Intramyocellular lipid and mitochondrial morphology.

<p>Data are presented as means ± SEM. IMCL, intramyocellular lipid.</p

Participant characteristics.

<p>Data are presented as means ± SEM.</p>A<p>Obese group data significantly different from lean group data, <i>P</i>≤0.01.</p>B<p>Obese group data significantly different from lean group data, <i>P</i>≤0.02.</p>C<p>Post-training significantly different from pre-training (main effect), <i>P</i>≤0.001.</p

Insulin signaling and lipid metabolite data.

<p>(<b>A</b>) Akt phosphorylation at Ser473 residue and GLUT4 protein content assessed by Western blot and (<b>B</b>) diacylglycerol and ceramide lipid content in skeletal muscle of lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. (<b>A</b>) p-Akt, Akt phosphorylation at Ser473; GLUT4, glucose transporter 4. Results were normalized to β-actin protein content. * <i>P</i>≤0.03 pre- <i>vs.</i> post-training (main effect).</p

Metabolic characteristics.

<p>Data are presented as means ± SEM.</p>A<p>Obese group data significantly different from lean group data, <i>P</i>≤0.04.</p>B<p>Obese group data significantly different from lean group data, <i>P</i>≤0.01.</p>C<p>Post-training significantly different from pre-training (main effect), <i>P</i>≤0.03.</p><p>2-h PG, 2-h plasma glucose; 2-h PI, 2-h plasma insulin; FFA, free fatty acid; FPG, fasting plasma glucose; FPI, fasting plasma insulin.</p

Transmission electron microscopy assessment of intramyocellular lipid and mitochondrial proximity.

<p>Representative electron micrographs of a skeletal muscle cell illustrating subsarcolemmal (<b>A</b>) and intermyofibrillar (<b>B</b>) intramyocellular lipid (IMCL) juxtaposed with mitochondria prior to (<b>A</b>,<b>B</b>) and following 12-wk endurance training (<b>C</b>,<b>D</b>). The micrographs (X6,500 magnification, scale bar: 1 µm) were obtained from a biopsy of the <i>vastus lateralis</i> muscle from an obese participant. Graph represents the proportion of IMCL juxtaposed with mitochondrial (i.e., the proportion of IMCL in contact with mitochondria) in subsarcolemmal and intermyofibrillar regions of skeletal muscle of lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. *<i>P</i>≤0.02 pre- <i>vs</i>. post-training (main effect).</p

Transmission electron microscopy assessment of intramyocellular lipid and mitochondrial content.

<p>Micrographs of a skeletal muscle cell illustrating subsarcolemmal (<b>A</b>) and intermyofibrillar (<b>B</b>) intramyocellular lipid (IMCL) and mitochondria prior to (<b>A</b>,<b>B</b>) and following 12-wk endurance training (<b>C</b>,<b>D</b>). Subsarcolemmal (SS) IMCL and mitochondria are located between the sarcolemma and the most superficial myofibrils. The intermyofibrillar (IMF) IMCL and mitochondria are located between parallel bundles of myofibrils. The micrographs (X6,500 magnification, scale bar: 1 µm) were obtained from a biopsy of the <i>vastus lateralis</i> muscle from an obese participant. L, intramyocellular lipid droplet; M, mitochondria, Z, Z-line. IMCL size (<b>E</b>), number (<b>F</b>), and density (<b>G</b>) in SS and IMF regions of skeletal muscle of lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. *<i>P</i>≤0.05 pre- <i>vs.</i> post-training (main effect). Mitochondria size (<b>H</b>), number (<b>I</b>), and density (<b>J</b>) in SS and IMF regions of skeletal muscle of lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. *<i>P</i>≤0.01 pre- <i>vs.</i> post-training (main effect).</p

Markers of mitochondrial function.

<p>(<b>A</b>) Mitochondrial protein content assessed by Western blot and (<b>B</b>) mitochondrial maximal enzyme activity in skeletal muscle of lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. (<b>A</b>) PGC-1α, peroxisome proliferator-activated receptor-γ coactivator-1α; CS, citrate synthase; COX, cytochrome <i>c</i> oxidase - subunits II and IV. Results were normalized to β-actin protein content. *<i>P</i>≤0.04 pre- <i>vs.</i> post-training (main effect). (<b>B</b>) CS, citrate synthase; COX, cytochrome <i>c</i> oxidase; SCHAD, short-chain β-hydroxyacyl-CoA dehydrogenase. *<i>P</i>≤0.03 pre- <i>vs.</i> post-training (main effect). (<b>C</b>) Mitochondrial DNA (mtDNA) copy number determined by real-time quantitative PCR using a TaqMan probe against NADH dehydrogenase 4 (ND4) and β-globin. mtDNA copy number was calculated as the ratio of ND4 to β-globin in skeletal muscle of lean (<i>n</i> = 3) and obese (<i>n</i> = 5) men prior to and following 12-wk endurance training. *<i>P</i> = 0.10 pre- <i>vs.</i> post-training (main effect).</p

Results of the oral glucose tolerance test.

<p>Mean plasma concentrations of glucose (<b>A</b>) and insulin (<b>B</b>) during a 75-g oral glucose tolerance test, and (<b>C</b>) the homeostasis model assessment index of insulin resistance (HOMA-IR) in lean (<i>n</i> = 9) and obese (<i>n</i> = 9) men prior to and following 12-wk endurance training. (<b>A</b>) <i>P</i> = 0.04 and <i>P</i> = 0.28 for the comparison of the areas under the curve for glucose (AUC_glucose) of lean and obese men, pre- and post-training, respectively. 2-hr plasma glucose concentration: *<i>P</i>≤0.01 lean <i>vs.</i> obese pre-training; † <i>P</i>≤0.01 pre- <i>vs.</i> post-training (main effect). (<b>B</b>) <i>P</i> = 0.02 and <i>P</i> = 0.02 for the comparison of the areas under the curve for insulin (AUC_insulin) of lean and obese men, pre- and post-training, respectively. Fasting plasma insulin concentration: *<i>P</i>≤0.03 lean <i>vs.</i> obese pre-training; 2-hr plasma insulin concentration: ^†<i>P</i>≤0.02 lean <i>vs.</i> obese pre-training; ^‡P = 0.07 pre- <i>vs.</i> post-training (main effect). (<b>C</b>) HOMA-IR was 68% higher in the obese <i>vs.</i> lean men pre-training and decreased by 17% post-training. *<i>P</i>≤0.02 lean <i>vs.</i> obese pre-training; <i>P</i> = 0.10 pre- <i>vs.</i> post-training (main effect).</p

Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concordance of targeted TCRB-Seq and ROP based on three TCGA samples from kidney renal clear cell carcinoma (KIRC). Table S4. RNA-seq datasets overview. Table S5. Genomic profile of unmapped reads reported for each dataset (S1, S2, S3). Table S6. Relative genomic abundance of microbial taxa at different levels of taxonomic classification after removal of reads with human origin (average over all samples of three tissues, performed for in-house RNA-Seqdata). Table S7. Genomic profile of unmapped reads across two SRA RNA-seq samples using ROP v1.0.8. Percentage for each category is calculated as a fraction from the total number of reads. (PDF 100 kb

Additional file 1: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Supplementary methods. (PDF 789 kb