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unpublished data
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Carstea, E.D.1
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1842357304
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note
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Patient DNA samples consist of a pan-ethnic selection from more than 40 NPC1 families whose genotype (4) and phenotype (3) were established. All patient and control DNA samples were obtained under the guidelines approved by clinical and research committees of the National Institutes of Health.
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11
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0030639315
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BAC DNA was subcloned into exon-trapping vectors pSPL3 and pTAG4 as described [D. B. Krizman et al., Methods Mol. Biol. 68, 167 (1997)].
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1842271607
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note
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Long-range polymerase chain reaction (PCR) was performed on a human fetal brain Marathon-Ready cDNA library with Advantage Klentaq Polymerase Mix (Clontech). An antisense primer, 5′-TATTCTGCACAGACACTGCATCGTG-3′, was designed on the basis of the 5′ sequence of EST clone H11600 (GenBank), and its reverse primer was provided by the manufacturer. Amplification products were subcloned into TA-vector (Invitrogen) and sequenced. For further 5′ extension from human Marathon-Ready cDNA libraries, additional antisense primers (5′-CGCTTGTTCCATCTTCAGCACCTCTGACAC-3′ 5′-CAGAAAGTGCGTGTGGTAATCGGCATACAC-3′, 5′-GTGCAGTTCGTGTTATACGGTGAAAGAGGG-3′) were designed from newly identified NPC1 sequence. Full-length NPC1 was generated by PCR amplification of human fibroblast and human ovary Marathon-Ready cDNA libraries, performed with 5′ untranslated region (UTR) primer 704F (5′-TGCTCCTGCTCCTCCGCTC-3′) or 87F (5′-AACCAGCCGAACGCCGCC-3′) paired with the 3′ UTR primer G-60 (5′-GTCCCTCATTTCATGCCACATC-3′. PCR products were cloned into expression vector pCR3.1 (Invitrogen). Orientation was determined by digestion with Sac I.
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14
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0021760092
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Molecular mass determinations were made with the GCG program PEPTIDESORT [J. Deveraux, P. Haeberil, O. Smithies, Nucleic Acids Res. 12, 387 (1984)]. PSORT {D. J. McGeogh, Virus Res. 3, 271 (1985), modified by K. Nakai and M. Kanehisa [Proteins Struct. Funct. Genet. 11, 95 (1991)} was used to detect signal peptide sequence. The same sequence was predicted by GCG-MOTIFS. TM domains were predicted with TMbase [K. Hofmann and W. Stoffel, Biol. Chem. Hoppe-Seyler 374, 166 (1993)] and the method described by P. Klein, M. Kanehisha, and C. DeLisi [Biochim. Biophys. Acta 815, 468 (1985)].
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Molecular mass determinations were made with the GCG program PEPTIDESORT [J. Deveraux, P. Haeberil, O. Smithies, Nucleic Acids Res. 12, 387 (1984)]. PSORT {D. J. McGeogh, Virus Res. 3, 271 (1985), modified by K. Nakai and M. Kanehisa [Proteins Struct. Funct. Genet. 11, 95 (1991)} was used to detect signal peptide sequence. The same sequence was predicted by GCG-MOTIFS. TM domains were predicted with TMbase [K. Hofmann and W. Stoffel, Biol. Chem. Hoppe-Seyler 374, 166 (1993)] and the method described by P. Klein, M. Kanehisha, and C. DeLisi [Biochim. Biophys. Acta 815, 468 (1985)].
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Molecular mass determinations were made with the GCG program PEPTIDESORT [J. Deveraux, P. Haeberil, O. Smithies, Nucleic Acids Res. 12, 387 (1984)]. PSORT {D. J. McGeogh, Virus Res. 3, 271 (1985), modified by K. Nakai and M. Kanehisa [Proteins Struct. Funct. Genet. 11, 95 (1991)} was used to detect signal peptide sequence. The same sequence was predicted by GCG-MOTIFS. TM domains were predicted with TMbase [K. Hofmann and W. Stoffel, Biol. Chem. Hoppe-Seyler 374, 166 (1993)] and the method described by P. Klein, M. Kanehisha, and C. DeLisi [Biochim. Biophys. Acta 815, 468 (1985)].
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Molecular mass determinations were made with the GCG program PEPTIDESORT [J. Deveraux, P. Haeberil, O. Smithies, Nucleic Acids Res. 12, 387 (1984)]. PSORT {D. J. McGeogh, Virus Res. 3, 271 (1985), modified by K. Nakai and M. Kanehisa [Proteins Struct. Funct. Genet. 11, 95 (1991)} was used to detect signal peptide sequence. The same sequence was predicted by GCG-MOTIFS. TM domains were predicted with TMbase [K. Hofmann and W. Stoffel, Biol. Chem. Hoppe-Seyler 374, 166 (1993)] and the method described by P. Klein, M. Kanehisha, and C. DeLisi [Biochim. Biophys. Acta 815, 468 (1985)].
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Molecular mass determinations were made with the GCG program PEPTIDESORT [J. Deveraux, P. Haeberil, O. Smithies, Nucleic Acids Res. 12, 387 (1984)]. PSORT {D. J. McGeogh, Virus Res. 3, 271 (1985), modified by K. Nakai and M. Kanehisa [Proteins Struct. Funct. Genet. 11, 95 (1991)} was used to detect signal peptide sequence. The same sequence was predicted by GCG-MOTIFS. TM domains were predicted with TMbase [K. Hofmann and W. Stoffel, Biol. Chem. Hoppe-Seyler 374, 166 (1993)] and the method described by P. Klein, M. Kanehisha, and C. DeLisi [Biochim. Biophys. Acta 815, 468 (1985)].
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32P]dCTP. Samples were subjected to electrophoresis on 0.6× tris-borate EDTA-buffered Mutation Detection Enhancement (MDE) (FMC Products, Rockland, ME) SSCP at 4 W for 14 hours. SSCP conformers were excised from the gel and reamplified by means of the original primer set. Reamplification products were sequenced (Applied Biosystems, Foster City, CA) and compared to normal controls.
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1842314819
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For transient transfection, DNA vectors 5-4 (704F/ G60), 8-1 (87F/G60), 1-1 (704F/G60), and antisense 7-5 (704F/G60) were extracted by alkaline lysis and CsCI gradient centrifugation. On day 0, NPC1 fibroblasts (GM-3123) were plated (70,000 cells per well) in Lab-Tek Chamber Slides (Nunc, Napeeville, IL). On day 1, lipofectamine transfection was done according to the manufacturer's recommendations (Gibco-BRL). On day 2, cells were rinsed once with phosphate-buffered saline, and Eagle's minimum essential medium containing 10% lipoprotein-deficient serum (LPDS) was then added to the cells for 36 hours and then replaced with LPDS medium with or without LDL (50 μg/ml) for 24 hours. The NPC1-genotyped cells were fixed, stained with filipin, and cytochemically viewed [E. J. Blanchette-Mackie et al., Proc. Natl. Acad. Sci. U.S.A. 85, 8022 (1988)]. For evaluation, 8 to 11 fields each consisting of ∼200 cells, were randomly selected and viewed with a 25× objective. Intense filipin fluorescence staining of cholesterol in perinuclear vacuoles was used as a marker of the lysosomal cholesterol accumulation characteristic of NP-C cells. Individual cells free of this intense fluorescence were scored as "corrected." Frequently, the corrected cells appeared in patches of two or more cells, and their lysosomes were often seen scattered throughout the cytoplasm. In untransfected, vector-only transfected, and antisense NPC1 transfected cultures, 1.9, 0.4, and 2.4%, respectively, of the mutant NPC1 cells showed no filipin staining of perinuclear vesicles. By contrast, in cultures transfected with the NPC1 vectors 5-4, 8-1, and 1-1, 23, 22, and 19% , respectively, of the mutant cells showed no filipin staining.
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1842358254
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note
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We thank D. Mosbrook and N. Dietrich for nucleotide sequencing, F. S. Collins for advice, E. A. Dawidowicz for many helpful discussions, D. Schoenberg for assistance in the preparation of the manuscript, and J. M. Trent for encouragement and mentoring. We thank the Ara Parseghian Medical Research Foundation and the National Niemann-Pick Disease Foundation for research support and the United Kingdom Niemann-Pick Foundation for helpful interactions. We foremost acknowledge the wisdom, courage, understanding, and faith of the Niemann-Pick C patients and their families who have made this work possible.
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