Muscle fiber size, degree of central nucleation and percentage of fibrotic/necrotic tissue.

<p>A. Regenerating and hypertrophic fibers were mainly observed in the <i>mdx</i> mice. A dystrophin level depend trend towards wild type distribution was observed for <i>mdx-Xist</i>^Δhs mice where <15% dystrophin already resulted in improvement. B. Dystrophin levels between 15–30% and >30% resulted in a reduction of the percentage of centralized nuclei of 40% and 60% respectively. C. The quadriceps of all mice was significantly more severely affected compared to <i>Xist</i>^Δhs mice. D. The diaphragm was the most severely affected muscle with on average 20% fibrotic/necrotic tissue in <i>mdx</i> mice. All mice were significantly more severely affected compared to <i>Xist</i>^Δhs mice. <i>Mdx-Xist</i>^Δhs mice with >30% dystrophin had less fibrotic/necrotic tissue than <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice with <15% dystrophin, but this difference was only significant between both <i>mdx-Xist</i>^Δhs groups. # indicates a significant difference of that bar with all the other groups. Single asterisks indicate a <i>P</i><0.05 and double asterisks indicate a <i>P</i><0.01.</p

Expression of several genes involved in disease pathology.

<p>A and B. For most biomarkers a clear dystrophin level dependent restoration of gene expression levels was observed in the <i>mdx-Xist</i>^Δhs mice, where intermediate dystrophin levels resulted in low expression of genes involved in disease pathology. For some genes, dystrophin levels <15% were enough to reduce gene expression while for other genes >30% was necessary. C. In the heart, even dystrophin levels of <15% decreased expression of fibrotic biomarkers like <i>Timp-1</i>. Since the mice were young, no difference in expression levels in heart function was observed, except for <i>Nppa</i>. Double asterisks indicate a <i>P</i><0.01.</p

<i>Mdx-Xist</i>^Δhs mice.

<p>A. To breed mice with low dystrophin levels, female <i>Xist</i>^Δhs mice, carrying a mutation in the <i>Xist</i> promoter which coordinates X-inactivation, were crossed with dystrophin negative <i>mdx</i> males. During embryogenesis, the maternal X-chromosome encoding a functional dystrophin gene will be preferentially (60–90%) inactivated as a result of the mutated <i>Xist</i> promoter. The <i>Xist</i>^Δhs mice were a kind gift from N. Brockdorff (MRC Clinical Sciences Center, London, UK, current affiliation Department of Biochemistry, University of Oxford, UK). B. Picture of a representative Western blot. The percentage of dystrophin was determined for the quadriceps of all <i>mdx-Xist</i>^Δhs mice by Western blot (2–9 technical replicates per mouse). The percentage of individual mice was determined using a concentration curve made from wild type samples. Myosin was used as a loading control. C. Skewed X-inactivation resulted in dystrophin levels of 3–47% (mean 22.7, stdev 12.1, <i>n</i> = 24) (as determined by Western blot) in the female <i>mdx-Xist</i>^Δhs offspring. Each bar represents the dystrophin level of an individual mouse. The dystrophin levels of the individual mice belonging to the three dystrophin groups can be appreciated from this graph. D. Dystrophin levels determined by Western blot and manual counting of dystrophin positive fibers demonstrate a strong correlation (R = 0.97). E. Longitudinal sections of a quadriceps stained with dystrophin (green) and spectrin (red). From the pictures it can be appreciated that dystrophin expression is not homogeneously expressed across the fiber but rather confined to certain nuclear domains.</p

Exercise induced histopathology and biomarker gene expression.

<p>A. Wild type mice were less severely affected than <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice. Due to high variation between individual <i>mdx</i> mice, the difference between <i>mdx</i> and wild type mice was not significant. <i>Mdx-Xist</i>^Δhs mice had slightly less fibrotic tissue than <i>mdx</i> mice. B. No difference in expression of genes involved in disease pathology was found between <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice. Both mouse strains did differ significantly from wild type mice, of which the expression levels were low. Single and double asterisks indicate a <i>P</i><0.05 and <i>P</i><0.01, respectively. # Indicates a significant difference from all other groups, average dystrophin levels of <i>mdx-Xist</i>^Δhs mice was 21% (2%–45% median 25.8).</p

Functional performance measured directly after treadmill exercise.

<p>A. Longest hanging time with the two limb hanging test was achieved by wild type and <i>mdx-Xist</i>^Δhs mice which both performed significantly (<i>P</i><0.001) better than <i>mdx</i> mice. B. Fore limb grip strength of <i>mdx-Xist</i>^Δhs mice was significantly (<i>P</i><0.001) better than that of <i>mdx</i> mice. C. Wild type mice outperformed <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice on the rotarod, while no significant difference was observed between <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice. Average dystrophin level of <i>mdx-Xist</i>^Δhs mice was 21% (2%–45% median 25.8).</p

Serum and plasma biomarkers assessed before and directly after treadmill running.

<p>A. CK levels assessed before and directly after treadmill running. CK levels collected before exercise were significantly (<i>P</i><0.01) lower than those collected directly after exercise in <i>mdx-Xist</i>^Δhs and <i>mdx</i> mice. This exercise induced increase was absent in wild type mice. B. CK levels determined before exercise were significantly (<i>P</i><0.01) elevated in <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice compared to wild type, but this was less pronounced for the <i>mdx-Xist</i>^Δhs mice as <i>mdx</i> mice had significantly (<i>P</i><0.05) higher CK levels. C. Plasma collected directly after exercise contained extremely high CK levels, in both <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice but not in wild type mice. D. Serum levels of MMP-9 were elevated in <i>mdx</i> mice compared to <i>Xist</i>^Δhs mice at both 8 and 14 weeks of age, while levels were normalized in <i>mdx-Xist</i>^Δhs mice. E. TIMP-1 levels were elevated in serum of both <i>mdx</i> and <i>mdx-Xist</i>^Δhs mice. In wild type mice we found an age related increase of the serum TIMP-1 level. Interestingly, at the age of 8 weeks, levels of <i>mdx-Xist</i>^Δhs mice were significantly lower than those of <i>mdx</i> mice. F. <i>Mdx</i> mice had significantly elevated OPN levels compared to both wild type and <i>mdx-Xist</i>^Δhs at 8 weeks of age. Single asterisks indicate a <i>P</i><0.05, average dystrophin level of <i>mdx-Xist</i>^Δhs mice was 21% (2%–45% median 25.8).</p

Effect of post-mortem delay on N-terminal huntingtin protein fragments in human control and Huntington disease brain lysates

<div><p>Huntington disease is associated with elongation of a CAG repeat in the <i>HTT</i> gene that results in a mutant huntingtin protein. Several studies have implicated N-terminal huntingtin protein fragments in Huntington disease pathogenesis. Ideally, these fragments are studied in human brain tissue. However, the use of human brain tissue comes with certain unavoidable variables such as post mortem delay, artefacts from freeze-thaw cycles and subject-to-subject variation. Knowledge on how these variables might affect N-terminal huntingtin protein fragments in post mortem human brain is important for a proper interpretation of study results. The effect of post mortem delay on protein in human brain is known to vary depending on the protein of interest. In the present study, we have assessed the effect of post mortem delay on N-terminal huntingtin protein fragments using western blot. We mimicked post mortem delay in one individual control case and one individual Huntington disease case with low initial post mortem delay. The influence of subject-to-subject variation on N-terminal huntingtin fragments was assessed in human cortex and human striatum using two cohorts of control and Huntington disease subjects. Our results show that effects of post mortem delay on N-terminal huntingtin protein fragments are minor in our individual subjects. Additionally, one freeze-thaw cycle decreases the huntingtin western blot signal intensity in the cortex control subject, but does not introduce additional N-terminal huntingtin fragments. Our results suggest that subject-to-subject variation contributes more to variability in N-terminal huntingtin fragments than post mortem delay.</p></div

Comparison of N-terminal huntingtin fragments in human post mortem control and HD cortex and striatum tissue.

<p>Western blot analysis of (A) Cortex control subjects, (B) Cortex HD subjects, (C) Striatum control subjects and (D) Striatum HD subjects. Control and HD subjects were age, gender and post mortem delay matched. Upper blot: full length htt (fl htt). Middle and lower blot: N-terminal htt fragments with β-actin loading control. Arrows: position of bands associated with a post mortem delay related increase in intensity. kDa = Molecular weight in kilodaltons, Post mortem delay in hours (hr). High sensitivity: Blot analyzed at a higher viewing-sensitivity. mut = full length mutant htt, wt = full length wild-type htt.</p

Genome Annotation using Nanopublications: An Approach to Interoperability of Genetic Data

<p>With the wide spread use of Next Generation Sequencing (NGS) technologies, the primary bottleneck of genetic research has shifted from data production to data analysis. However, annotated datasets produced by different research groups are often in different formats, making genetic comparisons and integration with other datasets challenging and time consuming tasks. Here, we propose a new data interoperability approach that provides unambiguous (machine readable) description of genomic annotations based on a novel method of data publishing called nanopublication. A nanopublication is a schema built on top of existing semantic web technologies that consists of three components: an individual assertion (i.e., the genomic annotation); provenance (containing links to the experimental information and data processing steps); and publication info (information about data ownership and rights, allowing each genomic annotation to be citable and its scientific impact tracked ). We use nanopublications to demonstrate automatic interoperability between individual genomic annotations from the FANTOM5 consortium (transcription start sites) and the Leiden Open Variation Database (genetic variants). The nanopublications can also be integrated with the data of the other semantic web frameworks like COEUS. Exposing legacy information and new NGS data as nanopublications promises tremendous scaling advantages when integrating very large and heterogeneous genetic datasets.</p

PCR analysis of targeted clones and confirmation of deletion exon 52 on RNA level.

<p>Single ES clones were cultured in 96-well plates and DNA was isolated and used as template in a multiplex PCR. Here the exons 46, 51 and 52 of the <i>hDMD</i> gene were analysed where exon 46 and 51 are positive controls and exon 52 the target to be deleted. <b>A</b>) An example is shown where candidate samples 2 and 5 are of interest because they are negative for exon 52 but positive for the control exons. <b>B</b>) For a large number of clones additional fragments were found for exon 52, suggesting non-homologues end joining (NHEJ) of TALEN induced double stranded breaks <b>C</b>) Representative image of LR-PCR performed on DNA of sub-clones of four exon 52 negative clones (9B4, 10H2, 11C9 and 11E7). LR-PCR was performed with primers targeting intron 51 (outside the targeting arm) and blasticidin (only present after homologous recombination), to rule out loss of PCR primer recognition sites by NHEJ and to confirm true targeting. <b>D</b>) RT-PCR was performed for RNA isolated from embryoid bodies of selected clones. The different fragments were isolated, purified and Sanger sequence analysed. In the wild type situation exon 52 was present, whereas in the properly targeted clones exon 52 was not present. This confirmed the exon 52 deletion on RNA level.</p