Electron micrographs of cultured DRG neurons from wild-type and <i>Nefl</i>^{<i>N98S/+</i>} mice.

<p>(A and B) EM of cell soma of wild-type. Fig B is a higher magnification view of the asterisk-labeled area in Fig A. Filamentous structures formed by intermediate filaments can been seen throughout the cell body, next to organelles such as mitochondria. (C) A longitudinal section of processes of <i>Nefl</i>^<i>+/+</i> DRG. Bundles of microtubules and intermediate filaments are running in parallel alongside the processes. (D and E) EM of cell soma of <i>Nefl</i>^{<i>N98S/+</i>} DRG. Fig E is a higher magnification view of the asterisk-labeled area in Fig D. Massive accumulation of disordered neurofilaments is observed in the soma of <i>Nefl</i>^{<i>N98S/+</i>} DRG (D). The density of neurofilaments is very high and few other cytoplasmic elements can be seen within the accumulations (E). (F) A longitudinal section of processes of <i>Nefl</i>^{<i>N98S/+</i>} DRG. An enlarged process area of disorganized filamentous accumulation can be seen. Scale bars = 2 μm (A and D) and 500 nm (B, C, E and F).</p

Immunofluorescence micrographs of cultured DRG neurons from <i>Nefl</i>^<i>+/+</i> and <i>Nefl</i>^{<i>N98S/+</i>} mice labeling NFL.

<p>(A and C) Low power views of DRG neurons from <i>Nefl</i>^<i>+/+</i> (A) and <i>Nefl</i>^{<i>N98S/+</i>} (C) mice. Note that in <i>Nefl</i>^{<i>N98S/+</i>} DRG neurons, the processes are characterized by large amounts of enlarged and bright particles along the processes, pointed by arrows (C). (B and D) High-magnification images of DRG neurons as seen in Fig A and C. Note the filamentous structure in <i>Nefl</i>^<i>+/+</i> DRG neuron (B). In contrast, disrupted neurofilament network and enlarged neurofilament particles (pointed by arrows) along the processes can be seen in <i>Nefl</i>^{<i>N98S/+</i>} DRG neurons (D). A low intensity image of DRG neurons pointed by the arrowhead is shown in the inset (D) that also shows the broken neurofilamentous network. <i>Nefl</i>^{<i>N98S/+</i>}, n = 8; <i>Nefl</i>^<i>+/+</i>, n = 5. Scale bars = 50 μm (A and C) and 25 μm (B and D).</p

Immunofluorescence micrographs of cultured DRG explants from wild-type and <i>Nefl</i>^{<i>N98S/+</i>} mice embryos (E15) labeling NFL.

<p>(A and C) Low power views of DRG explants from <i>Nefl</i>^<i>+/+</i> (A) and <i>Nefl</i>^{<i>N98S/+</i>} (C) embryos cultured on the laminin-coated coverslip for 3 days. (B) Higher magnification of the boxed area of wild-type DRG in Fig A. Note the processes are labeled quite uniformly with anti-NFL antibody. (D) Higher magnification of the boxed area of <i>Nefl</i>^{<i>N98S/+</i>} DRG in Fig C. Note the processes are characterized by a large amount of bright particles along the processes. 3 <i>Nefl</i>^<i>+/+</i> females bred with <i>Nefl</i>^{<i>N98S/+</i>} males were sacrificed, and embryos were collected and genotyped. DRG explants from those embryos were cultured. Embryos for <i>Nefl</i>^<i>+/+</i>, n = 10. Embryos for <i>Nefl</i>^{<i>N98S/+</i>}, n = 11. Scale bars = 500 μm (A and C) and 100 μm (B and D).</p

Electron micrographs of cross sections of DRG axons of wild-type and <i>Nefl</i>^{<i>N98S/+</i>} mice.

<p>(A, C and E) Low power views of DRG axons from <i>Nefl</i>^<i>+/+</i> (A) and <i>Nefl</i>^{<i>N98S/+</i>} (C and E) mice. (B) A high power view of the asterisk-labeled area in <i>Nefl</i>^<i>+/+</i> DRG axons from Fig A. Microtubules (pointed by an arrowhead) and neurofilaments (pointed by an arrow) are interspersed. (D) A high power view of the asterisk-labeled area in one cross section of <i>Nefl</i>^{<i>N98S/+</i>} DRG axons from Fig C. Neurofilaments are barely seen and replaced by more microtubules (pointed by an arrowhead). (F) A high power view of the asterisk-labeled area in another cross section of <i>Nefl</i>^{<i>N98S/+</i>} DRG axons from Fig E. Microtubules (pointed by an arrowhead) and barely any neurofilaments can be seen in this area. (G) A high power view of the diamond-labeled area in another cross section of <i>Nefl</i>^{<i>N98S/+</i>} DRG axons from Fig E. Neurofilaments are packed at high density in this area, almost exclusive of any other organelles. (E, F and G) Microtubules and other organelles are segregated from the neurofilament aggregates in this cross section of <i>Nefl</i>^{<i>N98S/+</i>} DRG axons. Scale bars = 500 nm (A, C and E) and 200 nm (B, D, F and G).</p

<i>Nefl</i>^{<i>N98S/+</i>} mice showing reduced protein levels of NFL in both triton-X 100 soluble and triton-X 100 insoluble fractions of cerebellum, DRG and spinal cord.

<p>A, D and G) Quantitative data from western blots of triton soluble fraction of cerebellum, DRG and spinal cord, respectively. The intensity of NFL was normalized to that of GAPDH. NFL levels in <i>Nefl</i>^<i>+/+</i> were further normalized to 100. (B, E and H) Quantitative data from western blots of triton insoluble fraction of cerebellum, DRG and spinal cord, respectively. NFL levels in <i>Nefl</i>^<i>+/+</i> were normalized to 100. (C, F and I) The ratio of triton soluble NFL to triton insoluble NFL in cerebellum, DRG and spinal cord, respectively. The ratio of <i>Nefl</i>^<i>+/+</i> was normalized to 100. A litter of 4 <i>Nefl</i>^<i>+/+</i> and 4 <i>Nefl</i>^{<i>N98S/+</i>} mice was used in this study. * <i>p</i> < 0.05.</p

Electron micrographs of DRG cell soma of wild-type and <i>Nefl</i>^{<i>N98S/+</i>} mice.

<p>(A and C) Low power views of cell soma of DRG from wild-type (A) and <i>Nefl</i>^{<i>N98S/+</i>} (C) mice. Note the large amount of aggregates throughout the soma of <i>Nefl</i>^{<i>N98S/+</i>} DRG (C). (B and D) High power views of asterisk-labeled areas in Fig A and C. The filamentous structure formed by intermediate filaments is pointed by the arrow in <i>Nefl</i>^<i>+/+</i> DRG (B). Massive accumulation of disordered neurofilaments is observed in <i>Nefl</i>^{<i>N98S/+</i>} DRG (D). The density of neurofilaments is very high and few other cytoplasmic elements can be seen within the aggregates. Scale bars = 2 μm (A and C) and 500 nm (B and D).</p

MOESM1 of Clinical utility of serum biomarkers in Duchenne muscular dystrophy

Additional file 1: Table S1. List of serum protein biomarkers indentified by mass spectrometry based proteome profiling and SomaScan technique References [44, 45]

Additional file 12: of Proteomic analysis of Medulloblastoma reveals functional biology with translational potential

Figure S8. Expression of HMAG1 isoforms in medulloblastoma tumors. a) Schematic representation of HMGA11 isoforms and Boxplots representing the mRNA expression levels for HMGA1 isoforms. b). Western blot of HMGA1 isoforms in the four medulloblastoma subgroups. Both HMAG1 isoforms are highly expressed in group 3 medulloblastoma. c) Kaplan–Meier survival curve shows that increased levels of HMGA1 are associated with poor survival in Group 3 Medulloblastoma. d) Expression level of HMGA1 is highly correlated with the expression of the oncogene MYC in Group 3 Medulloblastoma. (PDF 1.94 mb

Additional file 17: of Proteomic analysis of Medulloblastoma reveals functional biology with translational potential

Table S8. List of pathways representative for each medulloblastoma subgroup. (XLSX 72.6 kb

Additional file 11: of Proteomic analysis of Medulloblastoma reveals functional biology with translational potential

Figure S7. Expression of CALD1 isoforms in medulloblastoma tumors. The protein expression level of CALD1 isoforms in medulloblastoma subgroups is confirmed at the epigenetic (H3K27Ac Chip-seq) and mRNA level. a) Schematic representation of CALD1 isoforms. b) H3K27Ac Chip-seq genome tracks in medulloblastoma tumors. Active transcription region marks (H3K27Ac) are observed in the alternative transcription start site for the isoforms HeLa l-CaD I and II correlating with higher expression of these protein isoforms. c) Boxplots representing the mRNA expression levels for CALD1 isoforms. (PDF 2.2 mb