The effect of dietary fat intake on hepatic gene expression in LG/J AND SM/J mice

Background The liver plays a major role in regulating metabolic homeostasis and is vital for nutrient metabolism. Identifying the genetic factors regulating these processes could lead to a greater understanding of how liver function responds to a high-fat diet and how that response may influence susceptibilities to obesity and metabolic syndrome. In this study we examine differences in hepatic gene expression between the LG/J and SM/J inbred mouse strains and how gene expression in these strains is affected by high-fat diet. LG/J and SM/J are known to differ in their responses to a high-fat diet for a variety of obesity- and diabetes-related traits, with the SM/J strain exhibiting a stronger phenotypic response to diet. Results Dietary intake had a significant effect on gene expression in both inbred lines. Genes up-regulated by a high-fat diet were involved in biological processes such as lipid and carbohydrate metabolism; protein and amino acid metabolic processes were down regulated on a high-fat diet. A total of 259 unique transcripts exhibited a significant diet-by-strain interaction. These genes tended to be associated with immune function. In addition, genes involved in biochemical processes related to non-alcoholic fatty liver disease (NAFLD) manifested different responses to diet between the two strains. For most of these genes, SM/J had a stronger response to the high-fat diet than LG/J. Conclusions These data show that dietary fat impacts gene expression levels in SM/J relative to LG/J, with SM/J exhibiting a stronger response. This supports previous data showing that SM/J has a stronger phenotypic response to high-fat diet. Based upon these findings, we suggest that SM/J and its cross with the LG/J strain provide a good model for examining non-alcoholic fatty liver disease and its role in metabolic syndrome

Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish

We thank Scott Colborne for his help in collecting bluegill, Dave Bridges for providing the R script to convert Ensemble IDs to stickleback homologs, and David Winter and Jeramia Ory for providing Python script used in the bioinformatics analyses. We thank Doug Haywick for producing Fig 1. We also thank Shawn Garner, Tim Hain, Lauren Kordonowy, and Lindsay Havens, and three anonymous reviewers for helpful comments on the manuscript.Bluegill sunfish (Lepomis macrochirus) are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental life history is fixed, whereas individuals who enter the cuckolder life history transition from sneaker to satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of the three male tactics and females during spawning to identify gene ontology (GO) categories and potential candidate genes associated with each tactic. We found that sneaker males had higher levels of gene expression differentiation compared to the other two male tactics. Sneaker males also had higher expression in ionotropic glutamate receptor genes, specifically AMPA receptors, compared to other males, which may be important for increased spatial working memory while attempting to cuckold parental males at their nests. Larger differences in gene expression also occurred among male tactics than between males and females. We found significant expression differences in several candidate genes that were previously identified in other species with ARTs and suggest a previously undescribed role for cAMP-responsive element modulator (crem) in influencing parental male behaviors during spawning.Yeshttp://www.plosone.org/static/editorial#pee

Biological Invasions on a Large Scale: Investigating the Spread of Baby’s Breath (\u3ci\u3eGypsophila paniculata\u3c/i\u3e) Across North America

PURPOSE: This study investigates the invasion of baby’s breath (Gypsophila paniculata) across North America, particularly the potential adaptations that allow it to succeed in harsh ecoregions, such as Washington sage-steppes and Michigan dune shores. SUBJECTS: A database of herbarium samples was compiled and analyzed. Tissue samples from nine current populations of invasive baby’s breath were collected from four U.S. states: Washington, North Dakota, Minnesota, and Michigan. Seeds were collected from two populations of special interest: Chelan, Washington and Petoskey, Michigan. METHODS AND MATERIALS: Samples were genotyped at 14 microsatellite loci to infer relatedness between populations. RNA-seq based transcriptomes were established for populations in Chelan, WA and Petoskey, MI. A germination growth trial was conducted between these two populations. ANALYSES: Using Bayesian and multivariate methods, the number of genetic clusters across the sampling area was established. FST and DST were used to examine genetic similarity among populations. Principal Coordinates Analysis was used to explore transcriptome data. A time-to-event analysis was conducted on germination data. RESULTS: Cluster analyses revealed two distinct genetic clusters. Surprisingly, Petoskey, MI clustered separately from other MI populations and was most closely related to WA populations. Transcriptome analysis comparing WA and MI populations shows differential expression of genes related to flowering time, drought response, and circadian rhythms. Germination trials show that seeds from WA germinate significantly faster than those collected in MI. CONCLUSIONS: Results suggest more than one invasion event of G. paniculata. Further analyses reveal potential adaptations that may help this invader succeed in diverse, harsh environments

G. paniculata color morph data files

This folder contains raw sequence files, fasta files for the color morphs & reference sequences, aligned files for MEGA, and the nexus file used to create the haplotype network in PopART

Data from: Brain transcriptional profiles of male alternative reproductive tactics and females in bluegill sunfish

Bluegill sunfish (Lepomis macrochirus) are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental life history is fixed, whereas individuals who enter the cuckolder life history transition from sneaker to satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of the three male tactics and females during spawning to identify gene ontology (GO) categories and potential candidate genes associated with each tactic. We found that sneaker males had higher levels of gene expression differentiation compared to the other two male tactics. Sneaker males also had higher expression in ionotropic glutamate receptor genes, specifically AMPA receptors, compared to other males, which may be important for increased spatial working memory while attempting to cuckold parental males at their nests. Larger differences in gene expression also occurred among male tactics than between males and females. We found significant expression differences in several candidate genes that were previously identified in other species with ARTs and suggest a previously undescribed role for cAMP-responsive element modulator (crem) in influencing parental male behaviors during spawning

Genetic Structure of Invasive Baby’s Breath (Gypsophila paniculata L.) Populations in a Michigan Dune System

Coastal sand dunes are dynamic ecosystems with elevated levels of disturbance and are highly susceptible to plant invasions. One invasive plant that is of concern to the Great Lakes system is Gypsophila paniculata L. (perennial baby’s breath). The presence of G. paniculata negatively impacts native species and has the potential to alter ecosystem dynamics. Our research goals were to (1) estimate the genetic structure of invasive G. paniculata along the Michigan dune system and (2) identify landscape features that influence gene flow in this area. We analyzed 12 populations at 14 nuclear and two chloroplast microsatellite loci. We found strong genetic structure among populations (global FST = 0.228), and pairwise comparisons among all populations yielded significant FST values. Results from clustering analysis via STRUCTURE and discriminant analysis of principal components (DAPC) suggest two main genetic clusters that are separated by the Leelanau Peninsula, and this is supported by the distribution of chloroplast haplotypes. Land cover and topography better explained pairwise genetic distances than geographic distance alone, suggesting that these factors influence the genetic distribution of populations within the dunes system. Together, these data aid in our understanding of how invasive populations move through the dune landscape, providing valuable information for managing the spread of this species

Heatmap of transcripts differentially expressed in at least one group comparison.

<p>Only transcripts with a log2 fold change of 1.5 or greater are included in the heatmap, representing 1,400 transcripts. Count values were averaged within each group and are scaled by row. Sneak = sneaker males, Sat = satellite males, Parent = parental males, Fem = females, NS_P = non-spawning parental males.</p

Alternative reproductive tactics of bluegill sunfish.

<p>This figure has been modified from Gross and Charnov [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167509#pone.0167509.ref035" target="_blank">35</a>] and Neff and Knapp [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167509#pone.0167509.ref036" target="_blank">36</a>]. Ages are based on data from Gross and Charnov [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167509#pone.0167509.ref035" target="_blank">35</a>] but may differ among populations [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167509#pone.0167509.ref033" target="_blank">33</a>].</p

Differentially expressed transcripts associated with each male mating tactic and females.

<p>Differentially expressed transcripts associated with each male mating tactic and females.</p