Clinical characterisation of Becker muscular dystrophy patients predicts favourable outcome in exon-skipping therapy.

Science.gov (United States)

van den Bergen, J C; Schade van Westrum, S M; Dekker, L; van der Kooi, A J; de Visser, M; Wokke, B H A; Straathof, C S; Hulsker, M A; Aartsma-Rus, A; Verschuuren, J J; Ginjaar, H B

2014-01-01

Duchenne and Becker muscular dystrophy (DMD/BMD) are both caused by mutations in the DMD gene. Out-of-frame mutations in DMD lead to absence of the dystrophin protein, while in-frame BMD mutations cause production of internally deleted dystrophin. Clinically, patients with DMD loose ambulance around the age of 12, need ventilatory support at their late teens and die in their third or fourth decade due to pulmonary or cardiac failure. BMD has a more variable disease course. The disease course of patients with BMD with specific mutations could be very informative to predict the outcome of the exon-skipping therapy, aiming to restore the reading-frame in patients with DMD. Patients with BMD with a mutation equalling a DMD mutation after successful exon skipping were selected from the Dutch Dystrophinopathy Database. Information about disease course was gathered through a standardised questionnaire. Cardiac data were collected from medical correspondence and a previous study on cardiac function in BMD. Forty-eight patients were included, representing 11 different mutations. Median age of patients was 43 years (range 6-67). Nine patients were wheelchair users (26-56 years). Dilated cardiomyopathy was present in 7/36 patients. Only one patient used ventilatory support. Three patients had died at the age of 45, 50 and 76 years, respectively. This study provides mutation specific data on the course of disease in patients with BMD. It shows that the disease course of patients with BMD, with a mutation equalling a 'skipped' DMD mutation is relatively mild. This finding strongly supports the potential benefit of exon skipping in patients with DMD.

Nucleobase-modified antisense oligonucleotides containing 5-(phenyltriazol)-2′-deoxyuridine nucleotides induce exon-skipping

DEFF Research Database (Denmark)

Le, Bao T.; Hornum, Mick; Sharma, Pawan K.

2017-01-01

Chemically-modified antisense oligonucleotide-mediated exon-skipping has been validated as a therapeutic strategy for tackling several disease pathologies, particularly duchenne muscular dystrophy. To date, only sugar-modified and internucleotide linkage-modified oligonucleotide chemistries have...

Long-Term Efficacy of Systemic Multiexon Skipping Targeting Dystrophin Exons 45–55 With a Cocktail of Vivo-Morpholinos in Mdx52 Mice

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Yusuke Echigoya

2015-01-01

Full Text Available Antisense-mediated exon skipping, which can restore the reading frame, is a most promising therapeutic approach for Duchenne muscular dystrophy. Remaining challenges include the limited applicability to patients and unclear function of truncated dystrophin proteins. Multiexon skipping targeting exons 45–55 at the mutation hotspot of the dystrophin gene could overcome both of these challenges. Previously, we described the feasibility of exons 45–55 skipping with a cocktail of Vivo-Morpholinos in vivo; however, the long-term efficacy and safety of Vivo-Morpholinos remains to be determined. In this study, we examined the efficacy and toxicity of exons 45–55 skipping by intravenous injections of 6 mg/kg 10-Vivo-Morpholino cocktail (0.6 mg/kg each vPMO every 2 weeks for 18 weeks to dystrophic exon-52 knockout (mdx52 mice. Systemic skipping of the entire exons 45–55 region was induced, and the Western blot analysis exhibited the restoration of 5–27% of normal levels of dystrophin protein in skeletal muscles, accompanied by improvements in histopathology and muscle strength. No obvious immune response and renal and hepatic toxicity were detected at the end-point of the treatment. We demonstrate our new regimen with the 10-Vivo-Morpholino cocktail is effective and safe for long-term repeated systemic administration in the dystrophic mouse model.

Exon skipping and translation in patients with frameshift deletions in the dystrophin gene

Energy Technology Data Exchange (ETDEWEB)

Sherratt, T.G.; Dubowitz, V.; Sewry, C.A.; Strong, P.N. (Royal Postgraduate Medical School, London (United Kingdom)); Vulliamy, T. (Hammersmith Hospital, London (United Kingdom))

1993-11-01

Although many Duchenne muscular dystrophy patients have a deletion in the dystrophin gene which disrupts the translational reading frame, they express dystrophin in a small proportion of skeletal muscle fibers ([open quotes]revertant fibers[close quotes]). Antibody studies have shown, indirectly, that dystrophin synthesis in revertant fibers is facilitated by a frame-restoring mechanism; in the present study, the feasibility of mRNA splicing was investigated. Dystrophin transcripts were analyzed in skeletal muscle from individuals possessing revertant fibers and a frameshift deletion in the dystrophin gene. In each case a minor in-frame transcript was detected, in which exons adjacent to those deleted from the genome had been skipped. There appeared to be some correlation between the levels of in-frame transcripts and the predicted translation products. Low levels of alternatively spliced transcripts were also present in normal muscle. The results provide further evidence of exon skipping in the dystrophin gene and indicate that this may be involved in the synthesis of dystrophin by revertant fibers. 44 refs., 12 figs.

A duchenne muscular dystrophy gene hot spot mutation in dystrophin-deficient cavalier king charles spaniels is amenable to exon 51 skipping.

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Gemma L Walmsley

2010-01-01

Full Text Available Duchenne muscular dystrophy (DMD, which afflicts 1 in 3500 boys, is one of the most common genetic disorders of children. This fatal degenerative condition is caused by an absence or deficiency of dystrophin in striated muscle. Most affected patients have inherited or spontaneous deletions in the dystrophin gene that disrupt the reading frame resulting in unstable truncated products. For these patients, restoration of the reading frame via antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach. The major DMD deletion "hot spot" is found between exons 45 and 53, and skipping exon 51 in particular is predicted to ameliorate the dystrophic phenotype in the greatest number of patients. Currently the mdx mouse is the most widely used animal model of DMD, although its mild phenotype limits its suitability in clinical trials. The Golden Retriever muscular dystrophy (GRMD model has a severe phenotype, but due to its large size, is expensive to use. Both these models have mutations in regions of the dystrophin gene distant from the commonly mutated DMD "hot spot".Here we describe the severe phenotype, histopathological findings, and molecular analysis of Cavalier King Charles Spaniels with dystrophin-deficient muscular dystrophy (CKCS-MD. The dogs harbour a missense mutation in the 5' donor splice site of exon 50 that results in deletion of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein. Antisense oligonucleotide-mediated skipping of exon 51 in cultured myoblasts from an affected dog restored the reading frame and protein expression.Given the small size of the breed, the amiable temperament and the nature of the mutation, we propose that CKCS-MD is a valuable new model for clinical trials of antisense oligonucleotide-induced exon skipping and other therapeutic approaches for DMD.

Long-term Exon Skipping Studies With 2′-O-Methyl Phosphorothioate Antisense Oligonucleotides in Dystrophic Mouse Models

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Christa L Tanganyika-de Winter

2012-01-01

Full Text Available Antisense-mediated exon skipping for Duchenne muscular dystrophy (DMD is currently tested in phase 3 clinical trials. The aim of this approach is to modulate splicing by skipping a specific exon to reframe disrupted dystrophin transcripts, allowing the synthesis of a partly functional dystrophin protein. Studies in animal models allow detailed analysis of the pharmacokinetic and pharmacodynamic profile of antisense oligonucleotides (AONs. Here, we tested the safety and efficacy of subcutaneously administered 2′-O-methyl phosphorothioate AON at 200 mg/kg/week for up to 6 months in mouse models with varying levels of disease severity: mdx mice (mild phenotype and mdx mice with one utrophin allele (mdx/utrn+/−; more severe phenotype. Long-term treatment was well tolerated and exon skipping and dystrophin restoration confirmed for all animals. Notably, in the more severely affected mdx/utrn+/− mice the therapeutic effect was larger: creatine kinase (CK levels were more decreased and rotarod running time was more increased. This suggests that the mdx/utrn+/− model may be a more suitable model to test potential therapies than the regular mdx mouse. Our results also indicate that long-term subcutaneous treatment in dystrophic mouse models with these AONs is safe and beneficial.

Skipping of exon 27 in C3 gene compromises TED domain and results in complete human C3 deficiency.

Science.gov (United States)

da Silva, Karina Ribeiro; Fraga, Tatiana Rodrigues; Lucatelli, Juliana Faggion; Grumach, Anete Sevciovic; Isaac, Lourdes

2016-05-01

Primary deficiency of complement C3 is rare and usually associated with increased susceptibility to bacterial infections. In this work, we investigated the molecular basis of complete C3 deficiency in a Brazilian 9-year old female patient with a family history of consanguinity. Hemolytic assays revealed complete lack of complement-mediated hemolytic activity in the patient's serum. While levels of the complement regulatory proteins Factor I, Factor H and Factor B were normal in the patient's and family members' sera, complement C3 levels were undetectable in the patient's serum and were reduced by at least 50% in the sera of the patient's parents and brother. Additionally, no C3 could be observed in the patient's plasma and cell culture supernatants by Western blot. We also observed that patient's skin fibroblasts stimulated with Escherichia coli LPS were unable to secrete C3, which might be accumulated within the cells before being intracellularly degraded. Sequencing analysis of the patient's C3 cDNA revealed a genetic mutation responsible for the complete skipping of exon 27, resulting in the loss of 99 nucleotides (3450-3549) located in the TED domain. Sequencing of the intronic region between the exons 26 and 27 of the C3 gene (nucleotides 6690313-6690961) showed a nucleotide exchange (T→C) at position 6690626 located in a splicing donor site, resulting in the complete skipping of exon 27 in the C3 mRNA. Copyright © 2016. Published by Elsevier GmbH.

Muscle function recovery in golden retriever muscular dystrophy after AAV1-U7 exon skipping.

Science.gov (United States)

Vulin, Adeline; Barthélémy, Inès; Goyenvalle, Aurélie; Thibaud, Jean-Laurent; Beley, Cyriaque; Griffith, Graziella; Benchaouir, Rachid; le Hir, Maëva; Unterfinger, Yves; Lorain, Stéphanie; Dreyfus, Patrick; Voit, Thomas; Carlier, Pierre; Blot, Stéphane; Garcia, Luis

2012-11-01

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder resulting from lesions of the gene encoding dystrophin. These usually consist of large genomic deletions, the extents of which are not correlated with the severity of the phenotype. Out-of-frame deletions give rise to dystrophin deficiency and severe DMD phenotypes, while internal deletions that produce in-frame mRNAs encoding truncated proteins can lead to a milder myopathy known as Becker muscular dystrophy (BMD). Widespread restoration of dystrophin expression via adeno-associated virus (AAV)-mediated exon skipping has been successfully demonstrated in the mdx mouse model and in cardiac muscle after percutaneous transendocardial delivery in the golden retriever muscular dystrophy dog (GRMD) model. Here, a set of optimized U7snRNAs carrying antisense sequences designed to rescue dystrophin were delivered into GRMD skeletal muscles by AAV1 gene transfer using intramuscular injection or forelimb perfusion. We show sustained correction of the dystrophic phenotype in extended muscle areas and partial recovery of muscle strength. Muscle architecture was improved and fibers displayed the hallmarks of mature and functional units. A 5-year follow-up ruled out immune rejection drawbacks but showed a progressive decline in the number of corrected muscle fibers, likely due to the persistence of a mild dystrophic process such as occurs in BMD phenotypes. Although AAV-mediated exon skipping was shown safe and efficient to rescue a truncated dystrophin, it appears that recurrent treatments would be required to maintain therapeutic benefit ahead of the progression of the disease.

Dynamics of co-transcriptional pre-mRNA folding influences the induction of dystrophin exon skipping by antisense oligonucleotides.

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Keng Boon Wee

Full Text Available Antisense oligonucleotides (AONs mediated exon skipping offers potential therapy for Duchenne muscular dystrophy. However, the identification of effective AON target sites remains unsatisfactory for lack of a precise method to predict their binding accessibility. This study demonstrates the importance of co-transcriptional pre-mRNA folding in determining the accessibility of AON target sites for AON induction of selective exon skipping in DMD. Because transcription and splicing occur in tandem, AONs must bind to their target sites before splicing factors. Furthermore, co-transcriptional pre-mRNA folding forms transient secondary structures, which redistributes accessible binding sites. In our analysis, to approximate transcription elongation, a "window of analysis" that included the entire targeted exon was shifted one nucleotide at a time along the pre-mRNA. Possible co-transcriptional secondary structures were predicted using the sequence in each step of transcriptional analysis. A nucleotide was considered "engaged" if it formed a complementary base pairing in all predicted secondary structures of a particular step. Correlation of frequency and localisation of engaged nucleotides in AON target sites accounted for the performance (efficacy and efficiency of 94% of 176 previously reported AONs. Four novel insights are inferred: (1 the lowest frequencies of engaged nucleotides are associated with the most efficient AONs; (2 engaged nucleotides at 3' or 5' ends of the target site attenuate AON performance more than at other sites; (3 the performance of longer AONs is less attenuated by engaged nucleotides at 3' or 5' ends of the target site compared to shorter AONs; (4 engaged nucleotides at 3' end of a short target site attenuates AON efficiency more than at 5' end.

A novel mutation in SURF1 causes skipping of exon 8 in a patient with cytochrome c oxidase-deficient leigh syndrome and hypertrichosis

Czech Academy of Sciences Publication Activity Database

Williams, S. L.; Taanman, J. W.; Hansíková, H.; Houšťková, H.; Chowdhury, Subir; Zeman, J.; Houštěk, Josef

2001-01-01

Roč. 73, č. 4 (2001), s. 340-343 ISSN 1096-7192 R&D Projects: GA MŠk LN00A079; GA ČR GA302/99/0648; GA MZd NE6533 Grant - others:The Wellcome Trust(XX) 048410 Institutional research plan: CEZ:AV0Z5011922 Keywords : SURF1 * exon skipping * mitochondrial disorder Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.345, year: 2001

Antisense PMO found in dystrophic dog model was effective in cells from exon 7-deleted DMD patient.

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Takashi Saito

Full Text Available BACKGROUND: Antisense oligonucleotide-induced exon skipping is a promising approach for treatment of Duchenne muscular dystrophy (DMD. We have systemically administered an antisense phosphorodiamidate morpholino oligomer (PMO targeting dystrophin exons 6 and 8 to a dog with canine X-linked muscular dystrophy in Japan (CXMD(J lacking exon 7 and achieved recovery of dystrophin in skeletal muscle. To date, however, antisense chemical compounds used in DMD animal models have not been directly applied to a DMD patient having the same type of exon deletion. We recently identified a DMD patient with an exon 7 deletion and tried direct translation of the antisense PMO used in dog models to the DMD patient's cells. METHODOLOGY/PRINCIPAL FINDINGS: We converted fibroblasts of CXMD(J and the DMD patient to myotubes by FACS-aided MyoD transduction. Antisense PMOs targeting identical regions of dog and human dystrophin exons 6 and 8 were designed. These antisense PMOs were mixed and administered as a cocktail to either dog or human cells in vitro. In the CXMD(J and human DMD cells, we observed a similar efficacy of skipping of exons 6 and 8 and a similar extent of dystrophin protein recovery. The accompanying skipping of exon 9, which did not alter the reading frame, was different between cells of these two species. CONCLUSION/SIGNIFICANCE: Antisense PMOs, the effectiveness of which has been demonstrated in a dog model, achieved multi-exon skipping of dystrophin gene on the FACS-aided MyoD-transduced fibroblasts from an exon 7-deleted DMD patient, suggesting the feasibility of systemic multi-exon skipping in humans.

Exon silencing by UAGG motifs in response to neuronal excitation.

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Ping An

2007-02-01

Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

Stemcell Information: SKIP000837 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 50-59 Male ... Yes No TPB11(DNAVEC) is iPSC line reprogrammed from a Parkinson disease patient's T-cells, wh... SKIP000837 ... Diseased TPB11 (DNAVEC) TPB11 (DNAVEC) ... 家族性パーキンソン病 ... G20 ... ...ich deleated exon 6 and 7 in parkin gene.DNAVEC: SeV vectors, which were produced by DNAVEC Corp.(Cytotune). パーキンソン

Stemcell Information: SKIP000838 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 50-59 Male ... Yes No TPB27(DNAVEC) is iPSC line reprogrammed from a Parkinson disease patient's T-cells, wh... SKIP000838 ... Diseased TPB27 (DNAVEC) TPB27 (DNAVEC) ... 家族性パーキンソン病 ... G20 ... ...ich deleated exon 6 and 7 in parkin gene.DNAVEC: SeV vectors, which were produced by DNAVEC Corp.(Cytotune). パーキンソン

Stemcell Information: SKIP000836 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 50-59 Male ... Yes No TPB8(DNAVEC) is iPSC line reprogrammed from a Parkinson disease patient's T-cells, which... SKIP000836 ... Diseased TPB8 (DNAVEC) TPB8 (DNAVEC) ... 家族性パーキンソン病 ... G20 ... ... deleated exon 6 and 7 in parkin gene.DNAVEC: SeV vectors, which were produced by DNAVEC Corp.(Cytotune). パーキンソン

Stemcell Information: SKIP000835 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 50-59 Male ... Yes No TPB4(DNAVEC) is iPSC line reprogrammed from a Parkinson disease patient's T-cells, which... SKIP000835 ... Diseased TPB4 (DNAVEC) TPB4 (DNAVEC) ... 家族性パーキンソン病 ... G20 ... ... deleated exon 6 and 7 in parkin gene.DNAVEC: SeV vectors, which were produced by DNAVEC Corp.(Cytotune). パーキンソン

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues [v2; ref status: indexed, http://f1000r.es/2dl

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Liliana Florea

2013-11-01

Full Text Available Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina’s Human Body Map project (>2.5 billion reads.  Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60% were novel, involving new exons (~3000, new introns (~16000, or both. When tracing these events across the sixteen tissues, only a small number (4-7% appeared to be differentially expressed (‘switched’ between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared.  Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository (http://zenodo.org/record/7068; doi:10.5281/zenodo.7068 and from our web site http://ccb.jhu.edu/software/ASprofile.

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues [v1; ref status: indexed, http://f1000r.es/1p0

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Liliana Florea

2013-09-01

Full Text Available Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina’s Human Body Map project (>2.5 billion reads.  Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60% were novel, involving new exons (~3000, new introns (~16000, or both. When tracing these events across the sixteen tissues, only a small number (4-7% appeared to be differentially expressed (‘switched’ between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared.  Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository (http://zenodo.org/record/7068; doi:10.5281/zenodo.7068 and from our web site http://ccb.jhu.edu/software/ASprofile.

Splicing of phenylalanine hydroxylase (PAH) exon 11 is vulnerable - Molecular pathology of mutations in PAH exon 11

DEFF Research Database (Denmark)

Heintz, Caroline; Dobrowolski, Steven F.; Andersen, Henriette Skovgaard

2012-01-01

as a vulnerable exon and used patient derived lymphoblast cell lines and PAH minigenes to study the molecular defect that impacted pre-mRNA processing. We showed that the c.1144T>C and c.1066-3C>T mutations cause exon 11 skipping, while the c.1139C>T mutation is neutral or slightly beneficial. The c.1144T......In about 20-30% of phenylketonuria (PKU) patients, phenylalanine (Phe) levels can be controlled by cofactor 6R-tetrahydrobiopterin (BH(4)) administration. The phenylalanine hydroxylase (PAH) genotype has a predictive value concerning BH(4)-response and therefore a correct assessment of the mutation...... molecular pathology is important. Mutations that disturb the splicing of exons (e.g. interplay between splice site strength and regulatory sequences like exon splicing enhancers (ESEs)/exon splicing silencers (ESSs)) may cause different severity of PKU. In this study, we identified PAH exon 11...

Deletion of exon 26 of the dystrophin gene is associated with a mild Becker muscular dystrophy phenotype

DEFF Research Database (Denmark)

Witting, Nanna; Duno, Morten; Vissing, John

2011-01-01

With the possible introduction of exon skipping therapy in Duchenne muscular dystrophy, it has become increasingly important to know the role of each exon of the dystrophin gene to protein expression, and thus the phenotype. In this report, we present two related men with an unusually mild BMD...... skipping therapy for Duchenne muscular dystrophy. This report also shows that BMD may present with a normal CK....... associated with an exon 26 deletion. The proband, a 23-year-old man, had slightly delayed motor milestones, walking 1 1/2 years old. He had no complaints of muscle weakness, but had muscle pain. Clinical examination revealed no muscle wasting or loss of power, but his CK was 1500-7000 U/l. Muscle biopsy...

Abnormal splicing switch of DMD's penultimate exon compromises muscle fibre maintenance in myotonic dystrophy.

Science.gov (United States)

Rau, Frédérique; Lainé, Jeanne; Ramanoudjame, Laetitita; Ferry, Arnaud; Arandel, Ludovic; Delalande, Olivier; Jollet, Arnaud; Dingli, Florent; Lee, Kuang-Yung; Peccate, Cécile; Lorain, Stéphanie; Kabashi, Edor; Athanasopoulos, Takis; Koo, Taeyoung; Loew, Damarys; Swanson, Maurice S; Le Rumeur, Elisabeth; Dickson, George; Allamand, Valérie; Marie, Joëlle; Furling, Denis

2015-05-28

Myotonic Dystrophy type 1 (DM1) is a dominant neuromuscular disease caused by nuclear-retained RNAs containing expanded CUG repeats. These toxic RNAs alter the activities of RNA splicing factors resulting in alternative splicing misregulation and muscular dysfunction. Here we show that the abnormal splicing of DMD exon 78 found in dystrophic muscles of DM1 patients is due to the functional loss of MBNL1 and leads to the re-expression of an embryonic dystrophin in place of the adult isoform. Forced expression of embryonic dystrophin in zebrafish using an exon-skipping approach severely impairs the mobility and muscle architecture. Moreover, reproducing Dmd exon 78 missplicing switch in mice induces muscle fibre remodelling and ultrastructural abnormalities including ringed fibres, sarcoplasmic masses or Z-band disorganization, which are characteristic features of dystrophic DM1 skeletal muscles. Thus, we propose that splicing misregulation of DMD exon 78 compromises muscle fibre maintenance and contributes to the progressive dystrophic process in DM1.

Dual Myostatin and Dystrophin Exon Skipping by Morpholino Nucleic Acid Oligomers Conjugated to a Cell-penetrating Peptide Is a Promising Therapeutic Strategy for the Treatment of Duchenne Muscular Dystrophy

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Alberto Malerba

2012-01-01

Full Text Available The knockdown of myostatin, a negative regulator of skeletal muscle mass may have important implications in disease conditions accompanied by muscle mass loss like cancer, HIV/AIDS, sarcopenia, muscle atrophy, and Duchenne muscular dystrophy (DMD. In DMD patients, where major muscle loss has occurred due to a lack of dystrophin, the therapeutic restoration of dystrophin expression alone in older patients may not be sufficient to restore the functionality of the muscles. We recently demonstrated that phosphorodiamidate morpholino oligomers (PMOs can be used to re-direct myostatin splicing and promote the expression of an out-of-frame transcript so reducing the amount of the synthesized myostatin protein. Furthermore, the systemic administration of the same PMO conjugated to an octaguanidine moiety (Vivo-PMO led to a significant increase in the mass of soleus muscle of treated mice. Here, we have further optimized the use of Vivo-PMO in normal mice and also tested the efficacy of the same PMO conjugated to an arginine-rich cell-penetrating peptide (B-PMO. Similar experiments conducted in mdx dystrophic mice showed that B-PMO targeting myostatin is able to significantly increase the tibialis anterior (TA muscle weight and when coadministered with a B-PMO targeting the dystrophin exon 23, it does not have a detrimental interaction. This study confirms that myostatin knockdown by exon skipping is a potential therapeutic strategy to counteract muscle wasting conditions and dual myostatin and dystrophin skipping has potential as a therapy for DMD.

The Splicing Efficiency of Activating HRAS Mutations Can Determine Costello Syndrome Phenotype and Frequency in Cancer.

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Anne-Mette Hartung

2016-05-01

Full Text Available Costello syndrome (CS may be caused by activating mutations in codon 12/13 of the HRAS proto-oncogene. HRAS p.Gly12Val mutations have the highest transforming activity, are very frequent in cancers, but very rare in CS, where they are reported to cause a severe, early lethal, phenotype. We identified an unusual, new germline p.Gly12Val mutation, c.35_36GC>TG, in a 12-year-old boy with attenuated CS. Analysis of his HRAS cDNA showed high levels of exon 2 skipping. Using wild type and mutant HRAS minigenes, we confirmed that c.35_36GC>TG results in exon 2 skipping by simultaneously disrupting the function of a critical Exonic Splicing Enhancer (ESE and creation of an Exonic Splicing Silencer (ESS. We show that this vulnerability of HRAS exon 2 is caused by a weak 3' splice site, which makes exon 2 inclusion dependent on binding of splicing stimulatory proteins, like SRSF2, to the critical ESE. Because the majority of cancer- and CS- causing mutations are located here, they affect splicing differently. Therefore, our results also demonstrate that the phenotype in CS and somatic cancers is not only determined by the different transforming potentials of mutant HRAS proteins, but also by the efficiency of exon 2 inclusion resulting from the different HRAS mutations. Finally, we show that a splice switching oligonucleotide (SSO that blocks access to the critical ESE causes exon 2 skipping and halts proliferation of cancer cells. This unravels a potential for development of new anti-cancer therapies based on SSO-mediated HRAS exon 2 skipping.

Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease

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Lorena Suarez-Artiles

2018-01-01

Full Text Available Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing. Using predictive bioinformatics tools, we selected thirteen missense mutations and one synonymous mutation based on their potential effects on splicing regulatory elements or splice sites. These mutations were analyzed in a minigene splicing assay. Results of the RNA analysis showed that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation c.741G>T; p.(Trp247Cys generated splicing silencer sequences and disrupted splicing enhancer motifs that resulted in skipping of exon 9, while mutations c.2581G>A; p.(Ala861Thr and c.2581G>C; p.(Ala861Pro abolished a 5′ splice site leading to skipping of exon 23. Mutation c.741G>T represents the first OCRL exonic variant outside the conserved splice site dinucleotides that results in alteration of pre-mRNA splicing. Our results highlight the importance of evaluating the effects of OCRL exonic mutations at the mRNA level.

Deletion of exon 26 of the dystrophin gene is associated with a mild Becker muscular dystrophy phenotype

DEFF Research Database (Denmark)

Witting, Nanna; Duno, Morten; Vissing, John

2011-01-01

With the possible introduction of exon skipping therapy in Duchenne muscular dystrophy, it has become increasingly important to know the role of each exon of the dystrophin gene to protein expression, and thus the phenotype. In this report, we present two related men with an unusually mild BMD...... calf hypertrophy was noted. Creatine kinase was normal or raised maximally to 500 U/l. The muscle biopsy was myopathic with increased fiber size variation and many internal nuclei, but no dystrophy. No comorbidity was found. In both cases, western blot showed a reduced dystrophin band. Genetic...... skipping therapy for Duchenne muscular dystrophy. This report also shows that BMD may present with a normal CK....

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

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Maayan Amit

2012-05-01

Full Text Available During evolution segments of homeothermic genomes underwent a GC content increase. Our analyses reveal that two exon-intron architectures have evolved from an ancestral state of low GC content exons flanked by short introns with a lower GC content. One group underwent a GC content elevation that abolished the differential exon-intron GC content, with introns remaining short. The other group retained the overall low GC content as well as the differential exon-intron GC content, and is associated with longer introns. We show that differential exon-intron GC content regulates exon inclusion level in this group, in which disease-associated mutations often lead to exon skipping. This group's exons also display higher nucleosome occupancy compared to flanking introns and exons of the other group, thus “marking” them for spliceosomal recognition. Collectively, our results reveal that differential exon-intron GC content is a previously unidentified determinant of exon selection and argue that the two GC content architectures reflect the two mechanisms by which splicing signals are recognized: exon definition and intron definition.

Modulation of splicing of the preceding intron by antisense oligonucleotide complementary to intra-exon sequence deleted in dystrophin Kobe

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Takeshima, Y.; Matuso, M.; Sakamoto, H.; Nishio, H. [Kobe Univ. School of Medicine and Science (Japan)

1994-09-01

Molecular analysis of dystrophin Kobe showed that exon 19 of the dystrophin gene bearing a 52 bp deletion was skipped during splicing, although the known consensus sequences at the 5{prime} and 3{prime} splice site of exon 19 were maintained. These data suggest that the deleted sequence of exon 19 may function as a cis-acting factor for exact splicing for the upstream intron. To investigate this potential role, an in vitro splicing system using dystrophin precursors was established. A two-exon precursor containing exon 18, truncated intron 18, and exon 19 was accurately spliced. However, splicing of intron 18 was dramatically inhibited when wild exon 19 was replaced with mutated exon 19. Even though the length of exon 19 was restored to normal by replacing the deleted sequence with other sequence, splicing of intron 18 was not fully reactivated. Characteristically, splicing of intron 18 was inactivated more markedly when the replaced sequence contained less polypurine stretches. These data suggested that modification of the exon sequence would result in a splicing abnormality. Antisense 31 mer 2`-O-methyl ribonucleotide was targeted against 5{prime} end of deleted region of exon 19 to modulate splicing of the mRNA precursor. Splicing of intron 18 was inhibited in a dose- and time-dependent manner. This is the first in vitro evidence to show splicing of dystrophin pre-mRNA can be managed by antisense oligonucleotides. These experiments represent an approach in which antisense oligonucleotides are used to restore the function of a defective dystrophin gene in Duchenne muscular dystrophy by inducing skipping of certain exons during splicing.

Functional understanding of the diverse exon-intron structures of human GPCR genes.

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Hammond, Dorothy A; Olman, Victor; Xu, Ying

2014-02-01

The GPCR genes have a variety of exon-intron structures even though their proteins are all structurally homologous. We have examined all human GPCR genes with at least two functional protein isoforms, totaling 199, aiming to gain an understanding of what may have contributed to the large diversity of the exon-intron structures of the GPCR genes. The 199 genes have a total of 808 known protein splicing isoforms with experimentally verified functions. Our analysis reveals that 1301 (80.6%) adjacent exon-exon pairs out of the total of 1,613 in the 199 genes have either exactly one exon skipped or the intron in-between retained in at least one of the 808 protein splicing isoforms. This observation has a statistical significance p-value of 2.051762 * e(-09), assuming that the observed splicing isoforms are independent of the exon-intron structures. Our interpretation of this observation is that the exon boundaries of the GPCR genes are not randomly determined; instead they may be selected to facilitate specific alternative splicing for functional purposes.

An intronic variation in SLC52A1 causes exon skipping and transient riboflavin-responsive multiple acyl-CoA dehydrogenation deficiency

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Mosegaard, Signe; Bruun, Gitte Hoffmann; Flyvbjerg, Karen Freund

2017-01-01

Vitamin B2, riboflavin is essential for cellular function, as it participates in a diversity of redox reactions central to human metabolism, through its role as precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which are electron carriers. The electron...... site for the splice inhibitory hnRNP A1 protein and causes exon 4 skipping. Riboflavin deficiency and maternal malnutrition during pregnancy might have been the determining factor in the outcome of this case....... transfer flavoprotein (ETF) and its dehydrogenase (ETFDH), uses FAD as cofactor. The ETF and ETFDH are forming the electron transport pathway for many mitochondrial flavoprotein dehydrogenases involved in fatty acid, amino acid and choline metabolism. A variation in either ETF or ETFDH causes multiple acyl......-CoA dehydrogenation deficiency (MADD), but genetic variations in the riboflavin metabolism or transportation of riboflavin can also cause MADD. The most common variations are located in the riboflavin transporter 2 (RFVT2) and 3 (RFVT3), that are highly expressed in brain and intestinal tissues, respectively...

Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

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Calogero Raffaele A

2008-11-01

Full Text Available Abstract Background A new microarray platform (GeneChip® Exon 1.0 ST has recently been developed by Affymetrix http://www.affymetrix.com. This microarray platform changes the conventional view of transcript analysis since it allows the evaluation of the expression level of a transcript by querying each exon component. The Exon 1.0 ST platform does however raise some issues regarding the approaches to be used in identifying genome-wide alternative splicing events (ASEs. In this study an exon-level data analysis workflow is dissected in order to detect limit and strength of each step, thus modifying the overall workflow and thereby optimizing the detection of ASEs. Results This study was carried out using a semi-synthetic exon-skipping benchmark experiment embedding a total of 268 exon skipping events. Our results point out that summarization methods (RMA, PLIER do not affect the efficacy of statistical tools in detecting ASEs. However, data pre-filtering is mandatory if the detected number of false ASEs are to be reduced. MiDAS and Rank Product methods efficiently detect true ASEs but they suffer from the lack of multiple test error correction. The intersection of MiDAS and Rank Product results efficiently moderates the detection of false ASEs. Conclusion To optimize the detection of ASEs we propose the following workflow: i data pre-filtering, ii statistical selection of ASEs using both MiDAS and Rank Product, iii intersection of results derived from the two statistical analyses in order to moderate family-wise errors (FWER.

Alternative splicing of mutually exclusive exons--a review.

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Pohl, Martin; Bortfeldt, Ralf H; Grützmann, Konrad; Schuster, Stefan

2013-10-01

Alternative splicing (AS) of pre-mRNAs in higher eukaryotes and several viruses is one major source of protein diversity. Usually, the following major subtypes of AS are distinguished: exon skipping, intron retention, and alternative 3' and 5' splice sites. Moreover, mutually exclusive exons (MXEs) represent a rare subtype. In the splicing of MXEs, two (or more) splicing events are not independent anymore, but are executed or disabled in a coordinated manner. In this review, several bioinformatics approaches for analyzing MXEs are presented and discussed. In particular, we revisit suitable definitions and nomenclatures, and bioinformatics tools for finding MXEs, adjacent and non-adjacent MXEs, clustered and grouped MXEs. Moreover, the molecular mechanisms for splicing MXEs proposed in the literature are reviewed and discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A novel point mutation (G[sup [minus]1] to T) in a 5[prime] splice donor site of intron 13 of the dystrophin gene results in exon skipping and is responsible for Becker Muscular Dystrophy

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Hagiwara, Yoko; Nishio, Hisahide; Kitoh, Yoshihiko; Takeshima, Yasuhiro; Narita, Naoko; Wada, Hiroko; Yokoyama, Mitsuhiro; Nakamura, Hajime; Matsuo, Masafumi (Kobe Univ. School of Medicine (Japan))

1994-01-01

The mutations in one-third of Duchenne and Becker muscular dystrophy patients remain unknown, as they do not involve gross rearrangements of the dystrophin gene. The authors now report a defect in the splicing of precursor mRNA (pre-mRNA), resulting from a maternally inherited mutation of the dystrophin gene in a patient with Becker muscular dystrophy. This defect results from a G-to-T transversion at the terminal nucleotide of exon 13, within the 5[prime] splice site of intron 13, and causes complete skipping of exon 13 during processing of dystrophin pre-mRNA. The predicted polypeptide encoded by the aberrant mRNA is a truncated dystrophin lacking 40 amino acids from the amino-proximal end of the rod domain. This is the first report of an intraexon point mutation that completely inactivates a 5[prime] splice donor site in dystrophin pre-mRNA. Analysis of the genomic context of the G[sup [minus]1]-to-T mutation at the 5[prime] splice site supports the exon-definition model of pre-mRNA splicing and contributes to the understanding of splice-site selection. 48 refs., 5 figs.

Antisense Oligonucleotides Promote Exon Inclusion and Correct the Common c.-32-13T>G GAA Splicing Variant in Pompe Disease

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Erik van der Wal

2017-06-01

Full Text Available The most common variant causing Pompe disease is c.-32-13T>G (IVS1 in the acid α-glucosidase (GAA gene, which weakens the splice acceptor of GAA exon 2 and induces partial and complete exon 2 skipping. It also allows a low level of leaky wild-type splicing, leading to a childhood/adult phenotype. We hypothesized that cis-acting splicing motifs may exist that could be blocked using antisense oligonucleotides (AONs to promote exon inclusion. To test this, a screen was performed in patient-derived primary fibroblasts using a tiling array of U7 small nuclear RNA (snRNA-based AONs. This resulted in the identification of a splicing regulatory element in GAA intron 1. We designed phosphorodiamidate morpholino oligomer-based AONs to this element, and these promoted exon 2 inclusion and enhanced GAA enzyme activity to levels above the disease threshold. These results indicate that the common IVS1 GAA splicing variant in Pompe disease is subject to negative regulation, and inhibition of a splicing regulatory element using AONs is able to restore canonical GAA splicing and endogenous GAA enzyme activity.

First Exon Length Controls Active Chromatin Signatures and Transcription

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Nicole I. Bieberstein

2012-07-01

Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

A one base pair deletion in the canine ATP13A2 gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier.

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Anne Wöhlke

2011-10-01

Full Text Available Neuronal ceroid lipofuscinosis (NCL is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells. Tibetan terriers show a late-onset lethal form of NCL manifesting first visible signs at 5-7 years of age. Genome-wide association analyses for 12 Tibetan-terrier-NCL-cases and 7 Tibetan-terrier controls using the 127K canine Affymetrix SNP chip and mixed model analysis mapped NCL to dog chromosome (CFA 2 at 83.71-84.72 Mb. Multipoint linkage and association analyses in 376 Tibetan terriers confirmed this genomic region on CFA2. A mutation analysis for 14 positional candidate genes in two NCL-cases and one control revealed a strongly associated single nucleotide polymorphism (SNP in the MAPK PM20/PM21 gene and a perfectly with NCL associated single base pair deletion (c.1620delG within exon 16 of the ATP13A2 gene. The c.1620delG mutation in ATP13A2 causes skipping of exon 16 presumably due to a broken exonic splicing enhancer motif. As a result of this mutation, ATP13A2 lacks 69 amino acids. All known 24 NCL cases were homozygous for this deletion and all obligate 35 NCL-carriers were heterozygous. In a sample of 144 dogs from eleven other breeds, the c.1620delG mutation could not be found. Knowledge of the causative mutation for late-onset NCL in Tibetan terrier allows genetic testing of these dogs to avoid matings of carrier animals. ATP13A2 mutations have been described in familial Parkinson syndrome (PARK9. Tibetan terriers with these mutations provide a valuable model for a PARK9-linked disease and possibly for manganese toxicity in synucleinopathies.

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

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Awan, Ali R; Manfredo, Amanda; Pleiss, Jeffrey A

2013-07-30

Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in S. pombe reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.

The Splicing Efficiency of Activating HRAS Mutations Can Determine Costello Syndrome Phenotype and Frequency in Cancer

DEFF Research Database (Denmark)

Hartung, Anne-Mette; Swensen, Jeff; Uriz, Inaki E

2016-01-01

by the efficiency of exon 2 inclusion resulting from the different HRAS mutations. Finally, we show that a splice switching oligonucleotide (SSO) that blocks access to the critical ESE causes exon 2 skipping and halts proliferation of cancer cells. This unravels a potential for development of new anti......-cancer therapies based on SSO-mediated HRAS exon 2 skipping....

Morpholino oligomer-mediated exon skipping averts the onset of dystrophic pathology in the mdx mouse.

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Fletcher, Sue; Honeyman, Kaite; Fall, Abbie M; Harding, Penny L; Johnsen, Russell D; Steinhaus, Joshua P; Moulton, Hong M; Iversen, Patrick L; Wilton, Stephen D

2007-09-01

Duchenne and Becker muscular dystrophies are allelic disorders arising from mutations in the dystrophin gene. Duchenne muscular dystrophy is characterized by an absence of functional protein, whereas Becker muscular dystrophy, commonly caused by in-frame deletions, shows synthesis of partially functional protein. Anti-sense oligonucleotides can induce specific exon removal during processing of the dystrophin primary transcript, while maintaining or restoring the reading frame, and thereby overcome protein-truncating mutations. The mdx mouse has a non-sense mutation in exon 23 of the dystrophin gene that precludes functional dystrophin production, and this model has been used in the development of treatment strategies for dystrophinopathies. A phosphorodiamidate morpholino oligomer (PMO) has previously been shown to exclude exon 23 from the dystrophin gene transcript and induce dystrophin expression in the mdxmouse, in vivo and in vitro. In this report, a cell-penetrating peptide (CPP)-conjugated oligomer targeted to the mouse dystrophin exon 23 donor splice site was administered to mdxmice by intraperitoneal injection. We demonstrate dystrophin expression and near-normal muscle architecture in all muscles examined, except for cardiac muscle. The CPP greatly enhanced uptake of the PMO, resulting in widespread dystrophin expression.

Alternative splicing of exon 17 and a missense mutation in exon 20 of the insulin receptor gene in two brothers with a novel syndrome of insulin resistance (congenital fiber-type disproportion myopathy)

DEFF Research Database (Denmark)

Vorwerk, P; Christoffersen, C T; Müller, J

1999-01-01

to be compound heterozygotes for mutations in the IR gene. The maternal allele was alternatively spliced in exon 17 due to a point mutation in the -1 donor splice site of the exon. The abnormal skipping of exon 17 shifts the amino acid reading frame and leads to a truncated IR, missing the entire tyrosine kinase......The insulin receptor (IR) in two brothers with a rare syndrome of congenital muscle fiber type disproportion myopathy (CFTDM) associated with diabetes and severe insulin resistance was studied. By direct sequencing of Epstein-Barr virus-transformed lymphocytes both patients were found...... domain. In the correct spliced variant, the point mutation is silent and results in a normally translated IR. The paternal allele carries a missense mutation in the tyrosine kinase domain. All three cDNA variants were present in the lymphocytes of the patients. Purified IR from 293 cells overexpressing...

A mutation in an alternative untranslated exon of hexokinase 1 associated with hereditary motor and sensory neuropathy -- Russe (HMSNR).

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Hantke, Janina; Chandler, David; King, Rosalind; Wanders, Ronald J A; Angelicheva, Dora; Tournev, Ivailo; McNamara, Elyshia; Kwa, Marcel; Guergueltcheva, Velina; Kaneva, Radka; Baas, Frank; Kalaydjieva, Luba

2009-12-01

Hereditary Motor and Sensory Neuropathy -- Russe (HMSNR) is a severe autosomal recessive disorder, identified in the Gypsy population. Our previous studies mapped the gene to 10q22-q23 and refined the gene region to approximately 70 kb. Here we report the comprehensive sequencing analysis and fine mapping of this region, reducing it to approximately 26 kb of fully characterised sequence spanning the upstream exons of Hexokinase 1 (HK1). We identified two sequence variants in complete linkage disequilibrium, a G>C in a novel alternative untranslated exon (AltT2) and a G>A in the adjacent intron, segregating with the disease in affected families and present in the heterozygote state in only 5/790 population controls. Sequence conservation of the AltT2 exon in 16 species with invariable preservation of the G allele at the mutated site, strongly favour the exonic change as the pathogenic mutation. Analysis of the Hk1 upstream region in mouse mRNA from testis and neural tissues showed an abundance of AltT2-containing transcripts generated by extensive, developmentally regulated alternative splicing. Expression is very low compared with ubiquitous Hk1 and all transcripts skip exon1, which encodes the protein domain responsible for binding to the outer mitochondrial membrane, and regulation of energy production and apoptosis. Hexokinase activity measurement and immunohistochemistry of the peripheral nerve showed no difference between patients and controls. The mutational mechanism and functional effects remain unknown and could involve disrupted translational regulation leading to increased anti-apoptotic activity (suggested by the profuse regenerative activity in affected nerves), or impairment of an unknown HK1 function in the peripheral nervous system (PNS).

Two novel exonic point mutations in HEXA identified in a juvenile Tay-Sachs patient: role of alternative splicing and nonsense-mediated mRNA decay.

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Levit, A; Nutman, D; Osher, E; Kamhi, E; Navon, R

2010-06-01

We have identified three mutations in the beta-hexoseaminidase A (HEXA) gene in a juvenile Tay-Sachs disease (TSD) patient, which exhibited a reduced level of HEXA mRNA. Two mutations are novel, c.814G>A (p.Gly272Arg) and c.1305C>T (p.=), located in exon 8 and in exon 11, respectively. The third mutation, c.1195A>G (p.Asn399Asp) in exon 11, has been previously characterized as a common polymorphism in African-Americans. Hex A activity measured in TSD Glial cells, transfected with HEXA cDNA constructs bearing these mutations, was unaltered from the activity level measured in normal HEXA cDNA. Analysis of RT-PCR products revealed three aberrant transcripts in the patient, one where exon 8 was absent, one where exon 11 was absent and a third lacking both exons 10 and 11. All three novel transcripts contain frameshifts resulting in premature termination codons (PTCs). Transfection of mini-gene constructs carrying the c.814G>A and c.1305C>T mutations proved that the two mutations result in exon skipping. mRNAs that harbor a PTC are detected and degraded by the nonsense-mediated mRNA decay (NMD) pathway to prevent synthesis of abnormal proteins. However, although NMD is functional in the patient's fibroblasts, aberrant transcripts are still present. We suggest that the level of correctly spliced transcripts as well as the efficiency in which NMD degrade the PTC-containing transcripts, apparently plays an important role in the phenotype severity of the unique patient and thus should be considered as a potential target for drug therapy.

A mutation in an alternative untranslated exon of hexokinase 1 associated with Hereditary Motor and Sensory Neuropathy – Russe (HMSNR)

Science.gov (United States)

Hantke, Janina; Chandler, David; King, Rosalind; Wanders, Ronald JA; Angelicheva, Dora; Tournev, Ivailo; McNamara, Elyshia; Kwa, Marcel; Guergueltcheva, Velina; Kaneva, Radka; Baas, Frank; Kalaydjieva, Luba

2009-01-01

Hereditary Motor and Sensory Neuropathy – Russe (HMSNR) is a severe autosomal recessive disorder, identified in the Gypsy population. Our previous studies mapped the gene to 10q22-q23 and refined the gene region to ∼70 kb. Here we report the comprehensive sequencing analysis and fine mapping of this region, reducing it to ∼26 kb of fully characterised sequence spanning the upstream exons of Hexokinase 1 (HK1). We identified two sequence variants in complete linkage disequilibrium, a G>C in a novel alternative untranslated exon (AltT2) and a G>A in the adjacent intron, segregating with the disease in affected families and present in the heterozygote state in only 5/790 population controls. Sequence conservation of the AltT2 exon in 16 species with invariable preservation of the G allele at the mutated site, strongly favour the exonic change as the pathogenic mutation. Analysis of the Hk1 upstream region in mouse mRNA from testis and neural tissues showed an abundance of AltT2-containing transcripts generated by extensive, developmentally regulated alternative splicing. Expression is very low compared with ubiquitous Hk1 and all transcripts skip exon1, which encodes the protein domain responsible for binding to the outer mitochondrial membrane, and regulation of energy production and apoptosis. Hexokinase activity measurement and immunohistochemistry of the peripheral nerve showed no difference between patients and controls. The mutational mechanism and functional effects remain unknown and could involve disrupted translational regulation leading to increased anti-apoptotic activity (suggested by the profuse regenerative activity in affected nerves), or impairment of an unknown HK1 function in the peripheral nervous system (PNS). PMID:19536174

Exon-skipping strategy by ratio modulation between cytoprotective versus pro-apoptotic clusterin forms increased sensitivity of LNCaP to cell death.

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Abdellatif Essabbani

Full Text Available BACKGROUND: In prostate cancer the secreted form of clusterin (sCLU has been described as an anti-apoptotic protein whose expression is increased after therapeutic intervention, whereas, the nuclear protein form nCLU was reported to have pro-apoptotic properties. METHODOLOGY: In order to provide new therapeutic approaches targeting CLU, we developed a strategy based on exon skipping by using a lentiviral construct to preferentially induce the nuclear spliced form of the protein. The molecular construct was transduced in LNCaP cells for testing the modulation of sensitivity of the transduced cells to pro-apoptotic stress. RESULTS AND CONCLUSIONS: We showed an increase of nCLU/sCLU expression ratio in the prostate cancer cell line "LNCaP" after lentiviral vector-U7 nCLU transduction. Moreover, we showed a significant inhibition of cell proliferation in nCLU-U7 LNCaP cells after treatment with cisplatin and after exposure to ionizing radiation compared to control cells. Finally, we showed that nCLU-U7 LNCaP cells exposure to UV-C significantly reduced an increase of cell death compared to control. Finally, we showed that modulating nCLU expression had profound impact on Ku70/Bax interaction as well as Rad17 expression which could be a key mechanism in sensitizing cells to cell death. In conclusion, this is the first report showing that increasing of nCLU/sCLU expression ratio by using an "on demand alternative splicing" strategy successfully increased sensitivity to radiotherapy and chemotherapy of prostate cancer cells.

Modulation of mdm2 pre-mRNA splicing by 9-aminoacridine-PNA (peptide nucleic acid conjugates targeting intron-exon junctions

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Nielsen Peter E

2010-06-01

Full Text Available Abstract Background Modulation of pre-mRNA splicing by antisense molecules is a promising mechanism of action for gene therapeutic drugs. In this study, we have examined the potential of peptide nucleic acid (PNA 9-aminoacridine conjugates to modulate the pre-mRNA splicing of the mdm2 human cancer gene in JAR cells. Methods We screened 10 different 15 mer PNAs targeting intron2 at both the 5' - and the 3'-splice site for their effects on the splicing of mdm2 using RT-PCR analysis. We also tested a PNA (2512 targeting the 3'-splice site of intron3 with a complementarity of 4 bases to intron3 and 11 bases to exon4 for its splicing modulation effect. This PNA2512 was further tested for the effects on the mdm2 protein level as well as for inhibition of cell growth in combination with the DNA damaging agent camptothecin (CPT. Results We show that several of these PNAs effectively inhibit the splicing thereby producing a larger mRNA still containing intron2, while skipping of exon3 was not observed by any of these PNAs. The most effective PNA (PNA2406 targeting the 3'-splice site of intron2 had a complementarity of 4 bases to intron2 and 11 bases to exon3. PNA (2512 targeting the 3'-splice site of intron3 induced both splicing inhibition (intron3 skipping and skipping of exon4. Furthermore, treatment of JAR cells with this PNA resulted in a reduction in the level of MDM2 protein and a concomitant increase in the level of tumor suppressor p53. In addition, a combination of this PNA with CPT inhibited cell growth more than CPT alone. Conclusion We have identified several PNAs targeting the 5'- or 3'-splice sites in intron2 or the 3'-splice site of intron3 of mdm2 pre-mRNA which can inhibit splicing. Antisense targeting of splice junctions of mdm2 pre-mRNA may be a powerful method to evaluate the cellular function of MDM2 splice variants as well as a promising approach for discovery of mdm2 targeted anticancer drugs.

Effects of systemic multiexon skipping with peptide-conjugated morpholinos in the heart of a dog model of Duchenne muscular dystrophy.

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Echigoya, Yusuke; Nakamura, Akinori; Nagata, Tetsuya; Urasawa, Nobuyuki; Lim, Kenji Rowel Q; Trieu, Nhu; Panesar, Dharminder; Kuraoka, Mutsuki; Moulton, Hong M; Saito, Takashi; Aoki, Yoshitsugu; Iversen, Patrick; Sazani, Peter; Kole, Ryszard; Maruyama, Rika; Partridge, Terry; Takeda, Shin'ichi; Yokota, Toshifumi

2017-04-18

Duchenne muscular dystrophy (DMD) is a lethal genetic disorder caused by an absence of the dystrophin protein in bodywide muscles, including the heart. Cardiomyopathy is a leading cause of death in DMD. Exon skipping via synthetic phosphorodiamidate morpholino oligomers (PMOs) represents one of the most promising therapeutic options, yet PMOs have shown very little efficacy in cardiac muscle. To increase therapeutic potency in cardiac muscle, we tested a next-generation morpholino: arginine-rich, cell-penetrating peptide-conjugated PMOs (PPMOs) in the canine X-linked muscular dystrophy in Japan (CXMD J ) dog model of DMD. A PPMO cocktail designed to skip dystrophin exons 6 and 8 was injected intramuscularly, intracoronarily, or intravenously into CXMD J dogs. Intravenous injections with PPMOs restored dystrophin expression in the myocardium and cardiac Purkinje fibers, as well as skeletal muscles. Vacuole degeneration of cardiac Purkinje fibers, as seen in DMD patients, was ameliorated in PPMO-treated dogs. Although symptoms and functions in skeletal muscle were not ameliorated by i.v. treatment, electrocardiogram abnormalities (increased Q-amplitude and Q/R ratio) were improved in CXMD J dogs after intracoronary or i.v. administration. No obvious evidence of toxicity was found in blood tests throughout the monitoring period of one or four systemic treatments with the PPMO cocktail (12 mg/kg/injection). The present study reports the rescue of dystrophin expression and recovery of the conduction system in the heart of dystrophic dogs by PPMO-mediated multiexon skipping. We demonstrate that rescued dystrophin expression in the Purkinje fibers leads to the improvement/prevention of cardiac conduction abnormalities in the dystrophic heart.

Identification of evolutionarily conserved exons as regulated targets for the splicing activator tra2β in development.

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Sushma Grellscheid

2011-12-01

Full Text Available Alternative splicing amplifies the information content of the genome, creating multiple mRNA isoforms from single genes. The evolutionarily conserved splicing activator Tra2β (Sfrs10 is essential for mouse embryogenesis and implicated in spermatogenesis. Here we find that Tra2β is up-regulated as the mitotic stem cell containing population of male germ cells differentiate into meiotic and post-meiotic cells. Using CLIP coupled to deep sequencing, we found that Tra2β binds a high frequency of exons and identified specific G/A rich motifs as frequent targets. Significantly, for the first time we have analysed the splicing effect of Sfrs10 depletion in vivo by generating a conditional neuronal-specific Sfrs10 knock-out mouse (Sfrs10(fl/fl; Nestin-Cre(tg/+. This mouse has defects in brain development and allowed correlation of genuine physiologically Tra2β regulated exons. These belonged to a novel class which were longer than average size and importantly needed multiple cooperative Tra2β binding sites for efficient splicing activation, thus explaining the observed splicing defects in the knockout mice. Regulated exons included a cassette exon which produces a meiotic isoform of the Nasp histone chaperone that helps monitor DNA double-strand breaks. We also found a previously uncharacterised poison exon identifying a new pathway of feedback control between vertebrate Tra2 proteins. Both Nasp-T and the Tra2a poison exon are evolutionarily conserved, suggesting they might control fundamental developmental processes. Tra2β protein isoforms lacking the RRM were able to activate specific target exons indicating an additional functional role as a splicing co-activator. Significantly the N-terminal RS1 domain conserved between flies and humans was essential for the splicing activator function of Tra2β. Versions of Tra2β lacking this N-terminal RS1 domain potently repressed the same target exons activated by full-length Tra2β protein.

Is breakfast skipping associated with physical activity among U.S. adolescents? A cross-sectional study of adolescents aged 12-19 years, National Health and Nutrition Examination Survey (NHANES).

Science.gov (United States)

Lyerly, Jordan E; Huber, Larissa R; Warren-Findlow, Jan; Racine, Elizabeth F; Dmochowski, Jacek

2014-04-01

To examine the association between breakfast skipping and physical activity among US adolescents aged 12-19 years. A cross-sectional study of nationally representative 2007-2008 National Health and Nutrition Examination Survey (NHANES) data. Breakfast skipping was assessed by two 24 h dietary recalls. Physical activity was self-reported by participants and classified based on meeting national recommendations for physical activity for the appropriate age group. Multiple logistic regression analysis was used to model the association between breakfast skipping and physical activity while controlling for confounders. A total of 936 adolescents aged 12-19 years in the USA. After adjusting for family income, there was no association between breakfast skipping and meeting physical activity guidelines for age among adolescents aged 12-19 years (OR = 0.95, 95% CI 0.56, 1.32). Findings from the study differ from previous research findings on breakfast skipping and physical activity. Therefore, further research that uses large, nationally representative US samples and national recommended guidelines for physical activity is needed.

O vzniku a činnosti SKIP v letech 1968 - 1970

Czech Academy of Sciences Publication Activity Database

Burgetová, Jarmila

2008-01-01

Roč. 17, č. 1 (2008), s. 26-28 ISSN 1210-0927 Institutional research plan: CEZ:AV0Z70830501 Keywords : Association of Library and Information Professionals (SKIP)- foundation in 1968 * Association of Library and Information Professionals (SKIP) - activities in 1968-1970 Subject RIV: AF - Documentation, Librarianship, Information Studies

Analysis of 30 putative BRCA1 splicing mutations in hereditary breast and ovarian cancer families identifies exonic splice site mutations that escape in silico prediction.

Directory of Open Access Journals (Sweden)

Barbara Wappenschmidt

Full Text Available Screening for pathogenic mutations in breast and ovarian cancer genes such as BRCA1/2, CHEK2 and RAD51C is common practice for individuals from high-risk families. However, test results may be ambiguous due to the presence of unclassified variants (UCV in the concurrent absence of clearly cancer-predisposing mutations. Especially the presence of intronic or exonic variants within these genes that possibly affect proper pre-mRNA processing poses a challenge as their functional implications are not immediately apparent. Therefore, it appears necessary to characterize potential splicing UCV and to develop appropriate classification tools. We investigated 30 distinct BRCA1 variants, both intronic and exonic, regarding their spliceogenic potential by commonly used in silico prediction algorithms (HSF, MaxEntScan along with in vitro transcript analyses. A total of 25 variants were identified spliceogenic, either causing/enhancing exon skipping or activation of cryptic splice sites, or both. Except from a single intronic variant causing minor effects on BRCA1 pre-mRNA processing in our analyses, 23 out of 24 intronic variants were correctly predicted by MaxEntScan, while HSF was less accurate in this cohort. Among the 6 exonic variants analyzed, 4 severely impair correct pre-mRNA processing, while the remaining two have partial effects. In contrast to the intronic alterations investigated, only half of the spliceogenic exonic variants were correctly predicted by HSF and/or MaxEntScan. These data support the idea that exonic splicing mutations are commonly disease-causing and concurrently prone to escape in silico prediction, hence necessitating experimental in vitro splicing analysis.

Identification of protein features encoded by alternative exons using Exon Ontology.

Science.gov (United States)

Tranchevent, Léon-Charles; Aubé, Fabien; Dulaurier, Louis; Benoit-Pilven, Clara; Rey, Amandine; Poret, Arnaud; Chautard, Emilie; Mortada, Hussein; Desmet, François-Olivier; Chakrama, Fatima Zahra; Moreno-Garcia, Maira Alejandra; Goillot, Evelyne; Janczarski, Stéphane; Mortreux, Franck; Bourgeois, Cyril F; Auboeuf, Didier

2017-06-01

Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press.

Stemcell Information: SKIP000418 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available Princess ... Fetus Unknown ... -- No MRC-iPS-05|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like R... SKIP000418 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-5 MRC-iPS-5 Princess...e.0013017 Lectin microarray analysis of pluripotent and multipotent stem cells.--DNA methylation dynamics in... human induced pluripotent stem cells over time.--Mesenchymal to embryonic incomp...lete transition of human cells by chimeric OCT4/3 (POU5F1) with physiological co-activator EWS.--Defining hy

Skipping breakfast and associated factors among Brazilian adolescents

Directory of Open Access Journals (Sweden)

Rosemeyre França de Paula FIUZA

Full Text Available ABSTRACT Objective To analyze the prevalence and factors associated with breakfast skipping among adolescents. Methods Cross-sectional study, with adolescents aged 10-17 years, evaluated between 2009 and 2011, belonging to a cohort study in the Central-West region of Brazil. Breakfast skipping was considered as not having breakfast every day. Demographic, socioeconomic, and lifestyle factors were evaluated through a questionnaire. Anthropometric assessment included measurement of weight and height, which were used to classify weight status using body mass index. Poisson regression was used to assess the association of breakfast skipping with demographic and socioeconomic variables, lifestyle factors, and weight status. Results Among 1,716 Brazilian adolescents evaluated, 36.2% reported not consuming breakfast every day, with the highest prevalence among girls (p=0.03. After adjusting for age and economic class, breakfast skipping was associated with not consuming breakfast with parents and morning shift at school, in both genders, and with obesity only in boys. Lifestyle factors such as alcohol consumption, physical activity, diet quality, and smoking were not associated with skipping breakfast. Conclusion The omission of breakfast was observed in more than a third of adolescents, being associated with demographic and lifestyle factors. In the public health perspective, the importance of encouraging the consumption of this meal is highlighted, with actions involving the school environment and the family.

Exonization of active mouse L1s: a driver of transcriptome evolution?

Directory of Open Access Journals (Sweden)

Badge Richard

2007-10-01

Full Text Available Abstract Background Long interspersed nuclear elements (LINE-1s, L1s have been recently implicated in the regulation of mammalian transcriptomes. Results Here, we show that members of the three active mouse L1 subfamilies (A, GF and TF contain, in addition to those on their sense strands, conserved functional splice sites on their antisense strands, which trigger multiple exonization events. The latter is particularly intriguing in the light of the strong antisense orientation bias of intronic L1s, implying that the toleration of antisense insertions results in an increased potential for exonization. Conclusion In a genome-wide analysis, we have uncovered evidence suggesting that the mobility of the large number of retrotransposition-competent mouse L1s (~2400 potentially active L1s in NCBIm35 has significant potential to shape the mouse transcriptome by continuously generating insertions into transcriptional units.

ExonMiner: Web service for analysis of GeneChip Exon array data

Directory of Open Access Journals (Sweden)

Imoto Seiya

2008-11-01

Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

Nanopolymers improve delivery of exon skipping oligonucleotides and concomitant dystrophin expression in skeletal muscle of mdx mice

Directory of Open Access Journals (Sweden)

Sirsi Shashank R

2008-04-01

Full Text Available Abstract Background Exon skipping oligonucleotides (ESOs of 2'O-Methyl (2'OMe and morpholino chemistry have been shown to restore dystrophin expression in muscle fibers from the mdx mouse, and are currently being tested in phase I clinical trials for Duchenne Muscular Dystrophy (DMD. However, ESOs remain limited in their effectiveness because of an inadequate delivery profile. Synthetic cationic copolymers of poly(ethylene imine (PEI and poly(ethylene glycol (PEG are regarded as effective agents for enhanced delivery of nucleic acids in various applications. Results We examined whether PEG-PEI copolymers can facilitate ESO-mediated dystrophin expression after intramuscular injections into tibialis anterior (TA muscles of mdx mice. We utilized a set of PEG-PEI copolymers containing 2 kDa PEI and either 550 Da or 5 kDa PEG, both of which bind 2'OMe ESOs with high affinity and form stable nanoparticulates with a relatively low surface charge. Three weekly intramuscular injections of 5 μg of ESO complexed with PEI2K-PEG550 copolymers resulted in about 500 dystrophin-positive fibers and about 12% of normal levels of dystrophin expression at 3 weeks after the initial injection, which is significantly greater than for injections of ESO alone, which are known to be almost completely ineffective. In an effort to enhance biocompatibility and cellular uptake, the PEI2K-PEG550 and PEI2K-PEG5K copolymers were functionalized by covalent conjugation with nanogold (NG or adsorbtion of colloidal gold (CG, respectively. Surprisingly, using the same injection and dosing regimen, we found no significant difference in dystrophin expression by Western blot between the NG-PEI2K-PEG550, CG-PEI2K-PEG5K, and non-functionalized PEI2K-PEG550 copolymers. Dose-response experiments using the CG-PEI2K-PEG5K copolymer with total ESO ranging from 3–60 μg yielded a maximum of about 15% dystrophin expression. Further improvements in dystrophin expression up to 20% of normal

Stemcell Information: SKIP000576 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000576 ... Normal PB PB ... -- -- ... -- No Nomal human IPS cell line 正常iPS細胞...phem.2014.03.010 Generation of induced pluripotent stem cells derived from primary and secondary myelofibros

The Dynamics of Compound, Transcript, and Protein Effects After Treatment With 2OMePS Antisense Oligonucleotides in mdx Mice

Directory of Open Access Journals (Sweden)

Ingrid E C Verhaart

2014-01-01

Full Text Available Antisense-mediated exon skipping is currently in clinical development for Duchenne muscular dystrophy (DMD to amend the consequences of the underlying genetic defect and restore dystrophin expression. Due to turnover of compound, transcript, and protein, chronic treatment with effector molecules (antisense oligonucleotides will be required. To investigate the dynamics and persistence of antisense 2′-O-methyl phosphorothioate oligonucleotides, exon skipping, and dystrophin expression after dosing was concluded, mdx mice were treated subcutaneously for 8 weeks with 100 mg/kg oligonucleotides twice weekly. Thereafter, mice were sacrificed at different time points after the final injection (36 hours–24 weeks. Oligonucleotide half-life was longer in heart (~65 days compared with that in skeletal muscle, liver, and kidney (~35 days. Exon skipping half-lives varied between 33 and 53 days, whereas dystrophin protein showed a long half-life (>100 days. Oligonucleotide and exon-skipping levels peaked in the first week and declined thereafter. By contrast, dystrophin expression peaked after 3–8 weeks and then slowly declined, remaining detectable after 24 weeks. Concordance between levels of oligonucleotides, exon skipping, and proteins was observed, except in heart, wherein high oligonucleotide levels but low exon skipping and dystrophin expression were seen. Overall, these results enhance our understanding of the pharmacokinetics and pharmacodynamics of 2′-O-methyl phosphorothioate oligos used for the treatment of DMD.

Stemcell Information: SKIP000147 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000147 ... Blastocyst 胚盤胞 Unknown KhES-1 KhES-1 ... -- -- ... -- No Embryonic stem cell 胚性幹細胞...nt establishment of human embryonic stem cell lines and long-term maintenance wit

Stemcell Information: SKIP000326 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 0.1007/s00401-013-1149-y Modeling key pathological features of frontotemporal dementia... SKIP000326 ... Diseased Carrier2 #1 Carrier2 #1 ... 前頭側頭型認知症 G310 FrontoTemporal D

Stemcell Information: SKIP000593 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000593 ... Diseased PDB3F-9 PDB3F-9 ... パーキンソン病 G20 Parkinson disease 168600 ... ... ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induc

Stemcell Information: SKIP000598 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000598 ... Diseased PDB4F-4 PDB4F-4 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000604 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000604 ... Diseased PDD4F-1 PDD4F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000605 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000605 ... Diseased PDD4F-4 PDD4F-4 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000608 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000608 ... Diseased PDD4F-9 PDD4F-9 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000606 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000606 ... Diseased PDD4F-5 PDD4F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000595 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000595 ... Diseased PDB4F-1 PDB4F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000599 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000599 ... Diseased PDB4F-5 PDB4F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000597 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000597 ... Diseased PDB4F-3 PDB4F-3 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000607 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000607 ... Diseased PDD4F-8 PDD4F-8 ... パーキンソン病 G20 Parkinson disease 168600 ... ...head Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patie

Stemcell Information: SKIP000592 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000592 ... Diseased PDB3F-8 PDB3F-8 ... パーキンソン病 G20 Parkinson disease 168600 ... ...ute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived

Stemcell Information: SKIP000296 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000296 ... Normal C2 C2 ... -- Female ... -- No Healthy control lin...e for L2-1,2,3Mut. Born in 1931 Healthy control line for L2-1,2,3Mut. Born in　1931 -- -- -- ... -- ... Yes I

Stemcell Information: SKIP000325 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available School ... 23836290 10.1007/s00401-013-1149-y Modeling key pathological features of frontotemporal dementia... SKIP000325 ... Diseased Carrier1 #6 Carrier1 #6 ... 前頭側頭型認知症 G310 FrontoTemporal D

Stemcell Information: SKIP000327 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available cal School ... 23836290 10.1007/s00401-013-1149-y Modeling key pathological features of frontotemporal dementia... SKIP000327 ... Diseased Carrier2 #11 Carrier2 #11 ... 前頭側頭型認知症 G310 FrontoTemporal

Stemcell Information: SKIP000324 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available School ... 23836290 10.1007/s00401-013-1149-y Modeling key pathological features of frontotemporal dementia... SKIP000324 ... Diseased Carrier1 #5 Carrier1 #5 ... 前頭側頭型認知症 G310 FrontoTemporal D

Stemcell Information: SKIP000610 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000610 ... Diseased PDE3F-4 PDE3F-4 ... パーキンソン病 G20 Parkinson disease 168600 ... ...69371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced plur

Stemcell Information: SKIP000603 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000603 ... Diseased PDD3F-7 PDD3F-7 ... パーキンソン病 G20 Parkinson disease 168600 ... ...19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced p

Stemcell Information: SKIP000590 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000590 ... Diseased PDB3F-1 PDB3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...e ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived in

Stemcell Information: SKIP000601 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000601 ... Diseased PDD3F-1 PDD3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced p

Stemcell Information: SKIP000602 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000602 ... Diseased PDD3F-4 PDD3F-4 ... パーキンソン病 G20 Parkinson disease 168600 ... ...19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced p

Stemcell Information: SKIP000609 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000609 ... Diseased PDE3F-3 PDE3F-3 ... パーキンソン病 G20 Parkinson disease 168600 ... ...69371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced plur

Skip segment Hirschsprung's disease: a systematic review.

LENUS (Irish Health Repository)

O'Donnell, Anne-Marie

2012-02-01

PURPOSE: Hirschsprung\\'s disease is characterised by the congenital absence of ganglion cells beginning in the distal rectum and extending proximally for varying distances. \\'Zonal aganglionosis\\' is a phenomenon involving a zone of aganglionosis occurring within normally innervated intestine. \\'Skip segment\\' Hirschsprung\\'s disease (SSHD) involves a \\'skip area\\' of normally ganglionated intestine, surrounded proximally and distally by aganglionosis. While Hirschsprung\\'s disease is believed to be the result of incomplete craniocaudal migration of neural crest-derived cells, the occurrence of SSHD has no clear embryological explanation. The aim of this study was to perform a systematic review of SSHD, reported in the literature between 1954 and 2009, in order to determine the clinical characteristics of this rare entity and its significance. METHODS: The first reported case of SSHD was published in 1954. A systematic review of SSHD cases in the literature, from 1954 to 2009, was carried out using the electronic database \\'Pubmed\\'. Detailed information was recorded regarding the age, gender, presenting symptoms and location of the skip segment in each patient. RESULTS: 24 cases of SSHD have been reported in the literature to date. 18\\/24 (75%) of these cases were males and 6\\/24 (25%) were females. Of these, 22\\/24 (92%) were cases of total colonic aganglionosis (TCA), and 2\\/24 (8%) were rectosigmoid Hirschsprung\\'s disease. Of the 22 TCA cases, 9 (41%) had a skip segment in the transverse colon, 6 (27%) in the ascending colon, 2 (9%) in the caecum and 5 (23%) had multiple skip segments. In both rectosigmoid Hirschsprung\\'s disease cases, the skip segment was in the sigmoid colon. Overall, the length of the skip segment was variable, with the entire transverse colon ganglionated in some cases. CONCLUSION: SSHD occurs predominantly in patients with TCA. The existence of a skip area of normally innervated colon in TCA may influence surgical

Stemcell Information: SKIP000241 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000241 ... Diseased HPS0183 HPS0183 ... 封入体筋炎 G724 Inclusion body myositis 147...421 ... -- -- ... Yes No intractable disease-specific iPSC derived from Inclution body myositis. 封入体筋炎患者由

Stemcell Information: SKIP000243 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000243 ... Diseased HPS0174 HPS0174 ... 皮膚筋炎 M339 Dermatopolymyositis 613825 ... ... ... -- -- ... Yes No intractable disease-specific iPSC derived from Dermatomyositis (DM). 皮膚筋炎患者由来iPS細胞株。|

Stemcell Information: SKIP000600 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000600 ... Diseased PDC3F-1 PDC3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...titute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived

Stemcell Information: SKIP000292 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneration ... SKIP000292 ... Diseased L1-2Mut L1-2Mut ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP000297 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneratio... SKIP000297 ... Diseased L2-1Mut L2-1Mut ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP001117 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001117 ... Diseased D3-1 D3-1 ... 大うつ病 F33.3 major depression 605210 ... ...-- Male ... Yes No iPS cells derived from fibroblasts of a patient in which a frameshift mutation of disrupted in major depression

Stemcell Information: SKIP001118 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001118 ... Diseased D3-2 D3-2 ... 大うつ病 F33.3 major depression 605210 ... ...-- Male ... Yes No iPS cells derived from fibroblasts of a patient in which a frameshift mutation of disrupted in major depression

Stemcell Information: SKIP000594 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000594 ... Diseased PDB3F-d12 PDB3F-d12 ... パーキンソン病 G20 Parkinson disease 1686...he Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced

Stemcell Information: SKIP000763 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000763 ... Diseased PDB2lox-17 PDB2lox-17 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

Stemcell Information: SKIP000765 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000765 ... Diseased PDB2lox-22 PDB2lox-22 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

Stemcell Information: SKIP000542 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000542 ... Diseased PDA3F-1 PDA3F-1 ... パーキンソン病 G20 Parkinson disease 168600 ... ...udolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000953 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000953 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP06.1 SP06.1 ... パーキンソン病 G20 Parkinson...om human iPS-based models of genetic and sporadic Parkinson's disease. Sanchez-Da

Stemcell Information: SKIP000591 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000591 ... Diseased PDB3F-5 PDB3F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...dolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000762 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000762 ... Diseased PDB2lox-5 PDB2lox-5 ... パーキンソン病 G20 Parkinson disease 1686...71 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of vir

Stemcell Information: SKIP000856 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000856 ... Diseased HPS0256 HPS0256 ... アルツハイマー病 G309 Alzheimer disease 104300... ... -- -- ... No No Disease specific iPS cell line derived from a patient with Alzheimer disease アルツハイマー

Stemcell Information: SKIP000764 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000764 ... Diseased PDB2lox-21 PDB2lox-21 ... パーキンソン病 G20 Parkinson disease 16...9371 10.1016/j.cell.2009.02.013 Parkinson's disease patient-derived induced pluripotent stem cells free of v

Potential applications of skip SMV with thrust engine

Science.gov (United States)

Wang, Weilin; Savvaris, Al

2016-11-01

This paper investigates the potential applications of Space Maneuver Vehicles (SMV) with skip trajectory. Due to soaring space operations over the past decades, the risk of space debris has considerably increased such as collision risks with space asset, human property on ground and even aviation. Many active debris removal methods have been investigated and in this paper, a debris remediation method is first proposed based on skip SMV. The key point is to perform controlled re-entry. These vehicles are expected to achieve a trans-atmospheric maneuver with thrust engine. If debris is released at altitude below 80 km, debris could be captured by the atmosphere drag force and re-entry interface prediction accuracy is improved. Moreover if the debris is released in a cargo at a much lower altitude, this technique protects high value space asset from break up by the atmosphere and improves landing accuracy. To demonstrate the feasibility of this concept, the present paper presents the simulation results for two specific mission profiles: (1) descent to predetermined altitude; (2) descent to predetermined point (altitude, longitude and latitude). The evolutionary collocation method is adopted for skip trajectory optimization due to its global optimality and high-accuracy. This method is actually a two-step optimization approach based on the heuristic algorithm and the collocation method. The optimal-control problem is transformed into a nonlinear programming problem (NLP) which can be efficiently and accurately solved by the sequential quadratic programming (SQP) procedure. However, such a method is sensitive to initial values. To reduce the sensitivity problem, genetic algorithm (GA) is adopted to refine the grids and provide near optimum initial values. By comparing the simulation data from different scenarios, it is found that skip SMV is feasible in active debris removal and the evolutionary collocation method gives a truthful re-entry trajectory that satisfies the

Stemcell Information: SKIP000300 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinson... SKIP000300 ... Diseased L2-1GC L2-1GC ... パーキンソン病 G20 Parkinson's disease 607060 ...

Stemcell Information: SKIP000290 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegene... SKIP000290 ... Diseased L1-1Mut L1-1Mut ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP000299 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinsoni... SKIP000299 ... Diseased L2-3Mut L2-3Mut ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP000298 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinsoni... SKIP000298 ... Diseased L2-2Mut L2-2Mut ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP000235 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000235 ... Diseased HPS0270 HPS0270 ... アトピー性皮膚炎 L209 Atopic dermatitis 603165... ... -- -- ... Yes No iPS cell line derived from Atopic dermatitis patient. Same patient as HPS0271| アトピー性皮膚炎

Stemcell Information: SKIP000236 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000236 ... Diseased HPS0271 HPS0271 ... アトピー性皮膚炎 L210 Atopic dermatitis 603166... ... -- -- ... Yes No iPS cell line derived from Atopic dermatitis patient. Same patient as HPS0270| アトピー性皮膚炎

Stemcell Information: SKIP000968 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000968 ... Diseased PDB1lox-21Puro-12 PDB1lox-21Puro-12 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000974 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000974 ... Diseased PDB1lox-21GFP-41 PDB1lox-21GFP-41 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000948 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000948 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP14.2 SP14.2 ... パーキンソン病 G20 Parkinson...ic phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000943 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000943 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP08.2 SP08.2 ... パーキンソン病 G20 Parkinson...ific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000957 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000957 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP13.2 SP13.2 ... パーキンソン病 G20 Parkinson...cific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000960 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000960 ... Diseased PDB1lox-17GFP-55 PDB1lox-17GFP-55 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000973 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000973 ... Diseased PDB1lox-21Puro-28 PDB1lox-21Puro-28 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000951 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000951 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP05.1 SP05.1 ... パーキンソン病 G20 Parkinson... of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimenez

Stemcell Information: SKIP000969 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000969 ... Diseased PDB1lox-21Puro-13 PDB1lox-21Puro-13 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000962 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000962 ... Diseased PDB1lox-17Puro-10 PDB1lox-17Puro-10 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000971 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000971 ... Diseased PDB1lox-21Puro-20 PDB1lox-21Puro-20 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000967 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000967 ... Diseased PDB1lox-21Puro-5 PDB1lox-21Puro-5 ... パーキンソン病 G20 Parkinson... Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000966 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000966 ... Diseased PDB1lox-21GFP-19 PDB1lox-21GFP-19 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000937 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000937 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP01.4 SP01.4 ... パーキンソン病 G20 Parkinson...ific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000956 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000956 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP12.4 SP12.4 ... パーキンソン病 G20 Parkinson...cific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000954 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000954 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP06.2 SP06.2 ... パーキンソン病 G20 Parkinson... of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimenez

Stemcell Information: SKIP000952 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000952 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP05.2 SP05.2 ... パーキンソン病 G20 Parkinson...fic phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000950 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000950 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP16.3 SP16.3 ... パーキンソン病 G20 Parkinson...ific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000959 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000959 ... Diseased PDB1lox-17GFP-29 PDB1lox-17GFP-29 ... パーキンソン病 G20 Parkinson...Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000972 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000972 ... Diseased PDB1lox-21Puro-26 PDB1lox-21Puro-26 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000970 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000970 ... Diseased PDB1lox-21Puro-18 PDB1lox-21Puro-18 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000964 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000964 ... Diseased PDB1lox-17Puro-31 PDB1lox-17Puro-31 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000963 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000963 ... Diseased PDB1lox-17Puro-12 PDB1lox-17Puro-12 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000855 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000855 ... Diseased HPS0255 HPS0255 ... アルツハイマー病 G309 Alzheimer disease 104300... ... -- -- Japanese Japanese No No Disease specific iPS cell line derived from a patient with Alzheimer disease アルツハイマー

Stemcell Information: SKIP000854 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000854 ... Diseased HPS0254 HPS0254 ... アルツハイマー病 G309 Alzheimer disease 104300... ... -- -- Japanese Japanese No No Disease specific iPS cell line derived from a patient with Alzheimer disease アルツハイマー

Stemcell Information: SKIP000939 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000939 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP02.2 SP02.2 ... パーキンソン病 G20 Parkinson...ic phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson

Stemcell Information: SKIP000961 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000961 ... Diseased PDB1lox-17Puro-5 PDB1lox-17Puro-5 ... パーキンソン病 G20 Parkinson... Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000965 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000965 ... Diseased PDB1lox-17Puro-33 PDB1lox-17Puro-33 ... パーキンソン病 G20 Parkinson...ch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkinson

Stemcell Information: SKIP000293 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinson... SKIP000293 ... Diseased L1-1GC2 L1-1GC2 ... パーキンソン病 G20 Parkinson's disease 607060

Stemcell Information: SKIP000302 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... Information Only ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinso... SKIP000302 ... Diseased L2-3GC L2-3GC ... パーキンソン病 G20 Parkinson's disease 607060 ...

Stemcell Information: SKIP000253 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 21490598 10.1038/nature09915 Modelling schizophrenia using human induced pluripo... SKIP000253 ... Diseased GM23760 GM23760 ... 統合失調症 F20 Schizophrenia 181500 ... ...(SCZD) .episodes of agitatation, delusions of persecutation, fear of assassination, father also affected. 統合失調症

Stemcell Information: SKIP000245 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000245 ... Diseased HPS0164 HPS0164 ... デュシェンヌ型筋ジストロフィー G710 Duchenne Muscular... Dystrophy 310200 ... -- -- ... Yes No intractable disease-specific iPSC derived from Duchenne Muscular Dystrophy. デュシェンヌ

Stemcell Information: SKIP000955 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000955 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP12.3 SP12.3 ... パーキンソン病 G20 Parkinson...ls of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimen

Stemcell Information: SKIP000945 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000945 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP10.1 SP10.1 ... パーキンソン病 G20 Parkinson...e neurons from human iPS-based models of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-

Stemcell Information: SKIP000946 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000946 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP10.2 SP10.2 ... パーキンソン病 G20 Parkinson...sease-specific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinso

Stemcell Information: SKIP000958 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000958 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP13.4 SP13.4 ... パーキンソン病 G20 Parkinson...ls of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimen

Stemcell Information: SKIP000936 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000936 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP01.1 SP01.1 ... パーキンソン病 G20 Parkinson...s of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimene

Stemcell Information: SKIP000949 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000949 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP16.2 SP16.2 ... パーキンソン病 G20 Parkinson...s of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimene

Stemcell Information: SKIP000942 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000942 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP08.1 SP08.1 ... パーキンソン病 G20 Parkinson...s of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimene

Stemcell Information: SKIP000301 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... Information Only ... 23472874 10.1016/j.stem.2013.01.008 Genetic correction of a LRRK2 mutation in human iPSCs links parkinson... SKIP000301 ... Diseased L2-2GC L2-2GC ... パーキンソン病 G20 Parkinson's disease 607060 ...

Skipping of Chinese characters does not rely on word-based processing.

Science.gov (United States)

Lin, Nan; Angele, Bernhard; Hua, Huimin; Shen, Wei; Zhou, Junyi; Li, Xingshan

2018-02-01

Previous eye-movement studies have indicated that people tend to skip extremely high-frequency words in sentence reading, such as "the" in English and "/de" in Chinese. Two alternative hypotheses have been proposed to explain how this frequent skipping happens in Chinese reading: one assumes that skipping happens when the preview has been fully identified at the word level (word-based skipping); the other assumes that skipping happens whenever the preview character is easy to identify regardless of whether lexical processing has been completed or not (character-based skipping). Using the gaze-contingent display change paradigm, we examined the two hypotheses by substituting the preview of the third character of a four-character Chinese word with the high-frequency Chinese character "/de", which should disrupt the ongoing word-level processing. The character-based skipping hypothesis predicts that this manipulation will enhance the skipping probability of the target character (i.e., the third character of the target word), because the character "/de" has much higher character frequency than the original character. The word-based skipping hypothesis instead predicts a reduction of the skipping probability of the target character because the presence of the character "/de" is lexically infelicitous at word level. The results supported the character-based skipping hypothesis, indicating that in Chinese reading the decision of skipping a character can be made before integrating it into a word.

Designing optimum diameter of skip shafts in mines with inclined or steep coal seams

Energy Technology Data Exchange (ETDEWEB)

Durov, E.M.

1981-07-01

This paper discusses methods of increasing depth of operating shaft mines considering optimization of hoisting systems. The following solutions are analyzed: removing mined rock material to the surface, to operating horizon, to the deepest horizon, removing rock to the deepest horizon by enlarging a large diameter borehole. It is suggested that removing rock material to the surface is most economical. This solution is sometimes difficult to implement due to design of mine shafts. If a shaft is equipped with two pairs of skips, or with a pair of skips and two independent skips, one skip or a pair of skips can be removed to form free space for buckets used to hoist mined rock and coal. The bucket moves along rope shaft guides. Analysis of the optimum hoisting systems in shaft mines for coal mines with the following design capacity is carried out: 0.9, 1.2, 1.5 and 1.8 Mmt a year. The following depth of working horizons is evaluated: 600, 800, 1000, 1200, 1400 and 1600 m. It is assumed that coal and rock are hoisted separately. Advance rate ranges from 10 to 50 m/month. The results of analysis are shown in two tables. It is suggested that from the point of view of increasing depth of active mine shafts the following solutions are optimum: 7 m shaft with a system of three independently moving skips (two for coal, one for rock material), and 8 m shaft equipped with a pair of skips and two independent skips (one of the independently moving skips is used for rock hoisting). 4 refs.

Stemcell Information: SKIP001141 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001141 ... cardiac fibroblast 心臓線維芽細胞 Normal ATCC-CYS0105 ATCC-CYS0105 ... ...mary cardiac fibroblasts obtained from a healthy donor. ... 健常人の心臓線維芽細胞由来iPS細胞。 human ES-like Research Grade Se

Stemcell Information: SKIP000816 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000816 ... Diseased ACH-8858-6 ACH-8858-6 ... 軟骨無形成症 Q774 Achondroplasia 10080...0 ... 30 30-39 Female Japanese Japanese Yes No Achondroplasia(GM08858)-specific iPSC.GM08858 is from the mother of GM08859. 軟骨無形成

Stemcell Information: SKIP000265 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000265 ... Diseased HPS0264 HPS0264 ... パーキンソン病 G20 Parkinson disease ... ... ... 40-49 Male ... Yes No iPS cell line derived from Parkinson disease patient. パーキンソン病患者由来| human ES-like -- Re

Valence skipping driven superconductivity and charge Kondo effect

International Nuclear Information System (INIS)

Yanagisawa, Takashi; Hase, Izumi

2013-01-01

Highlights: •Valence skipping in metallic compounds can give rise to an unconventional superconductivity. •Several elements in the periodic table show valence skipping (or valence missing), for example, Bi forms the compounds in valence states +3 and +5. •The doping of valence skipping elements will induce superconductivity and this will lead to a possibility of high temperature superconductivity. •We consider the Wolf model with negative-U impurities, and show a phase diagram including superconducting phase. •There is a high temperature region near the boundary. -- Abstract: Valence skipping in metallic compounds can give rise to an unconventional superconductivity. Several elements in the periodic table show valence skipping (or valence missing), for example, Bi forms the compounds in valence states +3 and +5. The doping of valence skipping elements will induce superconductivity and this will lead to a possibility of high temperature superconductivity. We consider the Wolf model with negative-U impurities, and show a phase diagram including superconducting phase. The superconducting state is changed into a metallic state with a local singlet as the attractive interaction |U| increases. There is a high temperature region near the boundary

Stemcell Information: SKIP000151 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000151 ... Blastocyst 胚盤胞 Unknown KhES-2 KhES-2 ... -- -- ... -- No Embryonic Stem cell 胚性幹細胞...京都大学再生医科学研究所 ... 16707099 10.1016/j.bbrc.2006.04.135 Efficient establishment of human embryonic stem cell l

Stemcell Information: SKIP000888 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000888 ... T cells T細胞 Normal 24HM 24HM ... 24 20-29 Male Japanese 日本人 -- No iPS cell...s from healthy human T cells ヒト健常人由来iPS細胞 human ES-like Research Grade Plasmid OCT4,SOX2,KL

Stemcell Information: SKIP000815 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000815 ... Diseased ACH-8857-1 ACH-8857-1 ... 軟骨無形成症 Q774 Achondroplasia 10080...0 ... 34 30-39 Male Japanese Japanese Yes No Achondroplasia(GM08857)-specific iPSC.GM08857 is from the father of GM08859. 軟骨無形成症

Stemcell Information: SKIP000733 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000733 ... Diseased GM24666 GM24666 sAD2 sAD2 アルツハイマー病 G309 ALZHEIMER DISEAS...E 104300 ... 83 80-89 Male ... Yes Yes ALZHEIMER DISEASE(Sporadic AD) hiPSC derived from fibroblast アルツハイマー

Rope skipping increases bone mineral density at calcanei of pubertal girls in Hong Kong: A quasi-experimental investigation.

Directory of Open Access Journals (Sweden)

Amy S Ha

Full Text Available Bone mineral accrual during puberty is important, especially in girls, because it is related to reduced risks of osteoporosis in adulthood. Previous research has shown that jumping or plyometric exercises may be effective in increasing bone mineral density in adolescents. Rope skipping is a form of activity that involves jumping, thus regular skipping may also increase bone mineral density in pubertal girls. To this end, we conducted a quasi-experimental to examine the effects of rope skipping on girls' bone mineral density and cardiovascular fitness. 176 Hong Kong girls (age = 12.23 ± 1.80 years at baseline were recruited to take part in the study. Bone density at their forearms and calcanei were measured twice over two academic years (mean time between visits was 10.3 months. Using multilevel modeling analyses and adjusting for participants' height and physical activity, we found that girls who participated in weekly rope skipping activities, compared to those who did not, had higher levels of bone density at the calcanei (B = 0.023, p < .01. However, no differences were found for bone density at forearms or participants' cardiovascular fitness. The rates of change of these variables across time were also not significantly different. Results suggest that regular rope skipping may increase girls' bone density at the lower extremities, irrespective of the amount of self-report physical activity. However, further research is required to examine the potential dose-response relation between skipping behaviors and the measured outcomes.

SparseLeap: Efficient Empty Space Skipping for Large-Scale Volume Rendering

KAUST Repository

Hadwiger, Markus; Al-Awami, Ali K.; Beyer, Johanna; Agus, Marco; Pfister, Hanspeter

2017-01-01

Recent advances in data acquisition produce volume data of very high resolution and large size, such as terabyte-sized microscopy volumes. These data often contain many fine and intricate structures, which pose huge challenges for volume rendering, and make it particularly important to efficiently skip empty space. This paper addresses two major challenges: (1) The complexity of large volumes containing fine structures often leads to highly fragmented space subdivisions that make empty regions hard to skip efficiently. (2) The classification of space into empty and non-empty regions changes frequently, because the user or the evaluation of an interactive query activate a different set of objects, which makes it unfeasible to pre-compute a well-adapted space subdivision. We describe the novel SparseLeap method for efficient empty space skipping in very large volumes, even around fine structures. The main performance characteristic of SparseLeap is that it moves the major cost of empty space skipping out of the ray-casting stage. We achieve this via a hybrid strategy that balances the computational load between determining empty ray segments in a rasterization (object-order) stage, and sampling non-empty volume data in the ray-casting (image-order) stage. Before ray-casting, we exploit the fast hardware rasterization of GPUs to create a ray segment list for each pixel, which identifies non-empty regions along the ray. The ray-casting stage then leaps over empty space without hierarchy traversal. Ray segment lists are created by rasterizing a set of fine-grained, view-independent bounding boxes. Frame coherence is exploited by re-using the same bounding boxes unless the set of active objects changes. We show that SparseLeap scales better to large, sparse data than standard octree empty space skipping.

SparseLeap: Efficient Empty Space Skipping for Large-Scale Volume Rendering

KAUST Repository

Hadwiger, Markus

2017-08-28

Recent advances in data acquisition produce volume data of very high resolution and large size, such as terabyte-sized microscopy volumes. These data often contain many fine and intricate structures, which pose huge challenges for volume rendering, and make it particularly important to efficiently skip empty space. This paper addresses two major challenges: (1) The complexity of large volumes containing fine structures often leads to highly fragmented space subdivisions that make empty regions hard to skip efficiently. (2) The classification of space into empty and non-empty regions changes frequently, because the user or the evaluation of an interactive query activate a different set of objects, which makes it unfeasible to pre-compute a well-adapted space subdivision. We describe the novel SparseLeap method for efficient empty space skipping in very large volumes, even around fine structures. The main performance characteristic of SparseLeap is that it moves the major cost of empty space skipping out of the ray-casting stage. We achieve this via a hybrid strategy that balances the computational load between determining empty ray segments in a rasterization (object-order) stage, and sampling non-empty volume data in the ray-casting (image-order) stage. Before ray-casting, we exploit the fast hardware rasterization of GPUs to create a ray segment list for each pixel, which identifies non-empty regions along the ray. The ray-casting stage then leaps over empty space without hierarchy traversal. Ray segment lists are created by rasterizing a set of fine-grained, view-independent bounding boxes. Frame coherence is exploited by re-using the same bounding boxes unless the set of active objects changes. We show that SparseLeap scales better to large, sparse data than standard octree empty space skipping.

Stemcell Information: SKIP000242 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000242 ... Diseased HPS0178 HPS0178 ... 全身性強皮症 M340 Systemic Scleroderma 18175...), Systematic Sclerosis (SSc)| 全身性強皮症 ... 全身性硬化症　患者由来iPS細胞株。| human ES-like -- Sendai virus Sendai Virus Vector

Stemcell Information: SKIP000240 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000240 ... Diseased HPS0184 HPS0184 ... 全身性強皮症 M340 Systemic Scleroderma 18175...), Systematic Sclerosis (SSc)| 全身性強皮症、全身性硬化症　患者由来iPS細胞株。| human ES-like -- Sendai virus Sendai Virus Vector

Stemcell Information: SKIP000382 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000382 ... Diseased HPS0244 HPS0244 ... X連鎖αサラセミア·精神遅滞（ATR-X）症候群 D560 X-Linked alpha-Thalassemia...fic iPS cell line derived from a patient : X-Linked alpha-Thalassemia, Mental Retardation Syndrome (ATR-X sy

Stemcell Information: SKIP000596 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000596 ... Diseased PDB4F-2 PDB4F-2 ... パーキンソン病 G20 Parkinson disease 168600 ... ...f Jaenisch Rudolf Jaenisch Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkins...on's disease patient-derived induced pluripotent stem ce

Stemcell Information: SKIP000589 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000589 ... Diseased PDA3F-5 PDA3F-5 ... パーキンソン病 G20 Parkinson disease 168600 ... ...Available The Whitehead Institute The Whitehead Institute ... 19269371 10.1016/j.cell.2009.02.013 Parkins...on's disease patient-derived induced pluripotent stem cells free of viral reprogram

Stemcell Information: SKIP000771 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available e PARK6 600116 ... -- -- ... Yes No iPS cell line derived from a patient with Parkinson's disease, Familial type, PARK6. 家族性パーキンソン... SKIP000771 ... Diseased PKA13 PKA13 ... 家族性パーキンソン病 G20 familial parkinson's diseas

Stemcell Information: SKIP000770 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available PARK6 600116 ... -- -- ... Yes No iPS cell line derived from a patient with Parkinson's disease, Familial type, PARK6. 家族性パーキンソン... SKIP000770 ... Diseased PKA5 PKA5 ... 家族性パーキンソン病 G20 familial parkinson's disease

Stemcell Information: SKIP000175 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available le Black Black -- No Apparently healthy iPSCs from fetal lung fibroblast cell culture (GM06114) 健常胎児肺線維芽細胞(GM06114)由来iPS細胞... SKIP000175 ... Lung Fibroblast 肺線維芽細胞 Normal GM23392 GM23392 ... 0-9 Ma

Novel compound heterozygous Thyroglobulin mutations c.745+1G>A/c.7036+2T>A associated with congenital goiter and hypothyroidism in a Vietnamese family. Identification of a new cryptic 5' splice site in the exon 6.

Science.gov (United States)

Citterio, Cintia E; Morales, Cecilia M; Bouhours-Nouet, Natacha; Machiavelli, Gloria A; Bueno, Elena; Gatelais, Frédérique; Coutant, Regis; González-Sarmiento, Rogelio; Rivolta, Carina M; Targovnik, Héctor M

2015-03-15

Several patients were identified with dyshormonogenesis caused by mutations in the thyroglobulin (TG) gene. These defects are inherited in an autosomal recessive manner and affected individuals are either homozygous or compound heterozygous for the mutations. The aim of the present study was to identify new TG mutations in a patient of Vietnamese origin affected by congenital hypothyroidism, goiter and low levels of serum TG. DNA sequencing identified the presence of compound heterozygous mutations in the TG gene: the maternal mutation consists of a novel c.745+1G>A (g.IVS6 + 1G>A), whereas the hypothetical paternal mutation consists of a novel c.7036+2T>A (g.IVS40 + 2T>A). The father was not available for segregation analysis. Ex-vivo splicing assays and subsequent RT-PCR analyses were performed on mRNA isolated from the eukaryotic-cells transfected with normal and mutant expression vectors. Minigene analysis of the c.745+1G>A mutant showed that the exon 6 is skipped during pre-mRNA splicing or partially included by use of a cryptic 5' splice site located to 55 nucleotides upstream of the authentic exon 6/intron 6 junction site. The functional analysis of c.7036+2T>A mutation showed a complete skipping of exon 40. The theoretical consequences of splice site mutations, predicted with the bioinformatics tool NNSplice, Fsplice, SPL, SPLM and MaxEntScan programs were investigated and evaluated in relation with the experimental evidence. These analyses predicted that both mutant alleles would result in the abolition of the authentic splice donor sites. The c.745+1G>A mutation originates two putative truncated proteins of 200 and 1142 amino acids, whereas c.7036+2T>A mutation results in a putative truncated protein of 2277 amino acids. In conclusion, we show that the c.745+1G>A mutation promotes the activation of a new cryptic donor splice site in the exon 6 of the TG gene. The functional consequences of these mutations could be structural changes in the protein

Common pathological mutations in PQBP1 induce nonsense-mediated mRNA decay and enhance exclusion of the mutant exon.

Science.gov (United States)

Musante, Luciana; Kunde, Stella-Amrei; Sulistio, Tina O; Fischer, Ute; Grimme, Astrid; Frints, Suzanna G M; Schwartz, Charles E; Martínez, Francisco; Romano, Corrado; Ropers, Hans-Hilger; Kalscheuer, Vera M

2010-01-01

The polyglutamine binding protein 1 (PQBP1) gene plays an important role in X-linked mental retardation (XLMR). Nine of the thirteen PQBP1 mutations known to date affect the AG hexamer in exon 4 and cause frameshifts introducing premature termination codons (PTCs). However, the phenotype in this group of patients is variable. To investigate the pathology of these PQBP1 mutations, we evaluated their consequences on mRNA and protein expression. RT-PCRs revealed mutation-specific reduction of PQBP1 mRNAs carrying the PTCs that can be partially restored by blocking translation, thus indicating a role for the nonsense-mediated mRNA decay pathway. In addition, these mutations resulted in altered levels of PQBP1 transcripts that skipped exon 4, probably as a result of altering important splicing motifs via nonsense-associated altered splicing (NAS). This hypothesis is supported by transfection experiments using wild-type and mutant PQBP1 minigenes. Moreover, we show that a truncated PQBP1 protein is indeed present in the patients. Remarkably, patients with insertion/deletion mutations in the AG hexamer express significantly increased levels of a PQBP1 isoform, which is very likely encoded by the transcripts without exon 4, confirming the findings at the mRNA level. Our study provides significant insight into the early events contributing to the pathogenesis of the PQBP1 related XLMR disease.

Stemcell Information: SKIP000388 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000388 ... Diseased HPS0207 HPS0207 ... X連鎖アルファ-サラセミア・精神遅滞(ATR-X)症候群 ... Alpha-Thalassemia...l line derived from a patient :Alpha-Thalassemia/Mental Retardation Syndrome, X-Linked; ATRX. ... 疾患特異的iPS細胞株。X

Stemcell Information: SKIP001076 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001076 ... Fibroblast 線維芽細胞 Diseased ND35666 ND35666 ... 筋萎縮性側索硬化症 G122 amyotrop...mutation. Same subject as ND20522 (LCL) ALS 由来 (ND29509線維芽細胞)　SOD1 D91A変異 LCL (ND20522)有 human ES-like Resea

Stemcell Information: SKIP000182 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000182 ... Diseased GM23226 GM23226 ... 1型糖尿病 E10 diabetes (mellitus), juvenil...roblast. Multifactorial Defect 遺伝性若年発症I型糖尿病患者線維芽細胞（GM02416)由来iPS細胞 多因子の異常 human ES-like -- Retrovirus Oct4,

Stemcell Information: SKIP001077 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001077 ... Fibroblast 線維芽細胞 Diseased ND35668 ND35668 ... 筋萎縮性側索硬化症 G122 amyotrop...1 E49K mutation ALS 由来 (ND39026 線維芽細胞)　SOD1 E49K 変異 ... human ES-like Research Grade Retrovirus Oct4, Sox2, Klf

Stemcell Information: SKIP000941 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000941 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP04.2 SP04.2 ... パーキンソン病 G20 Parkinson...of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimenez-...0215 Disease-specific phenotypes in dopamine neurons from human iPS-based models

Stemcell Information: SKIP000938 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000938 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP02.1 SP02.1 ... パーキンソン病 G20 Parkinson...of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimenez-...0215 Disease-specific phenotypes in dopamine neurons from human iPS-based models

Stemcell Information: SKIP000947 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000947 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP14.1 SP14.1 ... パーキンソン病 G20 Parkinson...of genetic and sporadic Parkinson's disease. Sanchez-Danes A, Richaud-Patin Y, Carballo-Carbajal I, Jimenez-...0215 Disease-specific phenotypes in dopamine neurons from human iPS-based models

26 CFR 26.2662-1 - Generation-skipping transfer tax return requirements.

Science.gov (United States)

2010-04-01

... at death, the executor of the decedent's estate is liable for the tax imposed on that direct skip by...) Direct skip. In the case of a direct skip, on or before the date on which an estate or gift tax return is... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Generation-skipping transfer tax return...

See Before You Jump: Full Recognition of Parafoveal Words Precedes Skips During Reading

Science.gov (United States)

Gordon, Peter C.; Plummer, Patrick; Choi, Wonil

2013-01-01

Serial attention models of eye-movement control during reading were evaluated in an eye-tracking experiment that examined how lexical activation combines with visual information in the parafovea to affect word skipping (where a word is not fixated during first-pass reading). Lexical activation was manipulated by repetition priming created through prime-target pairs embedded within a sentence. The boundary technique (Rayner, 1975) was used to determine whether the target word was fully available during parafoveal preview or whether it was available with transposed letters (e.g., Herman changed to Hreman). With full parafoveal preview, the target word was skipped more frequently when it matched the earlier prime word (i.e., was repeated) than when it did not match the earlier prime word (i.e., was new). With transposed-letter (TL) preview, repetition had no effect on skipping rates despite the great similarity of the TL preview string to the target word and substantial evidence that TL strings activate the words from which they are derived (Perea & Lupker, 2003). These results show that lexically-based skipping is based on full recognition of the letter string in parafoveal preview and does not involve using the contextual constraint to compensate for the reduced information available from the parafovea. These results are consistent with models of eye-movement control during reading in which successive words in a text are processed one at a time (serially) and in which word recognition strongly influences eye movements. PMID:22686842

The relation between breakfast skipping and school performance in Adolescents

NARCIS (Netherlands)

Boschloo, A.M.; Ouwehand, C.; Dekker, S.J.; Lee, N.C.; de Groot, R.H.M.; Krabbendam, A.C.; Jolles, J.

2012-01-01

Breakfast skipping is common in adolescents, but research on the effects of breakfast skipping on school performance is scarce. This current cross-sectional survey study of 605 adolescents aged 11-18 years investigated whether adolescents who habitually skip breakfast have lower end-of-term grades

Social Inequalities in Young Children's Meal Skipping Behaviors: The Generation R Study.

Directory of Open Access Journals (Sweden)

Anne I Wijtzes

Full Text Available Regular meal consumption is considered an important aspect of a healthy diet. While ample evidence shows social inequalities in breakfast skipping among adolescents, little is known about social inequalities in breakfast skipping and skipping of other meals among young school-aged children. Such information is crucial in targeting interventions aimed to promote a healthy diet in children.We examined data from 4704 ethnically diverse children participating in the Generation R Study, a population-based prospective cohort study in Rotterdam, the Netherlands. Information on family socioeconomic position (SEP, ethnic background, and meal skipping behaviors was assessed by parent-reported questionnaire when the child was 6 years old. Multiple logistic regression analyses were performed to assess the associations of family SEP (educational level, household income, employment status, family composition and ethnic background with meal skipping behaviors, using high SEP children and native Dutch children as reference groups.Meal skipping prevalence ranged from 3% (dinner to 11% (lunch. The prevalence of meal skipping was higher among low SEP children and ethnic minority children. Maternal educational level was independently associated with breakfast skipping ([low maternal educational level] OR: 2.21; 95% CI: 1.24,3.94. Paternal educational level was independently associated with lunch skipping ([low paternal educational level] OR: 1.53; 95% CI: 1.06,2.20 and dinner skipping ([mid-high paternal educational level] OR: 0.39; 95% CI: 0.20,0.76. Household income was independently associated with breakfast skipping ([low income] OR: 2.43, 95% CI: 1.40,4.22 and dinner skipping ([low income] OR: 2.44; 95% CI: 1.22,4.91. In general, ethnic minority children were more likely to skip breakfast, lunch, and dinner compared with native Dutch children. Adjustment for family SEP attenuated the associations of ethnic minority background with meal skipping behaviors

A novel point mutation within the EDA gene causes an exon dropping in mature RNA in Holstein Friesian cattle breed affected by X-linked anhidrotic ectodermal dysplasia

Directory of Open Access Journals (Sweden)

Pariset Lorraine

2011-07-01

Full Text Available Abstract Background X-linked anhidrotic ectodermal dysplasia is a disorder characterized by abnormal development of tissues and organs of ectodermal origin caused by mutations in the EDA gene. The bovine EDA gene encodes the ectodysplasin A, a membrane protein expressed in keratinocytes, hair follicles and sweat glands, which is involved in the interactions between cell and cell and/or cell and matrix. Four mutations causing ectodermal dysplasia in cattle have been described so far. Results We identified a new single nucleotide polymorphism (SNP at the 9th base of exon 8 in the EDA gene in two calves of Holstein Friesian cattle breed affected by ectodermal dysplasia. This SNP is located in the exonic splicing enhancer (ESEs recognized by SRp40 protein. As a consequence, the spliceosome machinery is no longer able to recognize the sequence as exonic and causes exon skipping. The mutation determines the deletion of the entire exon (131 bp in the RNA processing, causing a severe alteration of the protein structure and thus the disease. Conclusion We identified a mutation, never described before, that changes the regulation of alternative splicing in the EDA gene and causes ectodermal dysplasia in cattle. The analysis of the SNP allows the identification of carriers that can transmit the disease to the offspring. This mutation can thus be exploited for a rational and efficient selection of unequivocally healthy cows for breeding.

Stemcell Information: SKIP001078 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001078 ... Fibroblast 線維芽細胞 Diseased ND35669 ND35669 NDS00076 NDS00076 筋萎縮性側索硬...(SNP, no amino acid change) ... ALS 患者由来 (線維芽細胞)　FIG4 27C>T (SNP アミノ酸置換なし） ... human ES-like Research Grade Retrov

Stemcell Information: SKIP000920 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000920 ... fibroblast 線維芽細胞 Diseased SLE#100H SLE#100H ... 全身性紅斑性狼瘡 M32.9 System...ic lupus erythematosus 152700 ... -- -- ... No No iPS cell line iPS cell line human ES-like Research Grad...Medicine, Mayo Clinic ... 22142803 10.1186/scrt89 Successful disease-specific induced pluripotent stem cell

Stemcell Information: SKIP000282 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000282 ... Diseased HPS0272 HPS0272 ... アトピー性皮膚炎 L209 Atopic dermatitis 603165...atitis. HPS0270 and HPS0271 are derived from the same patient. 疾患特異的iPS細胞株。アトピー性皮膚炎患者由来。HPS0270、HPS0271と同一人由

Stemcell Information: SKIP000734 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000734 ... Diseased GM24675 GM24675 APPDp2 APPDp2 アルツハイマー病 G309 ALZHEIMER DI... hiPSC derived from fibroblast 家族性アルツハイマー病患者（APP遺伝子重複)維芽細胞由来iPS細胞 human ES-like Research Grade Retrovirus OC

Stemcell Information: SKIP000279 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000279 ... Diseased HPS0192 HPS0192 ... 杉花粉症 J301 Allergic rhinitis (Pollen allergy) 607154 食物アレルギー...cell line derived from a patient: Allergic rhinitis (Pollen allergy). ... 疾患特異的iPS細胞株。杉花粉症 (カニアレルギーも)患者由来。 huma

Skip segment Hirschsprung disease and Waardenburg syndrome

OpenAIRE

Gross, Erica R.; Geddes, Gabrielle C.; McCarrier, Julie A.; Jarzembowski, Jason A.; Arca, Marjorie J.

2015-01-01

Skip segment Hirschsprung disease describes a segment of ganglionated bowel between two segments of aganglionated bowel. It is a rare phenomenon that is difficult to diagnose. We describe a recent case of skip segment Hirschsprung disease in a neonate with a family history of Waardenburg syndrome and the genetic profile that was identified.

Occipital horn syndrome and classical Menkes syndrome caused by deep intronic mutations, leading to the activation of ATP7A pseudo-exon

DEFF Research Database (Denmark)

Yasmeen, Saiqa; Lund, Katrine; De Paepe, Anne

2014-01-01

Menkes disease is an X-linked disorder of copper metabolism caused by mutations in the ATP7A gene. Whereas most of the patients exhibit a severe classical form, about 9% of the patients exhibit a milder form of Menkes disease. The mildest form is called occipital horn syndrome (OHS). Mutations...... patients: two patients with OHS and one patient with classical Menkes disease. The pseudo-exons were inserted between exons 10 and 11, between exons 16 and 17 and between exons 14 and 15 in the three patients, as a result of deep intronic mutations. This is the first time the activation of pseudo...... mechanism, which has hitherto been overlooked.European Journal of Human Genetics advance online publication, 4 September 2013; doi:10.1038/ejhg.2013.191....

Efficient use of a translation start codon in BDNF exon I.

Science.gov (United States)

Koppel, Indrek; Tuvikene, Jürgen; Lekk, Ingrid; Timmusk, Tõnis

2015-09-01

The brain-derived neurotrophic factor (BDNF) gene contains a number of 5' exons alternatively spliced with a common 3' exon. BDNF protein is synthesized from alternative transcripts as a prepro-precursor encoded by the common 3' exon IX, which has a translation start site 21 bp downstream of the splicing site. BDNF mRNAs containing exon I are an exception to this arrangement as the last three nucleotides of this exon constitute an in-frame AUG. Here, we show that this AUG is efficiently used for translation initiation in PC12 cells and cultured cortical neurons. Use of exon I-specific AUG produces higher levels of BDNF protein than use of the common translation start site, resulting from a higher translation rate. No differences in protein degradation, constitutive or regulated secretion were detected between BDNF isoforms with alternative 5' termini. As the BDNF promoter preceding exon I is known to be highly regulated by neuronal activity, our results suggest that the function of this translation start site may be efficient stimulus-dependent synthesis of BDNF protein. The brain-derived neurotrophic factor (BDNF) gene contains multiple untranslated 5' exons alternatively spliced to one common protein-coding 3' exon. However, exon I contains an in-frame ATG in a favorable translation context. Here, we show that use of this ATG is associated with more efficient protein synthesis than the commonly used ATG in exon IX. © 2015 International Society for Neurochemistry.

The Relation between Breakfast Skipping and School Performance in Adolescents

Science.gov (United States)

Boschloo, Annemarie; Ouwehand, Carolijn; Dekker, Sanne; Lee, Nikki; de Groot, Renate; Krabbendam, Lydia; Jolles, Jelle

2012-01-01

Breakfast skipping is common in adolescents, but research on the effects of breakfast skipping on school performance is scarce. This current cross-sectional survey study of 605 adolescents aged 11-18 years investigated whether adolescents who habitually skip breakfast have lower end-of-term grades than adolescents who eat breakfast daily.…

Skip segment Hirschsprung disease and Waardenburg syndrome

Directory of Open Access Journals (Sweden)

Erica R. Gross

2015-04-01

Full Text Available Skip segment Hirschsprung disease describes a segment of ganglionated bowel between two segments of aganglionated bowel. It is a rare phenomenon that is difficult to diagnose. We describe a recent case of skip segment Hirschsprung disease in a neonate with a family history of Waardenburg syndrome and the genetic profile that was identified.

Origins and Impacts of New Mammalian Exons

Directory of Open Access Journals (Sweden)

Jason J. Merkin

2015-03-01

Full Text Available Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from five mammals and one bird, identifying thousands of species- and lineage-specific exons. Most new exons derived from unique rather than repetitive intronic sequence. Unlike exons conserved across mammals, species-specific internal exons were mostly located in 5′ UTRs and alternatively spliced. They were associated with upstream intronic deletions, increased nucleosome occupancy, and RNA polymerase II pausing. Genes containing new internal exons had increased gene expression, but only in tissues in which the exon was included. Increased expression correlated with the level of exon inclusion, promoter proximity, and signatures of cotranscriptional splicing. Altogether, these findings suggest that increased splicing at the 5′ ends of genes enhances expression and that changes in 5′ end splicing alter gene expression between tissues and between species.

Longitudinal effect of eteplirsen versus historical control on ambulation in Duchenne muscular dystrophy

Science.gov (United States)

Goemans, Nathalie; Lowes, Linda P.; Alfano, Lindsay N.; Berry, Katherine; Shao, James; Kaye, Edward M.; Mercuri, Eugenio; Hamid, Hoda Abdel; Byrne, Barry J.; Connolly, Anne M.; Dracker, Robert A.; Matthew Frank, L.; Heydemann, Peter T.; O'Brien, Kevin C.; Sparks, Susan E.; Specht, Linda A.; Rodino‐Klapac, Louise; Sahenk, Zarife; Al‐Zaidy, Samiah; Cripe, Linda H.; Lewis, Sarah; M, Pane; E, Mazzone; S, Messina; GL, Vita; Bertini, D Amico A; Casimiro, Berardinelli A; Y, Torrente; F, Magri; GP, Comi; G, Baranello; T, Mongini; A, Pini; R, Battini; E, Pegoraro; C, Bruno; L, Politano; S, Previtali

2016-01-01

Objective To continue evaluation of the long‐term efficacy and safety of eteplirsen, a phosphorodiamidate morpholino oligomer designed to skip DMD exon 51 in patients with Duchenne muscular dystrophy (DMD). Three‐year progression of eteplirsen‐treated patients was compared to matched historical controls (HC). Methods Ambulatory DMD patients who were ≥7 years old and amenable to exon 51 skipping were randomized to eteplirsen (30/50mg/kg) or placebo for 24 weeks. Thereafter, all received eteplirsen on an open‐label basis. The primary functional assessment in this study was the 6‐Minute Walk Test (6MWT). Respiratory muscle function was assessed by pulmonary function testing (PFT). Longitudinal natural history data were used for comparative analysis of 6MWT performance at baseline and months 12, 24, and 36. Patients were matched to the eteplirsen group based on age, corticosteroid use, and genotype. Results At 36 months, eteplirsen‐treated patients (n = 12) demonstrated a statistically significant advantage of 151m (p < 0.01) on 6MWT and experienced a lower incidence of loss of ambulation in comparison to matched HC (n = 13) amenable to exon 51 skipping. PFT results remained relatively stable in eteplirsen‐treated patients. Eteplirsen was well tolerated. Analysis of HC confirmed the previously observed change in disease trajectory at age 7 years, and more severe progression was observed in patients with mutations amenable to exon skipping than in those not amenable. The subset of patients amenable to exon 51 skipping showed a more severe disease course than those amenable to any exon skipping. Interpretation Over 3 years of follow‐up, eteplirsen‐treated patients showed a slower rate of decline in ambulation assessed by 6MWT compared to untreated matched HC. Ann Neurol 2016;79:257–271 PMID:26573217

Stemcell Information: SKIP000261 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available Sample_Detail.aspx?Ref=GM23762&PgId=166 ... 21490598 10.1038/nature09915 Modelling schizophrenia using human... SKIP000261 ... Diseased GM23762 GM23762 ... 統合失調症 F20 Schizophrenia 181500 ... ...cally affected with Shizophrenia(SCZD) . 統合失調症患者線維芽細胞(GM02497)由来iPS細胞株。 | human ES-like -- Retrovirus Oct4,

Stemcell Information: SKIP000176 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available male Black Black -- No Apparently healthy iPSCs from APPARENTLY HEALTHY FETAL lung fibroblast cell culture (GM06112) 健常胎児肺線維芽細胞... SKIP000176 ... Lung Fibroblast 肺線維芽細胞 Normal GM23413 GM23413 ... 0-9 Fe...(GM06112)由来iPS細胞株 human ES-like -- Retrovirus Oct4, Sox2, Klf, c-Myc, retroviral vectors

Power inverter implementing phase skipping control

Science.gov (United States)

Somani, Utsav; Amirahmadi, Ahmadreza; Jourdan, Charles; Batarseh, Issa

2016-10-18

A power inverter includes a DC/AC inverter having first, second and third phase circuitry coupled to receive power from a power source. A controller is coupled to a driver for each of the first, second and third phase circuitry (control input drivers). The controller includes an associated memory storing a phase skipping control algorithm, wherein the controller is coupled to receive updating information including a power level generated by the power source. The drivers are coupled to control inputs of the first, second and third phase circuitry, where the drivers are configured for receiving phase skipping control signals from the controller and outputting mode selection signals configured to dynamically select an operating mode for the DC/AC inverter from a Normal Control operation and a Phase Skipping Control operation which have different power injection patterns through the first, second and third phase circuitry depending upon the power level.

Stemcell Information: SKIP001115 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001115 ... Diseased D2-1 D2-1 ... 統合失調症 F209 schizophrenia ... 605210 ... 39 ...30-39 Female ... Yes No iPS cells derived from fibroblasts of a patient in which a frameshift mutation of disrupted in schizophrenia... 1 ( DISC1 ) 統合失調症患者由来iPS細胞 human ES-like Research Grade Plasmid OCT4,SOX2,KLF4,c-MYC,

Stemcell Information: SKIP001116 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001116 ... Diseased D2-2 D2-2 ... 統合失調症 F209 schizophrenia ... 605210 ... 39 ...30-39 Female ... Yes No iPS cells derived from fibroblasts of a patient in which a frameshift mutation of disrupted in schizophrenia... 1 ( DISC1 ) 統合失調症患者由来iPS細胞 human ES-like Research Grade Plasmid OCT4,SOX2,KLF4,c-MYC,

Stemcell Information: SKIP000260 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available x?Ref=GM23761&PgId=166 ... 21490598 10.1038/nature09915 Modelling schizophrenia using human induced pluripot... SKIP000260 ... Diseased GM23761 GM23761 ... 統合失調症 F20 Schizophrenia 181500 ... ...h Shizophrenia(SCZD) . | 統合失調症患者線維芽細胞(GM01835)由来iPS細胞株| human ES-like -- Lentivirus Oct4, Sox2, Klf4, c-Myc,

Optimized Exon-Exon Junction Library and its Application on Rodents' Brain Transcriptome Analysis

Directory of Open Access Journals (Sweden)

Tong-Hai Dou

2017-05-01

Full Text Available ABSTRACT Background: Alternative splicing (AS, which plays an important role in gene expression and functional regulation, has been analyzed on genome-scale by various bioinformatic approaches based on RNA-seq data. Compared with the huge number of studies on mouse, the AS researches approaching the rat, whose genome is intermedia between mouse and human, were still limited. To enrich the knowledge on AS events in rodents' brain, we perfomed a comprehensive analysis on four transcriptome libraries (mouse cerebrum, mouse cerebellum, rat cerebrum, and rat cerebellum, recruiting high-throughput sequencing technology. An optimized exon-exon junction library approach was introduced to adapt the longer RNA-seq reads and to improve mapping efficiency. Results: In total, 7,106 mouse genes and 2,734 rat genes were differentially expressed between cerebrum and cerebellum, while 7,125 mouse genes and 1,795 rat genes exhibited varieties on transcript variant level. Only half of the differentially expressed exon-exon junctions could be reflected at gene expression level. Functional cluster analysis showed that 32 pathways in mouse and 9 pathways in rat were significantly enriched, and 6 of them were in both. Interestingly, some differentially expressed transcript variants did not show difference on gene expression level, such as PLCβ1 and Kcnma1. Conclusion: Our work provided a case study of a novel exon-exon junction strategy to analyze the expression of genes and isoforms, helping us understand which transcript contributes to the overall expression and further functional change.

Identification of five novel FBN1 mutations by non-radioactive single-strand conformation analysis

Energy Technology Data Exchange (ETDEWEB)

Liu, W.; Qian, C.; Comeau, K.; Francke, U. [Stanford Univ. Medical Center, Stanford, CA (United States)

1994-09-01

Marfan syndrome (MFS), one of the most common genetic disorders of connective tissue, is characterized by variable manifestations in skeletal, cardiovascular and ocular systems. Mutations in the fibrillin gene on chromosome 15 (FBN1) have been shown to cause MFS. To examine the relationship between FBN1 gene mutations, fibrillin protein function and MFS phenotypes, we screened for alternations in the fibrillin coding sequence in fibroblast derived cDNA from MFS patients. To date, abnormally migrating bands in more than 20 unrelated MFS patients have been identified by using non-radioactive single-strand conformation analysis and silver staining. Five altered bands have been directly sequenced. Two missense mutations and three splice site mutations have been identified. Both missense mutations substitute another amino acid for a cysteine residue (C1402W and C1672R) in EGF-like motifs of the fibrillin polypeptide chain. The two splice site mutations are at nucleotide positions 6994+1 (G{yields}A), and 7205-2 (A{yields}G) and result in in-frame skipping of exon 56 and 58, respectively. Skipping of exon 56 occurs in 50% of mutant transcripts. Use of a cryptic splice site 51 bp upstream of the normal donor site results in half of the mutant transcripts containing part of exon 56. Both products contain in-frame deletions. Another splice site mutation, identified by exon screening from patient genomic DNA using intron primers, is at nucleotide position 2293+2 (T{yields}A), but the predicted exon skipping has not been detected at the RT-PCR level. This may be due to instability of the mutant transcript. Including the mutations reported here, a total of 8 out of 36 published FBN1 gene mutations involve exon skipping. It may be inferred that FBN1 exon skipping plays an important pathogenic role in MFS.

Stemcell Information: SKIP000330 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000330 ... mesenchymal stem cell 間葉系幹細胞 polydactylous human fingers 指 Normal Yub...ovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3377 ... ...621BMC Yub621BMC JCRB1113 JCRB1113 ... -- -- ... -- No JCRB1113 ... bone marrow-derived mesenchymal stem cell

Stemcell Information: SKIP000333 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000333 ... mesenchymal stem cell 間葉系幹細胞 polydactylous human fingers 指 Normal Yub...ター研究所 ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cell... 10F Yub 10F JCRB1116 JCRB1116 ... -- -- ... -- No JCRB1116 mesenchymal stem cell finite proliferatio

Optimized Skip-Stop Metro Line Operation Using Smart Card Data

Directory of Open Access Journals (Sweden)

Peitong Zhang

2017-01-01

Full Text Available Skip-stop operation is a low cost approach to improving the efficiency of metro operation and passenger travel experience. This paper proposes a novel method to optimize the skip-stop scheme for bidirectional metro lines so that the average passenger travel time can be minimized. Different from the conventional “A/B” scheme, the proposed Flexible Skip-Stop Scheme (FSSS can better accommodate spatially and temporally varied passenger demand. A genetic algorithm (GA based approach is then developed to efficiently search for the optimal solution. A case study is conducted based on a real world bidirectional metro line in Shenzhen, China, using the time-dependent passenger demand extracted from smart card data. It is found that the optimized skip-stop operation is able to reduce the average passenger travel time and transit agencies may benefit from this scheme due to energy and operational cost savings. Analyses are made to evaluate the effects of that fact that certain number of passengers fail to board the right train (due to skip operation. Results show that FSSS always outperforms the all-stop scheme even when most passengers of the skipped OD pairs are confused and cannot get on the right train.

Antisense-mediated isoform switching of steroid receptor coactivator-1 in the central nucleus of the amygdala of the mouse brain

Directory of Open Access Journals (Sweden)

Zalachoras Ioannis

2013-01-01

Full Text Available Abstract Background Antisense oligonucleotide (AON-mediated exon skipping is a powerful tool to manipulate gene expression. In the present study we investigated the potential of exon skipping by local injection in the central nucleus of the amygdala (CeA of the mouse brain. As proof of principle we targeted the splicing of steroid receptor coactivator-1 (SRC-1, a protein involved in nuclear receptor function. This nuclear receptor coregulator exists in two splice variants (SRC-1a and SRC-1e which display differential distribution and opposing activities in the brain, and whose mRNAs differ in a single SRC-1e specific exon. Methods For proof of principle of feasibility, we used immunofluorescent stainings to study uptake by different cell types, translocation to the nucleus and potential immunostimulatory effects at different time points after a local injection in the CeA of the mouse brain of a control AON targeting human dystrophin with no targets in the murine brain. To evaluate efficacy we designed an AON targeting the SRC-1e-specific exon and with qPCR analysis we measured the expression ratio of the two splice variants. Results We found that AONs were taken up by corticotropin releasing hormone expressing neurons and other cells in the CeA, and translocated into the cell nucleus. Immune responses after AON injection were comparable to those after sterile saline injection. A successful shift of the naturally occurring SRC-1a:SRC-1e expression ratio in favor of SRC-1a was observed, without changes in total SRC-1 expression. Conclusions We provide a proof of concept for local neuropharmacological use of exon skipping by manipulating the expression ratio of the two splice variants of SRC-1, which may be used to study nuclear receptor function in specific brain circuits. We established that exon skipping after local injection in the brain is a versatile and useful tool for the manipulation of splice variants for numerous genes that are relevant

A novel whole exon deletion in WWOX gene causes early epilepsy, intellectual disability and optic atrophy.

Science.gov (United States)

Ben-Salem, Salma; Al-Shamsi, Aisha M; John, Anne; Ali, Bassam R; Al-Gazali, Lihadh

2015-05-01

Recent studies have implicated the WW domain-containing oxidoreductase encoding gene (WWOX) in a severe form of autosomal recessive neurological disorder. This condition showed an overlapping spectrum of clinical features including spinocerebellar ataxia associated with generalized seizures and delayed psychomotor development to growth retardation, spasticity, and microcephaly. We evaluated a child from a consanguineous Emirati family that presented at birth with growth retardation, microcephaly, epileptic seizures, and later developed spasticity and delayed psychomotor development. Screening for deletions and duplications using whole-chromosomal microarray analysis identified a novel homozygous microdeletion encompassing exon 5 of the WWOX gene. Analysis of parental DNA indicated that this deletion was inherited from both parents and lies within a large region of homozygosity. Sanger sequencing of the cDNA showed that the deletion resulted in exon 5 skipping leading to a frame-shift and creating a premature stop codon at amino acid position 212. Quantification of mRNA revealed striking low level of WWOX expression in the child and moderate level of expression in the mother compared to a healthy control. To the best of our knowledge, this is the first homozygous germline structural variation in WWOX gene resulting in truncated transcripts that were presumably subject to NMD pathway. Our findings extend the clinical and genetic spectrum of WWOX mutations and support a crucial role of this gene in neurological development.

Oncogenic exon 2 mutations in Mediator subunit MED12 disrupt allosteric activation of cyclin C-CDK8/19.

Science.gov (United States)

Park, Min Ju; Shen, Hailian; Spaeth, Jason M; Tolvanen, Jaana H; Failor, Courtney; Knudtson, Jennifer F; McLaughlin, Jessica; Halder, Sunil K; Yang, Qiwei; Bulun, Serdar E; Al-Hendy, Ayman; Schenken, Robert S; Aaltonen, Lauri A; Boyer, Thomas G

2018-03-30

Somatic mutations in exon 2 of the RNA polymerase II transcriptional Mediator subunit MED12 occur at high frequency in uterine fibroids (UFs) and breast fibroepithelial tumors as well as recurrently, albeit less frequently, in malignant uterine leimyosarcomas, chronic lymphocytic leukemias, and colorectal cancers. Previously, we reported that UF-linked mutations in MED12 disrupt its ability to activate cyclin C (CycC)-dependent kinase 8 (CDK8) in Mediator, implicating impaired Mediator-associated CDK8 activity in the molecular pathogenesis of these clinically significant lesions. Notably, the CDK8 paralog CDK19 is also expressed in myometrium, and both CDK8 and CDK19 assemble into Mediator in a mutually exclusive manner, suggesting that CDK19 activity may also be germane to the pathogenesis of MED12 mutation-induced UFs. However, whether and how UF-linked mutations in MED12 affect CDK19 activation is unknown. Herein, we show that MED12 allosterically activates CDK19 and that UF-linked exon 2 mutations in MED12 disrupt its CDK19 stimulatory activity. Furthermore, we find that within the Mediator kinase module, MED13 directly binds to the MED12 C terminus, thereby suppressing an apparent UF mutation-induced conformational change in MED12 that otherwise disrupts its association with CycC-CDK8/19. Thus, in the presence of MED13, mutant MED12 can bind, but cannot activate, CycC-CDK8/19. These findings indicate that MED12 binding is necessary but not sufficient for CycC-CDK8/19 activation and reveal an additional step in the MED12-dependent activation process, one critically dependent on MED12 residues altered by UF-linked exon 2 mutations. These findings confirm that UF-linked mutations in MED12 disrupt composite Mediator-associated kinase activity and identify CDK8/19 as prospective therapeutic targets in UFs. © 2018 Park et al.

Stemcell Information: SKIP000924 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000924 ... dermal fibroblast 表皮繊維芽細胞 Diseased CPVT-iPS c5 CPVT-iPS c5 ... カテコラミン... line iPS細胞 human ES-like Research Grade Retrovirus SOX2, KLF4, OCT3/4 and c-MYC (pMX-based...誘発多形性心室頻拍 I47.2 Catecholaminergic polymorphic ventricular tachycardia type 1 604772 ... 46 40-49 Female ... Yes No iPS cell

Stemcell Information: SKIP000328 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000328 ... mesenchymal stem cell 間葉系幹細胞 polydactylous human fingers 指 Normal Yub... ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3375 ... ...621c Yub621c JCRB1111 JCRB1111 ... -- -- ... -- No JCRB1111 cartilige-derived messenchymal stem cell.

Stemcell Information: SKIP000748 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available B1345. Ph1 chromosome-positive human acute lymphoblastic leukemia cell line. Single Ph1 chromosome observed. 白血病... SKIP000748 ... acute lymphoblastic leukemia cell line 急性リンパ芽球 ... Diseased PALL-2 PALL...c and molecular analysis of Ph1-chromosome-positive acute lymphoblastic leukemia cell lines. Miyagi T, Ohyas...-2 JCRB1345 JCRB1345 急性リンパ性白血病 C910 Acute lymphoblastic leukaemia [ALL] 613065 ... -- Male ... Yes No JCR

Stemcell Information: SKIP000280 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000280 ... Diseased HPS0209 HPS0209 ... 肺性高血圧症 I270 Pulmonary hypertension 178...600 ... -- -- Japanese Japanese Yes No Disease specific iPS cell line derived from a patient: Pulmonary hypertension.... ... 疾患特異的iPS細胞株。肺性高血圧症患者由来。 human ES-like -- Sendai virus SeV18+HS-OCT3/4/TSΔF, SeV18+HS-SOX2/TS

Stemcell Information: SKIP000865 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000865 ... Diseased HPS0211 HPS0211 ... 肺性高血圧症 I270 Pulmonary hypertension 178...600 ... -- -- Japanese 日本人 Yes No Disease specific iPS cell line derived from a patient : Pulmonary hypertension.... HPS0209 was derived from the same patient. ... 疾患特異的iPS細胞株。肺性高血圧症患者由来。HPS0209と同一人由来。 human ES-like R

Stemcell Information: SKIP000329 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000329 ... mesenchymal stem cell 間葉系幹細胞 polydactylous human fingers 指 Normal Yub... Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3376 ... ...621b Yub621b JCRB1112 JCRB1112 ... -- -- ... -- No JCRB1112 bone-derived mesenchymal stem cell. finit

Word skipping: effects of word length, predictability, spelling and reading skill.

Science.gov (United States)

Slattery, Timothy J; Yates, Mark

2017-08-31

Readers eyes often skip over words as they read. Skipping rates are largely determined by word length; short words are skipped more than long words. However, the predictability of a word in context also impacts skipping rates. Rayner, Slattery, Drieghe and Liversedge (2011) reported an effect of predictability on word skipping for even long words (10-13 characters) that extend beyond the word identification span. Recent research suggests that better readers and spellers have an enhanced perceptual span (Veldre & Andrews, 2014). We explored whether reading and spelling skill interact with word length and predictability to impact word skipping rates in a large sample (N=92) of average and poor adult readers. Participants read the items from Rayner et al. (2011) while their eye movements were recorded. Spelling skill (zSpell) was assessed using the dictation and recognition tasks developed by Sally Andrews and colleagues. Reading skill (zRead) was assessed from reading speed (words per minute) and accuracy of three 120 word passages each with 10 comprehension questions. We fit linear mixed models to the target gaze duration data and generalized linear mixed models to the target word skipping data. Target word gaze durations were significantly predicted by zRead while, the skipping likelihoods were significantly predicted by zSpell. Additionally, for gaze durations, zRead significantly interacted with word predictability as better readers relied less on context to support word processing. These effects are discussed in relation to the lexical quality hypothesis and eye movement models of reading.

Asthma and COPD in cystic fibrosis intron-8 5T carriers. A population-based study

DEFF Research Database (Denmark)

Dahl, Morten; Tybjaerg-Hansen, Anne; Lange, Peter

2005-01-01

Carriers of cystic fibrosis intron-8 5T alleles with high exon-9 skipping could have increased annual lung function decline and increased risk for asthma or chronic obstructive pulmonary disease (COPD).......Carriers of cystic fibrosis intron-8 5T alleles with high exon-9 skipping could have increased annual lung function decline and increased risk for asthma or chronic obstructive pulmonary disease (COPD)....

Stemcell Information: SKIP000817 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000817 ... Diseased ACHhomo-8859-3 ACHhomo-8859-3 ... 軟骨無形成症 Q774 Achondroplasia... 100800 ... 0-9 Female Japanese Japanese Yes No Achondroplasia(GM08859)-specific iPSC.GM08859 is from... the homozygous child of GM08857 and GM08858. 軟骨無形成症患者(GM08859)繊維芽細胞由来iPS細胞。|GM08859はGM08858の母親とGM08857の父親の子

Stemcell Information: SKIP000993 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ISEASE 8, AUTOSOMAL DOMINANT; PARK8 607060 ... 78 70-79 Female ... Yes No iPS cells from familial Parkinson... SKIP000993 ... Diseased PARK8-LB16 PARK8-LB16 ... 遺伝性パーキンソン病：PARK8 G20 PARKINSON D...'s disease patient ... 遺伝性パーキンソン病患者由来iPS細胞 human ES-like Research Grade Lentivirus Klf4, Sox2, Oct4, c-Myc ... Ye

Stemcell Information: SKIP000991 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available EASE 8, AUTOSOMAL DOMINANT; PARK8 607060 ... 66 60-69 Female ... Yes No iPS cells from familial Parkinson's disease patient ... 遺伝性パーキ... SKIP000991 ... Diseased PARK8-LA5 PARK8-LA5 ... 遺伝性パーキンソン病：PARK8 G20 PARKINSON DIS...ンソン病患者由来iPS細胞 human ES-like Research Grade Lentivirus Klf4, Sox2, Oct4, c-Myc ... Yes

Stemcell Information: SKIP000992 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ISEASE 8, AUTOSOMAL DOMINANT; PARK8 607060 ... 66 60-69 Female ... Yes No iPS cells from familial Parkinson... SKIP000992 ... Diseased PARK8-LA11 PARK8-LA11 ... 遺伝性パーキンソン病：PARK8 G20 PARKINSON D...'s disease patient ... 遺伝性パーキンソン病患者由来iPS細胞 human ES-like Research Grade Lentivirus Klf4, Sox2, Oct4, c-Myc ... Ye

Stemcell Information: SKIP000994 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ISEASE 8, AUTOSOMAL DOMINANT; PARK8 607060 ... 78 70-79 Female ... Yes No iPS cells from familial Parkinson... SKIP000994 ... Diseased PARK8-LB21 PARK8-LB21 ... 遺伝性パーキンソン病：PARK8 G20 PARKINSON D...'s disease patient ... 遺伝性パーキンソン病患者由来iPS細胞 human ES-like Research Grade Lentivirus Klf4, Sox2, Oct4, c-Myc ... Ye

Stemcell Information: SKIP000845 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000845 ... unknown 不明 Diseased Sporadic PD-1 Sporadic PD-1 10005.117.01 10005.117.01 パーキンソン病 G20 Parkin...son Disease 168600 ... 65 60-69 Female ... No No Transgene-free iPS cells from Sporadic Parkinson...lrep.2014.10.023 iPSC-derived dopamine neurons reveal differences between monozygotic twins discordant for Parkinson... Disease patient.Using CytoTune iPS Sendai reprogramming protocol (Life Technologies). 孤発性パーキンソン

Alternative splicing at exon 2 results in the loss of the catalytic activity of mouse DNA polymerase iota in vitro.

Science.gov (United States)

Kazachenko, Konstantin Y; Miropolskaya, Nataliya A; Gening, Leonid V; Tarantul, Vyacheslav Z; Makarova, Alena V

2017-02-01

Y-family DNA polymerase iota (Pol ι) possesses both DNA polymerase and dRP lyase activities and was suggested to be involved in DNA translesion synthesis and base excision repair in mammals. The 129 strain of mice and its derivatives have a natural nonsense codon mutation in the second exon of the Pol ι gene resulting in truncation of the Pol ι protein. These mice were widely used as a Pol ι-null model for in vivo studies of the Pol ι function. However whether 129-derived strains of mice are fully deficient in the Pol ι functions was a subject of discussion since Pol ι mRNA undergoes alternative splicing at exon 2. Here we report purification of mouse Pol ι lacking the region encoded by exon 2, which includes several conserved residues involved in catalysis. We show that the deletion abrogates both the DNA polymerase and dRP lyase activities of Pol ι in the presence of either Mg 2+ or Mn 2+ ions. Thus, 129-derived strains of mice express catalytically inactive alternatively spliced Pol ι variant, whose cellular functions, if any exist, remain to be established. Copyright © 2017 Elsevier B.V. All rights reserved.

Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene

Directory of Open Access Journals (Sweden)

Shomron Noam

2007-11-01

Full Text Available Abstract Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes. Results Genome-wide analysis of exonization of transposed elements revealed a higher rate of exonization within duplicated genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, underwent a humanoid-specific triplication, all three copies of the gene are active transcriptionally, although only one copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted into the first intron. In one of the non-protein coding copies, this Alu is exonized. We identified a single point mutation leading to exonization in one of the gene duplicates. When this mutation was introduced into the TIF-IA coding copy, exonization was activated and the level of the protein-coding mRNA was reduced substantially. A very low level of exonization was detected in normal human cells. However, this exonization was abundant in most leukemia cell lines evaluated, although the genomic sequence is unchanged in these cancerous cells compared to normal cells. Conclusion The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. These results further our understanding of the delicate interplay between gene duplication and alternative splicing and of the molecular evolutionary mechanisms leading to genetic innovations. This implies the existence of purifying selection against exonization in single copy genes, with duplicate genes free from such constrains.

Dystrophin quantification and clinical correlations in Becker muscular dystrophy: implications for clinical trials.

Science.gov (United States)

Anthony, Karen; Cirak, Sebahattin; Torelli, Silvia; Tasca, Giorgio; Feng, Lucy; Arechavala-Gomeza, Virginia; Armaroli, Annarita; Guglieri, Michela; Straathof, Chiara S; Verschuuren, Jan J; Aartsma-Rus, Annemieke; Helderman-van den Enden, Paula; Bushby, Katherine; Straub, Volker; Sewry, Caroline; Ferlini, Alessandra; Ricci, Enzo; Morgan, Jennifer E; Muntoni, Francesco

2011-12-01

Duchenne muscular dystrophy is caused by mutations in the DMD gene that disrupt the open reading frame and prevent the full translation of its protein product, dystrophin. Restoration of the open reading frame and dystrophin production can be achieved by exon skipping using antisense oligonucleotides targeted to splicing elements. This approach aims to transform the Duchenne muscular dystrophy phenotype to that of the milder disorder, Becker muscular dystrophy, typically caused by in-frame dystrophin deletions that allow the production of an internally deleted but partially functional dystrophin. There is ongoing debate regarding the functional properties of the different internally deleted dystrophins produced by exon skipping for different mutations; more insight would be valuable to improve and better predict the outcome of exon skipping clinical trials. To this end, we have characterized the clinical phenotype of 17 patients with Becker muscular dystrophy harbouring in-frame deletions relevant to on-going or planned exon skipping clinical trials for Duchenne muscular dystrophy and correlated it to the levels of dystrophin, and dystrophin-associated protein expression. The cohort of 17 patients, selected exclusively on the basis of their genotype, included 4 asymptomatic, 12 mild and 1 severe patient. All patients had dystrophin levels of >40% of control and significantly higher dystrophin (P = 0.013), β-dystroglycan (P = 0.025) and neuronal nitric oxide synthase (P = 0.034) expression was observed in asymptomatic individuals versus symptomatic patients with Becker muscular dystrophy. Furthermore, grouping the patients by deletion, patients with Becker muscular dystrophy with deletions with an end-point of exon 51 (the skipping of which could rescue the largest group of Duchenne muscular dystrophy deletions) showed significantly higher dystrophin levels (P = 0.034) than those with deletions ending with exon 53. This is the first quantitative study on both

A novel deletion in the splice donor site of MLH1 exon 6 in a Japanese colon cancer patient with Lynch syndrome.

Science.gov (United States)

Yamaguchi, Junya; Sato, Yuri; Kita, Mizuho; Nomura, Sachio; Yamamoto, Noriko; Kato, Yo; Ishikawa, Yuichi; Arai, Masami

2015-10-01

Lynch syndrome is an autosomal dominantly inherited disease that is characterized by a predisposition to cancers, mainly colorectal cancer. Germline mutations of DNA mismatch repair genes such as MLH1, MSH2, MSH6 and PMS2 have been described in patients with Lynch syndrome. Here, we report deletion of 2 bp in the splice donor site of the MLH1 exon 6 (c.545+4_545+5delCA) in a 48-year-old Japanese woman with Lynch syndrome. RT-PCR direct sequencing analysis revealed that this mutation led to an increase in the level of an MLH1 transcript in which exon 6 was skipped, and may cause a frameshift (p.E153FfsX8). Therefore, this mutation appears to be pathogenic and is responsible for Lynch syndrome. Additionally, analysis of the patient's tumor cells indicated microsatellite instability high phenotype and loss of the MLH1 and PMS2 proteins. To our knowledge, this is a germline splice site mutation of MLH1 that has not been reported previously. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Stemcell Information: SKIP000944 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available inson disease 168006 ... 66 60-69 Female ... No No iPS cell line iPS細胞 human ES-like Research Grade Retrov... SKIP000944 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP08.3 SP08.3 ... パーキンソン病 G20 Park...irus SOX2, KLF4 and OCT3/4 Yes Yes MEFs Lines of patient-specific iPS cells were maintained by mechanical di...ssociation of colonies and splitting 1:3 onto feeder cells in hESC medium or by l

Stemcell Information: SKIP000644 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000644 ... umbilical cord 臍帯(線維芽細胞) Normal HiPS-RIKEN-2D HiPS-RIKEN-2D ... ...bilical cord fibroblast, male) 臍帯由来線維芽細胞（RCB0197 HUC-Fm)iPS細胞. human ES-like Research Grade Retrovirus ... Oct3... ... Fetus Male Japanese Japanese -- No Human iPS cell line. Parent cell line of RCB0197 HUC-Fm(Normal um...010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shimizu

Stemcell Information: SKIP000706 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000706 ... mesenchymal stem cell 間葉系幹細胞 placenta 胎盤 Normal PL502 PL502 ... ... ... -- -- ... -- No JCRB1125 mesenchymal stem cell. finite prolieferation 胎盤由来間葉系幹細胞(有限増殖) fibroblast-like -...lable National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3548 ...

Stemcell Information: SKIP001095 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(1439 KURABO)| 新生児皮膚繊維芽細胞(1439 KURABO)由来iPS細胞 human ES-like Research ...on, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001095 ... Normal WT-1-#1 WT-1-#1 ... 0-9 Male ... -- No Nomal human iPS cell...ling type II collagenopathy skeletal dysplasia by directed conversion and induced pluripotent stem cell

Stemcell Information: SKIP000940 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available inson disease 168006 ... 46 40-49 Male ... No No iPS cell line iPS細胞 human ES-like Research Grade Retrovir... SKIP000940 ... dermal fibroblast 表皮繊維芽細胞 Diseased SP04.1 SP04.1 ... パーキンソン病 G20 Park...us SOX2, KLF4 and OCT3/4 Yes Yes MEFs Lines of patient-specific iPS cells were maintained by mechanical diss...ociation of colonies and splitting 1:3 onto feeder cells in hESC medium or by lim

Stemcell Information: SKIP000637 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000637 ... umbilical cord 臍帯(線維芽細胞) Normal HiPS-RIKEN-1B HiPS-RIKEN-1B ... ...umbilical cord fibroblast,Female) 臍帯由来線維芽細胞（RCB0436 HUC-F2)iPS細胞. human ES-like Research Grade Retrovirus Oc... ... Fetus Female Japanese Japanese -- No Human iPS cell line. Parent cell line of RCB0436 HUC-F2(Normal ...774.2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shi

Stemcell Information: SKIP000639 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000639 ... umbilical cord 臍帯(線維芽細胞) Normal HiPS-RIKEN-1D HiPS-RIKEN-1D ... ... umbilical cord fibroblast,Female) 臍帯由来線維芽細胞（RCB0436 HUC-F2)iPS細胞. human ES-like Research Grade Retrovirus O... ... Fetus Female Japanese Japanese -- No Human iPS cell line. Parent cell line of ... RCB0436 HUC-F2(Normal...774.2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shi

Stemcell Information: SKIP000648 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000648 ... umbilical cord 臍帯(線維芽細胞) Normal HiPS-RIKEN-13B HiPS-RIKEN-13B ... ... cord fibroblast, male) 臍帯由来線維芽細胞（HUC-5)iPS細胞. human ES-like Research Grade Retrovirus Oct3/4, Sox2, Klf4,c-... ... Fetus Male Japanese Japanese -- No Human iPS cell line. Parent cell line of HUC-5(Normal umbilical...blishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shimizu N, Yoshino K, Mi

Stemcell Information: SKIP000652 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available both neonatal and maternal cells. 羊膜(母胎・胎児）由来線維芽細胞（HFM-1)由来iPS細胞. human ES-like Research Grade Retrovirus Oc... SKIP000652 ... amnion 羊膜 Normal HiPS-RIKEN-3D HiPS-RIKEN-3D ... Fetus Male ... -- No Human iPS cel...l line. Parent cell line of HFM-1(amniotic membrane cells).HFM-1 were derived from ...2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shimizu

Stemcell Information: SKIP000640 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000640 ... umbilical cord 臍帯(線維芽細胞) Normal HiPS-RIKEN-1E HiPS-RIKEN-1E ... ...umbilical cord fibroblast,Female) 臍帯由来線維芽細胞（RCB0436 HUC-F2)iPS細胞. human ES-like Research Grade Retrovirus Oc... ... Fetus Female Japanese Japanese -- No Human iPS cell line. Parent cell line of RCB0436 HUC-F2(Normal ...74.2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shim

Stemcell Information: SKIP000655 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available both neonatal and maternal cells. 羊膜(母胎・胎児）由来線維芽細胞（HFM-1)由来iPS細胞. human ES-like Research Grade Lentivirus Oc... SKIP000655 ... amnion 羊膜 Normal HiPS-RIKEN-4B HiPS-RIKEN-4B ... Fetus Male ... -- No Human iPS cel...l line. Parent cell line of HFM-1(amniotic membrane cells).HFM-1 were derived from ...4.2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shimi

Stemcell Information: SKIP001097 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(1439 KURABO)| 新生児皮膚繊維芽細胞(1439 KURABO)由来iPS細胞 human ES-like Research ...n, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001097 ... Normal WT-1-#3 WT-1-#3 ... 0-9 Male ... -- No Nomal human iPS cell...ing type II collagenopathy skeletal dysplasia by directed conversion and induced pluripotent stem cell

Stemcell Information: SKIP000653 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available both neonatal and maternal cells. 羊膜(母胎・胎児）由来線維芽細胞（HFM-1)由来iPS細胞. human ES-like Research Grade Retrovirus Oc... SKIP000653 ... amnion 羊膜 Normal HiPS-RIKEN-3E HiPS-RIKEN-3E ... Fetus Male ... -- No Human iPS cel...l line. Parent cell line of HFM-1(amniotic membrane cells).HFM-1 were derived from ...2010.00091.x Establishment of induced pluripotent stem cells from human neonatal tissues. Fujioka T, Shimizu

Stemcell Information: SKIP000617 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000617 ... Diseased HPS0097 HPS0097 ... 家族性パーキンソン病 PARK2 G20 Parkinson's disea...se, Familial type, PARK2 600116 ... -- -- Japanese Japanese No No Disease specific iPS cell line derived from a patient: Parkins...on's disease, Familial type, PARK2. 疾患特異的iPS細胞株。家族性パーキンソン病 PARK2患者由来。レトロウイルスベクターにより

Stemcell Information: SKIP001068 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available DISEASE, PARK4 605543 ... 42 40-49 Male ... Yes No Disease specific iPS cell lines derived from patient with Parkinson...rsity Stanford University ... 22110584 10.1371/journal.pone.0026159 SNCA triplication Parkinson... SKIP001068 ... Diseased Trpl17 Trpl17 ... 家族性パーキンソン病 PARK4 G20 Familial PARKINSON ... disease (PARK4) パーキンソン病（PARK4）患者由来iPS細胞 human ES-like Research Grade Retrovirus KLF4,SOX2,OCT4,

Stemcell Information: SKIP001096 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(1439 KURABO)| 新生児皮膚繊維芽細胞(1439 KURABO)由来iPS細胞 human ES-like Research ...n, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001096 ... Normal WT-1-#2 WT-1-#2 ... 0-9 Male ... -- No Nomal human iPS cell...ing type II collagenopathy skeletal dysplasia by directed conversion and induced pluripotent stem cell

26 CFR 26.2653-1 - Taxation of multiple skips.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Taxation of multiple skips. 26.2653-1 Section 26.2653-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE...-1 Taxation of multiple skips. (a) General rule. If property is held in trust immediately after a GST...

Gait biomechanics of skipping are substantially different than those of running.

Science.gov (United States)

McDonnell, Jessica; Willson, John D; Zwetsloot, Kevin A; Houmard, Joseph; DeVita, Paul

2017-11-07

The inherit injury risk associated with high-impact exercises calls for alternative ways to achieve the benefits of aerobic exercise while minimizing excessive stresses to body tissues. Skipping presents such an alternative, incorporating double support, flight, and single support phases. We used ground reaction forces (GRFs), lower extremity joint torques and powers to compare skipping and running in 20 healthy adults. The two consecutive skipping steps on each limb differed significantly from each other, and from running. Running had the longest step length, the highest peak vertical GRF, peak knee extensor torque, and peak knee negative and positive power and negative and positive work. Skipping had the greater cadence, peak horizontal GRF, peak hip and ankle extensor torques, peak ankle negative power and work, and peak ankle positive power. The second vs first skipping step had the shorter step length, higher cadence, peak horizontal GRF, peak ankle extensor torque, and peak ankle negative power, negative work, and positive power and positive work. The first skipping step utilized predominately net negative joint work (eccentric muscle action) while the second utilized predominately net positive joint work (concentric muscle action). The skipping data further highlight the persistence of net negative work performed at the knee and net positive work performed at the ankle across locomotion gaits. Evidence of step segregation was seen in distribution of the braking and propelling impulses and net work produced across the hip, knee, and ankle joints. Skipping was substantially different than running and was temporally and spatially asymmetrical with successive foot falls partitioned into a dominant function, either braking or propelling whereas running had a single, repeated step in which both braking and propelling actions were performed equally. Copyright © 2017 Elsevier Ltd. All rights reserved.

Large exon size does not limit splicing in vivo.

Science.gov (United States)

Chen, I T; Chasin, L A

1994-03-01

Exon sizes in vertebrate genes are, with a few exceptions, limited to less than 300 bases. It has been proposed that this limitation may derive from the exon definition model of splice site recognition. In this model, a downstream donor site enhances splicing at the upstream acceptor site of the same exon. This enhancement may require contact between factors bound to each end of the exon; an exon size limitation would promote such contact. To test the idea that proximity was required for exon definition, we inserted random DNA fragments from Escherichia coli into a central exon in a three-exon dihydrofolate reductase minigene and tested whether the expanded exons were efficiently spliced. DNA from a plasmid library of expanded minigenes was used to transfect a CHO cell deletion mutant lacking the dhfr locus. PCR analysis of DNA isolated from the pooled stable cotransfectant populations displayed a range of DNA insert sizes from 50 to 1,500 nucleotides. A parallel analysis of the RNA from this population by reverse transcription followed by PCR showed a similar size distribution. Central exons as large as 1,400 bases could be spliced into mRNA. We also tested individual plasmid clones containing exon inserts of defined sizes. The largest exon included in mRNA was 1,200 bases in length, well above the 300-base limit implied by the survey of naturally occurring exons. We conclude that a limitation in exon size is not part of the exon definition mechanism.

Skipped spawning in fishes: More common than you might think

DEFF Research Database (Denmark)

Rideout, Rick M.; Tomkiewicz, Jonna

2011-01-01

The traditional view of iteroparity in fishes is one of an annual reproductive cycle that culminates each year in spawning. More recently, a more flexible view of fish reproduction has been adopted, including the potential for mature fish to skip spawning. Here, we review the abundance of recent...... on elemental and isotope signatures. Skipped spawning is most commonly attributed to deficient diet and poor nutritional condition. Advances made in this field of study in recent years include descriptions of hormonal changes that precede and perhaps initiate skipped spawning, the development of life history...

Dynamics of Leading-strand Lesion Skipping by the Replisome

Science.gov (United States)

Yeeles, Joseph T.P.; Marians, Kenneth J.

2013-01-01

SUMMARY The E. coli replisome stalls transiently when it encounters a lesion in the leading-strand template, skipping over the damage by reinitiating replication at a new primer synthesized downstream by the primase. We report here that template unwinding and lagging-strand synthesis continue downstream of the lesion at a reduced rate after replisome stalling, that one replisome is capable of skipping multiple lesions, and that the rate limiting steps of replication restart involve the synthesis and activation of the new primer downstream. We also find little support for the concept that polymerase uncoupling, where extensive lagging-strand synthesis proceeds downstream in the absence of leading-strand synthesis, involves physical separation of the leading-strand polymerase from the replisome. Instead, our data indicate that extensive uncoupled replication likely results from a failure of the leading-strand polymerase still associated with the DNA helicase and the lagging-strand polymerase that are proceeding downstream to reinitiate synthesis. PMID:24268579

Update History of This Database - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us SKIP Stemcell Database Update History of This Database Date Update contents 2017/03/13 SKIP Stemcell Database... English archive site is opened. 2013/03/29 SKIP Stemcell Database ( https://www.skip.med.k...eio.ac.jp/SKIPSearch/top?lang=en ) is opened. About This Database Database Description Download License Update History of This Databa...se Site Policy | Contact Us Update History of This Database - SKIP Stemcell Database | LSDB Archive ...

See before You Jump: Full Recognition of Parafoveal Words Precedes Skips during Reading

Science.gov (United States)

Gordon, Peter C.; Plummer, Patrick; Choi, Wonil

2013-01-01

Serial attention models of eye-movement control during reading were evaluated in an eye-tracking experiment that examined how lexical activation combines with visual information in the parafovea to affect word skipping (where a word is not fixated during first-pass reading). Lexical activation was manipulated by repetition priming created through…

26 CFR 26.2611-1 - Generation-skipping transfer defined.

Science.gov (United States)

2010-04-01

... AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX REGULATIONS UNDER THE TAX REFORM ACT OF 1986 § 26.2611... either a direct skip, a taxable distribution, or a taxable termination. See § 26.2612-1 for the definition of these terms. The determination as to whether an event is a GST is made by reference to the most...

Skip Regulates TGF-β1-Induced Extracellular Matrix Degrading Proteases Expression in Human PC-3 Prostate Cancer Cells

Directory of Open Access Journals (Sweden)

Victor Villar

2013-01-01

Full Text Available Purpose. To determine whether Ski-interacting protein (SKIP regulates TGF-β1-stimulated expression of urokinase-type plasminogen activator (uPA, matrix metalloproteinase-9 (MMP-9, and uPA Inhibitor (PAI-1 in the androgen-independent human prostate cancer cell model. Materials and Methods. PC-3 prostate cancer cell line was used. The role of SKIP was evaluated using synthetic small interference RNA (siRNA compounds. The expression of uPA, MMP-9, and PAI-1 was evaluated by zymography assays, RT-PCR, and promoter transactivation analysis. Results. In PC-3 cells TGF-β1 treatment stimulated uPA, PAI-1, and MMP-9 expressions. The knockdown of SKIP in PC-3 cells enhanced the basal level of uPA, and TGF-β1 treatment inhibited uPA production. Both PAI-1 and MMP-9 production levels were increased in response to TGF-β1. The ectopic expression of SKIP inhibited both TGF-β1-induced uPA and MMP-9 promoter transactivation, while PAI-1 promoter response to the factor was unaffected. Conclusions. SKIP regulates the expression of uPA, PAI-1, and MMP-9 stimulated by TGF-β1 in PC-3 cells. Thus, SKIP is implicated in the regulation of extracellular matrix degradation and can therefore be suggested as a novel therapeutic target in prostate cancer treatment.

Stemcell Information: SKIP000390 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available lections/NIGMS/ipsc_list.aspx?PgId=696 ... 21490598 10.1038/nature09915 Modelling schizophrenia using human ... SKIP000390 ... Diseased GM23764 GM23764 ... 統合失調症 F209 Schizophrenia 181500 ... ...より人工多能性幹細胞 (iPSC) を樹立。23回継代の凍結サンプル。同一人由来のリンパ球GM01490も参照。青年期から神経性無食欲症を発症。鬱＜統合失調症。

Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

Science.gov (United States)

Yokota, Toshifumi; Wood, Matthew J. A.

2013-01-01

Duchenne muscular dystrophy (DMD) is an incurable, X-linked progressive muscle degenerative disorder that results from the absence of dystrophin protein and leads to premature death in affected individuals due to respiratory and/or cardiac failure typically by age of 30. Very recently the exciting prospect of an effective oligonucleotide therapy has emerged which restores dystrophin protein expression to affected tissues in DMD patients with highly promising data from a series of clinical trials. This therapeutic approach is highly mutation specific and thus is personalised. Therefore DMD has emerged as a model genetic disorder for understanding and overcoming of the challenges of developing personalised genetic medicines. One of the greatest weaknesses of the current oligonucleotide approach is that it is a mutation-specific therapy. To address this limitation, we have recently demonstrated that exons 45–55 skipping therapy has the potential to treat clusters of mutations that cause DMD, which could significantly reduce the number of compounds that would need to be developed in order to successfully treat all DMD patients. Here we discuss and review the latest preclinical work in this area as well as a variety of accompanying issues, including efficacy and potential toxicity of antisense oligonucleotides, prior to human clinical trials. PMID:23984357

Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes.

Directory of Open Access Journals (Sweden)

Jonàs Juan-Mateu

Full Text Available DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.

Stemcell Information: SKIP000203 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 20iPSにおいてExon 6, 7のhomozygous deletionを確認。|HIV : 未実施|HTLV-1 : 未実施|HBV : 実施　陰性|HCV : 実施　陰性|病歴・治療歴等 : 28歳発症|家族

Stemcell Information: SKIP000202 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 20iPSにおいてExon 6, 7のhomozygous deletionを確認。|HIV : 未実施|HTLV-1 : 未実施|HBV : 実施　陰性|HCV : 実施　陰性|病歴・治療歴等 : 28歳発症|家族

Deep Temporal Models using Identity Skip-Connections for Speech Emotion Recognition

NARCIS (Netherlands)

Kim, Jaebok; Englebienne, Gwenn; Truong, Khiet P.; Evers, Vanessa

2017-01-01

Deep architectures using identity skip-connections have demonstrated groundbreaking performance in the field of image classification. Recently, empirical studies suggested that identity skip-connections enable ensemble-like behaviour of shallow networks, and that depth is not a solo ingredient for

Stemcell Information: SKIP000474 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available Gideon ... Fetus Unknown ... -- No MRC-iPS-62|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like Res... SKIP000474 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-62 MRC-iPS-62 Gideon...459.x--10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.--D...NA methylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Itaku...med/21155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000494 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available eyes Snake eyes ... Fetus Unknown ... -- No MRC-iPS-83|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-... SKIP000494 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-83 MRC-iPS-83 Snake ....2010.01459.x--10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cell...s.--DNA methylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue ....gov/pubmed/21155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000498 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available y Diggity ... Fetus Unknown ... -- No MRC-iPS-86|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like R... SKIP000498 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-86 MRC-iPS-86 Diggit...01459.x--10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.-...-DNA methylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Ita...ubmed/21155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP001099 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(789013 KURABO)| 新生児皮膚繊維芽細胞(789013 KURABO)由来iPS細胞 human ES-like Res...ication, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001099 ... Normal WT-2-#32 WT-2-#32 ... 0-9 Male ... -- No Nomal human iPS cell... Modeling type II collagenopathy skeletal dysplasia by directed conversion and in...duced pluripotent stem cells. Okada M, Ikegawa S, Morioka M, Yamashita A, Saito A, Sawai H, Murotsuki J, Oha

Stemcell Information: SKIP000433 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available pper Gobstopper ... Fetus Unknown ... -- No MRC-iPS-21|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-... SKIP000433 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-21 MRC-iPS-21 Gobsto....2010.01459.x--10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cell...s.--DNA methylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue ....gov/pubmed/21155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000478 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available g ... Fetus Unknown ... -- No MRC-iPS-66|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like Research ... SKIP000478 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-66 MRC-iPS-66 Tug Tu...-10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.--DNA met...hylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Itakura Y, ...155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000457 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available s Jimmies ... Fetus Unknown ... -- No MRC-iPS-45|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like R... SKIP000457 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-45 MRC-iPS-45 Jimmie...01459.x--10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.-...-DNA methylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Ita...ubmed/21155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000437 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available c ... Fetus Unknown ... -- No MRC-iPS-25|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like Research ... SKIP000437 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-25 MRC-iPS-25 Tic Ti...-10.1371/journal.pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.--DNA met...hylation dynamics in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Itakura Y, ...155951--http://www.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP000444 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available b ... Fetus Unknown ... -- No MRC-iPS-32|MRC5-derived iPS cells| MRC5由来iPS細胞| human ES-like Research ... SKIP000444 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-32 MRC-iPS-32 Bob Bo....pgen.1002085 Lectin microarray analysis of pluripotent and multipotent stem cells.--DNA methylation dynamic...s in human induced pluripotent stem cells over time. Toyoda M, Yamazaki-Inoue M, Itakura Y, Kuno A, Ogawa T,...ww.ncbi.nlm.nih.gov/pubmed/21637780 -- Some of clones of the same original cells have been used in the papers.

Stemcell Information: SKIP001098 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(789013 KURABO)| 新生児皮膚繊維芽細胞(789013 KURABO)由来iPS細胞 human ES-like Res...ication, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001098 ... Normal WT-2-#31 WT-2-#31 ... 0-9 Male ... -- No Nomal human iPS cell... Modeling type II collagenopathy skeletal dysplasia by directed conversion and in...duced pluripotent stem cells. Okada M, Ikegawa S, Morioka M, Yamashita A, Saito A, Sawai H, Murotsuki J, Oha

Stemcell Information: SKIP000708 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000708 ... mesenchymal stem cell 間葉系幹細胞 placenta 胎盤 Normal PL505 PL505 ... ... ... -- -- ... -- No JCRB1128 mesenchymal stem cell finite proliferation 胎盤由来間葉系幹細胞(有限増殖) fibroblast-like -- ...opment 国立成育医療研究センター研究所 ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞...バンク http://cellbank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3558 ...

Stemcell Information: SKIP001100 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a neonate.(789013 KURABO)| 新生児皮膚繊維芽細胞(789013 KURABO)由来iPS細胞 human ES-like Res...ication, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞... SKIP001100 ... Normal WT-2-#33 WT-2-#33 ... 0-9 Male ... -- No Nomal human iPS cell... Modeling type II collagenopathy skeletal dysplasia by directed conversion and in...duced pluripotent stem cells. Okada M, Ikegawa S, Morioka M, Yamashita A, Saito A, Sawai H, Murotsuki J, Oha

Skipping meals and alcohol consumption. The regulation of energy intake and expenditure among weight loss participants.

Science.gov (United States)

Carels, Robert A; Young, Kathleen M; Coit, Carissa; Clayton, Anna Marie; Spencer, Alexis; Wagner, Marissa

2008-11-01

Research suggests that specific eating patterns (e.g., eating breakfast) may be related to favorable weight status. This investigation examined the relationship between eating patterns (i.e., skipping meals; consuming alcohol) and weight loss treatment outcomes (weight loss, energy intake, energy expenditure, and duration of exercise). Fifty-four overweight or obese adults (BMI> or =27 kg/m(2)) participated in a self-help or therapist-assisted weight loss program. Daily energy intake from breakfast, lunch, dinner, and alcoholic beverages, total daily energy intake, total daily energy expenditure, physical activity, and weekly weight loss were assessed. On days that breakfast or dinner was skipped, or alcoholic beverages were not consumed, less total daily energy was consumed compared to days that breakfast, dinner, or alcoholic beverages were consumed. On days that breakfast or alcohol was consumed, daily energy expenditure (breakfast only) and duration of exercise were higher compared to days that breakfast or alcohol was not consumed. Individuals who skipped dinner or lunch more often had lower energy expenditure and exercise duration than individuals who skipped dinner or lunch less often. Individuals who consumed alcohol more often had high daily energy expenditure than individuals who consumed alcohol less often. Skipping meals or consuming alcoholic beverages was not associated with weekly weight loss. In this investigation, weight loss program participants may have compensated for excess energy intake from alcoholic beverages and meals with greater daily energy expenditure and longer exercise duration.

Naturally- and experimentally-designed restorations of the Parkin gene deficit in autosomal recessive juvenile parkinsonism

International Nuclear Information System (INIS)

Asai, Hirohide; Hirano, Makito; Kiriyama, Takao; Ikeda, Masanori; Ueno, Satoshi

2010-01-01

Intranuclear events due to mutations in the Parkin gene remain elusive in autosomal recessive juvenile parkinsonism (ARJP). We identified a mutant PARKIN protein in fibroblast cultures from a pair of siblings with ARJP who were homozygous for the exon 4-deleted Parkin gene. Disease was mild in one patient and debilitating in the other. The detected mutant, encoded by a transcript lacking exon 3 as well as exon 4, is an in-frame deletion that removes 121 aa, resulting in a 344-aa protein (PaDel3,4). Cell culture and transfection studies revealed negative correlations between expression levels of PaDel3,4 and those of cell cycle proteins, including cyclin E, CDK2, ppRb, and E2F-1, and demonstrated that GFP-PaDel3,4 entered nucleus and ubiquitinated cyclin E as a part of SCF hSel-10 ligase complex in the patient cells. In addition, nuclear localization signal-tagged PaDel3,4 expressed in the transfected patient cells most effectively ubiquitinated cyclin E and reduced DNA damage, protecting cells from oxidative stress. Antisense-oligonucleotide treatment promoted skipping of exon 3 and thus generated PaDel3,4, increasing cell survival. Collectively, we propose that naturally- and experimentally-induced exon skipping at least partly restores the mutant Parkin gene deficit, providing a molecular basis for the development of therapeutic exon skipping.

Effect of skipping breakfast on subsequent energy intake.

Science.gov (United States)

Levitsky, David A; Pacanowski, Carly R

2013-07-02

The objective was to examine the effect of consuming breakfast on subsequent energy intake. Participants who habitually ate breakfast and those who skipped breakfast were recruited for two studies. Using a randomized crossover design, the first study examined the effect of having participants consume either (a) no breakfast, (b) a high carbohydrate breakfast (335 kcals), or (c) a high fiber breakfast (360 kcals) on three occasions and measured ad libitum intake at lunch. The second study again used a randomized crossover design but with a larger, normal carbohydrate breakfast consumed ad libtum. Intake averaged 624 kcals and subsequent food intake was measured throughout the day. Participants ate only foods served from the Cornell Human Metabolic Research Unit where all foods were weighed before and after consumption. In the first study, neither eating breakfast nor the kind of breakfast consumed had an effect on the amount consumed at lunch despite a reduction in hunger ratings. In the second study, intake at lunch as well as hunger ratings were significantly increased after skipping breakfast (by 144 kcal), leaving a net caloric deficit of 408 kcal by the end of the day. These data are consistent with published literature demonstrating that skipping a meal does not result in accurate energy compensation at subsequent meals and suggests that skipping breakfast may be an effective means to reduce daily energy intake in some adults. Copyright © 2013 Elsevier Inc. All rights reserved.

The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Shazia Mahamdallie

2017-05-01

Full Text Available Detection of deletions and duplications of whole exons (exon CNVs is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel together with Multiplex Ligation-dependent Probe Amplification (MLPA results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA under the accession number EGAS00001002428.

Is snack consumption associated with meal skipping in children and adolescents? The CASPIAN-IV study.

Science.gov (United States)

Kelishadi, Roya; Mozafarian, Nafiseh; Qorbani, Mostafa; Motlagh, Mohammad Esmaeil; Safiri, Saeid; Ardalan, Gelayol; Keikhah, Mojtaba; Rezaei, Fatemeh; Heshmat, Ramin

2017-06-01

The present inquiry set to assess the relationship between snack consumption and meal skipping in Iranian children and adolescents. Overall, 14,880 students, aged 6-18 years, were selected via multistage cluster sampling method from rural and urban areas of 30 provinces of Iran. A validated questionnaire of food behaviors including questions on snacks consumption and taking/skipping meals was completed. Consuming and skipping meals and their related factors were reported in both crude and adjusted models. Overall, 13,486 students with a mean age of 12.47 ± 3.36 years completed the study (90.6% participation rate). Among them, 32.08, 8.89, and 10.90% skipped breakfast, lunch, and dinner, respectively. Compared to their counterpart groups, the frequency of meal skipping was higher in girls, urban inhabitants, and students in higher school grades (P Snack consumption was associated with an increased odds ratio of meal skipping in many types of snack groups. Meal skipping and snack consumption were frequent among Iranian children and adolescents. Evidence based interventions are proposed to improve the students' eating habits.

Short (16-mer locked nucleic acid splice-switching oligonucleotides restore dystrophin production in Duchenne Muscular Dystrophy myotubes.

Directory of Open Access Journals (Sweden)

Vanessa Borges Pires

Full Text Available Splice-switching antisense oligonucleotides (SSOs offer great potential for RNA-targeting therapies, and two SSO drugs have been recently approved for treating Duchenne Muscular Dystrophy (DMD and Spinal Muscular Atrophy (SMA. Despite promising results, new developments are still needed for more efficient chemistries and delivery systems. Locked nucleic acid (LNA is a chemically modified nucleic acid that presents several attractive properties, such as high melting temperature when bound to RNA, potent biological activity, high stability and low toxicity in vivo. Here, we designed a series of LNA-based SSOs complementary to two sequences of the human dystrophin exon 51 that are most evolutionary conserved and evaluated their ability to induce exon skipping upon transfection into myoblasts derived from a DMD patient. We show that 16-mers with 60% of LNA modification efficiently induce exon skipping and restore synthesis of a truncated dystrophin isoform that localizes to the plasma membrane of patient-derived myotubes differentiated in culture. In sum, this study underscores the value of short LNA-modified SSOs for therapeutic applications.

Skip cycle method with a valve-control mechanism for spark ignition engines

International Nuclear Information System (INIS)

Baykara, Cemal; Akin Kutlar, O.; Dogru, Baris; Arslan, Hikmet

2017-01-01

Highlights: • A normal four-stroke cycle followed by a skip cycle without gas exchange is tested. • The normal and skipped mode results are compared at equal power levels. • The throttle valve is opened wider, thereby resulting in a higher volumetric efficiency. • The pumping work during the gas exchange decreases significantly. • The fuel consumption (BSFC) is reduced by approximately 14–26% under part load conditions. - Abstract: The efficiency decrease of spark ignition (SI) engines under part-load conditions is a considerable issue. Changing the effective stroke volume based on the load level is one of the methods using to improve the part-load efficiency. In this study, a novel alternative engine valve control technique in order to perform a cycle without gas exchange (skip cycle), is examined. The goal of skip cycle strategy is to reduce the effective stroke volume of an engine under part load conditions by skipping several of the four stroke cycles by cutting off the fuel injection and simultaneously deactivating the inlet and exhaust valves. To achieve the same power level in the skip cycle, the cylinder pressure level reaches higher values compared to those in a normal four stroke cycle operation, but inherently not higher than the maximum one at full load of normal cycle. According to the experimental results, the break specific fuel consumption (BSFC) was reduced by 14–26% at a 1–3 bar break mean effective pressure (BMEP) and a 1200–1800 rpm engine speed of skip cycle operation, in comparison to normal engine operation. The significant decrease in the pumping work from the gas exchange is one of the primary factors for an increase in efficiency under part load conditions. As expected, the fuel consumption reduction rate at lower load conditions was higher. These experimental results indicate a promising potential of the skip cycle system for reducing the fuel consumption under part load conditions.

Canine and human gastrointestinal stromal tumors display similar mutations in c-KIT exon 11

International Nuclear Information System (INIS)

Gregory-Bryson, Emmalena; Bartlett, Elizabeth; Kiupel, Matti; Hayes, Schantel; Yuzbasiyan-Gurkan, Vilma

2010-01-01

Gastrointestinal stromal tumors (GISTs) are common mesenchymal neoplasms in the gastrointestinal tract of humans and dogs. Little is known about the pathogenesis of these tumors. This study evaluated the role of c-KIT in canine GISTs; specifically, we investigated activating mutations in exons 8, 9, 11, 13, and 17 of c-KIT and exons 12, 14, and 18 of platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), all of which have been implicated in human GISTs. Seventeen canine GISTs all confirmed to be positive for KIT immunostaining were studied. Exons 8, 9, 11, 13 and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA, were amplified from DNA isolated from formalin-fixed paraffin-embedded samples. Of these seventeen cases, six amplicons of exon 11 of c-KIT showed aberrant bands on gel electrophoresis. Sequencing of these amplicons revealed heterozygous in-frame deletions in six cases. The mutations include two different but overlapping six base pair deletions. Exons 8, 9, 13, and 17 of c-KIT and exons 12, 14, and 18 of PDGFRA had no abnormalities detected by electrophoresis and sequencing did not reveal any mutations, other than synonymous single nucleotide polymorphisms (SNPs) found in exon 11 of c-KIT and exons 12 and 14 of PDGFRA. The deletion mutations detected in canine GISTs are similar to those previously found in the juxtamembrane domain of c-KIT in canine cutaneous mast cell tumors in our laboratory as well as to those reported in human GISTs. Interestingly, none of the other c-KIT or PDGFRA exons showed any abnormalities in our cases. This finding underlines the critical importance of c-KIT in the pathophysiology of canine GISTs. The expression of KIT and the identification of these activating mutations in c-KIT implicate KIT in the pathogenesis of these tumors. Our results indicate that mutations in c-KIT may be of prognostic significance and that targeting KIT may be a rational approach to treatment of these malignant tumors. This study further

Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor

Energy Technology Data Exchange (ETDEWEB)

Hou, Zhiqiang; Su, Lijing; Pei, Jimin; Grishin, Nick V.; Zhang, Hong (UTSMC)

2017-08-01

In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.

Cycle-skipping strategies for pumping loss reduction in spark ignition engines: An experimental approach

International Nuclear Information System (INIS)

Yüksek, Levent; Özener, Orkun; Sandalcı, Tarkan

2012-01-01

Highlights: ► A cycle density variation technique called cycle-skipping was applied. ► Effect on fuel consumption and gaseous emissions was investigated. ► Fuel consumption and gaseous tail-pipe emissions improved at partial loading conditions. - Abstract: Spark ignition (SI) engines are widely used for power generation, especially in the automotive industry. SI engines have a lower thermal efficiency than diesel engines due to a lower compression ratio, higher charge-induction work and lower end of compression stroke pressure. A significant amount of charge induction work is lost when an SI engine runs under partial loading conditions. Under partial loading conditions, a lower intake charge is required, which can be theoretically achieved by varying the displacement volume or the stroke number of the engine without using a throttle. Reducing the displacement volume to control the engine load can be achieved by skipping cycles in single-cylinder engines. This study investigates the effect of cycle-skipping strategies on the brake specific fuel consumption (BSFC) and exhaust emissions of an SI engine under partial loading conditions. Three different skipping modes were applied: normal, normal-skip and normal-normal-skip. A significant improvement in BSFC and carbon monoxide emission was obtained by applying cycle-skipping strategies.

Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations

DEFF Research Database (Denmark)

Nielsen, Karsten Bork; Sørensen, Suzette; Cartegni, Luca

2007-01-01

assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing...

Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

Science.gov (United States)

Vouille, V; Amiche, M; Nicolas, P

1997-09-01

We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

Investigation of ANGPTL3 expression, exon sequence and promotor ...

African Journals Online (AJOL)

like proteins, has been demonstrated to affect lipid metabolism by inhibiting the activity of lipoprotein lipase (LPL). Objective: To compare the ANGPTL3 mRNA and protein expression, exon mutation and promoter district CpG island methylation ...

Eye movements and word skipping during reading: Effects of word length and predictability

Science.gov (United States)

Rayner, Keith; Slattery, Timothy J.; Drieghe, Denis; Liversedge, Simon P.

2012-01-01

The extent to which target words were predictable from prior context was varied: half of the target words were predictable and the other half were unpredictable. In addition, the length of the target word varied: the target words were short (4–6 letters), medium (7–9 letters), or long (10–12 letters). Length and predictability both yielded strong effects on the probability of skipping the target words and on the amount of time readers fixated the target words (when they were not skipped). However, there was no interaction in any of the measures examined for either skipping or fixation time. The results demonstrate that word predictability (due to contextual constraint) and word length have strong and independent influences on word skipping and fixation durations. Furthermore, since the long words extended beyond the word identification span, the data indicate that skipping can occur on the basis of partial information in relation to word identity. PMID:21463086

The relationship between breakfast skipping, chronotype, and glycemic control in type 2 diabetes.

Science.gov (United States)

Reutrakul, Sirimon; Hood, Megan M; Crowley, Stephanie J; Morgan, Mary K; Teodori, Marsha; Knutson, Kristen L

2014-02-01

Breakfast skipping is associated with obesity and an increased risk of type 2 diabetes. Later chronotypes, individuals who have a preference for later bed and wake times, often skip breakfast. The aim of the study was to explore the relationships among breakfast skipping, chronotype, and glycemic control in type 2 diabetes patients. We collected sleep timing and 24-h dietary recall from 194 non-shift-working type 2 diabetes patients who were being followed in outpatient clinics. Mid-sleep time on free days (MSF) was used as an indicator of chronotype. Hemoglobin A1C (HbA1C) values were obtained from medical records. Hierarchical linear regression analyses controlling for demographic, sleep, and dietary variables were computed to determine whether breakfast skipping was associated with HbA1C. Additional regression analyses were performed to test if this association was mediated by chronotype. There were 22 participants (11.3%) who self-reported missing breakfast. Breakfast skippers had significantly higher HbA1C levels, higher body mass indices (BMI), and later MSF than breakfast eaters. Breakfast skipping was significantly associated with higher HbA1C values (B = 0.108, p = 0.01), even after adjusting for age, sex, race, BMI, number of diabetes complications, insulin use, depressive symptoms, perceived sleep debt, and percentage of daily caloric intake at dinner. The relationship between breakfast skipping and HbA1C was partially mediated by chronotype. In summary, breakfast skipping is associated with a later chronotype. Later chronotype and breakfast skipping both contribute to poorer glycemic control, as indicated by higher HbA1C levels. Future studies are needed to confirm these findings and determine whether behavioral interventions targeting breakfast eating or sleep timing may improve glycemic control in patients with type 2 diabetes.

Database Description - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us SKIP Stemcell Database Database Description General information of database Database name SKIP Stemcell Database...rsity Journal Search: Contact address http://www.skip.med.keio.ac.jp/en/contact/ Database classification Human Genes and Diseases Dat...abase classification Stemcell Article Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database...ks: Original website information Database maintenance site Center for Medical Genetics, School of medicine, ...lable Web services Not available URL of Web services - Need for user registration Not available About This Database Database

Computer method to detect and correct cycle skipping on sonic logs

International Nuclear Information System (INIS)

Muller, D.C.

1985-01-01

A simple but effective computer method has been developed to detect cycle skipping on sonic logs and to replace cycle skips with estimates of correct traveltimes. The method can be used to correct observed traveltime pairs from the transmitter to both receivers. The basis of the method is the linearity of a plot of theoretical traveltime from the transmitter to the first receiver versus theoretical traveltime from the transmitter to the second receiver. Theoretical traveltime pairs are calculated assuming that the sonic logging tool is centered in the borehole, that the borehole diameter is constant, that the borehole fluid velocity is constant, and that the formation is homogeneous. The plot is linear for the full range of possible formation-rock velocity. Plots of observed traveltime pairs from a sonic logging tool are also linear but have a large degree of scatter due to borehole rugosity, sharp boundaries exhibiting large velocity contrasts, and system measurement uncertainties. However, this scatter can be reduced to a level that is less than scatter due to cycle skipping, so that cycle skips may be detected and discarded or replaced with estimated values of traveltime. Advantages of the method are that it can be applied in real time, that it can be used with data collected by existing tools, that it only affects data that exhibit cycle skipping and leaves other data unchanged, and that a correction trace can be generated which shows where cycle skipping occurs and the amount of correction applied. The method has been successfully tested on sonic log data taken in two holes drilled at the Nevada Test Site, Nye County, Nevada

High-throughput proteomics detection of novel splice isoforms in human platelets.

LENUS (Irish Health Repository)

Power, Karen A

2009-01-01

Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS\\/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS\\/MS datasets.

Relationships between bullying victimization psychological distress and breakfast skipping among boys and girls.

Science.gov (United States)

Sampasa-Kanyinga, Hugues; Willmore, Jacqueline

2015-06-01

The purpose of this study was to further explore the association between bullying victimization and breakfast skipping in children and adolescents. Compared to the previous study, we have used a larger and representative sample of middle and high school students, examined the effect of gender, different forms (physical, verbal, theft/vandalism and cyber) and severity of bullying on breakfast eating behaviour. Data from students (2286 boys and 2859 girls) aged 11 to 19 years (mean ± SD age: 14.6 ± 1.9 years) from the 2013 Ontario Student Drug Use and Health Survey (OSDUHS) were analysed using self-reports of being bullied, diet, psychological distress, demographics, socio-economic status, weight status, and substance use. Results revealed greater odds of breakfast skipping in girl victims of physical, verbal, and cyber bullying, and in boy victims of verbal and cyber bullying. There was a dose-response relationship between experience of both school and cyber bullying victimization and breakfast skipping behaviour for both genders. Mediation analysis indicated that psychological distress fully mediated the relationship between both verbal and physical bullying victimization and breakfast skipping in girls, and partially mediated the relationship between verbal bullying victimization and breakfast skipping in boys. Psychological distress also partially mediated the link between cyber bullying victimization and breakfast skipping in both boys and girls. These results corroborate previous findings on the association between bullying victimization and breakfast skipping in children and adolescents. The strong and consistent associations with different forms of bullying victimization, the dose-response relationship, and the mediating role of psychological distress suggest a causal relationship. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stemcell Information: SKIP000707 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available 胎盤由来間葉系幹細胞 fibroblast-like -- -- ... -- ... When the cultures reached subconfluence, the cell...evelopment 国立成育医療研究センター研究所 ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cell... SKIP000707 ... placenta 胎盤 Normal PL504 PL504 ... -- -- ... -- No JCRB1126 mesenchymal stem cell...s were harvested with 0.25% trypsin and 1mM EDTA and replated with one-quarter of harvested cells ... 5% ... ...bank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3549 ...

Stemcell Information: SKIP001176 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001176 ... Normal 253F5 253F5 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP000287 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000287 ... mesenchymal stem cell 間葉系幹細胞 Umbilical cord blood 臍帯血 Normal UCB408E7...ot Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cell...s with transgenic HPV E7. finite proliferation 臍帯血由来間葉系幹細胞 (有限増殖) fibroblast-like -- Retr...-32 UCB408E7-32 JCRB1109 JCRB1109 ... -- -- ... -- No JCRB1109 ... Human umbilical cord blood-derived mesenchymal stem cell...bank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID=3373 ... 15647378 ... Immortalization of human fetal cell

Stemcell Information: SKIP001169 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001169 ... Normal 246B4 246B4 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP000414 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available bba ... Fetus Male ... -- No MRC-iPS-01|MRC5(a 14-week male foetal lung tissue)-derived iPS cells| MRC5(14週男性胎児胚線維芽細胞）由来iPS細胞... SKIP000414 ... fetal lung fibroblast 胎児肺線維芽細胞 Unknown MRC-iPS-1 MRC-iPS-1 Bubba Bu...10.1016/j.yexcr.2009.06.016--10.1371/journal.pone.0013017 Lectin microarray analysis of pluripotent and multipotent stem cell...s.--DNA methylation dynamics in human induced pluripotent stem cell...s over time.--Mesenchymal to embryonic incomplete transition of human cells by chimeric OCT4/3 (POU5F1) w

Stemcell Information: SKIP001173 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001173 ... Normal 253F2 253F2 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001165 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001165 ... Normal 246B2 246B2 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001168 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001168 ... Normal 246B6 246B6 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001164 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001164 ... Normal 246B1 246B1 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001166 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001166 ... Normal 246B3 246B3 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001175 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001175 ... Normal 253F4 253F4 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001167 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available plication (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese... iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Ap... SKIP001167 ... Normal 246B5 246B5 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from adult human fibrob

Stemcell Information: SKIP001162 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information Only ... 18035408 10.1016/j.cell... line derived from a healthy individual dermal fibroblasts. 健常人の皮膚線維芽細胞由来のヒトiPS細胞株。 human ES-like Rese...山中 伸弥 Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell... SKIP001162 ... Normal 201B3 201B3 ... 36 30-39 Female ... -- No Human iPS cell....2007.11.019 Induction of pluripotent stem cells from ad

Frame Filtering and Skipping for Point Cloud Data Video Transmission

Directory of Open Access Journals (Sweden)

Carlos Moreno

2017-01-01

Full Text Available Sensors for collecting 3D spatial data from the real world are becoming more important. They are a prime research area topic and have applications in consumer markets, such as medical, entertainment, and robotics. However, a primary concern with collecting this data is the vast amount of information being generated, and thus, needing to be processed before being transmitted. To address the issue, we propose the use of filtering methods and frame skipping. To collect the 3D spatial data, called point clouds, we used the Microsoft Kinect sensor. In addition, we utilized the Point Cloud Library to process and filter the data being generated by the Kinect. Two different computers were used: a client which collects, filters, and transmits the point clouds; and a server that receives and visualizes the point clouds. The client is also checking for similarity in consecutive frames, skipping those that reach a similarity threshold. In order to compare the filtering methods and test the effectiveness of the frame skipping technique, quality of service (QoS metrics such as frame rate and percentage of filter were introduced. These metrics indicate how well a certain combination of filtering method and frame skipping accomplishes the goal of transmitting point clouds from one location to another. We found that the pass through filter in conjunction with frame skipping provides the best relative QoS. However, results also show that there is still too much data for a satisfactory QoS. For a real-time system to provide reasonable end-to-end quality, dynamic compression and progressive transmission need to be utilized.

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity

Directory of Open Access Journals (Sweden)

Rouet Fabien

2009-10-01

Full Text Available Abstract Background Commercially available microarrays have been used in many settings to generate expression profiles for a variety of applications, including target selection for disease detection, classification, profiling for pharmacogenomic response to therapeutics, and potential disease staging. However, many commercially available microarray platforms fail to capture transcript diversity produced by alternative splicing, a major mechanism for driving proteomic diversity through transcript heterogeneity. Results The human Genome-Wide SpliceArray™ (GWSA, a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and exon junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC Project. The array was shown to be highly quantitative, and displayed greater than 85% correlation with the HG-U133 Plus 2.0 array at the gene level while providing more extensive coverage of each gene. Almost 60% of splice events among genes demonstrating differential expression of greater than 3 fold also contained extensive splicing alterations. Importantly, almost 10% of splice events within the gene set displaying constant overall expression values had evidence of transcript diversity. Two examples illustrate the types of events identified: LIM domain 7 showed no differential expression at the gene level, but demonstrated deregulation of an exon skip event, while erythrocyte membrane protein band 4.1 -like 3 was differentially expressed and also displayed deregulation of a skipped exon isoform. Conclusion Significant changes were detected independent of

Clinical Expression and New SPINK5 Splicing Defects in Netherton Syndrome: Unmasking a Frequent Founder Synonymous Mutation and Unconventional Intronic Mutations

DEFF Research Database (Denmark)

Lacroix, Matthieu; Lacaze-Buzy, Laetitia; Furio, Laetitia

2012-01-01

a clinical triad suggestive of NS with variations in inter- and intra-familial disease expression. We identified a new and frequent synonymous mutation c.891C>T (p.Cys297Cys) in exon 11 of the 12 NS patients. This mutation disrupts an exonic splicing enhancer sequence and causes out-of-frame skipping of exon...

Mathematical modeling for optimizing skip-stop rail transit operation strategy using genetic algorithm.

Science.gov (United States)

2012-03-01

"With skip-stop rail transit operation, transit agencies can reduce their operating costs and fleet size, : and passengers can experience reduced in-transit travel times without extra track and technological : improvement. However, since skip-stop op...

The role of germline promoters and I exons in cytokine-induced gene-specific class switch recombination.

Science.gov (United States)

Dunnick, Wesley A; Shi, Jian; Holden, Victoria; Fontaine, Clinton; Collins, John T

2011-01-01

Germline transcription precedes class switch recombination (CSR). The promoter regions and I exons of these germline transcripts include binding sites for activation- and cytokine-induced transcription factors, and the promoter regions/I exons are essential for CSR. Therefore, it is a strong hypothesis that the promoter/I exons regions are responsible for much of cytokine-regulated, gene-specific CSR. We tested this hypothesis by swapping the germline promoter and I exons for the murine γ1 and γ2a H chain genes in a transgene of the entire H chain C-region locus. We found that the promoter/I exon for γ1 germline transcripts can direct robust IL-4-induced recombination to the γ2a gene. In contrast, the promoter/I exon for the γ2a germline transcripts works poorly in the context of the γ1 H chain gene, resulting in expression of γ1 H chains that is level. Nevertheless, the small amount of recombination to the chimeric γ1 gene is induced by IFN-γ. These results suggest that cytokine regulation of CSR, but not the magnitude of CSR, is regulated by the promoter/I exons.

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution.

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Pawandeep Dhami

2010-08-01

Full Text Available It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II occupancy show preferential association with exons ("exon-intron marking", linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

Breakfast skipping is associated with cyberbullying and school bullying victimization. A school-based cross-sectional study.

Science.gov (United States)

Sampasa-Kanyinga, Hugues; Roumeliotis, Paul; Farrow, Claire V; Shi, Yuanfeng F

2014-08-01

Breakfast skipping is a health concern that has well-known negative consequences physically and psychologically. It is therefore important to understand why children skip breakfast. The purpose of this study was to establish whether the experience of bullying and cyberbullying impacts upon breakfast skipping and to further evaluate whether the inability for youths to cope with bullying victimization affects their mental health (depression), and in turn predicts breakfast skipping. Data were obtained from the Eastern Ontario 2011 Youth Risk Behaviour Survey, a cross-sectional regional school-based survey of middle and high school students (11-20 years old) across the five counties of Eastern Ontario, Canada (N = 3035). Self-reported data about children's experiences of bullying victimization, breakfast eating habits, socio-economical status, depression, and other risk behaviours were analysed. Approximately half of the participants (50.4%) reported not eating breakfast on a regular basis: 26.3% and 24.1% reported often (usually eat breakfast three times or more per week) and frequent (usually eat breakfast twice a week or less) breakfast skipping behaviour, respectively. Victims of both cyberbullying and school bullying presented greater likelihood of often (adjusted relative risk ratio (RR) = 1.55; 95% confidence interval (CI) = 1.17-2.06) and frequent (RR = 1.97; 95% CI = 1.28-3.03) breakfast skipping. Mediation analysis further showed that depression fully mediated the relationship between school bullying victimization and frequent breakfast skipping. Moreover, depression partially mediated the associations between both cyberbullying and school bullying with frequent breakfast skipping. These findings highlight the potential interrelationships between cyberbullying, school bullying and depression in predicting unhealthy breakfast skipping behaviour in children. Copyright © 2014 Elsevier Ltd. All rights reserved.

Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

DEFF Research Database (Denmark)

Irimia, Manuel; Rukov, Jakob L; Penny, David

2007-01-01

Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern...... in Caenorhabditis nematodes-more than 92% of cassette exons from Caenorhabditis elegans are conserved in Caenorhabditis briggsae and/or Caenorhabditis remanei. High levels of conservation extend to minor-form exons (present in a minority of transcripts) and are particularly pronounced for exons showing complex...... patterns of splicing. The functionality of the vast majority of cassette exons is underscored by various other features. We suggest that differences in conservation between lineages reflect differences in levels of functionality and further suggest that these differences are due to differences in intron...

Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

Science.gov (United States)

Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

2016-01-01

The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with MPL exon-10 mutation should be pursued.

Evaluating approaches to find exon chains based on long reads.

Science.gov (United States)

Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

2018-05-01

Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

Exon - ASTRA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ontents Exons in variants Data file File name: astra_exon.zip File URL: ftp://ftp.biosciencedbc.jp/archive/a... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Exon - ASTRA | LSDB Archive ...

Ewing sarcoma of the left big toe with trans-articular skip lesion

Directory of Open Access Journals (Sweden)

Ahmad F. Kamal

2009-06-01

Full Text Available We report the case of the patient who had Ewing Sarcoma in whom radiological and hystopathological appearances revealed a tumor mass in the left big toe along with trans-artikular skip lesion on the left diaphysis of tibia. In Cipto Mangunkusomo Hospital since 1995 until 2004 we have found 20 Ewing sarcoma cases, but only one skip lesion Ewing sarcoma was found. The diagnosis of transarticular skip lesion in association of Ewing sarcoma was confirmed in clinicopathological conferrence. The initial evaluation of all patients included the recording of the medical history, physical examination, and hematological studies. Radiographs of the chest and the site of the primary tumor were made routinely. Systemic staging was performed with use of total-body bone scan. Ray amputation of left big toe and open biopsy from mass of mid-shaft of tibia had been done to confirm the diagnosis. The patient underwent induction chemotherapy and above knee amputation. Ten months after diagnosis, he died because of advanced-distant metastasis. (Med J Indones 2008; 18: 139-44Key words: Ewing sarcoma, trans-articular skip lesion

Health, behavioral, cognitive, and social correlates of breakfast skipping among women living in socioeconomically disadvantaged neighborhoods.

Science.gov (United States)

Smith, Kylie J; McNaughton, Sarah A; Cleland, Verity J; Crawford, David; Ball, Kylie

2013-11-01

Breakfast skipping is a potentially modifiable behavior that has negative effects on health and is socioeconomically patterned. This study aimed to examine the intrapersonal (health, behavioral, and cognitive) and social factors associated with breakfast skipping. Nonpregnant women (n = 4123) aged 18-45 y from socioeconomically disadvantaged neighborhoods throughout Victoria, Australia, completed a postal questionnaire. Sociodemographic characteristics, diet, physical activity, sedentary behaviors, and cognitive and social factors were assessed by self-report. Breakfast skipping was defined in 2 ways: 1) "rarely/never" eating breakfast (n = 498) and 2) eating breakfast ≤2 d/wk (includes those who rarely/never ate breakfast; n = 865). Poisson regression was used to calculate prevalence ratios and linear trends, adjusting for covariates. The P values for linear trends are reported below. Compared with breakfast consumers, women who reported rarely/never eating breakfast tended to have poorer self-rated health (P-trend pay less attention to health (P-trend lower proportion were trying to control their weight (P-trend lower leisure-time physical activity (P-trend = 0.012) and less self-efficacy for eating a healthy diet (P-trend women living in socioeconomically disadvantaged areas. Acknowledging the cross-sectional design and need for causal confirmation, programs that aim to promote breakfast consumption in this population group should consider targeting family-related barriers to healthy eating and nutrition knowledge.

Multiple splicing defects in an intronic false exon.

Science.gov (United States)

Sun, H; Chasin, L A

2000-09-01

Splice site consensus sequences alone are insufficient to dictate the recognition of real constitutive splice sites within the typically large transcripts of higher eukaryotes, and large numbers of pseudoexons flanked by pseudosplice sites with good matches to the consensus sequences can be easily designated. In an attempt to identify elements that prevent pseudoexon splicing, we have systematically altered known splicing signals, as well as immediately adjacent flanking sequences, of an arbitrarily chosen pseudoexon from intron 1 of the human hprt gene. The substitution of a 5' splice site that perfectly matches the 5' consensus combined with mutation to match the CAG/G sequence of the 3' consensus failed to get this model pseudoexon included as the central exon in a dhfr minigene context. Provision of a real 3' splice site and a consensus 5' splice site and removal of an upstream inhibitory sequence were necessary and sufficient to confer splicing on the pseudoexon. This activated context also supported the splicing of a second pseudoexon sequence containing no apparent enhancer. Thus, both the 5' splice site sequence and the polypyrimidine tract of the pseudoexon are defective despite their good agreement with the consensus. On the other hand, the pseudoexon body did not exert a negative influence on splicing. The introduction into the pseudoexon of a sequence selected for binding to ASF/SF2 or its replacement with beta-globin exon 2 only partially reversed the effect of the upstream negative element and the defective polypyrimidine tract. These results support the idea that exon-bridging enhancers are not a prerequisite for constitutive exon definition and suggest that intrinsically defective splice sites and negative elements play important roles in distinguishing the real splicing signal from the vast number of false splicing signals.

Potential Association between Breakfast Skipping and Concomitant Late-Night-Dinner Eating with Metabolic Syndrome and Proteinuria in the Japanese Population

Directory of Open Access Journals (Sweden)

Ayano Kutsuma

2014-01-01

Full Text Available Skipping breakfast is considered to be an unhealthy eating habit linked to predispositions to obesity and type 2 diabetes. Because eating dinner late at night can elicit subsequent breakfast skipping, we investigated if skipping breakfast concomitant with late-night-dinner eating (LNDE was associated with metabolic syndrome (MetS and proteinuria in the general Japanese population. We examined self-reported habitual breakfast skipping and LNDE, MetS (modified ATP-III criteria, and proteinuria in a cross-sectional study of 60,800 Japanese adults aged 20–75 years. A total of 14,068 subjects (23.1% skipped breakfast, of whom approximately half (52.8% skipped breakfast alone (without LNDE. The percentages of subjects who skipped breakfast showed a J-shaped relationship with body mass index (BMI. Multivariate logistic regression analysis showed that skipping breakfast concomitant with LNDE (n = 6,645 was significantly associated with MetS and proteinuria, even after adjusting for relevant confounders (odds ratio (95% CI, 1.17 (1.08–1.28, P=0.0003, and 1.37 (1.24–1.52, P<0.0001, resp.. Skipping breakfast alone and LNDE alone were not associated with MetS and proteinuria, respectively. In conclusion, habitual breakfast skipping concomitant with LNDE may represent poorer eating behavior than skipping breakfast alone, associated with MetS, asymptomatic proteinuria, obesity, and low body weight in the general Japanese population.

Potential Association between Breakfast Skipping and Concomitant Late-Night-Dinner Eating with Metabolic Syndrome and Proteinuria in the Japanese Population.

Science.gov (United States)

Kutsuma, Ayano; Nakajima, Kei; Suwa, Kaname

2014-01-01

Skipping breakfast is considered to be an unhealthy eating habit linked to predispositions to obesity and type 2 diabetes. Because eating dinner late at night can elicit subsequent breakfast skipping, we investigated if skipping breakfast concomitant with late-night-dinner eating (LNDE) was associated with metabolic syndrome (MetS) and proteinuria in the general Japanese population. We examined self-reported habitual breakfast skipping and LNDE, MetS (modified ATP-III criteria), and proteinuria in a cross-sectional study of 60,800 Japanese adults aged 20-75 years. A total of 14,068 subjects (23.1%) skipped breakfast, of whom approximately half (52.8%) skipped breakfast alone (without LNDE). The percentages of subjects who skipped breakfast showed a J-shaped relationship with body mass index (BMI). Multivariate logistic regression analysis showed that skipping breakfast concomitant with LNDE (n = 6,645) was significantly associated with MetS and proteinuria, even after adjusting for relevant confounders (odds ratio (95% CI), 1.17 (1.08-1.28), P = 0.0003, and 1.37 (1.24-1.52), P < 0.0001, resp.). Skipping breakfast alone and LNDE alone were not associated with MetS and proteinuria, respectively. In conclusion, habitual breakfast skipping concomitant with LNDE may represent poorer eating behavior than skipping breakfast alone, associated with MetS, asymptomatic proteinuria, obesity, and low body weight in the general Japanese population.

A dystrophic Duchenne mouse model for testing human antisense oligonucleotides.

Directory of Open Access Journals (Sweden)

Marcel Veltrop

Full Text Available Duchenne muscular dystrophy (DMD is a severe muscle-wasting disease generally caused by reading frame disrupting mutations in the DMD gene resulting in loss of functional dystrophin protein. The reading frame can be restored by antisense oligonucleotide (AON-mediated exon skipping, allowing production of internally deleted, but partially functional dystrophin proteins as found in the less severe Becker muscular dystrophy. Due to genetic variation between species, mouse models with mutations in the murine genes are of limited use to test and further optimize human specific AONs in vivo. To address this we have generated the del52hDMD/mdx mouse. This model carries both murine and human DMD genes. However, mouse dystrophin expression is abolished due to a stop mutation in exon 23, while the expression of human dystrophin is abolished due to a deletion of exon 52. The del52hDMD/mdx model, like mdx, shows signs of muscle dystrophy on a histological level and phenotypically mild functional impairment. Local administration of human specific vivo morpholinos induces exon skipping and dystrophin restoration in these mice. Depending on the number of mismatches, occasional skipping of the murine Dmd gene, albeit at low levels, could be observed. Unlike previous models, the del52hDMD/mdx model enables the in vivo analysis of human specific AONs targeting exon 51 or exon 53 on RNA and protein level and muscle quality and function. Therefore, it will be a valuable tool for optimizing human specific AONs and genome editing approaches for DMD.

Stemcell Information: SKIP001159 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 0-9 Male ... -- No Human iPS cell lines derived from BJ human foreskin fibroblasts. 新生児包皮から得た線維芽細胞由来のヒトiPS細胞... SKIP001159 ... BJ Human Foreskin Fibroblasts 新生児包皮由来の線維芽細胞 Unknown 246G6 246G6 ... ... Shinya 山中 伸弥 Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for ...iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Information On...ly ... 18035408--22146343 10.1016/j.cell.2007.11.019--10.1038/mt.2011.266 Indu

Stemcell Information: SKIP001144 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available l line derived from a healthy individual cord blood. ... 健常人の臍帯血由来のヒトiPS細胞株。 human ES-...for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and... Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Available RIKEN BioResource Center ... SKIP001144 ... cord blood 臍帯血 Normal HPS0331 HPS0331 610B1 610B1 ... -- Male ... -- No Human iPS cel...理化学研究所 バイオリソースセンター ... http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0331&

Stemcell Information: SKIP001156 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ... 0-9 Male ... -- No Human iPS cell lines derived from BJ human foreskin fibroblasts. 新生児包皮から得た線維芽細胞由来のヒトiPS細胞... SKIP001156 ... BJ Human Foreskin Fibroblasts 新生児包皮由来の線維芽細胞 Unknown 246G3 246G3 ... ...amanaka Shinya 山中 伸弥 Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Cent...er for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Informa...tion Only ... 18035408--22146343 10.1016/j.cell.2007.11.019--10.1038/mt.2011.2

Stemcell Information: SKIP000823 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line, derived from fibloblast(JCRB TIG114). TIG114線維芽細胞由来iPS細胞。エピゾーマルベクターによる樹立、導入細胞には...suke Okita 沖田　圭介 Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 Center for iPS ...Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 Shinya Yamanaka 山中伸弥... Information Only Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 http://www.cir... SKIP000823 ... Normal 418C-1 418C-1 ... 36 30-39 Male Japanese Japanese -- No Human iPS cell

Stemcell Information: SKIP001190 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001190 ... blood mononuclear cell 血中単核細胞 Diseased HPS0414 HPS0414 ... 原発性側索硬化症 G...m a patient :Primary lateral sclerosis (PLS). ... 原発性側索硬化症由来iPS細胞株。 human ES-like Research Grade Other Oct3/4, ...122 Primary Lateral Sclerosis ... -- -- Japanese 日本人 Yes No Disease specific iPS cell line derived fro...EN BioResource Center 理化学研究所 バイオリソースセンター ... Available RIKEN BioResource Center 理化学研究所 バイオリソースセンター ... http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0414&type=1 ...

Stemcell Information: SKIP001192 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001192 ... blood mononuclear cell 血中単核細胞 Diseased HPS0429 HPS0429 CiRA00142 Ci...d from a patient :Charcot-Marie-Tooth disease . ... シャルコー·マリー·トゥース病患者由来iPS細胞株。 human ES-like Research Grade Pla...ll Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research and Applicati...on (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Available RIKEN Bi...RA00142 シャルコー・マリー・トゥース病 G600 Charcot-Marie-Tooth disease 118210 ... -- -- ... Yes No iPS cell line derive

Stemcell Information: SKIP001006 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available e AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europ...e AB. タカラバイオヨーロッパAB Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clonte... SKIP001006 ... Normal ChiPSC21 ChiPSC21 Y00315 Y00315 ... 26 20-29 Male Europe...ovirus Oct4,SOX2,KLF4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europ...an/North African European/North African -- No Cellartis human iPS cell line 21 (ChiPSC21)|Research Gra

Stemcell Information: SKIP001004 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available e AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europ...e AB. タカラバイオヨーロッパAB Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clonte... SKIP001004 ... Normal ChiPSC12 ChiPSC12 Y00285 Y00285 ... 24 20-29 Male Europe...ovirus Oct4,SOX2,KLF4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europ...an/North African European/North African -- No Cellartis human iPS cell line 12 (ChiPSC12)|Research Gra

Stemcell Information: SKIP001005 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available e AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europ...e AB. タカラバイオヨーロッパAB Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clonte... SKIP001005 ... Normal ChiPSC18 ChiPSC18 Y00305 Y00305 ... 32 30-39 Male Europe...ovirus Oct4,SOX2,KLF4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europ...an/North African European/North African -- No Cellartis human iPS cell line 18 (ChiPSC18)|Research Gra

Stemcell Information: SKIP001007 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available e AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europ...e AB. タカラバイオヨーロッパAB Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clonte... SKIP001007 ... Normal ChiPSC22 ChiPSC22 Y00325 Y00325 ... 32 30-39 Male Europe...ovirus Oct4,SOX2,KLF4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europ...an/North African European/North African -- No Cellartis human iPS cell line 22 (ChiPSC22)|Research Gra

Stemcell Information: SKIP001003 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe... AB. タカラバイオヨーロッパAB Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clontech.c... SKIP001003 ... Normal ChiPSC7 ChiPSC7 Y00275 Y00275 ... 20 20-29 Female Europe...us Oct4,SOX2,KLF4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europe...an/North African European/North African -- No Cellartis human iPS cell line 7 (ChiPSC7)|Research Grade

Stemcell Information: SKIP000824 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line, derived from fibloblast(JCRB TIG107). TIG107線維芽細胞由来iPS細胞。エピゾーマルベクターによる樹立、導入細胞...and ... No ... Keisuke Okita 沖田　圭介 Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 ...Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 Shiny...a Yamanaka 山中伸弥 Information Only Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所... SKIP000824 ... Normal 421C-1 421C-1 ... 81 80-89 Female Japanese Japanese -- No Human iPS cell

Stemcell Information: SKIP001145 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from a healthy individual peripheral blood. ... 健常人の末梢血由来のヒトiPS細胞株。 human ES-li... Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Rese...arch and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Available RIKEN BioResource... SKIP001145 ... Normal HPS0360 HPS0360 648A1 648A1 ... 30 30-39 Male ... -- No Human iPS cell... Center 理化学研究所 バイオリソースセンター ... http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=

Stemcell Information: SKIP000821 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line, derived from fibloblast(Cell applications Inc. Lot1388). Lot1388線維芽細胞由来iPS細胞。エピゾーマルベクターによる樹立、導入細胞...No ... No ... Keisuke Okita 沖田　圭介 Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 ...Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 Shiny...a Yamanaka 山中伸弥 Information Only Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所... SKIP000821 ... Normal 404C-2 404C-2 ... 36 30-39 Female ... -- No Human iPS cell

Stemcell Information: SKIP000288 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000288 ... mesenchymal stem cell 間葉系幹細胞 Umbilical cord blood 臍帯血 Normal UCB408E6...d-derived mesenchymal stem cells with transgenic hTERT, HPV E6 and E7. Immortalized ... 臍帯血由来間葉系幹細胞, ... 不死化細胞株 fi...evelopment 国立成育医療研究センター研究所 ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cell...bank.nibio.go.jp/~cellbank/cgi-bin/search_res_det.cgi?DB_NUM=1&ID...=3374 ... 15647378 ... Immortalization of human fetal cells: the life span of umbilical cord blood-derived cell

Stemcell Information: SKIP000286 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP000286 ... mesenchymal stem cell 間葉系幹細胞 Umbilical cord blood 臍帯血 Normal UCB408E6...医療研究センター研究所 ... Not Available National Institute of Biomedical Innovation. 独立行政法人医薬基盤研究所ＪＣＲＢ細胞バンク http://cellbank.nibio.go.jp/~cell...s with transgenic HPV E6 and E7. finite proliferation 臍帯血由来間葉系幹細胞(有限増殖) fibroblast-li...E7-31 UCB408E6E7-31 JCRB1108 JCRB1108 ... -- -- ... -- No JCRB1108 ... Human umbilical cord blood-derived mesenchymal stem cell...378 ... Immortalization of human fetal cells: the life span of umbilical cord blood-derived cells can be prolon

The combined unhealthy behaviors of breakfast skipping and smoking are associated with the prevalence of diabetes mellitus.

Science.gov (United States)

Nishiyama, Midori; Muto, Takashi; Minakawa, Toshihiro; Shibata, Toshie

2009-08-01

Skipping breakfast has been considered a representative unhealthy behavior, but there is little information about the combined effects of breakfast skipping and other unhealthy health habits, especially smoking. First this cross-sectional study investigated unhealthy behaviors among breakfast skippers, and then examined the impact of the combined association of skipping breakfast and smoking on health. A total of 1,200 adults living in one Japanese community were sent questionnaires to elicit data on age, gender, breakfast-eating frequency, and other lifestyle habits. A total 603 of people returned their questionnaires (response rate: 50.3%), and 493 (230 men and 263 women) questionnaires were considered appropriate for analysis. Smoking rate in men (mean age, 53.7 years) and women (mean age, 50.4 years) was 41.3%, and 9.5%, respectively. Skipping breakfast was more prevalent in people under age 50 years (p related to other unhealthy behaviors. Binary logistic regression identified current smoking as the most significant factor related to breakfast skipping (3.10, 95%CI 1.50-6.39). Other factors included, age younger than 50 years (3.04, 95%CI 1.31-7.06) and poor sleeping quality (2.06, 95%CI 1.00-4.25). After examining the combined impact of skipping breakfast and smoking, the highest odds ratio for a diagnosis of diabetes mellitus was found among those who smoked and skipped breakfast (4.68, 95% CI: 1.46-15.05). Moreover, skipping breakfast among non-smokers showed a high association with perceived stress (2.83, 95% CI: 1.05-7.61). In conclusion, the combined unhealthy behaviors of skipping breakfast and smoking are associated with the prevalence of diabetes mellitus.

Performance Analysis of Stop-Skipping Scheduling Plans in Rail Transit under Time-Dependent Demand.

Science.gov (United States)

Cao, Zhichao; Yuan, Zhenzhou; Zhang, Silin

2016-07-13

Stop-skipping is a key method for alleviating congestion in rail transit, where schedules are sometimes difficult to implement. Several mechanisms have been proposed and analyzed in the literature, but very few performance comparisons are available. This study formulated train choice behavior estimation into the model considering passengers' perception. If a passenger's train path can be identified, this information would be useful for improving the stop-skipping schedule service. Multi-performance is a key characteristic of our proposed five stop-skipping schedules, but quantified analysis can be used to illustrate the different effects of well-known deterministic and stochastic forms. Problems in the novel category of forms were justified in the context of a single line rather than transit network. We analyzed four deterministic forms based on the well-known A/B stop-skipping operating strategy. A stochastic form was innovatively modeled as a binary integer programming problem. We present a performance analysis of our proposed model to demonstrate that stop-skipping can feasibly be used to improve the service of passengers and enhance the elasticity of train operations under demand variations along with an explicit parametric discussion.

Performance Analysis of Stop-Skipping Scheduling Plans in Rail Transit under Time-Dependent Demand

Directory of Open Access Journals (Sweden)

Zhichao Cao

2016-07-01

Full Text Available Stop-skipping is a key method for alleviating congestion in rail transit, where schedules are sometimes difficult to implement. Several mechanisms have been proposed and analyzed in the literature, but very few performance comparisons are available. This study formulated train choice behavior estimation into the model considering passengers’ perception. If a passenger’s train path can be identified, this information would be useful for improving the stop-skipping schedule service. Multi-performance is a key characteristic of our proposed five stop-skipping schedules, but quantified analysis can be used to illustrate the different effects of well-known deterministic and stochastic forms. Problems in the novel category of forms were justified in the context of a single line rather than transit network. We analyzed four deterministic forms based on the well-known A/B stop-skipping operating strategy. A stochastic form was innovatively modeled as a binary integer programming problem. We present a performance analysis of our proposed model to demonstrate that stop-skipping can feasibly be used to improve the service of passengers and enhance the elasticity of train operations under demand variations along with an explicit parametric discussion.

Thread-Skip: An Undefined Common Observation.

Science.gov (United States)

McDermott, Peter; Allan, William DE

When a screw-retained implant prosthesis is removed, a click is heard and a slight axial shift is felt, indicating the screw has been fully removed from the retaining thread. This common observation has never been described in the literature. This article describes the click, and it is proposed it be termed thread-skip.

Novel splice-affecting variants in CYP27A1 gene in two Chilean patients with Cerebrotendinous Xanthomatosis

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Susan V. Smalley

2015-03-01

Full Text Available Cerebrotendinous Xanthomatosis (CTX, a rare lipid storage disorder, is caused by recessive loss-of-function mutations of the 27-sterol hydroxylase (CYP27A1, producing an alteration of the synthesis of bile acids, with an accumulation of cholestanol. Clinical characteristics include juvenile cataracts, diarrhea, tendon xanthomas, cognitive impairment and other neurological manifestations. Early diagnosis is critical, because treatment with chenodeoxycholic acid may prevent neurological damage. We studied the CYP27A1 gene in two Chilean CTX patients by sequencing its nine exons, exon-intron boundaries, and cDNA from peripheral blood mononuclear cells. Patient 1 is a compound heterozygote for the novel substitution c.256-1G > T that causes exon 2 skipping, leading to a premature stop codon in exon 3, and for the previously-known pathogenic mutation c.1183C > T (p.Arg395Cys. Patient 2 is homozygous for the novel mutation c.1185-1G > A that causes exon 7 skipping and the generation of a premature stop codon in exon 8, leading to the loss of the crucial adrenoxin binding domain of CYP27A1.

Kinematic characteristics of motor patterns in rope skipping

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Luiz Henrique da Silva

2009-09-01

Full Text Available Rope skipping seems to be an easy task to be performed. However, careful analysis of this motor skill shows how complex the execution of this task is. The objective of this study was to examine kinematic variables of jump patterns as a function of skipping frequency. Eight male university students performed a sequence of 30 rope jumps using two jump patterns (alternating support of the feet and simultaneous support of the feet at three skipping frequencies (1.5, 1.7,1.9 Hz. Frequencies were determined with a digital metronome and the rope was turned by the student himself. Rope jumping performance was recorded with two digital cameras for 3Danalysis. Passive markers were attached to the rope and to the ankle, knee and hip joints forcollection of the following dependent variables: continuous relative phase, time interval betweenthe loss of contact of the feet with the ground and cross of the rope under the feet of the volunteer,jump height, and rope height. ANOVA showed that for the pattern with alternating support ofthe feet the jump is executed at a lower height. In addition, analysis of the time interval revealeda delay in the withdrawal of the feet for crossing the rope in the case of the jump pattern with simultaneous support of the feet.

Stemcell Information: SKIP000222 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available EN-12A HPS0029 HPS0029 ... -- Male ... -- No Human iPS cell line. ヒトiPS細胞株。臍帯由来線維芽細胞由来。 human ES-like... SKIP000222 ... Umbilical cord(Fibroblast) 臍帯（線維芽細胞） Normal HiPS-RIKEN-12A HiPS-RIK... -- Retrovirus Retroviral vector pMXs, Oct3/4, Sox2, Klf4 ... Yes MEF (X-rays:5000R or MMC) 1-1.5x10^(6) cells/...N BRC 理化学研究所バイオリソースセンター Yukio Nakamura 中村幸夫 Available RIKEN BRC 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0029&type=1 ...

Stemcell Information: SKIP001194 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001194 ... blood mononuclear cell 血中単核細胞 Diseased HPS0508 HPS0508 CiRA00161 Ci... line derived from a patient :Charcot-Marie-Tooth disease . ... シャルコー·マリー·トゥース病患者由来iPS細胞株。 huma...ya 山中 伸弥 Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS C...ell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shiny...RA00161 シャルコー・マリー・トゥース病 G600 Charcot-Marie-Tooth disease 118210 ... -- -- Japanese 日本人 Yes No Disease specific iPS cell

Stemcell Information: SKIP001001 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available F4,c-Myc ... -- ... Negative ... Yes ... Yes ... Yes G-banding Yes ... Yes ... Takara Bio Europe AB. タカラバイオヨーロッパ...AB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパAB Takara Bio Europe AB. タカラバイオヨーロッパ...AB Not Available Takara Bio Europe AB. タカラバイオヨーロッパAB http://www.clontech.com/JP/Support/Contact_Technical_Support?sitex=10025:22372:US ... takarabio ... SKIP001001 ... Normal P11032 P11032 Y00225 Y00225 ... 38 30-39 Female European/North African Euro...pean/North African -- No Cellartis human iPS cell line P11032|Research Grade(commer

Stemcell Information: SKIP000219 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available l line. ヒトiPS細胞。歯髄細胞由来。 human ES-like -- Plasmid Episomal vector pCXLE, Oct3/4, Sox...Yamanaka 山中伸弥 Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所 ... Available RIKE... SKIP000219 ... Pulp 歯髄 Normal 454E2 454E2 HPS0077 HPS0077 ... 16 10-19 Female ... -- No Human iPS cel...2, Klf4, L-Myc, Lin28, p53 shRNA ... Yes SNL 76/7 (X-rays:5000R or MMC) 1.5-2.5x10^(6) cells/100mm dish Primate...N BRC 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0077&type=1 ...

Stemcell Information: SKIP000277 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available l1 retrotransposition in the neuronal genome in schizophrenia. Bundo M, Toyoshima... SKIP000277 ... Diseased KO-001-25 KO-001-25 ... 統合失調症 F209 Schizophrenia 181500 ... ... |HCV : |その他の感染症 : 梅毒　陰性（梅毒定性RPR（ラテックス比濁法）、梅毒定性TP抗体（ラテックス比濁法）|病歴・治療歴等 : 28歳時、注意力の低下、記憶障害、独語、空笑、幻聴などの精神病症状が亜急性に出現。|　　　　　　　　精神科受診し統合失調症

Stemcell Information: SKIP001193 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001193 ... blood mononuclear cell 血中単核細胞 Diseased HPS0507 HPS0507 CiRA00160 Ci...line derived from a patient :Charcot-Marie-Tooth disease . ... シャルコー·マリー·トゥース病患者由来iPS細胞株。 human ES-like Researc... for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Cell Research an...d Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya 山中 伸弥 Availab...RA00160 シャルコー・マリー・トゥース病 G600 Charcot-Marie-Tooth disease 118210 ... -- -- Japanese 日本人 Yes No iPS cell

Stemcell Information: SKIP001191 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001191 ... blood mononuclear cell 血中単核細胞 Diseased HPS0426 HPS0426 CiRA00139 Ci... line derived from a patient :Charcot-Marie-Tooth disease . シャルコー·マリー·トゥース病患者由来iPS細胞株。 human...a 山中 伸弥 Center for iPS Cell Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Center for iPS Ce...ll Research and Application (CiRA), Kyoto University 京都大学iPS細胞研究所 Yamanaka Shinya...RA00139 シャルコー・マリー・トゥース病 G600 Charcot-Marie-Tooth disease 118210 ... -- -- Japanese 日本人 Yes No Disease specific iPS cell

The effect of skipping meals and daily activities of university students regarding the body mass index (BMI

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Selen Ozakar Akca

2015-10-01

Full Text Available Background: If we assume that the group of 18-24 years old young people are university students, their proper eating habits present social importance for their own health. With this present study it was aimed to determine the effect of eating habits and daily activity situations of university students regarding obesity. Methods: This descriptive and cross-sectional type study has been carried out in the Health College of the Hitit University. No sample selection was performed, the sample consisted of students visiting the school during the study dates (10- 21.03.2014 and participated voluntarily (n=197 in the study. Questionnaires were used as data collection tool. The data was evaluated with appropriate statistical methods. P < 0.05 has been accepted as statistically significant. Results: 73.1% of the students, participating in the study were female and 26,9% male. The overweight and obesity frequency rate of female students (16% was lower in comparison to male students (17%, whereas the students' BMI average was 22.595+/-3.57. 13.7% of participating students were thin and 8.5% obese. It was seen that 68% of participants in the study skip meals and 28.9% eat 1-2 meals per day. Additionally it was determined that students' skipping meal status is according to the BMI classification statistically significant (p<0.05 Apart from this it was stated that 90.7% of students are doing and #8804;2 hours/week sports. Conclusions: If we assume that one out of every three student is overweight/obese and that the majority do not have a proper nutrition and sport habit, it reveals the importance of BMI screenings and trainings regarding eating habits in school [TAF Prev Med Bull 2015; 14(5.000: 394-400

Two genetic determinants acquired late in Mus evolution regulate the inclusion of exon 5, which alters mouse APOBEC3 translation efficiency.

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Jun Li

2012-01-01

Full Text Available Mouse apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like editing complex 3 (mA3, an intracellular antiviral factor, has 2 allelic variations that are linked with different susceptibilities to beta- and gammaretrovirus infections among various mouse strains. In virus-resistant C57BL/6 (B6 mice, mA3 transcripts are more abundant than those in susceptible BALB/c mice both in the spleen and bone marrow. These strains of mice also express mA3 transcripts with different splicing patterns: B6 mice preferentially express exon 5-deficient (Δ5 mA3 mRNA, while BALB/c mice produce exon 5-containing full-length mA3 mRNA as the major transcript. Although the protein product of the Δ5 mRNA exerts stronger antiretroviral activities than the full-length protein, how exon 5 affects mA3 antiviral activity, as well as the genetic mechanisms regulating exon 5 inclusion into the mA3 transcripts, remains largely uncharacterized. Here we show that mA3 exon 5 is indeed a functional element that influences protein synthesis at a post-transcriptional level. We further employed in vitro splicing assays using genomic DNA clones to identify two critical polymorphisms affecting the inclusion of exon 5 into mA3 transcripts: the number of TCCT repeats upstream of exon 5 and the single nucleotide polymorphism within exon 5 located 12 bases upstream of the exon 5/intron 5 boundary. Distribution of the above polymorphisms among different Mus species indicates that the inclusion of exon 5 into mA3 mRNA is a relatively recent event in the evolution of mice. The widespread geographic distribution of this exon 5-including genetic variant suggests that in some Mus populations the cost of maintaining an effective but mutagenic enzyme may outweigh its antiviral function.

Media use as a reason for meal skipping and fast eating in secondary school children.

Science.gov (United States)

Van den Bulck, J; Eggermont, S

2006-04-01

This study examined self-reported meal skipping and eating faster than usual with the goal of watching television or playing computer games. Respondents reported their media use and indicated how often they skipped a meal to watch a favourite television programme or to play a computer game, and how often they ate faster than usual in order to watch television or play a computer game. Respondents were 2546 adolescents of 13 (first year of secondary school) and 16 years (fourth year of secondary school) of age. About one respondent in 10 skipped at least one meal every week for either television viewing or computer game playing. Weekly meal skipping for television viewing occurs more regularly in boys and first-year students, but particularly in teenagers who view 5 h or more daily (15% of the sample). The category of teenagers who play computer games four times a week or more (25.3% of the sample) is at increased risk of meal skipping; those who play more than four times a week are 10 times more likely weekly to skip a meal. A quarter of the adolescents eat faster at least once a week to be able to watch television or play a computer game. Regardless of gender and school year, teenagers' risk of eating faster progressively increases with their use of the media. Those who watch 4 h or more daily are about seven times more likely to skip a meal for television and those who play computer games at least four times a week are nine times more likely weekly to skip a meal. Unhealthy eating habits can be a side effect of heavy or excessive media use. Teenagers' use of television or game computers during nonworking or out-of-school hours partly displaces the amount of time that needs to be spent at meals. Practitioners and educators may try to encourage or restore a pattern of healthful meal consumption habits by reducing the amount of media use, and by supporting parental rule-making regarding children's eating habits and media use.

Lex-SVM: exploring the potential of exon expression profiling for disease classification.

Science.gov (United States)

Yuan, Xiongying; Zhao, Yi; Liu, Changning; Bu, Dongbo

2011-04-01

Exon expression profiling technologies, including exon arrays and RNA-Seq, measure the abundance of every exon in a gene. Compared with gene expression profiling technologies like 3' array, exon expression profiling technologies could detect alterations in both transcription and alternative splicing, therefore they are expected to be more sensitive in diagnosis. However, exon expression profiling also brings higher dimension, more redundancy, and significant correlation among features. Ignoring the correlation structure among exons of a gene, a popular classification method like L1-SVM selects exons individually from each gene and thus is vulnerable to noise. To overcome this limitation, we present in this paper a new variant of SVM named Lex-SVM to incorporate correlation structure among exons and known splicing patterns to promote classification performance. Specifically, we construct a new norm, ex-norm, including our prior knowledge on exon correlation structure to regularize the coefficients of a linear SVM. Lex-SVM can be solved efficiently using standard linear programming techniques. The advantage of Lex-SVM is that it can select features group-wisely, force features in a subgroup to take equal weihts and exclude the features that contradict the majority in the subgroup. Experimental results suggest that on exon expression profile, Lex-SVM is more accurate than existing methods. Lex-SVM also generates a more compact model and selects genes more consistently in cross-validation. Unlike L1-SVM selecting only one exon in a gene, Lex-SVM assigns equal weights to as many exons in a gene as possible, lending itself easier for further interpretation.

Persistent Dystrophin Protein Restoration 90 Days after a Course of Intraperitoneally Administered Naked 2′OMePS AON and ZM2 NP-AON Complexes in mdx Mice

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Elena Bassi

2012-01-01

Full Text Available In Duchenne muscular dystrophy, the exon-skipping approach has obtained proof of concept in animal models, myogenic cell cultures, and following local and systemic administration in Duchenne patients. Indeed, we have previously demonstrated that low doses (7.5 mg/Kg/week of 2′-O-methyl-phosphorothioate antisense oligoribonucleotides (AONs adsorbed onto ZM2 nanoparticles provoke widespread dystrophin restoration 7 days after intraperitoneal treatment in mdx mice. In this study, we went on to test whether this dystrophin restoration was still measurable 90 days from the end of the same treatment. Interestingly, we found that both western blot and immunohistochemical analysis (up to 7% positive fibres were still able to detect dystrophin protein in the skeletal muscles of ZM2-AON-treated mice at this time, and the level of exon-23 skipping could still be assessed by RT real-time PCR (up to 10% of skipping percentage. In contrast, the protein was undetectable by western blot analysis in the skeletal muscles of mdx mice treated with an identical dose of naked AON, and the percentage of dystrophin-positive fibres and exon-23 skipping were reminiscent of those of untreated mdx mice. Our data therefore demonstrate the long-term residual efficacy of this systemic low-dose treatment and confirm the protective effect nanoparticles exert on AON molecules.

KRAS exon 2 mutations influence activity of regorafenib in an SW48-based disease model of colorectal cancer.

Science.gov (United States)

Camaj, Peter; Primo, Stefano; Wang, Yan; Heinemann, Volker; Zhao, Yue; Laubender, Ruediger Paul; Stintzing, Sebastian; Giessen-Jung, Clemens; Jung, Andreas; Gamba, Sebastian; Bruns, Christiane Josephine; Modest, Dominik Paul

2015-01-01

To investigate the impact of KRAS mutation variants on the activity of regorafenib in SW48 colorectal cancer cells. Activity of regorafenib was evaluated in isogenic SW48 KRAS wild-type (WT) and mutant cells. Subcutaneous xenografts (KRAS WT and G12C mutant variants) in NOD/SCID mice were analyzed to elucidate the effect of regorafenib treatment in vivo. Compared with KRAS WT cells, all mutant variants seemed associated with some degree of resistance to regorafenib-treatment in vitro. In vivo, activation of apoptosis (TUNEL) and reduction of proliferation (Ki67) after treatment with regorafenib were more pronounced in KRAS WT tumors as compared with G12C variants. In SW48 cells, exon 2 mutations of the KRAS gene may influence antitumor effects of regorafenib.

Concurrent mutation in exons 1 and 2 of the K-ras oncogene in colorectal cancer

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Fiorella Guadagni

2012-01-01

Full Text Available The K-ras gene is frequently mutated in colorectal cancer and has been associated with tumor initiation and progression; approximately 90% of the activating mutations are found in codons 12 and 13 of exon 1 and just under 5% in codon 61 located in exon 2. These mutations determine single aminoacidic substitutions in the GTPase pocket leading to a block of the GTP hydrolytic activity of the K-ras p21 protein, and therefore to its constitutive activation. Point mutations in sites of the K-ras gene, other than codons 12, 13 and 61, and other types of genetic alterations, may occur in a minority of cases, such as in the less frequent cases of double mutations in the K-ras gene. However, all mutations in this gene, even those which occur in non-canonical sites or double mutations, are relevant oncogenic alterations in colorectal cancer and may underlie K-ras pathway hyperactivation. In the present study, we report the case of a patient with colorectal cancer presenting a concurrent point mutation in exons 1 and 2 of the K-ras gene, a GGT to TGT substitution (Glycine to Cysteine at codon 12, and a GAC to AAC substitution (Aspartic Acid to Asparagine at codon 57. In addition, we found in the same patient’s sample a silent polymorphism at codon 11 (Ala11Ala of exon 1. (Folia Histochemica et Cytobiologica 2011; Vol. 49, No. 4, pp. 729–733

Stemcell Information: SKIP001101 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001101 ... o induced chondrogenic (iChon) cells ダイレクトリプログラミングで作製した軟骨細胞 ... Normal ...man Dermal Fibroblasts(1439 KURABO). 新生児皮膚繊維芽細胞(1439 KURABO)をダイレクトリプログラミングにより軟骨細胞へと誘導（iChon細胞） Other Researc... Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Research ...and Application,Kyoto University 京都大学iPS細胞研究所　CiRA https://www.cira.kyoto-u.ac.jp/e/index.html ... 25187577 ...WT-1-iChon WT-1-iChon ... 0-9 Male ... -- No Direct iInduction of Chondrogenic(iChon) cells from Hu

Stemcell Information: SKIP000678 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available ns in the ratio 3:1:1:1:1. 胎児肺線維芽細胞由来iPS細胞。|低酸素下でKlf4, c-Myc, Oct4, Sox2とLIN28を3:...1:1:1:1の割合でコードした合成RNAを、線維芽細胞株に20日間毎日添加し、遺伝子を細胞へ導入した。 human ES-like Research Grade Other OCT4 , SOX2 , KLF4 ,... SKIP000678 ... Lung Lung Normal MRC5-RiPS-1.8 MRC5-RiPS-1.8 ... Fetus Male ... -- No hiPS-cell...s derived from human fetal lung fibroblast cells (MRC-5 Line).They were derived using m....1016/j.stem.2010.08.012 Highly efficient reprogramming to pluripotency and directed differentiation of human cell

Stemcell Information: SKIP001102 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001102 ... induced chondrogenic (iChon) cells ダイレクトリプログラミングで作製した軟骨細胞 ... Normal WT...n Dermal Fibroblasts(789013 KURABO). 新生児皮膚繊維芽細胞(789013 KURABO)をダイレクトリプログラミングにより軟骨細胞へと誘導（iChon細胞） Other Resea...n, Kyoto University 京都大学iPS細胞研究所 ... Information Only Center for iPS Cell Researc...h and Application,Kyoto University 京都大学iPS細胞研究所　CiRA https://www.cira.kyoto-u.ac.jp/e/index.html ... 2518757...-2-iChon WT-2-iChon ... 0-9 Male ... -- No Direct iInduction of Chondrogenic(iChon) cells from Huma

Stemcell Information: SKIP000674 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available rous hESC-like colonies in BJ cultures that were mechanically picked at day 18, 20, 21, and 25, respectively. BJ新生児線維芽細胞由来iPS細胞...。|低酸素下でKlf4, c-Myc, Oct4, Sox2とLIN28を3:1:1:1:1の割合でコードした合成RNAを、線維芽細胞株に20日間毎日添加し、遺伝子を細胞へ導入し... SKIP000674 ... foreskin foreskin Normal BJ-RiPS1.1 BJ-RiPS1.1 ... 0-9 Male ... -- No hiPS-cell...cy and directed differentiation of human cells with synthetic modified mRNA.--Som...atic coding mutations in human induced pluripotent stem cells. Warren L, Manos PD, Ahfeldt T, Loh YH, Li H,

JAK2 Exon 12 Mutations in Polycythemia Vera and Idiopathic Erythrocytosis

Science.gov (United States)

Scott, Linda M.; Tong, Wei; Levine, Ross L.; Scott, Mike A.; Beer, Philip A.; Stratton, Michael R.; Futreal, P. Andrew; Erber, Wendy N.; McMullin, Mary Frances; Harrison, Claire N.; Warren, Alan J.; Gilliland, D. Gary; Lodish, Harvey F.; Green, Anthony R.

2010-01-01

BACKGROUND The V617F mutation, which causes the substitution of phenylalanine for valine at position 617 of the Janus kinase (JAK) 2 gene (JAK2), is often present in patients with polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis. However, the molecular basis of these myeloproliferative disorders in patients without the V617F mutation is unclear. METHODS We searched for new mutations in members of the JAK and signal transducer and activator of transcription (STAT) gene families in patients with V617F-negative polycythemia vera or idiopathic erythrocytosis. The mutations were characterized biochemically and in a murine model of bone marrow transplantation. RESULTS We identified four somatic gain-of-function mutations affecting JAK2 exon 12 in 10 V617F-negative patients. Those with a JAK2 exon 12 mutation presented with an isolated erythrocytosis and distinctive bone marrow morphology, and several also had reduced serum erythropoietin levels. Erythroid colonies could be grown from their blood samples in the absence of exogenous erythropoietin. All such erythroid colonies were heterozygous for the mutation, whereas colonies homozygous for the mutation occur in most patients with V617F-positive polycythemia vera. BaF3 cells expressing the murine erythropoietin receptor and also carrying exon 12 mutations could proliferate without added interleukin-3. They also exhibited increased phosphorylation of JAK2 and extracellular regulated kinase 1 and 2, as compared with cells transduced by wild-type JAK2 or V617F JAK2. Three of the exon 12 mutations included a substitution of leucine for lysine at position 539 of JAK2. This mutation resulted in a myeloproliferative phenotype, including erythrocytosis, in a murine model of retroviral bone marrow transplantation. CONCLUSIONS JAK2 exon 12 mutations define a distinctive myeloproliferative syndrome that affects patients who currently receive a diagnosis of polycythemia vera or idiopathic erythrocytosis

Skipping breakfast is detrimental for primary school children: cross-sectional analysis of determinants for targeted prevention

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Dorothea Kesztyüs

2017-03-01

Full Text Available Abstract Background Skipping breakfast was found to be associated with abdominal obesity in primary school children. The aim of this research was to examine factors associated with skipping breakfast in primary school children in order to develop targeted preventive measures. Methods Baseline data assessment (2010 of a cluster-randomized controlled trial for the evaluation of a school-based health promotion program in primary school children in the state of Baden-Württemberg, Germany. Anthropometric measures of 1,943 primary school children aged 7.1 ± 0.6 years (51.2% boys were conducted according to ISAK-standards (International Standard for Anthropometric Assessment by trained staff. Further information on the health and living conditions of the children and their parents were assessed in parental questionnaires. Generalized linear mixed regression analysis was calculated to define correlates for skipping breakfast in terms of odds ratios (OR and 95% confidence intervals (CI. Results According to the final regression models, significant correlates of skipping breakfast can be divided into modifiable behavioral components (high consumption of soft drinks (OR 2.49, 95% CI 1.81; 3.43, screen media (OR 2.48, 95% CI 1.77; 3.46 and high levels of physical activity (OR 0.64, 95% CI 0.44; 0.93 on the one hand, and more or less static socio-economic factors (migration background (OR 2.81, 95% CI 2.02; 3.91, single parenting (OR 2.13, 95% CI 1.34; 3.40, and high family education level (OR 0.42, 95% CI 0.28; 0.64 on the other hand, and finally individual factors (female gender (OR 1.43, 95% CI 1.03; 1.99 and having a percentage of body fat at or above the 95th percentile (OR 1.47, 95% CI 1.00; 2.17. Conclusion Targeted prevention should aim at health-related behaviors accompanying the habit of skipping breakfast. Focusing on vulnerable groups, characterized by not so easily modifiable socio-economic as well as individual factors, may improve

Characterization of novel RS1 exonic deletions in juvenile X-linked retinoschisis.

Science.gov (United States)

D'Souza, Leera; Cukras, Catherine; Antolik, Christian; Craig, Candice; Lee, Ji-Yun; He, Hong; Li, Shibo; Smaoui, Nizar; Hejtmancik, James F; Sieving, Paul A; Wang, Xinjing

2013-01-01

X-linked juvenile retinoschisis (XLRS) is a vitreoretinal dystrophy characterized by schisis (splitting) of the inner layers of the neuroretina. Mutations within the retinoschisis (RS1) gene are responsible for this disease. The mutation spectrum consists of amino acid substitutions, splice site variations, small indels, and larger genomic deletions. Clinically, genomic deletions are rarely reported. Here, we characterize two novel full exonic deletions: one encompassing exon 1 and the other spanning exons 4-5 of the RS1 gene. We also report the clinical findings in these patients with XLRS with two different exonic deletions. Unrelated XLRS men and boys and their mothers (if available) were enrolled for molecular genetics evaluation. The patients also underwent ophthalmologic examination and in some cases electroretinogram (ERG) recording. All the exons and the flanking intronic regions of the RS1 gene were analyzed with direct sequencing. Two patients with exonic deletions were further evaluated with array comparative genomic hybridization to define the scope of the genomic aberrations. After the deleted genomic region was identified, primer walking followed by direct sequencing was used to determine the exact breakpoints. Two novel exonic deletions of the RS1 gene were identified: one including exon 1 and the other spanning exons 4 and 5. The exon 1 deletion extends from the 5' region of the RS1 gene (including the promoter) through intron 1 (c.(-35)-1723_c.51+2664del4472). The exon 4-5 deletion spans introns 3 to intron 5 (c.185-1020_c.522+1844del5764). Here we report two novel exonic deletions within the RS1 gene locus. We have also described the clinical presentations and hypothesized the genomic mechanisms underlying these schisis phenotypes.

Loss of Endocan tumorigenic properties after alternative splicing of exon 2

International Nuclear Information System (INIS)

Depontieu, Florence; Grigoriu, Bogdan-Dragos; Scherpereel, Arnaud; Adam, Estelle; Delehedde, Maryse; Gosset, Philippe; Lassalle, Philippe

2008-01-01

Endocan was originally described as a dermatan sulfate proteoglycan found freely circulating in the blood. Endocan expression confers tumorigenic properties to epithelial cell lines or accelerate the growth of already tumorigenic cells. This molecule is the product of a single gene composed of 3 exons. Previous data showed that endocan mRNA is subject to alternative splicing with possible generation of two protein products. In the present study we identified, and functionally characterized, the alternative spliced product of the endocan gene: the exon 2-deleted endocan, called endocanΔ2. Stable, endocanΔ2-overexpressing cell lines were generated to investigate the biological activities of this new alternatively spliced product of endocan gene. Tumorigenesis was studied by inoculating endocan and endocanΔ2 expressing cell lines subcutaneously in SCID mice. Biochemical properties of endocan and endocanΔ2 were studied after production of recombinant proteins in various cell lines of human and murine origin. Our results showed that the exon 2 deletion impairs synthesis of the glycan chain, known to be involved in the pro-tumoral effect of endocan. EndocanΔ2 did not promote tumor formation by 293 cells implanted in the skin of severe combined immunodeficient (SCID) mice. Our results emphasize the key role of the polypeptide sequence encoded by the exon 2 of endocan gene in tumorigenesis, and suggest that this sequence could be a target for future therapies against cancer

Correlating In Vitro Splice Switching Activity With Systemic In Vivo Delivery Using Novel ZEN-modified Oligonucleotides

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Suzan M Hammond

2014-01-01

Full Text Available Splice switching oligonucleotides (SSOs induce alternative splicing of pre-mRNA and typically employ chemical modifications to increase nuclease resistance and binding affinity to target pre-mRNA. Here we describe a new SSO non-base modifier (a naphthyl-azo group, “ZEN™” to direct exon exclusion in mutant dystrophin pre-mRNA to generate functional dystrophin protein. The ZEN modifier is placed near the ends of a 2′-O-methyl (2′OMe oligonucleotide, increasing melting temperature and potency over unmodified 2′OMe oligonucleotides. In cultured H2K cells, a ZEN-modified 2′OMe phosphorothioate (PS oligonucleotide delivered by lipid transfection greatly enhanced dystrophin exon skipping over the same 2′OMePS SSO lacking ZEN. However, when tested using free gymnotic uptake in vitro and following systemic delivery in vivo in dystrophin deficient mdx mice, the same ZEN-modified SSO failed to enhance potency. Importantly, we show for the first time that in vivo activity of anionic SSOs is modelled in vitro only when using gymnotic delivery. ZEN is thus a novel modifier that enhances activity of SSOs in vitro but will require improved delivery methods before its in vivo clinical potential can be realized.

The role of exon shuffling in shaping protein-protein interaction networks

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França Gustavo S

2010-12-01

Full Text Available Abstract Background Physical protein-protein interaction (PPI is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains, self-interacting (able to interact with another copy of themselves and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Potential Association between Breakfast Skipping and Concomitant Late-Night-Dinner Eating with Metabolic Syndrome and Proteinuria in the Japanese Population

OpenAIRE

Kutsuma, Ayano; Nakajima, Kei; Suwa, Kaname

2014-01-01

Skipping breakfast is considered to be an unhealthy eating habit linked to predispositions to obesity and type 2 diabetes. Because eating dinner late at night can elicit subsequent breakfast skipping, we investigated if skipping breakfast concomitant with late-night-dinner eating (LNDE) was associated with metabolic syndrome (MetS) and proteinuria in the general Japanese population. We examined self-reported habitual breakfast skipping and LNDE, MetS (modified ATP-III criteria), and proteinur...

Inactivating Mutation screening of Exon 6 and Exon 10E of FSHR gene in women with Polycystic Ovarian Syndrome in Vellore population

Science.gov (United States)

Sekar, Nishu; Sapre, Madhura; Kale, Vaikhari; Prabhu, Yogamaya D.; Renu, Kaviyarasi; Ramgir, Shalaka S.; Abilash, V. G.

2017-11-01

Polycystic Ovarian syndrome (PCOS) is a major cause of infertility in females of reproducing age and is typified by oligo-anovulation, hyperandrogenism, hirsutism and polycystic ovaries. FSHR gene located on chromosome 2 p21 is responsible for the normal follicular development and any deletion or mutation in the gene affects the interaction of FSH with its receptor. Thus, it becomes the candidate gene for PCOS study. Inactivating mutation in FSHR gene limits the receptor’s function by creating a complete block, changing the receptor-ligand complex or the basic hormone signal transduction.To screen the inactivating mutations in Exon 6 and Exon 10E of FSHR gene in women diagnosed with PCOS.PCR-RFLP analysis indicated that there were no inactivating mutations found in Exon 6 and Exon 10E. Variations in hormone levels were seen amongst the PCOS patients. There were no inactivating mutations found in FSHR gene of the women diagnosed with PCOS according to the Rotterdam criteria in Vellore population.

Clinical and molecular consequences of exon 78 deletion in DMD gene.

Science.gov (United States)

Traverso, Monica; Assereto, Stefania; Baratto, Serena; Iacomino, Michele; Pedemonte, Marina; Diana, Maria Cristina; Ferretti, Marta; Broda, Paolo; Minetti, Carlo; Gazzerro, Elisabetta; Madia, Francesca; Bruno, Claudio; Zara, Federico; Fiorillo, Chiara

2018-03-19

We present a 13-year-old patient with persistent increase of serum Creatine Kinase (CK) and myalgia after exertion. Skeletal muscle biopsy showed marked reduction of dystrophin expression leading to genetic analysis of DMD gene by MLPA, which detected a single deletion of exon 78. To the best of our knowledge, DMD exon 78 deletion has never been described in literature and, according to prediction, it should lead to loss of reading frame in the dystrophin gene. To further assess the actual effect of exon 78 deletion, we analysed cDNA from muscle mRNA. This analysis confirmed the absence of 32 bp of exon 78. Exclusion of exon 78 changes the open reading frame of exon 79 and generate a downstream stop codon, producing a dystrophin protein of 3703 amino acids instead of 3685 amino acids. Albeit loss of reading frame usually leads to protein degradation and severe phenotype, in this case, we demonstrated that deletion of DMD exon 78 can be associated with a functional protein able to bind DGC complex and a very mild phenotype. This study adds a novel deletion in DMD gene in human and helps to define the compliance between maintaining/disrupting the reading frame and clinical form of the disease.

Skipping of meals has a significant impact on dietary intake and nutritional status of old (65+ y) nursing home residents.

Science.gov (United States)

Beck, A M; Ovesen, L

2004-01-01

In spite of a high prevalence of undernutrition among old nursing home residents, studies have generally reported a mean intake of energy sufficient to cover the mean estimated energy requirement. This discrepancy could be due to skipping of meals and hence periods of insufficient energy intake too intermittent to be identified, when mean results are presented. To examine the significance of skipping of (part of) meals on dietary intake and nutritional status of old (65+y) nursing home residents. Participants were 132 nursing home residents (84 (82-85) y). They were characterised according to activity of daily living-functions (ADL-functions), cognitive performance, intake of energy and protein (4-days dietary record), skipping of meals, energy and protein balance, and nutritional status (body mass index (BMI)). The participants had an energy intake, which was significantly higher than the estimated energy requirement (p eat or only had desert at one or more meals during the 4-day registration period. Participants who were skipping meals had a lower BMI, energy and protein intake (all p <0.001) and a higher prevalence of negative protein balance (p <0.01), than the other residents. More focus should be given to individualized nutritional assessment in order to discover the cause to this problem and target individuals who could be helped by nutritional intervention.

Stemcell Information: SKIP000206 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available RK2 600116 ... 71 70-79 Female ... Yes No PARK2 iPSC, Exon 2-4 homozygous deletions in parkin PARK2 iPS細胞,...kin遺伝子のexon毎に設計したprimerを用いてgenomic PCR解析を行った。|　　　　　　その結果、患者由来線維芽細胞およびPA1.9.22iPSにおいてExon2,3,4のhomozygous del...625)|8.Feeder Cellの使用: 使用する|　細胞名 : SNL細胞|　使用時の細胞密度 : 1.5 x 10^(6)/10cm dish|　使用前処理方法 : Mitomycin C処理 : 400mi...)|　Total 50ml|　Aliquot and store at -20 degree|10.パッセージの際の細胞播種時の細胞密度|　Confluentの10cm dish 1枚から、10cm dish 3〜8...形成実験 : 実施　胚葉体形成確認|テラトーマ形成実験 : 実施　テラトーマ形成確認|in vitro分化能解析 : 実施　神経への分化確認|マイコプラズマ汚染検査 : 実施　陰性|細胞同定検査（STR多型解析） : 未実施|クローニング : ||その他の特性情報 : 樹立に用いた外来遺伝子の発現抑制を確認した。

Risk of mental health problems in adolescents skipping meals: The Korean National Health and Nutrition Examination Survey 2010 to 2012.

Science.gov (United States)

Lee, Gyungjoo; Han, Kyungdo; Kim, Hyunju

Adolescents frequently skip meals, doing so even more than once per day. This is associated with more mental health problems. This study identified mental health problems' associations with skipping meals and the frequency thereof among adolescents. This cross-sectional population-based study used a data set of 1,413 adolescents from the 2010 to 2012 Korean National Health and Nutrition Examination Survey. Hierarchical multivariable logistic regression was conducted to determine the risk of mental health problems, including stress, depressive mood, and suicidal ideation in relation to skipping meals and the frequency thereof per day. Breakfast skipping significantly increased the risks of stress and depressive mood. Stress, depressive mood, and suicidal ideation were significantly prevalent as the daily frequency of skipping meals increased. Specific strategies should be developed at government or school level to decrease the frequency of skipping meals per day, associated with serious mental health problems in adolescents. Copyright © 2017 Elsevier Inc. All rights reserved.

Stemcell Information: SKIP001103 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available SKIP001103 ... induced chondrogenic (iChon) cells ダイレクトリプログラミングで作製した軟骨細胞 ... Diseased ...s have elevated ER stress and undergo apoptosis. 軟骨無発症患者線維芽細胞(GM07892)をダイレクトリプログラミングにより軟骨細胞...へと誘導（iChon細胞）。|小胞体ストレスが生じ、過度のアポトーシスが引き起こされていた。 Other Research Grade Retrovirus c-MYC, KLF4... ... Minoru Okada 岡田　稔 Center for iPS Cell Research and Application, Kyoto University 京都大学iPS細胞研究所... ... Information Only Center for iPS Cell Research and Application,Kyoto University 京都大学iPS細胞研究所　CiRA https:

Stemcell Information: SKIP000221 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available N-2A HPS0009 HPS0009 ... -- Male ... -- No Human iPS cell line. ヒトiPS細胞。臍帯由来線維芽細胞（RCB0197 HUC-Fm）由来。 ... SKIP000221 ... Umbilical cord(Fibroblast) 臍帯（線維芽細胞） Normal HiPS-RIKEN-2A HiPS-RIKE...human ES-like -- Retrovirus Retroviral vector pMXs, Oct3/4, Sox2, Klf4, c-Myc ... Yes MEF (X-rays:5000R or MMC) 1-1.5x10^(6) cell.../www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0009&type=1 ... ...学研究所バイオリソースセンター RIKEN BRC 理化学研究所バイオリソースセンター Yukio Nakamura 中村幸夫 Available RIKEN BRC 理化学研究所バイオリソースセンター http:/

Cloud-based adaptive exon prediction for DNA analysis.

Science.gov (United States)

Putluri, Srinivasareddy; Zia Ur Rahman, Md; Fathima, Shaik Yasmeen

2018-02-01

Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database.

Reduced anxiety-like behavior and altered hippocampal morphology in female p75NTR exon IV-/- mice.

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Zoe ePuschban

2016-06-01

Full Text Available The presence of the neurotrophin receptor p75NTR in adult basal forebrain cholinergic neurons, precursor cells in the subventricular cell layer and the subgranular cell layer of the hippocampus has been linked to alterations in learning as well as anxiety- and depression- related behaviors. In contrast to previous studies performed in a p75NTR exonIII-/- model still expressing the short isoform of the p75NTR, we focused on locomotor and anxiety–associated behavior in p75NTR exonIV-/- mice lacking both p75NTR isoforms. Comparing p75NTR exonIV-/- and wildtype mice for both male and female animals showed an anxiolytic-like behavior as evidenced by increased central activities in the open field paradigm and flex field activity system as well as higher numbers of open arm entries in the elevated plus maze test in female p75NTR knockout mice.Morphometrical analyses of dorsal and ventral hippocampus revealed a reduction of width of the dentate gyrus and the granular cell layer in the dorsal but not ventral hippocampus in male and female p75NTR exonIV -/- mice. We conclude that germ-line deletion of p75NTR seems to differentially affect morphometry of dorsal and ventral dentate gyrus and that p75NTR may play a role in anxiety-like behavior, specifically in female mice.

Screening for mutations in two exons of FANCG gene in Pakistani population.

Science.gov (United States)

Aymun, Ujala; Iram, Saima; Aftab, Iram; Khaliq, Saba; Nadir, Ali; Nisar, Ahmed; Mohsin, Shahida

2017-06-01

Fanconi anemia is a rare autosomal recessive disorder of genetic instability. It is both molecularly and clinically, a heterogeneous disorder. Its incidence is 1 in 129,000 births and relatively high in some ethnic groups. Sixteen genes have been identified among them mutations in FANCG gene are most common after FANCA and FANCC gene mutations. To study mutations in exon 3 and 4 of FANCG gene in Pakistani population. Thirty five patients with positive Diepoxybutane test were included in the study. DNA was extracted and amplified for exons 3 and 4. Thereafter Sequencing was done and analyzed for the presence of mutations. No mutation was detected in exon 3 whereas a carrier of known mutation c.307+1 G>T was found in exon 4 of the FANCG gene. Absence of any mutation in exon 3 and only one heterozygous mutation in exon 4 of FANCG gene points to a different spectrum of FA gene pool in Pakistan that needs extensive research in this area.

Intron Retention and TE Exonization Events in ZRANB2

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Sang-Je Park

2012-01-01

Full Text Available The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2, contains arginine/serine-rich (RS domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3 between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3. Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species. Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3. RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys and were expressed via intron retention (IR. Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.

Tracking the evolution of alternatively spliced exons within the Dscam family

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Vision Todd J

2006-02-01

Full Text Available Abstract Background The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17, potentially generating 38,016 protein isoforms. This degree of transcript diversity has not been found in mammalian homologs of Dscam. We examined the molecular evolution of exons within this gene family to locate the point of divergence for this alternative splicing pattern. Results Using the fruit fly Dscam exons 4, 6, 9 and 17 as seed sequences, we iteratively searched sixteen genomes for homologs, and then performed phylogenetic analyses of the resulting sequences to examine their evolutionary history. We found homologs in the nematode, arthropod and vertebrate genomes, including homologs in several vertebrates where Dscam had not been previously annotated. Among these, only the arthropods contain homologs arranged in tandem arrays indicative of mutually exclusive splicing. We found no homologs to these exons within the Arabidopsis, yeast, tunicate or sea urchin genomes but homologs to several constitutive exons from fly Dscam were present within tunicate and sea urchin. Comparing the rate of turnover within the tandem arrays of the insect taxa (fruit fly, mosquito and honeybee, we found the variants within exons 4 and 17 are well conserved in number and spatial arrangement despite 248–283 million years of divergence. In contrast, the variants within exons 6 and 9 have undergone considerable turnover since these taxa diverged, as indicated by deeply branching taxon-specific lineages. Conclusion Our results suggest that at least one Dscam exon array may be an ancient duplication that predates the divergence of deuterostomes from protostomes but that there is no evidence for the presence of arrays in the common ancestor of vertebrates. The different patterns of conservation and turnover among the Dscam exon arrays

Skipping breakfast and overweight in 2-and 5-year-old Dutch children-the GECKO Drenthe cohort

NARCIS (Netherlands)

Kupers, L. K.; de Pijper, J. J.; Sauer, P. J. J.; Stolk, R. P.; Corpeleijn, E.

Skipping breakfast is associated with higher BMI in children aged 5 years and older. However, not much is known about this association in younger children. In the Dutch GECKO Drenthe birth cohort we examined the association between breakfast skipping and objectively measured overweight at the age of

THE EXON 5, 6, 7, 8 OF P53 MUTATIONS IN ORAL SQUAMOUS CELLS CARCINOMA

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Retno P Rahayu

2012-04-01

Full Text Available Genetic instability may underlie the etiology of multistep carcinogenesis. The altered p53 gene observed in tumors may represent the expression of such instability and may allow the accumulation of other gene alterations caused by multiple mechanism. p53 gene is the guardian of the genome, that is why we pay more attention to this gene. In this study, we evaluated the significance of p53 mutation in 55 patient with oral squamous carcinoma. Thirty among them underwent well-differentiated carcinoma, while the remaining 25 patients underwent poorly differentiated carcinoma. The mutations were detected by PCR-SSCP (Single strand Conformational Polymorphism analysis in the region between exon 5 and exon 8. The results indicated that the p53 mutation in exon 5 (40%, exon 6 (28%, exon 7 (24% and exon 8 (8% were associated with poorly differentiated carcinoma, whereas mutation in exon 5 (10%, exon 6 (30%, exon 7 (40% and exon 8 (20% were associated with well-differentiated carcinoma. These observations suggest that p53 mutation in exon 5, 6, and 7 have strong correlation with poorly differentiated in oral squamous carcinoma while well-differentiated level was related with mutation in exon 6,7 and 8.

breakfast skipping and academic / social development of pupils

African Journals Online (AJOL)

Abasiama Akpan

“Assessment of the effects of skipping breakfast on the children by pupils was the basic ... concludes that since proper feeding is necessary for the child's academic and social development, the ... people feed influence their behaviour in a variety ... J. C. Duruamaku-Dim, Department of Curriculum & Teaching, Faculty of ...

Multiple splice defects in ABCA1 cause low HDL-C in a family with Hypoalphalipoproteinemia and premature coronary disease

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Miller Michael

2009-01-01

Full Text Available Abstract Background Mutations at splice junctions causing exon skipping are uncommon compared to exonic mutations, and two intronic mutations causing an aberrant phenotype have rarely been reported. Despite the high number of functional ABCA1 mutations reported to date, splice variants have been reported infrequently. We screened DNA from a 41 year-old male with low HDL-C (12 mg/dL [0.31 mmol/L] and a family history of premature coronary heart disease (CHD using polymerase chain reaction single-strand conformation polymorphism (SSCP analysis. Methods Family members with low levels of HDL-C (n = 6 were screened by SSCP for mutations in ABCA1. Samples with altered SSCP patterns were sequenced directly using either an ABI 3700 or ABI3730Xl DNA Analyzer. To screen for splicing defects, cDNA was isolated from the proband's RNA and was sequenced as above. A series of minigenes were constructed to determine the contribution of normal and defective alleles. Results Two novel splice variants in ABCA1 were identified. The first mutation was a single base pair change (T->C in IVS 7, 6 bps downstream from the exon7/intron7 junction. Amplification of cDNA and allelic subcloning identified skipping of Exon 7 that results in the elimination of 59 amino acids from the first extracellular loop of the ABCA1 protein. The second mutation was a single base pair change (G->C at IVS 31 -1, at the intron/exon junction of exon 32. This mutation causes skipping of exon 32, resulting in 8 novel amino acids followed by a stop codon and a predicted protein size of 1496 AA, compared to normal (2261 AA. Bioinformatic studies predicted an impact on splicing as confirmed by in vitro assays of constitutive splicing. Conclusion In addition to carnitine-acylcarnitine translocase (CACT deficiency and Hermansky-Pudlak syndrome type 3, this represents only the third reported case in which 2 different splice mutations has resulted in an aberrant clinical phenotype.

Skipping on uneven ground: trailing leg adjustments simplify control and enhance robustness.

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Müller, Roy; Andrada, Emanuel

2018-01-01

It is known that humans intentionally choose skipping in special situations, e.g. when descending stairs or when moving in environments with lower gravity than on Earth. Although those situations involve uneven locomotion, the dynamics of human skipping on uneven ground have not yet been addressed. To find the reasons that may motivate this gait, we combined experimental data on humans with numerical simulations on a bipedal spring-loaded inverted pendulum model (BSLIP). To drive the model, the following parameters were estimated from nine subjects skipping across a single drop in ground level: leg lengths at touchdown, leg stiffness of both legs, aperture angle between legs, trailing leg angle at touchdown (leg landing first after flight phase), and trailing leg retraction speed. We found that leg adjustments in humans occur mostly in the trailing leg (low to moderate leg retraction during swing phase, reduced trailing leg stiffness, and flatter trailing leg angle at lowered touchdown). When transferring these leg adjustments to the BSLIP model, the capacity of the model to cope with sudden-drop perturbations increased.

Handover Management in 5G and Beyond: A Topology Aware Skipping Approach

KAUST Repository

Arshad, Rabe

2016-12-21

Network densification is foreseen as a potential solution to fulfill the 5G spectral efficiency requirements. The spectral efficiency is improved by shrinking base stations’ (BSs) footprints, thus improving the spatial frequency reuse and reducing the number of users sharing the resources of each BS. However, the foreseen densification gains are achieved at the expense of increasing handover (HO) rates. Hence, HO rate is a key performance limiting factor that should be carefully considered in densification planning. This paper sheds light on the HO problem that appears in dense 5G networks and proposes an effective solution via topology aware HO skipping. Different skipping techniques are considered and compared with the conventional best connected scheme. To this end, the proposed schemes are validated via the average user rate in downlink single-tier and two-tier cellular networks, which are modeled using the Poisson point process and the Poisson cluster process, respectively. The proposed skipping schemes show up to 47% gains in the average throughput, which would maximize the benefit of network densification.

Handover Management in 5G and Beyond: A Topology Aware Skipping Approach

KAUST Repository

Arshad, Rabe; Elsawy, Hesham; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

2016-01-01

Network densification is foreseen as a potential solution to fulfill the 5G spectral efficiency requirements. The spectral efficiency is improved by shrinking base stations’ (BSs) footprints, thus improving the spatial frequency reuse and reducing the number of users sharing the resources of each BS. However, the foreseen densification gains are achieved at the expense of increasing handover (HO) rates. Hence, HO rate is a key performance limiting factor that should be carefully considered in densification planning. This paper sheds light on the HO problem that appears in dense 5G networks and proposes an effective solution via topology aware HO skipping. Different skipping techniques are considered and compared with the conventional best connected scheme. To this end, the proposed schemes are validated via the average user rate in downlink single-tier and two-tier cellular networks, which are modeled using the Poisson point process and the Poisson cluster process, respectively. The proposed skipping schemes show up to 47% gains in the average throughput, which would maximize the benefit of network densification.

Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses

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van der Klift, Heleen M; Jansen, Anne M L; van der Steenstraten, Niki; Bik, Elsa C; Tops, Carli M J; Devilee, Peter; Wijnen, Juul T

2015-01-01

A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants. PMID:26247049

EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

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Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

2014-11-01

The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. © 2014 John Wiley & Sons Ltd.

Effects of social determinants on food choice and skipping meals among Turkish adolescents.

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Soyer, Meral Turk; Ergin, Isil; Gursoy, Safak Taner

2008-01-01

To present data that contributes to understanding factors that influence food choice and skipping meals in adolescents. A cross sectional study is carried in selected high schools in Bornova. Study sample compromises of 527 students chosen randomly by class from a population of 2410 first year in high school students. Self-administered questionnaires containing sociodemographic determinants, self reported weight and height, food choices and meal patterns were used. A psychosocial factor that affects almost all of the students is the "taste and sensory perception of food". The second noticable factor is the "health and nutritious value of food". The time conserved and the convenience in the preparation of food is one of the lifestyle factors that affect more than half of the students. The cost of the food was also found to have an effect. Among the third group of factors categorized as "media", the leading factor is advertisement, effective in one third of the students. Among boys and girls, there was no statistical difference in the type of meal skipped. Living in Izmir for more than 10 years compared to less than ten years, being in a nuclear family to extended family, and belonging to the "owner" social class to "wage laborer" class also do not statistically differ with regard to skipping meals. However, the mother's and father's education level and having a working mother are associated with skipping meals. These results provide important evidence to support opportunities to positively influence the adoption of healthful eating.

Acetylcholinesterase (AChE) gene modification in transgenic animals: functional consequences of selected exon and regulatory region deletion.

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Camp, Shelley; Zhang, Limin; Marquez, Michael; de la Torre, Brian; Long, Jeffery M; Bucht, Goran; Taylor, Palmer

2005-12-15

. delaTorre, P. Taylor, Knockout mice with deletions of alternatively spliced exons of Acetylcholinesterase, in: N.C. Inestrosa, E.O. Campus (Eds.), VII International Meeting on Cholinesterases, Pucon-Chile Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects. P. Universidad Catholica de Chile-FONDAP Biomedicina, 2004, pp. 43-48; R.Y.Y. Chan, C. Boudreau-Larivière, L.A. Angus, F. Mankal, B.J. Jasmin, An intronic enhancer containing an N-box motif is required for synapse- and tissue-specific expression of the acetylcholinesterase gene in skeletal muscle fibers. Proc. Natl. Acad. Sci. USA 96 (1999) 4627-4632], is also presented. The intronic region was floxed and then deleted by mating with Ella-cre transgenic mice. The deletion of this region produced a dramatic phenotype; a mouse with near normal AChE expression in brain and other CNS tissues, but no AChE expression in muscle. Phenotype and AChE tissue activities are compared with the total AChE knockout mouse [W. Xie, J.A. Chatonnet, P.J. Wilder, A. Rizzino, R.D. McComb, P. Taylor, S.H. Hinrichs, O. Lockridge, Postnatal developmental delay and supersensitivity to organophosphate in gene-targeted mice lacking acetylcholinesterase. J. Pharmacol. Exp. Ther. 293 (3) (2000) 896-902].

Skipping Syntactically Illegal "the" Previews: The Role of Predictability

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Abbott, Matthew J.; Angele, Bernhard; Ahn, Y. Danbi; Rayner, Keith

2015-01-01

Readers tend to skip words, particularly when they are short, frequent, or predictable. Angele and Rayner (2013) recently reported that readers are often unable to detect syntactic anomalies in parafoveal vision. In the present study, we manipulated target word predictability to assess whether contextual constraint modulates…

The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene.

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Vaughn, Cecily P; Baker, Christine L; Samowitz, Wade S; Swensen, Jeffrey J

2013-01-01

Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology. Copyright © 2012 Wiley Periodicals, Inc.

Dietary selenomethionine increases exon-specific DNA methylation of the p53 gene in rat liver and colon mucosa.

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Zeng, Huawei; Yan, Lin; Cheng, Wen-Hsing; Uthus, Eric O

2011-08-01

The regulation of site-specific DNA methylation of tumor suppressor genes has been considered as a leading mechanism by which certain nutrients exert their anticancer property. This study was to investigate whether selenium (Se) affects the methylation of globe genomic DNA and the exon-specific p53 gene. Three groups of rats (n = 6-7/group) were fed the AIN-93G basal diet supplemented with 0 [Se deficient (D)], 0.15 [Se adequate (A)], or 4 mg [Se supranutritional (S)] (Se as l-selenomethionine)/kg diet for 104 d, respectively. Rats fed the A or S diet had greater plasma and liver glutathione peroxidase activity, liver thioredoxin reductase activity, and plasma homocysteine concentration than those fed the D diet. However, compared with the A diet, rats fed the S diet did not further increase these Se-dependent enzyme activities or homocysteine concentration. In contrast, Se concentrations in kidney, liver, gastrocnemius muscle, and plasma were increased in a Se-dose-dependent manner. Interestingly, rats fed the S diet had significantly less global liver genomic DNA methylation than those fed the D diet. However, the S diet significantly increased the methylation of the p53 gene (exons 5-8) but not the β-actin gene (exons 2-3) DNA in liver and colon mucosa compared with those fed the D diet. Taken together, long-term Se consumption not only affects selenoprotein enzyme activities, homocysteine, tissue Se concentrations, and global genomic DNA methylation but also increases exon-specific DNA methylation of the p53 gene in a Se-dose-dependent manner in rat liver and colon mucosa.

Naturally occuring nucleosome positioning signals in human exons and introns

DEFF Research Database (Denmark)

Baldi, Pierre; Brunak, Søren; Chauvin, Yves

1996-01-01

We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity of rou...

Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms*

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Gabbai, Carolina B.; Yeeles, Joseph T. P.; Marians, Kenneth J.

2014-01-01

A number of different enzymatic pathways have evolved to ensure that DNA replication can proceed past template base damage. These pathways include lesion skipping by the replisome, replication fork regression followed by either correction of the damage and origin-independent replication restart or homologous recombination-mediated restart of replication downstream of the lesion, and bypass of the damage by a translesion synthesis DNA polymerase. We report here that of two translesion synthesis polymerases tested, only DNA polymerase IV, not DNA polymerase II, could engage productively with the Escherichia coli replisome to bypass leading strand template damage, despite the fact that both enzymes are shown to be interacting with the replicase. Inactivation of the 3′ → 5′ proofreading exonuclease of DNA polymerase II did not enable bypass. Bypass by DNA polymerase IV required its ability to interact with the β clamp and act as a translesion polymerase but did not require its “little finger” domain, a secondary region of interaction with the β clamp. Bypass by DNA polymerase IV came at the expense of the inherent leading strand lesion skipping activity of the replisome, indicating that they are competing reactions. PMID:25301949

Outlier Detection in Regression Using an Iterated One-Step Approximation to the Huber-Skip Estimator

DEFF Research Database (Denmark)

Johansen, Søren; Nielsen, Bent

2013-01-01

In regression we can delete outliers based upon a preliminary estimator and reestimate the parameters by least squares based upon the retained observations. We study the properties of an iteratively defined sequence of estimators based on this idea. We relate the sequence to the Huber-skip estima......In regression we can delete outliers based upon a preliminary estimator and reestimate the parameters by least squares based upon the retained observations. We study the properties of an iteratively defined sequence of estimators based on this idea. We relate the sequence to the Huber...... that the normalized estimation errors are tight and are close to a linear function of the kernel, thus providing a stochastic expansion of the estimators, which is the same as for the Huber-skip. This implies that the iterated estimator is a close approximation of the Huber-skip...

A study on single nucleotide polymorphism of exon 7 T/C (locus 593 of platelet-activating factor acetylhydrolase gene in healthy Han population in the Shanghai region

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Tian-bao XIA

2012-08-01

Full Text Available Objective To investigate the distribution of single nucleotide polymorphism (SNP in platelet-activating factor acetylhydrolase (PAF-AH gene exon 7 T/C (locus 593 in healthy Han population in Shanghai region and the features different from other races. Methods The SNP in PAF-AH gene exon 7 T/C (locus 593 was detected and analyzed by PCR and sequencing in 110 healthy Han people from Shanghai areas. The genotype and allele frequency were then calculated and compared with that in other races in combination with review of relevant literature. Results The amplified product of the SNP in PAF-AH gene exon 7 T/C (locus 593 was 240 bp in 110 healthy Han people, of whom 97 were with TT genotype and 13 with TC genotype, but no CC genotype was found. As to the allele frequency distribution, T type allele took the highest position, and C type followed. The genotype frequency of TT and TC was 88.2% and 11.8%, respectively, and they were markedly different from that in German population (0.95%, while not statistically significant different from that in British population (7.67%. Conclusions There exists SNP in PAF-AH gene exon 7 T/C (position 593 in healthy Han people in Shanghai region, with a higher frequency of T→C mutation. The mutational genotype frequency is found to be located at the locus 593 is 11.81%, and it is markedly different from that in German population, but not significantly different from that in British population.

Impact of breakfast skipping on the health status of the population

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Raksha Goyal

2014-01-01

Full Text Available Background: Obesity has become a worldwide epidemic and its prevalence continues to increase at a rapid rate in various populations and across all age-group. The effect of meal skipping, both behaviorally and physiologically, may have an impact on the outcome of weight-loss efforts. Aims and Objectives: Therefore, the aim of this study was to examine the prevalence of breakfast skipping and obesity in subjects. Materials and Methods: A retrospective analysis of the patients visited to a metabolic clinic of the city was done. Results: One hundred and eighty-six eligible subjects were included for the study. A questionnaire was used for data collection which included information regarding dietary factors and exercise schedule/physical activity. A 24-hour dietary recall method was used to assess the amount of food consumed. Anthropometric measurements were taken. Results: Overweight is generally higherin females than males. The prevalence of overweight was higher among those who consumed more than recommended calories than those who were taking recommended or fewer calories per day. The average intake of fat and protein by the study subjects was quite different than the recommended intake of these food items. There was positive association between fat (oil intake and overweight status and a negative association between protein intake and overweight status which was statistically significant. Conclusion: The higher prevalence of overweight and obesity in the present study could be because of imbalance in the diet and faulty food habits prevalent in the region.

Intravitreal Injection of Splice-switching Oligonucleotides to Manipulate Splicing in Retinal Cells

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Xavier Gérard

2015-01-01

Full Text Available Leber congenital amaurosis is a severe hereditary retinal dystrophy responsible for neonatal blindness. The most common disease-causing mutation (c.2991+1655A>G; 10–15% creates a strong splice donor site that leads to insertion of a cryptic exon encoding a premature stop codon. Recently, we reported that splice-switching oligonucleotides (SSO allow skipping of the mutant cryptic exon and the restoration of ciliation in fibroblasts of affected patients, supporting the feasibility of a SSO-mediated exon skipping strategy to correct the aberrant splicing. Here, we present data in the wild-type mouse, which demonstrate that intravitreal administration of 2’-OMePS-SSO allows selective alteration of Cep290 splicing in retinal cells, including photoreceptors as shown by successful alteration of Abca4 splicing using the same approach. We show that both SSOs and Cep290 skipped mRNA were detectable for at least 1 month and that intravitreal administration of oligonucleotides did not provoke any serious adverse event. These data suggest that intravitreal injections of SSO should be considered to bypass protein truncation resulting from the c.2991+1655A>G mutation as well as other truncating mutations in genes which like CEP290 or ABCA4 have a mRNA size that exceed cargo capacities of US Food and Drug Administration (FDA-approved adeno-associated virus (AAV-vectors, thus hampering gene augmentation therapy.

Television viewing, computer game play and book reading during meals are predictors of meal skipping in a cross-sectional sample of 12-, 14- and 16-year-olds.

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Custers, Kathleen; Van den Bulck, Jan

2010-04-01

To examine whether television viewing, computer game playing or book reading during meals predicts meal skipping with the aim of watching television, playing computer games or reading books (media meal skipping). A cross-sectional study was conducted using a standardized self-administered questionnaire. Analyses were controlled for age, gender and BMI. Data were obtained from a random sample of adolescents in Flanders, Belgium. Seven hundred and ten participants aged 12, 14 and 16 years. Of the participants, 11.8 % skipped meals to watch television, 10.5 % skipped meals to play computer games and 8.2 % skipped meals to read books. Compared with those who did not use these media during meals, the risk of skipping meals in order to watch television was significantly higher for those children who watched television during meals (2.9 times higher in those who watched television during at least one meal a day). The risk of skipping meals for computer game playing was 9.5 times higher in those who played computer games weekly or more while eating, and the risk of meal skipping in order to read books was 22.9 times higher in those who read books during meals less than weekly. The more meals the respondents ate with the entire family, the less likely they were to skip meals to watch television. The use of media during meals predicts meal skipping for using that same medium. Family meals appear to be inversely related to meal skipping for television viewing.

The effects of multiple features of alternatively spliced exons on the KA/KS ratio test

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Chen Feng-Chi

2006-05-01

Full Text Available Abstract Background The evolution of alternatively spliced exons (ASEs is of primary interest because these exons are suggested to be a major source of functional diversity of proteins. Many exon features have been suggested to affect the evolution of ASEs. However, previous studies have relied on the KA/KS ratio test without taking into consideration information sufficiency (i.e., exon length > 75 bp, cross-species divergence > 5% of the studied exons, leading to potentially biased interpretations. Furthermore, which exon feature dominates the results of the KA/KS ratio test and whether multiple exon features have additive effects have remained unexplored. Results In this study, we collect two different datasets for analysis – the ASE dataset (which includes lineage-specific ASEs and conserved ASEs and the ACE dataset (which includes only conserved ASEs. We first show that information sufficiency can significantly affect the interpretation of relationship between exons features and the KA/KS ratio test results. After discarding exons with insufficient information, we use a Boolean method to analyze the relationship between test results and four exon features (namely length, protein domain overlapping, inclusion level, and exonic splicing enhancer (ESE frequency for the ASE dataset. We demonstrate that length and protein domain overlapping are dominant factors, and they have similar impacts on test results of ASEs. In addition, despite the weak impacts of inclusion level and ESE motif frequency when considered individually, combination of these two factors still have minor additive effects on test results. However, the ACE dataset shows a slightly different result in that inclusion level has a marginally significant effect on test results. Lineage-specific ASEs may have contributed to the difference. Overall, in both ASEs and ACEs, protein domain overlapping is the most dominant exon feature while ESE frequency is the weakest one in affecting

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

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Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2015-01-01

Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

Meal pattern among Norwegian primary-school children and longitudinal associations between meal skipping and weight status.

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Stea, Tonje H; Vik, Frøydis N; Bere, Elling; Svendsen, Martin V; Oellingrath, Inger M

2015-02-01

To investigate meal pattern longitudinally and explore whether meal skipping was associated with overweight among Norwegian children and adolescents. Longitudinal study. Children's meal frequencies were reported by their parents using a retrospective FFQ. Weight and height were measured by public health nurses. Descriptive data comparing 4th and 7th grade were analysed by paired-sample t tests for continuous variables and χ 2 tests for categorical variables. Odds ratio estimates, including confidence intervals, with BMI category (normal/overweight) as the dependent variable, were determined through logistic regression analyses. Primary schools, Telemark County, Norway. A cohort of 428 Norwegian boys and girls; 4th graders in 2007, 7th graders in 2010. The number of children eating four main meals per day (regular meal frequency) decreased from 4th grade (47 %) to 7th grade (38 %; P = 0·001). Those who ate regular meals in 4th grade but not in 7th grade had higher odds (OR = 3·1; 95 % CI 1·1, 9·0) of being overweight in 7th grade after adjusting for gender, maternal education and physical activity, but the odds ratio was not statistically significant after adjusting for overweight in 4th grade (OR = 2·8; 95 % CI 0·7, 11·6). The present study showed significant increases in overall meal skipping among children between 4th and 7th grade. The results indicate an association between overweight and meal skipping, but additional prospective and longitudinal analyses and intervention trials are warranted to confirm this relationship.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

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Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

The proximal first exon architecture of the murine ghrelin gene is highly similar to its human orthologue

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Seim Inge

2009-05-01

Full Text Available Abstract Background The murine ghrelin gene (Ghrl, originally sequenced from stomach tissue, contains five exons and a single transcription start site in a short, 19 bp first exon (exon 0. We recently isolated several novel first exons of the human ghrelin gene and found evidence of a complex transcriptional repertoire. In this report, we examined the 5' exons of the murine ghrelin orthologue in a range of tissues using 5' RACE. Findings 5' RACE revealed two transcription start sites (TSSs in exon 0 and four TSSs in intron 0, which correspond to 5' extensions of exon 1. Using quantitative, real-time RT-PCR (qRT-PCR, we demonstrated that extended exon 1 containing Ghrl transcripts are largely confined to the spleen, adrenal gland, stomach, and skin. Conclusion We demonstrate that multiple transcription start sites are present in exon 0 and an extended exon 1 of the murine ghrelin gene, similar to the proximal first exon organisation of its human orthologue. The identification of several transcription start sites in intron 0 of mouse ghrelin (resulting in an extension of exon 1 raises the possibility that developmental-, cell- and tissue-specific Ghrl mRNA species are created by employing alternative promoters and further studies of the murine ghrelin gene are warranted.

Antisense Oligonucleotide-mediated Exon Skipping as a Systemic Therapeutic Approach for Recessive Dystrophic Epidermolysis Bullosa : Exon Skipping as Systemic Therapy for RDEB

NARCIS (Netherlands)

Bremer, Jeroen; Bornert, Olivier; Nyström, Alexander; Gostynski, Antoni; Jonkman, Marcel F; Aartsma-Rus, Annemieke; van den Akker, Peter C; Pasmooij, Anna MG

2016-01-01

The "generalized severe" form of recessive dystrophic epidermolysis bullosa (RDEB-gen sev) is caused by bi-allelic null mutations in COL7A1, encoding type VII collagen. The absence of type VII collagen leads to blistering of the skin and mucous membranes upon the slightest trauma. Because most

Mucopolysaccharidosis IVA: Four new exonic mutations in patients with N-acetylgalactosamine-6-sulfate sulfatase deficiency

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Tomatsu, Shunji; Fukuda, Seiji; Yamagishi, Atsushi [Gifu Univ. (Japan)] [and others

1996-05-01

We report four new mutations in Japanese patients with mucopolysaccharidosis IVA (MPSIVA) who were heterozygous for a common double gene deletion. A nonsense mutation of CAG to TAG at codon 148 in exon 4 was identified, resulting in a change of Q to a stop codon and three missense mutations: V (GTC) to A (GCC) at codon 138 in exon 4, P (CCC) to S (TCC) at codon 151 in exon 5, and P (CCC) to L (CTC) at codon 151 in exon 5. Introduction of these mutations into the normal GALNS cDNA and transient expression in cultured fibroblasts resulted in a significant decrease in the enzyme activity. V138A and Q148X mutations result in changes of restriction site, which were analyzed by restriction-enzyme assay. P151S and P151L mutations that did not alter the restriction site were detected by direct sequencing or allele specific oligohybridization. Detection of the double gene deletion was initially done using Southern blots and was confirmed by PCR. Haplotypes were determined using seven polymorphisms to the GALNS locus in families with the double gene deletion. Haplotype analysis showed that the common double gene deletion occurred on a single haplotype, except for some variation in a VNTR-like polymorphism. This finding is consistent with a common founder for all individuals with this mutation. 48 refs., 5 figs., 1 tab.

JAK2 V617F, MPL W515L and JAK2 Exon 12 Mutations in Chinese Patients with Primary Myelofibrosis.

Science.gov (United States)

Xia, Jun; Lu, Mi-Ze; Jiang, Yuan-Qiang; Yang, Guo-Hua; Zhuang, Yun; Sun, Hong-Li; Shen, Yun-Feng

2012-03-01

JAK2 V617F, MPL W515L and JAK2 exon 12 mutations are novel acquired mutations that induce constitutive cytokine-independent activation of the JAK-STAT pathway in myeloproliferative disorders (MPD). The discovery of these mutations provides novel mechanism for activation of signal transduction in hematopoietic malignancies. This research was to investigate their prevalence in Chinese patients with primary myelofibrosis (PMF). We introduced allele-specific PCR (AS-PCR) combined with sequence analysis to simultaneously screen JAK2 V617F, MPL W515L and JAK2 exon 12 mutations in 30 patients with PMF. Fifteen PMF patients (50.0%) carried JAK2 V617F mutation, and only two JAK2 V617F-negative patients (6.7%) harbored MPL W515L mutation. None had JAK2 exon 12 mutations. Furthermore, these three mutations were not detected in 50 healthy controls. MPL W515L and JAK2 V617F mutations existed in PMF patients but JAK2 exon 12 mutations not. JAK2 V617F and MPL W515L and mutations might contribute to the primary molecular pathogenesis in patients with PMF.

The relation between breakfast skipping and school performance in adolescents

NARCIS (Netherlands)

Boschloo, Annemarie; Ouwehand, Carolijn; Dekker, Sanne; Lee, Nikki; De Groot, Renate; Krabbendam, Lydia; Jolles, Jelle

2012-01-01

Boschloo, A., Ouwehand, C., Dekker, S., Lee, N., De Groot, R., Krabbendam, L., & Jolles, J. (2012). The relation between breakfast skipping and school performance in adolescents. Mind, Brain, and Education, 6(2), 81-88. doi:10.1111/j.1751-228x.2012.01138.x

40 CFR 61.243-2 - Alternative standards for valves in VHAP service-skip period leak detection and repair.

Science.gov (United States)

2010-07-01

... VHAP service-skip period leak detection and repair. 61.243-2 Section 61.243-2 Protection of Environment... AIR POLLUTANTS National Emission Standard for Equipment Leaks (Fugitive Emission Sources) § 61.243-2 Alternative standards for valves in VHAP service—skip period leak detection and repair. (a)(1) An owner or...

Double-target Antisense U1snRNAs Correct Mis-splicing Due to c.639+861C>T and c.639+919G>A GLA Deep Intronic Mutations

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Lorenzo Ferri

2016-01-01

Full Text Available Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one. Here, we built a wild-type GLA minigene and two minigenes that carry mutations c.639+861C>T and c.639+919G>A. Once transfected into cells, the minigenes recapitulate the molecular patterns observed in patients, at the mRNA, protein, and enzymatic level. We constructed a set of specific double-target U1asRNAs to correct c.639+861C>T and c.639+919G>A GLA mutations. Efficacy of U1asRNAs in inducing the skipping of the cryptic exon was evaluated upon their transient co-transfection with the minigenes in COS-1 cells, by real-time polymerase chain reaction (PCR, western blot analysis, and α-Gal A enzyme assay. We identified a set of U1asRNAs that efficiently restored α-Gal A enzyme activity and the correct splicing pathways in reporter minigenes. We also identified a unique U1asRNA correcting both mutations as efficently as the mutation-specific U1asRNAs. Our study proves that an exon skipping-based approach recovering α-Gal A activity in the c.639+861C>T and c.639+919G>A GLA mutations is active.

E-cadherin gene re-expression in chronic lymphocytic leukemia cells by HDAC inhibitors

International Nuclear Information System (INIS)

Jordaan, Gwen; Liao, Wei; Sharma, Sanjai

2013-01-01

The tumor suppressor gene E-cadherin gene is frequently silenced in chronic lymphocytic leukemia (CLL) cells and results in wnt-pathway activation. We analyzed the role of histone epigenetic modifications in E-cadherin gene silencing. CLL specimens were treated with histone deacetylase inhibitor (HDACi) MS-275 and analyzed for E-cadherin expression with western blot and RT-PCR analysis. The downstream effects of HDACi treated leukemic cells were studied by analyzing the effect on wnt-pathway signaling. HDACi induced alterations in E-cadherin splicing were investigated by transcript specific real time PCR analysis. Treatment of CLL specimens with histone deacetylase inhibitors (HDACi) treatment resulted in an increase of the E-cadherin RNA transcript (5 to 119 fold increase, n=10) in eight out of ten CLL specimens indicating that this gene is down regulated by histone hypoacetylation in a majority of CLL specimens. The E-cadherin re-expression in CLL specimens was noted by western blot analysis as well. Besides epigenetic silencing another mechanism of E-cadherin inactivation is aberrant exon 11 splicing resulting in an alternatively spliced transcript that lacks exon 11 and is degraded by the non-sense mediated decay (NMD) pathway. Our chromatin immunoprecipitation experiments show that HDACi increased the acetylation of histones H3 and H4 in the E-cadherin promoter region. This also affected the E-cadherin exon 11 splicing pattern as HDACi treated CLL specimens preferentially expressed the correctly spliced transcript and not the exon 11 skipped aberrant transcript. The re-expressed E- cadherin binds to β-catenin with inhibition of the active wnt-beta-catenin pathway in these cells. This resulted in a down regulation of two wnt target genes, LEF and cyclinD1 and the wnt pathway reporter. The E-cadherin gene is epigenetically modified and hypoacetylated in CLL leukemic cells. Treatment of CLL specimens with HDACi MS-275 activates transcription from this silent

Exon-primed intron-crossing (EPIC markers for non-model teleost fishes

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Riethoven Jean-Jack M

2010-03-01

Full Text Available Abstract Background Exon-primed intron-crossing (EPIC markers have three advantages over anonymous genomic sequences in studying evolution of natural populations. First, the universal primers designed in exon regions can be applied across a broad taxonomic range. Second, the homology of EPIC-amplified sequences can be easily determined by comparing either their exon or intron portion depending on the genetic distance between the taxa. Third, having both the exon and intron fragments could help in examining genetic variation at the intraspecific and interspecific level simultaneously, particularly helpful when studying species complex. However, the paucity of EPIC markers has hindered multilocus studies using nuclear gene sequences, particularly in teleost fishes. Results We introduce a bioinformatics pipeline for developing EPIC markers by comparing the whole genome sequences between two or more species. By applying this approach on five teleost fishes whose genomes were available in the Ensembl database http://www.ensembl.org, we identified 210 EPIC markers that have single-copy and conserved exon regions with identity greater than 85% among the five teleost fishes. We tested 12 randomly chosen EPIC markers in nine teleost species having a wide phylogenetic range. The success rate of amplifying and sequencing those markers varied from 44% to 100% in different species. We analyzed the exon sequences of the 12 EPIC markers from 13 teleosts. The resulting phylogeny contains many traditionally well-supported clades, indicating the usefulness of the exon portion of EPIC markers in reconstructing species phylogeny, in addition to the value of the intron portion of EPIC markers in interrogating the population history. Conclusions This study illustrated an effective approach to develop EPIC markers in a taxonomic group, where two or more genome sequences are available. The markers identified could be amplified across a broad taxonomic range of teleost

Late-night overeating is associated with smaller breakfast, breakfast skipping, and obesity in children: The Healthy Growth Study.

Science.gov (United States)

Karatzi, Kalliopi; Moschonis, George; Choupi, Eurikleia; Manios, Yannis

2017-01-01

Excessive energy intake during evening hours is associated with several health problems. The aim of this study was to investigate for the first time the possible association of late-night overeating with breakfast habits and obesity in a large sample of Greek children ages 9 to 13 y. In all, 2655 schoolchildren (9-13 y) participated in the Healthy Growth Study, a cross-sectional epidemiologic study conducted in 77 primary schools in four large regions in Greece. The present study presents results on 1912 children having full data regarding anthropometric, dietary, physical activity, and physical examination indices. High-energy intake at dinner and evening snack was associated with higher likelihood of skipping breakfast (odds ratio, 1.85; 95% confidence interval 1.42-2.39) and with lower caloric intake at breakfast (β = 0.14; P overeating is associated with skipping and/or consuming a smaller breakfast. In children with low levels of physical activity, it is associated with increased body mass index. Future relevant studies are essential to further explore and confirm the findings of the present study. Copyright © 2016 Elsevier Inc. All rights reserved.

N1303K (c.3909C>G) Mutation and Splicing: Implication of Its c.[744-33GATT(6); 869+11C>T] Complex Allele in CFTR Exon 7 Aberrant Splicing

Science.gov (United States)

Farhat, Raëd; Puissesseau, Géraldine; El-Seedy, Ayman; Pasquet, Marie-Claude; Adolphe, Catherine; Corbani, Sandra; Megarbané, André; Kitzis, Alain; Ladeveze, Véronique

2015-01-01

Cystic Fibrosis is the most common recessive autosomal rare disease found in Caucasians. It is caused by mutations on the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) that encodes a protein located on the apical membrane of epithelial cells. c.3909C>G (p.Asn1303Lys, old nomenclature: N1303K) is one of the most common worldwide mutations. This mutation has been found at high frequencies in the Mediterranean countries with the highest frequency in the Lebanese population. Therefore, on the genetic level, we conducted a complete CFTR gene screening on c.3909C>G Lebanese patients. The complex allele c.[744-33GATT(6); 869+11C>T] was always associated with the c.3909C>G mutation in cis in the Lebanese population. In cellulo splicing studies, realized by hybrid minigene constructs, revealed no impact of the c.3909C>G mutation on the splicing process, whereas the associated complex allele induces minor exon skipping. PMID:26075213

Breakfast-skipping in children and young adolescents in the Netherlands

NARCIS (Netherlands)

Brugman, E.; Meulmeester, J.F.; Spee-Wekke, A. van der; Verloove-Vanhorick, S.P.

1998-01-01

Background: The objective of this study was to provide national figures on the prevalence of breakfast-skipping and the association with sociodemographic variables in 4-15 year old children. Methods: Data of 4,377 children were collected. A food questionnaire (24 h recall) was completed by the

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

Science.gov (United States)

Peng, Tao; Xue, Chenghai; Bi, Jianning; Li, Tingting; Wang, Xiaowo; Zhang, Xuegong; Li, Yanda

2008-04-26

Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown. Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation) patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1) The vast majority of positively-correlated pairs are old, (2) most of the weakly-correlated pairs are relatively young, and (3) negatively-correlated pairs are a mixture of old and young events. We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.

Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.

Science.gov (United States)

Pantazatos, S P; Huang, Y-Y; Rosoklija, G B; Dwork, A J; Arango, V; Mann, J J

2017-05-01

Brain gene expression profiling studies of suicide and depression using oligonucleotide microarrays have often failed to distinguish these two phenotypes. Moreover, next generation sequencing approaches are more accurate in quantifying gene expression and can detect alternative splicing. Using RNA-seq, we examined whole-exome gene and exon expression in non-psychiatric controls (CON, N=29), DSM-IV major depressive disorder suicides (MDD-S, N=21) and MDD non-suicides (MDD, N=9) in the dorsal lateral prefrontal cortex (Brodmann Area 9) of sudden death medication-free individuals post mortem. Using small RNA-seq, we also examined miRNA expression (nine samples per group). DeSeq2 identified 35 genes differentially expressed between groups and surviving adjustment for false discovery rate (adjusted Pdepression, altered genes include humanin-like-8 (MTRNRL8), interleukin-8 (IL8), and serpin peptidase inhibitor, clade H (SERPINH1) and chemokine ligand 4 (CCL4), while exploratory gene ontology (GO) analyses revealed lower expression of immune-related pathways such as chemokine receptor activity, chemotaxis and cytokine biosynthesis, and angiogenesis and vascular development in (adjusted Psuicide and depression, and provisional evidence for altered DNA-dependent ATPase expression in suicide only. DEXSEq analysis identified differential exon usage in ATPase, class II, type 9B (adjusted Pdepression. Differences in miRNA expression or structural gene variants were not detected. Results lend further support for models in which deficits in microglial, endothelial (blood-brain barrier), ATPase activity and astrocytic cell functions contribute to MDD and suicide, and identify putative pathways and mechanisms for further study in these disorders.

Stemcell Information: SKIP000783 [SKIP Stemcell Database[Archive

Lifescience Database Archive (English)

Full Text Available line derived from T cell in Peripheral Blood (TiPS) 正常iPS細胞株（末梢血由来T細胞から樹立(TiPS)） ... human ES-like Resear...5)|8.Feeder Cellの使用: 使用する|　細胞名 : SNL細胞|　使用時の細胞密度 : 1.5 x 10^(6)/10cm dish|　使用前処理方法 : Mitomycin C処理 : 400micr...　Total 50ml|　Aliquot and store at -20 degree|10.パッセージの際の細胞播種時の細胞密度|　Confluentの10c...析 : 未実施|胚葉体形成実験 : 実施　胚葉体形成確認|テラトーマ形成実験 : 未実施|in vitro分化能解析 : 実施　神経への分化確認|マイコプラズマ汚染検査 : 未実施|細胞同定検査（STR多型解析） : 未実施|クローニング : 未実施 ... SKIP000783 ... Normal aTKA9 aTKA9 ... 40 40-49 Male ... -- No Normal iPS cell

Roles of viral and cellular proteins in the expression of alternatively spliced HTLV-1 pX mRNAs

International Nuclear Information System (INIS)

Princler, Gerald L.; Julias, John G.; Hughes, Stephen H.; Derse, David

2003-01-01

The human T cell leukemia virus type 1 (HTLV-1) genome contains a cluster of at least five open reading frames (ORFs) near the 3' terminus within the pX region. The pX ORFs are encoded by mono- or bicistronic mRNAs that are generated by alternative splicing. The various pX mRNAs result from skipping of the internal exon (2-exon versus 3-exon isofoms) or from the utilization of alternative splice acceptor sites in the terminal exon. The Rex and Tax proteins, encoded by ORFs X-III and X-IV, have been studied intensively and are encoded by the most abundant of the alternative 3-exon mRNAs. The protein products of the other pX ORFs have not been detected in HTLV-1-infected cell lines and the levels of the corresponding mRNAs have not been accurately established. We have used real-time RT-PCR with splice-site specific primers to accurately measure the levels of individual pX mRNA species in chronically infected T cell lines. We have asked whether virus regulatory proteins or ectopic expression of cellular factors influence pX mRNA splicing in cells that were transfected with HTLV-1 provirus clones. In chronically infected cell lines, the pX-tax/rex mRNA was present at 500- to 2500-fold higher levels than the pX-tax-orfII mRNA and at approximately 1000-fold higher levels than pX-rex-orfI mRNA. Chronically infected cell lines that contain numerous defective proviruses expressed 2-exon forms of pX mRNAs at significantly higher levels compared to cell lines that contain a single full-length provirus. Cells transfected with provirus expression plasmids expressed similar relative amounts of 3-exon pX mRNAs but lower levels of 2-exon mRNA forms compared to cells containing a single, full-length provirus. The pX mRNA expression patterns were nearly identical in cells transfected with wild-type, Tax-minus, or Rex-minus proviruses. Cotransfection of cells with HTLV-1 provirus in combination with SF2/ASF expression plasmid resulted in a relative increase in pX-tax/rex m

Multi-exon deletions of the FBN1 gene in Marfan syndrome

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Schrijver Iris

2001-10-01

Full Text Available Abstract Background Mutations in the fibrillin -1 gene (FBN1 cause Marfan syndrome (MFS, an autosomal dominant multi-system connective tissue disorder. The 200 different mutations reported in the 235 kb, 65 exon-containing gene include only one family with a genomic multi-exon deletion. Methods We used long-range RT-PCR for mutation detection and long-range genomic PCR and DNA sequencing for identification of deletion breakpoints, allele-specific transcript analyses to determine stability of the mutant RNA, and pulse-chase studies to quantitate fibrillin synthesis and extracellular matrix deposition in cultured fibroblasts. Southern blots of genomic DNA were probed with three overlapping fragments covering the FBN1 coding exons Results Two novel multi-exon FBN1 deletions were discovered. Identical nucleotide pentamers were found at or near the intronic breakpoints. In a Case with classic MFS, an in-frame deletion of exons 42 and 43 removed the C-terminal 24 amino acids of the 5th LTBP (8-cysteine domain and the adjacent 25th calcium-binding EGF-like (6-cysteine domain. The mutant mRNA was stable, but fibrillin synthesis and matrix deposition were significantly reduced. A Case with severe childhood-onset MFS has a de novo deletion of exons 44–46 that removed three EGF-like domains. Fibrillin protein synthesis was normal, but matrix deposition was strikingly reduced. No genomic rearrangements were detected by Southern analysis of 18 unrelated MFS samples negative for FBN1 mutation screening. Conclusions Two novel deletion cases expand knowledge of mutational mechanisms and genotype/phenotype correlations of fibrillinopathies. Deletions or mutations affecting an LTBP domain may result in unstable mutant protein cleavage products that interfere with microfibril assembly.

Skip cycle system for spark ignition engines: An experimental investigation of a new type working strategy

International Nuclear Information System (INIS)

Kutlar, Osman Akin; Arslan, Hikmet; Calik, Alper T.

2007-01-01

A new type working strategy for spark ignition engine, named skip cycle, is examined. The main idea is to reduce the effective stroke volume of an engine by cutting off fuel injection and spark ignition in some of the classical four stroke cycles. When the cycle is skipped, additionally, a rotary valve is used in the intake to reduce pumping losses in part load conditions. The effect of this strategy is similar to that of variable displacement engines. Alternative power stroke fractions in one cycle and applicability in single cylinder engines are specific advantageous properties of the proposed system. A thermodynamic model, besides experimental results, is used to explain the skip cycle strategy in more detail. This theoretical investigation shows considerable potential to increase the efficiency at part load conditions. Experimental results obtained with this novel strategy show that the throttle valve of the engine opens wider and the minimum spark advance for maximum brake torque decreases in comparison to those of the classical operation system. The brake specific fuel consumption decreases at very low speed and load, while it increases at higher speed and load due to the increased fuel loss within the skipped cycles. In this working mode, the engine operates at lower idle speed without any stability problem; and moreover with less fuel consumption

Poly(ester amine Composed of Polyethylenimine and Pluronic Enhance Delivery of Antisense Oligonucleotides In Vitro and in Dystrophic mdx Mice

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Mingxing Wang

2016-01-01

Full Text Available A series of poly(esteramines (PEAs constructed from low molecular weight polyethyleneimine (LPEI and Pluronic were evaluated for the delivery of antisense oligonuclotides (AOs, 2′-O-methyl phosphorothioate RNA (2′-OMePS and phosphorodiamidate morpholino oligomer (PMO in cell culture and dystrophic mdx mice. Improved exon-skipping efficiency of both 2′-OMePS and PMO was observed in the C2C12E50 cell line with all PEA polymers compared with PEI 25k or LF-2k. The degree of efficiency was found in the order of PEA 01, PEA 04 > PEA 05 > others. The in vivo study in mdx mice demonstrated enhanced exon-skipping of 2′-OMePS with the order of PEA 06 > PEA 04, PEA 07 > PEA 03 > PEA 01 > others, and much higher than PEI 25k formulated 2′-OMePS. Exon-skipping efficiency of PMO in formulation with the PEAs were significantly enhanced in the order of PEA 02 > PEA 10 > PEA 01, PEA 03 > PEA 05, PEA 07, PEA 08 > others, with PEA 02 reaching fourfold of Endo-porter formulated PMO. PEAs improve PMO delivery more effectively than 2′-OMePS delivery in vivo, and the systemic delivery evaluation further highlight the efficiency of PEA for PMO delivery in all skeletal muscle. The results suggest that the flexibility of PEA polymers could be explored for delivery of different AO chemistries, especially for antisense therapy.

The human cytochrome P450 3A locus. Gene evolution by capture of downstream exons.

Science.gov (United States)

Finta, C; Zaphiropoulos, P G

2000-12-30

Using a bacterial artificial chromosome (BAC) clone, we have mapped the human cytochrome P450 3A (CYP3A) locus containing the genes encoding for CYP3A4, CYP3A5 and CYP3A7. The genes lie in a head-to-tail orientation in the order of 3A4, 3A7 and 3A5. In both intergenic regions (3A4-3A7 and 3A7-3A5), we have detected several additional cytochrome P450 3A exons, forming two CYP3A pseudogenes. These pseudogenes have the same orientation as the CYP3A genes. To our surprise, a 3A7 mRNA species has been detected in which the exons 2 and 13 of one of the pseudogenes (the one that is downstream of 3A7) are spliced after the 3A7 terminal exon. This results in an mRNA molecule that consists of the 13 3A7 exons and two additional exons at the 3' end. The additional two exons originating from the pseudogene are in an altered reading frame and consequently have the capability to code a completely different amino acid sequence than the canonical CYP3A exons 2 and 13. These findings may represent a generalized evolutionary process with genes having the potential to capture neighboring sequences and use them as functional exons.

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.

Science.gov (United States)

Ramírez-Sánchez, Obed; Pérez-Rodríguez, Paulino; Delaye, Luis; Tiessen, Axel

2016-12-01

Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

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Obed Ramírez-Sánchez

2016-12-01

Full Text Available Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa, average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt]. Streptophyta have on average only ∼5.7 exons of medium size (∼230 nt. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt. Among subcellular compartments, membrane proteins are the largest (∼520 aa, whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240 aa. Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

Skipping Posterior Dynamic Transpedicular Stabilization for Distant Segment Degenerative Disease

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Bilgehan Solmaz

2012-01-01

Full Text Available Objective. To date, there is still no consensus on the treatment of spinal degenerative disease. Current surgical techniques to manage painful spinal disorders are imperfect. In this paper, we aimed to evaluate the prospective results of posterior transpedicular dynamic stabilization, a novel surgical approach that skips the segments that do not produce pain. This technique has been proven biomechanically and radiologically in spinal degenerative diseases. Methods. A prospective study of 18 patients averaging 54.94 years of age with distant spinal segment degenerative disease. Indications consisted of degenerative disc disease (57%, herniated nucleus pulposus (50%, spinal stenosis (14.28%, degenerative spondylolisthesis (14.28%, and foraminal stenosis (7.1%. The Oswestry Low-Back Pain Disability Questionnaire and visual analog scale (VAS for pain were recorded preoperatively and at the third and twelfth postoperative months. Results. Both the Oswestry and VAS scores showed significant improvement postoperatively (P<0.05. We observed complications in one patient who had spinal epidural hematoma. Conclusion. We recommend skipping posterior transpedicular dynamic stabilization for surgical treatment of distant segment spinal degenerative disease.

Live-Cell Imaging Visualizes Frequent Mitotic Skipping During Senescence-Like Growth Arrest in Mammary Carcinoma Cells Exposed to Ionizing Radiation

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Suzuki, Masatoshi, E-mail: msuzuki@nagasaki-u.ac.jp [Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (Japan); Yamauchi, Motohiro; Oka, Yasuyoshi; Suzuki, Keiji; Yamashita, Shunichi [Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (Japan)

2012-06-01

Purpose: Senescence-like growth arrest in human solid carcinomas is now recognized as the major outcome of radiotherapy. This study was designed to analyze cell cycle during the process of senescence-like growth arrest in mammary carcinoma cells exposed to X-rays. Methods and Materials: Fluorescent ubiquitination-based cell cycle indicators were introduced into the human mammary carcinoma cell line MCF-7. Cell cycle was sequentially monitored by live-cell imaging for up to 5 days after exposure to 10 Gy of X-rays. Results: Live-cell imaging revealed that cell cycle transition from G2 to G1 phase without mitosis, so-called mitotic skipping, was observed in 17.1% and 69.8% of G1- and G2-irradiated cells, respectively. Entry to G1 phase was confirmed by the nuclear accumulation of mKO{sub 2}-hCdt1 as well as cyclin E, which was inversely correlated to the accumulation of G2-specific markers such as mAG-hGeminin and CENP-F. More than 90% of cells skipping mitosis were persistently arrested in G1 phase and showed positive staining for the senescent biochemical marker, which is senescence-associated ss-galactosidase, indicating induction of senescence-like growth arrest accompanied by mitotic skipping. While G2 irradiation with higher doses of X-rays induced mitotic skipping in approximately 80% of cells, transduction of short hairpin RNA (shRNA) for p53 significantly suppressed mitotic skipping, suggesting that ionizing radiation-induced mitotic skipping is associated with p53 function. Conclusions: The present study found the pathway of senescence-like growth arrest in G1 phase without mitotic entry following G2-irradiation.

Live-Cell Imaging Visualizes Frequent Mitotic Skipping During Senescence-Like Growth Arrest in Mammary Carcinoma Cells Exposed to Ionizing Radiation

International Nuclear Information System (INIS)

Suzuki, Masatoshi; Yamauchi, Motohiro; Oka, Yasuyoshi; Suzuki, Keiji; Yamashita, Shunichi

2012-01-01

Purpose: Senescence-like growth arrest in human solid carcinomas is now recognized as the major outcome of radiotherapy. This study was designed to analyze cell cycle during the process of senescence-like growth arrest in mammary carcinoma cells exposed to X-rays. Methods and Materials: Fluorescent ubiquitination-based cell cycle indicators were introduced into the human mammary carcinoma cell line MCF-7. Cell cycle was sequentially monitored by live-cell imaging for up to 5 days after exposure to 10 Gy of X-rays. Results: Live-cell imaging revealed that cell cycle transition from G2 to G1 phase without mitosis, so-called mitotic skipping, was observed in 17.1% and 69.8% of G1- and G2-irradiated cells, respectively. Entry to G1 phase was confirmed by the nuclear accumulation of mKO 2 -hCdt1 as well as cyclin E, which was inversely correlated to the accumulation of G2-specific markers such as mAG-hGeminin and CENP-F. More than 90% of cells skipping mitosis were persistently arrested in G1 phase and showed positive staining for the senescent biochemical marker, which is senescence-associated ß-galactosidase, indicating induction of senescence-like growth arrest accompanied by mitotic skipping. While G2 irradiation with higher doses of X-rays induced mitotic skipping in approximately 80% of cells, transduction of short hairpin RNA (shRNA) for p53 significantly suppressed mitotic skipping, suggesting that ionizing radiation-induced mitotic skipping is associated with p53 function. Conclusions: The present study found the pathway of senescence-like growth arrest in G1 phase without mitotic entry following G2-irradiation.

Characterization of major histocompatibility complex (MHC DRB exon 2 and DRA exon 3 fragments in a primary terrestrial rabies vector (Procyon lotor.

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Sarrah Castillo

Full Text Available The major histocompatibility complex (MHC presents a unique system to explore links between genetic diversity and pathogens, as diversity within MHC is maintained in part by pathogen driven selection. While the majority of wildlife MHC studies have investigated species that are of conservation concern, here we characterize MHC variation in a common and broadly distributed species, the North American raccoon (Procyon lotor. Raccoons host an array of broadly distributed wildlife diseases (e.g., canine distemper, parvovirus and raccoon rabies virus and present important human health risks as they persist in high densities and in close proximity to humans and livestock. To further explore how genetic variation influences the spread and maintenance of disease in raccoons we characterized a fragment of MHC class II DRA exon 3 (250 bp and DRB exon 2 (228 bp. MHC DRA was found to be functionally monomorphic in the 32 individuals screened; whereas DRB exon 2 revealed 66 unique alleles among the 246 individuals screened. Between two and four alleles were observed in each individual suggesting we were amplifying a duplicated DRB locus. Nucleotide differences between DRB alleles ranged from 1 to 36 bp (0.4-15.8% divergence and translated into 1 to 21 (1.3-27.6% divergence amino acid differences. We detected a significant excess of nonsynonymous substitutions at the peptide binding region (P = 0.005, indicating that DRB exon 2 in raccoons has been influenced by positive selection. These data will form the basis of continued analyses into the spatial and temporal relationship of the raccoon rabies virus and the immunogenetic response in its primary host.

Association of KIT exon 9 mutations with nongastric primary site and aggressive behavior: KIT mutation analysis and clinical correlates of 120 gastrointestinal stromal tumors.

Science.gov (United States)

Antonescu, Cristina R; Sommer, Gunhild; Sarran, Lisa; Tschernyavsky, Sylvia J; Riedel, Elyn; Woodruff, James M; Robson, Mark; Maki, Robert; Brennan, Murray F; Ladanyi, Marc; DeMatteo, Ronald P; Besmer, Peter

2003-08-15

Activating mutations of the KIT juxtamembrane region are the most common genetic events in gastrointestinal stromal tumors (GISTs) and have been noted as independent prognostic factors. The impact of KIT mutation in other regions, such as the extracellular or kinase domains, is not well-defined and fewer than 30 cases have been published to date. One hundred twenty GISTs, confirmed by KIT immunoreactivity, were evaluated for the presence of KIT exon 9, 11, 13, and 17 mutations. The relation between the presence/type of KIT mutation and clinicopathological factors was analyzed using Fisher's exact test and log-rank test. Forty-four % of the tumors were located in the stomach, 47% in the small bowel, 6% in the rectum, and 3% in the retroperitoneum. Overall, KIT mutations were detected in 78% of patients as follows: 67% in exon 11, 11% in exon 9, and none in exon 13 or 17. The types of KIT exon 11 mutations were heterogeneous and clustered in the classic "hot spot" at the 5' end of exon 11. Seven % of cases showed internal tandem duplications (ITD) at the 3' end of exon 11, in a region that we designate as a second hot spot for KIT mutations. Interestingly, these cases were associated with: female predominance, stomach location, occurrence in older patients, and favorable outcome. There were significant associations between exon 9 mutations and large tumor size (P < 0.001) and extragastric location (P = 0.02). Ten of these 13 patients with more than 1-year follow-up have developed recurrent disease. Most KIT-expressing GISTs show KIT mutations that are preferentially located within the classic hot spot of exon 11. In addition, we found an association between a second hot spot at the 3'end of exon 11, characterized by ITDs, and a subgroup of clinically indolent gastric GISTs in older females. KIT exon 9 mutations seem to define a distinct subset of GISTs, located predominantly in the small bowel and associated with an unfavorable clinical course.

Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia.

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Nathalie Boone

Full Text Available BACKGROUND: Familial dysautonomia (FD is a hereditary neuropathy caused by mutations in the IKBKAP gene, the most common of which results in variable tissue-specific mRNA splicing with skipping of exon 20. Defective splicing is especially severe in nervous tissue, leading to incomplete development and progressive degeneration of sensory and autonomic neurons. The specificity of neuron loss in FD is poorly understood due to the lack of an appropriate model system. To better understand and modelize the molecular mechanisms of IKBKAP mRNA splicing, we collected human olfactory ecto-mesenchymal stem cells (hOE-MSC from FD patients. hOE-MSCs have a pluripotent ability to differentiate into various cell lineages, including neurons and glial cells. METHODOLOGY/PRINCIPAL FINDINGS: We confirmed IKBKAP mRNA alternative splicing in FD hOE-MSCs and identified 2 novel spliced isoforms also present in control cells. We observed a significant lower expression of both IKBKAP transcript and IKAP/hELP1 protein in FD cells resulting from the degradation of the transcript isoform skipping exon 20. We localized IKAP/hELP1 in different cell compartments, including the nucleus, which supports multiple roles for that protein. We also investigated cellular pathways altered in FD, at the genome-wide level, and confirmed that cell migration and cytoskeleton reorganization were among the processes altered in FD. Indeed, FD hOE-MSCs exhibit impaired migration compared to control cells. Moreover, we showed that kinetin improved exon 20 inclusion and restores a normal level of IKAP/hELP1 in FD hOE-MSCs. Furthermore, we were able to modify the IKBKAP splicing ratio in FD hOE-MSCs, increasing or reducing the WT (exon 20 inclusion:MU (exon 20 skipping ratio respectively, either by producing free-floating spheres, or by inducing cells into neural differentiation. CONCLUSIONS/SIGNIFICANCE: hOE-MSCs isolated from FD patients represent a new approach for modeling FD to better

Exonal deletion of SLC24A4 causes hypomaturation amelogenesis imperfecta.

Science.gov (United States)

Seymen, F; Lee, K-E; Tran Le, C G; Yildirim, M; Gencay, K; Lee, Z H; Kim, J-W

2014-04-01

Amelogenesis imperfecta is a heterogeneous group of genetic conditions affecting enamel formation. Recently, mutations in solute carrier family 24 member 4 (SLC24A4) have been identified to cause autosomal recessive hypomaturation amelogenesis imperfecta. We recruited a consanguineous family with hypomaturation amelogenesis imperfecta with generalized brown discoloration. Sequencing of the candidate genes identified a 10-kb deletion, including exons 15, 16, and most of the last exon of the SLC24A4 gene. Interestingly, this deletion was caused by homologous recombination between two 354-bp-long homologous sequences located in intron 14 and the 3' UTR. This is the first report of exonal deletion in SLC24A4 providing confirmatory evidence that the function of SLC24A4 in calcium transport has a crucial role in the maturation stage of amelogenesis.

Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11.

Science.gov (United States)

Baert, Annelot; Machackova, Eva; Coene, Ilse; Cremin, Carol; Turner, Kristin; Portigal-Todd, Cheryl; Asrat, Marie Jill; Nuk, Jennifer; Mindlin, Allison; Young, Sean; MacMillan, Andree; Van Maerken, Tom; Trbusek, Martin; McKinnon, Wendy; Wood, Marie E; Foulkes, William D; Santamariña, Marta; de la Hoya, Miguel; Foretova, Lenka; Poppe, Bruce; Vral, Anne; Rosseel, Toon; De Leeneer, Kim; Vega, Ana; Claes, Kathleen B M

2018-04-01

For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies. © 2017 Wiley Periodicals, Inc.

Skipping Breakfast is Correlated with Obesity.

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Watanabe, Yoko; Saito, Isao; Henmi, Ikuyo; Yoshimura, Kana; Maruyama, Kotatsu; Yamauchi, Kanako; Matsuo, Tatsuhiro; Kato, Tadahiro; Tanigawa, Takeshi; Kishida, Taro; Asada, Yasuhiko

2014-01-01

Despite the fact that the total energy intake of Japanese people has decreased, the percentage of obese people has increased. This suggests that the timing of meals is related to obesity. The purpose of the study was to investigate the relationship between the timing of meals and obesity, based on analyses of physical measurements, serum biochemical markers, nutrient intake, and lifestyle factors in the context of Chrononutrition. We analyzed data derived from 766 residents of Toon City (286 males and 480 females) aged 30 to 79 years who underwent detailed medical examinations between 2011 and 2013. These medical examinations included. (1) physical measurements (waist circumference, blood pressure, etc.); (2) serum biochemical markers (total cholesterol, etc.); (3) a detailed questionnaire concerning lifestyle factors such as family structure and daily habits (22 issues), exercise and eating habits (28 issues), alcohol intake and smoking habits; (4) a food frequency questionnaire based on food groups (FFQg); and (5) a questionnaire concerning the times at which meals and snacks are consumed. The values for body mass index (BMI) and waist circumference were higher for participants who ate dinner less than three hours before bedtime (3-h group). The Chi-square test showed that there was a significant difference in eating habits, e.g., eating snacks, eating snacks at night, having dinner after 8 p.m., and having dinner after 9 p.m., between the 3-h group. Multiple linear regression analysis showed that skipping breakfast significantly influenced both waist circumference (β = 5.271) and BMI (β = 1.440) and that eating dinner influenced BMI (β = 0.581). Skipping breakfast had a greater influence on both waist circumference and BMI than eating dinner <3-h before going to bed.

Targeting TGF-β Signaling by Antisense Oligonucleotide-mediated Knockdown of TGF-β Type I Receptor

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Dwi U Kemaladewi

2014-01-01

Full Text Available Duchenne muscular dystrophy (DMD is caused by lack of functional dystrophin and results in progressive myofiber damage and degeneration. In addition, impaired muscle regeneration and fibrosis contribute to the progressive pathology of DMD. Importantly, transforming growth factor-β (TGF-β is implicated in DMD pathology and is known to stimulate fibrosis and inhibit muscle regeneration. In this study, we present a new strategy to target TGF-β signaling cascades by specifically inhibiting the expression of TGF-β type I receptor TGFBR1 (ALK5. Antisense oligonucleotides (AONs were designed to specifically induce exon skipping of mouse ALK5 transcripts. AON-induced exon skipping of ALK5 resulted in specific downregulation of full-length receptor transcripts in vitro in different cell types, repression of TGF-β activity, and enhanced C2C12 myoblast differentiation. To determine the effect of these AONs in dystrophic muscles, we performed intramuscular injections of ALK5 AONs in mdx mice, which resulted in a decrease in expression of fibrosis-related genes and upregulation of Myog expression compared to control AON-injected muscles. In summary, our study presents a novel method to target TGF-β signaling cascades with potential beneficial effects for DMD.

Velocity Building by Reflection Waveform Inversion without Cycle-skipping

KAUST Repository

Guo, Qiang

2017-05-26

Reflection waveform inversion (RWI) provides estimation of low wavenumber model components using reflections generated from a migration/demigration process. The resulting model tends to be a good initial model for FWI. In fact, the optimization images to combine the migration velocity analysis (MVA) objectives (given here by RWI) and the FWI ones. However, RWI may still encounter cycle-skipping at far offsets if the velocity model is highly inaccurate. Similar to MVA, RWI is devoted to focusing reflection data to its true image positions, yet because of the cycle skipping potential we tend to initially use only near offsets. To make the inversion procedure more robust, we introduce the extended image into our RWI. Extending the model perturbations (or image) allows us to better fit the data at larger offsets even with an inaccurate velocity. Thus, we implement a nested approach to optimize the velocity and extended image simultaneously using the objective function of RWI. We slowly reduce the extension, as the image becomes focused, to allow wavepath updates from far offsets to near as a natural progression from long wavelength updates to shorter ones. Applications on synthetic data demonstrate the effectiveness of our method without much additional cost to RWI.

MET gene exon 14 deletion created using the CRISPR/Cas9 system enhances cellular growth and sensitivity to a MET inhibitor.

Science.gov (United States)

Togashi, Yosuke; Mizuuchi, Hiroshi; Tomida, Shuta; Terashima, Masato; Hayashi, Hidetoshi; Nishio, Kazuto; Mitsudomi, Tetsuya

2015-12-01

MET splice site mutations resulting in an exon 14 deletion have been reported to be present in about 3% of all lung adenocarcinomas. Patients with lung adenocarcinoma and a MET splice site mutation who have responded to MET inhibitors have been reported. The CRISPR/Cas9 system is a recently developed genome-engineering tool that can easily and rapidly cause small insertions or deletions. We created an in vitro model for MET exon 14 deletion using the CRISPR/Cas9 system and the HEK293 cell line. The phenotype, which included MET inhibitor sensitivity, was then investigated in vitro. Additionally, MET splice site mutations were analyzed in several cancers included in The Cancer Genome Atlas (TCGA) dataset. An HEK293 cell line with a MET exon 14 deletion was easily and rapidly created; this cell line had a higher MET protein expression level, enhanced MET phosphorylation, and prolonged MET activation. In addition, a direct comparison of phenotypes using this system demonstrated enhanced cellular growth, colony formation, and MET inhibitor sensitivity. In the TCGA dataset, lung adenocarcinomas had the highest incidence of MET exon 14 deletions, while other cancers rarely carried such mutations. Approximately 10% of the lung adenocarcinoma samples without any of driver gene alterations carried the MET exon 14 deletion. These findings suggested that this system may be useful for experiments requiring the creation of specific mutations, and the present experimental findings encourage the development of MET-targeted therapy against lung cancer carrying the MET exon 14 deletion. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Efficient and fast functional screening of microdystrophin constructs in vivo and in vitro for therapy of duchenne muscular dystrophy

DEFF Research Database (Denmark)

Jørgensen, Louise Helskov; Larochelle, Nancy; Orlopp, Kristian

2009-01-01

Duchenne muscular dystrophy (DMD) is an X-linked, lethal genetic disorder affecting the skeletal muscle compartment, and is caused by mutation(s) in the dystrophin gene. Gene delivery of microdystrophin constructs using adeno-associated virus (AAV) and antisense-mediated exon skipping restoring...

TNF-α-Induced microRNAs Control Dystrophin Expression in Becker Muscular Dystrophy.

Science.gov (United States)

Fiorillo, Alyson A; Heier, Christopher R; Novak, James S; Tully, Christopher B; Brown, Kristy J; Uaesoontrachoon, Kitipong; Vila, Maria C; Ngheim, Peter P; Bello, Luca; Kornegay, Joe N; Angelini, Corrado; Partridge, Terence A; Nagaraju, Kanneboyina; Hoffman, Eric P

2015-09-08

The amount and distribution of dystrophin protein in myofibers and muscle is highly variable in Becker muscular dystrophy and in exon-skipping trials for Duchenne muscular dystrophy. Here, we investigate a molecular basis for this variability. In muscle from Becker patients sharing the same exon 45-47 in-frame deletion, dystrophin levels negatively correlate with microRNAs predicted to target dystrophin. Seven microRNAs inhibit dystrophin expression in vitro, and three are validated in vivo (miR-146b/miR-374a/miR-31). microRNAs are expressed in dystrophic myofibers and increase with age and disease severity. In exon-skipping-treated mdx mice, microRNAs are significantly higher in muscles with low dystrophin rescue. TNF-α increases microRNA levels in vitro whereas NFκB inhibition blocks this in vitro and in vivo. Collectively, these data show that microRNAs contribute to variable dystrophin levels in muscular dystrophy. Our findings suggest a model where chronic inflammation in distinct microenvironments induces pathological microRNAs, initiating a self-sustaining feedback loop that exacerbates disease progression. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

TNF-α-Induced microRNAs Control Dystrophin Expression in Becker Muscular Dystrophy

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Alyson A. Fiorillo

2015-09-01

Full Text Available The amount and distribution of dystrophin protein in myofibers and muscle is highly variable in Becker muscular dystrophy and in exon-skipping trials for Duchenne muscular dystrophy. Here, we investigate a molecular basis for this variability. In muscle from Becker patients sharing the same exon 45–47 in-frame deletion, dystrophin levels negatively correlate with microRNAs predicted to target dystrophin. Seven microRNAs inhibit dystrophin expression in vitro, and three are validated in vivo (miR-146b/miR-374a/miR-31. microRNAs are expressed in dystrophic myofibers and increase with age and disease severity. In exon-skipping-treated mdx mice, microRNAs are significantly higher in muscles with low dystrophin rescue. TNF-α increases microRNA levels in vitro whereas NFκB inhibition blocks this in vitro and in vivo. Collectively, these data show that microRNAs contribute to variable dystrophin levels in muscular dystrophy. Our findings suggest a model where chronic inflammation in distinct microenvironments induces pathological microRNAs, initiating a self-sustaining feedback loop that exacerbates disease progression.

Relationship between the functional exon 3 deleted growth hormone receptor polymorphism and symptomatic osteoarthritis in women

NARCIS (Netherlands)

Claessen, K. M. J. A.; Kloppenburg, M.; Kroon, H. M.; Bijsterbosch, J.; Pereira, A. M.; Romijn, J. A.; van der Straaten, T.; Nelissen, R. G. H. H.; Hofman, A.; Uitterlinden, A. G.; Duijnisveld, B. J.; Lakenberg, N.; Beekman, M.; van Meurs, J. B.; Slagboom, P. E.; Biermasz, N. R.; Meulenbelt, I.

2014-01-01

Background Several studies suggest a role of the growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis in the pathophysiology of primary osteoarthritis (OA). A common polymorphism of the GH receptor (exon 3 deletion, d3-GHR) is associated with increased GH/IGF-1 activity. Objective To study

Delineation of the Marfan phenotype associated with mutations in exons 23-32 of the FBN1 gene

Energy Technology Data Exchange (ETDEWEB)

Putnam, E.A.; Cho, M.; Milewicz, D.M. [Univ. of Texas-Houston Medical School, Houston, TX (United States)] [and others

1996-03-29

Marfan syndrome is a dominantly inherited connective tissue disorder with a wide range of phenotypic severity. The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. We screened 8 patients with either neonatal Marfan syndrome or severe cardiovascular complications of Marfan syndrome for mutations in this region of the gene. Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. This analysis documented mutations in exons 25-27 of the FBN1 mutations in 6 of these patients. These results, taken together with previously published FBN1 mutations in this region, further define the phenotype associated with mutations in exons 24-32 of the FBN1 gene, information important for the development of possible diagnostic tests and genetic counseling. 49 refs., 4 figs., 2 tabs.

Redox-mediated bypass of restriction point via skipping of G1pm

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Greene James J

2006-07-01

Full Text Available Abstract Background It is well known that cancer cells bypass the restriction point, R, and undergo uncontrolled cell proliferation. Hypothesis and evidence We suggest here that fibrosarcoma cells enter G1ps directly from M, skipping G1pm, hence bypassing R, in response to redox modulation. Evidence is presented from the published literature that demonstrate a shortening of the cycle period of transformed fibroblasts (SV-3T3 compared to the nontransformed 3T3 fibroblasts, corresponding to the duration of G1pm in the 3T3 fibroblasts. Evidence is also presented that demonstrate that redox modulation can induce the CUA-4 fibroblasts to bypass R, resulting in a cycle period closely corresponding to the cycle period of fibrosarcoma cells (HT1080. Conclusion The evidence supports our hypothesis that a low internal redox potential can cause fibrosarcoma cells to skip the G1pm phase of the cell cycle.

Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array

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Wu Yonghong

2009-03-01

Full Text Available Abstract Background The balance between endothelial cell survival and apoptosis during stress is an important cellular process for vessel integrity and vascular homeostasis, and it is also pivotal in angiogenesis during the development of many vascular diseases. However, the underlying molecular mechanisms remain largely unknown. Although both transcription and alternative splicing are important in regulating gene expression in endothelial cells under stress, the regulatory mechanisms underlying this state and their interactions have not yet been studied on a genome-wide basis. Results Human umbilical vein endothelial cells (HUVECs were treated with cobalt chloride (CoCl2 both to mimic hypoxia and to induce cell apoptosis and alternative splicing responses. Cell apoptosis rate analysis indicated that HUVECs exposed to 300 μM CoCl2 for 24 hrs were initially counterbalancing apoptosis with cell survival. We therefore used the Affymetrix exon array system to determine genome-wide transcript- and exon-level differential expression. Other than 1583 differentially expressed transcripts, 342 alternatively spliced exons were detected and classified by different splicing types. Sixteen alternatively spliced exons were validated by RT-PCR. Furthermore, direct evidence for the ongoing balance between HUVEC survival and apoptosis was provided by Gene Ontology (GO and protein function, as well as protein domain and pathway enrichment analyses of the differentially expressed transcripts. Importantly, a novel molecular module, in which the heat shock protein (HSP families play a significant role, was found to be activated under mimicked hypoxia conditions. In addition, 46% of the transcripts containing stress-modulated exons were differentially expressed, indicating the possibility of combinatorial regulation of transcription and splicing. Conclusion The exon array system effectively profiles gene expression and splicing on the genome-wide scale. Based on

Characterization of a spliced exon product of herpes simplex type-1 latency-associated transcript in productively infected cells

International Nuclear Information System (INIS)

Kang, Wen; Mukerjee, Ruma; Gartner, Jared J.; Hatzigeorgiou, Artemis G.; Sandri-Goldin, Rozanne M.; Fraser, Nigel W.

2006-01-01

The latency-associated transcripts (LATs) of herpes simplex virus type-1 (HSV-1) are the only viral RNAs accumulating during latent infections in the sensory ganglia of the peripheral nervous system. The major form of LAT that accumulates in latently infected neurons is a 2 kb intron, spliced from a much less abundant 8.3 primary transcript. The spliced exon mRNA has been hard to detect. However, in this study, we have examined the spliced exon RNA in productively infected cells using ribonuclease protection (RPA), and quantitative RT-PCR (q-PCR) assays. We were able to detect the LAT exon RNA in productively infected SY5Y cells (a human neuronal cell line). The level of the LAT exon RNA was found to be approximately 5% that of the 2 kb intron RNA and thus is likely to be relatively unstable. Quantitative RT-PCR (q-PCR) assays were used to examine the LAT exon RNA and its properties. They confirmed that the LAT exon mRNA is present at a very low level in productively infected cells, compared to the levels of other viral transcripts. Furthermore, experiments showed that the LAT exon mRNA is expressed as a true late gene, and appears to be polyadenylated. In SY5Y cells, in contrast to most late viral transcripts, the LAT exon RNA was found to be mainly nuclear localized during the late stage of a productive infection. Interestingly, more LAT exon RNA was found in the cytoplasm in differentiated compared to undifferentiated SY5Y cells, suggesting the nucleocytoplasmic distribution of the LAT exon RNA and its related function may be influenced by the differentiation state of cells

Analysis of KIT expression and KIT exon 11 mutations in canine oral malignant melanomas.

Science.gov (United States)

Murakami, A; Mori, T; Sakai, H; Murakami, M; Yanai, T; Hoshino, Y; Maruo, K

2011-09-01

KIT, a transmembrane receptor tyrosine kinase, is one of the specific targets for anti-cancer therapy. In humans, its expression and mutations have been identified in malignant melanomas and therapies using molecular-targeted agents have been promising in these tumours. As human malignant melanoma, canine malignant melanoma is a fatal disease with metastases and the poor response has been observed with all standard protocols. In our study, KIT expression and exon 11 mutations in dogs with histologically confirmed malignant oral melanomas were evaluated. Although 20 of 39 cases were positive for KIT protein, there was no significant difference between KIT expression and overall survival. Moreover, polymerase chain reaction amplification and sequencing of KIT exon 11 in 17 samples did not detect any mutations and proved disappointing. For several reasons, however, KIT expression and mutations of various exons including exon 11 should be investigated in more cases. © 2011 Blackwell Publishing Ltd.

Origin of introns by 'intronization' of exonic sequences

DEFF Research Database (Denmark)

Irimia, Manuel; Rukov, Jakob Lewin; Penny, David

2008-01-01

The mechanisms of spliceosomal intron creation have proved elusive. Here we describe a new mechanism: the recruitment of internal exonic sequences ('intronization') in Caenorhabditis species. The numbers of intronization events and introns gained by other mechanisms are similar, suggesting that i...

Personnel reliability impact on petrochemical facilities monitoring system's failure skipping probability

Science.gov (United States)

Kostyukov, V. N.; Naumenko, A. P.

2017-08-01

The paper dwells upon urgent issues of evaluating impact of actions conducted by complex technological systems operators on their safe operation considering application of condition monitoring systems for elements and sub-systems of petrochemical production facilities. The main task for the research is to distinguish factors and criteria of monitoring system properties description, which would allow to evaluate impact of errors made by personnel on operation of real-time condition monitoring and diagnostic systems for machinery of petrochemical facilities, and find and objective criteria for monitoring system class, considering a human factor. On the basis of real-time condition monitoring concepts of sudden failure skipping risk, static and dynamic error, monitoring systems, one may solve a task of evaluation of impact that personnel's qualification has on monitoring system operation in terms of error in personnel or operators' actions while receiving information from monitoring systems and operating a technological system. Operator is considered as a part of the technological system. Although, personnel's behavior is usually a combination of the following parameters: input signal - information perceiving, reaction - decision making, response - decision implementing. Based on several researches on behavior of nuclear powers station operators in USA, Italy and other countries, as well as on researches conducted by Russian scientists, required data on operator's reliability were selected for analysis of operator's behavior at technological facilities diagnostics and monitoring systems. The calculations revealed that for the monitoring system selected as an example, the failure skipping risk for the set values of static (less than 0.01) and dynamic (less than 0.001) errors considering all related factors of data on reliability of information perception, decision-making, and reaction fulfilled is 0.037, in case when all the facilities and error probability are under

Do Vaccines Cause Autism? Is it OK to Skip Certain Vaccines? Get the facts

Science.gov (United States)

... Lifestyle Infant and toddler health Do vaccines cause autism? Is it OK to skip certain vaccines? Get ... their potentially serious complications. Vaccines do not cause autism. Despite much controversy on the topic, researchers haven' ...

Blau syndrome-associated mutations in exon 4 of the caspase activating recruitment domain 15 (CARD 15) gene are not found in ethnic Danes with sarcoidosis

DEFF Research Database (Denmark)

Milman, Nils; Nielsen, Finn Cilius; Hviid, Thomas Vauvert F

2007-01-01

BACKGROUND: Distinct mutations of the caspase activating recruitment domain 15 (CARD15) gene (also known as nucleotide-binding oligomerisation domain protein 2) on chromosome 16q are associated with the chronic granulomatous disease called Blau syndrome. Sarcoidosis is a systemic granulomatous...... disease, which has features in common with Blau syndrome. AIM: The aim of this study was to evaluate whether ethnic Danes with sarcoidosis have CARD15 mutations associated with Blau syndrome. METHODS: Analysis of exon 4 of the CARD15 gene containing mutations associated with Blau syndrome was performed...

Measuring Physical Activity Intensity

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Duchenne muscular dystrophy in a female with compound heterozygous contiguous exon deletions.

Science.gov (United States)

Takeshita, Eri; Minami, Narihiro; Minami, Kumiko; Suzuki, Mikiya; Awashima, Takeya; Ishiyama, Akihiko; Komaki, Hirofumi; Nishino, Ichizo; Sasaki, Masayuki

2017-06-01

Females with Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) mutations rarely exhibit clinical symptoms from childhood, although potential mechanisms for symptoms associated with DMD and BMD in females have been reported. We report the case of a female DMD patient with a clinical course indistinguishable from that of a male DMD patient, and who possessed compound heterozygous contiguous exon deletions in the dystrophin gene. She exhibited Gowers' sign, calf muscle hypertrophy, and a high serum creatine kinase level at 2 years. Her muscle pathology showed most of the fibers were negative for dystrophin immunohistochemical staining. She lost ambulation at 11 years. Multiplex ligation-dependent probe amplification analysis of this gene detected one copy of exons 48-53; she was found to be a BMD carrier with an in-frame deletion. Messenger RNA from her muscle demonstrated out-of-frame deletions of exons 48-50 and 51-53 occurring on separate alleles. Genomic DNA from her lymphocytes demonstrated the accurate deletion region on each allele. To our knowledge, this is the first report on a female patient possessing compound heterozygous contiguous exon deletions in the dystrophin gene, leading to DMD. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy

Energy Technology Data Exchange (ETDEWEB)

Nguyen thi Man; Morris, G.E. (North East Wales Inst., Clwyd (United Kingdom))

1993-06-01

The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random [open quotes]libraries[close quotes] of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25--60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1--41, and the authors now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes. 38 refs., 2 figs., 4 tabs.

PMO Delivery System Using Bubble Liposomes and Ultrasound Exposure for Duchenne Muscular Dystrophy Treatment.

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Negishi, Yoichi; Ishii, Yuko; Nirasawa, Kei; Sasaki, Eri; Endo-Takahashi, Yoko; Suzuki, Ryo; Maruyama, Kazuo

2018-01-01

Duchenne muscular dystrophy (DMD) is a genetic disorder characterized by progressive muscle degeneration, caused by nonsense or frameshift mutations in the dystrophin (DMD) gene. Antisense oligonucleotides can be used to induce specific exon skipping; recently, a phosphorodiamidate morpholino oligomer (PMO) has been approved for clinical use in DMD. However, an efficient PMO delivery strategy is required to improve the therapeutic efficacy in DMD patients. We previously developed polyethylene glycol (PEG)-modified liposomes containing ultrasound contrast gas, "Bubble liposomes" (BLs), and found that the combination of BLs with ultrasound exposure is a useful gene delivery tool. Here, we describe an efficient PMO delivery strategy using the combination of BLs and ultrasound exposure to treat muscles in a DMD mouse model (mdx). This ultrasound-mediated BL technique can increase the PMO-mediated exon-skipping efficiency, leading to significantly increased dystrophin expression. Thus, the combination of BLs and ultrasound exposure may be a feasible PMO delivery method to improve therapeutic efficacy and reduce the PMO dosage for DMD treatment.

Targeted exon sequencing in Usher syndrome type I.

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Bujakowska, Kinga M; Consugar, Mark; Place, Emily; Harper, Shyana; Lena, Jaclyn; Taub, Daniel G; White, Joseph; Navarro-Gomez, Daniel; Weigel DiFranco, Carol; Farkas, Michael H; Gai, Xiaowu; Berson, Eliot L; Pierce, Eric A

2014-12-02

Patients with Usher syndrome type I (USH1) have retinitis pigmentosa, profound congenital hearing loss, and vestibular ataxia. This syndrome is currently thought to be associated with at least six genes, which are encoded by over 180 exons. Here, we present the use of state-of-the-art techniques in the molecular diagnosis of a cohort of 47 USH1 probands. The cohort was studied with selective exon capture and next-generation sequencing of currently known inherited retinal degeneration genes, comparative genomic hybridization, and Sanger sequencing of new USH1 exons identified by human retinal transcriptome analysis. With this approach, we were able to genetically solve 14 of the 47 probands by confirming the biallelic inheritance of mutations. We detected two likely pathogenic variants in an additional 19 patients, for whom family members were not available for cosegregation analysis to confirm biallelic inheritance. Ten patients, in addition to primary disease-causing mutations, carried rare likely pathogenic USH1 alleles or variants in other genes associated with deaf-blindness, which may influence disease phenotype. Twenty-one of the identified mutations were novel among the 33 definite or likely solved patients. Here, we also present a clinical description of the studied cohort at their initial visits. We found a remarkable genetic heterogeneity in the studied USH1 cohort with multiplicity of mutations, of which many were novel. No obvious influence of genotype on phenotype was found, possibly due to small sample sizes of the genotypes under study. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

The calreticulin (CALR) exon 9 mutations are promising targets for cancer immune therapy

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Holmström, M O; Martinenaite, E; Ahmad, S M

2017-01-01

The calreticulin (CALR) exon 9 mutations are found in ∼30% of patients with essential thrombocythemia and primary myelofibrosis. Recently, we reported spontaneous immune responses against the CALR mutations. Here, we describe that CALR-mutant (CALRmut)-specific T cells are able to specifically re...... CALR exon 9 mutations.Leukemia advance online publication, 15 August 2017; doi:10.1038/leu.2017.214....

Exon sequencing of PKD1 gene in an Iranian patient with autosomal-dominant polycystic kidney disease.

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Hafizi, Atousa; Khatami, Saeid Reza; Galehdari, Hamid; Shariati, Gholamreza; Saberi, Ali Hossein; Hamid, Mohammad

2014-07-01

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic kidney disorders with the incidence of 1 in 1,000 births. ADPKD is genetically heterogeneous with two genes identified: PKD1 (16p13.3, 46 exons) and PKD2 (4q21, 15 exons). Eighty five percent of the patients with ADPKD have at least one mutation in the PKD1 gene. Genetic studies have demonstrated an important allelic variability among patients, but very few data are known about the genetic variation among Iranian populations. In this study, exon direct sequencing of PKD1 was performed in a seven-year old boy with ADPKD and in his parents. The patient's father was ADPKD who was affected without any kidney dysfunction, and the patient's mother was congenitally missing one kidney. Molecular genetic testing found a mutation in all three members of this family. It was a missense mutation GTG>ATG at position 3057 in exon 25 of PKD1. On the other hand, two novel missense mutations were reported just in the 7-year-old boy: ACA>GCA found in exon 15 at codon 2241 and CAC>AAC found in exon 38 at codon 3710. For checking the pathogenicity of these mutations, exons 15, 25, and 38 of 50 unrelated normal cases were sequenced. our findings suggested that GTG>ATG is a polymorphism with high frequency (60%) as well as ACA>GCA and CAC>AAC are polymorphisms with frequencies of 14% and 22%, respectively in the population of Southwest Iran.

DMD Mutations in 576 Dystrophinopathy Families: A Step Forward in Genotype-Phenotype Correlations.

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Jonas Juan-Mateu

Full Text Available Recent advances in molecular therapies for Duchenne muscular dystrophy (DMD require precise genetic diagnosis because most therapeutic strategies are mutation-specific. To understand more about the genotype-phenotype correlations of the DMD gene we performed a comprehensive analysis of the DMD mutational spectrum in a large series of families. Here we provide the clinical, pathological and genetic features of 576 dystrophinopathy patients. DMD gene analysis was performed using the MLPA technique and whole gene sequencing in blood DNA and muscle cDNA. The impact of the DNA variants on mRNA splicing and protein functionality was evaluated by in silico analysis using computational algorithms. DMD mutations were detected in 576 unrelated dystrophinopathy families by combining the analysis of exonic copies and the analysis of small mutations. We found that 471 of these mutations were large intragenic rearrangements. Of these, 406 (70.5% were exonic deletions, 64 (11.1% were exonic duplications, and one was a deletion/duplication complex rearrangement (0.2%. Small mutations were identified in 105 cases (18.2%, most being nonsense/frameshift types (75.2%. Mutations in splice sites, however, were relatively frequent (20%. In total, 276 mutations were identified, 85 of which have not been previously described. The diagnostic algorithm used proved to be accurate for the molecular diagnosis of dystrophinopathies. The reading frame rule was fulfilled in 90.4% of DMD patients and in 82.4% of Becker muscular dystrophy patients (BMD, with significant differences between the mutation types. We found that 58% of DMD patients would be included in single exon-exon skipping trials, 63% from strategies directed against multiexon-skipping exons 45 to 55, and 14% from PTC therapy. A detailed analysis of missense mutations provided valuable information about their impact on the protein structure.

Fibrillin mutations in the Marfan syndrome

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Price, C.E.; Wang, M.; Wang, J.; Godfrey, M. [Univ. of Nebraska Medical Center, Omaha, NE (United States)

1994-09-01

The Marfan syndrome (MFS) is an autosomal dominant heritable disorder of connective tissue manifested by variable and pleiotropic defect in the skeletal, ocular, and cardiovascular systems. We have recently begun to use intron-specific primers that have become available through the International Marfan Syndrome Consortium to screen for fibrillin mutations in MFS patients. Using the genomic PCR-based approach in addition to RT-PCR methodologies, we have identified several novel mutations. A single base insertion was identified in all affected individuals of one family. The insertion of an {open_quote}A{close_quote} at position 1891 in exon 15 causes a premature stop codon and thus a truncated polypeptide. The truncated protein of 617 amino acids has an expected molecular weight of 63 kD. Metabolic labeling and immunoprecipitation studies are in progress. A C{r_arrow}T transition at position 1634 in exon 12 causing a 5th position Cys to Phe substitution in an EGF-like motif was observed in another MFS patient. Finally, we have identified a G{r_arrow}A transition at the +1 position of the donor splice site that causes the deletion of fibrillin exon 32 in a patient with the neonatal form of MFS. Exon 32 is a precursor EGF-like calcium binding motif that is located in a single stretch of 12 similar domains. We had previously identified the skipping of this exon due to an A{r_arrow}T transversion at the -2 position of the consensus acceptor splice site in another patient with neonatal MFS. The reason that the skipping of exon 32 causes a neonatal lethal MFS phenotype is presently unclear. These studies will help elucidate the role of diverse regions of fibrillin.

Transtheoretical Model Based Exercise Counseling Combined with Music Skipping Rope Exercise on Childhood Obesity.

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Ham, Ok Kyung; Sung, Kyung Mi; Lee, Bo Gyeong; Choi, Hee Won; Im, Eun-Ok

2016-06-01

The purpose was to evaluate the effects of a transtheoretical model (TTM) based exercise counseling offered with music skipping rope exercise on components of the TTM (stages of change, decisional balance, and self-efficacy), body mass index, glucose, and lipid profile of overweight/obese children in Korea. This study used a nonequivalent pretest and posttest experimental study design. A total of 75 overweight/obese children participated in the study. Eight sessions of exercise counseling combined with music skipping rope exercise for 12 weeks were offered for children in the experimental group, while one session of exercise counseling with music skipping rope exercise for 12 weeks was offered for children in the control group. Outcomes were measured at baseline, and 6 months after the intervention. After the intervention, self-efficacy significantly improved among children in the experimental group (p = .049), while these children maintained their baseline BMI at 6-month follow-up (p > .05). Among children in the control group, BMI significantly increased (p effective in maintaining BMI and improving self-efficacy of overweight/obese children. The TTM-based counseling combined with exercise classes has potential to control weight among overweight/obese children, while involvement of parents and children in the development of the theory-based intervention may generate further benefits regarding health and well-being of overweight/obese children. Copyright © 2016. Published by Elsevier B.V.

Breakfast skipping in prepubertal obese children: hormonal, metabolic and cognitive consequences.

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Maffeis, C; Fornari, E; Surano, M G; Comencini, E; Corradi, M; Tommasi, M; Fasan, I; Cortese, S

2012-03-01

Skipping breakfast influences cognitive performance. The aim of our study was to investigate the relationship between the variation of hormonal and metabolic postprandial parameters induced by breakfast consumption or fasting and cognitive performance in obese children. Cross-sectional study for repeated measures. Memory and attention assessment tests, hormones and nutrient oxidation were measured before and after consuming breakfast vs fasting in 10 prepubertal obese children. Fasting induced a significant (PContinuous Performance Test II (a global index of inattention) and the Test of Memory and Learning Word Selective Reminding (a test of verbal memory), whereas no changes were found after breakfast. Fasting was associated with a reduction of insulin and an increase in glucagon, with no changes in glucose. The increase in inattention was associated with a reduction of carbohydrate oxidation (ρ=-0.66, Pbreakfast or fasting, whereas Ghrelin was significantly lower. No association between postprandial hormone variation and cognitive performance was found. Attention and visual memory performance in the morning were reduced when the children skipped breakfast. No association was found with hormones or metabolic changes, but we did find an association with a reduction of carbohydrate oxidation. Nevertheless, these preliminary findings need confirmation in larger sample size.

Comparable clinical and radiological outcomes between skipped-level and all-level plating for open-door laminoplasty.

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Cheung, Jason Pui Yin; Cheung, Prudence Wing Hang; Cheung, Amy Yim Ling; Lui, Darren; Cheung, Kenneth M C

2018-06-01

To compare the clinical and radiological outcomes between skipped-level and all-level plating for cervical laminoplasty. Patients with cervical spondylotic myelopathy (CSM) treated by open-door laminoplasty with minimum 2-year postoperative follow-up were included. All patients had opening from C3-6 or C3-7 and were divided into skipped-level or all-level plating groups. Japanese Orthopaedic Association (JOA) scores and canal measurements were obtained preoperatively, immediate (within 1 week) postoperatively, and at 2, 6 weeks, 3, 6 and 12 months postoperatively. Paired t test was used for comparative analysis. Receiver operating characteristic analysis was used to determine the canal expansion cutoff for spring-back closure. A total of 74 subjects were included with mean age of 66.1 ± 11.3 years at surgery. Of these, 32 underwent skipped-level plating and 42 underwent all-level plating. No significant differences were noted between the two groups at baseline and follow-up. Spring-back closure was observed in up to 50% of the non-plated levels within 3 months postoperatively. The cutoff for developing spring-back closure was 7 mm canal expansion for C3-6. No differences were observed in JOA scores and recovery rates between the two groups. None of the patients with spring-back required reoperation. There were no significant differences between skipped-level and all-level plating in terms of JOA or recovery rate, and canal diameter differences. This has tremendous impact on saving costs in CSM management as up to two plates per patient undergoing a standard C3-6 laminoplasty may be omitted instead of four plates to every level to achieve similar clinical and radiological outcomes. III. These slides can be retrieved under Electronic Supplementary Material.

Multiplex amplification of large sets of human exons.

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Porreca, Gregory J; Zhang, Kun; Li, Jin Billy; Xie, Bin; Austin, Derek; Vassallo, Sara L; LeProust, Emily M; Peck, Bill J; Emig, Christopher J; Dahl, Fredrik; Gao, Yuan; Church, George M; Shendure, Jay

2007-11-01

A new generation of technologies is poised to reduce DNA sequencing costs by several orders of magnitude. But our ability to fully leverage the power of these technologies is crippled by the absence of suitable 'front-end' methods for isolating complex subsets of a mammalian genome at a scale that matches the throughput at which these platforms will routinely operate. We show that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify approximately 10,000 human exons in a single multiplex reaction. Additionally, we show integration of this protocol with ultra-high-throughput sequencing for targeted variation discovery. Although the multiplex capture reaction is highly specific, we found that nonuniform capture is a key issue that will need to be resolved by additional optimization. We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing.

SKIPing with Head Start Teachers: Influence of T-SKIP on Object-Control Skills

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Brian, Ali; Goodway, Jacqueline D.; Logan, Jessica A.; Sutherland, Sue

2017-01-01

Purpose: Children from disadvantaged settings are at risk for delays in their object-control (OC) skills. Fundamental motor skill interventions, such as the Successful Kinesthetic Instruction for Preschoolers (SKIP) Program, are highly successful when led by motor development experts. However, few preschools employ such experts. This study…

High resolution melting for mutation scanning of TP53 exons 5–8

International Nuclear Information System (INIS)

Krypuy, Michael; Dobrovic, Alexander; Ahmed, Ahmed Ashour; Etemadmoghadam, Dariush; Hyland, Sarah J; Australian Ovarian Cancer Study Group; Fazio, Anna de; Fox, Stephen B; Brenton, James D; Bowtell, David D

2007-01-01

p53 is commonly inactivated by mutations in the DNA-binding domain in a wide range of cancers. As mutant p53 often influences response to therapy, effective and rapid methods to scan for mutations in TP53 are likely to be of clinical value. We therefore evaluated the use of high resolution melting (HRM) as a rapid mutation scanning tool for TP53 in tumour samples. We designed PCR amplicons for HRM mutation scanning of TP53 exons 5 to 8 and tested them with DNA from cell lines hemizygous or homozygous for known mutations. We assessed the sensitivity of each PCR amplicon using dilutions of cell line DNA in normal wild-type DNA. We then performed a blinded assessment on ovarian tumour DNA samples that had been previously sequenced for mutations in TP53 to assess the sensitivity and positive predictive value of the HRM technique. We also performed HRM analysis on breast tumour DNA samples with unknown TP53 mutation status. One cell line mutation was not readily observed when exon 5 was amplified. As exon 5 contained multiple melting domains, we divided the exon into two amplicons for further screening. Sequence changes were also introduced into some of the primers to improve the melting characteristics of the amplicon. Aberrant HRM curves indicative of TP53 mutations were observed for each of the samples in the ovarian tumour DNA panel. Comparison of the HRM results with the sequencing results revealed that each mutation was detected by HRM in the correct exon. For the breast tumour panel, we detected seven aberrant melt profiles by HRM and subsequent sequencing confirmed the presence of these and no other mutations in the predicted exons. HRM is an effective technique for simple and rapid scanning of TP53 mutations that can markedly reduce the amount of sequencing required in mutational studies of TP53

Germline mutations of BRCA1 gene exon 11 are not associated with platinum response neither with survival advantage in patients with primary ovarian cancer: understanding the clinical importance of one of the biggest human exons. A study of the Tumor Bank Ovarian Cancer (TOC) Consortium.

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Dimitrova, Desislava; Ruscito, Ilary; Olek, Sven; Richter, Rolf; Hellwag, Alexander; Türbachova, Ivana; Woopen, Hannah; Baron, Udo; Braicu, Elena Ioana; Sehouli, Jalid

2016-09-01

Germline mutations in BRCA1 gene have been reported in up to 20 % of epithelial ovarian cancer (EOC) patients. Distinct clinical characteristics have been attributed to this special EOC population. We hypothesized that mutations in different BRCA1 gene exons may differently affect the clinical course of the disease. The aim of this study was to analyze, in a large cohort of primary EOCs, the clinical impact of mutations in BRCA1 gene exon 11, the largest exon of the gene sequence encoding the 60 % of BRCA1 protein. Two hundred sixty-three primary EOC patients, treated between 2000 and 2008 at Charité University Hospital of Berlin, were included. Patients' blood samples were obtained from the Tumor Ovarian Cancer (TOC) Network ( www.toc-network.de ). Direct sequencing of BRCA1 gene exon 11 was performed for each patient to detect mutations. Based on their BRCA1 exon 11 mutational status, patients were compared regarding clinico-pathological variables and survival. Mutations in BRCA1 exon 11 were found in 18 out of 263 patients (6.8 %). Further 10/263 (3.8 %) cases showed variants of uncertain significance (VUS). All exon 11 BRCA1-positive tumors (100 %) were Type 2 ovarian carcinomas (p = 0.05). Age at diagnosis was significantly younger in Type 2 exon 11 mutated patients (p = 0.01). On multivariate analysis, BRCA1 exon 11 mutational status was not found to be an independent predictive factor for optimal cytoreduction, platinum response, or survival. Mutations in BRCA1 gene exon 11 seem to predispose women to exclusively develop a Type 2 ovarian cancer at younger age. Exon 11 BRCA1-mutated EOC patients showed distinct clinico-pathological features but similar clinical outcome with respect to sporadic EOC patients.

Construction and applications of exon-trapping gene-targeting vectors with a novel strategy for negative selection.

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Saito, Shinta; Ura, Kiyoe; Kodama, Miho; Adachi, Noritaka

2015-06-30

Targeted gene modification by homologous recombination provides a powerful tool for studying gene function in cells and animals. In higher eukaryotes, non-homologous integration of targeting vectors occurs several orders of magnitude more frequently than does targeted integration, making the gene-targeting technology highly inefficient. For this reason, negative-selection strategies have been employed to reduce the number of drug-resistant clones associated with non-homologous vector integration, particularly when artificial nucleases to introduce a DNA break at the target site are unavailable or undesirable. As such, an exon-trap strategy using a promoterless drug-resistance marker gene provides an effective way to counterselect non-homologous integrants. However, constructing exon-trapping targeting vectors has been a time-consuming and complicated process. By virtue of highly efficient att-mediated recombination, we successfully developed a simple and rapid method to construct plasmid-based vectors that allow for exon-trapping gene targeting. These exon-trap vectors were useful in obtaining correctly targeted clones in mouse embryonic stem cells and human HT1080 cells. Most importantly, with the use of a conditionally cytotoxic gene, we further developed a novel strategy for negative selection, thereby enhancing the efficiency of counterselection for non-homologous integration of exon-trap vectors. Our methods will greatly facilitate exon-trapping gene-targeting technologies in mammalian cells, particularly when combined with the novel negative selection strategy.

Emerging genetic therapies to treat Duchenne muscular dystrophy

Science.gov (United States)

Nelson, Stanley F.; Crosbie, Rachelle H.; Miceli, M. Carrie; Spencer, Melissa J.

2010-01-01

Purpose of review Duchenne muscular dystrophy is a progressive muscle degenerative disease caused by dystrophin mutations. The purpose of this review is to highlight two emerging therapies designed to repair the primary genetic defect, called `exon skipping' and `nonsense codon suppression'. Recent findings A drug, PTC124, was identified that suppresses nonsense codon translation termination. PTC124 can lead to restoration of some dystrophin expression in human Duchenne muscular dystrophy muscles with mutations resulting in premature stops. Two drugs developed for exon skipping, PRO051 and AVI-4658, result in the exclusion of exon 51 from mature mRNA. They can restore the translational reading frame to dystrophin transcripts from patients with a particular subset of dystrophin gene deletions and lead to some restoration of dystrophin expression in affected boys' muscle in vivo. Both approaches have concluded phase I trials with no serious adverse events. Summary These novel therapies that act to correct the primary genetic defect of dystrophin deficiency are among the first generation of therapies tailored to correct specific mutations in humans. Thus, they represent paradigm forming approaches to personalized medicine with the potential to lead to life changing treatment for those affected by Duchenne muscular dystrophy. PMID:19745732

Defense Human Resources Activity > PERSEREC

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Early-onset seizures due to mosaic exonic deletions of CDKL5 in a male and two females.

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Bartnik, Magdalena; Derwińska, Katarzyna; Gos, Monika; Obersztyn, Ewa; Kołodziejska, Katarzyna E; Erez, Ayelet; Szpecht-Potocka, Agnieszka; Fang, Ping; Terczyńska, Iwona; Mierzewska, Hanna; Lohr, Naomi J; Bellus, Gary A; Reimschisel, Tyler; Bocian, Ewa; Mazurczak, Tadeusz; Cheung, Sau Wai; Stankiewicz, Paweł

2011-05-01

Mutations in the CDKL5 gene have been associated with an X-linked dominant early infantile epileptic encephalopathy-2. The clinical presentation is usually of severe encephalopathy with refractory seizures and Rett syndrome (RTT)-like phenotype. We attempted to assess the role of mosaic intragenic copy number variation in CDKL5. We have used comparative genomic hybridization with a custom-designed clinical oligonucleotide array targeting exons of selected disease and candidate genes, including CDKL5. We have identified mosaic exonic deletions of CDKL5 in one male and two females with developmental delay and medically intractable seizures. These three mosaic changes represent 60% of all deletions detected in 12,000 patients analyzed by array comparative genomic hybridization and involving the exonic portion of CDKL5. We report the first case of an exonic deletion of CDKL5 in a male and emphasize the importance of underappreciated mosaic exonic copy number variation in patients with early-onset seizures and RTT-like features of both genders.

Fox-2 Splicing Factor Binds to a Conserved Intron Motif to PromoteInclusion of Protein 4.1R Alternative Exon 16

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