AON-mediated Exon Skipping Restores Ciliation in Fibroblasts Harboring the Common Leber Congenital Amaurosis CEP290 Mutation

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Xavier Gerard

2012-01-01

Full Text Available Leber congenital amaurosis (LCA is a severe hereditary retinal dystrophy responsible for congenital or early-onset blindness. The most common disease-causing mutation (>10% is located deep in intron 26 of the CEP290 gene (c.2991+1655A>G. It creates a strong splice donor site that leads to insertion of a cryptic exon encoding a premature stop codon. In the present study, we show that the use of antisense oligonucleotides (AONs allow an efficient skipping of the mutant cryptic exon and the restoration of ciliation in fibroblasts of affected patients. These data support the feasibility of an AON-mediated exon skipping strategy to correct the aberrant splicing.

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

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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.

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.

Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

Czech Academy of Sciences Publication Activity Database

Divina, Petr; Kvitkovicova, Andrea; Buratti, E.; Vorechovsky, I.

2009-01-01

Roč. 17, č. 6 (2009), s. 759-765 ISSN 1018-4813 Institutional research plan: CEZ:AV0Z50520514 Keywords : mutation * cryptic splice site * exon skipping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.564, year: 2009

Modulating Calcium Signals to Boost AON Exon Skipping for DMD

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2017-10-01

for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT AON-mediated exon skipping is currently advancing as therapy for DMD...9 9. Appendices…………………………………………………………… 9 1 1. INTRODUCTION AON-AON-mediated exon skipping is currently advancing as therapy for DMD...CDMD inter-group meetings, an annual retreat, and hosting and attending seminars. While not a stated objective of this grant, trainee career

A dystrophic Duchenne mouse model for testing human antisense oligonucleotides.

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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.

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

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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.

Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies.

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Zhi Yon Charles Toh

Full Text Available Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.

Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

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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

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.

Context Dependent Effects of Chimeric Peptide Morpholino Conjugates Contribute to Dystrophin Exon-skipping Efficiency.

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Yin, Haifang; Boisguerin, Prisca; Moulton, Hong M; Betts, Corinne; Seow, Yiqi; Boutilier, Jordan; Wang, Qingsong; Walsh, Anthony; Lebleu, Bernard; Wood, Matthew Ja

2013-09-24

We have recently reported that cell-penetrating peptides (CPPs) and novel chimeric peptides containing CPP (referred as B peptide) and muscle-targeting peptide (referred as MSP) motifs significantly improve the systemic exon-skipping activity of morpholino phosphorodiamidate oligomers (PMOs) in dystrophin-deficient mdx mice. In the present study, the general mechanistic significance of the chimeric peptide configuration on the activity and tissue uptake of peptide conjugated PMOs in vivo was investigated. Four additional chimeric peptide-PMO conjugates including newly identified peptide 9 (B-9-PMO and 9-B-PMO) and control peptide 3 (B-3-PMO and 3-B-PMO) were tested in mdx mice. Immunohistochemical staining, RT-PCR and western blot results indicated that B-9-PMO induced significantly higher level of exon skipping and dystrophin restoration than its counterpart (9-B-PMO), further corroborating the notion that the activity of chimeric peptide-PMO conjugates is dependent on relative position of the tissue-targeting peptide motif within the chimeric peptide with respect to PMOs. Subsequent mechanistic studies showed that enhanced cellular uptake of B-MSP-PMO into muscle cells leads to increased exon-skipping activity in comparison with MSP-B-PMO. Surprisingly, further evidence showed that the uptake of chimeric peptide-PMO conjugates of both orientations (B-MSP-PMO and MSP-B-PMO) was ATP- and temperature-dependent and also partially mediated by heparan sulfate proteoglycans (HSPG), indicating that endocytosis is likely the main uptake pathway for both chimeric peptide-PMO conjugates. Collectively, our data demonstrate that peptide orientation in chimeric peptides is an important parameter that determines cellular uptake and activity when conjugated directly to oligonucleotides. These observations provide insight into the design of improved cell targeting compounds for future therapeutics studies.Molecular Therapy-Nucleic Acids (2013) 2, e124; doi:10.1038/mtna.2013

Context Dependent Effects of Chimeric Peptide Morpholino Conjugates Contribute to Dystrophin Exon-skipping Efficiency

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HaiFang Yin

2013-01-01

Full Text Available We have recently reported that cell-penetrating peptides (CPPs and novel chimeric peptides containing CPP (referred as B peptide and muscle-targeting peptide (referred as MSP motifs significantly improve the systemic exon-skipping activity of morpholino phosphorodiamidate oligomers (PMOs in dystrophin-deficient mdx mice. In the present study, the general mechanistic significance of the chimeric peptide configuration on the activity and tissue uptake of peptide conjugated PMOs in vivo was investigated. Four additional chimeric peptide-PMO conjugates including newly identified peptide 9 (B-9-PMO and 9-B-PMO and control peptide 3 (B-3-PMO and 3-B-PMO were tested in mdx mice. Immunohistochemical staining, RT-PCR and western blot results indicated that B-9-PMO induced significantly higher level of exon skipping and dystrophin restoration than its counterpart (9-B-PMO, further corroborating the notion that the activity of chimeric peptide-PMO conjugates is dependent on relative position of the tissue-targeting peptide motif within the chimeric peptide with respect to PMOs. Subsequent mechanistic studies showed that enhanced cellular uptake of B-MSP-PMO into muscle cells leads to increased exon-skipping activity in comparison with MSP-B-PMO. Surprisingly, further evidence showed that the uptake of chimeric peptide-PMO conjugates of both orientations (B-MSP-PMO and MSP-B-PMO was ATP- and temperature-dependent and also partially mediated by heparan sulfate proteoglycans (HSPG, indicating that endocytosis is likely the main uptake pathway for both chimeric peptide-PMO conjugates. Collectively, our data demonstrate that peptide orientation in chimeric peptides is an important parameter that determines cellular uptake and activity when conjugated directly to oligonucleotides. These observations provide insight into the design of improved cell targeting compounds for future therapeutics studies.

Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells.

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Winston Koh

Full Text Available Circular RNAs comprise a poorly understood new class of noncoding RNA. In this study, we used a combination of targeted deletion, high-resolution splicing detection, and single-cell sequencing to deeply probe ASXL1 circular splicing. We found that efficient circular splicing required the canonical transcriptional start site and inverted AluSx elements. Sequencing-based interrogation of isoforms after ASXL1 overexpression identified promiscuous linear splicing between all exons, with the two most abundant non-canonical linear products skipping the exons that produced the circular isoforms. Single-cell sequencing revealed a strong preference for either the linear or circular ASXL1 isoforms in each cell, and found the predominant exon skipping product is frequently co-expressed with its reciprocal circular isoform. Finally, absolute quantification of ASXL1 isoforms confirmed our findings and suggests that standard methods overestimate circRNA abundance. Taken together, these data reveal a dynamic new view of circRNA genesis, providing additional framework for studying their roles in cellular biology.

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.

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

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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.

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.

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

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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.

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.

Context Dependent Effects of Chimeric Peptide Morpholino Conjugates Contribute to Dystrophin Exon-skipping Efficiency

OpenAIRE

HaiFang Yin; Prisca Boisguerin; Hong M Moulton; Corinne Betts; Yiqi Seow; Jordan Boutilier; Qingsong Wang; Anthony Walsh; Bernard Lebleu; Matthew JA Wood

2013-01-01

We have recently reported that cell-penetrating peptides (CPPs) and novel chimeric peptides containing CPP (referred as B peptide) and muscle-targeting peptide (referred as MSP) motifs significantly improve the systemic exon-skipping activity of morpholino phosphorodiamidate oligomers (PMOs) in dystrophin-deficient mdx mice. In the present study, the general mechanistic significance of the chimeric peptide configuration on the activity and tissue uptake of peptide conjugated PMOs in vivo was ...

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

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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

Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts

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Herington Adrian C

2007-08-01

Full Text Available Abstract Background Ghrelin is a multifunctional peptide hormone expressed in a range of normal tissues and pathologies. It has been reported that the human ghrelin gene consists of five exons which span 5 kb of genomic DNA on chromosome 3 and includes a 20 bp non-coding first exon (20 bp exon 0. The availability of bioinformatic tools enabling comparative analysis and the finalisation of the human genome prompted us to re-examine the genomic structure of the ghrelin locus. Results We have demonstrated the presence of an additional novel exon (exon -1 and 5' extensions to exon 0 and 1 using comparative in silico analysis and have demonstrated their existence experimentally using RT-PCR and 5' RACE. A revised exon-intron structure demonstrates that the human ghrelin gene spans 7.2 kb and consists of six rather than five exons. Several ghrelin gene-derived splice forms were detected in a range of human tissues and cell lines. We have demonstrated ghrelin gene-derived mRNA transcripts that do not code for ghrelin, but instead may encode the C-terminal region of full-length preproghrelin (C-ghrelin, which contains the coding region for obestatin and a transcript encoding obestatin-only. Splice variants that differed in their 5' untranslated regions were also found, suggesting a role of these regions in the post-transcriptional regulation of preproghrelin translation. Finally, several natural antisense transcripts, termed ghrelinOS (ghrelin opposite strand transcripts, were demonstrated via orientation-specific RT-PCR, 5' RACE and in silico analysis of ESTs and cloned amplicons. Conclusion The sense and antisense alternative transcripts demonstrated in this study may function as non-coding regulatory RNA, or code for novel protein isoforms. This is the first demonstration of putative obestatin and C-ghrelin specific transcripts and these findings suggest that these ghrelin gene-derived peptides may also be produced independently of preproghrelin

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.

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

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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.

Recent advances in antisense oligonucleotide therapy in genetic neuromuscular diseases

Directory of Open Access Journals (Sweden)

Ashok Verma

2018-01-01

Full Text Available Genetic neuromuscular diseases are caused by defective expression of nuclear or mitochondrial genes. Mutant genes may reduce expression of wild-type proteins, and strategies to activate expression of the wild-type proteins might provide therapeutic benefits. Also, a toxic mutant protein may cause cell death, and strategies that reduce mutant gene expression may provide therapeutic benefit. Synthetic antisense oligonucleotide (ASO can recognize cellular RNA and control gene expression. In recent years, advances in ASO chemistry, creation of designer ASO molecules to enhance their safety and target delivery, and scientific controlled clinical trials to ascertain their therapeutic safety and efficacy have led to an era of plausible application of ASO technology to treat currently incurable neuromuscular diseases. Over the past 1 year, for the first time, the United States Food and Drug Administration has approved two ASO therapies in genetic neuromuscular diseases. This overview summarizes the recent advances in ASO technology, evolution and use of synthetic ASOs as a therapeutic platform, and the mechanism of ASO action by exon-skipping in Duchenne muscular dystrophy and exon-inclusion in spinal muscular atrophy, with comments on their advantages and limitations.

Antisense pre-treatment increases gene therapy efficacy in dystrophic muscles.

Science.gov (United States)

Peccate, Cécile; Mollard, Amédée; Le Hir, Maëva; Julien, Laura; McClorey, Graham; Jarmin, Susan; Le Heron, Anita; Dickson, George; Benkhelifa-Ziyyat, Sofia; Piétri-Rouxel, France; Wood, Matthew J; Voit, Thomas; Lorain, Stéphanie

2016-08-15

In preclinical models for Duchenne muscular dystrophy, dystrophin restoration during adeno-associated virus (AAV)-U7-mediated exon-skipping therapy was shown to decrease drastically after six months in treated muscles. This decline in efficacy is strongly correlated with the loss of the therapeutic AAV genomes, probably due to alterations of the dystrophic myofiber membranes. To improve the membrane integrity of the dystrophic myofibers at the time of AAV-U7 injection, mdx muscles were pre-treated with a single dose of the peptide-phosphorodiamidate morpholino (PPMO) antisense oligonucleotides that induced temporary dystrophin expression at the sarcolemma. The PPMO pre-treatment allowed efficient maintenance of AAV genomes in mdx muscles and enhanced the AAV-U7 therapy effect with a ten-fold increase of the protein level after 6 months. PPMO pre-treatment was also beneficial to AAV-mediated gene therapy with transfer of micro-dystrophin cDNA into muscles. Therefore, avoiding vector genome loss after AAV injection by PPMO pre-treatment would allow efficient long-term restoration of dystrophin and the use of lower and thus safer vector doses for Duchenne patients. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

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.

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

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.

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

Directory of Open Access Journals (Sweden)

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.

Polyethylenimine-modified Pluronics (PCMs) Improve Morpholino Oligomer Delivery in Cell Culture and Dystrophic mdx Mice

OpenAIRE

Wang, Mingxing; Wu, Bo; Lu, Peijuan; Cloer, Caryn; Tucker, Jay D; Lu, Qilong

2012-01-01

We investigated a series of small-sized polyethylenimine (PEI, 0.8/1.2 k)-conjugated pluronic copolymers (PCMs) for their potential to enhance delivery of an antisense phosphorodiamidate morpholino oligomer (PMO) in vitro and in dystrophic mdx mice. PCM polymers containing pluronics of molecular weight (Mw) ranging 2–6 k, with hydrophilic-lipophilic balance (HLB) 7–23, significantly enhanced PMO-induced exon-skipping in a green fluorescent protein (GFP) reporter-based myoblast culture system....

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

Directory of Open Access Journals (Sweden)

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...

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...

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.

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

Science.gov (United States)

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.

Electroporation Enhanced Effect of Dystrophin Splice Switching PNA Oligomers in Normal and Dystrophic Muscle

Directory of Open Access Journals (Sweden)

Camilla Brolin

2015-01-01

Full Text Available Peptide nucleic acid (PNA is a synthetic DNA mimic that has shown potential for discovery of novel splice switching antisense drugs. However, in vivo cellular delivery has been a limiting factor for development, and only few successful studies have been reported. As a possible modality for improvement of in vivo cellular availability, we have investigated the effect of electrotransfer upon intramuscular (i.m. PNA administration in vivo. Antisense PNA targeting exon 23 of the murine dystrophin gene was administered by i.m. injection to the tibialis anterior (TA muscle of normal NMRI and dystrophic mdx mice with or without electroporation. At low, single PNA doses (1.5, 3, or 10 µg/TA, electroporation augmented the antisense exon skipping induced by an unmodified PNA by twofold to fourfold in healthy mouse muscle with optimized electric parameters, measured after 7 days. The PNA splice switching was detected at the RNA level up to 4 weeks after a single-dose treatment. In dystrophic muscles of the MDX mouse, electroporation increased the number of dystrophin-positive fibers about 2.5-fold at 2 weeks after a single PNA administration compared to injection only. In conclusion, we find that electroporation can enhance PNA antisense effects in muscle tissue.

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.

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...

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

Directory of Open Access Journals (Sweden)

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.

Identification of antisense long noncoding RNAs that function as SINEUPs in human cells.

Science.gov (United States)

Schein, Aleks; Zucchelli, Silvia; Kauppinen, Sakari; Gustincich, Stefano; Carninci, Piero

2016-09-20

Mammalian genomes encode numerous natural antisense long noncoding RNAs (lncRNAs) that regulate gene expression. Recently, an antisense lncRNA to mouse Ubiquitin carboxyl-terminal hydrolase L1 (Uchl1) was reported to increase UCHL1 protein synthesis, representing a new functional class of lncRNAs, designated as SINEUPs, for SINE element-containing translation UP-regulators. Here, we show that an antisense lncRNA to the human protein phosphatase 1 regulatory subunit 12A (PPP1R12A), named as R12A-AS1, which overlaps with the 5' UTR and first coding exon of the PPP1R12A mRNA, functions as a SINEUP, increasing PPP1R12A protein translation in human cells. The SINEUP activity depends on the aforementioned sense-antisense interaction and a free right Alu monomer repeat element at the 3' end of R12A-AS1. In addition, we identify another human antisense lncRNA with SINEUP activity. Our results demonstrate for the first time that human natural antisense lncRNAs can up-regulate protein translation, suggesting that endogenous SINEUPs may be widespread and present in many mammalian species.

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

Directory of Open Access Journals (Sweden)

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

Directory of Open Access Journals (Sweden)

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.

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

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

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.

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: 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: 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

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.

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

DEFF Research Database (Denmark)

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...

Induced-Decay of Glycine Decarboxylase Transcripts as an Anticancer Therapeutic Strategy for Non-Small-Cell Lung Carcinoma

Directory of Open Access Journals (Sweden)

Jing Lin

2017-12-01

Full Text Available Self-renewing tumor-initiating cells (TICs are thought to be responsible for tumor recurrence and chemo-resistance. Glycine decarboxylase, encoded by the GLDC gene, is reported to be overexpressed in TIC-enriched primary non-small-cell lung carcinoma (NSCLC. GLDC is a component of the mitochondrial glycine cleavage system, and its high expression is required for growth and tumorigenic capacity. Currently, there are no therapeutic agents against GLDC. As a therapeutic strategy, we have designed and tested splicing-modulating steric hindrance antisense oligonucleotides (shAONs that efficiently induce exon skipping (half maximal inhibitory concentration [IC50] at 3.5–7 nM, disrupt the open reading frame (ORF of GLDC transcript (predisposing it for nonsense-mediated decay, halt cell proliferation, and prevent colony formation in both A549 cells and TIC-enriched NSCLC tumor sphere cells (TS32. One candidate shAON causes 60% inhibition of tumor growth in mice transplanted with TS32. Thus, our shAONs candidates can effectively inhibit the expression of NSCLC-associated metabolic enzyme GLDC and may have promising therapeutic implications.

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

First Exon Length Controls Active Chromatin Signatures and Transcription

Directory of Open Access Journals (Sweden)

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.

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

Directory of Open Access Journals (Sweden)

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.

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.

Optimization of Peptide Nucleic Acid Antisense Oligonucleotides for Local and Systemic Dystrophin Splice Correction in the mdx Mouse

Science.gov (United States)

Yin, HaiFang; Betts, Corinne; Saleh, Amer F; Ivanova, Gabriela D; Lee, Hyunil; Seow, Yiqi; Kim, Dalsoo; Gait, Michael J; Wood, Matthew JA

2010-01-01

Antisense oligonucleotides (AOs) have the capacity to alter the processing of pre-mRNA transcripts in order to correct the function of aberrant disease-related genes. Duchenne muscular dystrophy (DMD) is a fatal X-linked muscle degenerative disease that arises from mutations in the DMD gene leading to an absence of dystrophin protein. AOs have been shown to restore the expression of functional dystrophin via splice correction by intramuscular and systemic delivery in animal models of DMD and in DMD patients via intramuscular administration. Major challenges in developing this splice correction therapy are to optimize AO chemistry and to develop more effective systemic AO delivery. Peptide nucleic acid (PNA) AOs are an alternative AO chemistry with favorable in vivo biochemical properties and splice correcting abilities. Here, we show long-term splice correction of the DMD gene in mdx mice following intramuscular PNA delivery and effective splice correction in aged mdx mice. Further, we report detailed optimization of systemic PNA delivery dose regimens and PNA AO lengths to yield splice correction, with 25-mer PNA AOs providing the greatest splice correcting efficacy, restoring dystrophin protein in multiple peripheral muscle groups. PNA AOs therefore provide an attractive candidate AO chemistry for DMD exon skipping therapy. PMID:20068555

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: 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: 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

Alternative splicing of mutually exclusive exons--a review.

Science.gov (United States)

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.

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

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

Energy Technology Data Exchange (ETDEWEB)

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 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

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

Dopamine-induced apoptosis in human neuronal cells: inhibition by nucleic acides antisense to the dopamine transporter

International Nuclear Information System (INIS)

Porat, S.; Gabbay, M.; Tauber, M.; Ratovitski, T.; Blinder, E.; Simantov, R.

1996-01-01

Human neuroblastoma NMB cells take up [ 3 H]dopamine in a selective manner indicating that dopamine transporters are responsible for this uptake. These cells were therefore used as a model to study dopamine neurotoxicity, and to elucidate the role of dopamine transporters in controlling cell death. Treatment with 0.05-0.4 mM dopamine changed cells' morphology within 4 h, accompanied by retraction of processes, shrinkage, apoptosis-like atrophy, accumulation of apoptotic particles, DNA fragmentation and cell death. Cycloheximide inhibited dopamine's effect, suggesting that induction of apoptosis by dopamine was dependent upon protein synthesis. Dopamine cytotoxicity, monitored morphologically by flow cytometric analysis, and by lactate dehydrogenase released, was blocked by cocaine but not by the noradrenaline and serotonin uptake blockers desimipramine and imipramine, respectively. Attempting to inhibit dopamine transport and toxicity in a drug-free and highly selective way, three 18-mer dopamine transporter antisense phosphorothioate oligonucleotides (numbers 1, 2 and 3) and a new plasmid vector expressing the entire rat dopamine transporter complementary DNA in the antisense orientation were prepared and tested. Antisense phosphorothioate oligonucleotide 3 inhibited [ 3 H]dopamine uptake in a time- and dose-dependent manner. Likewise, transient transfection of NMB cells with the plasmid expressing dopamine transporter complementary DNA in the antisense orientation partially blocked [ 3 H]dopamine uptake. Antisense phosphorothioate oligonucleotide 3 also decreased, dose-dependently, the toxic effect of dopamine and 6-hydroxydopamine. Western blot analysis with newly prepared anti-human dopamine transporter antibodies showed that antisense phosphorothioate oligonucleotide 3 decreased the transporter protein level. These studies contribute to better understand the mechanism of dopamine-induced apoptosis and neurotoxicity. (Copyright (c) 1996 Elsevier Science B

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

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

Directory of Open Access Journals (Sweden)

López-Barragán María J

2011-11-01

Full Text Available Abstract Background It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene models for those expressed in sexual or mosquito stages have not been validated. Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown. Results We have sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 parasites. Alignment of the cDNA sequences to the 3D7 reference genome revealed stage-specific antisense transcripts and novel intron-exon splicing junctions. Sequencing of strand-specific cDNA libraries suggested that more genes are expressed in one direction in gametocyte than in schizont. Alternatively spliced genes, antisense transcripts, and stage-specific expressed genes were also characterized. Conclusions It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression.

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

Directory of Open Access Journals (Sweden)

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.

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

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.

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: 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

Preclinical Studies on Intestinal Administration of Antisense Oligonucleotides as a Model for Oral Delivery for Treatment of Duchenne Muscular Dystrophy

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Maaike van Putten

2014-01-01

Full Text Available Antisense oligonucleotides (AONs used to reframe dystrophin mRNA transcripts for Duchenne muscular dystrophy (DMD patients are tested in clinical trials. Here, AONs are administered subcutaneously and intravenously, while the less invasive oral route would be preferred. Oral delivery of encapsulated AONs supplemented with a permeation enhancer, sodium caprate, has been successfully used to target tumor necrosis factor (TNF-α expression in liver. To test the feasibility of orally delivered AONs for DMD, we applied 2′-O-methyl phosphorothioate AONs (with or without sodium caprate supplementation directly to the intestine of mdx mice and compared pharmacokinetics and -dynamics with intravenous, intraperitoneal, and subcutaneous delivery. Intestinally infused AONs were taken up, but resulted in lower plasma levels compared to other delivery routes, although bioavailability could be largely improved by supplementation of sodium caprate. After intestinal infusion, AON levels in all tissues were lower than for other administration routes, as were the ratios of target versus nontarget organ levels, except for diaphragm and heart where comparable levels and ratios were observed. For each administration route, low levels of exon skipping in triceps was observed 3 hours post-AON administration. These data suggest that oral administration of naked 2′-O-methyl phosphorothioate AONs may be feasible, but only when high AON concentrations are used in combination with sodium caprate.

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.

Suppression of cell division by pKi-67 antisense-RNA and recombinant protein.

Science.gov (United States)

Duchrow, M; Schmidt, M H; Zingler, M; Anemüller, S; Bruch, H P; Broll, R

2001-01-01

The human antigen defined by the monoclonal antibody Ki-67 (pKi-67) is a human nuclear protein strongly associated with cell proliferation and found in all tissues studied. It is widely used as a marker of proliferating cells, yet its function is unknown. To investigate its function we suppressed pKi-67 expression by antisense RNA and overexpressed a partial structure of pKi-67 in HeLa cells. A BrdU-incorporation assay showed a significant decrease in DNA synthesis after antisense inhibition. Cell cycle analysis indicated a higher proportion of cells in G1 phase and a lower proportion of cells in S phase while the number of G(2)/M phase cells remained constant. Overexpression of a recombinant protein encoding three of the repetitive elements from exon 13 of pKi-67 had a similar effect to that obtained by antisense inhibition. The similarity of the effect of expressing 'Ki-67 repeats' and pKi-67 antisense RNA could be explained by a negative effect on the folding of the endogenous protein in the endoplasmatic reticulum. Furthermore excessive self-association of pKi-67 via the repeat structure could inhibit its nuclear transport, preventing it from getting to its presumptive site of action. We conclude that the Ki-67 protein has an important role in the regulation of the cell cycle, which is mediated in part by its repetitive elements. Copyright 2001 S. Karger AG, Basel

Identification of sequence motifs significantly associated with antisense activity

Directory of Open Access Journals (Sweden)

Peek Andrew S

2007-06-01

mediators to speed the process along like the RNA Induced Silencing Complex (RISC in RNAi. The independence of motif position and antisense activity also allows us to bypass consideration of this feature in the modelling process, promoting model efficiency and reducing the chance of overfitting when predicting antisense activity. The increase in SVR correlation with significant features compared to nearest-neighbour features indicates that thermodynamics alone is likely not the only factor in determining antisense efficiency.

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...

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

Directory of Open Access Journals (Sweden)

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.

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,

Antiviral effects of herpes simplex virus specific anti-sense nucleic acids.

Science.gov (United States)

Cantin, E M; Podsakoff, G; Willey, D E; Openshaw, H

1992-01-01

We have targeted mRNA sequences encompassing the translation initiation codon of the essential herpes simplex virus type 1 (HSV-1) IE3 gene with three kinds of anti-sense molecule. Addition of a 15mer oligodeoxyribonucleoside methylphosphonate to tissue culture cells resulted in suppression of viral replication. HSV-1 replication was also inhibited in cultured cells containing anti-sense vectors expressing transcripts complementary to the IE3 mRNA. We have also constructed a ribozyme which upon base pairing with the target IE3 mRNA induces cleavage at the predicted GUC site. A major obstacle to anti-sense studies in animals is drug delivery of preformed antisense molecules to ganglionic neurons, the site of HSV latency and reactivation. We speculate as to how this may be accomplished through carrier compounds which are taken up by nerve terminals and transported by retrograde axoplasmic flow. By the same route, HSV itself may be used as an anti-sense vector.

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: 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: 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: 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

Glycogen Reduction in Myotubes of Late-Onset Pompe Disease Patients Using Antisense Technology.

Science.gov (United States)

Goina, Elisa; Peruzzo, Paolo; Bembi, Bruno; Dardis, Andrea; Buratti, Emanuele

2017-09-06

Glycogen storage disease type II (GSDII) is a lysosomal disorder caused by the deficient activity of acid alpha-glucosidase (GAA) enzyme, leading to the accumulation of glycogen within the lysosomes. The disease has been classified in infantile and late-onset forms. Most late-onset patients share a splicing mutation c.-32-13T > G in intron 1 of the GAA gene that prevents efficient recognition of exon 2 by the spliceosome. In this study, we have mapped the splicing silencers of GAA exon 2 and developed antisense morpholino oligonucleotides (AMOs) to inhibit those regions and rescue normal splicing in the presence of the c.-32-13T > G mutation. Using a minigene approach and patient fibroblasts, we successfully increased inclusion of exon 2 in the mRNA and GAA enzyme production by targeting a specific silencer with a combination of AMOs. Most importantly, the use of these AMOs in patient myotubes results in a decreased accumulation of glycogen. To our knowledge, this is the only therapeutic approach resulting in a decrease of glycogen accumulation in patient tissues beside enzyme replacement therapy (ERT) and TFEB overexpression. As a result, it may represent a highly novel and promising therapeutic line for GSDII. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

An antisense oligodeoxynucleotide targeted against the type IIβ regulatory subunit mRNA of protein kinase inhibits cAMP-induced differentiation in HL-60 leukemia cells without affecting phorbol ester effects

International Nuclear Information System (INIS)

Tortora, G.; Clair, T.; Cho-Chung, Y.S.

1990-01-01

The type II β regulatory subunit of cAMP-dependent protein kinase (RII β ) has been hypothesized to play an important role in the growth inhibition and differentiation induced by site-selective cAMP analogs in human cancer cells, but direct proof of this function has been lacking. To address this tissue, HL-60 human promyelocytic leukemia cells were exposed to RII β antisense synthetic oligodeoxynucleotide, and the effects on cAMP-induced growth regulation were examined. Exposure of these cells to RII β antisense oligodeoxynucleotide resulted in a decrease in cAMP analog-induced growth inhibition and differentiation without apparent effect on differentiation induced by phorbol esters. This loss in cAMP growth regulatory function correlated with a decrease in basal and induced levels of RII β protein. Exposure to RII β sense, RI α and RII α antisense, or irrelevant oligodeoxynucleotides had no such effect. These results show that the RII β regulatory subunit of protein kinase plays a critical role in the cAMP-induced growth regulation of HL-60 leukemia cells

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

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

Science.gov (United States)

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.

Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

Directory of Open Access Journals (Sweden)

Kristel Kaer

Full Text Available Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

Antisense oligonucleotides suppress cell-volume-induced activation of chloride channels.

Science.gov (United States)

Gschwentner, M; Nagl, U O; Wöll, E; Schmarda, A; Ritter, M; Paulmichl, M

1995-08-01

Cell volume regulation is an essential feature of most cells. After swelling in hypotonic media, the simultaneous activation of potassium and chloride channels is believed to be the initial, time-determining step in cell volume regulation. The activation of both pathways is functionally linked and enables the cells to lose ions and water, subsequently leading to cell shrinkage and readjustment of the initial volume. NIH 3T3 fibroblasts efficiently regulate their volume after swelling and bear chloride channels that are activated by decreasing extracellular osmolarity. The chloride current elicited in these cells after swelling is reminiscent of the current found in oocytes expressing an outwardly rectifying chloride current termed ICln. Introduction of antisense oligodeoxynucleotides complementary to the first 30 nucleotides of the coding region of the ICln channel into NIH 3T3 fibroblasts suppresses the activation of the swelling-induced chloride current. The experiments directly demonstrate an unambiguous link between a volume-activated chloride current and a cloned protein involved in chloride transport.

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

OpenAIRE

Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

2012-01-01

In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription ...

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: 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

Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

Science.gov (United States)

Chen, Huei-Mei; Rosebrock, Adam P; Khan, Sohail R; Futcher, Bruce; Leatherwood, Janet K

2012-01-01

In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

Functional comparison of antisense proteins of HTLV-1 and HTLV-2 in viral pathogenesis

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Benoit eBarbeau

2013-08-01

Full Text Available The production of antisense transcripts from the 3’ long terminal repeat (LTR in human T-lymphotropic retroviruses has now been clearly demonstrated. After the identification of the antisense strand-encoded HTLV-1 bZIP (HBZ factor, we reported that HBZ could interact with CREB transcription factors and consequently turn off the important activating potential of the viral Tax protein on HTLV-1 5’ LTR promoter activity. We have recently accumulated new results demonstrating that antisense transcripts also exist in HTLV-2, -3 and -4. Furthermore, our data have confirmed the existence of encoded proteins from these antisense transcripts (termed antisense proteins of HTLVs or APHs. APHs are also involved in the down-regulation of Tax-dependent viral transcription. In this review, we will focus on the different molecular mechanisms used by HBZ and APH-2 to control viral expression. While HBZ interacts with CREB through its basic zipper domain, APH-2 binds to this cellular factor through a five amino acid motif localized in its carboxyl terminus. Moreover, unlike APH-2, HBZ possesses an N-terminal activation domain that also contributes to the inhibition of the viral transcription by interacting with the KIX domain of p300/CBP. On the other hand, HBZ was found to induce T-cell proliferation while APH-2 was unable to promote such proliferation. Interestingly, HTLV-2 has not been causally linked to human T-cell leukemia, while HTLV-1 is responsible for the development of the Adult T-cell Leukemia/Lymphoma (ATLL. We will further discuss the possible role played by antisense proteins in the establishment of pathologies induced by viral infection.

Cocaine alters Homer1 natural antisense transcript in the nucleus accumbens.

Science.gov (United States)

Sartor, Gregory C; Powell, Samuel K; Velmeshev, Dmitry; Lin, David Y; Magistri, Marco; Wiedner, Hannah J; Malvezzi, Andrea M; Andrade, Nadja S; Faghihi, Mohammad A; Wahlestedt, Claes

2017-12-01

Natural antisense transcripts (NATs) are an abundant class of long noncoding RNAs that have recently been shown to be key regulators of chromatin dynamics and gene expression in nervous system development and neurological disorders. However, it is currently unclear if NAT-based mechanisms also play a role in drug-induced neuroadaptations. Aberrant regulation of gene expression is one critical factor underlying the long-lasting behavioral abnormalities that characterize substance use disorder, and it is possible that some drug-induced transcriptional responses are mediated, in part, by perturbations in NAT activity. To test this hypothesis, we used an automated algorithm that mines the NCBI AceView transcriptomics database to identify NAT overlapping genes linked to addiction. We found that 22% of the genes examined contain NATs and that expression of Homer1 natural antisense transcript (Homer1-AS) was altered in the nucleus accumbens (NAc) of mice 2h and 10days following repeated cocaine administration. In in vitro studies, depletion of Homer1-AS lead to an increase in the corresponding sense gene expression, indicating a potential regulatory mechanisms of Homer1 expression by its corresponding antisense transcript. Future in vivo studies are needed to definitely determine a role for Homer1-AS in cocaine-induced behavioral and molecular adaptations. Copyright © 2017 Elsevier Inc. All rights reserved.

Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress.

Science.gov (United States)

Servant, Géraldine; Pinson, Benoit; Tchalikian-Cosson, Aurélie; Coulpier, Fanny; Lemoine, Sophie; Pennetier, Carole; Bridier-Nahmias, Antoine; Todeschini, Anne Laure; Fayol, Hélène; Daignan-Fornier, Bertrand; Lesage, Pascale

2012-07-01

Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

Science.gov (United States)

Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

2012-01-01

In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression. PMID:22238674

Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

Directory of Open Access Journals (Sweden)

Huei-Mei Chen

Full Text Available In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

Challenges to oligonucleotides-based therapeutics for Duchenne muscular dystrophy

Directory of Open Access Journals (Sweden)

Goyenvalle Aurélie

2011-02-01

Full Text Available Abstract Antisense oligonucleotides are short nucleic acids designed to bind to specific messenger RNAs in order to modulate splicing patterns or inhibit protein translation. As such, they represent promising therapeutic tools for many disorders and have been actively developed for more than 20 years as a form of molecular medicine. Although significant progress has been made in developing these agents as drugs, they are yet not recognized as effective therapeutics and several hurdles remain to be overcome. Within the last few years, however, the prospect of successful oligonucleotides-based therapies has moved a step closer, in particular for Duchenne muscular dystrophy. Clinical trials have recently been conducted for this myopathy, where exon skipping is being used to achieve therapeutic outcomes. In this review, the recent developments and clinical trials using antisense oligonucleotides for Duchenne muscular dystrophy are discussed, with emphasis on the challenges ahead for this type of therapy, especially with regards to delivery and regulatory issues.

Peripheral reduction of FGFR4 with antisense oligonucleotides increases metabolic rate and lowers adiposity in diet-induced obese mice.

Directory of Open Access Journals (Sweden)

Xing Xian Yu

Full Text Available Obesity is a primary risk factor for multiple metabolic disorders. Many drugs for the treatment of obesity, which mainly act through CNS as appetite suppressants, have failed during development or been removed from the market due to unacceptable adverse effects. Thus, there are very few efficacious drugs available and remains a great unmet medical need for anti-obesity drugs that increase energy expenditure by acting on peripheral tissues without severe side effects. Here, we report a novel approach involving antisense inhibition of fibroblast growth factor receptor 4 (FGFR4 in peripheral tissues. Treatment of diet-induce obese (DIO mice with FGFR4 antisense oligonucleotides (ASO specifically reduced liver FGFR4 expression that not only resulted in decrease in body weight (BW and adiposity in free-feeding conditions, but also lowered BW and adiposity under caloric restriction. In addition, combination treatment with FGFR4 ASO and rimonabant showed additive reduction in BW and adiposity. FGFR4 ASO treatment increased basal metabolic rate during free-feeding conditions and, more importantly, prevented adaptive decreases of metabolic rate induced by caloric restriction. The treatment increased fatty acid oxidation while decreased lipogenesis in both liver and fat. Mechanistic studies indicated that anti-obesity effect of FGFR4 ASO was mediated at least in part through an induction of plasma FGF15 level resulted from reduction of hepatic FGFR4 expression. The anti-obesity effect was accompanied by improvement in plasma glycemia, whole body insulin sensitivity, plasma lipid levels and liver steatosis. Therefore, FGFR4 could be a potential novel target and antisense reduction of hepatic FGFR4 expression could be an efficacious therapy as an adjunct to diet restriction or to an appetite suppressant for the treatment of obesity and related metabolic disorders.

Peripheral reduction of FGFR4 with antisense oligonucleotides increases metabolic rate and lowers adiposity in diet-induced obese mice.

Science.gov (United States)

Yu, Xing Xian; Watts, Lynnetta M; Manchem, Vara Prasad; Chakravarty, Kaushik; Monia, Brett P; McCaleb, Michael L; Bhanot, Sanjay

2013-01-01

Obesity is a primary risk factor for multiple metabolic disorders. Many drugs for the treatment of obesity, which mainly act through CNS as appetite suppressants, have failed during development or been removed from the market due to unacceptable adverse effects. Thus, there are very few efficacious drugs available and remains a great unmet medical need for anti-obesity drugs that increase energy expenditure by acting on peripheral tissues without severe side effects. Here, we report a novel approach involving antisense inhibition of fibroblast growth factor receptor 4 (FGFR4) in peripheral tissues. Treatment of diet-induce obese (DIO) mice with FGFR4 antisense oligonucleotides (ASO) specifically reduced liver FGFR4 expression that not only resulted in decrease in body weight (BW) and adiposity in free-feeding conditions, but also lowered BW and adiposity under caloric restriction. In addition, combination treatment with FGFR4 ASO and rimonabant showed additive reduction in BW and adiposity. FGFR4 ASO treatment increased basal metabolic rate during free-feeding conditions and, more importantly, prevented adaptive decreases of metabolic rate induced by caloric restriction. The treatment increased fatty acid oxidation while decreased lipogenesis in both liver and fat. Mechanistic studies indicated that anti-obesity effect of FGFR4 ASO was mediated at least in part through an induction of plasma FGF15 level resulted from reduction of hepatic FGFR4 expression. The anti-obesity effect was accompanied by improvement in plasma glycemia, whole body insulin sensitivity, plasma lipid levels and liver steatosis. Therefore, FGFR4 could be a potential novel target and antisense reduction of hepatic FGFR4 expression could be an efficacious therapy as an adjunct to diet restriction or to an appetite suppressant for the treatment of obesity and related metabolic disorders.

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

Antisense imaging of epidermal growth factor-induced p21{sup WAF-1/CIP-1} gene expression in MDA-MB-468 human breast cancer xenografts

Energy Technology Data Exchange (ETDEWEB)

Wang, Judy; Chen, Paul; Mrkobrada, Marko [Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, M5S 2S2, Toronto, Ontario (Canada); Hu, Meiduo [Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, M5S 2S2, Toronto, Ontario (Canada); Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario (Canada); Vallis, Katherine A. [Department of Radiation Oncology, Princess Margaret Hospital, University Health Network, 610 University Avenue, Toronto, Ontario (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario (Canada); Department of Medical Biophysics, University of Toronto, Toronto, Ontario (Canada); Reilly, Raymond M. [Department of Medical Imaging, University of Toronto, Toronto, Ontario (Canada)

2003-09-01

Molecular imaging of the expression of key genes which determine the response to DNA damage following cancer treatment may predict the effectiveness of a particular treatment strategy. A prominent early response gene for DNA damage is the gene encoding p21{sup WAF-1/CIP-1}, a cyclin-dependent kinase inhibitor that regulates progression through the cell cycle. In this study, we explored the feasibility of imaging p21{sup WAF-1/CIP-1} gene expression at the mRNA level using an 18-mer phosphorothioated antisense oligodeoxynucleotide (ODN) labeled with {sup 111}In. The known induction of the p21{sup WAF-1/CIP-1} gene in MDA-MB-468 human breast cancer cells following exposure to epidermal growth factor (EGF) was used as an experimental tool. Treatment of MDA-MB-468 cells in vitro with EGF (20 nM) increased the ratio of p21{sup WAF-1/CIP-1} mRNA/{beta}-actin mRNA threefold within 2 h as measured by the reverse transcription polymerase chain reaction (RT-PCR). A concentration-dependent inhibition of EGF-induced p21{sup WAF-1/CIP-1} protein expression was achieved in MDA-MB-468 cells by treatment with antisense ODNs with up to a tenfold decrease observed at 1 {mu}M. There was a fourfold lower inhibition of p21{sup WAF-1/CIP-1} protein expression by control sense or random sequence ODNs. Intratumoral injections of EGF (15 {mu}g/day x 3 days) were employed to induce p21{sup WAF-1/CIP-1} gene expression in MDA-MB-468 xenografts implanted subcutaneously into athymic mice. RT-PCR of explanted tumors showed a threefold increased level of p21{sup WAF-1/CIP-1} mRNA compared with normal saline-treated tumors. Successful imaging of EGF-induced p21{sup WAF-1/CIP-1} gene expression in MDA-MB-468 xenografts was achieved at 48 h post injection of {sup 111}In-labeled antisense ODNs (3.7 MBq; 2 {mu}g). Tumors displaying basal levels of p21{sup WAF-1/CIP-1} gene expression in the absence of EGF treatment could not be visualized. Biodistribution studies showed a significantly higher tumor

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.

Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5.

Science.gov (United States)

Bahal, Raman; McNeer, Nicole Ali; Ly, Danith H; Saltzman, W Mark; Glazer, Peter M

2013-01-01

The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of chemokine receptor 5 (CC R5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer

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Adam Shlien

2016-08-01

Full Text Available Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.

ExonMiner: Web service for analysis of GeneChip Exon array data

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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: 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: 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: 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,

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: 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: 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

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

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....

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: 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: 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

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 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).

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

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

Science.gov (United States)

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.

Sense-antisense (complementary) peptide interactions and the proteomic code; potential opportunities in biology and pharmaceutical science.

Science.gov (United States)

Miller, Andrew D

2015-02-01

A sense peptide can be defined as a peptide whose sequence is coded by the nucleotide sequence (read 5' → 3') of the sense (positive) strand of DNA. Conversely, an antisense (complementary) peptide is coded by the corresponding nucleotide sequence (read 5' → 3') of the antisense (negative) strand of DNA. Research has been accumulating steadily to suggest that sense peptides are capable of specific interactions with their corresponding antisense peptides. Unfortunately, although more and more examples of specific sense-antisense peptide interactions are emerging, the very idea of such interactions does not conform to standard biology dogma and so there remains a sizeable challenge to lift this concept from being perceived as a peripheral phenomenon if not worse, into becoming part of the scientific mainstream. Specific interactions have now been exploited for the inhibition of number of widely different protein-protein and protein-receptor interactions in vitro and in vivo. Further, antisense peptides have also been used to induce the production of antibodies targeted to specific receptors or else the production of anti-idiotypic antibodies targeted against auto-antibodies. Such illustrations of utility would seem to suggest that observed sense-antisense peptide interactions are not just the consequence of a sequence of coincidental 'lucky-hits'. Indeed, at the very least, one might conclude that sense-antisense peptide interactions represent a potentially new and different source of leads for drug discovery. But could there be more to come from studies in this area? Studies on the potential mechanism of sense-antisense peptide interactions suggest that interactions may be driven by amino acid residue interactions specified from the genetic code. If so, such specified amino acid residue interactions could form the basis for an even wider amino acid residue interaction code (proteomic code) that links gene sequences to actual protein structure and function, even

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: 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.

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

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: 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

Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum.

Science.gov (United States)

Amit-Avraham, Inbar; Pozner, Guy; Eshar, Shiri; Fastman, Yair; Kolevzon, Netanel; Yavin, Eylon; Dzikowski, Ron

2015-03-03

The virulence of Plasmodium falciparum, the causative agent of the deadliest form of human malaria, is attributed to its ability to evade human immunity through antigenic variation. These parasites alternate between expression of variable antigens, encoded by members of a multicopy gene family named var. Immune evasion through antigenic variation depends on tight regulation of var gene expression, ensuring that only a single var gene is expressed at a time while the rest of the family is maintained transcriptionally silent. Understanding how a single gene is chosen for activation is critical for understanding mutually exclusive expression but remains a mystery. Here, we show that antisense long noncoding RNAs (lncRNAs) initiating from var introns are associated with the single active var gene at the time in the cell cycle when the single var upstream promoter is active. We demonstrate that these antisense transcripts are incorporated into chromatin, and that expression of these antisense lncRNAs in trans triggers activation of a silent var gene in a sequence- and dose-dependent manner. On the other hand, interference with these lncRNAs using complement peptide nucleic acid molecules down-regulated the active var gene, erased the epigenetic memory, and induced expression switching. Altogether, our data provide evidence that these antisense lncRNAs play a key role in regulating var gene activation and mutually exclusive expression.

Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9.

Science.gov (United States)

Li, Hongmei Lisa; Fujimoto, Naoko; Sasakawa, Noriko; Shirai, Saya; Ohkame, Tokiko; Sakuma, Tetsushi; Tanaka, Michihiro; Amano, Naoki; Watanabe, Akira; Sakurai, Hidetoshi; Yamamoto, Takashi; Yamanaka, Shinya; Hotta, Akitsu

2015-01-13

Duchenne muscular dystrophy (DMD) is a severe muscle-degenerative disease caused by a mutation in the dystrophin gene. Genetic correction of patient-derived induced pluripotent stem cells (iPSCs) by TALENs or CRISPR-Cas9 holds promise for DMD gene therapy; however, the safety of such nuclease treatment must be determined. Using a unique k-mer database, we systematically identified a unique target region that reduces off-target sites. To restore the dystrophin protein, we performed three correction methods (exon skipping, frameshifting, and exon knockin) in DMD-patient-derived iPSCs, and found that exon knockin was the most effective approach. We further investigated the genomic integrity by karyotyping, copy number variation array, and exome sequencing to identify clones with a minimal mutation load. Finally, we differentiated the corrected iPSCs toward skeletal muscle cells and successfully detected the expression of full-length dystrophin protein. These results provide an important framework for developing iPSC-based gene therapy for genetic disorders using programmable nucleases. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

G3139, a Bcl-2 antisense oligodeoxynucleotide, induces clinical responses in VAD refractory myeloma

NARCIS (Netherlands)

van de Donk, N. W. C. J.; de Weerdt, O.; Veth, G.; Eurelings, M.; van Stralen, E.; Frankel, S. R.; Hagenbeek, A.; Bloem, A. C.; Lokhorst, H. M.

2004-01-01

Expression of Bcl-2 in multiple myeloma is associated with resistance to chemotherapeutic drugs. Conversely, suppression of Bcl-2 enhanced the chemosensitivity of myeloma cells in vitro. G3139 is an antisense oligodeoxynucleotide targeted to the first six codons of the Bcl-2 mRNA open reading frame.

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: 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

Inhibition of B cell proliferation by antisense DNA to both alpha and beta forms of Fc epsilon R II.

Science.gov (United States)

Bhatti, L; Behle, K; Stevens, R H

1992-10-01

Epstein-Barr Virus (EBV) infection activates B lymphocyte proliferation through partially understood mechanisms, resulting in phenotypic changes, including the appearance of new antigens. One such antigen is Fc epsilon R II/CD-23 which may be relevant for B cell proliferation. We have used anti-sense oligonucleotides to study the importance of the two forms of this molecule for proliferation in the EBV-transformed, Fc epsilon R II +ve lymphoblastoid B cell line, RPMI 8866. Anti-sense oligodeoxynucleotides were generated to the two forms of Fc epsilon R II; Fc epsilon R IIa (alpha) and IIb (beta) which differ only in their intracytoplasmic domains. Addition of increasing concentrations of anti-sense oligonucleotides, ranging from 1 to 30 microM, significantly decreased cellular proliferation as measured by the incorporation of [3H]thymidine (inhibition range 8-88%). Optimum inhibition of cellular proliferation was apparent at 15 microM concentration of both anti-sense Fc epsilon R IIa and IIb (Fc epsilon R IIa, mean +/- SE = 75 +/- 7% inhibition, p less than 0.001; Fc epsilon R IIb, mean +/- SE = 71 +/- 7% inhibition, p less than 0.001). Anti-sense oligonucleotides complementary to the common part of Fc epsilon R II resulted in a similar inhibition of proliferation. Sense oligonucleotides did not induce significant inhibition. Preincubation of sense and anti-sense oligonucleotides resulted in an abrogation of proliferation inhibition. Moreover, none of these oligonucleotides had any effect on a Fc epsilon R II -ve cell line. Incubation with both anti-sense IIa and IIb resulted in additive, but not synergistic inhibition of proliferation. Addition of soluble Fc epsilon R II did not reverse inhibition of proliferation, suggesting that membrane-bound or intracellular rather than soluble Fc epsilon R II was important for the induced proliferation. Analysis of cell surface expression for Fc epsilon II indicated that while there was a pronounced effect on cell number

Antisense downregulation of mutant huntingtin in a cell model

DEFF Research Database (Denmark)

Hasholt, L.; Abell, K.; Norremolle, A.

2003-01-01

or by addition to the culture medium. Results Expression of the fusion protein containing the mutant huntingtin fragment resulted in diffuse green fluorescence in the cytoplasm and formation of aggregates in some of the NT2 cells and NT2-N neurons. We obtained antisense sequence-specific inhibition of expression...... of the fusion protein and/or suppression of the aggregate formation in both cell types. In the NT2 cells the antisense effect was dependent on the way of administration of the oligo. Conclusions The PS-antisense oligo is effective in downregulation of mutant huntingtin, and the reduction of aggregate formation...... is a sensitive biological marker. The findings suggest that antisense knockdown of huntingtin could be a useful strategy for treatment of HD, and could also be suitable for studies of the normal and pathological function of huntingtin in different cellular model systems....

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

Peptide nucleic acid (PNA) antisense effects in Escherichia coli

DEFF Research Database (Denmark)

Good, L; Nielsen, P E

1999-01-01

Antisense peptide nucleic acid (PNA) can be used to control cell growth, gene expression and growth phenotypes in the bacteria Escherichia coli. PNAs targeted to the RNA components of the ribosome can inhibit translation and cell growth, and PNAs targeted to mRNA can limit gene expression with gene...... and sequence specificity. In an E. coli cell extract, efficient inhibition is observed when using PNA concentrations in the nanomolar range, whereas micromolar concentrations are required for inhibition in growing cells. A mutant strain of E. coli that is more permeable to antibiotics also is more susceptible...... to antisense PNAs than the wild type. This chapter details methods for testing the antisense activities of PNA in E. coli. As an example of the specific antisense inhibition possible, we show the effects of an anti-beta-galactosidase PNA in comparison to control PNAs. With improvements in cell uptake...

Complex organisation and structure of the ghrelin antisense strand gene GHRLOS, a candidate non-coding RNA gene

Directory of Open Access Journals (Sweden)

Herington Adrian C

2008-10-01

Full Text Available Abstract Background The peptide hormone ghrelin has many important physiological and pathophysiological roles, including the stimulation of growth hormone (GH release, appetite regulation, gut motility and proliferation of cancer cells. We previously identified a gene on the opposite strand of the ghrelin gene, ghrelinOS (GHRLOS, which spans the promoter and untranslated regions of the ghrelin gene (GHRL. Here we further characterise GHRLOS. Results We have described GHRLOS mRNA isoforms that extend over 1.4 kb of the promoter region and 106 nucleotides of exon 4 of the ghrelin gene, GHRL. These GHRLOS transcripts initiate 4.8 kb downstream of the terminal exon 4 of GHRL and are present in the 3' untranslated exon of the adjacent gene TATDN2 (TatD DNase domain containing 2. Interestingly, we have also identified a putative non-coding TATDN2-GHRLOS chimaeric transcript, indicating that GHRLOS RNA biogenesis is extremely complex. Moreover, we have discovered that the 3' region of GHRLOS is also antisense, in a tail-to-tail fashion to a novel terminal exon of the neighbouring SEC13 gene, which is important in protein transport. Sequence analyses revealed that GHRLOS is riddled with stop codons, and that there is little nucleotide and amino-acid sequence conservation of the GHRLOS gene between vertebrates. The gene spans 44 kb on 3p25.3, is extensively spliced and harbours multiple variable exons. We have also investigated the expression of GHRLOS and found evidence of differential tissue expression. It is highly expressed in tissues which are emerging as major sites of non-coding RNA expression (the thymus, brain, and testis, as well as in the ovary and uterus. In contrast, very low levels were found in the stomach where sense, GHRL derived RNAs are highly expressed. Conclusion GHRLOS RNA transcripts display several distinctive features of non-coding (ncRNA genes, including 5' capping, polyadenylation, extensive splicing and short open reading

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

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

Advancements of antisense oligonucleotides in treatment of breast cancer

Institute of Scientific and Technical Information of China (English)

YANGShuan-Ping; SONGSan-Tai; 等

2003-01-01

Breast cancer is one kind of multi-gene related malignancy.Overexpression of some oncogenes such as HER-2(c-erbB-2,Neu),bcl-2/bcl-xL,protein kinase A(PKA),and transferrin receptor gene(TfR gene),etc significantly affect the prognosis of breast cancer.It was shown that specific suppression of the overexpressed genes above resulted in the improvement of the therapy of breast cancer.Antisense interference.one of useful tools for inhibiting the overexpression of specific oncogenes,was involved in the therapy of breast cancer in recent years. Data indicated that antisense oligonucleotides(ON)could inhibit specially the expression of the target genes on mRNA or protein levels in most of cases;some ON candidates showed encouraging therapeutic effects in vitro and in vivo on breast cancer cell lines or xenografts.Furthermore,the combination use of the antisense ON and normal chemotherapeutic agents indicated synergistic antitumor effects,which was probably the best utilization of antisense ON in the treatment of breast cancer.

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...

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.

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Christopher A Lavender

2016-08-01

Full Text Available Antisense transcription is a prevalent feature at mammalian promoters. Previous studies have primarily focused on antisense transcription initiating upstream of genes. Here, we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells, investigating the genomic context of downstream antisense transcription. We find extensive correlations between antisense transcription and features associated with the chromatin environment at gene promoters. Antisense transcription downstream of promoters is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Antisense transcription initiates between nucleosomes regularly positioned downstream of these promoters. The nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. This region is bound by chromatin remodeling and histone modifying complexes including SWI/SNF subunits and HDACs, suggesting that antisense transcription or resulting RNA transcripts contribute to the creation and maintenance of a promoter-associated chromatin environment. Downstream antisense transcription overlays additional regulatory features, such as transcription factor binding, DNA accessibility, and the downstream edge of promoter-associated CpG islands. These features suggest an important role for antisense transcription in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment.

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

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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.

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: 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.

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

Energy Technology Data Exchange (ETDEWEB)

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.

Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

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Xiaoling Zhang

2013-01-01

Full Text Available We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs at a false discovery rate (FDR <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.

New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals

Directory of Open Access Journals (Sweden)

RENATA V. VELHO

2015-08-01

Full Text Available With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals.

Science.gov (United States)

Velho, Renata V; Sperb-Ludwig, Fernanda; Schwartz, Ida V D

2015-08-01

With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

Antisense Oligonucleotide (AON-based Therapy for Leber Congenital Amaurosis Caused by a Frequent Mutation in CEP290

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Rob WJ Collin

2012-01-01

Full Text Available Leber congenital amaurosis (LCA is the most severe form of inherited retinal degeneration, with an onset in the first year of life. The most frequent mutation that causes LCA, present in at least 10% of individuals with LCA from North-American and Northern-European descent, is an intronic mutation in CEP290 that results in the inclusion of an aberrant exon in the CEP290 mRNA. Here, we describe a genetic therapy approach that is based on antisense oligonucleotides (AONs, small RNA molecules that are able to redirect normal splicing of aberrantly processed pre-mRNA. Immortalized lymphoblastoid cells of individuals with LCA homozygously carrying the intronic CEP290 mutation were transfected with several AONs that target the aberrant exon that is incorporated in the mutant CEP290 mRNA. Subsequent RNA isolation and reverse transcription-PCR analysis revealed that a number of AONs were capable of almost fully redirecting normal CEP290 splicing, in a dose-dependent manner. Other AONs however, displayed no effect on CEP290 splicing at all, indicating that the rescue of aberrant CEP290 splicing shows a high degree of sequence specificity. Together, our data show that AON-based therapy is a promising therapeutic approach for CEP290-associated LCA that warrants future research in animal models to develop a cure for this blinding disease.

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.…

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.

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.

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

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

Antisense Treatments for Biothreat Agents

National Research Council Canada - National Science Library

Warfield, Kelly L; Panchal, Rekha G; Aman, M J; Bavari, Sina

2006-01-01

... a variety of pathogens in cell culture studies and nonhuman primate models of infection. For these reasons, antisense technologies are being pursued as treatments against biothreat agents such as Ebola virus, dengue virus and Bacillus anthracis...

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

Science.gov (United States)

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.

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.

Knockdown of long noncoding antisense RNA brain-derived neurotrophic factor attenuates hypoxia/reoxygenation-induced nerve cell apoptosis through the BDNF-TrkB-PI3K/Akt signaling pathway.

Science.gov (United States)

Zhong, Jian-Bin; Li, Xie; Zhong, Si-Ming; Liu, Jiu-Di; Chen, Chi-Bang; Wu, Xiao-Yan

2017-09-27

Brain-derived neurotrophic factor (BDNF) plays an important role in neuronal cell apoptosis. The antisense RNA of brain-derived neurotrophic factor (BDNF-AS) is a natural antisense transcript that is transcribed opposite the gene that encodes BDNF. The aim of this study was to determine whether knockdown of BDNF-AS can suppress hypoxia/reoxygenation (H/R)-induced neuronal cell apoptosis and whether this is mediated by the BDNF-TrkB-PI3K/Akt pathway. We detected the expression of BDNF and BDNF-AS in brain tissue from 20 patients with cerebral infarction and five patients with other diseases (but no cerebral ischemia). We found that BDNF expression was significantly downregulated in patients with cerebral infarction, whereas the expression of BDNF-AS was significantly upregulated. In both human cortical neurons (HCN2) and human astrocytes, H/R significantly induced the expression of BDNF-AS, but significantly decreased BDNF expression. H/R also significantly induced apoptosis and reduced the mitochondrial membrane potential in these cells. Following downregulation of BDNF-AS by siRNA in human cortical neurons and human astrocyte cells, BDNF expression was significantly upregulated and the H/R-induced upregulation of BDNF-AS was significantly attenuated. BDNF-AS siRNA inhibited H/R-induced cell apoptosis and ameliorated the H/R-induced suppression of mitochondrial membrane potential. H/R inhibited the expression of BDNF, p-AKT/AKT, and TrKB, and this inhibition was recovered by BDNF-AS siRNA. In summary, this study indicates that BDNF-AS siRNA induces activation of the BDNF-TrkB-PI3K/Akt pathway following H/R-induced neurotoxicity. These findings will be useful toward the application of BDNF-AS siRNA for the treatment of neurodegenerative diseases.

Antisense targeting of TGF-β1 augments BMP-induced upregulation of osteopontin, type I collagen and Cbfa1 in human Saos-2 cells

International Nuclear Information System (INIS)

Shen, Zhong-Jian; Kook Kim, Sang; Youn Jun, Do; Park, Wan; Ho Kim, Young; Malter, James S.; Jo Moon, Byung

2007-01-01

Despite commonalities in signal transduction in osteoblasts from different species, the role of TGF-β1 on bone formation remains elusive. In particular, the role of autocrine TGF-β1 on human osteoblasts is largely unknown. Here we show the effect of TGF-β1 knock-down on the proliferation and differentiation of osteoblasts induced by BMP2. Treatment with antisense TGF-β1 moderately increased the rate of cell proliferation, which was completely reversed by the exogenous addition of TGF-β1. Notably, TGF-β1 blockade significantly enhanced BMP2-induced upregulation of mRNAs encoding osteopontin, type I collagen and Cbfa1, which was suppressed by exogenous TGF-β1. Moreover, TGF-β1 knock-down increased BMP2-induced phosphorylation of Smad1/5 as well as their nuclear import, which paralleled a reduction of inhibitory Smad6. These data suggest autocrine TGF-β1 antagonizes BMP signaling through modulation of inducible Smad6 and the activity of BMP specific Smad1/5

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,

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

Directory of Open Access Journals (Sweden)

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.

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.

Comparison of three techniques for generation of tolerogenic dendritic cells: siRNA, oligonucleotide antisense, and antibody blocking.

Science.gov (United States)

Karimi, Mohammad Hossein; Ebadi, Padideh; Pourfathollah, Ali Akbar; Moazzeni, Mohammad; Soheili, Zahra Soheila; Samiee, Shahram

2010-12-01

In recent years, a new view of dendritic cells (DCs) as a main regulator of immunity to induce and maintain tolerance has been established. In vitro manipulation of their development and maturation is a topic of DC therapeutic application, which utilizes their inherent tolerogenicity. In this field, the therapeutic potential of antisense, siRNA, and blocking antibody are an interesting goal. In the present study, the efficiency of these three methods--siRNA, antisense, and blocking antibody--against CD40 molecule and its function in DCs and BCL1 cell line are compared. DCs were separated from mouse spleen and then cultured in vitro using Lipofectamine 2000 to deliver both silencers; the efficacy of transfection was estimated by flow cytometry. mRNA expression and protein synthesis were assessed by real time-PCR and flow cytometry, respectively. By Annexin V and propidium iodine staining, we could evaluate the viability of transfected cells. Knocking down the CD40 gene into separate groups of DCs by siRNA, antisense, and blocking antibody treated DCs can cause an increase in IL-4, decrease in IL-12, IFN-γ production, and allostimulation activity. Our results indicated that, in comparison to antisense and blocking antibody, siRNAs appear to be quantitatively more efficient in CD40 downregulation and their differences are significant.

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.

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.

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.

Dyslipidemia, sense, antisense or nonsense?

NARCIS (Netherlands)

Visser, M.E.

2011-01-01

Maartje Visser onderzocht het remmen van de synthese van apoB met behulp van antisense - een nieuwe farmacologische techniek. Dit blijkt het slechte LDL-cholesterol op een effectieve manier te verlagen. Bij sommige proefpersonen resulteerde dit in leververvetting. Of dit op de lange termijn

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.

Scintigraphic imaging of oncogenes with antisense probes: does it make sense?

International Nuclear Information System (INIS)

Urbain, J.L.C.; Shore, S.K.; Vekemans, M.C.; Cosenza, S.C.; DeRiel, K.; Patel, G.V.; Charkes, N.D.; Malmud, L.S.; Reddy, E.P.

1995-01-01

The aim of this study was to demonstrate that cells which are expressing a particular mRNA transcript do preferentially and specifically retain the antisense probe targeting that mRNA. Using a mouse plasmacytoma cell line (MOPC315) which produces high levels of IgA heavy chain mRNA, a control mouse pre B cell line (7OZ/3B), a human mammary cell line (MCF7) which expresses the erbB2 or neu oncogene, MOPC315 cells as neu-negative controls, and antisense DNA oligonucleotides complementary to the 5' region of the mRNAs and the sense sequence, we have shown that there is a preferential, specific retention of the IgA and neu antisense sequence in MOPC315 and MCF7 cells, respectively. We have further demonstrated that this retention is time and concentration dependent with a maximum at 24 h. We conclude that cancer cells which express a particular oncogene are suitable targets for radiolabeled antisense deoxyoligonucleotides directed toward the oncogene transcript. (orig.)

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

Bcl-2 antisense therapy in B-cell malignancies.

Science.gov (United States)

Chanan-Khan, Asher

2005-07-01

Bcl-2 is an apoptosis regulating protein, overexpression of which is associated with chemotherapy resistant disease, aggressive clinical course, and poor survival in patients with B-cell lymphoproliferative disorders. Overexpression of Bcl-2 protein results in an aberrant intrinsic apoptotic pathway that confers a protective effect on malignant cells against a death signal (e.g., chemotherapy or radiotherapy). Downregulation of this oncoprotein, thus, represents a possible new way to target clinically aggressive disease. Preclinical studies have shown that this oncoprotein can be effectively decreased by Bcl-2 antisense in malignant lymphoid cells and can reverse chemotherapy resistance, as well as enhance the anti-apoptotic potential of both chemotherapeutic and biologic agents. Ongoing clinical trials are exploring the role of Bcl-2 downregulation with oblimersen (Bcl-2 antisense) in patients with non-Hodgkin's lymphoma, chronic lymphocytic leukemia and multiple myeloma. Early results from these studies are promising and support the proof of the principle. As these studies are completed and mature data emerges, the role of Bcl-2 antisense therapy in the treatment of B-cell malignancies will become clearer.

CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells.

Science.gov (United States)

Xia, Heng; Chen, Dong; Wu, Qijia; Wu, Gang; Zhou, Yanhong; Zhang, Yi; Zhang, Libin

2017-09-01

The current RIP-seq approach has been developed for the identification of genome-wide interaction between RNA binding protein (RBP) and the bound RNA transcripts, but still rarely for identifying its binding sites. In this study, we performed RIP-seq experiments in HeLa cells using a monoclonal antibody against CELF1. Mapping of the RIP-seq reads showed a biased distribution at the 3'UTR and intronic regions. A total of 15,285 and 1384 CELF1-specific sense and antisense peaks were identified using the ABLIRC software tool. Our bioinformatics analyses revealed that 5' and 3' splice site motifs and GU-rich motifs were highly enriched in the CELF1-bound peaks. Furthermore, transcriptome analyses revealed that alternative splicing was globally regulated by CELF1 in HeLa cells. For example, the inclusion of exon 16 of LMO7 gene, a marker gene of breast cancer, is positively regulated by CELF1. Taken together, we have shown that RIP-seq data can be used to decipher RBP binding sites and reveal an unexpected landscape of the genome-wide CELF1-RNA interactions in HeLa cells. In addition, we found that CELF1 globally regulates the alternative splicing by binding the exon-intron boundary in HeLa cells, which will deepen our understanding of the regulatory roles of CELF1 in the pre-mRNA splicing process. Copyright © 2017 Elsevier B.V. All rights reserved.

Developmental transitions in Arabidopsis are regulated by antisense RNAs resulting from bidirectionally transcribed genes.

Science.gov (United States)

Krzyczmonik, Katarzyna; Wroblewska-Swiniarska, Agata; Swiezewski, Szymon

2017-07-03

Transcription terminators are DNA elements located at the 3' end of genes that ensure efficient cleavage of nascent RNA generating the 3' end of mRNA, as well as facilitating disengagement of elongating DNA-dependent RNA polymerase II. Surprisingly, terminators are also a potent source of antisense transcription. We have recently described an Arabidopsis antisense transcript originating from the 3' end of a master regulator of Arabidopsis thaliana seed dormancy DOG1. In this review, we discuss the broader implications of our discovery in light of recent developments in yeast and Arabidopsis. We show that, surprisingly, the key features of terminators that give rise to antisense transcription are preserved between Arabidopsis and yeast, suggesting a conserved mechanism. We also compare our discovery to known antisense-based regulatory mechanisms, highlighting the link between antisense-based gene expression regulation and major developmental transitions in plants.

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: 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: 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: 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,

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.

Effective intracellular delivery of oligonucleotides in order to make sense of antisense

NARCIS (Netherlands)

Shi, FX; Hoekstra, D

2004-01-01

For more than two decades, antisense oligonucleotides (ODNs) have been used to modulate gene expression for the purpose of applications in cell biology and for development of novel sophisticated medical therapeutics. Conceptually, the antisense approach represents an elegant strategy, involving the

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...

Redox-mediated bypass of restriction point via skipping of G1pm

Directory of Open Access Journals (Sweden)

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.

Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa.

Directory of Open Access Journals (Sweden)

Jeferson Gross

Full Text Available RNAi (RNA interference relies on the production of small RNAs (sRNAs from double-stranded RNA and comprises a major pathway in eukaryotes to restrict the propagation of selfish genetic elements. Amplification of the initial RNAi signal by generation of multiple secondary sRNAs from a targeted mRNA is catalyzed by RNA-dependent RNA polymerases (RdRPs. This phenomenon is known as transitivity and is particularly important in plants to limit the spread of viruses. Here we describe, using a genome-wide approach, the distribution of sRNAs in the glaucophyte alga Cyanophora paradoxa. C. paradoxa is a member of the supergroup Plantae (also known as Archaeplastida that includes red algae, green algae, and plants. The ancient (>1 billion years ago split of glaucophytes within Plantae suggests that C. paradoxa may be a useful model to learn about the early evolution of RNAi in the supergroup that ultimately gave rise to plants. Using next-generation sequencing and bioinformatic analyses we find that sRNAs in C. paradoxa are preferentially associated with mRNAs, including a large number of transcripts that encode proteins arising from different functional categories. This pattern of exonic sRNAs appears to be a general trend that affects a large fraction of mRNAs in the cell. In several cases we observe that sRNAs have a bias for a specific strand of the mRNA, including many instances of antisense predominance. The genome of C. paradoxa encodes four sequences that are homologous to RdRPs in Arabidopsis thaliana. We discuss the possibility that exonic sRNAs in the glaucophyte may be secondarily derived from mRNAs by the action of RdRPs. If this hypothesis is confirmed, then transitivity may have had an ancient origin in Plantae.

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 ...

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

Directory of Open Access Journals (Sweden)

Settles Matthew L

2009-05-01

Full Text Available Abstract Background Natural antisense transcripts (NATs are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded or a different locus (trans-encoded. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept. Results By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense-antisense

Search for antisense copies of beta-globin mRNA in anemic mouse spleen

Directory of Open Access Journals (Sweden)

Taylor John M

2001-03-01

Full Text Available Abstract Background Previous studies by Volloch and coworkers have reported that during the expression of high levels of β-globin mRNA in the spleen of anemic mice, they could also detect small but significant levels of an antisense (AS globin RNA species, which they postulated might have somehow arisen by RNA-directed RNA synthesis. For two reasons we undertook to confirm and possibly extend these studies. First, previous studies in our lab have focussed on what is an unequivocal example of host RNA-directed RNA polymerase activity on the RNA genome of human hepatitis delta virus. Second, if AS globin species do exist they could in turn form double-stranded RNA species which might induce post-transcriptional gene silencing, a phenomenon somehow provoked in eukaryotic cells by AS RNA sequences. Results We reexamined critical aspects of the previous globin studies. We used intraperitoneal injections of phenylhydrazine to induce anemia in mice, as demonstrated by the appearance and ultimate disappearance of splenomegaly. While a 30-fold increase in globin mRNA was detected in the spleen, the relative amount of putative AS RNA could be no more than 0.004%. Conclusions Contrary to earlier reports, induction of a major increase in globin transcripts in the mouse spleen was not associated with a detectable level of antisense RNA to globin mRNA.

Inhaled ENaC antisense oligonucleotide ameliorates cystic fibrosis-like lung disease in mice.

Science.gov (United States)

Crosby, Jeff R; Zhao, Chenguang; Jiang, Chong; Bai, Dong; Katz, Melanie; Greenlee, Sarah; Kawabe, Hiroshi; McCaleb, Michael; Rotin, Daniela; Guo, Shuling; Monia, Brett P

2017-11-01

Epithelial sodium channel (ENaC, Scnn1) hyperactivity in the lung leads to airway surface dehydration and mucus accumulation in cystic fibrosis (CF) patients and in mice with CF-like lung disease. We identified several potent ENaC specific antisense oligonucleotides (ASOs) and tested them by inhalation in mouse models of CF-like lung disease. The inhaled ASOs distributed into lung airway epithelial cells and decreased ENaC expression by inducing RNase H1-dependent degradation of the targeted Scnn1a mRNA. Aerosol delivered ENaC ASO down-regulated mucus marker expression and ameliorated goblet cell metaplasia, inflammation, and airway hyper-responsiveness. Lack of systemic activity of ASOs delivered via the aerosol route ensures the safety of this approach. Our results demonstrate that antisense inhibition of ENaC in airway epithelial cells could be an effective and safe approach for the prevention and reversal of lung symptoms in CF and potentially other inflammatory diseases of the lung. Copyright © 2017 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

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...

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

Directory of Open Access Journals (Sweden)

Lonardi Stefano

2008-01-01

Full Text Available Abstract Background In spite of large intergenic spaces in plant and animal genomes, 7% to 30% of genes in the genomes encode overlapping cis-natural antisense transcripts (cis-NATs. The widespread occurrence of cis-NATs suggests an evolutionary advantage for this type of genomic arrangement. Experimental evidence for the regulation of two cis-NAT gene pairs by natural antisense transcripts-generated small interfering RNAs (nat-siRNAs via the RNA interference (RNAi pathway has been reported in Arabidopsis. However, the extent of siRNA-mediated regulation of cis-NAT genes is still unclear in any genome. Results The hallmarks of RNAi regulation of NATs are 1 inverse regulation of two genes in a cis-NAT pair by environmental and developmental cues and 2 generation of siRNAs by cis-NAT genes. We examined Arabidopsis transcript profiling data from public microarray databases to identify cis-NAT pairs whose sense and antisense transcripts show opposite expression changes. A subset of the cis-NAT genes displayed negatively correlated expression profiles as well as inverse differential expression changes under at least one of the examined developmental stages or treatment conditions. By searching the Arabidopsis Small RNA Project (ASRP and Massively Parallel Signature Sequencing (MPSS small RNA databases as well as our stress-treated small RNA dataset, we found small RNAs that matched at least one gene in 646 pairs out of 1008 (64% protein-coding cis-NAT pairs, which suggests that siRNAs may regulate the expression of many cis-NAT genes. 209 putative siRNAs have the potential to target more than one gene and half of these small RNAs could target multiple members of a gene family. Furthermore, the majority of the putative siRNAs within the overlapping regions tend to target only one transcript of a given NAT pair, which is consistent with our previous finding on salt- and bacteria-induced nat-siRNAs. In addition, we found that genes encoding plastid- or

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。

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.

Alzheimer's disease presenilin-1 exon 9 deletion and L250S mutations sensitize SH-SY5Y neuroblastoma cells to hyperosmotic stress-induced apoptosis

DEFF Research Database (Denmark)

Tanii, H; Ankarcrona, M; Flood, F

2000-01-01

. In the present study, we determined whether PS1 mutations also sensitize cells to hyperosmotic stress-induced apoptosis. For this, we established SH-SY5Y neuroblastoma cell lines stably transfected with wild-type PS1 or either the PS1 exon 9 deletion (deltaE9) or PS1 L250S mutants. Cultured cells were exposed...

Targeting antisense mitochondrial ncRNAs inhibits murine melanoma tumor growth and metastasis through reduction in survival and invasion factors.

Science.gov (United States)

Lobos-González, Lorena; Silva, Verónica; Araya, Mariela; Restovic, Franko; Echenique, Javiera; Oliveira-Cruz, Luciana; Fitzpatrick, Christopher; Briones, Macarena; Villegas, Jaime; Villota, Claudio; Vidaurre, Soledad; Borgna, Vincenzo; Socias, Miguel; Valenzuela, Sebastián; Lopez, Constanza; Socias, Teresa; Varas, Manuel; Díaz, Jorge; Burzio, Luis O; Burzio, Verónica A

2016-09-06

We reported that knockdown of the antisense noncoding mitochondrial RNAs (ASncmtRNAs) induces apoptotic death of several human tumor cell lines, but not normal cells, suggesting this approach for selective therapy against different types of cancer. In order to translate these results to a preclinical scenario, we characterized the murine noncoding mitochondrial RNAs (ncmtRNAs) and performed in vivo knockdown in syngeneic murine melanoma models. Mouse ncmtRNAs display structures similar to the human counterparts, including long double-stranded regions arising from the presence of inverted repeats. Knockdown of ASncmtRNAs with specific antisense oligonucleotides (ASO) reduces murine melanoma B16F10 cell proliferation and induces apoptosis in vitro through downregulation of pro-survival and metastasis markers, particularly survivin. For in vivo studies, subcutaneous B16F10 melanoma tumors in C57BL/6 mice were treated systemically with specific and control antisense oligonucleotides (ASO). For metastasis studies, tumors were resected, followed by systemic administration of ASOs and the presence of metastatic nodules in lungs and liver was assessed. Treatment with specific ASO inhibited tumor growth and metastasis after primary tumor resection. In a metastasis-only assay, mice inoculated intravenously with cells and treated with the same ASO displayed reduced number and size of melanoma nodules in the lungs, compared to controls. Our results suggest that ASncmtRNAs could be potent targets for melanoma therapy. To our knowledge, the ASncmtRNAs are the first potential non-nuclear targets for melanoma therapy.

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

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

Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

Directory of Open Access Journals (Sweden)

Hsiao Chiu-Bin

2006-11-01

Full Text Available Abstract Background While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1 long terminal repeat (LTR. Results Inspection of published sequences revealed a potential transcription initiator element (INR situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP sequences identified HAPs from HIV+ human peripheral blood lymphocytes. Conclusion HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The

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: 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 ...

Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus

DEFF Research Database (Denmark)

tang, T. H.; Polacek, N.; Zywicki, M.

2005-01-01

By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus, we have identified 57 novel small non-coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong to one of two classes, either antisense or antisense...... elements by inhibiting expression of the transposase mRNA. Surprisingly, the class of antisense RNAs also contained RNAs complementary to tRNAs or sRNAs (small-nucleolar-like RNAs). For the antisense-box ncRNAs, the majority could be assigned to the class of C/D sRNAs, which specify 2'-O-methylation sites...... on rRNAs or tRNAs. Five C/D sRNAs of this group are predicted to target methylation at six sites in 13 different tRNAs, thus pointing to the widespread role of these sRNA species in tRNA modification in Archaea. Another group of antisense-box RNAs, lacking typical C/D sRNA motifs, was predicted...

Bcl-2 antisense therapy in B-cell malignant proliferative disorders.

Science.gov (United States)

Chanan-Khan, Asher; Czuczman, Myron S

2004-08-01

Overexpression of Bcl-2 oncogene has been clinically associated with an aggressive clinical course, chemotherapy and radiotherapy resistance, and poor survival in patients with malignant B-cell disorders. Patients with relapsed or refractory chronic lymphocytic leukemia, multiple myeloma, or non-Hodgkin's lymphoma have limited therapeutic options. Preclinical and early clinical data have shown that Bcl-2 oncoprotein can be decreased by Bcl-2 antisense therapy. Also, downregulation of Bcl-2 protein can result in reversal of chemotherapy resistance and improved antitumor activity of biologic agents. Various clinical trials are evaluating the role of targeting Bcl-2 as a mechanism to enhance the antitumor potential of chemotherapy and immunotherapy. Early results from these clinical studies are encouraging and confirm the proof of principle for antisense therapy. As current data mature, these trials will hopefully validate preliminary results and establish Bcl-2 antisense as an important addition to the current armamentarium used in the treatment of patients with B-cell neoplasms.

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

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.

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.

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.

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...

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

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

Directory of Open Access Journals (Sweden)

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

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.

Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

Energy Technology Data Exchange (ETDEWEB)

Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile; Hoglund, Anna-Stina; Jansson, Christer

2008-01-15

Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos sarcoma virus could inhibit virus replication in tissue cultures of chick embryo fibroblasts. Since then the antisense ODN technology has been widely used in animal sciences and as an important emerging therapeutic approach in clinical medicine. However, antisense ODN inhibition has been an under-exploited strategy for plant tissues, although the prospects for plant cells in suspension cultures to take up single-stranded ODNs was reported over a decade ago. In 2001, two reports from Malho and coworker demonstrated the use of cationic-complexed antisense ODNs to suppress expression of genes encoding pollen

Modulation of lipoprotein metabolism by antisense technology: preclinical drug discovery methodology.

Science.gov (United States)

Crooke, Rosanne M; Graham, Mark J

2013-01-01

Antisense oligonucleotides (ASOs) are a new class of specific therapeutic agents that alter the intermediary metabolism of mRNA, resulting in the suppression of disease-associated gene products. ASOs exert their pharmacological effects after hybridizing, via Watson-Crick base pairing, to a specific target RNA. If appropriately designed, this event results in the recruitment of RNase H, the degradation of targeted mRNA or pre-mRNA, and subsequent inhibition of the synthesis of a specific protein. A key advantage of the technology is the ability to selectively inhibit targets that cannot be modulated by traditional therapeutics such as structural proteins, transcription factors, and, of topical interest, lipoproteins. In this chapter, we will first provide an overview of antisense technology, then more specifically describe the status of lipoprotein-related genes that have been studied using the antisense platform, and finally, outline the general methodology required to design and evaluate the in vitro and in vivo efficacy of those drugs.

Combination of vascular endothelial growth factor antisense oligonucleotide therapy and radiotherapy increases the curative effects against maxillofacial VX2 tumors in rabbits

Energy Technology Data Exchange (ETDEWEB)

Zheng Linfeng, E-mail: zhenglinfeng04@yahoo.com.cn [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Li Yujie, E-mail: yujieli01@yahoo.com.cn [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Wang Han, E-mail: bingowh@hotmail.com [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Zhao Jinglong, E-mail: jinglongz@yahoo.com [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Wang Xifu, E-mail: wangxiechen001@163.com [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Hu Yunsheng, E-mail: springmorninghu@163.com [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China); Zhang Guixiang, E-mail: guixiangzhang@sina.com [Department of Radiology, Shanghai First People' s Hospital, Medical College, Shanghai Jiaotong University, Hanning Road, 100, 200080 Shanghai (China)

2011-05-15

Purpose: To study the effects of combination of vascular endothelial growth factor (VEGF) antisense oligonucleotide therapy and radiotherapy on maxillofacial VX2 tumors in rabbits. Methods: We used 24 New Zealand white rabbits as a model to induce maxillofacial VX2 tumor. The rabbits were randomly divided into the following 4 groups: radiotherapy group (group A), treated with 16 Gy of radiotherapy; VEGF antisense oligonucleotide treatment group (group B), treated with an injection of 150 {mu}g of VEGF antisense oligonucleotide into the local tumor; VEGF antisense oligonucleotide combined with radiotherapy group (group C), treated with an injection of 150 {mu}g of VEGF antisense oligonucleotide into the local tumor immediately after 16 Gy of radiotherapy; and control group (group D), treated with an injection of 300 {mu}l 5% aqueous glucose solution into the local tumor. On days 3 and 14 after treatment, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was performed to calculate maximal enhancement ratio (MER), slope of enhancement (SLE), and tumor volume change. Rabbits were killed on day 14 to obtain samples for pathological examination and immunohistochemical staining for VEGF. Results: In group C, tumor volume was significantly reduced on day 14 after treatment, and the difference was statistically different as compared to that before treatment, on day 3 after treatment and other groups (P < 0.01). Values of both MER and SLE after treatment were significantly lower than the values before treatment (P < 0.05). Pathological specimen revealed tumor cell edema, bleeding, necrosis, vascular wall thickening and occlusion, and decreased VEGF expression. The immunohistochemical score (IHS) of group C was significantly different from groups A and D respectively (P < 0.05). Conclusion: Injecting the tumor with VEGF antisense oligonucleotide immediately after radiotherapy can enhance the curative effect on rabbit maxillofacial VX2 tumor, and DCE-MRI can serve

GPR39 splice variants versus antisense gene LYPD1: expression and regulation in gastrointestinal tract, endocrine pancreas, liver, and white adipose tissue

DEFF Research Database (Denmark)

Egerod, Kristoffer L; Holst, Birgitte; Petersen, Pia S

2007-01-01

nervous system as characterized with both quantitative RT-PCR and in situ hybridization analysis. A functional analysis of the GPR39 promoter region identified sites for the hepatocyte nuclear factors 1alpha and 4alpha (HNF-1alpha and -4alpha) and specificity protein 1 (SP1) transcription factors as being......G protein-coupled receptor 39 (GPR39) is a constitutively active, orphan member of the ghrelin receptor family that is activated by zinc ions. GPR39 is here described to be expressed in a full-length, biologically active seven-transmembrane form, GPR39-1a, as well as in a truncated splice variant...... five-transmembrane form, GPR39-1b. The 3' exon of the GPR39 gene overlaps with an antisense gene called LYPD1 (Ly-6/PLAUR domain containing 1). Quantitative RT-PCR analysis demonstrated that GPR39-1a is expressed selectively throughout the gastrointestinal tract, including the liver and pancreas...

A Simple Three-Step Method for Design and Affinity Testing of New Antisense Peptides: An Example of Erythropoietin

Directory of Open Access Journals (Sweden)

Nikola Štambuk

2014-05-01

Full Text Available Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense–antisense (epitope–paratope peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.

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: 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

Functional Analysis of Polyphenol Oxidases by Antisense/Sense Technology

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Jutharat Attajarusit

2007-07-01

Full Text Available Polyphenol oxidases (PPOs catalyze the oxidation of phenolics to quinones, the secondary reactions of which lead to oxidative browning and postharvest losses of many fruits and vegetables. PPOs are ubiquitous in angiosperms, are inducible by both biotic and abiotic stresses, and have been implicated in several physiological processes including plant defense against pathogens and insects, the Mehler reaction, photoreduction of molecular oxygen by PSI, regulation of plastidic oxygen levels, aurone biosynthesis and the phenylpropanoid pathway. Here we review experiments in which the roles of PPO in disease and insect resistance as well as in the Mehler reaction were investigated using transgenic tomato (Lycopersicon esculentum plants with modified PPO expression levels (suppressed PPO and overexpressing PPO. These transgenic plants showed normal growth, development and reproduction under laboratory, growth chamber and greenhouse conditions. Antisense PPO expression dramatically increased susceptibility while PPO overexpression increased resistance of tomato plants to Pseudomonas syringae. Similarly, PPO-overexpressing transgenic plants showed an increase in resistance to various insects, including common cutworm (Spodoptera litura (F., cotton bollworm (Helicoverpa armigera (Hübner and beet army worm (Spodoptera exigua (Hübner, whereas larvae feeding on plants with suppressed PPO activity had higher larval growth rates and consumed more foliage. Similar increases in weight gain, foliage consumption, and survival were also observed with Colorado potato beetles (Leptinotarsa decemlineata (Say feeding on antisense PPO transgenic tomatoes. The putative defensive mechanisms conferred by PPO and its interaction with other defense proteins are discussed. In addition, transgenic plants with suppressed PPO exhibited more favorable water relations and decreased photoinhibition compared to nontransformed controls and transgenic plants

Frame Filtering and Skipping for Point Cloud Data Video Transmission

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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.

Folding Landscape of Mutant Huntingtin Exon1: Diffusible Multimers, Oligomers and Fibrils, and No Detectable Monomer.

Directory of Open Access Journals (Sweden)

Bankanidhi Sahoo

Full Text Available Expansion of the polyglutamine (polyQ track of the Huntingtin (HTT protein above 36 is associated with a sharply enhanced risk of Huntington's disease (HD. Although there is general agreement that HTT toxicity resides primarily in N-terminal fragments such as the HTT exon1 protein, there is no consensus on the nature of the physical states of HTT exon1 that are induced by polyQ expansion, nor on which of these states might be responsible for toxicity. One hypothesis is that polyQ expansion induces an alternative, toxic conformation in the HTT exon1 monomer. Alternative hypotheses posit that the toxic species is one of several possible aggregated states. Defining the nature of the toxic species is particularly challenging because of facile interconversion between physical states as well as challenges to identifying these states, especially in vivo. Here we describe the use of fluorescence correlation spectroscopy (FCS to characterize the detailed time and repeat length dependent self-association of HTT exon1-like fragments both with chemically synthesized peptides in vitro and with cell-produced proteins in extracts and in living cells. We find that, in vitro, mutant HTT exon1 peptides engage in polyQ repeat length dependent dimer and tetramer formation, followed by time dependent formation of diffusible spherical and fibrillar oligomers and finally by larger, sedimentable amyloid fibrils. For expanded polyQ HTT exon1 expressed in PC12 cells, monomers are absent, with tetramers being the smallest molecular form detected, followed in the incubation time course by small, diffusible aggregates at 6-9 hours and larger, sedimentable aggregates that begin to build up at 12 hrs. In these cell cultures, significant nuclear DNA damage appears by 6 hours, followed at later times by caspase 3 induction, mitochondrial dysfunction, and cell death. Our data thus defines limits on the sizes and concentrations of different physical states of HTT exon1 along the

Tumor delivery of antisense oligomer using trastuzumab within a streptavidin nanoparticle

Energy Technology Data Exchange (ETDEWEB)

Wang, Yi [University of Massachusetts Medical School, Division of Nuclear Medicine, Department of Radiology, Worcester, MA (United States); Yale University, Yale PET Center, Department of Diagnostic Radiology, New Haven, CT (United States); Liu, Xinrong; Chen, Ling; Cheng, Dengfeng; Rusckowski, Mary [University of Massachusetts Medical School, Division of Nuclear Medicine, Department of Radiology, Worcester, MA (United States); Hnatowich, Donald J. [University of Massachusetts Medical School, Division of Nuclear Medicine, Department of Radiology, Worcester, MA (United States); Umass Medical School, Department of Radiology, Worcester, MA (United States)

2009-12-15

Trastuzumab (Herceptin trademark) is often internalized following binding to Her2+ tumor cells. The objective of this study was to investigate whether trastuzumab can be used as a specific carrier to deliver antisense oligomers into Her2+ tumor cells both in vitro and in vivo. A biotinylated MORF oligomer antisense to RhoC mRNA and its biotinylated sense control were labeled with either lissamine for fluorescence detection or {sup 99m}Tc for radioactivity detection and were linked to biotinylated trastuzumab via streptavidin. The nanoparticles were studied in SUM190 (RhoC+, Her2+) study and SUM149 (RhoC+, Her2-) control cells in culture and as xenografts in mice. As evidence of unimpaired Her2+ binding of trastuzumab within the nanoparticle, accumulations were clearly higher in SUM190 compared to SUM149 cells and, by whole-body imaging, targeting of SUM190 tumor was similar to that expected for a radiolabeled trastuzumab. As evidence of internalization, fluorescence microscopy images of cells grown in culture and obtained from xenografts showed uniform cytoplasm distribution of the lissamine-MORF. An invasion assay showed decreased RhoC expression in SUM190 cells when incubated with the antisense MORF nanoparticles at only 100 nM. Both in cell culture and in animals, the nanoparticle with trastuzumab as specific carrier greatly improved tumor delivery of the antisense oligomer against RhoC mRNA into tumor cells overexpressing Her2 and may be of general utility. (orig.)

Increased cell survival by inhibition of BRCA1 using an antisense approach in an estrogen responsive ovarian carcinoma cell line

International Nuclear Information System (INIS)

Annab, Lois A; Hawkins, Rebecca E; Solomon, Greg; Barrett, J Carl; Afshari, Cynthia A

2000-01-01

phosphoprotein that is regulated in response to DNA damaging agents [5,6,7] and in response to estrogen-induced growth [8,9,10,11]. Germline mutations that cause breast and ovarian cancer predisposition frequently result in truncated and presumably inactive BRCA1 protein [12]. BG-1 cells were derived from a patient with stage III, poorly differentiated ovarian adenocarcinoma [13]. This cell line, which expresses wild-type BRCA1, is estrogen responsive and withdrawal of estrogen results in eventual cell death. Previous studies suggest that BRCA1 is stimulated as a result of estrogen treatment [8,9,10,11], and also that BRCA1 may be involved in the cell death process [14]. Therefore, we examined the effect of reduction of BRCA1 levels in BG-1 cells on the cellular response to hormone depletion as well as estrogen stimulation. The results suggest that reduced levels of BRCA1 correlates with a survival advantage when BG-1 cells are placed under growth-restrictive and hormone-depleted conditions. In optimum growth conditions, significantly reduced levels of BRCA1 correlates with enhanced growth both in vitro and in vivo. To test the hypothesis that BRCA1 may play a role in the regulation of ovarian tumor cell death as well as in the inhibition of ovarian cell proliferation. The estrogen receptor-positive, BG-1 cell line [13], which contains an abundant amount of estrogen receptors (600 fmoles/100 μg DNA), was infected using a pLXSN retroviral vector (provided by AD Miller) containing an inverted partial human cDNA 900-base-pair sequence of BRCA1 (from nucleotide 121 in exon 1 to nucleotide 1025 in exon 11, accession #U14680). After 2 weeks of selection in 800 μg/ml of geneticin-G418 (Gibco/Life Technologies, Gaithersburg, MD, USA), BG-1 G418-resistant colonies were pooled, or individually isolated, and assayed for growth in the presence or absence of supplemented estrogen. Virally infected pooled populations of BG-1 cells were examined for BRCA1 message levels by ribonuclease

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...

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.

Re-sensitizing drug-resistant bacteria to antibiotics by designing Antisense Therapeutics

Science.gov (United States)

Courtney, Colleen; Chatterjee, Anushree

2014-03-01

``Super-bugs'' or ``multi-drug resistant organisms'' are a serious international health problem, with devastating consequences to patient health care. The Center for Disease Control has identified antibiotic resistance as one of the world's most pressing public health problems as a significant fraction of bacterial infections contracted are drug resistant. Typically, antibiotic resistance is encoded by ``resistance-genes'' which express proteins that carryout the resistance causing functions inside the bacterium. We present a RNA based therapeutic strategy for designing antimicrobials capable of re-sensitizing resistant bacteria to antibiotics by targeting labile regions of messenger RNAs encoding for resistance-causing proteins. We perform in silico RNA secondary structure modeling to identify labile target regions in an mRNA of interest. A synthetic biology approach is then used to administer antisense nucleic acids to our model system of ampicillin resistant Escherichia coli. Our results show a prolonged lag phase and decrease in viability of drug-resistant E. colitreated with antisense molecules. The antisense strategy can be applied to alter expression of other genes in antibiotic resistance pathways or other pathways of interest.

Brief report: Afatinib and cetuximab in four patients with EGFR exon 20 insertion positive advanced non-small-cell lung cancer.

Science.gov (United States)

van Veggel, Bianca; de Langen, Adrianus J; Hashemi, Sayed; Monkhorst, Kim; Heideman, Daniëlle A M; Thunnissen, Erik; Smit, Egbert F

2018-04-24

Epidermal growth factor receptor (EGFR) exon 20 insertions comprise 4-9% of EGFR mutated non-small-cell lung cancer (NSCLC). Despite being an oncogenic driver, they are associated with primary resistance to EGFR tyrosine kinase inhibitors (TKIs). We hypothesized that dual EGFR blockade with afatinib, an irreversible EGFR TKI, and cetuximab, a monoclonal antibody against EGFR, could induce tumor responses. Four patients with EGFR exon 20 insertion positive NSCLC were treated with afatinib 40 mg once daily and cetuximab 250-500 mg/m 2 every two weeks. All patients had stage IV adenocarcinoma of the lung harboring an EGFR exon 20 insertion mutation. Previous lines of treatment consisted of platinum doublet chemotherapy (n=4) and EGFR TKI (n=2). Three out of four patients showed a partial response according to RECIST 1.1. Median progression-free survival was 5.4 months (95% confidence interval 0.0 - 14.2 months; range 2.7 - 17.6 months). Toxicity was manageable with appropriate skin management and dose reduction being required in two patients. Dual EGFR blockade with afatinib and cetuximab may induce tumor responses in patients with EGFR exon 20 insertion positive NSCLC. Copyright © 2018. Published by Elsevier Inc.

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

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.

Functional characterization of the spf/ash splicing variation in OTC deficiency of mice and man.

Directory of Open Access Journals (Sweden)

Ana Rivera-Barahona

Full Text Available The spf/ash mouse model of ornithine transcarbamylase (OTC deficiency, a severe urea cycle disorder, is caused by a mutation (c.386G>A; p.R129H in the last nucleotide of exon 4 of the Otc gene, affecting the 5' splice site and resulting in partial use of a cryptic splice site 48 bp into the adjacent intron. The equivalent nucleotide change and predicted amino acid change is found in OTC deficient patients. Here we have used liver tissue and minigene assays to dissect the transcriptional profile resulting from the "spf/ash" mutation in mice and man. For the mutant mouse, we confirmed liver transcripts corresponding to partial intron 4 retention by the use of the c.386+48 cryptic site and to normally spliced transcripts, with exon 4 always containing the c.386G>A (p.R129H variant. In contrast, the OTC patient exhibited exon 4 skipping or c.386G>A (p.R129H-variant exon 4 retention by using the natural or a cryptic splice site at nucleotide position c.386+4. The corresponding OTC tissue enzyme activities were between 3-6% of normal control in mouse and human liver. The use of the cryptic splice sites was reproduced in minigenes carrying murine or human mutant sequences. Some normally spliced transcripts could be detected in minigenes in both cases. Antisense oligonucleotides designed to block the murine cryptic +48 site were used in minigenes in an attempt to redirect splicing to the natural site. The results highlight the relevance of in depth investigations of the molecular mechanisms of splicing mutations and potential therapeutic approaches. Notably, they emphasize the fact that findings in animal models may not be applicable for human patients due to the different genomic context of the mutations.

Hydrogel-Assisted Antisense LNA Gapmer Delivery for In Situ Gene Silencing in Spinal Cord Injury

DEFF Research Database (Denmark)

Moreno, Pedro M.D.; Ferreira, Ana R.; Salvador, Daniela

2018-01-01

)-modified AON gapmers in combination with a fibrin hydrogel bridging material to induce gene silencing in situ at a SCI lesion site. LNA gapmers were effectively developed against two promising gene targets aiming at enhancing axonal regeneration—RhoA and GSK3β. The fibrin-matrix-assisted AON delivery system......After spinal cord injury (SCI), nerve regeneration is severely hampered due to the establishment of a highly inhibitory microenvironment at the injury site, through the contribution of multiple factors. The potential of antisense oligonucleotides (AONs) to modify gene expression at different levels...

Lysine metabolism in antisense C-hordein barley grains

DEFF Research Database (Denmark)

Schmidt, Daiana; Rizzi, Vanessa; Gaziola, Salete A

2015-01-01

The grain proteins of barley are deficient in lysine and threonine due to their low concentrations in the major storage protein class, the hordeins, especially in the C-hordein subgroup. Previously produced antisense C-hordein transgenic barley lines have an improved amino acid composition, with ...

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

Simultaneous Expression from Both the Sense and Antisense Strand of the Erythropoietin Receptor Gene Mitigates Acute Lung Injury

Science.gov (United States)

2017-09-01

concept efficacy that increasing EpoR or RopE expression by cDNA delivery to lung cells in vitro enhances cytoprotection against hyperoxia-induced injury...oxidative damage, cell culture, rodent model, inhalation cDNA delivery, sense and antisense erythropoietin receptor transcripts 16. SECURITY...prevention of acute lung injury. 1-6 50% Subtask 1: Prepare plasmid cDNA of EpoR and RopE in nanoparticle formulation. 1 Completed 06.2017 Subtask 2

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.

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.

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.

Peptide nucleic acid (PNA) cell penetrating peptide (CPP) conjugates as carriers for cellular delivery of antisense oligomers

DEFF Research Database (Denmark)

Shiraishi, Takehiko; Nielsen, Peter E

2012-01-01

We have explored the merits of a novel delivery strategy for the antisense oligomers based on cell penetrating peptide (CPP) conjugated to a carrier PNA with sequence complementary to part of the antisense oligomer. The effect of these carrier CPP-PNAs was evaluated by using antisense PNA targeting......-PNA (cPNA1(7)-(D-Arg)8) and hexamer carrier decanoyl-CPP-PNA (Deca-cPNA1(6)-(D-Arg)8), respectively, without showing significant additional cellular toxicity. Most interestingly, the activity reached the same level obtained by enhancement with endosomolytic chloroquine (CQ) treatment, suggesting...... that the carrier might facilitate endosomal escape. Furthermore, 50% downregulation of luciferase expression at 60 nM siRNA was obtained using this carrier CPP-PNA delivery strategy (with CQ co-treatment) for a single stranded antisense RNA targeting normal luciferase mRNA. These results indicated that CPP...

Scientific and Regulatory Policy Committee Points-to-consider Paper*: Drug-induced Vascular Injury Associated with Nonsmall Molecule Therapeutics in Preclinical Development: Part 2. Antisense Oligonucleotides.

Science.gov (United States)

Engelhardt, Jeffery A; Fant, Pierluigi; Guionaud, Silvia; Henry, Scott P; Leach, Michael W; Louden, Calvert; Scicchitano, Marshall S; Weaver, James L; Zabka, Tanja S; Frazier, Kendall S

2015-10-01

Drug-induced vascular injury (DIVI) is a recurrent challenge in the development of novel pharmaceutical agents. In recent years, DIVI has been occasionally observed in nonhuman primates given RNA-targeting therapeutics such as antisense oligonucleotide therapies (ASOs) during chronic toxicity studies. While DIVI in laboratory animal species has been well characterized for vasoactive small molecules, and immune-mediated responses against large molecule biotherapeutics have been well described, there is little published information regarding DIVI induced by ASOs to date. Preclinical DIVI findings in monkeys have caused considerable delays in development of promising new ASO therapies, because of the uncertainty about whether DIVI in preclinical studies is predictive of effects in humans, and the lack of robust biomarkers of DIVI. This review of DIVI discusses clinical and microscopic features of vasculitis in monkeys, their pathogenic mechanisms, and points to consider for the toxicologist and pathologist when confronted with ASO-related DIVI. Relevant examples of regulatory feedback are included to provide insight into risk assessment of ASO therapies. © 2015 by The Author(s).

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

Directory of Open Access Journals (Sweden)

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.

Transfection of mouse cytotoxic T lymphocyte with an antisense granzyme A vector reduces lytic activity.

Science.gov (United States)

Talento, A; Nguyen, M; Law, S; Wu, J K; Poe, M; Blake, J T; Patel, M; Wu, T J; Manyak, C L; Silberklang, M

1992-12-15

Murine CTL have seven serine proteases, known as granzymes, in their lytic granules. Despite considerable effort, convincing evidence that these enzymes play an obligatory role in the lytic process has not been presented. To investigate the function of one of these proteases, granzyme A (GA), we utilized an antisense expression vector to lower the level of the enzyme in the cells. An expression vector containing antisense cDNA for GA and the gene for hygromycin B resistance was constructed and electroporated into the murine CTL line, AR1. Transfectants were selected based on resistance to hygromycin B, and a number of stable lines were developed. One of the antisense lines had greatly reduced levels of GA mRNA, when compared to the parental cells or to control lines transfected with the vector lacking the antisense DNA. The message levels for two other CTL granule proteins, granzyme B and perforin, were unaffected by the antisense vector. The amount of GA, as measured by enzymatic activity, was 3- to 10-fold lower in the transfectant. Most significantly, this line also consistently showed 50 to 70% lower ability to lyse nucleated target cells and to degrade their DNA. Furthermore, it exhibited 90 to 95% lower lytic activity to anti-CD3-coated SRBC. Conjugate formation with target cells, however, was normal. These data provide strong evidence that GA plays an important role in the cytolytic cycle, and that the quantity of enzyme is a limiting factor in these cytolytic cells.

Kinematic characteristics of motor patterns in rope skipping

Directory of Open Access Journals (Sweden)

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.

Review on investigations of antisense oligonucleotides with the use of mass spectrometry.

Science.gov (United States)

Studzińska, Sylwia

2018-01-01

Antisense oligonucleotides have been investigated as potential drugs for years. They inhibit target gene or protein expression. The present review summarizes their modifications, modes of action, and applications of liquid chromatography coupled with mass spectrometry for qualitative and quantitative analysis of these compounds. The most recent reports on a given topic were given prominence, while some early studies were reviewed in order to provide a theoretical background. The present review covers the issues of using ion-exchange chromatography, ion-pair reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography for the separation of antisense oligonucleotides. The application of mass spectrometry was described with regard to the ionization type used for the determination of these potential therapeutics. Moreover, the current approaches and applications of mass spectrometry for quantitative analysis of antisense oligonucleotides and their metabolites as well as their impurities during in vitro and in vivo studies were discussed. Finally, certain conclusions and perspectives on the determination of therapeutic oligonucleotides in various samples were briefly described. Copyright © 2017 Elsevier B.V. All rights reserved.

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: 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

Technetium-99m labeled antisense oligonucleotide-noninvasive tumor imaging in mice

International Nuclear Information System (INIS)

Qin, G.M.; Zhang, Y.X.; An, R.; Gao, Z.R.; Cao, W.; Cao, G.X.; Hnatowich, D.J.

2002-01-01

Single-stranded RNA and DNA oligonucleotides may be useful as radiopharmaceuticals for antisense and other in vivo applications if convenient methods for stably attaching radionuclides such as 99m Tc can be developed. The c-myc oncogene works in cooperation with other oncogenes in a variety of malignant tumors. The concentration of c-myc messenger RNA increases rapidly 30 to 50 fold during DNA synthesis, thus making it a suitable target for following the progression of malignancy by noninvasive imaging with radiolabeled antisense oligonucleotide probes. Methods: 1 Oligonucleotide Conjugation: A solution of single stranded amine-derivatized DNA (100-1000μg) was prepared at a concentration of 2 mg/ml in 0.25M sodium bicarbonate, 1 M sodium chloride, 1mM EDTA, pH8.5. 2 Oligonucleotide Labeling: A fresh 50mg/ml solution of sodium tartrate was prepared in sterile 0.5 M ammonium The ability of the labeled DNA to hybridize to its complement was analyzed by Sep-Pak column chromatography before and after the addition of the complementary DNA. 3 Biodistribution and Tumor Imaging Studies: A colony of KM mice (15-20g) were inoculated with 1x10 6 Ehrlich carcinoma tumor cells in the right thigh, and the tumors were allowed to grow for 6-7 days to a size of 1.0-1.5 cm in diameter. Biodistribution studies were performed in 32 KM mice after 50 μCi per mouse of 99m Tc-labeled oncogene probes were injected intravenously. A total of 8 mice were injected intravenously in the tail vein with 1-2 mCi of 99m Tc-labeled sense or antisense probes, immobilized with ketamine hydrochloride and imaged periodically from 0.5hr to 24hr with a gamma camera. Results: Essentially complete conjugation was achieved by reverse-phase Sep-Pak C18 chromatography analysis. The labeled antisense DNA still remained the ability to hybridize with its complementary DNA. The highest accumulation of label was in the liver first, with the kidney and small bowel next. The injected activity localized in the lesion

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.

Factor XI Antisense Oligonucleotide for Prevention of Venous Thrombosis

NARCIS (Netherlands)

Büller, Harry R.; Bethune, Claudette; Bhanot, Sanjay; Gailani, David; Monia, Brett P.; Raskob, Gary E.; Segers, Annelise; Verhamme, Peter; Weitz, Jeffrey I.; Weitz, Jeffrey; Prins, Martin; Beenen, Ludo; Otten, Hans-Martin; Roos, Yvo; Slagboom, Ton; Vandenbriele, Christophe; Vanassche, Thomas; Dani, Vidhi; Schulz, Dan; Shapiro, Cara; Kwoh, Katherine; Jung, Bill; Gawinek-Samelczak, Agata; Kaemmer, Christina; Angelov, S.; Stavrev, V.; Kinov, P.; Dessouki, E.; Abuzgaya, F.; Baurovskis, A.; Peredistijs, A.; Petronis, S.; Danilyak, V.; Driagin, V.; Kuropatkin, G.; Parfeev, S.; Safronov, A.; Ankin, M.; Korzh, M.; Olinichenko, G.; Polivoda, A.; Shevchenko, V.; Sulyma, V.

2015-01-01

Background Experimental data indicate that reducing factor XI levels attenuates thrombosis without causing bleeding, but the role of factor XI in the prevention of postoperative venous thrombosis in humans is unknown. FXI-ASO (ISIS 416858) is a second-generation antisense oligonucleotide that

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.

Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

Directory of Open Access Journals (Sweden)

Casey R Richardson

2010-05-01

Full Text Available MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery.We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes.Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non-coding RNAs in plants and potentially other

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

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.

Regulation of Peripheral Myelination through Transcriptional Buffering of Egr2 by an Antisense Long Non-coding RNA

Directory of Open Access Journals (Sweden)

Margot Martinez-Moreno

2017-08-01

Full Text Available Precise regulation of Egr2 transcription is fundamentally important to the control of peripheral myelination. Here, we describe a long non-coding RNA antisense to the promoter of Egr2 (Egr2-AS-RNA. During peripheral nerve injury, the expression of Egr2-AS-RNA is increased and correlates with decreased Egr2 transcript and protein levels. Ectopic expression of Egr2-AS-RNA in dorsal root ganglion (DRG cultures inhibits the expression of Egr2 mRNA and induces demyelination. In vivo inhibition of Egr2-AS-RNA using oligonucleotide GapMers released from a biodegradable hydrogel following sciatic nerve injury reverts the EGR2-mediated gene expression profile and significantly delays demyelination. Egr2-AS-RNA gradually recruits H3K27ME3, AGO1, AGO2, and EZH2 on the Egr2 promoter following sciatic nerve injury. Furthermore, expression of Egr2-AS-RNA is regulated through ERK1/2 signaling to YY1, while loss of Ser184 of YY1 regulates binding to Egr2-AS-RNA. In conclusion, we describe functional exploration of an antisense long non-coding RNA in peripheral nervous system (PNS biology.

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

Directory of Open Access Journals (Sweden)

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.

Divergently overlapping cis-encoded antisense RNA regulating toxin-antitoxin systems from E. coli: hok/sok, ldr/rdl, symE/symR.

Science.gov (United States)

Kawano, Mitsuoki

2012-12-01

Toxin-antitoxin (TA) systems are categorized into three classes based on the type of antitoxin. In type I TA systems, the antitoxin is a small antisense RNA that inhibits translation of small toxic proteins by binding to the corresponding mRNAs. Those type I TA systems were originally identified as plasmid stabilization modules rendering a post-segregational killing (PSK) effect on the host cells. The type I TA loci also exist on the Escherichia coli chromosome but their biological functions are less clear. Genetic organization and regulatory elements of hok/sok and ldr/rdl families are very similar and the toxins are predicted to contain a transmembrane domain, but otherwise share no detectable sequence similarity. This review will give an overview of the type I TA modules of E. coli K-12, especially hok/sok, ldr/rdl and SOS-inducible symE/symR systems, which are regulated by divergently overlapping cis-encoded antisense RNAs.

Alteration of rice growth and development via antisense expression ...

African Journals Online (AJOL)

user

OsGA20ox2 in regulating plant growth and development, we used reverse genomic approach to ... pathways. Similarly, Carmen et al. (2007) suggested that. Carrizo citrange plants have produced antisense ... universal SP6 and T7 primers to conform their reality (Sangon, ..... Optimising the tissue culture conditions for.

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...

Photodynamic antisense regulation of mRNA having a point mutation with psoralen-conjugated oligonucleotide.

Science.gov (United States)

Higuchi, Maiko; Yamayoshi, Asako; Kobori, Akio; Murakami, Akira

2008-01-01

Nucleic acid-based drugs, such as antisense oligonucleotide, ribozyme, and small interfering RNA, are specific compounds that inhibit gene expression at the post-transcriptional level. To develop more effective nucleic acid-based drugs, we focused on photo-reactive antisense oligonucleotides. We have optimized the structure of psoralen-conjugated oligonucleotide to improve their sequence selectivity and photo-crosslinking efficiency. Previously, we reported that photo reactive oligonucleotides containing 2'-O-psoralenyl-methoxyethyl adenosine (2'-Ps-eom) showed drastic photo-reactivity with a strictly sequence specific manner in vitro. In this report, we evaluated the binding ability toward intracellular target mRNA. The 2'-Ps-eom selectively photo-cross-linked to the target mRNA extracted from cells. The 2'-Ps-eom also cross-linked to target mRNA in cells. Furthermore, 2'-Ps-eom did not cross-link to mRNA having a mismatch base. These results suggest that 2'-Ps-eom is a powerful antisense molecule to inhibit the expression of mRNA having a point mutation.

Cellular delivery and antisense effects of peptide nucleic acid conjugated to polyethyleneimine via disulfide linkers

DEFF Research Database (Denmark)

Berthold, Peter R; Shiraishi, Takehiko; Nielsen, Peter E

2010-01-01

Peptide nucleic acid (PNA) is potentially an attractive antisense and antigene agent for which more efficient cellular delivery systems are still warranted. The cationic polymer polyethylenimine (PEI) is commonly used for cellular transfection of DNA and RNA complexes, but is not readily applicable...... moiety) and further reacted this with a cysteine PNA. The level of modification was determined spectrophotometrically with high accuracy, and the PNA transfection efficiency of the conjugates was evaluated in an antisense luciferase splice-correction assay using HeLa pLuc705 cells. We find that PEI...... is an efficient vector for PNA delivery yielding significantly higher (up to 10-fold) antisense activity than an analogous PNA-octaarginine conjugate, even in the presence of chloroquine, which only slightly enhances the PEI-PNA activity. The PEI-PEG conjugates are preferred due to lower acute cellular toxicity...

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.

Transcript-specific effects of adrenalectomy on seizure-induced BDNF expression in rat hippocampus

DEFF Research Database (Denmark)

Lauterborn, J C; Poulsen, F R; Stinis, C T

1998-01-01

Activity-induced brain-derived neurotrophic factor (BDNF) expression is negatively modulated by circulating adrenal steroids. The rat BDNF gene gives rise to four major transcript forms that each contain a unique 5' exon (I-IV) and a common 3' exon (V) that codes for BDNF protein. Exon-specific i......Activity-induced brain-derived neurotrophic factor (BDNF) expression is negatively modulated by circulating adrenal steroids. The rat BDNF gene gives rise to four major transcript forms that each contain a unique 5' exon (I-IV) and a common 3' exon (V) that codes for BDNF protein. Exon...... and in exon II-containing mRNA with 30-days survival. In the dentate gyrus granule cells, adrenalectomy markedly potentiated increases in exon I and II cRNA labeling, but not increases in exon III and IV cRNA labeling, elicited by one hippocampal afterdischarge. Similarly, for the granule cells and CA1...... no effect on exon IV-containing mRNA content. These results demonstrate that the negative effects of adrenal hormones on activity-induced BDNF expression are by far the greatest for transcripts containing exons I and II. Together with evidence for region-specific transcript expression, these results suggest...

Role of natural antisense transcripts pertaining to tumor suppressor genes in human carcinomas

International Nuclear Information System (INIS)

Pelicci, G.; Pierotti, M.

2009-01-01

Overlapping transcripts in opposite orientations can potentially form perfect sense-antisense duplex RNA. Recently, several studies have revealed the extent of natural antisense transcripts (NATs) and their role in important biological phenomena also in higher organisms. In order to test the hypothesis that the function of NATs in man might represent an essential element in the regulation of gene expression, especially at transcriptional level, in this study we planned to look for, systematically examine, and characterize NATs belonging in the human genome to the tumour suppressor class of genes, so to identify physiological (and potentially pathological) modulators in this gene class

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.

Antisense RNA: a genetic approach to cell resistance against Parvovirus; RNA antisentido: una aproximacion de resistencia genetica a Parvovirus

Energy Technology Data Exchange (ETDEWEB)

Ramirez Martinez, J.C.

1992-12-31

The Minute Virus of Mice (MVMp), an autonomous Parvovirus that replicates cytolytically in the A9 mouse fibroblast cell line, was interfered by constitutive expression of an antisense RNA targeted against the major non-structural NS-1 protein. Permanently transfected A9 clones expressing NS-1 antisense, showed increased proliferative capacity upon virus infection, and likewise cultures infected at low multiplicity by MVMp reached confluence overcoming virus growth. Correspondingly, an inhibition in virus multiplication was demonstrated by a significant lower virus production and plaque forming ability in clones expressing antisense RNa. At the molecular level, several fold reduction in viral DNA, RNA and proteins was quantitated by respective analysis of Southern, RNase protection and bidimensional gels. Remarkably, the accumulation of all three viral messengers(R1,R2,R3) was decreased both in the cytoplasm and in the nucleus, suggesting that antisense-mediated inhibition is primarily exerted at the level of viral transcription or nuclear post-transcriptional events. Thus, this system illustrates the possibility to create an antisense-mediated protective stage to highly cytotoxic viruses in permissive cells, by down-modulation the expression of a transactivator of virus genes. (author)180 refs., 25 figs.

Antisense RNA: a genetic approach to cell resistance against Parvovirus. RNA antisentido: una aproximacion de resistencia genetica a Parvovirus

Energy Technology Data Exchange (ETDEWEB)

Ramirez Martinez, J.C.

1992-01-01

The Minute Virus of Mice (MVMp), an autonomous Parvovirus that replicates cytolytically in the A9 mouse fibroblast cell line, was interfered by constitutive expression of an antisense RNA targeted against the major non-structural NS-1 protein. Permanently transfected A9 clones expressing NS-1 antisense, showed increased proliferative capacity upon virus infection, and likewise cultures infected at low multiplicity by MVMp reached confluence overcoming virus growth. Correspondingly, an inhibition in virus multiplication was demonstrated by a significant lower virus production and plaque forming ability in clones expressing antisense RNa. At the molecular level, several fold reduction in viral DNA, RNA and proteins was quantitated by respective analysis of Southern, RNase protection and bidimensional gels. Remarkably, the accumulation of all three viral messengers(R1,R2,R3) was decreased both in the cytoplasm and in the nucleus, suggesting that antisense-mediated inhibition is primarily exerted at the level of viral transcription or nuclear post-transcriptional events. Thus, this system illustrates the possibility to create an antisense-mediated protective stage to highly cytotoxic viruses in permissive cells, by down-modulation the expression of a transactivator of virus genes. (author)180 refs., 25 figs.

Encapsulation of c-myc antisense oligodeoxynucleotides in lipid particles improves antitumoral efficacy in vivo in a human melanoma line.

Science.gov (United States)

Leonetti, C; Biroccio, A; Benassi, B; Stringaro, A; Stoppacciaro, A; Semple, S C; Zupi, G

2001-06-01

Phosphorothioate c-myc antisense oligodeoxynucleotides [S]ODNs (free INX-6295) were encapsulated in a new liposome formulation and the antitumor activity was compared to the unencapsulated antisense in a human melanoma xenograft. The systemic administration of INX-6295 encapsulated in stabilized antisense lipid particles (SALP INX-6295) improved plasma AUC (area under the plasma concentration-time curve) and initial half-life of free INX-6295, resulting in a significant enhancement in tumor accumulation and improvement in tumor distribution of antisense oligodeoxynucleotides. Animals treated with SALP INX-6295 exhibited a prolonged reduction of c-myc expression, reduced tumor growth and increased mice survival. When administered in combination with cisplatin (DDP), SALP INX-6295 produced a complete tumor regression in approximately 30% of treated mice, which persisted for at least 60 days following the first cycle of treatment. Finally, the median survival of mice treated with DDP/SALP INX-6295 increased by 105% compared to 84% for animals treated with the combination DDP/free INX-6295. These data indicate that the biological activity and the therapeutic efficacy of c-myc antisense therapy may be improved when these agents are administered in lipid-based delivery systems.

Effective photo-enhancement of cellular activity of fluorophore-octaarginine antisense PNA conjugates correlates with singlet oxygen formation, endosomal escape and chromophore lipophilicity

DEFF Research Database (Denmark)

Yarani, Reza; Shiraishi, Takehiko; Nielsen, Peter E.

2018-01-01

Photochemical internalization (PCI) is a cellular drug delivery method based on the generation of light-induced reactive oxygen species (ROS) causing damage to the endosomal membrane and thereby resulting in drug release to the cytoplasm. In our study a series of antisense fluorophore octaarginin...... indicate that efficient photodynamic endosomal escape is strongly dependent on the quantum yield for photochemical singlet oxygen formation, photostability as well as the lipophilicity of the chromophore....

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: 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.

Antisense silencing of the creA gene in Aspergillus nidulans

DEFF Research Database (Denmark)

Bautista, L. F.; Aleksenko, Alexei Y.; Hentzer, Morten

2000-01-01

Antisense expression of a portion of the gene encoding the major carbon catabolite repressor CREA in Aspergillus nidulans resulted in a substantial increase in the levels of glucose-repressible enzymes, both endogenous and heterologous, in the presence of glucose. The derepression effect was appr...

Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

Directory of Open Access Journals (Sweden)

Xiaolong Wang

Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools

Science.gov (United States)

Soukarieh, Omar; Gaildrat, Pascaline; Hamieh, Mohamad; Drouet, Aurélie; Baert-Desurmont, Stéphanie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra

2016-01-01

The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient’s RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants), including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs). We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZEI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases. PMID:26761715

Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools.

Directory of Open Access Journals (Sweden)

Omar Soukarieh

2016-01-01

Full Text Available The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient's RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants, including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs. We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZEI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases.

BC047440 antisense eukaryotic expression vectors inhibited HepG2 cell proliferation and suppressed xenograft tumorigenicity

International Nuclear Information System (INIS)

Lu, Zheng; Ping, Liang; JianBo, Zhou; XiaoBing, Huang; Yu, Wen; Zheng, Wang; Jing, Li

2012-01-01

The biological functions of the BC047440 gene highly expressed by hepatocellular carcinoma (HCC) are unknown. The objective of this study was to reconstruct antisense eukaryotic expression vectors of the gene for inhibiting HepG 2 cell proliferation and suppressing their xenograft tumorigenicity. The full-length BC047440 cDNA was cloned from human primary HCC by RT-PCR. BC047440 gene fragments were ligated with pMD18-T simple vectors and subsequent pcDNA3.1(+) plasmids to construct the recombinant antisense eukaryotic vector pcDNA3.1(+)BC047440AS. The endogenous BC047440 mRNA abundance in target gene-transfected, vector-transfected and naive HepG 2 cells was semiquantitatively analyzed by RT-PCR and cell proliferation was measured by the MTT assay. Cell cycle distribution and apoptosis were profiled by flow cytometry. The in vivo xenograft experiment was performed on nude mice to examine the effects of antisense vector on tumorigenicity. BC047440 cDNA fragments were reversely inserted into pcDNA3.1(+) plasmids. The antisense vector significantly reduced the endogenous BC047440 mRNA abundance by 41% in HepG 2 cells and inhibited their proliferation in vitro (P < 0.01). More cells were arrested by the antisense vector at the G 1 phase in an apoptosis-independent manner (P = 0.014). Additionally, transfection with pcDNA3.1(+) BC047440AS significantly reduced the xenograft tumorigenicity in nude mice. As a novel cell cycle regulator associated with HCC, the BC047440 gene was involved in cell proliferation in vitro and xenograft tumorigenicity in vivo through apoptosis-independent mechanisms

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

Directory of Open Access Journals (Sweden)

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