Metaproteomics of the Resistant Starch-fed Chronic Kidney Disease Rats
ABSTRACT: Background- Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction. Methods- Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins. Results - 5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved – with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Conclusions- Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.
Project description:Conventionally raised and germ-free newly weaned male Sprague-Dawley rats were fed a basal diet or a diet supplemented with digestion resistant carbohydrates in the form of inulin, resistant starch or konjac flour. Gene expression in colon tissue was measured to characterise interaction between food, microbes and host. 2 colour microarray, reference design. Biological replicates: 6 for all groups except for conventionally raised rats fed inulin, which consisted of 5 biological replicates
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.
Project description:The 791spin is the spinosad-selected strain derived from 791a, a laboratory strain derived from a multi-resistant field-collected sample of houseflies. The 791a strain proved highly resistant to pyrethroids and some anticholinesterases and showed some resistance to the chitin synthesis-disrupting larvicides.In order to understand the evolution of insecticide resistance, de novo assembly of a spinosad resistant housefly strain 791spin using 454 technology was initiated Transcriptome analysis of insecticide resistant housefly strain compared to susceptible strain
Project description:Sardinian alcohol-preferring (sP) and Sardinina alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. The project proposed to identify salivary markers distinguishing the two rat lines possibly correlated to alcohol preference, by a proteomic approach.
Project description:We use a genome wide transcriptomic approach to assess the effects of protein supplementation on gene expression in the small intestine of periparturient rats during a secondary infection with the rat nematode Nippostrongylus brasiliensis
Project description:Analysis of hormone effects on irradiated LBNF1 rat testes, which contain only somatic cells except for a few type A spermatgogonia. Rats were treated for 2 weeks with either sham treatment (group X), hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide, group XAF), testosterone supplementation (GnRH antagonist and testosterone, group XAT), and FSH supplementation ((GnRH antagonist, androgen receptor antagonist, and FSH, group XAFF). Results provide insight into identifying genes in the somatic testis cells regulated by testosterone, LH, or FSH. Experiment Overall Design: 14 Sample replicates of sham treatment, 11 Sample replicates of hormonal ablation, 5 Sample replicates of testosterone supplementation, and 5 Sample replicates of FSH supplementation were studied.
Project description:Conventionally raised and germ-free newly weaned male Sprague-Dawley rats were fed a basal diet or a diet supplemented with digestion resistant carbohydrates in the form of inulin, resistant starch or konjac flour. Gene expression in colon tissue was measured to characterise interaction between food, microbes and host. Overall design: 2 colour microarray, reference design. Biological replicates: 6 for all groups except for conventionally raised rats fed inulin, which consisted of 5 biological replicates
Project description:We used Affymetrix microarrays to investigate gene expression changes in the liver of lean female Zucker rats exposed to a normal diet supplemented with a rosemary extract rich in the diterpenic compound, carnosic acid (CA). The aim of this work was to determine whether the daily intake (with the standard diet) of the rosemary extract (RE) enriched in CA (40%) for 64 days exerted any modulatory effects, at the level of gene expression, in the liver of lean Zucker female rats. Female lean Zucker rats were randomly assigned to two experimental groups (n= 7 animals per group) as follows: (1) control group, fed a standard diet (CT); (2) treated group, fed a standard diet supplemented (0.05% w/w) with the RE rich in CA (RE). At the end of the experimental procedure (64 days), total RNA was extracted from the liver to compare differential gene expression between the two groups. Liver differential gene expression after 64 days of supplementation between the CT group and the RE group (effects of the extract supplementation).
Project description:Spatial regulation analysis across multiple condition comparisons revealed distinct patterns of gene expression. We combined these transcriptome data with spatial CNS data to produce the spatio-transcripto map of the ganglia chain. The Hirudo Medicinalis set of transcripts generated here provides a resource for gene discovery and gene regulation within the nervous system. In addition, the strategy for de novo assembly of transcriptome data presented here may be helpful in other similar transcriptome studies. Examination of 3 different ganglia in 3 different leeches.