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Spliceosome-mediated RNA trans-splicing has become an emergent tool for the repair of mutated pre-mRNAs in the treatment of genetic diseases. RNA trans-splicing molecules (RTMs) are designed to induce a specific trans-splicing reaction via a binding domain for a respective target pre-mRNA region. A previously established reporter-based screening system allows us to analyze the impact of various factors on the RTM trans-splicing efficiency in vitro. Using this system, we are further able to investigate the potential of antisense RNAs (AS RNAs), presuming to improve the trans-splicing efficiency of a selected RTM, specific for intron 102 of COL7A1. Mutations in the COL7A1 gene underlie the dystrophic subtype of the skin blistering disease epidermolysis bullosa (DEB). We have shown that co-transfections of the RTM and a selected AS RNA, interfering with competitive splicing elements on a COL7A1-minigene (COL7A1-MG), lead to a significant increase of the RNA trans-splicing efficiency. Thereby, accurate trans-splicing between the RTM and the COL7A1-MG is represented by the restoration of full-length green fluorescent protein GFP on mRNA and protein level. This mechanism can be crucial for the improvement of an RTM-mediated correction, especially in cases where a high trans-splicing efficiency is required.

We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3' splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

Genetic disorders affecting the skin, genodermatoses, constitute a large and heterogeneous group of diseases, for which treatment is generally limited to management of symptoms. RNA-based therapies are emerging as a powerful tool to treat genodermatoses. In this review, we discuss in detail RNA splicing modulation by antisense oligonucleotides and RNA trans-splicing, transcript replacement and genome editing by in vitro-transcribed mRNAs, and gene knockdown by small interfering RNA and anti-sense oligonucleotides. We present the current state of these therapeutic approaches and critically discuss their opportunities, limitations and the challenges that remain to be solved. The aim of this review was to set the stage for the development of new and better therapies to improve the lives of patients and families affected by a genodermatosis.

A fast and validated supercritical fluid chromatography method for the quantitative determination of major lactones in Piper methysticum, a plant used against nervous anxiety, stress, and restlessness, was developed. The baseline separation of dihydrokavain, demethoxyyangonin, kavain, yangonin, dihydromethysticin, and methysticin was possible in less than 4 min on an Aquity UPC2 BEH 1.7 µm column, in combination with a mobile phase comprising CO2 and methanol with diethylamine. The column temperature had a great impact on the results because only at 70 °C could kavain and yangonin be fully resolved. With correlation coefficients above 0.998, recovery rates between 95.9 and 104.1 % as well as limit of detection values below 1.5 ng on-column, the procedure fulfilled all validation requirements and was well suited for the quantitative analysis of commercial products containing P. methysticum root powder and/or extract. All of them contained the target analytes, however, the absolute content of lactones was quite variable. Accordingly, depending on the product, the total daily intake of lactones varied from 56 to 312 mg. Concerning speed, selectivity, and environmental friendly operation, this supercritical fluid chromatography approach surpasses all previously reported ones.

The analysis of natural products is a challenging task, because the investigated matrices are usually complex, relevant compounds are sometimes present in small amounts, and they often show similar structures. Thus only techniques fulfilling high demands with respect to selectivity, versatility, and sensitivity will be suitable for their analysis especially in real-life samples. That SFC is such a technique is shown in this chapter. The number of relevant applications is still on a manageable level; however, analytes successfully studied by SFC range from alkaloids to carotenoids, phenols, anthraquinones, terpenes, and steroids. The described technical variability is impressive and not limited to the mobile or stationary phase only, but also includes detectors like MS, NMR, and FTIR or the hyphenation to GC and UPLC. The analysis of natural products by SFC is an interesting option, whose relevance will definitely increase in the future.

We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

(VLID)2704563

Social media has become an important part of the lives of their hundreds of millions of users. Hackers make use of the large target audience by sending malicious content, often by hijacking existing accounts. This phenomenon has caused widespread research on how to detect hacked accounts, where different approaches exist. This work sets out to analyze the possibilities of including the reactions of hacked Twitter accounts’ peers into a detection system. Based on a dataset of six million tweets crawled from Twitter over the course of two years, we select a subset of tweets in which users react to alleged hacks of other accounts. We then gather and analyze the responses to those messages to reconstruct the conversations made. A quantitative analysis of these conversations shows that 30% of the users that are allegedly being hacked reply to the accusations, suggesting that these users acknowledge that their account was hacked.

submitted by Michaela Murauer, BSc. Universität Linz, Masterarbeit, 2017

In the treatment of genetic disorders, repairing defective pre-mRNAs by RNA trans-splicing has become an emerging alternative to conventional gene therapy. Previous studies have made clear that the design of the binding domains of the corrective RNA trans-splicing molecules (RTMs) is crucial for their optimal functionality. We established a reporter-based screening method that allows for selection of highly functional RTMs from a large pool of variants. The efficiency and functionality of the screen were validated in the COL7A1 gene, in which mutations are the cause of the skin disease dystrophic epidermolysis bullosa. Comparison of RTMs containing different binding domains hybridizing to COL7A1 intron 64/exon 65 revealed highly different trans-splicing efficiencies. Isolated RTMs were then adapted for endogenous trans-splicing in a recessive dystrophic epidermolysis bullosa (RDEB) keratinocyte cell line expressing reduced levels of COL7A1 mRNA. Our results confirm the applicability and relevance of prescreening reporter RTMs, as significant levels of endogenous COL7A1 mRNA repair were seen with RTMs identified as being highly efficient in our screening system.

The fact that supercritical fluid chromatography (SFC) offers many desirable features is known for a long time. Yet, the number of applications on natural products is still limited, because robust and user-friendly instrumentation became available just a few years ago. As coumarins hardly have been studied by this technique we developed the first SFC assay for their determination in crude plant material. After method optimization eight standard compounds, including simple coumarins, linear and angular furanocoumarins, could be baseline separated in 6min using an Acquity UPC(2) CSH Fluoro-Phenyl 1.7μm column with supercritical CO2, methanol and diethylamine as mobile phase. Method validation confirmed that the assay is linear (R(2)≥0.9995), precise (intra-day variation≤5.8%; inter-day variation≤4.4%) and accurate (recovery rates from 96.5 to 104.2%). Detection limits determined at 300nm were below 2ng on-column, and the method showed to be well suited for the analysis of coumarins in Angelica dahurica roots. It was observed that qualitative as well as quantitative composition vary significantly. In all samples Imperatorin (0.09-0.28%) was the major coumarin, followed either by Isoimperatorin or Oxypeucedanin; the total coumarin content ranged from 0.16 to 0.77%. The results were in good agreement to published data, so that because of its speed and green nature SFC is definitely an interesting alternative for the analysis of this important class of natural products.

Fur ein konkretes Projekt der Entwickhmgszusammenarbeit (EZA) in einer Region am Rande der Sahelzone wird ein Simulationsmodell des Typs System Dynamics vorgestellt. Die praktischen Probleme des Modellbildungsprozesses werden reflektiert. Mit diesem Modell werden verschiedene Strategien der EZA durchgerechnet und deren Ergebnisse diskutiert. Dabei werden die Ergebnisse sowohl unter dem Gesichtspunkt der inharenten Probleme und Grenzen von Simulationsverfahren erortert als auch zu den Grenzen der Moglichkeiten der EZA, wie sie von NGOs getatigt wird, in Bezug gesetzt.

Spliceosome-mediated RNA trans-splicing (SMaRT) is an RNA-based technology to reprogram genes for diagnostic and therapeutic purposes. For the correction of genetic diseases, SMaRT offers several advantages over traditional gene-replacement strategies. SMaRT protocols have recently been used for in vitro phenotypic correction of a variety of genetic disorders, ranging from epidermolysis bullosa to neurodegenerative diseases. In vivo studies are currently bringing trans-splicing RNA therapy toward clinical application. In this review, we summarize the progress made toward the medical use of SMaRT and provide an outlook on its upcoming applications.

Patients suffering from recessive dystrophic epidermolysis bullosa (RDEB), a hereditary blistering disease of epithelia, show susceptibility to develop highly aggressive squamous cell carcinoma (SCC). Tumors metastasize early and are associated with mortality in the 30th–40th years of life in this patient group. So far, no adequate therapy is available for RDEB SCC. An approach is suicide gene therapy, in which a cell death-inducing agent is introduced to cancer cells. However, lack of specificity has constrained clinical application of this modality. Therefore, we used spliceosome-mediated RNA trans-splicing technology, capable of replacing a tumor-specific transcript with one encoding a cell death-inducing peptide/toxin, to provide tumor-restricted expression. We designed 3′ pre–trans-splicing molecules (PTM) and evaluated their efficiency to trans-splice an RDEB SCC-associated target gene, the matrix metalloproteinase-9 (MMP9), in a fluorescence-based test system. A highly efficient PTM was further adapted to insert the toxin streptolysin O (SLO) of Streptococcus pyogenes into the MMP9 gene. Transfection of RDEB SCC cells with the SLO-PTM resulted in cell death and induction of toxin function restricted to RDEB SCC cells. Thus, RNA trans-splicing is a suicide gene therapy approach with increased specificity to treat highly malignant SCC tumors. Mol Cancer Ther; 10(2); 233–41. ©2011 AACR.

Purpose: The objective of the study was to determine whether the various breast biopsy procedures specified in the S3 guidelines are sensibly represented within the current German health system as considered from a cost evaluation perspective. Materials and Methods: This prospectively designed multicenter study analyzed 221 breast biopsies at 7 institutions from 04/2006 to 01/2007. Core needle biopsies, vacuum-assisted biopsies and surgical open biopsies under sonographic or mammographic guidance were evaluated. During an analysis of process costs, the individual process steps were recorded in diagrammatic form and assigned to the true consumption of resources. The actual resource consumption costs were entered. A process-related breakeven analysis was conducted to check whether the reimbursement of individual biopsy types covers the costs. Results: Only sonographically guided core needle biopsy and surgical open biopsy are adequately reimbursed in the current German health system. All other breast biopsies indicate a negative profit margin. The principal reasons for underfunding are found in the area of reimbursement of investment and non-personnel costs. Conclusion: The reimbursement of breast biopsies must be improved in order to guarantee nationwide care of the population using the breast biopsy methods recommended in the S3 guidelines and to avoid disincentives with respect to breast biopsy indications.

The major challenge to a successful gene therapy of autosomal dominant genetic diseases is a highly efficient and specific knock-down or repair of the disease-causing allele. In epidermolysis bullosa simplex-type Dowling-Meara (EBS-DM), a single amino acid exchange in exon 1 of the keratin 14 gene (K14) triggers a severe skin phenotype, characterized by blistering of the skin and mucous membranes after minor trauma. We chose spliceosome-mediated RNA trans-splicing to specifically replace exons 1-7 of the K14 gene. In this approach, the mutated coding region is replaced by an RNA-trans-splicing molecule (RTM) that incorporates a binding domain (BD) and the wild-type sequence of K14. Since the BD is crucial for the trans-splicing functionality, we developed a fluorescence-based RTM screen consisting of an RTM library containing random BDs. Co-transfection of the library with a target molecule enabled us to identify highly functional RTMs. The best RTMs were adapted for endogenous trans-splicing in an EBS-DM patient cell line. In this cell line, we were able to detect functional, efficient and correct trans-splicing on RNA and protein levels. Scratch assays confirmed phenotypic reversion in vitro. Owing to concomitant knock-down and repair of the mutated allele, we assume that trans-splicing is a promising tool for the treatment of autosomal dominant genetic disease.

Wafer bonding behavior of plasma activated Si and SiO2 surfaces was investigated. Process evaluation was performed by various experiments. Surface energy of wafer pairs bonded after different storage times at room temperature and after thermal annealing at 300oC was investigated as a measure of surface activation lifetime. Plasma activation was studied also for room temperature storage of pre-bonded pairs, as well as for low temperature annealing (50{degree sign}C) of the bonded pairs. The effect of the plasma treatment on the surface microroughness was studied. The quality of the bonded interfaces was explored by TEM cross section analysis.