Gene Expression in Rats Fed a Western Diet
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE32312 | GEO | 2012/12/01
SECONDARY ACCESSION(S): PRJNA147299
REPOSITORIES: GEO
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Project description:Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments. Distal colon tissues from Sprague Dawley rats fed a variety of diets (see summary) were removed from RNAlater stabilisation reagent (Sigma, Australia) they had been stored in,, placed in 1 ml of TRIzol® Reagent (Invitrogen, Australia) and homogenised usingbeads (mix of 2.5 mm glass and 0.1 - 1.0 mm diameter silicon-zirconian beads) in a MiniBeadbeater-8 (BioSpec Products Inc., USA). Total RNA was extracted (using TRIzol® Reagent manufacturer's instructions) and further purified using RNAeasy mini spin columns (QIAGEN, Australia) with a DNase on-column digestion as per manufacturer's instructions.RNA integrity was checked using a Bioanalyzer 2100 (Agilent Technologies, USA) andquantified using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). RNA samples with insufficinet quality and quantity were not assayed. The numbers of rats arrayed from each diet were as follows: CON, 5;LAMS, 7; HAMS, 8; HAMSB, 9; LAW, 6; HAW , 8. This gives a total of 43 arrays.
2012-12-01 | E-GEOD-32312 | biostudies-arrayexpress
Project description:The starch, acting as the major energy-producing component of the daily diet, is the main carbohydrate in mammal nutrition. However, the nutritional value of starch can vary widely depending upon its source and site of digestion. The distinct physiological responses were previously observed both in human and other mammals, but still little is known about the underlying mechanisms regarding the metabolic shifts due to the intake of various dietary starches. Here, we assessed the overall metabolic changes in weaned pigs induced by different dietary starch sources at the transcriptome level. Sixteen weaned pigs (DurocÃLandraceÃYorkshire) were selected and randomly allotted to diets containing either wheat (WH) or cassava (CA) starch as the energy source (n=8). We measured serum metabolites and hormones and generated transcriptional profiles of liver. 648 genes in liver were differentially expressed in response to dietary starch sources. Pathway analysis indicated that dietary starch sources altered both carbohydrate and lipid metabolism in liver. In contrast, CA may be more healthful as dietary energy source than WH by down-regulating lipogenesis and steroidogenesis in liver. Sixteen weaned pigs (DurocÃLandraceÃYorkshire) with an average initial body weight of 7.37±0.25 kg were selected and randomly allotted to two dietary treatments (either wheat or cassava starch as the energy source) for 21 d. At the end of the trial, the liver tissue were collected for transcriptome analysis using Agilent porcine microarrays.
2010-09-09 | E-GEOD-20721 | biostudies-arrayexpress
Project description:Cereal crops accumulate starch in seeds as an energy reserve. Sucrose synthase (SuSy) plays an important role in grain starch synthesis. In this study, ZmSUS1 was transformed into maize inbred line KN5585, and transgenic plants were obtained. Compared with the control, the content and activity of SuSy were significantly increased, the amylose content in mature seeds of transgenic maize increased by 41.1-69.2%, the total starch content increased by 5.0-13.5%, The 100-grain weight increased by 19.0-26.2% and the average diameter of starch granules increased by 10.8-17.2%. These results indicated that overexpression of ZmSUS1 can significantly improve the traits of maize kernels and obtain new lines with high amylose content. It was also found that ZmSUS1 may increase the amylose content by regulating the expression of Shrunken2 (Sh2) and Brittle2 (Bt2) which encodes endosperm ADP-glucose pyrophosphorylase (AGPase) size subunits, and the expression of Granule bound starchsynthase1 (GBSS1) and Starch synthase1 (SS1) which encodes starch synthase. This study proved the important role of ZmSUS1 in maize starch synthesis, and provided a new technology strategy for improving corn starch content and yield.
2022-09-07 | GSE212465 | GEO
Project description:Resistant starches (RS) are dietary compounds processed by the gut microbiota into metabolites, such as butyrate, that are beneficial to the host. The production of butyrate by the microbiome appears to be affected by the plant source and type of RS as well as the individual’s microbiota. In this study, we used in vitro culture and metaproteomic methods to explore the consistency and variations in individual microbiome's functional responses to three types of RS - RS2(Hi Maize 260), RS3(Novelose 330) and RS4(Fibersym RW). Results showed that RS2 and RS3 significantly altered the levels of protein expression in the individual gut microbiomes, while RS4 did not result in significant protein changes. Significantly elevated protein groups were enriched in carbohydrate metabolism and transport functions of families Eubacteriaceae, Lachnospiraceae and Ruminococcaceae. In addition, Bifidobacteriaceae was significantly increased in response to RS3. We also observed taxon-specific enrichments of starch metabolism and pentose phosphate pathways corresponding to this family. Functions related to starch utilization, ABC transporters and pyruvate metabolism pathways were consistently increased in the individual microbiomes in response to RS2 and RS3; in contrast, the downstream butyrate producing pathway response varied. Our study confirm that different types of RS have markedly variable functional effects on the human gut microbiome, and also found considerable inter-individual differences in microbiome pathway responses.
2021-09-08 | PXD017907 | Pride
Project description:Waxy starch has an important influence on bread dough and the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. The waxy and non-waxy wheats had similar starch granule morphological features and developmental patterns, and similar amylopectin quality in the grain. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Dynamic transcriptional expression profiling of starch biosynthesis-related genes indicated similar transcriptional expression profiles in both cultivars. Our results revealed that phosphorylation modifications played critical roles in amylose and amylopectin biosynthesis, but the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
2017-10-30 | PXD002805 | Pride
Project description:Waxy starch has an important influence on the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and grain yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Our results revealed the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
2017-01-17 | PXD000646 | Pride
Project description:Diets rich in carbohydrates not only lead to obesity but also contribute to the liver metabolic diseases. Starch is the major energy source of the daily diet. However, little is known about the metabolic changes due to the intake of different dietary starches. Our aim was to assess the overall metabolic changes at the transcriptome level. Animal model was used, and a total of 16 weaned pigs were randomly allotted to two experimental diets containing either of cassava starch (CS) or maize starch (MS) during 21 days. At the end of the trial, liver tissues were sampled and used for analysis of digestive enzymes, metabolites and transcriptomes. The growth performance was not affected by dietary starch sources. However, CS-feeding significantly increased the serum insulin and cholesterol concentrations (P<0.05). The liver triglyceride and cholesterol content were both elevated by CS-feeding (P<0.05). Microarray analysis led to the identification of 648 genes differentially expressed in liver (P<0.05). The CS-feeding activated the transcription of lipogenic genes such as HMGR and FASN, but decreased the expression of lipolytic genes such as ACOX1, PPARA and FBP. The microarray results correlated well with the measurements of several key enzymes involved in hepatic lipid metabolisms. These results suggested that dietary starch source alters hepatic transcriptome in weaned pigs. The slowly digestible starch (i.e. MS) seemed to be more healthful for mammals as the dietary energy supplier by transcriptional down-regulation of lipogenesis and steroidogenesis.
2010-03-11 | GSE20721 | GEO
Project description:Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to adhere to and degrade RS. Sas20 is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based upon amino acid sequence. Here, we perform a structure-function analysis of Sas20 which features two discrete starch-binding domains separated by a flexible linker. Sas20 domain 1 has an N-terminal β-sandwich followed by a cluster of α-helices and captures the non-reducing end of maltooligosaccharides between these structural features. The crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical 1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose within starch granules. Affinity PAGE and isothermal titration calorimetry demonstrate both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd 20 M) but exhibit limited or no binding to cyclodextrins. Small angle x-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency.
2022-06-09 | PXD032013 | Pride
Project description:The gene expression profiling analyses by DNA chip showed that the gene expression pattern of mice fed resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone, respectively, modifying expression of genes related to aging regulation, cell differentiation, extracellular matrix, neurogenesis, or secretion. (1) Ctrl (The control mice fed a NFD in which the carbohydrate source was corn starch and sucrose), (2) RS (resveratrol mice fed a NFD in which the carbohydrate source was corn starch and sucrose except containing resveratrol), (3) DJ (Dongjin mice fed a NFD in which the corn starch and sucrose were replaced with Dongjin rice), and (4) DJ526 (DJ526 mice fed a NFD in which the corn starch and sucrose were replaced with the resveratrol-enriched rice DJ526)
2016-03-12 | E-GEOD-79109 | biostudies-arrayexpress
Project description:Objective: An altered gut bacterial composition is associated with the pathogenesis of type 1 diabetes and short-chain fatty acids are known to play a pivotal role in maintaining gut homeostasis. The effects of short-chain fatty acids on pancreatic islet cell function, insulin production and local immune-infiltration, however, remain elusive.Methods: Five-week-old female NOD mice were fed with an acetylated and butyrylated high-amylose maize-resistant starch (HAMSAB) or control diet for five consecutive weeks. The pancreata were harvested, islets isolated using collagenase, and dispersed into single cells by trypsin. Single-cell RNA sequencing was performed with 10x Chromium. The raw counts were analysed using RStudio with the Seurat package. Human embryonic stem cell-differentiated beta-like cells, mouse islets and INS-1E beta cell line were treated with acetate, butyrate and/or combination. Pro-inflammatory cytokines (IFN- + IL-1) were used for stress response and viability assays. Results: single-cell RNA sequencing analysis mapped the gene expression profiles of 4,301 and 4,113 individual islet cells from HAMSAB or HAMS fed mice, respectively. Cells were annotated into 11 clusters: 5 immune, 4 endocrine, acinar and endothelial cell types. The scRNA seq dataset indicated that T cells, B cells, macrophages, and dendritic cell subsets infiltrated the islets of Langerhans from both HAMSAB and HAMS-fed mice. Interestingly, HAMSAB induced an immune tolerogenic profile and lower cytotoxic Gzma+ CD8+ T cells. Moreover, HAMSAB maintained the expression of beta cell functional genes (i.e., Ins1, Ins2, G6pc2, Prlr and Iapp) and decreased the expression of genes associated with cellular stress (i.e., Fos, Impact, Stat1, Dusp1 and Hsp40/Dnajb1). Short-chain fatty acid treatment decreased pro-inflammatory cytokine-induced stress in mouse islets and INS-1E beta cells. In addition, HAMSAB preserved the identity of endocrine cells, evaluated by a decrease in dedifferentiated poly-hormonal cells expressing endocrine progenitor genes (MafA, Nfix). Importantly, short-chain fatty acids increased insulin levels in human embryonic stem cell-differentiated beta-like cells and improve transplantation outcome in NOD/SCID mice. Conclusions: Short-chain fatty acids prevent diabetes development in NOD mice, at least in part, by enhancing beta cell function and preserving the cell identity of endocrine cells under inflammatory-mediated autoimmune stress.
2024-01-18 | GSE234704 | GEO