35 results on '"Rot G"'
Search Results
2. The TIA1/TIAL1 and TDP-43 proteins regulate alternative polyA site selection and thereby mRNA isoform expression: SW01.S2–33
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Modic, M., Rot, G., Lence, T., Attig, J., and Ule, J.
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- 2013
3. Charging technology for modern electric-arc furnaces
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Burgmann, W., Lur'e, W., and Rot, G. -L.
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- 1999
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4. Substantiation of a noninvasive method of administration of drugs at the prelymphatic level
- Author
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Pedder, V. V., Grigor’ev, V. N., Rot, G. Z., Afanas’ev, V. P., Novikov, A. A., Letyagin, A. Yu., and Shkuro, Yu. V.
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- 1998
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5. A system for collecting, processing, archiving, and transmitting X-ray images
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Alekseev, L. V., Antonov, A. O., Antonov, O. S., Burnashov, N. A., Duntau, A. P., Rot, G. Z., Spektor, B. I., Tret'yakov, V. P., Fetisov, Yu. I., Shtark, M. B., and Yarokhno, V. I.
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- 1997
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6. USE OF A 3' RNA SEQUENCING APPROACH TO DETERMINE DIFFERENTIAL TRANSCRIPT EXPRESSION AND ALTERNATIVE POLYADENYLATION SITE USAGE BETWEEN AGE MATCHED, HEALTHY AND OSTEOARTHRITIC KNEE CARTILAGE.
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Winstanley-Zarach, P., Kuba, S., Smagul, A., Peffers, M.J., Rot, G., and Tew, S.R.
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- 2022
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7. THE REVENUE ACT OF 1932.
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Blakey, Rot G. and Blakey, Gladys C.
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REVENUE ,UNITED States federal budget ,ADMINISTRATIVE acts ,TAXATION ,FINANCE ,GOLD standard ,COMMERCIAL policy - Abstract
The Treasury deficit resulting from the prolonged depression brought to the U.S. Congress of 1931-32 the problem of balancing the budget in order to maintain national credit. The annual report of the Treasury, submitted In December, 1931, stated actual and prospective deficits and proposed additional revenues and a reduction of expenditures to meet the situation. The report was supplemented by similar statements before the House Ways and Means Committee in January, 1932 and before the Senate Finance Committee in April, 1932, each successive estimate indicating larger deficits and lower yields from revenue measures. The Revenue act of 1932 is the result of an attempt to balance the federal budget and to maintain the national credit. The current depression had brought a Treasury deficit of $900,000,000 for the fiscal year ending June 30, 1931 and threatened larger deficits for 1932 and 1933. Despite the efforts to keep the tariff issue out of the revenue bill, it got in early and stayed in till the last. It increased the log-rolling tactics and delayed procedure with the revenue bill, in spite of the appeals for haste to balance the budget in order to arrest the financial panic and to restore confidence in the gold standard of the United States.
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- 1932
8. dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
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Rot Gregor, Parikh Anup, Curk Tomaz, Kuspa Adam, Shaulsky Gad, and Zupan Blaz
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.
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- 2009
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9. 1038 Increased prevalence of aortic valve calcification and stenosis in patients with left ventricular hypertrophy and dynamic outflow tract obstruction
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Monakier, D., Paz, R., Shapira, Y., Weisenberg, D., Vaturi, M., Rot, G., Battler, A., and Sagie, A.
- Abstract
An abstract of the article "Increased prevalence of aortic valve calcification and stenosis in patients with left ventricular hypertrophy and dynamic outflow tract obstruction," by D. Monakier and colleagues is presented.
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- 2006
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10. The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.
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Mangilet AF, Weber J, Schüler S, Adler M, Mjema EY, Heilmann P, Herold A, Renneberg M, Nagel L, Droste-Borel I, Streicher S, Schmutzer T, Rot G, Macek B, Schmidtke C, and Laubinger S
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- RNA 3' End Processing, RNA, Plant metabolism, RNA, Plant genetics, Gene Expression Regulation, Plant, Introns genetics, Polyadenylation, Arabidopsis genetics, Arabidopsis metabolism, Ribonucleoprotein, U1 Small Nuclear metabolism, Ribonucleoprotein, U1 Small Nuclear genetics, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, RNA, Messenger metabolism, RNA, Messenger genetics
- Abstract
The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns-a mechanism known as telescripting in metazoans-while also influencing alternative polyadenylation site selection in 3'-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3'-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs., (© 2024. The Author(s).)
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- 2024
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11. splicekit : an integrative toolkit for splicing analysis from short-read RNA-seq.
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Rot G, Wehling A, Schmucki R, Berntenis N, Zhang JD, and Ebeling M
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Motivation: Analysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. To the best of our knowledge, there is currently no integrative open-source software dedicated to this task., Results: Here, we introduce splicekit , a Python package that provides and integrates a set of existing and novel splicing analysis tools for conducting splicing analysis., Availability and Implementation: The software splicekit is open-source and available at Github (https://github.com/bedapub/splicekit) and via the Python Package Index., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)
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- 2024
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12. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
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Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, and Zavolan M
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- RNA-Seq, Polyadenylation, Sequence Analysis, RNA methods, RNA genetics, Benchmarking
- Abstract
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets., (© 2023 Bryce-Smith et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
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- 2023
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13. Analysis of RNA Polyadenylation in Healthy and Osteoarthritic Human Articular Cartilage.
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Winstanley-Zarach P, Rot G, Kuba S, Smagul A, Peffers MJ, and Tew SR
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- Humans, Polyadenylation genetics, Transcriptome, Sequence Analysis, RNA, RNA genetics, RNA metabolism, Cartilage, Articular metabolism, Osteoarthritis, Knee genetics, Osteoarthritis, Knee metabolism
- Abstract
Polyadenylation (polyA) defines the 3' boundary of a transcript's genetic information. Its position can vary and alternative polyadenylation (APA) transcripts can exist for a gene. This causes variance in 3' regulatory domains and can affect coding sequence if intronic events occur. The distribution of polyA sites on articular chondrocyte transcripts has not been studied so we aimed to define their transcriptome-wide location in age-matched healthy and osteoarthritic knee articular cartilage. Total RNA was isolated from frozen tissue samples and analysed using the QuantSeq-Reverse 3' RNA sequencing approach, where each read runs 3' to 5' from within the polyA tail into the transcript and contains a distinct polyA site. Differential expression of transcripts was significant altered between healthy and osteoarthritic samples with enrichment for functionalities that were strongly associated with joint pathology. Subsequent examination of polyA site data allowed us to define the extent of site usage across all the samples. When comparing healthy and osteoarthritic samples, we found that differential use of polyadenylation sites was modest. However, in the genes affected, there was potential for the APA to have functional relevance. We have characterised the polyadenylation landscape of human knee articular chondrocytes and conclude that osteoarthritis does not elicit a widespread change in their polyadenylation site usage. This finding differentiates knee osteoarthritis from pathologies such as cancer where APA is more commonly observed., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.
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- 2023
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14. The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians.
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Spruce T, Plass M, Gohr A, Ray D, Martínez de Lagrán M, Rot G, Nóvoa A, Burguera D, Permanyer J, Miret M, Zheng H, Swanson MS, Morris Q, Mallo M, Dierssen M, Hughes TR, Pernaute B, and Irimia M
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- Alternative Splicing genetics, Animals, Eutheria genetics, Female, Pregnancy, RNA metabolism, Placenta metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism
- Abstract
Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process of evolutionary specialization in eutherian mammals resulting in the emergence of a novel placental function for the gene. Mbnl3 belongs to a family of RNA-binding proteins whose members regulate multiple aspects of RNA metabolism. We find that, in eutherians, while both Mbnl3 and its paralog Mbnl2 are strongly expressed in placenta, Mbnl3 expression has been lost from nonplacental tissues in association with the evolution of a novel promoter. Moreover, Mbnl3 has undergone accelerated protein sequence evolution leading to changes in its RNA-binding specificities and cellular localization. While Mbnl2 and Mbnl3 share partially redundant roles in regulating alternative splicing, polyadenylation site usage and, in turn, placenta maturation, Mbnl3 has also acquired novel biological functions. Specifically, Mbnl3 knockout (M3KO) alone results in increased placental growth associated with higher Myc expression. Furthermore, Mbnl3 loss increases fetal resource allocation during limiting conditions, suggesting that location of Mbnl3 on the X chromosome has led to its role in limiting placental growth, favoring the maternal side of the parental genetic conflict., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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15. Correction to: A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells.
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Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, and Lehner CF
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- 2022
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16. A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells.
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Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, and Lehner CF
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- Animals, Cold Temperature, Regulatory Sequences, Nucleic Acid, Temperature, Drosophila, Drosophila melanogaster genetics
- Abstract
Background: Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown., Results: The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14-29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D., Conclusion: Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range., (© 2021. The Author(s).)
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- 2021
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17. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.
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Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, and Drukker M
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- Animals, Cell Nucleus genetics, Cell Nucleus metabolism, DNA-Binding Proteins metabolism, Humans, Mice, MicroRNAs genetics, Pluripotent Stem Cells metabolism, Polyadenylation genetics, RNA, Long Noncoding metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Cell Differentiation genetics, DNA-Binding Proteins genetics, Mouse Embryonic Stem Cells metabolism, RNA, Long Noncoding genetics
- Abstract
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2019
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18. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.
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Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, and Ule J
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- HEK293 Cells, Humans, Protein Binding, RNA 3' Polyadenylation Signals, RNA, Messenger chemistry, RNA, Messenger genetics, DNA-Binding Proteins metabolism, Polyadenylation, RNA Splicing, RNA, Messenger metabolism
- Abstract
Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we developed expressRNA, a web platform encompassing computational tools for integration of iCLIP and RNA motif analyses with RNA-seq and 3' mRNA sequencing. This reveals at nucleotide resolution the "RNA maps" describing how the RNA binding positions of RBPs relate to their regulatory functions. We use this approach to examine how TDP-43, an RBP involved in several neurodegenerative diseases, binds around its regulated poly(A) sites. Binding close to the poly(A) site generally represses, whereas binding further downstream enhances use of the site, which is similar to TDP-43 binding around regulated exons. Our RNAmotifs2 software also identifies sequence motifs that cluster together with the binding motifs of TDP-43. We conclude that TDP-43 directly regulates diverse types of pre-mRNA processing according to common position-dependent principles., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
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19. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.
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Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, and Ule J
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- Animals, Brain cytology, Brain metabolism, Cell Line, Exons, Heart physiology, Humans, Mice, Mice, Knockout, Microarray Analysis, RNA-Binding Proteins metabolism, Software, Alternative Splicing genetics, Nucleotide Motifs genetics, RNA-Binding Proteins genetics, Sequence Analysis, RNA methods
- Abstract
RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs.
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- 2014
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20. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions.
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Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, and Kuspa A
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- Dictyostelium genetics, Gene Expression Profiling, Genes, Bacterial, Genes, Protozoan, Gram-Negative Bacteria genetics, Gram-Positive Bacteria genetics, Host-Pathogen Interactions genetics, Mutation, Transcription, Genetic, Dictyostelium physiology, Gram-Negative Bacteria physiology, Gram-Positive Bacteria physiology
- Abstract
Background: Amoebae and bacteria interact within predator-prey and host-pathogen relationships, but the general response of amoeba to bacteria is not well understood. The amoeba Dictyostelium discoideum feeds on, and is colonized by, diverse bacterial species, including Gram-positive [Gram(+)] and Gram-negative [Gram(-)] bacteria, two major groups of bacteria that differ in structure and macromolecular composition., Results: Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+) or with Gram(-) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell-surface protein gp130, as well as several genes that are only required for growth on Gram(-) bacteria, including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways., Conclusions: We have defined genes that are critical for amoebal survival during feeding on Gram(+), or Gram(-), bacteria that we propose form part of a regulatory network that allows D. discoideum to elicit specific cellular responses to different species of bacteria in order to optimize survival., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
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21. Transcriptional profiling of Dictyostelium with RNA sequencing.
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Miranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G, and Zupan B
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- Base Sequence, DNA Primers, DNA, Complementary genetics, Data Mining, Dictyostelium metabolism, Gene Library, Genome, Protozoan, High-Throughput Nucleotide Sequencing methods, Molecular Sequence Annotation, Molecular Sequence Data, Polymerase Chain Reaction, Protozoan Proteins genetics, Protozoan Proteins metabolism, RNA, Messenger genetics, RNA, Messenger isolation & purification, RNA, Messenger metabolism, RNA, Protozoan genetics, RNA, Protozoan isolation & purification, RNA, Protozoan metabolism, Software, Dictyostelium genetics, Gene Expression Profiling methods, Sequence Analysis, RNA methods
- Abstract
Transcriptional profiling methods have been utilized in the analysis of various biological processes in Dictyostelium. Recent advances in high-throughput sequencing have increased the resolution and the dynamic range of transcriptional profiling. Here we describe the utility of RNA sequencing with the Illumina technology for production of transcriptional profiles. We also describe methods for data mapping and storage as well as common and specialized tools for data analysis, both online and offline.
- Published
- 2013
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22. Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain.
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Rogelj B, Easton LE, Bogu GK, Stanton LW, Rot G, Curk T, Zupan B, Sugimoto Y, Modic M, Haberman N, Tollervey J, Fujii R, Takumi T, Shaw CE, and Ule J
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- Animals, Base Sequence, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Exons, Gene Expression Regulation, Gene Order, Humans, Male, Mice, Mice, Knockout, Neurons metabolism, Protein Binding, RNA Isoforms, RNA-Binding Protein FUS genetics, Alternative Splicing, Brain metabolism, RNA Precursors genetics, RNA Precursors metabolism, RNA-Binding Protein FUS metabolism
- Abstract
Fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43) are RNA-binding proteins pathogenetically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), but it is not known if they regulate the same transcripts. We addressed this question using crosslinking and immunoprecipitation (iCLIP) in mouse brain, which showed that FUS binds along the whole length of the nascent RNA with limited sequence specificity to GGU and related motifs. A saw-tooth binding pattern in long genes demonstrated that FUS remains bound to pre-mRNAs until splicing is completed. Analysis of FUS(-/-) brain demonstrated a role for FUS in alternative splicing, with increased crosslinking of FUS in introns around the repressed exons. We did not observe a significant overlap in the RNA binding sites or the exons regulated by FUS and TDP-43. Nevertheless, we found that both proteins regulate genes that function in neuronal development.
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- 2012
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23. CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function.
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Wagnon JL, Briese M, Sun W, Mahaffey CL, Curk T, Rot G, Ule J, and Frankel WN
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- Animals, CELF Proteins, Cerebral Cortex metabolism, Hippocampus metabolism, Humans, Mice, NAV1.6 Voltage-Gated Sodium Channel metabolism, Pyramidal Cells metabolism, RNA Stability, Synapses genetics, Synapses metabolism, Synaptic Transmission genetics, Transcriptome, Epilepsy genetics, Epilepsy metabolism, Neurons cytology, Neurons metabolism, Protein Biosynthesis, RNA, Messenger genetics, RNA, Messenger metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism
- Abstract
RNA-binding proteins have emerged as causal agents of complex neurological diseases. Mice deficient for neuronal RNA-binding protein CELF4 have a complex neurological disorder with epilepsy as a prominent feature. Human CELF4 has recently been associated with clinical features similar to those seen in mutant mice. CELF4 is expressed primarily in excitatory neurons, including large pyramidal cells of the cerebral cortex and hippocampus, and it regulates excitatory but not inhibitory neurotransmission. We examined mechanisms underlying neuronal hyperexcitability in Celf4 mutants by identifying CELF4 target mRNAs and assessing their fate in the absence of CELF4 in view of their known functions. CELF4 binds to at least 15%-20% of the transcriptome, with striking specificity for the mRNA 3' untranslated region. CELF4 mRNA targets encode a variety of proteins, many of which are well established in neuron development and function. While the overall abundance of these mRNA targets is often dysregulated in Celf4 deficient mice, the actual expression changes are modest at the steady-state level. In contrast, by examining the transcriptome of polysome fractions and the mRNA distribution along the neuronal cell body-neuropil axis, we found that CELF4 is critical for maintaining mRNA stability and availability for translation. Among biological processes associated with CELF4 targets that accumulate in neuropil of mutants, regulation of synaptic plasticity and transmission are the most prominent. Together with a related study of the impact of CELF4 loss on sodium channel Na(v)1.6 function, we suggest that CELF4 deficiency leads to abnormal neuronal function by combining a specific effect on neuronal excitation with a general impairment of synaptic transmission. These results also expand our understanding of the vital roles RNA-binding proteins play in regulating and shaping the activity of neural circuits., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2012
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24. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.
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Tollervey JR, Wang Z, Hortobágyi T, Witten JT, Zarnack K, Kayikci M, Clark TA, Schweitzer AC, Rot G, Curk T, Zupan B, Rogelj B, Shaw CE, and Ule J
- Subjects
- Adolescent, Adult, Age Factors, Aged, Aged, 80 and over, Antigens, Neoplasm genetics, Antigens, Neoplasm metabolism, Cell Adhesion Molecules genetics, Down-Regulation, Exons, Gene Expression Profiling, Humans, Ion Channels genetics, Middle Aged, Nerve Tissue Proteins genetics, Nerve Tissue Proteins metabolism, Neuro-Oncological Ventral Antigen, Oligonucleotide Array Sequence Analysis, Polypyrimidine Tract-Binding Protein metabolism, Principal Component Analysis, Protein Isoforms metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Synaptic Transmission genetics, Temporal Lobe metabolism, Transcription, Genetic, Young Adult, Aging, Alternative Splicing, Alzheimer Disease genetics, Frontotemporal Lobar Degeneration genetics
- Abstract
Age is the most important risk factor for neurodegeneration; however, the effects of aging and neurodegeneration on gene expression in the human brain have most often been studied separately. Here, we analyzed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages who were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer's disease (AD). We identified age-related splicing changes in cognitively normal individuals and found that these were present also in 95% of individuals with FTLD or AD, independent of their age. These changes were consistent with increased polypyrimidine tract binding protein (PTB)-dependent splicing activity. We also identified disease-specific splicing changes that were present in individuals with FTLD or AD, but not in cognitively normal individuals. These changes were consistent with the decreased neuro-oncological ventral antigen (NOVA)-dependent splicing regulation, and the decreased nuclear abundance of NOVA proteins. As expected, a dramatic down-regulation of neuronal genes was associated with disease, whereas a modest down-regulation of glial and neuronal genes was associated with aging. Whereas our data indicated that the age-related splicing changes are regulated independently of transcript-level changes, these two regulatory mechanisms affected expression of genes with similar functions, including metabolism and DNA repair. In conclusion, the alternative splicing changes identified in this study provide a new link between aging and neurodegeneration.
- Published
- 2011
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25. SNPsyn: detection and exploration of SNP-SNP interactions.
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Curk T, Rot G, and Zupan B
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- Chromosome Mapping, Internet, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Software
- Abstract
SNPsyn (http://snpsyn.biolab.si) is an interactive software tool for the discovery of synergistic pairs of single nucleotide polymorphisms (SNPs) from large genome-wide case-control association studies (GWAS) data on complex diseases. Synergy among SNPs is estimated using an information-theoretic approach called interaction analysis. SNPsyn is both a stand-alone C++/Flash application and a web server. The computationally intensive part is implemented in C++ and can run in parallel on a dedicated cluster or grid. The graphical user interface is written in Adobe Flash Builder 4 and can run in most web browsers or as a stand-alone application. The SNPsyn web server hosts the Flash application, receives GWAS data submissions, invokes the interaction analysis and serves result files. The user can explore details on identified synergistic pairs of SNPs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.
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- 2011
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26. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.
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Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, and Ule J
- Subjects
- DNA, Complementary genetics, DNA, Complementary metabolism, Immunoprecipitation methods, RNA genetics, RNA metabolism, RNA radiation effects, RNA Splicing, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, RNA-Binding Proteins radiation effects, Ultraviolet Rays, Gene Expression Profiling methods, RNA analysis, RNA-Binding Proteins analysis
- Abstract
The unique composition and spatial arrangement of RNA-binding proteins (RBPs) on a transcript guide the diverse aspects of post-transcriptional regulation. Therefore, an essential step towards understanding transcript regulation at the molecular level is to gain positional information on the binding sites of RBPs. Protein-RNA interactions can be studied using biochemical methods, but these approaches do not address RNA binding in its native cellular context. Initial attempts to study protein-RNA complexes in their cellular environment employed affinity purification or immunoprecipitation combined with differential display or microarray analysis (RIP-CHIP). These approaches were prone to identifying indirect or non-physiological interactions. In order to increase the specificity and positional resolution, a strategy referred to as CLIP (UV cross-linking and immunoprecipitation) was introduced. CLIP combines UV cross-linking of proteins and RNA molecules with rigorous purification schemes including denaturing polyacrylamide gel electrophoresis. In combination with high-throughput sequencing technologies, CLIP has proven as a powerful tool to study protein-RNA interactions on a genome-wide scale (referred to as HITS-CLIP or CLIP-seq). Recently, PAR-CLIP was introduced that uses photoreactive ribonucleoside analogs for cross-linking. Despite the high specificity of the obtained data, CLIP experiments often generate cDNA libraries of limited sequence complexity. This is partly due to the restricted amount of co-purified RNA and the two inefficient RNA ligation reactions required for library preparation. In addition, primer extension assays indicated that many cDNAs truncate prematurely at the crosslinked nucleotide. Such truncated cDNAs are lost during the standard CLIP library preparation protocol. We recently developed iCLIP (individual-nucleotide resolution CLIP), which captures the truncated cDNAs by replacing one of the inefficient intermolecular RNA ligation steps with a more efficient intramolecular cDNA circularization (Figure 1). Importantly, sequencing the truncated cDNAs provides insights into the position of the cross-link site at nucleotide resolution. We successfully applied iCLIP to study hnRNP C particle organization on a genome-wide scale and assess its role in splicing regulation.
- Published
- 2011
- Full Text
- View/download PDF
27. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.
- Author
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Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, König J, Hortobágyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, and Ule J
- Subjects
- Cell Line, Cell Line, Tumor, DNA-Binding Proteins physiology, Gene Expression Regulation genetics, Humans, Protein Isoforms genetics, RNA, Messenger biosynthesis, RNA, Messenger genetics, RNA, Untranslated genetics, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Alternative Splicing genetics, Brain Chemistry genetics, DNA-Binding Proteins genetics, RNA Splicing physiology, RNA, Messenger metabolism
- Abstract
TDP-43 is a predominantly nuclear RNA-binding protein that forms inclusion bodies in frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). The mRNA targets of TDP-43 in the human brain and its role in RNA processing are largely unknown. Using individual nucleotide-resolution ultraviolet cross-linking and immunoprecipitation (iCLIP), we found that TDP-43 preferentially bound long clusters of UG-rich sequences in vivo. Analysis of RNA binding by TDP-43 in brains from subjects with FTLD revealed that the greatest increases in binding were to the MALAT1 and NEAT1 noncoding RNAs. We also found that binding of TDP-43 to pre-mRNAs influenced alternative splicing in a similar position-dependent manner to Nova proteins. In addition, we identified unusually long clusters of TDP-43 binding at deep intronic positions downstream of silenced exons. A substantial proportion of alternative mRNA isoforms regulated by TDP-43 encode proteins that regulate neuronal development or have been implicated in neurological diseases, highlighting the importance of TDP-43 for the regulation of splicing in the brain.
- Published
- 2011
- Full Text
- View/download PDF
28. iCLIP predicts the dual splicing effects of TIA-RNA interactions.
- Author
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Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, and Ule J
- Subjects
- Base Sequence, Exons, Genome, Human, HeLa Cells, Humans, Molecular Sequence Data, Poly(A)-Binding Proteins genetics, Protein Binding, RNA Splice Sites, RNA, Small Interfering genetics, RNA, Small Interfering metabolism, RNA-Binding Proteins genetics, T-Cell Intracellular Antigen-1, Alternative Splicing, Poly(A)-Binding Proteins metabolism, RNA genetics, RNA metabolism, RNA-Binding Proteins metabolism
- Abstract
The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites. T-cell intracellular antigen 1 (TIA1) and TIA1-like 1 (TIAL1) locally enhance exon inclusion by recruiting U1 snRNP to 5' splice sites. However, effects of TIA proteins on splicing of distal exons have not yet been explored. We used UV-crosslinking and immunoprecipitation (iCLIP) to find that TIA1 and TIAL1 bind at the same positions on human RNAs. Binding downstream of 5' splice sites was used to predict the effects of TIA proteins in enhancing inclusion of proximal exons and silencing inclusion of distal exons. The predictions were validated in an unbiased manner using splice-junction microarrays, RT-PCR, and minigene constructs, which showed that TIA proteins maintain splicing fidelity and regulate alternative splicing by binding exclusively downstream of 5' splice sites. Surprisingly, TIA binding at 5' splice sites silenced distal cassette and variable-length exons without binding in proximity to the regulated alternative 3' splice sites. Using transcriptome-wide high-resolution mapping of TIA-RNA interactions we evaluated the distal splicing effects of TIA proteins. These data are consistent with a model where TIA proteins shorten the time available for definition of an alternative exon by enhancing recognition of the preceding 5' splice site. Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2010
- Full Text
- View/download PDF
29. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
- Author
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König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, and Ule J
- Subjects
- Base Sequence, HeLa Cells, Humans, Molecular Sequence Data, Protein Binding, RNA Precursors genetics, RNA Precursors metabolism, Ultraviolet Rays, Uridine metabolism, Alternative Splicing, Heterogeneous-Nuclear Ribonucleoproteins metabolism, Immunoprecipitation methods, Nucleotides metabolism
- Abstract
In the nucleus of eukaryotic cells, nascent transcripts are associated with heterogeneous nuclear ribonucleoprotein (hnRNP) particles that are nucleated by hnRNP C. Despite their abundance, however, it remained unclear whether these particles control pre-mRNA processing. Here, we developed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to study the role of hnRNP C in splicing regulation. iCLIP data show that hnRNP C recognizes uridine tracts with a defined long-range spacing consistent with hnRNP particle organization. hnRNP particles assemble on both introns and exons but remain generally excluded from splice sites. Integration of transcriptome-wide iCLIP data and alternative splicing profiles into an 'RNA map' indicates how the positioning of hnRNP particles determines their effect on the inclusion of alternative exons. The ability of high-resolution iCLIP data to provide insights into the mechanism of this regulation holds promise for studies of other higher-order ribonucleoprotein complexes.
- Published
- 2010
- Full Text
- View/download PDF
30. Conserved developmental transcriptomes in evolutionarily divergent species.
- Author
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Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, and Shaulsky G
- Subjects
- Base Sequence, DNA, Complementary genetics, Dictyostelium cytology, Gene Expression Profiling, Molecular Sequence Data, RNA, Messenger genetics, Sequence Analysis, RNA, Species Specificity, Biological Evolution, Conserved Sequence genetics, Dictyostelium genetics, Gene Expression Regulation, Developmental genetics, Gene Regulatory Networks genetics, RNA, Messenger metabolism
- Abstract
Background: Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish., Results: Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression., Conclusions: These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum.
- Published
- 2010
- Full Text
- View/download PDF
31. [On the use of photoplasmodynamic method in treatment of suppurative wounds].
- Author
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Pedder VV, Kosenok VK, Belik DV, Rot GZ, Surgutskova IV, Shkuro IuV, Pedder AV, Naboka MV, Mironenko VN, and Shudina AV
- Subjects
- Electricity, Humans, Skin Diseases, Infectious drug therapy, Suppuration, Ozone therapeutic use, Skin Diseases, Infectious therapy, Wound Healing
- Abstract
A new photoplasmodynamic method and Elektroton-Pulsar hardware system for its implementation are described. The method provides treatment of suppurative wounds by exposure of the infection focus to a gas mixture containing highly active components: O*, O2*, 1O2, O(, O3 traces + UV, etc. The exposure is performed using high-voltage electric discharges interacting with the initial ozone-containing gas mixture. The photoplasmodynamic method and the Elektroton-Pulsar hardware system are used in clinical practice for treatment of suppurative wounds and cavities of various etiology.
- Published
- 2008
32. Relation of tricuspid inflow E-wave peak velocity to severity of tricuspid regurgitation.
- Author
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Danicek V, Sagie A, Vaturi M, Weisenberg DE, Rot G, and Shapira Y
- Subjects
- Echocardiography, Doppler, Color, Female, Follow-Up Studies, Humans, Male, Middle Aged, Prognosis, Prospective Studies, Severity of Illness Index, Tricuspid Valve diagnostic imaging, Tricuspid Valve Insufficiency diagnostic imaging, Blood Flow Velocity physiology, Tricuspid Valve physiopathology, Tricuspid Valve Insufficiency physiopathology
- Abstract
E-wave velocity in mitral flow has previously been shown to discriminate between severe and nonsevere mitral regurgitation. In this study, we sought to explore this association in the tricuspid position. The peak velocity of the tricuspid inflow E wave was measured in 118 patients (mean age 62 +/- 16.6 years; 48% women). Patients with tricuspid stenosis, transvenous pacemakers, and tricuspid prostheses were excluded. E-wave measurements were taken during shallow breathing. Tricuspid regurgitation (TR) was quantified as none or mild (group 1), moderate (group 2), or severe (group 3), according to American Society of Echocardiography guidelines. Forty-three patients had mild TR, 43 had moderate TR, and 33 had severe TR. Peak E-wave velocity was 48.6 +/- 13.8, 48.6 +/- 11.7, and 78.3 +/- 26.1 cm/s in groups 1, 2, and 3, respectively (p > 0.0001). Mean E-wave velocity was similar in groups 1 and 2 but greater in group 3 (p < 0.0001). A peak E-wave velocity of > or = 65 cm/s had a sensitivity of 73% and specificity of 88% for the detection of severe TR. In conclusion, increased peak tricuspid E-wave velocity is associated with severe TR and thus can be used as a simple measure of TR grade.
- Published
- 2006
- Full Text
- View/download PDF
33. [Rationale of noninvasive method of drug administration at the prelymphatic level].
- Author
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Pedder VV, Grigor'ev VN, Rot GZ, Afanas'ev VP, Novikov AA, Letiagin AIu, and Shkuro IuV
- Subjects
- Animals, Dogs, Humans, Lymph Nodes, Lymphatic System, Microcirculation, Microscopy, Electron, Physical Therapy Modalities, Rats, Rheology, Skin Absorption, Temperature, Drug Administration Routes, Iontophoresis instrumentation, Phonophoresis instrumentation
- Abstract
The paper deals with the mode of local drug administration into the biological tissue at the prelympathic level without damaging the skin, which is based on enhancement of skin permeability by exposing to physical factors, including the use of contrast temperatures in the cyclic process of heating-cooling, followed by exposure to contact low-frequency ultrasound. Experimental and clinical studies of the mode versus routine drug administration have shown it to be promising in physiotherapeutic use.
- Published
- 1998
34. [The system of collection, processing, storage and retrieval of x-ray diagnostic images].
- Author
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Alekseev LV, Antonov AO, Antonov OS, Burnashov NA, Duntau AP, Rot GZ, Spektor BI, Tret'iakov VP, Fetisov IuI, Shtark MB, and Iarokhno VI
- Subjects
- Databases as Topic, Hospitals, General, Hospitals, Special, Humans, Siberia, Software, Radiography, Radiology Information Systems
- Abstract
The paper describes a system able to combine conventional techniques of diagnostic x-ray imaging with direct digital imaging on the original receiver with a resolution of 1.2 lin/mm. Digital roentgenography may be introduced into medical practice basing on the system of computers at the working places of roentgenologist and his assistant. Data base of long-term storage of x-ray images and input software for each x-ray picture are outlined. The authors have some experience of utilizing the system in the random sequence of patients (20,000) in general and specialized hospitals of Novosibirsk.
- Published
- 1997
35. [Characteristics of the diagnostic errors in infectious forms of syphilis].
- Author
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Krivosheev BN, Bogatyreva AV, Rot GZ, Motovilova NN, and Koshuba SV
- Subjects
- Adolescent, Adult, Diagnosis, Differential, Female, Health Workforce, Humans, Male, Medication Errors, Middle Aged, Recurrence, Specialization, Syphilis drug therapy, Time Factors, Trichomonas Infections diagnosis, Diagnostic Errors, Syphilis diagnosis
- Published
- 1980
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