UniFrac distances between sequencing methods.

<p>(A) Weighted and (B) unweighted UniFrac distances. Reads by 454 Standard chemistry were compared with technical replicates of the same DNAs sequenced by 454 Standard chemistry (Standard), with 454 Titanium chemistry (no trim), and with 454 Titanium chemistry with sequences trimmed at 270 bp (trim). ** p<0.01, **** p<0.0001</p

Association between coverage and the number of OTUs.

<p>(A) The number of OTUs sampled as a function of number of reads. The data points represent mean ± SD of five randomized samplings. (B) Coverage to detect OTU with different frequencies with ≥95% of confidence. The data points were estimated based on the binomial distribution (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016952#s4" target="_blank">Materials and Methods</a>). The x axis is shown in logarithmic scale.</p

Association between coverage and UniFrac distances at different coverage.

<p>(A) Weighted and (B) unweighted UniFrac distances. For ‘Between individuals’ each data point includes 36 distances calculated from 6 samples of individual B and 6 samples of individual C. For ‘Within same individual’ each data point includes 18 distances (9 within sample B and 9 within sample C). Mean ± SD.</p

UniFrac distances between the seven biopsies and two sampling types of stools.

<p>Weighted distances are shown in the cells below the diagonal and unweighted distances are shown above the diagonal. Significance was tested with each UniFrac distance between that of two extractions from the same anatomic region (Mean ± SD, weighted: 0.084±0.027, unweighted: 0.415±0.068).</p><p>* p<0.05,</p><p>** p<0.01,</p><p>*** p<0.001,</p><p>**** p<0.0001. Significant p values after Bonferroni correction ( =  1.67×10⁻³) are underlined.</p

Proportion of the top 4 bacterial classes in the six biopsies of two individuals by different extraction kits (Mini Kit and Stool Kit).

<p>Proportion of the top 4 bacterial classes in the six biopsies of two individuals by different extraction kits (Mini Kit and Stool Kit).</p

UniFrac distances between different PCR conditions.

<p>(A) Weighted and (B) unweighted UniFrac distances. UniFrac distances were calculated between the most used PCR condition (annealing temperature: 55°C and the number of cycle: 25 cycles) and three PCR conditions; the same PCR condition (technical replication), the PCR condition of more cycles (55°C and 35 cycles), and the PCR condition of lower annealing temperature (50°C and 25 cycles). * p<0.05, ** p<0.01</p

data_123801SNP

data_123801SN

BearUCE_with_PartitionsRob

Nexus file of 996,381 nucleotides of concatenated Ultra Conserved Elements sequences from polar, brown, and black bears and other carnivora

High-Resolution Mapping of a Genetic Locus Regulating Preferential Carbohydrate Intake, Total Kilocalories, and Food Volume on Mouse Chromosome 17

<div><p>The specific genes regulating the quantitative variation in macronutrient preference and food intake are virtually unknown. We fine mapped a previously identified mouse chromosome 17 region harboring quantitative trait loci (QTL) with large effects on preferential macronutrient intake-carbohydrate (<i>Mnic1</i>), total kilcalories (<i>Kcal2</i>), and total food volume (<i>Tfv1</i>) using interval-specific strains. These loci were isolated in the [C57BL/6J.CAST/EiJ-17.1<i>-(D17Mit19</i>-<i>D17Mit50)</i>; B6.CAST-17.1] strain, possessing a ∼40.1 Mb region of CAST DNA on the B6 genome. In a macronutrient selection paradigm, the B6.CAST-17.1 subcongenic mice eat 30% more calories from the carbohydrate-rich diet, ∼10% more total calories, and ∼9% more total food volume per body weight. In the current study, a cross between carbohydrate-preferring B6.CAST-17.1 and fat-preferring, inbred B6 mice was used to generate a subcongenic-derived F₂ mapping population; genotypes were determined using a high-density, custom SNP panel. Genetic linkage analysis substantially reduced the 95% confidence interval for <i>Mnic1</i> (encompassing <i>Kcal2</i> and <i>Tfv1</i>) from 40.1 to 29.5 Mb and more precisely established its boundaries. Notably, no genetic linkage for self-selected fat intake was detected, underscoring the carbohydrate-specific effect of this locus. A second key finding was the separation of two energy balance QTLs: <i>Mnic1/Kcal2/Tfv1</i> for food intake and a newly discovered locus regulating short term body weight gain. The <i>Mnic1/Kcal2/Tfv1</i> QTL was further de-limited to 19.0 Mb, based on the absence of nutrient intake phenotypes in subcongenic HQ17IIa mice. Analyses of available sequence data and gene ontologies, along with comprehensive expression profiling in the hypothalamus of non-recombinant, <i>cast/cast</i> and <i>b6/b6</i> F₂ controls, focused our attention on candidates within the QTL interval. <i>Zfp811</i>, <i>Zfp870</i>, and <i>Btnl6</i> showed differential expression and also contain stop codons, but have no known biology related to food intake regulation. The genes <i>Decr2</i>, <i>Ppard</i> and <i>Agapt1</i> are more appealing candidates because of their involvement in lipid metabolism and down-regulation in carbohydrate-preferring animals.</p></div

The critical <i>Mnic1/Kcal1</i>/<i>Tfv1</i> QTL region on mouse chromosome 17 was reduced to 19.0 Mb.

<p>Legend: Congenic and subcongenic strains with CAST/EiJ alleles introgressed on the wild type C57BL/6J (B6) or mutant C57BL/6J-<i>^hg/hg</i> genome are illustrated. Solid bars indicate CAST donor regions, open bars indicate B6 genotype, and hatched bars designate intervals of undetermined genotype, as defined by SNP or Mit markers (top). The fine-mapped interval encompassing carbohydrate-specific macronutrient intake (<i>Mnic1</i>; peak at 32.49 Mb), total kilocalories (<i>Kcal1</i>; peak at 27.19 Mb) and total food volume (<i>Tfv1</i>; peak at 27.10) is specified by the bar outlined in red.</p