317 research outputs found
AGenDA: gene prediction by cross-species sequence comparison
No full textTaher L, Rinner O, Garg S, Sczyrba A, Morgenstern B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 2004;32(Web Server):W305-W308.Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/
Characterization of Ti-6A2-4V modified by nitrogen plasma immersion ion implantation
No full textCharacterization of Ti-6A2-4V modified by nitrogen plasma immersion ion implantation / M. Rinner ... - In: Surface and coatings technology. 93. 1997. S. 305-30
AGenDA: homology-based gene prediction
No full textTaher L, Rinner O, Garg S, et al. AGenDA: homology-based gene prediction. BIOINFORMATICS. 2003;19(12):1575-1577.We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment
Multi-camera object tracking using surprisal observations in visual sensor networks
No full textIn this work, we propose a multi-camera object tracking method with surprisal observations based on the cubature information filter in visual sensor networks. In multi-camera object tracking approaches, multiple cameras observe an object and exchange the object’s local information with each other to compute the global state of the object. The information exchange among the cameras suffers from certain bandwidth and energy constraints. Thus, allowing only a desired number of cameras with the most informative observations to participate in the information exchange is an efficient way to meet the stringent requirements of bandwidth and energy. In this paper, the concept of surprisal is used to calculate the amount of information associated with the observations of each camera. Furthermore, a surprisal selection mechanism is proposed to facilitate the cameras to take independent decision on whether their observations are informative or not. If the observations are informative, the cameras calculate the local information vector and matrix based on the cubature information filter and transmit them to the fusion center. These cameras are called as surprisal cameras. The fusion center computes the global state of the object by fusing the local information from the surprisal cameras. Moreover, the proposed scheme also ensures that on average, only a desired number of cameras participate in the information exchange. The proposed method shows a significant improvement in tracking accuracy over the multi-camera object tracking with randomly selected or fixed cameras for the same number of average transmissions to the fusion cente
Extracellular vesicles enhance the targeted delivery of immunogenic oncolytic adenovirus and paclitaxel in immunocompetent mice
No full textExtracellular vesicles (EVs), are naturally occurring cargo delivery tools with the potential to be used as drug vehicles of single agents or combination therapies. We previously demonstrated that human lung cancer cell-derived EVs could be used for the systemic delivery of oncolytic virus (OVs) and chemotherapy drugs such as paclitaxel (PTX), leading to enhanced anti-tumor effects in nude mice. In the current work, we evaluated the biodistribution of EVs by using bioluminescence and fluorescence imaging technologies, thus proving the ability of these EVs-formulations to specifically target the neoplasia, while leaving other body tissues unaffected. Moreover, in vivo imaging of NFκB activation in an immunocompetent reporter mouse model allowed to demonstrate the selective ability of EVs to induce tumor-associated inflammatory reactions, which are characterized by immunogenic cell death and CD3+/CD4+/CD8+ T-cell infiltration. While EVs have the potential to induce a systemic immune reaction by pro-inflammatory cytokines, our study provides compelling evidences of a localized inflammatory effect in the peritumoral area. Collectively, our findings strongly support the systemic administration of EVs formulations with OVs alone or in combination with chemotherapy agents as a novel strategy aimed at treating primary and metastatic cancers
Selectivity of the (S)-oxynitrilase from Hevea brasiliensis towards α- and β-substituted aldehydes
No full textThe performance of (S)-oxynitrilase from Hevea brasiliensis (HbHNL) has been investigated with several α- and β-substituted alkyl or alkoxy aldehydes and the results have been compared to the data previously obtained with the (R)-specific enzyme from almonds (PaHNL). With both enzymes there was no chiral discrimination between the enantiomers of the racemic substrates, therefore this reaction cannot be used as a preparative method to achieve both the kinetic resolution of the starting racemic aldehyde and the production of diastereomerically pure (or enriched) cyanohydrins. Additionally, in comparison with the (R)-PaHNL the (S)-selective enzyme from Hevea gave products with higher de, but was more negatively effected by oxygenated substituents
Supplementary_Table_1__2 – Supplemental material for A 3-Dimensional In Vitro Model of Zonally Organized Extracellular Matrix
No full textSupplemental material, Supplementary_Table_1__2 for A 3-Dimensional In Vitro Model of Zonally Organized Extracellular Matrix by Sonja M. Walzer, Stefan Toegel, Catharina Chiari, Sebastian Farr, Beate Rinner, Annelie-Martina Weinberg, Daniela Weinmann, Michael B. Fischer and Reinhard Windhager in CARTILAGE</p
MiR-4646-5p Acts as a Tumor-Suppressive Factor in Triple Negative Breast Cancer and Targets the Cholesterol Transport Protein GRAMD1B
No full textMicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression, and their deregulation contributes to many aspects of cancer development and progression. Thus, miRNAs provide insight into oncogenic mechanisms and represent promising targets for new therapeutic approaches. A type of cancer that is still in urgent need of improved treatment options is triple negative breast cancer (TNBC). Therefore, we aimed to characterize a novel miRNA with a potential role in TNBC. Based on a previous study, we selected miR-4646-5p, a miRNA with a still unknown function in breast cancer. We discovered that higher expression of miR-4646-5p in TNBC patients is associated with better survival. In vitro assays showed that miR-4646-5p overexpression reduces growth, proliferation, and migration of TNBC cell lines, whereas inhibition had the opposite effect. Furthermore, we found that miR-4646-5p inhibits the tube formation ability of endothelial cells, which may indicate anti-angiogenic properties. By whole transcriptome analysis, we not only observed that miR-4646-5p downregulates many oncogenic factors, like tumor-promoting cytokines and migration- and invasion-related genes, but were also able to identify a direct target, the GRAM domain-containing protein 1B (GRAMD1B). GRAMD1B is involved in cellular cholesterol transport and its knockdown phenocopied the growth-reducing effects of miR-4646-5p. We thus conclude that GRAMD1B may partly contribute to the diverse tumor-suppressive effects of miR-4646-5p in TNBC
Exon discovery by genomic sequence alignment.
No full textMotivation: During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating ‘junk DNA’ so local sequence similarity often indicates biological functionality. This fact can be used to identify functional elements in large eukaryotic DNA sequences by cross-species sequence comparison. In recent years, several gene-prediction methods have been proposed that work by comparing anonymous genomic sequences, for example from human and mouse. The main advantage of these methods is that they are based on simple and generally applicable measures of (local) sequence similarity; unlike standard gene-finding approaches they do not depend on species-specific training data or on the presence of cognate genes in data bases. As all comparative sequence-analysis methods, the new comparative gene-finding approaches critically rely on the quality of the underlying sequence alignments. Results: Herein, we describe a new implementation of the sequence-alignment program DIALIGN that has been developed for alignment of large genomic sequences. We compare our method to the alignment programs PipMaker, WABA and BLAST and we show that local similarities identified by these programs are highly correlated to protein-coding regions. In our test runs, PipMaker was the most sensitive method while DIALIGN was most specific
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