, and feeding turmeric oleoresin upregulated (P < 0.05) CFTR, COX2, and p38 MAPK expression, but downregulated (P < 0.05) p65 NFkB expression in the ileal mucosa of weaned pigs. No differences were observed from feeding garlic botanical. DISCUSSION Beneficial effects of plant extracts on weaned pigs have been reported by several studies, which reduced disease incidence and diarrhea (Manzanilla et al., 2004; Michiels et al., 2010; Liu et al., 2013). However, little is known about the modes of action. The microarray as used in this study characterized gene expression as indicated by abundance of mRNA. We applied it to ileal mucosa of pigs fed 3 different plant extracts to understand the intestinal physiological responses to those extracts. The microarray results indicated that the 3 plant extracts had different effects on the transcriptional changes of ileal mucosa of pigs. Capsicum oleoresin is obtained from hot green and red peppers, with capsaicin as the major active ingredient (Abdel Salam et al., 2005). A high-throughput gene expression analysis of intestinal intraepithelial lymphocytes after feeding of capsicum oleoresin to broiler chickens indicated that capsicum oleoresin activated the network related to lipid metabolism, small molecule biochemistry, and cancer (Kim et al., 2010). It is possible that the present study is first to investigate the effects of feeding capsicum oleoresin to weaned pigs using a high-throughput gene expression analysis, the microarray. The supplementation of capsicum oleoresin increased the expression of genes related to activation of the immune response. These genes include C1qa, C5, ccl25, Cd46, CFB, FCN2, and others (Table 3). Among these genes, the C1qa and C5 encode components of the complement system (Sarma and Ward, 2011), whereas the Cd46 and CFB encode regulatory proteins in the complement system (Riley-Vargas et al., 2004). The FCN2 encodes ficolin-2, an oligomeric lectin that can activate the lectin pathway of complement activation and play an important role in innate immunity (Matsushita, 2010). The ccl25 encodes a chemokine with an important role in the development of T cells (Zaballos et al., 1999). The supplementation of capsicum oleoresin to pig diets also upregulated the expression of 68 genes related to cellular components integral to membranes. This category also included several immune genes, such as CCR9, CD3D, Cd3 g, CD46, CD9, DPP4, FCGR3B, FCGRT, KLRK1, SLA-1, SLA-2, SLA-DRB1, and TLR-2. The CCR9 encodes chemokine receptor type 9, which is expressed by T lymphocytes of the small intestine and contributes to the thymocyte recruitment and development that may permit functional specialization of immune responses in different segments of the gastrointestinal tract (Zaballos et al., 1999). The SLA-1, SLA-2, and SLA-DRB1 encode major histocompatibility complex I and II antigens involved in antigen processing and presentation (Radosevich and Ono, 2003; Yang, 2003). The increased expression of immune genes indicates the supplementation of capsicum oleoresin may enhance the gut mucosal immunity of weaned pigs, especially the innate immunity. This enhancement may be beneficial to the host by providing immediate defense (Parkin and Cohen, 2001). Our in vitro study also provided evidence that the administration of capsicum oleoresin stimulated the secretion of proinflammatory cytokines from alveolar macrophages (Liu et al., 2012). Otherwise, feeding capsicum oleoresin increased expression of CLDN3 and Ocln, which encode 2 integral membrane proteins, claudin 3 and occludin, that are required for the formation and maintenance of tight junctions (McCarthy et al., 1996; Elkouby-Naor and Ben-Yosef, 2010). The increased tight junction proteins indicate a potential benefit of feeding capsicum oleoresin on gut barrier function. Mucins play a central role in maintaining homeostasis of the gut through interfacing with food, water, and luminal microorganisms. Mucin2 is the major core polypeptide of membrane-associated and secretory gel-forming mucins in the intestine, and it plays an important role in defense against inflammation (Hollingsworth and Swanson, 2004; Nishida et al., 2009; Hansson, 2012). Therefore, the RT-PCR results showing that feeding capsicum oleoresin upregulated the expression of MUC2 also support a beneficial effect of capsicum oleoresin on the gut barrier. The present results showed that feeding capsicum oleoresin upregulated the expression of genes related to the transportation processes. Among these processes, several genes (SLC4A4, SLC5A1, SLC5A4, SLC7A7, SLC7a9, SLC9A2, SLC15A1, SLC30A7, SLC35A3, and CTR1) encode the members of solute carrier family (SLC), a group of membrane transport proteins. These proteins are important transporters or cotransporters that contribute to the transportation of bicarbonate (SLC4A4), sodium and glucose (SLC5A1 and SLC5A4), AA and oligopeptide (Slc15a1), nucleoside-sugar (SLC35A3), zinc (SLC30A7), copper (CTR1), and other nutrients (Hediger et al., 2004; Petris, 2004). Besides the solute carrier family, other genes associated with vitamin A transportation (rbp2 and RBP4; Takase et al., 2000), Na/K exchanger (ATP1A1, Atp1b1, and ATP9A; Boyer, 1997), reabsorption of water (AQP1, AQP3, AQP8iand AQP11; Borgnia et al., 1999), and cholesterol transportation (APOA1 and APOC3; Groenendijk et al., 2001) were also upregulated by feeding capsicum oleoresin. The increased transportation may facilitate the transport of glucose, different ions, and other nutrients and help to maintain the homoeostasis in the small intestine. In addition, feeding capsicum oleoresin upregulated the expression of tas1r3 that encodes a taste receptor; this may trigger the secretion of GLP-2 from enteroendocrine cells (Shirazi-Beechey et al., 2011). The GLP-2 has potent and specific trophic effects on the GI tract and has the capability to enhance the gut barrier function (Benjamin et al., 2000; Burrin et al., 2001). Therefore, the reduced diarrhea and increased growth rate by feeding capsicum oleoresin to weaned pigs (Liu et al., 2013) may be related to the potential benefits on the gut barrier function and the maintenance of gut homoeostasis. Moreover, the supplementation of capsicum oleoresin downregulated the expression level of genes involved in the cell cycle (Fig. 1). This observation was different from a previous report from Manzanilla et al. (2009), which indicated that feeding pigs with 200 mg/kg of a mixture of plant extracts increased mitosis in the distal jejunum, possibly because of the presence of nonabsorbed nutrients or changes in microbiota in the lumen. However, capsaicin, the major active component or capsicum oleoresin, has been observed to induce cell cycle arrest and inhibit the growth of several tumor cells by suppressing STAT signaling pathway or NF-κB pathway in vitro (Bhutani et al., 2007; Thoennissen et al., 2010; Shanmugam et al., 2011). Therefore, more research may be needed to clarify the effect of capsicum oleoresin on normal epithelial cells in vivo. Garlic botanical is an extract from garlic and standardized to 40% propyl thiosulfonates. Feeding 10 mg/kg garlic botanical did not show as many effects as feeding capsicum oleoresin to pigs, and expression levels of only 64 genes were changed, 33 upregulated and 31 downregulated. The supplementation of garlic botanical upregulated the expression level of genes related to defense responses (biological process) and complement and coagulation cascades (Kegg pathway). These genes included LYZ, CFB, C5, IRG6, AMCF-II, C6, and C9. The IRG encodes an interferon-induced antiviral protein, viperin, which is induced in lymphoid cells and dendritic cells during acute infection and highly induced in neutrophils and macrophages (Hinson et al., 2010). The LYZ encodes an enzyme, lysozyme that can kill the pathogenic bacteria by damaging bacterial cell walls and prevent the direct access of microorganisms to the intestinal mucosa (Luzio et al., 2007). The CFB, C5, C6, and C9 encode proteins associated with the complement system, indicating activation of the complement system by feeding garlic botanical. However, the mRNA expression level of genes involved in antigen processing and presentation and Fc γ R-mediated phagocytosis were reduced, indicating that feeding garlic botanical may alter the immune responses of pigs, but there is no clear implication based on the results due to the complexity of the immune system and its regulation. Turmeric oleoresin is specially known for its wound-healing and anti-inflammatory properties (Shishodia et al., 2005; Aggarwal et al., 2007; Krishnaswamy, 2008). Similar to feeding capsicum oleoresin and garlic botanical, feeding turmeric oleoresin also altered the mRNA expression of genes related to the immune responses. In the present study, the supplementation of turmeric oleoresin upregulated the expression of genes related to the recruitment of neutrophils (AMCF-II and IRG6; Goodman et al., 1991; Hinson et al., 2010), the complement system (C5; Sarma and Ward, 2011) and its regulatory proteins (Cd46, CFB, and FCN2; Riley-Vargas et al., 2004; Matsushita, 2010), chemokines (CCL5, ccl21, CCL28, and IL8; Bennett et al., 2011), cytokines (IL15 and TNFSF10; Micheau and Tschopp, 2003), and antigen processing and presentation (B2M, DDX58, and SLA-1; Yang, 2003; Takeuchi and Akira, 2008). The gene expression results indicated that, similar to capsicum oleoresin, feeding turmeric oleoresin may also enhance the gut mucosal immunity of weaned pigs. Our RT-PCR results showed that feeding turmeric oleoresin increased the expression of COX-2, which also indicates increased inflammatory responses in the ileal mucosa of weaned pigs (Abdalla et al., 2005). Otherwise, our previous in vitro study indicated the addition of turmeric oleoresin may enhance immune responses (Liu et al., 2012). The turmeric oleoresin used in this study was extracted oleoresin standardized to 98% curcuminoides, and 1 of the major components is curcumin. It is well known that curcumin possesses several pharmacological properties, including anti-inflammatory, antimicrobial, antiviral, and others (Mazumder et al., 1995; Jobin et al., 1999; Negi et al., 1999). Most literature indicates anti-inflammatory effects of curcumin in pathological conditions, such as stimulation by lipopolysaccharides or other proinflammatory stimuli (Jagetia and Aggarwal, 2007). However, curcumin also can differentially regulate the immune function in normal conditions (Jagetia and Aggarwal, 2007). Li and Liu (2005) showed that a low dose of curcumin increased the proliferation of splenic lymphocytes, whereas high-dose curcumin depressed it, indicating its ability to differentially regulate the proliferation of splenic lymphocytes. Churchill et al. (2000) have reported that curcumin treatment stimulates proliferation of B cells in the mucosa of intestine of mice, indicating its immunostimulatory activity. The RT-PCR results also show that feeding capsicum oleoresin upregulated the expression of p38 MAPK but downregulated the expression of p65 NFkB in ileal mucosa, indicating that the increased immune genes may be more attributed to the activation of p38 MAPK (Camacho-Barquero et al., 2007), which is a key modulator of several target genes that ultimately control infiltration of monocytic cells and acute intestinal inflammation (Kyriakis and Avruch, 2012). However, the exact mechanisms need to be elucidated. Feeding turmeric oleoresin upregulated the expression of genes related to tight junctions and cell-cell junctions (CLDN2, CLDN3, CLDN4, JUP, Olcn, and vcl). The CLDN2, CLDN3, and CLDN4 encode proteins claudin2, claudin 3, and claudin 4, which are considered major proteins in the structural backbone of tight junctions (Van Itallie et al., 2001; Elkouby-Naor and Ben-Yosef, 2010). The Ocln codes another transmembrane protein associated with tight junctions, occludin. Occludin interacts with claudin and is involved in the regulation of intermembrane diffusion and paracellular diffusion of small molecules (Balda et al., 1996: Tsukita and Furuse, 1999). The gene JUP encodes a protein called plakoglobin, which participates in the adherens junctions and play an important role in strengthening the cell adhesion (Yin et al., 2005). The gene vcl encodes vinculin, known to have the function of enhancing epithelial barrier formation and maintaining properly functional tissues (Twiss et al., 2012). The microarray results indicate that feeding turmeric oleoresin may strengthen the gut barrier function of weaned pigs, which may enhance the gut health and reduce weaning stress as indicated by the reduced diarrhea and growth retardation (Liu et al., 2013). This finding is consistent with Wang et al. (2012), who found curcumin protects epithelial dysfunction by increasing tight junction proteins. The mechanisms are not clear but may be partially related to the reduced NFκB activation. Ma et al. (2004) found curcumin prevented epithelial cell tight junction permeability by inhibiting NFκB activation and upregulation of zonula occludens-1 in the epithelial cells. Similar to capsicum oleoresin, turmeric oleoresin also downregulated the expression of genes related to the cell cycle. Curcumin was previously observed to be antiproliferative by interrupting the cell cycle, disrupting mitotic spindle structures, and inducing apoptosis and micronucleation (Chen and Huang, 1998; Jagetia and Aggarwal, 2007). However, there is little research on turmeric oleoresin or curcumin applied to normal epithelial cells. Overall, the analysis of gene expression patterns shows that dietary plant extracts affected the gene expression of ileal mucosa of weaned pigs. Feeding capsicum and turmeric oleoresins produced similar effects. They increased the mRNA abundance of several genes related to the activation of immune responses and genes involved in tight junctions, indicating both of them may enhance gut mucosal immunity and gut barrier function of weaned pigs. However, feeding those reduced the expression of genes related to the cell cycle, the implications of which are not clear. Feeding garlic botanical also enhanced the mRNA expression of genes related to defense responses but reduced the expression of genes associated with antigen processing and presentation. In conclusion, our findings provide new insights into the immunomodulatory and physiologically modulatory properties of plant extracts. Feeding plant extracts, especially capsicum and turmeric oleoresin, may provide benefits by enhancing the immune responses and gut physiological health at the transcriptional level. The changes at the transcription level may or may not correlate well with the changes at protein level because of the complicated regulation in the process by which information from genes is used in the synthesis of proteins. Further research at the protein level may be needed. LITERATURE CITED Abdalla S. I. Sanderson I. R. Fitzgerald R. C. 2005. Effect of inflammation on cyclooxygenase (COX)-2 expression in benign and malignant oesophageal cells. Carcinogenesis  26: 1627– 1633. Google Scholar CrossRef Search ADS PubMed  Abdel Salam O. M. E. Heikal O. A. El-Shenawy S. M. 2005. Effect of capsicum on bile secretion in the rat. Pharmacology  73: 121– 128. Google Scholar CrossRef Search ADS PubMed  Aggarwal B. B. Sundaram C. Malani N. Ichikawa H. 2007. Curcumin: The Indian solid gold. Adv. Exp. Med. Biol.  595: 1– 75. Bakkali F. Averbeck S. Averbeck D. Idaomar M. 2008. Biological effects of essential oils—A review. Food Chem. Toxicol.  46: 446– 475. Google Scholar CrossRef Search ADS PubMed  Balda M. S. Whitney J. A. Flores C. González S. Cereijido M. Matter K. 1996. Functional dissociation of paracellular permeability and transepithelial electrical resistance and disruption of the apical-basolaternal intramembrane diffusion barrier by expression a mutant tight junction membrane protein. J. Cell Biol.  134: 1031– 1049. Google Scholar CrossRef Search ADS PubMed  Benjamin M. A. McKay D. M. Yang P.-C. Cameron H. Perdue M. H. 2000. Glugacon-like peptide-2 enhances intestinal epithelial barrier function of both transcellular and paracellular pathways in the mouse. Gut  47: 112– 119. Google Scholar CrossRef Search ADS PubMed  Bennett L. D. Fox J. M. Signoret N. 2011. Mechanisms regulating chemokine receptor activity. Immunology  134: 246– 256. Google Scholar CrossRef Search ADS PubMed  Bhutani M. Pathak A. K. Nair A. S. Kunnumakkara A. B. Guha S. Sethi G. Aggarwal B. B. 2007. Capsaicin is a novel blocker of constitutive and interleukin-6-inducible STAT3 activation. Clin. Cancer Res.  13: 3024– 3032. Google Scholar CrossRef Search ADS PubMed  Borgnia M. Nielsen S. Engel A. Agre P. 1999. Cellular and molecular biology of the aquaporin water channels. Annu. Rev. Biochem.  68: 425– 458. Google Scholar CrossRef Search ADS PubMed  Boyer P. D 1997. The ATP synthase—A splendid molecular machine. Annu. Rev. Biochem.  66: 717– 749. Google Scholar CrossRef Search ADS PubMed  Burrin D. G. Petersen Y. Stoll B. Sangild P. 2001. Glucagon-like peptide 2: A nutrient-responsive gut growth factor. J. Nutr.  131: 709– 712. Google Scholar CrossRef Search ADS PubMed  Calsamiglia S. Busquet M. Cardozo P. W. Castillejos L. Ferret A. 2007. Invited review: Essential oils as modifiers of rumen microbial fermentation. J. Dairy Sci.  90: 2580– 2595. Google Scholar CrossRef Search ADS PubMed  Camacho-Barquero L. Villegas I. Sánchez J. M. Talero E. Sáanchez-Fidalgo S. Motilva V. Alarcón de la Lastra C. 2007. Curcumin, a Curcuma longa constituent, acts on MAPK p38 pathway modulating COX-2 and iNOS expression in chronic experimental colitis. Int. Immunopharmacol.  7: 333– 342. Google Scholar CrossRef Search ADS PubMed  Che T. M. Johnson R. W. Kelley K. W. Van Alstine W. G. Dawson K. A. Moran C. A. Pettigrew J. E. 2011. Mannan oligosaccharide modulates gene expression profile in pigs experimentally infected with porcine reproductive and respiratory syndrome virus. J. Anim. Sci.  89: 3016– 3029. Google Scholar CrossRef Search ADS PubMed  Chen H. Huang H. 1998. Effect of curcumin on cell cycle progression and apoptosis in vascular smooth muscle cells. Br. J. Pharmacol.  124: 1029– 1040. Google Scholar CrossRef Search ADS PubMed  Churchill M. Chadburn A. Bilinski R. T. Bertagnolli M. M. 2000. Inhibition of intestinal tumors by curcumin is associated with changes in the intestinal immune cell profile. J. Surg. Res.  89: 169– 175. Google Scholar CrossRef Search ADS PubMed  Elkouby-Naor L. Ben-Yosef R. 2010. Functions of claudin tight junction proteins and their complex interactions in various physiological systems. Int. Rev. Cell Mol. Biol.  279: 1– 32. Google Scholar CrossRef Search ADS PubMed  Gentleman R. C. Carey V. J. Bates D. M. Bolstad B. Dettling M. Dudoit S. Ellis B. Gautier L. Ge Y. Gentry J. Hornik K. Hothorn T. Huner W. Iacus S. Irizarry R. Leisch F. Li C. Maechler M. Rossini A.J. Sawitzki G. Smith C. Smyth G. Tierney L. Yang J. Y. H. Zhang J. 2004. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol.  5: R80. Google Scholar CrossRef Search ADS PubMed  Goodman R. B. Forstrom J. W. Osborn S. G. Chi E. Y. Martin T. R. 1991. Identification of two neutrophil chemotactic peptides produced by porcine alveolar macrophage. J. Biol. Chem.  266: 8455– 8463. Google Scholar PubMed  Groenendijk M. Cantor R. M. de Bruin T. W. Dallinga-Thie G. M. 2001. The apoAI-CIII-AIV gene cluster. Atherosclerosis  157: 1– 11. Google Scholar CrossRef Search ADS PubMed  Hansson G. C 2012. Role of mucus layers in gut infection and inflammation. Curr. Opin. Microbiol.  15: 57– 62. Google Scholar CrossRef Search ADS PubMed  Hediger M. A. Romero M. F. Peng J. Rolfs A. Takanaga H. Bruford E. A. 2004. The ABCs of solute carriers: Physiological, pathological, and therapeutic implications of human membrane transport proteins. Pflugers Arch.  447: 465– 468. Google Scholar CrossRef Search ADS PubMed  Hinson E. R. Joshi N. S. Chen J. H. Rahner C. Jung Y. W. Wang X. Kaech S. M. Cresswell P. 2010. Viperin is highly induced I neutrophils and macrophages during acute and chronic lymphocytic choriomeningitis virus infection. J. Immunol.  184: 5723– 5731. Google Scholar CrossRef Search ADS PubMed  Hollingsworth M. A. Swanson B. J. 2004. Mucins in cancer: Protection and control of the cell surface. Nat. Rev. Cancer  4: 45– 60. Google Scholar CrossRef Search ADS PubMed  Huang D. W. Sherman B. T. Lempicki R. A. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.  4: 44– 57. Google Scholar CrossRef Search ADS PubMed  Jagetia G. C. Aggarwal B. B. 2007. “Spicing up” of the immune system by curcumin. J. Clin. Immunol.  27: 19– 35. Google Scholar CrossRef Search ADS PubMed  Jobin C. Bradham C. A. Russo M. P. Juma B. Narula A. S. Brenner D. A. Sartor R. B. 1999. Curcumin blocks cytokine-mediated NF-kappa B activation and proinflammatory gene expression by inhibiting inhibitory factor I-kappa B kinase activity. J. Immunol.  163: 3474– 3483. Google Scholar PubMed  Kim D. K. Lillehoj H. S. Lee S. H. Jang S. I. Bravo D. 2010. High-throughput gene expression analysis of intestinal intraepithelial lymphocytes after oral feeding of carvacrol, cinnamaldehyde, or capsicum oleoresin. Poult. Sci.  89: 68– 81. Google Scholar CrossRef Search ADS PubMed  Krishnaswamy K 2008. Traditional Indian spices and their health significance. Asia Pac. J. Clin. Nutr.  17: 265– 268. Google Scholar PubMed  Kyriakis J. M. Avruch J. 2012. Mammalian MAPK signal transduction pathways activated by stress and inflammation: A 10-year update. Physiol. Rev.  92: 689– 737. Google Scholar CrossRef Search ADS PubMed  Lee K.-W. Events H. Beynen A. C. 2004. Essential oils in broiler nutrition. Int. J. Poult. Sci.  3: 738– 752. Google Scholar CrossRef Search ADS   Li X. Liu X. 2005. Effect of curcumin on immune function of mice. J. Huazhong Univ. Sci. Technol. Med. Sci.  25: 137– 140. Google Scholar CrossRef Search ADS PubMed  Liu Y. Song M. Che T. M. Bravo D. Pettigrew J. E. 2012. Anti-inflammatory effects of several plant extracts on porcine alveolar macrophages in vitro. J. Anim. Sci.  90: 2774– 2783. Google Scholar CrossRef Search ADS PubMed  Liu Y. Song M. Che T. M. Almeida J. A. S. Lee J. J. Bravo D. Maddox C. W. Pettigrew J. E. 2013. Dietary plant extracts alleviate diarrhea and alter immune responses of weaned pigs experimentally infected with a pathogenic Escherichia coli. J. Anim. Sci.  91: 5294– 5306. Google Scholar CrossRef Search ADS PubMed  Luzio J. P. Pryor P. R. Bright N. A. 2007. Lysosomes: Fusion and function. Nat. Rev. Mol. Cell Biol.  8: 622– 632. Google Scholar CrossRef Search ADS PubMed  Ma T. Y. Iwamoto G. K. Hoa N. T. Akotia V. Pedram A. Boivin M. A. Said H. M. 2004. TNF-α-induced increase in intestinal epithelial tight junction permeability requires NF-κB activation. Am. J. Physiol. Gastrointest. Liver Physiol.  286: G367– G376. Google Scholar CrossRef Search ADS PubMed  MacDonald J. W 2005. Affycoretools: Functions useful for those doing repetitive analyses with Affymetrix Genchips. R. Package version 1.14.1.  www.bioconductor.org/packages/2.6/biol/html/affycoretools.html. (Accessed 12 August 2013.) Manzanilla E. G. Perez J. F. Martin M. Kramel C. Baucells F. Gasa J. 2004. Effect of plant extracts and formic acid on the intestinal equilibrium of early-weaned pigs. J. Anim. Sci.  82: 3210– 3218. Google Scholar CrossRef Search ADS PubMed  Manzanilla E. G. Nofrarías M. Anguita M. Castillo M. Perez J. F. Martín-Orúe S. M. Kamel C. Gasa J. 2006. Effects of butyrate, avilamycin, and a plant extract combination on the intestinal equilibrium of early-weaned pigs. J. Anim. Sci.  84: 2743– 2751. Google Scholar CrossRef Search ADS PubMed  Manzanilla E. G. Pérez J. F. Martin M. Blandón J. C. Baucells F. Gasa J. 2009. Dietary protein modifies effect of plant extracts in the intestinal ecosystem of the pig at weaning. J. Anim. Sci.  87: 2029– 2037. Google Scholar CrossRef Search ADS PubMed  Matsushita M 2010. Ficolins: Complement-activating lectins involved in innate immunity. J. Innate Immun.  2: 24– 32. Google Scholar CrossRef Search ADS PubMed  Mazumder A. Raghavan K. Weinstein J. Kohn K. W. Pommier Y. 1995. Inhibition of human immunodeficiency virus type-1 integrase by curcumin. Biochem. Pharmacol.  49: 1165– 1170. Google Scholar CrossRef Search ADS PubMed  McCarthy K. M. Skare I. B. Stankewich M. C. Furuse M. Tsukita S. Rogers R. A. Lynch R. D. Schneeberger E. E. 1996. Occludin is a functional component of the tight junction. J. Cell Sci.  109: 2287– 2298. Google Scholar PubMed  Micheau O. Tschopp J. 2003. Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell  114: 181– 190. Google Scholar CrossRef Search ADS PubMed  Michiels J. Missotten J. Van Hoorick A. Ovyn A. Fremaut D. De Smet D. Dierick N. 2010. Effects of dose and formulation of carvacrol and thymol on bacteria and some functional traits of the gut in piglets after weaning. Arch. Anim. Nutr.  64: 136– 154. Google Scholar CrossRef Search ADS PubMed  Negi P. S. Jayaprakasha G. K. Jagan Mohan Rao L. Sakariah K. K. 1999. Antibacterial activity of turmeric oil: A byproduct from curcumin manufacture. J. Agric. Food Chem.  47: 4297– 4300. Google Scholar CrossRef Search ADS PubMed  Neill C. R. Nelssen J. L. Tokach M. D. Goodband R. D. DeRouchey J. M. Dritz S. S. Groesbeck C. N. Brown R. B. 2006. Effects of oregano oil on growth performance of nursery pigs. J. Swine Health Prod.  14: 312– 316. Nishida K. Kamizato M. Kawai T. Masuda K. Takeo K. Teshima-Kondo S. Tanahashi T. Rokutan K. 2009. Interleukin-18 is a crucial determinant of vulnerability of the mouse rectum to psychosocial stress. FASEB J.  23: 1797– 1805. Google Scholar CrossRef Search ADS PubMed  Nofrarías M. Manzanilla E. G. Pujols J. Gibert X. Majó N. Segalés J. Gasa J. 2006. Effects of spray-dried porcine plasma and plant extracts on intestinal morphology and on leukocyte cell subsets of weaned pigs. J. Anim. Sci.  84: 2735– 2742. Google Scholar CrossRef Search ADS PubMed  NRC 1998. Nutrient requirements of swine. 10th rev. ed. Natl. Acad. Press, Washington, DC. Parkin J. Cohen B. 2001. An overview of the immune system. Lancet  357: 1777– 1789. Google Scholar CrossRef Search ADS PubMed  Petris M. J 2004. The SLC31 (Ctr) copper transporter family. Pflugers Arch.  447: 752– 755. Google Scholar CrossRef Search ADS PubMed  R Development Core Team 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing  Vienna, Austria. ISBN 3-900051-07-0. www.R-project.org. Radosevich M. Ono S. J. 2003. Novel mechanisms of class I major histocompatibility complex gene regulation. Immunol. Res.  27: 85– 105. Google Scholar CrossRef Search ADS PubMed  Riley-Vargas R. C. Gill D. B. Kemper C. Liszewski M. K. Atkinson J. P. 2004. CD46: Expanding beyond complement regulation. Trends Immunol.  25: 496– 503. Google Scholar CrossRef Search ADS PubMed  Sads O. R. Bilkei G. 2003. The effect of oregano and vaccination against Glasser's disease and pathogenic Escherichia coli on postweaning performance of pigs. Ir. Vet. J.  56: 611– 615. Sarma J. V. Ward P. A. 2011. The complement system. Cell Tissue Res.  343: 227– 235. Google Scholar CrossRef Search ADS PubMed  Shanmugam M. K. Kannaiyan R. Sethi G. 2011. Targeting cell signaling and apoptotic pathways by dietary agents: Role in the prevention and treatment of cancer. Nutr. Cancer  63: 161– 173. Google Scholar CrossRef Search ADS PubMed  Shirazi-Beechey S. P. Moran A. W. Bravo D. Al-Rammahi M. 2011. NONRUMINANT NUTRITION SYMPOSIUM: Intestinal glucose sensing and regulation of glucose absorption: Implications for swine nutrition. J. Anim. Sci.  89: 1854– 1862. Google Scholar CrossRef Search ADS PubMed  Shishodia S. Sethi G. Aggarwal B. B. 2005. Curcumin: Getting back to the roots. Ann. N. Y. Acad. Sci.  1056: 206– 217. Google Scholar CrossRef Search ADS PubMed  Simonson R. R 2004. Antimicrobial properties of herbs and spices and their potential use in diets for pigs. Newport Laboratories, Inc., Worthington, MN. Smyth G. K 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol.  3: 1– 26. Google Scholar CrossRef Search ADS   Solano-Aguilar G. I. Vengroski K. G. Beshah E. Lunney J. K. 2000. Isolation and purification of lymphocyte subsets from gut-associated lymphoid tissue in neonatal swine. J. Immunol. Methods.  241: 185– 199. Google Scholar CrossRef Search ADS PubMed  Takase S. Suruga K. Goda T. 2000. Regulation of vitamin A metabolism-related gene expression. Br. J. Nutr.  84: S217– S221. Google Scholar CrossRef Search ADS PubMed  Takeuchi O. Akira S. 2008. MDA5/RIG-1 and virus recognition. Curr. Opin. Immunol.  20: 17– 22. Google Scholar CrossRef Search ADS PubMed  Thoennissen N. H. O'Kelly J. Lu D. Iwanski G. B. La D. T. Abbassi S. Leiter A. Karlan B. Mehta R. Koeffler H. P. 2010. Capsaicin causes cell-cycle arrest and apoptosis in ER-positive and negative breast cancer cells by modulating the EGFR/HER-2 pathway. Oncogene  29: 285– 296. Google Scholar CrossRef Search ADS PubMed  Tsukita S. Furuse M. 1999. Occludin and claudins in tight-junction strands: Leading or supporting players? Trends Cell Biol.  9: 268– 273. Google Scholar CrossRef Search ADS PubMed  Twiss F. le Duc Q. van der Horst S. Tabdili H. van der Krogt G. Wang N. Rehmann H. Huveneers S. Leckband D. E. de Rooij J. 2012. Vinculin-dependent cadherin mechanosensing regulates efficient epithelial barrier formation. Biol. Open.  1: 1128– 1140. Google Scholar CrossRef Search ADS PubMed  Van Itallie C. Rahner C. Anderson J. M. 2001. Regulated expression of claudi-4 decreases paracellular conductance through a selective decrease in sodium permeability. J. Clin. Invest.  107: 1319– 1327. Google Scholar CrossRef Search ADS PubMed  Wang N. Wang G. Hao J. Ma J. Wang Y. Jiang X. Jiang H. 2012. Curcumin ameliorates hydrogen peroxide-induced epithelial barrier disruption by upregulating heme oxygenase-1 expression in human intestinal epithelial cells. Dig. Dis. Sci.  57: 1792– 1801. Google Scholar CrossRef Search ADS PubMed  Windisch W. Schedle K. Plitzer C. Kroismayr A. 2008. Use of phytogenic products as feed additives for swine and poultry. J. Anim. Sci.  86: E140– E148. Google Scholar CrossRef Search ADS PubMed  Wu Z. Irizarry R. A. 2005. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J. Comput. Biol.  12: 882– 893. Google Scholar CrossRef Search ADS PubMed  Yang Y 2003. Generation of major histocompatibility complex class I antigens. Microbes Infect.  5: 39– 47. Google Scholar CrossRef Search ADS PubMed  Yin T. Getsios S. Caldelari R. Godsel L. M. Kowalczyk A. P. Müller E. J. Green K. J. 2005. Mechanisms of plakoglobin-dependent adhesion: Desmosome-specific functions in assembly and regulation by epidermal growth factor receptor. J. Biol. Chem.  280: 40355– 40363. Google Scholar CrossRef Search ADS PubMed  Zaballos A. Gutiérrez J. Varona R. Ardavín C. Márquez G. 1999. Cutting edge: Identification of the orphan chemokine receptor GPR-9–6 as CCR9, the receptor for the chemokine TECK. J. Immunol.  162: 5671– 5675. Google Scholar PubMed  Footnotes 1 Financial support from Pancosma SA (Geneva, Switzerland) is greatly appreciated. American Society of Animal Science
TI - Effects of capsicum oleoresin, garlic botanical, and turmeric oleoresin on gene expression profile of ileal mucosa in weaned pigs
JF - Journal of Animal Science
DO - 10.2527/jas.2013-6496
DA - 2014-08-01
UR - https://www.deepdyve.com/lp/oxford-university-press/effects-of-capsicum-oleoresin-garlic-botanical-and-turmeric-oleoresin-oJBELNpnyh
SP - 3426
EP - 3440
VL - 92
IS - 8
DP - DeepDyve
ER -