Gene expression profiles in rat lung following intratracheal instillation with short size single-wall and multi-wall carbon nanotubes
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: Katsuhide Fujita
PROVIDER: E-GEOD-75148 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Gene expression profiling of the rat lung following intratracheal instillation with SWCNTs was employed to gain insights into these molecular events. We attempted to characterize time-dependent changes in the gene expression until 754 days after intratracheal instillation with SWCNTs suspensions at 0.2 mg (L-SWCNT) and 0.4 mg (H-SWCNT) injected dose per rat, and to identify the shift from the acute-phase to the chronic-phase phase on the basis of evaluation at the molecular level. Groups of nine-week-old male Wistar rats (n= 6 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml distilled water including 0.1% Triton X-100 as a single injection 0.1 mg (L-SWCNT) and 0.4 mg (H-SWCNT) SWCNTs/ rat). Control groups received 0.1% Triton X-100 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 M-BM-0C with a chow diet ad libitum, and dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days and 754 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2013-09-07 | E-GEOD-50664 | biostudies-arrayexpress
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs). We have prepared two types of dispersed the SWCNTs, namely relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2), and attempted to characterize time-dependent changes in the gene expression of lung tissues until 90 days after intratracheal instillation with SWCNTs suspensions at 0.4 mg injected dose per rat. Groups of nine-week-old male Wistar rats (n= 4 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml of 1.0mg/mL bovine serum albumin (BSA) as a single injection 0.4 mg SWCNTs/ rat. Control groups received 1.0mg/mL BSA (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 M-BM-0C with a chow diet ad libitum, and dissected at 1day, 3 days, 7 days, 30 days, and 90 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2014-09-17 | E-GEOD-61483 | biostudies-arrayexpress
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of single-wall carbon nanotubes (SWCNTs). Two kinds of the impurity-free singlewall carbon nanotubes (SWCNTs), CNT-1 or CNT-2 induced gene expression in rat alveolar macrophages were measured at 24 hours exposure to doses of 0.1mg/mL. The experiments were performed using control for each experiment (n=4).
2014-09-11 | E-GEOD-61319 | biostudies-arrayexpress
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the molecular level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physico-chemical properties of single-wall carbon nanotubes (SWCNTs). Three kinds of single-wall carbon nanotubes (SWCNTs), CNT-1, CNT-2 or CNT-3 induced gene expression in human alveolar epithelial cell lines were measured at 24 and 48 hours exposure to doses of 90.8μg/mL (CNT-1), 109.0μg/mL (CNT-2), and 77.0μg/mL (CNT-2). Three independent experiments were performed at each time (24 or 48 hours) using different untreated control for each experiment (n=4).
2012-09-25 | E-GEOD-41101 | biostudies-arrayexpress
Project description:Although various mechanisms have been inferred for combinatorial actions of multiple carcinogens, these mechanisms have not been well demonstrated in experimental carcinogenesis models. We evaluated mammary carcinogenesis initiated by combined exposure to various doses of radiation and chemical carcinogens. Female rats at 7 weeks of age were M-NM-3-irradiated (0.2M-bM-^@M-^S2 Gy) and/or exposed to 1-methyl-1-nitrosourea (20 or 40 mg/kg, single intraperitoneal injection) or 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (40 mg/kg/day by gavage for 10 days) and were observed until 50 weeks of age. The incidence of mammary carcinoma increased steadily as a function of radiation dose in the absence of chemicals; mathematical analysis supported an additive increase when radiation was combined with a chemical carcinogen, irrespective of the chemical species and its dose. Hras mutations were characteristic of carcinomas that developed after chemical carcinogen treatments and were overrepresented in carcinomas induced by the combination of radiation and MNU (but not PhIP), indicating an interaction of radiation and MNU at the level of initiation. The expression profiles of seven classifier genes, previously shown to distinguish two classes of rat mammary carcinomas, categorized almost all examined carcinomas that developed after individual or combined treatments with radiation (1 Gy) and chemicals as belonging to a single class; more comprehensive screening using microarrays and a separate test sample set failed to identify differences in gene expression profiles among these carcinomas. These results suggest that a complex, multilevel interaction underlies the combinatorial action of radiation and chemical carcinogens in the experimental model. Mammary cancers were from untreated rats (n = 3) and rats treated with radiation (1 Gy; n = 4), MNU (40 mg/kg; H-rasM-bM-^@M-^Smutated cancers, n = 5; H-rasM-bM-^@M-^Snonmutated cancers, n = 4), PhIP (H-rasM-bM-^@M-^Smutated, n = 1; H-rasM-bM-^@M-^Snonmutated, n = 3), radiation 1 Gy plus MNU (40 mg/kg; H-rasM-bM-^@M-^Smutated, n = 5; H-rasM-bM-^@M-^Snonmutated, n = 4) and radiation 1 Gy plus PhIP (H-rasM-bM-^@M-^Snonmutated , n = 4). Normal mammary tissues were from untreated rats (n = 3).
2013-08-29 | E-GEOD-44786 | biostudies-arrayexpress
Project description:Soyfoods have been drawn the interrest in the roles that reducing risk of cardiovascular disease. Among various components, isoflavones have been come to the attention as beneficial soy ingredients. To evaluate the effectiveness of isoflavone content in dietary soybean (Glycine max) on modulating lipid metabolism, hepatic gene expressions involved in lipid metabolism were analyzed in rats. An isoflavone-rich cultivar (Yukipirika) and a conventional cultivar (Fukuyutaka) were employed. A principal component analysis (PCA) of microarray data was used to summarize characteristics of the experimental groups. As a result, the characteristics of the diets were largely explained by the first principal component (PC1). Soybean content in the diets distinctly separated in PC1. In contrast, isoflavone content had little effect on the mRNA expression. The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data. Male Splague-Dawley rats were randomly divided into 4 groups and fed an experimental diet for 21 days. The experimental diets were as follows: a diet containing 200 g/kg casein (Cas, n=7); a diet containing two proteins derived equally from casein and Fukuyutaka (conventional cultiver soybean) (F10, n=7); a diet containing two proteins derived from casein and Yukipirika (high-isoflavone soybean) in the proportion of three parts to one (Y05, n=7); a diet containing two proteins derived equally from casein and Yukipirika (Y10, n=8). In each of the groups, five rats with average food intake were used for microarray analysis.
2016-08-01 | E-GEOD-67782 | biostudies-arrayexpress
Project description:Iron deficiency-induced anemia is generally a representative nutritional problem in most populations. We reported that the anemia due to dietary iron deficiency causes a variety of changes in nutrient metabolism, even leading to apoptosis as a result of associated endoplasmic reticulum (ER) stress in the rat liver. On the other hand, it appears that non-anemic iron-deficiency causes no serious problem because no appreciable down-regulation of hemoglobin synthesis occurs. Biochemically, iron is essential for activation of cytochrome-related enzymes and its deficiency should yield some physiological problems. We performed a comprehensive transcriptome analysis to define the effects of non-anemic iron deficiency on hepatic gene expression. Four-week-old rats were fed a low-iron diet (ca. 3 ppm iron) for 2 days. These rats were compared with those fed a control diet (48 ppm iron) by pair feeding. On day 3, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. Rats in the iron-deficient diet group, showed that their serum ferritin and iron levels decreased with an increase in the serum total iron binding capacity (TIBC) level, while the hemoglobin level was not changed. In the DNA microarray study, we identified 91 up-regulated and 186 down-regulated probe sets that characterized the iron-deficient diet group. In the up-regulated probe sets, genes involved in glucose and lipid metabolic processes were significantly enriched, whereas genes related to organic acid metabolic process, cellular ketone metabolic process, lipid metabolic process, oxidation reduction, response to drug, response to extracellular stimulus and gas transport were significantly enriched in the down-regulated probe sets. These results suggest that even the non-anemic iron-deficiency exerts various influences on nutrient metabolisms in the liver. Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 M-BM-1 1M-BM-0C and 40 M-BM-1 5% humidity with a 12-h light/dark cycle (light 08:00M-bM-^@M-^S20:00; dark 20:00M-bM-^@M-^S08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n = 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater.
2013-03-21 | E-GEOD-30533 | biostudies-arrayexpress
Project description:Transcription profiling of intestinal tissue from germ free rats mono-colonised with one of two strains of Lactobacillus fermentum; AGR1485 or AGR 1487 Two colour microarray, reference design. 2 treatments (AGR1485 or AGR1487) and 2 tissues analysed (colon or duodenum): Biological replicates: 6
2014-06-25 | E-GEOD-58777 | biostudies-arrayexpress
Project description:We have previously showed that whey protein hydrolysate (WPH) causes a greater increase in muscle protein synthesis than an identical composition of amino acids mixture does. The present study was conducted to investigate a comparative effect of WPH on gene expression. Male Sprague-Dawley rats subjected to a 2-h swimming exercise were administered either a carbohydrate-amino acid diet or a carbohydrate-WPH diet immediately after exercise. One hour after exercise, epitrochlearis muscle mRNA was sampled and subjected to DNA microarray analysis. As a result, ingestion of WPH altered 189 genes in considering the false discovery rate. Among the upregulated genes, 8 Gene Ontology (GO) terms were enriched, which included key elements in muscle repair after exercise such as Cd24, Ccl2, Ccl7 and Cxcl1. On the other hand, 9 GO terms were enriched in the gene sets downregulated by ingestion of WPH and these GO terms fell into 2 clusters, 'regulation of ATPase activity' and 'immune response'. Furthermore, we found that WPH activate the 2 upstream proteins, extracellular signal-regulated kinase 1/2 (ERK1/2) and hypoxia-inducible factor-1a (HIF-1a), which may act as key factors for regulation of gene expression. These results suggest that ingestion of WPH, compared to an identical composition of amino acid mixture, induces greater changes in the after-exercise gene expression profile via activation of the proteins, ERK1/2 and HIF-1a. Male Sprague-Dawley rats (5-week-old) with body weights of approximately 150 g each (CLEA Japan, Inc., Tokyo, Japan) were used in this study. Rats were maintained at 23 +/- 2C, with lights on from 8:00 to 20:00 and off from 20:00 to 8:00. Rats had free access to food (protein 23.6%, fat 5.3%, carbohydrate 54.4%, ash 6.1%, fiber 2.9%, moisture 7.7%, MF, Oriental Yeast Co., Ltd., Osaka, Japan) and water. After 2- or 3-day acclimation, the rats were pre-trained to swimming exercise for 3 days. One day before the experiment, they were fed 5 g of a restricted diet (MF, Oriental Yeast Co., Ltd., Osaka, Japan). On the day of the experiment, rats swam for 2 hours, with 4 rats swimming simultaneously in a barrel filled with water to a depth of 50 cm, allowing an average surface area of 400 cm2 for each animal. The water temperature was maintained at a constant of 35C. Immediately following exercise, rats were given one of two isoenergetic test solutions by gavage. These solutions contained 44 kJ in a four-test dose that represented about 15% of daily energy needs and included either a mixed meal containing carbohydrate and amino acid mixture (AAM) or a mixed meal containing carbohydrate and whey protein hydrolysate (WPH; Meiji Co., Ltd., Japan). This study was approved by the Animal Committee of Food Science Research Lab., Meiji Co., Ltd., with the animals receiving care according to the guidelines laid down by this committee.
2014-04-15 | E-GEOD-49486 | biostudies-arrayexpress
Project description:Iron is an essential nutritional element; its deficiency in the body causes nutritional problems and a decrease in iron storage that can lead to anemia. The liver not only stores iron but is an important metabolic target as well. Dietary iron deficiency is associated with changes in the metabolism of nutrients such as lipids. However, to the best of our knowledge, a global analysis detailing the consequences of iron deficiency in the body has not yet been reported. We performed a comprehensive transcriptome analysis using DNA microarray technology to reveal the effects of iron deficiency on hepatic gene expression. Four-week-old rats were fed an iron-deficient diet or a control diet for 16 days. On day 17, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. We identified 600 up-regulated and 500 down-regulated probe sets to characterize the iron-deficient diet group. The up-regulated probe sets contained genes for enzymes that are involved in cholesterol, amino acid, and glucose metabolisms, as well as in apoptosis. The down-regulated probe sets included genes for enzymes associated with lipid metabolism. Additionally, the 16-day iron-deficient diet induced anemia. Our gene expression analysis revealed that, as a result, cholesterol biosynthesis, gluconeogenesis, and apoptosis due to endoplasmic reticulum stress were accelerated, while fatty acid biosynthesis was suppressed by dietary iron deficiency. Our analysis also showed that cholesterol metabolism, including bile acid biosynthesis, was accelerated in the initial stages of cholesterol accumulation. Experiment Overall Design: Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n = 7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the ratsâ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia. Livers were then excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan). Blood hemoglobin level of rats fed an iron-deficient diet decreased significantly over the course of the feeding. On day 17, the hemoglobin level in the iron-deficient diet group was 42% of that of the control diet group (P < 0.01).
2009-07-11 | E-GEOD-16899 | biostudies-arrayexpress