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Sample records for reporter gene fusion

  1. Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals

    SciTech Connect

    Gambhir, Sanjiv; Pritha, Ray

    2015-07-14

    Novel double and triple fusion reporter gene constructs harboring distinct imagable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.

  2. Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals

    DOEpatents

    Gambhir, Sanjiv [Portola Valley, CA; Pritha, Ray [Mountain View, CA

    2011-06-07

    Novel double and triple fusion reporter gene constructs harboring distinct imagable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.

  3. Multimodality imaging of reporter gene expression using a novel fusion vector in living cells and animals

    SciTech Connect

    Gambhir,; Sanjiv, Pritha; Ray,

    2009-04-28

    Novel double and triple fusion reporter gene constructs harboring distinct imageable reporter genes are provided, as well as applications for the use of such double and triple fusion constructs in living cells and in living animals using distinct imaging technologies.

  4. The fusion Vibrio campbellii luciferase as a eukaryotic gene reporter.

    PubMed

    Tinikul, Ruchanok; Thotsaporn, Kittisak; Thaveekarn, Wichit; Jitrapakdee, Sarawut; Chaiyen, Pimchai

    2012-12-31

    Bacterial luciferase from Vibrio campbellii is a thermostable enzyme with an in vitro thermal inactivation half-life of ~1020 min at 37°C. The enzyme also binds tightly to reduced FMN. In this study, a V. campbellii fusion luciferase construct in which the α and β subunits are linked with a decapeptide was made and characterized. In general, the overall enzymatic properties of the two enzymes are similar. Expression of the enzymes in Escherichia coli demonstrated that the V. campbellii fusion luciferase emits less light than the native luciferase, but still emits a much greater amount of light than native luciferase from Vibrio harveyi and Photobacterium leiognathi TH1. The intensity of light emitted by the V. campbellii fusion luciferase was more than 80-fold greater than that from the V. harveyi native luciferase when expressed at 37°C. Biochemical characterization has shown that the V. campbellii fusion luciferase also retains a high binding affinity for reduced flavin mononucleotide and high thermostability. The levels of bioluminescence emitted by the V. campbellii fusion luciferase expressed in HEK293T cells reached ~1×10(6) Relative Light Units/mg total protein. These findings suggest that the V. campbellii fusion luciferase is a promising candidate for further development as a luciferase-based reporter for eukaryotic systems.

  5. Xp11 neoplasm with melanocytic differentiation of the prostate harbouring the novel NONO-TFE3 gene fusion: report of a unique case expanding the gene fusion spectrum.

    PubMed

    Wang, Xiao-Tong; Xia, Qiu-Yuan; Ni, Hao; Wang, Zi-Yu; Ye, Sheng-Bing; Li, Rui; Wang, Xuan; Lv, Jing-Huan; Shi, Shan-Shan; Ma, Heng-Hui; Lu, Zhen-Feng; Shen, Qin; Zhou, Xiao-Jun; Rao, Qiu

    2016-09-01

    Recently, an increasing number of TFE3 rearrangement-associated tumours have been reported, such as TFE3 rearrangement-associated perivascular epithelioid cell tumours (PEComas), melanotic Xp11 translocation renal cancers and melanotic Xp11 neoplasms. We have suggested that these tumours belong to a single clinicopathological spectrum. 'Xp11 neoplasm with melanocytic differentiation' or 'melanotic Xp11 neoplasm' have been proposed to designate this unique neoplasm. Herein, we describe the first case of an Xp11 neoplasm with melanocytic differentiation to be described in the prostate, bearing the novel NONO-TFE3 gene fusion. This study both adds to the spectrum regarding melanotic Xp11 neoplasms and expands its gene fusion spectrum. Moreover, we discuss the relationship of these rare tumours to neoplasms such as conventional PEComas, alveolar soft part sarcomas, malignant melanomas, clear cell sarcomas and Xp11 translocation renal cancers.

  6. Dual-therapeutic reporter genes fusion for enhanced cancer gene therapy and imaging.

    PubMed

    Sekar, T V; Foygel, K; Willmann, J K; Paulmurugan, R

    2013-05-01

    Two of the successful gene-directed enzyme prodrug therapies include herpes simplex virus-thymidine kinase (HSV1-TK) enzyme-ganciclovir prodrug and the Escherichia coli nitroreductase (NTR) enzyme-CB1954 prodrug strategies; these enzyme-prodrug combinations produce activated cytotoxic metabolites of the prodrugs capable of tumor cell death by inhibiting DNA synthesis and killing quiescent cells, respectively. Both these strategies also affect significant bystander cell killing of neighboring tumor cells that do not express these enzymes. We have developed a dual-combination gene strategy, where we identified HSV1-TK and NTR fused in a particular orientation can effectively kill tumor cells when the tumor cells are treated with a fusion HSV1-TK-NTR gene- along with a prodrug combination of GCV and CB1954. In order to determine whether the dual-system demonstrate superior therapeutic efficacy than either HSV1-TK or NTR systems alone, we conducted both in vitro and in vivo tumor xenograft studies using triple negative SUM159 breast cancer cells, by evaluating the efficacy of cell death by apoptosis and necrosis upon treatment with the dual HSV1-TK genes-GCV-CB1954 prodrugs system, and compared the efficiency to HSV1-TK-GCV and NTR-CB1954. Our cell-based studies, tumor regression studies in xenograft mice, histological analyses of treated tumors and bystander studies indicate that the dual HSV1-TK-NTR-prodrug system is two times more efficient even with half the doses of both prodrugs than the respective single gene-prodrug system, as evidenced by enhanced apoptosis and necrosis of tumor cells in vitro in culture and xenograft of tumor tissues in animals.

  7. Regulation of Sinorhizobium meliloti 1021 rrnA-reporter gene fusions in response to cold shock.

    PubMed

    Gustafson, Ann M; O'Connell, Kevin P; Thomashow, Michael F

    2002-09-01

    We previously reported that mutants of Sinorhizobium meliloti 1021 carrying luxAB insertions in each of the three 16S rRNA genes exhibited a dramatic (> or = 28-fold) increase in luminescence following a temperature downshift from 30 to 15 degrees C. These results raised the possibility that the rRNA operons (rrn) of S. meliloti were cold shock loci. In testing this possibility, we found that fusion of the S. meliloti 1021 rrnA promoter to two different reporter genes, luxAB and uidA, resulted in hybrid genes that were transiently upregulated (as measured by transcript accumulation) about four- to sixfold in response to a temperature downshift. These results are consistent with the hypothesis that the rrn promoters are transiently upregulated in response to cold shock. However, much of the apparent cold shock regulation of the initial luxAB insertions was due to an unexpected mechanism: an apparent temperature-dependent inhibition of translation. Specifically, the rrnA sequences from +1 to +172 (relative to the start of transcription) were found to greatly decrease the ability of S. meliloti to translate hybrid rrn-luxAB transcripts into active protein at 30 degrees C. This effect, however, was largely eliminated at 15 degrees C. Possible mechanisms for the apparent transient increase in rrnA promoter activity and temperature-dependent inhibition of translation are discussed.

  8. Interkingdom gene fusions.

    PubMed

    Wolf, Y I; Kondrashov, A S; Koonin, E V

    2000-01-01

    Genome comparisons have revealed major lateral gene transfer between the three primary kingdoms of life - Bacteria, Archaea, and Eukarya. Another important evolutionary phenomenon involves the evolutionary mobility of protein domains that form versatile multidomain architectures. We were interested in investigating the possibility of a combination of these phenomena, with an invading gene merging with a pre-existing gene in the recipient genome. Complete genomes of fifteen bacteria, four archaea and one eukaryote were searched for interkingdom gene fusions (IKFs); that is, genes coding for proteins that apparently consist of domains originating from different primary kingdoms. Phylogenetic analysis supported 37 cases of IKF, each of which includes a 'native' domain and a horizontally acquired 'alien' domain. IKFs could have evolved via lateral transfer of a gene coding for the alien domain (or a larger protein containing this domain) followed by recombination with a native gene. For several IKFs, this scenario is supported by the presence of a gene coding for a second, stand-alone version of the alien domain in the recipient genome. Among the genomes investigated, the greatest number of IKFs has been detected in Mycobacterium tuberculosis, where they are almost always accompanied by a stand-alone alien domain. For most of the IKF cases detected in other genomes, the stand-alone counterpart is missing. The results of comparative genome analysis show that IKF formation is a real, but relatively rare, evolutionary phenomenon. We hypothesize that IKFs are formed primarily via the proposed two-stage mechanism, but other than in the Actinomycetes, in which IKF generation seems to be an active, ongoing process, most of the stand-alone intermediates have been eliminated, perhaps because of functional redundancy.

  9. Gene Fusion: A Genome Wide Survey

    NASA Technical Reports Server (NTRS)

    Liang, Ping; Riley, Monica

    2001-01-01

    As a well known fact, organisms form larger and complex multimodular (composite or chimeric) and mostly multi-functional proteins through gene fusion of two or more individual genes which have independent evolution histories and functions. We call each of these components a module. The existence of multimodular proteins may improves the efficiency in gene regulation and in cellular functions, and thus may give the host organism advantages in adaptation to environments. Analysis of all gene fusions in present-day organisms should allow us to examine the patterns of gene fusion in context with cellular functions, to trace back the evolution processes from the ancient smaller and uni-functional proteins to the present-day larger and complex multi-functional proteins, and to estimate the minimal number of ancestor proteins that existed in the last common ancestor for all life on earth. Although many multimodular proteins have been experimentally known, identification of gene fusion events systematically at genome scale had not been possible until recently when large number of completed genome sequences have been becoming available. In addition, technical difficulties for such analysis also exist due to the complexity of this biological and evolutionary process. We report from this study a new strategy to computationally identify multimodular proteins using completed genome sequences and the results surveyed from 22 organisms with the data from over 40 organisms to be presented during the meeting. Additional information is contained in the original extended abstract.

  10. Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions.

    PubMed

    Pandey, Naresh; Nobles, Christopher L; Zechiedrich, Lynn; Maresso, Anthony W; Silberg, Jonathan J

    2015-05-15

    Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein-protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein-protein interactions within whole animals.

  11. Fusion Simulation Project Workshop Report

    NASA Astrophysics Data System (ADS)

    Kritz, Arnold; Keyes, David

    2009-03-01

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved 46 physicists, applied mathematicians and computer scientists, from 21 institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a 3-day workshop in May 2007.

  12. Adamantinoma-like Ewing's sarcoma with EWS-FLI1 fusion gene: a case report.

    PubMed

    Fujii, Hiromasa; Honoki, Kanya; Enomoto, Yasunori; Kasai, Takahiko; Kido, Akira; Amano, Itsuto; Kumamoto, Makiko; Morishita, Toru; Mii, Yoshio; Nonomura, Akitaka; Takakura, Yoshinori

    2006-11-01

    Recent studies have advocated the genotypic and phenotypic delineation of a novel Ewing's sarcoma histologic variant showing epithelial features defined as "adamantinoma-like Ewing's sarcoma". We described an 18-year-old girl with a primary small round-cell sarcoma of the right tibia showing polyphenotypic differentiation with epithelioid features. The neoplastic cells had mainly round or oval nuclei with fine chromatin with a portion of epithelial arrangements. The immunohistochemical analysis showed the epithelial markers of cytokeratin 5/6/18, AE1/AE3, and cytokeratin high molecular weight were stained especially in the foci with epithelioid features, as well as MIC2, S100, and NSE. The diagnosis of the lesion was confirmed as Ewing's sarcoma by the presence of the EWS-FLI1 fusion transcript, and could be defined as the so-called "adamantinoma-like Ewing's sarcoma". After wide excision and high-dose chemotherapy with peripheral blood stem cell transfusion, the patient has been well and continuously event-free for 3 years since the initial diagnosis.

  13. Novel fusion genes and chimeric transcripts in ependymal tumors.

    PubMed

    Olsen, Thale Kristin; Panagopoulos, Ioannis; Gorunova, Ludmila; Micci, Francesca; Andersen, Kristin; Kilen Andersen, Hege; Meling, Torstein R; Due-Tønnessen, Bernt; Scheie, David; Heim, Sverre; Brandal, Petter

    2016-12-01

    We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  14. Development of detection method for novel fusion gene using GeneChip exon array

    PubMed Central

    2014-01-01

    Background Fusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired. Results We introduced a new method of detecting the novel fusion gene by using GeneChip Exon Array that enables exon expression analysis on a whole-genome scale and TAIL-PCR. To screen genes with abnormal exon expression profiles, we developed computational program, and confirmed that the program was able to search the fusion partner gene using Exon Array data of T-cell acute lymphocytic leukemia (T-ALL) cell lines. It was reported that the T-ALL cell lines, ALL-SIL, BE13 and LOUCY, harbored the fusion gene NUP214-ABL1, NUP214-ABL1 and SET-NUP214, respectively. The program extracted the candidate genes with abnormal exon expression profiles: 1 gene in ALL-SIL, 1 gene in BE13, and 2 genes in LOUCY. The known fusion partner gene NUP214 was included in the genes in ALL-SIL and LOUCY. Thus, we applied the proposed program to the detection of fusion partner genes in other tumors. To discover novel fusion genes, we examined 24 breast cancer cell lines and 20 pancreatic cancer cell lines by using the program. As a result, 20 and 23 candidate genes were obtained for the breast and pancreatic cancer cell lines respectively, and seven genes were selected as the final candidate gene based on information of the EST data base, comparison with normal cell samples and visual inspection of Exon expression profile. Finding of fusion partners for the final candidate genes was tried by TAIL-PCR, and three novel fusion genes were identified. Conclusions The usefulness of our detection method was confirmed. Using this method for more samples, it is thought that fusion genes can be identified. PMID:24533689

  15. Fusion Breeder Program interim report

    SciTech Connect

    Moir, R.; Lee, J.D.; Neef, W.

    1982-06-11

    This interim report for the FY82 Fusion Breeder Program covers work performed during the scoping phase of the study, December, 1981-February 1982. The goals for the FY82 study are the identification and development of a reference blanket concept using the fission suppression concept and the definition of a development plan to further the fusion breeder application. The context of the study is the tandem mirror reactor, but emphasis is placed upon blanket engineering. A tokamak driver and blanket concept will be selected and studied in more detail during FY83.

  16. Construction of a cytosolic firefly luciferase reporter cassette for use in PCR-mediated gene deletion and fusion in Saccharomyces cerevisiae.

    PubMed

    Ainsworth, W B; Rome, C M; Hjortsø, M A; Benton, M G

    2012-12-01

    Monitoring promoter response to environmental changes using reporter systems has provided invaluable information regarding cellular state. With the development of in vivo luciferase reporter systems, inexpensive, sensitive and accurate promoter assays have been developed without the variability reported between in vitro samplings. Current luciferase reporter systems, however, are largely inflexible to modifications to the promoter of interest. To overcome problems in flexibility and stability of these expression vectors, we report the creation of a novel vector system which introduces a cytosol-localized Photinus pyralis luciferase [LUC*(-SKL)] capable of one-step, in vivo measurements into a promoter-reporter system via PCR-based gene deletion and fusion. After introduction of the reporter under HUG1 promoter control, cytosolic localization was confirmed by fluorescence microscopy. The dose-response of this novel construct was then compared with that of a similar HUG1Δ::yEGFP1 promoter-reporter system and shown to give a similar response pattern.

  17. INTEGRATE: gene fusion discovery using whole genome and transcriptome data

    PubMed Central

    Zhang, Jin; White, Nicole M.; Schmidt, Heather K.; Fulton, Robert S.; Tomlinson, Chad; Warren, Wesley C.; Wilson, Richard K.; Maher, Christopher A.

    2016-01-01

    While next-generation sequencing (NGS) has become the primary technology for discovering gene fusions, we are still faced with the challenge of ensuring that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately. However, as both WGS and RNA-seq have their limitations when used independently, we hypothesize that the orthogonal validation from integrating both data could generate a sensitive and specific approach for detecting high-confidence gene fusion predictions. Fortunately, decreasing NGS costs have resulted in a growing quantity of patients with both data available. Therefore, we developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read mapping. To evaluate INTEGRATE, we compared it with eight additional gene fusion discovery tools using the well-characterized breast cell line HCC1395 and peripheral blood lymphocytes derived from the same patient (HCC1395BL). The predictions subsequently underwent a targeted validation leading to the discovery of 131 novel fusions in addition to the seven previously reported fusions. Overall, INTEGRATE only missed six out of the 138 validated fusions and had the highest accuracy of the nine tools evaluated. Additionally, we applied INTEGRATE to 62 breast cancer patients from The Cancer Genome Atlas (TCGA) and found multiple recurrent gene fusions including a subset involving estrogen receptor. Taken together, INTEGRATE is a highly sensitive and accurate tool that is freely available for academic use. PMID:26556708

  18. INTEGRATE: gene fusion discovery using whole genome and transcriptome data.

    PubMed

    Zhang, Jin; White, Nicole M; Schmidt, Heather K; Fulton, Robert S; Tomlinson, Chad; Warren, Wesley C; Wilson, Richard K; Maher, Christopher A

    2016-01-01

    While next-generation sequencing (NGS) has become the primary technology for discovering gene fusions, we are still faced with the challenge of ensuring that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately. However, as both WGS and RNA-seq have their limitations when used independently, we hypothesize that the orthogonal validation from integrating both data could generate a sensitive and specific approach for detecting high-confidence gene fusion predictions. Fortunately, decreasing NGS costs have resulted in a growing quantity of patients with both data available. Therefore, we developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read mapping. To evaluate INTEGRATE, we compared it with eight additional gene fusion discovery tools using the well-characterized breast cell line HCC1395 and peripheral blood lymphocytes derived from the same patient (HCC1395BL). The predictions subsequently underwent a targeted validation leading to the discovery of 131 novel fusions in addition to the seven previously reported fusions. Overall, INTEGRATE only missed six out of the 138 validated fusions and had the highest accuracy of the nine tools evaluated. Additionally, we applied INTEGRATE to 62 breast cancer patients from The Cancer Genome Atlas (TCGA) and found multiple recurrent gene fusions including a subset involving estrogen receptor. Taken together, INTEGRATE is a highly sensitive and accurate tool that is freely available for academic use.

  19. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

    PubMed

    Weirather, Jason L; Afshar, Pegah Tootoonchi; Clark, Tyson A; Tseng, Elizabeth; Powers, Linda S; Underwood, Jason G; Zabner, Joseph; Korlach, Jonas; Wong, Wing Hung; Au, Kin Fai

    2015-10-15

    We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.

  20. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

    PubMed Central

    Weirather, Jason L.; Afshar, Pegah Tootoonchi; Clark, Tyson A.; Tseng, Elizabeth; Powers, Linda S.; Underwood, Jason G.; Zabner, Joseph; Korlach, Jonas; Wong, Wing Hung; Au, Kin Fai

    2015-01-01

    We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes. PMID:26040699

  1. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.

    PubMed

    Marincevic-Zuniga, Yanara; Dahlberg, Johan; Nilsson, Sara; Raine, Amanda; Nystedt, Sara; Lindqvist, Carl Mårten; Berglund, Eva C; Abrahamsson, Jonas; Cavelier, Lucia; Forestier, Erik; Heyman, Mats; Lönnerholm, Gudmar; Nordlund, Jessica; Syvänen, Ann-Christine

    2017-08-14

    Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.

  2. ETS fusion genes in prostate cancer.

    PubMed

    Gasi Tandefelt, Delila; Boormans, Joost; Hermans, Karin; Trapman, Jan

    2014-06-01

    Prostate cancer is very common in elderly men in developed countries. Unravelling the molecular and biological processes that contribute to tumor development and progressive growth, including its heterogeneity, is a challenging task. The fusion of the genes ERG and TMPRSS2 is the most frequent genomic alteration in prostate cancer. ERG is an oncogene that encodes a member of the family of ETS transcription factors. At lower frequency, other members of this gene family are also rearranged and overexpressed in prostate cancer. TMPRSS2 is an androgen-regulated gene that is preferentially expressed in the prostate. Most of the less frequent ETS fusion partners are also androgen-regulated and prostate-specific. During the last few years, novel concepts of the process of gene fusion have emerged, and initial experimental results explaining the function of the ETS genes ERG and ETV1 in prostate cancer have been published. In this review, we focus on the most relevant ETS gene fusions and summarize the current knowledge of the role of ETS transcription factors in prostate cancer. Finally, we discuss the clinical relevance of TMRPSS2-ERG and other ETS gene fusions in prostate cancer.

  3. Mammary Analogue Secretory Carcinoma of Salivary Glands: Molecular Analysis of 25 ETV6 Gene Rearranged Tumors With Lack of Detection of Classical ETV6-NTRK3 Fusion Transcript by Standard RT-PCR: Report of 4 Cases Harboring ETV6-X Gene Fusion.

    PubMed

    Skálová, Alena; Vanecek, Tomas; Simpson, Roderick H W; Laco, Jan; Majewska, Hanna; Baneckova, Martina; Steiner, Petr; Michal, Michal

    2016-01-01

    ETV6 gene abnormalities are well described in tumor pathology. Many fusion partners of ETV6 have been reported in a variety of epithelial and hematological malignancies. In salivary gland tumor pathology, however, the ETV6-NTRK3 translocation is specific for mammary analogue secretory carcinoma (MASC), and has not been documented in any other salivary tumor type. The present study comprised a clinical and molecular analysis of 25 cases morphologically and immunohistochemically typical of MASC. They all also displayed the ETV6 rearrangement as visualized by fluorescent in situ hybridization but lacked the classical ETV6-NTRK3 fusion transcript by standard reverse-transcriptase-polymerase chain reaction. In 4 cases, the classical fusion transcript was found by more sensitive, nested reverse-transcription-polymerase chain reaction. Five other cases harbored atypical fusion transcripts as detected by both standard and nested reverse-transcription-polymerase chain reaction. In addition, fluorescent in situ hybridization with an NTRK3 break-apart probe was also performed; rearrangement of NTRK3 gene was detected in 16 of 25 cases. In 3 other cases, the tissue was not analyzable, and in 2 further cases analysis could not be performed because of a lack of appropriate tissue material. Finally, in the 4 remaining cases whose profile was NTRK3 split-negative and ETV6 split-positive, unknown (non-NTRK) genes appeared to fuse with ETV6 (ETV6-X fusion). In looking for possible fusion partners, analysis of rearrangement of other kinase genes known to fuse with ETV6 was also performed, but without positive results. Although numbers were small, correlating the clinico-pathologic features of the 4 ETV6-X fusion tumors and 5 MASC cases with atypical fusion transcripts raises the possibility of that they may behave more aggressively.

  4. FGFR-TACC gene fusions in human glioma.

    PubMed

    Lasorella, Anna; Sanson, Marc; Iavarone, Antonio

    2016-11-16

    Chromosomal translocations joining in-frame members of the fibroblast growth factor receptor-transforming acidic coiled-coil gene families (the FGFR-TACC gene fusions) were first discovered in human glioblastoma multiforme (GBM) and later in many other cancer types. Here, we review this rapidly expanding field of research and discuss the unique biological and clinical features conferred to isocitrate dehydrogenase wild-type glioma cells by FGFR-TACC fusions. FGFR-TACC fusions generate powerful oncogenes that combine growth-promoting effects with aneuploidy through the activation of as yet unclear intracellular signaling mechanisms. FGFR-TACC fusions appear to be clonal tumor-initiating events that confer strong sensitivity to FGFR tyrosine kinase inhibitors. Screening assays have recently been reported for the accurate identification of FGFR-TACC fusion variants in human cancer, and early clinical data have shown promising effects in cancer patients harboring FGFR-TACC fusions and treated with FGFR inhibitors. Thus, FGFR-TACC gene fusions provide a "low-hanging fruit" model for the validation of precision medicine paradigms in human GBM.

  5. Primary renal sclerosing epithelioid fibrosarcoma: report of 2 cases with EWSR1-CREB3L1 gene fusion.

    PubMed

    Argani, Pedram; Lewin, Jack R; Edmonds, Pamela; Netto, George J; Prieto-Granada, Carlos; Zhang, Lei; Jungbluth, Achim A; Antonescu, Cristina R

    2015-03-01

    We report the first 2 genetically confirmed cases of primary renal sclerosing epithelioid fibrosarcoma (SEF), occurring in a 17-year-old boy and a 61-year-old woman. In both cases, the tumors demonstrated the typical epithelioid clear cell morphology associated with extensive hyalinizing fibrosis, raising the differential diagnosis of solitary fibrous tumor, metanephric stromal tumor, and the sclerosing variant of clear cell sarcoma of the kidney. Both neoplasms demonstrated diffuse immunoreactivity for MUC4, a highly specific marker for SEF, and both demonstrated evidence of rearrangement of both the EWSR1 and CREB3L1 genes, which have recently been shown to be fused in this entity. Both neoplasms presented with metastatic disease. Primary renal SEF represents yet another translocation-associated sarcoma now shown to arise primarily in the kidney.

  6. INTRODUCTION: Status report on fusion research

    NASA Astrophysics Data System (ADS)

    Burkart, Werner

    2005-10-01

    A major milestone on the path to fusion energy was reached in June 2005 on the occasion of the signing of the joint declaration of all parties to the ITER negotiations, agreeing on future arrangements and on the construction site at Cadarache in France. The International Atomic Energy Agency has been promoting fusion activities since the late 1950s; it took over the auspices of the ITER Conceptual Design Activities in 1988, and of the ITER Engineering and Design Activities in 1992. The Agency continues its support to Member States through the organization of consultancies, workshops and technical meetings, the most prominent being the series of International Fusion Energy Conferences (formerly called the International Conference on Plasma Physics and Controlled Nuclear Fusion Research). The meetings serve as a platform for experts from all Member States to have open discussions on their latest accomplishments as well as on their problems and eventual solutions. The papers presented at the meetings and conferences are routinely published, many being sent to the journal it Nuclear Fusion, co-published monthly by Institute of Physics Publishing, Bristol, UK. The journal's reputation is reflected in the fact that it is a world-renowned publication, and the International Fusion Research Council has used it for the publication of a Status Report on Controlled Thermonuclear Fusion in 1978 and 1990. This present report marks the conclusion of the preparatory phases of ITER activities. It provides background information on the progress of fusion research within the last 15 years. The International Fusion Research Council (IFRC), which initiated the report, was fully aware of the complexities of including all scientific results in just one paper, and so decided to provide an overview and extensive references for the interested reader who need not necessarily be a fusion specialist. Professor Predhiman K. Kaw, Chairman, prepared the report on behalf of the IFRC, reflecting

  7. Gene Fusion Markup Language: a prototype for exchanging gene fusion data

    PubMed Central

    2012-01-01

    Background An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Results Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. Conclusion The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses. PMID:23072312

  8. Gene Fusion Markup Language: a prototype for exchanging gene fusion data.

    PubMed

    Kalyana-Sundaram, Shanker; Shanmugam, Achiraman; Chinnaiyan, Arul M

    2012-10-16

    An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses.

  9. Myeloid Neoplasms with t(5;12) and ETV6-ACSL6 Gene Fusion, Potential Mimickers of Myeloid Neoplasm with PDGFRB Rearrangement: Case Report with Imatinib Therapy and Review of the Literature

    PubMed Central

    Ninfea, Jose I. Ruades; Pearson, Lauren; Conant, Joanna; Bryant, Ronald; Zakai, Neil A.; Tang, Mary E.

    2016-01-01

    We report the second case of ETV6-ACSL6 associated myeloproliferative neoplasm that has received a full course of imatinib therapy. The patient was a 51-year-old previously healthy man who presented with three months of worsening dyspnea and was found to have a white count of 216,000/cmm, of which 84% were eosinophil lineage. Cytogenetic analysis revealed a t(5;12)(q31~33;p13). FISH was negative for PDGFRB rearrangement but additional FISH testing demonstrated an ACSL6 rearrangement. ETV6-ACSL6 gene fusion is a rare abnormality that most often presents as a myeloproliferative-type disorder with prominent eosinophilia or basophilia. Review of the literature yielded a total of 11 previous cases. This gene fusion results in a t(5;12)(q31~33;p13) that mimics the t(5;12) found in ETV6-PDGFRB neoplasms. Identification of the fusion genes involved in t(5;12) in eosinophilia-associated myeloproliferative disorders is crucial to direct an effective treatment plan. In particular, while tyrosine kinase inhibitor therapy is effective in patients with PDGFRB rearrangement, there is little information on imatinib efficacy in patients with ETV6-ACSL6 gene fusion. Our patient was found to be nonresponsive to imatinib therapy. PMID:27746819

  10. Optical coding of fusion genes using multicolor quantum dots for prostate cancer diagnosis.

    PubMed

    Lee, Hyojin; Kim, Chloe; Lee, Dongjin; Park, Jea Ho; Searson, Peter C; Lee, Kwan Hyi

    2017-01-01

    Recent studies have found that prostate cancer expresses abnormal genetic markers including multiple types of TMPRSS2-ERG fusion genes. The expression level of different TMPRSS2-ERG fusion genes is correlated to pathologic variables of aggressive prostate cancer and disease progression. State-of-the-art methods for detection of TMPRSS2-ERG fusion genes include reverse transcription polymerase chain reaction (RT-PCR) with a detection limit of 1 fmol at urinary condition. RT-PCR is time consuming, costly, and inapplicable for multiplexing. Ability to identify multiple fusion genes in a single sample has become important for diagnostic and clinical purposes. There is a need for a sensitive diagnostic test to detect multiple TMPRSS2-ERG fusion genes for an early diagnosis and prognosis of prostate cancer. Here, we propose to develop an assay for prostate cancer diagnosis using oligonucleotide-functionalized quantum dot and magnetic microparticle for optical detection of rearranged TMPRSS2-ERG fusion genes at a low concentration in urine. We found that our assay was able to identify three different types of fusion gene with a wide detection range and detection limit of 1 fmol (almost the same level of the RT-PCR result reported). Here, we show detection of multiple TMPRSS2-ERG fusion genes using color-coded oligonucleotides in cell lysate and urine.

  11. Identification of Targetable FGFR Gene Fusions in Diverse Cancers

    PubMed Central

    Wu, Yi-Mi; Su, Fengyun; Kalyana-Sundaram, Shanker; Khazanov, Nick; Ateeq, Bushra; Cao, Xuhong; Lonigro, Robert J.; Vats, Pankaj; Wang, Rui; Lin, Su-Fang; Cheng, Ann-Joy; Kunju, Lakshmi P.; Siddiqui, Javed; Tomlins, Scott A.; Wyngaard, Peter; Sadis, Seth; Roychowdhury, Sameek; Hussain, Maha H.; Feng, Felix Y.; Zalupski, Mark M.; Talpaz, Moshe; Pienta, Kenneth J.; Rhodes, Daniel R.; Robinson, Dan R.; Chinnaiyan, Arul M.

    2013-01-01

    Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2 including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR gene fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types. PMID:23558953

  12. Repeated Evolution of Chimeric Fusion Genes in the β-Globin Gene Family of Laurasiatherian Mammals

    PubMed Central

    Gaudry, Michael J.; Storz, Jay F.; Butts, Gary Tyler; Campbell, Kevin L.; Hoffmann, Federico G.

    2014-01-01

    The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB “Lepore” deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived “anti-Lepore” duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20–100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion. PMID:24814285

  13. Repeated evolution of chimeric fusion genes in the β-globin gene family of laurasiatherian mammals.

    PubMed

    Gaudry, Michael J; Storz, Jay F; Butts, Gary Tyler; Campbell, Kevin L; Hoffmann, Federico G

    2014-05-09

    The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB "Lepore" deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived "anti-Lepore" duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20-100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data.

    PubMed

    Thieme, Sebastian; Groth, Philip

    2013-03-15

    Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches. Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.

  15. Identification of targetable FGFR gene fusions in diverse cancers.

    PubMed

    Wu, Yi-Mi; Su, Fengyun; Kalyana-Sundaram, Shanker; Khazanov, Nickolay; Ateeq, Bushra; Cao, Xuhong; Lonigro, Robert J; Vats, Pankaj; Wang, Rui; Lin, Su-Fang; Cheng, Ann-Joy; Kunju, Lakshmi P; Siddiqui, Javed; Tomlins, Scott A; Wyngaard, Peter; Sadis, Seth; Roychowdhury, Sameek; Hussain, Maha H; Feng, Felix Y; Zalupski, Mark M; Talpaz, Moshe; Pienta, Kenneth J; Rhodes, Daniel R; Robinson, Dan R; Chinnaiyan, Arul M

    2013-06-01

    Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2, including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Because of the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts, which incorporate transcriptome analysis for gene fusions, are poised to identify rare, targetable FGFR fusions across diverse cancer types.

  16. Gene fusions with lacZ by duplication insertion in the radioresistant bacterium Deinococcus radiodurans

    SciTech Connect

    Lennon, E.; Minton, K.W. )

    1990-06-01

    Deinococcus radiodurans is the most-studied species of a eubacterial family characterized by extreme resistance to DNA damage. We have focused on developing molecular biological techniques to investigate the genetics of this organism. We report construction of lacZ gene fusions by a method involving both in vitro splicing and the natural transformation of D. radiodurans. Numerous fusion strains were identified by expression of beta-galactosidase. Among these fusion strains, several were inducible by exposure to the DNA-damaging agent mitomycin C, and four of the inducible fusion constructs were cloned in Escherichia coli. Hybridization studies indicate that one of the damage-inducible genes contains a sequence reiterated throughout the D. radiodurans chromosome. Survival measurements show that two of the fusion strains have increased sensitivity to mitomycin C, suggesting that the fusions within these strains inactivate repair functions.

  17. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer.

    PubMed

    Lu, Hengyu; Villafane, Nicole; Dogruluk, Turgut; Grzeskowiak, Caitlin L; Kong, Kathleen; Tsang, Yiu Huen; Zagorodna, Oksana; Pantazi, Angeliki; Yang, Lixing; Neill, Nicholas J; Kim, Young Won; Creighton, Chad J; Verhaak, Roel G; Mills, Gordon B; Park, Peter J; Kucherlapati, Raju; Scott, Kenneth L

    2017-07-01

    Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, BCR-ABL1, EML4-ALK, and ETV6-NTRK3, as well as 20 previously uncharacterized fusion genes identified in The Cancer Genome Atlas datasets. In addition to confirming oncogenic activity of the known fusion oncogenes engineered by our construction strategy, we validated five novel fusion genes involving MET, NTRK2, and BRAF kinases that exhibited potent transforming activity and conferred sensitivity to FDA-approved kinase inhibitors. Our fusion construction strategy also enabled domain-function studies of BRAF fusion genes. Our results confirmed other reports that the transforming activity of BRAF fusions results from truncation-mediated loss of inhibitory domains within the N-terminus of the BRAF protein. BRAF mutations residing within this inhibitory region may provide a means for BRAF activation in cancer, therefore we leveraged the modular design of our fusion gene construction methodology to screen N-terminal domain mutations discovered in tumors that are wild-type at the BRAF mutation hotspot, V600. We identified an oncogenic mutation, F247L, whose expression robustly activated the MAPK pathway and sensitized cells to BRAF and MEK inhibitors. When applied broadly, these tools will facilitate rapid fusion gene construction for subsequent functional characterization and translation into personalized treatment strategies. Cancer Res; 77(13); 3502-12. ©2017 AACR. ©2017 American Association for Cancer Research.

  18. Secretory carcinoma of the breast containing the ETV6-NTRK3 fusion gene in a male: case report and review of the literature

    PubMed Central

    Arce, C; Cortes-Padilla, D; Huntsman, DG; Miller, MA; Dueñnas-Gonzalez, A; Alvarado, A; Pérez, V; Gallardo-Rincón, D; Lara-Medina, F

    2005-01-01

    Background Secretory carcinoma (SC) of the breast is a rare and indolent tumor. Although originally described in children, it is now known to occur in adults of both sexes. Recently, the tumor was associated with the ETV6-NTRK3 gene translocation. Case presentation A 52-year-old male was diagnosed with secretory breast carcinoma and underwent a modified radical mastectomy. At 18 months the tumor recurred at the chest wall and the patient developed lung metastases. He was treated concurrently with radiation and chemotherapy without response. His tumor showed the ETV6-NTRK3 translocation as demonstrated by fluorescent in situ hybridization (FISH). Conclusion SC is a rare slow-growing tumor best treated surgically. There are insufficient data to support the use of adjuvant radiation or chemotherapy. Its association with the ETV6-NTRK3 fusion gene gives some clues for the better understanding of this neoplasm and eventually, the development of specific therapies. PMID:15963235

  19. A Plan for the Development of Fusion Energy. Final Report to Fusion Energy Sciences Advisory Committee, Fusion Development Path Panel

    SciTech Connect

    None, None

    2003-03-05

    This report presents a plan for the deployment of a fusion demonstration power plant within 35 years, leading to commercial application of fusion energy by mid-century. The plan is derived from the necessary features of a demonstration fusion power plant and from the time scale defined by President Bush. It identifies critical milestones, key decision points, needed major facilities and required budgets.

  20. BreakTrans: uncovering the genomic architecture of gene fusions.

    PubMed

    Chen, Ken; Navin, Nicholas E; Wang, Yong; Schmidt, Heather K; Wallis, John W; Niu, Beifang; Fan, Xian; Zhao, Hao; McLellan, Michael D; Hoadley, Katherine A; Mardis, Elaine R; Ley, Timothy J; Perou, Charles M; Wilson, Richard K; Ding, Li

    2013-08-23

    Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans.

  1. Gene Fusions in Soft Tissue Tumors: Recurrent and Overlapping Pathogenetic Themes

    PubMed Central

    Mertens, Fredrik; Antonescu, Cristina R.; Mitelman, Felix

    2016-01-01

    Gene fusions have been described in approximately one-third of soft tissue tumors (STT); of the 142 different fusions that have been reported, more than half are recurrent in the same histologic subtype. These gene fusions constitute pivotal driver mutations, and detailed studies of their cellular effects have provided important knowledge about pathogenetic mechanisms in STT. Furthermore, most fusions are strongly associated with a particular histotype, serving as ideal molecular diagnostic markers. In recent years, it has also become apparent that some chimeric proteins, directly or indirectly, constitute excellent treatment targets, making the detection of gene fusions in STT ever more important. Indeed, pharmacological treatment of STT displaying fusions that activate protein kinases, such as ALK and ROS1, or growth factors, such as PDGFB, is already in clinical use. However, the vast majority (52/78) of recurrent gene fusions create structurally altered and/or deregulated transcription factors, and a small but growing subset develops through rearranged chromatin regulators. The present review provides an overview of the spectrum of currently recognized gene fusions in STT, and, on the basis of the protein class involved, the mechanisms by which they exert their oncogenic effect are discussed. PMID:26684580

  2. Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes.

    PubMed

    Mertens, Fredrik; Antonescu, Cristina R; Mitelman, Felix

    2016-04-01

    Gene fusions have been described in approximately one-third of soft tissue tumors (STT); of the 142 different fusions that have been reported, more than half are recurrent in the same histologic subtype. These gene fusions constitute pivotal driver mutations, and detailed studies of their cellular effects have provided important knowledge about pathogenetic mechanisms in STT. Furthermore, most fusions are strongly associated with a particular histotype, serving as ideal molecular diagnostic markers. In recent years, it has also become apparent that some chimeric proteins, directly or indirectly, constitute excellent treatment targets, making the detection of gene fusions in STT ever more important. Indeed, pharmacological treatment of STT displaying fusions that activate protein kinases, such as ALK and ROS1, or growth factors, such as PDGFB, is already in clinical use. However, the vast majority (52/78) of recurrent gene fusions create structurally altered and/or deregulated transcription factors, and a small but growing subset develops through rearranged chromatin regulators. The present review provides an overview of the spectrum of currently recognized gene fusions in STT, and, on the basis of the protein class involved, the mechanisms by which they exert their oncogenic effect are discussed. © 2015 Wiley Periodicals, Inc.

  3. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma

    PubMed Central

    Parker, Brittany C.; Annala, Matti J.; Cogdell, David E.; Granberg, Kirsi J.; Sun, Yan; Ji, Ping; Li, Xia; Gumin, Joy; Zheng, Hong; Hu, Limei; Yli-Harja, Olli; Haapasalo, Hannu; Visakorpi, Tapio; Liu, Xiuping; Liu, Chang-gong; Sawaya, Raymond; Fuller, Gregory N.; Chen, Kexin; Lang, Frederick F.; Nykter, Matti; Zhang, Wei

    2013-01-01

    Fusion genes are chromosomal aberrations that are found in many cancers and can be used as prognostic markers and drug targets in clinical practice. Fusions can lead to production of oncogenic fusion proteins or to enhanced expression of oncogenes. Several recent studies have reported that some fusion genes can escape microRNA regulation via 3′–untranslated region (3′-UTR) deletion. We performed whole transcriptome sequencing to identify fusion genes in glioma and discovered FGFR3-TACC3 fusions in 4 of 48 glioblastoma samples from patients both of mixed European and of Asian descent, but not in any of 43 low-grade glioma samples tested. The fusion, caused by tandem duplication on 4p16.3, led to the loss of the 3′-UTR of FGFR3, blocking gene regulation of miR-99a and enhancing expression of the fusion gene. The fusion gene was mutually exclusive with EGFR, PDGFR, or MET amplification. Using cultured glioblastoma cells and a mouse xenograft model, we found that fusion protein expression promoted cell proliferation and tumor progression, while WT FGFR3 protein was not tumorigenic, even under forced overexpression. These results demonstrated that the FGFR3-TACC3 gene fusion is expressed in human cancer and generates an oncogenic protein that promotes tumorigenesis in glioblastoma. PMID:23298836

  4. Origin and Ascendancy of a Chimeric Fusion Gene: The β/δ-Globin Gene of Paenungulate Mammals

    PubMed Central

    Opazo, Juan C.; Sloan, Angela M.; Campbell, Kevin L.

    2009-01-01

    The δ-globin gene (HBD) of eutherian mammals exhibits a propensity for recombinational exchange with the closely linked β-globin gene (HBB) and has been independently converted by the HBB gene in multiple lineages. Here we report the presence of a chimeric β/δ fusion gene in the African elephant (Loxodonta africana) that was created by unequal crossing-over between misaligned HBD and HBB paralogs. The recombinant chromosome that harbors the β/δ fusion gene in elephants is structurally similar to the “anti-Lepore” duplication mutant of humans (the reciprocal exchange product of the hemoglobin Lepore deletion mutant). However, the situation in the African elephant is unique in that the chimeric β/δ fusion gene supplanted the parental HBB gene and is therefore solely responsible for synthesizing the β-chain subunits of adult hemoglobin. A phylogenetic survey of β-like globin genes in afrotherian and xenarthran mammals revealed that the origin of the chimeric β/δ fusion gene and the concomitant inactivation of the HBB gene predated the radiation of “Paenungulata,” a clade of afrotherian mammals that includes three orders: Proboscidea (elephants), Sirenia (dugongs and manatees), and Hyracoidea (hyraxes). The reduced fitness of the human Hb Lepore deletion mutant helps to explain why independently derived β/δ fusion genes (which occur on an anti-Lepore chromosome) have been fixed in a number of mammalian lineages, whereas the reciprocal δ/β fusion gene (which occurs on a Lepore chromosome) has yet to be documented in any nonhuman mammal. This illustrates how the evolutionary fates of chimeric fusion genes can be strongly influenced by their recombinational mode of origin. PMID:19332641

  5. Magnetized Target Fusion Collaboration. Final report

    SciTech Connect

    Slough, John

    2012-04-18

    Nuclear fusion has the potential to satisfy the prodigious power that the world will demand in the future, but it has yet to be harnessed as a practical energy source. The entry of fusion as a viable, competitive source of power has been stymied by the challenge of finding an economical way to provide for the confinement and heating of the plasma fuel. It is the contention here that a simpler path to fusion can be achieved by creating fusion conditions in a different regime at small scale (~ a few cm). One such program now under study, referred to as Magnetized Target Fusion (MTF), is directed at obtaining fusion in this high energy density regime by rapidly compressing a compact toroidal plasmoid commonly referred to as a Field Reversed Configuration (FRC). To make fusion practical at this smaller scale, an efficient method for compressing the FRC to fusion gain conditions is required. In one variant of MTF a conducting metal shell is imploded electrically. This radially compresses and heats the FRC plasmoid to fusion conditions. The closed magnetic field in the target plasmoid suppresses the thermal transport to the confining shell, thus lowering the imploding power needed to compress the target. The undertaking described in this report was to provide a suitable target FRC, as well as a simple and robust method for inserting and stopping the FRC within the imploding liner. The FRC must also survive during the time it takes for the metal liner to compress the FRC target. The initial work at the UW was focused on developing adequate preionization and flux trapping that were found to be essential in past experiments for obtaining the density, flux and most critically, FRC lifetime required for MTF. The timescale for testing and development of such a source can be rapidly accelerated by taking advantage of a new facility funded by the Department of Energy. At this facility, two inductive plasma accelerators (IPA) were constructed and tested. Recent experiments with

  6. Transforming fusions of FGFR and TACC genes in human glioblastoma.

    PubMed

    Singh, Devendra; Chan, Joseph Minhow; Zoppoli, Pietro; Niola, Francesco; Sullivan, Ryan; Castano, Angelica; Liu, Eric Minwei; Reichel, Jonathan; Porrati, Paola; Pellegatta, Serena; Qiu, Kunlong; Gao, Zhibo; Ceccarelli, Michele; Riccardi, Riccardo; Brat, Daniel J; Guha, Abhijit; Aldape, Ken; Golfinos, John G; Zagzag, David; Mikkelsen, Tom; Finocchiaro, Gaetano; Lasorella, Anna; Rabadan, Raul; Iavarone, Antonio

    2012-09-07

    The brain tumor glioblastoma multiforme (GBM) is among the most lethal forms of human cancer. Here, we report that a small subset of GBMs (3.1%; 3 of 97 tumors examined) harbors oncogenic chromosomal translocations that fuse in-frame the tyrosine kinase coding domains of fibroblast growth factor receptor (FGFR) genes (FGFR1 or FGFR3) to the transforming acidic coiled-coil (TACC) coding domains of TACC1 or TACC3, respectively. The FGFR-TACC fusion protein displays oncogenic activity when introduced into astrocytes or stereotactically transduced in the mouse brain. The fusion protein, which localizes to mitotic spindle poles, has constitutive kinase activity and induces mitotic and chromosomal segregation defects and triggers aneuploidy. Inhibition of FGFR kinase corrects the aneuploidy, and oral administration of an FGFR inhibitor prolongs survival of mice harboring intracranial FGFR3-TACC3-initiated glioma. FGFR-TACC fusions could potentially identify a subset of GBM patients who would benefit from targeted FGFR kinase inhibition.

  7. Molecular pathways: targeting ETS gene fusions in cancer.

    PubMed

    Feng, Felix Y; Brenner, J Chad; Hussain, Maha; Chinnaiyan, Arul M

    2014-09-01

    Rearrangements, or gene fusions, involving the ETS family of transcription factors are common driving events in both prostate cancer and Ewing sarcoma. These rearrangements result in pathogenic expression of the ETS genes and trigger activation of transcriptional programs enriched for invasion and other oncogenic features. Although ETS gene fusions represent intriguing therapeutic targets, transcription factors, such as those comprising the ETS family, have been notoriously difficult to target. Recently, preclinical studies have demonstrated an association between ETS gene fusions and components of the DNA damage response pathway, such as PARP1, the catalytic subunit of DNA protein kinase (DNAPK), and histone deactylase 1 (HDAC1), and have suggested that ETS fusions may confer sensitivity to inhibitors of these DNA repair proteins. In this review, we discuss the role of ETS fusions in cancer, the preclinical rationale for targeting ETS fusions with inhibitors of PARP1, DNAPK, and HDAC1, as well as ongoing clinical trials targeting ETS gene fusions. ©2014 American Association for Cancer Research.

  8. Inertial Confinement Fusion Annual Report 1997

    SciTech Connect

    Correll, D

    1998-06-01

    The ICF Annual Report provides documentation of the achievements of the LLNL ICF Program during the fiscal year by the use of two formats: (1) an Overview that is a narrative summary of important results for the fiscal year and (2) a compilation of the articles that previously appeared in the ICF Quarterly Report that year. Both the Overview and Quarterly Report are also on the Web at http://lasers.llnl.gov/lasers/pubs/icfq.html. Beginning in Fiscal Year 1997, the fourth quarter issue of the ICF Quarterly was no longer printed as a separate document but rather included in the ICF Annual. This change provided a more efficient process of documenting our accomplishments with-out unnecessary duplication of printing. In addition we introduced a new document, the ICF Program Monthly Highlights. Starting with the September 1997 issue and each month following, the Monthly Highlights will provide a brief description of noteworthy activities of interest to our DOE sponsors and our stakeholders. The underlying theme for LLNL's ICF Program research continues to be defined within DOE's Defense Programs missions and goals. In support of these missions and goals, the ICF Program advances research and technology development in major interrelated areas that include fusion target theory and design, target fabrication, target experiments, and laser and optical science and technology. While in pursuit of its goal of demonstrating thermonuclear fusion ignition and energy gain in the laboratory, the ICF Program provides research and development opportunities in fundamental high-energy-density physics and supports the necessary research base for the possible long-term application of inertial fusion energy for civilian power production. ICF technologies continue to have spin-off applications for additional government and industrial use. In addition to these topics, the ICF Annual Report covers non-ICF funded, but related, laser research and development and associated applications. We also

  9. Fusion Power Program biannual progress report, April-September 1979

    SciTech Connect

    Not Available

    1980-02-01

    This biannual report summarizes the Argonne National Laboratory work performed for the Office of Fusion Energy during the April-September 1979 quarter in the following research and development areas: materials; energy storage and transfer; tritium containment, recovery and control; advanced reactor design; atomic data; reactor safety; fusion-fission hybrid systems; alternate applications of fusion energy; and other work related to fusion power. Separate abstracts were prepared for three sections. (MOW)

  10. Primary intracerebral angiomatoid fibrous histiocytoma: report of a case with a t(12;22)(q13;q12) causing type 1 fusion of the EWS and ATF-1 genes.

    PubMed

    Dunham, Christopher; Hussong, Jerry; Seiff, Michael; Pfeifer, John; Perry, Arie

    2008-03-01

    Angiomatoid fibrous histiocytoma (AFH) is generally considered a soft tissue sarcoma of low malignant potential that occurs in children/young adults and most frequently affects the extremities. AFH infrequently recurs and rarely metastasizes. AFH has a characteristic histomorphology, and immunohistochemical reactivities for desmin and CD68 have led to myofibroblastic and fibrohistiocytic histogenetic hypotheses, respectively. Although only a limited number of AFH cases have been molecularly characterized, many have demonstrated evidence of an underlying translocation event. Reverse transcription-polymerase chain reaction and fluorescence in situ hybridization studies suggest that chromosomal rearrangement in AFH most frequently involve the EWS, CREB, ATF-1, and FUS genes. We report the first pathologically confirmed case of an AFH presenting as an intracerebral primary in a previously healthy 25-year-old man. Genetic analyses revealed a t(12;22)(q13;q12) and a unique underlying clear cell sarcomalike type 1 EWS/ATF-1 gene fusion.

  11. FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples.

    PubMed

    Paciello, Giulia; Ficarra, Elisa

    2017-01-23

    Latest Next Generation Sequencing technologies opened the way to a novel era of genomic studies, allowing to gain novel insights into multifactorial pathologies as cancer. In particular gene fusion detection and comprehension have been deeply enhanced by these methods. However, state of the art algorithms for gene fusion identification are still challenging. Indeed, they identify huge amounts of poorly overlapping candidates and all the reported fusions should be considered for in lab validation clearly overwhelming wet lab capabilities. In this work we propose a novel methodological approach and tool named FuGePrior for the prioritization of gene fusions from paired-end RNA-Seq data. The proposed pipeline combines state of the art tools for chimeric transcript discovery and prioritization, a series of filtering and processing steps designed by considering modern literature on gene fusions and an analysis on functional reliability of gene fusion structure. FuGePrior performance has been assessed on two publicly available paired-end RNA-Seq datasets: The first by Edgren and colleagues includes four breast cancer cell lines and a normal breast sample, whereas the second by Ren and colleagues comprises fourteen primary prostate cancer samples and their paired normal counterparts. FuGePrior results accounted for a reduction in the number of fusions output of chimeric transcript discovery tools that ranges from 65 to 75% depending on the considered breast cancer cell line and from 37 to 65% according to the prostate cancer sample under examination. Furthermore, since both datasets come with a partial validation we were able to assess the performance of FuGePrior in correctly prioritizing real gene fusions. Specifically, 25 out of 26 validated fusions in breast cancer dataset have been correctly labelled as reliable and biologically significant. Similarly, 2 out of 5 validated fusions in prostate dataset have been recognized as priority by FuGePrior tool.

  12. Particle beam fusion progress report for 1989

    SciTech Connect

    Sweeney, M.A.

    1994-08-01

    This report summarizes the progress on the pulsed power approach to inertial confinement fusion. In 1989, the authors achieved a proton focal intensity of 5 TW/cm{sup 2} on PBFA-II in a 15-cm-radius applied magnetic-field (applied-B) ion diode. This is an improvement by a factor of 4 compared to previous PBFA-II experiments. They completed development of the three-dimensional (3-D), electromagnetic, particle-in-cell code QUICKSILVER and obtained the first 3-D simulations of an applied-B ion diode. The simulations, together with analytic theory, suggest that control of electromagnetic instabilities could reduce ion divergence. In experiments using a lithium fluoride source, they delivered 26 kJ of lithium energy to the diode axis. Rutherford-scattered ion diagnostics have been developed and tested using a conical foil located inside the diode. They can now obtain energy density profiles by using range filters and recording ion images on nuclear track recording film. Timing uncertainties in power flow experiments on PBFA-II have been reduced by a factor of 5. They are investigating three plasma opening switches that use magnetic fields to control and confine the injected plasma. These new switches provide better power flow than the standard plasma erosion switch. Advanced pulsed-power fusion drivers will require extraction-geometry applied-B ion diodes. During this reporting period, progress was made in evaluating the generation, transport, and focus of multiple ion beams in an extraction geometry and in assessing the probable damage to a target chamber first wall.

  13. Pinpointing disease genes through phenomic and genomic data fusion

    PubMed Central

    2015-01-01

    Background Pinpointing genes involved in inherited human diseases remains a great challenge in the post-genomics era. Although approaches have been proposed either based on the guilt-by-association principle or making use of disease phenotype similarities, the low coverage of both diseases and genes in existing methods has been preventing the scan of causative genes for a significant proportion of diseases at the whole-genome level. Results To overcome this limitation, we proposed a rigorous statistical method called pgFusion to prioritize candidate genes by integrating one type of disease phenotype similarity derived from the Unified Medical Language System (UMLS) and seven types of gene functional similarities calculated from gene expression, gene ontology, pathway membership, protein sequence, protein domain, protein-protein interaction and regulation pattern, respectively. Our method covered a total of 7,719 diseases and 20,327 genes, achieving the highest coverage thus far for both diseases and genes. We performed leave-one-out cross-validation experiments to demonstrate the superior performance of our method and applied it to a real exome sequencing dataset of epileptic encephalopathies, showing the capability of this approach in finding causative genes for complex diseases. We further provided the standalone software and online services of pgFusion at http://bioinfo.au.tsinghua.edu.cn/jianglab/pgfusion. Conclusions pgFusion not only provided an effective way for prioritizing candidate genes, but also demonstrated feasible solutions to two fundamental questions in the analysis of big genomic data: the comparability of heterogeneous data and the integration of multiple types of data. Applications of this method in exome or whole genome sequencing studies would accelerate the finding of causative genes for human diseases. Other research fields in genomics could also benefit from the incorporation of our data fusion methodology. PMID:25708473

  14. Pinpointing disease genes through phenomic and genomic data fusion.

    PubMed

    Jiang, Rui; Wu, Mengmeng; Li, Lianshuo

    2015-01-01

    Pinpointing genes involved in inherited human diseases remains a great challenge in the post-genomics era. Although approaches have been proposed either based on the guilt-by-association principle or making use of disease phenotype similarities, the low coverage of both diseases and genes in existing methods has been preventing the scan of causative genes for a significant proportion of diseases at the whole-genome level. To overcome this limitation, we proposed a rigorous statistical method called pgFusion to prioritize candidate genes by integrating one type of disease phenotype similarity derived from the Unified Medical Language System (UMLS) and seven types of gene functional similarities calculated from gene expression, gene ontology, pathway membership, protein sequence, protein domain, protein-protein interaction and regulation pattern, respectively. Our method covered a total of 7,719 diseases and 20,327 genes, achieving the highest coverage thus far for both diseases and genes. We performed leave-one-out cross-validation experiments to demonstrate the superior performance of our method and applied it to a real exome sequencing dataset of epileptic encephalopathies, showing the capability of this approach in finding causative genes for complex diseases. We further provided the standalone software and online services of pgFusion at http://bioinfo.au.tsinghua.edu.cn/jianglab/pgfusion. pgFusion not only provided an effective way for prioritizing candidate genes, but also demonstrated feasible solutions to two fundamental questions in the analysis of big genomic data: the comparability of heterogeneous data and the integration of multiple types of data. Applications of this method in exome or whole genome sequencing studies would accelerate the finding of causative genes for human diseases. Other research fields in genomics could also benefit from the incorporation of our data fusion methodology.

  15. Patient Reported Outcomes from Sacroiliac Joint Fusion

    PubMed Central

    McGowan, Shane M.; Audley, Brittany N.; Sokunbi, Gbolabo; Puccio, Steven T.

    2017-01-01

    Study Design Retrospective, case series. Purpose The purpose of this study is to determine morbidity, complications, and patient reported outcomes from minimally invasive sacroiliac joint (SIJ) fusion. Overview of Literature Lumbar back pain emanating from the SIJ can be surgically treated via a percutaneous approach in the appropriately selected patient with minimal morbidity and acceptable functional outcomes. Methods Patients diagnosed by >2 physical examination maneuvers and subjective relief from a computed tomography–guided lidocaine-bupivacaine-steroid injection underwent SIJ fusion after failing conservative management with a combination of oral anti-inflammatory medications, physical therapy, and pelvic belt stabilization. Perioperative data collected include estimated blood loss (EBL) and operative time. Oswestry disability index, 12-item short form health survey (SF-12), visual analogue score, and functional status were analyzed. All complications were noted. Results The study cohort of 45 cases (69% female) achieved postoperative survey follow-up at 9.9 and 32.3 months. SF-12 physical component summary statistically improved while all other scores were equivalent. Mean EBL and operative time were 22 mL and 36 minutes, respectively. Initial survey showed that 64% of patients discontinued narcotics (29/45), 71% do not use an assistive device (32/45), and 15.6% do not work due to pain (7/45). 73% of patients stated they would have the surgery again (33/45). For the second survey, 65% of patients discontinued narcotics (26/40), 70% did not use an assistive device (28/40), and 17.5% did not work due to pain (7/40). A history of thoracolumbar instrumentation (16/45) did not significantly affect outcomes. Three complications described by screw malposition with neurologic deficit (6.7%) were treated with screw repositioning (1 case) and removal of a single superior implant (2 cases) with time to revision of 2.2 months. All three ultimately had resolution of

  16. Identification of KANSARL as the first cancer predisposition fusion gene specific to the population of European ancestry origin

    PubMed Central

    Wang, Ling; Wang, Kesheng; Zhang, Yanbin; Yuan, Fenghua; Li, Fengli; Zhuo, David D.; Tang, Liren; Zhuo, Degen

    2017-01-01

    Gene fusion is one of the hallmarks of cancer. Recent advances in RNA-seq of cancer transcriptomes have facilitated the discovery of fusion transcripts. In this study, we report identification of a surprisingly large number of fusion transcripts, including six KANSARL (KANSL1-ARL17A) transcripts that resulted from the fusion between the KANSL1 and ARL17A genes using a RNA splicingcode model. Five of these six KANSARL fusion transcripts are novel. By systematic analysis of RNA-seq data of glioblastoma, prostate cancer, lung cancer, breast cancer, and lymphoma from different regions of the World, we have found that KANSARL fusion transcripts were rarely detected in the tumors of individuals from Asia or Africa. In contrast, they exist in 30 - 52% of the tumors from North Americans cancer patients. Analysis of CEPH/Utah Pedigree 1463 has revealed that KANSARL is a familially-inherited fusion gene. Further analysis of RNA-seq datasets of the 1000 Genome Project has indicated that KANSARL fusion gene is specific to 28.9% of the population of European ancestry origin. In summary, we demonstrated that KANSARL is the first cancer predisposition fusion gene associated with genetic backgrounds of European ancestry origin. PMID:28881586

  17. Analysis of mammary specific gene locus regulation in differentiated cells derived by somatic cell fusion

    SciTech Connect

    Robinson, Claire; Kolb, Andreas F.

    2009-02-01

    The transcriptional regulation of a gene is best analysed in the context of its normal chromatin surroundings. However, most somatic cells, in contrast to embryonic stem cells, are refractory to accurate modification by homologous recombination. We show here that it is possible to introduce precise genomic modifications in ES cells and to analyse the phenotypic consequences in differentiated cells by using a combination of gene targeting, site-specific recombination and somatic cell fusion. To provide a proof of principle, we have analysed the regulation of the casein gene locus in mammary gland cells derived from modified murine ES cells by somatic cell fusion. A {beta}-galactosidase reporter gene was inserted in place of the {beta}-casein gene and the modified ES cells, which do not express the reporter gene, were fused with the mouse mammary gland cell line HC11. The resulting cell clones expressed the {beta}-galactosidase gene to a similar extent and with similar hormone responsiveness as the endogenous gene. However, a reporter gene under the control of a minimal {beta}-casein promoter (encompassing the two consensus STAT5 binding sites which mediate the hormone response of the casein genes) was unable to replicate expression levels or hormone responsiveness of the endogenous gene when inserted into the same site of the casein locus. As expected, these results implicate sequences other than the STAT5 sites in the regulation of the {beta}-casein gene.

  18. Mammary analogue secretory carcinoma of salivary glands with high-grade transformation: report of 3 cases with the ETV6-NTRK3 gene fusion and analysis of TP53, β-catenin, EGFR, and CCND1 genes.

    PubMed

    Skálová, Alena; Vanecek, Tomas; Majewska, Hanna; Laco, Jan; Grossmann, Petr; Simpson, Roderick H W; Hauer, Lukas; Andrle, Pavel; Hosticka, Lubor; Branžovský, Jindrich; Michal, Michal

    2014-01-01

    Mammary analogue secretory carcinoma of salivary gland origin (MASC) is a recently described tumor resembling secretory carcinoma of the breast characterized by strong S-100 protein, mammaglobin, and vimentin immunoexpression and which harbors a t(12;15) (p13;q25) translocation resulting in ETV6-NTRK3 fusion product. Histologically, conventional MASC displays bland histomorphology and a lobulated growth pattern and is often composed of microcystic, tubular, and solid structures with abundant eosinophilic homogenous or bubbly secretions. Colloid-like secretory material stains positively for periodic acid-Schiff with and without diastase as well as for Alcian Blue. We present for the first time, 3 patients with MASC of the parotid gland in which high-grade (HG) transformation developed in each case characterized by an accelerated clinical course and poor outcome. The HG component revealed strong membrane staining for EGFR and β-catenin, cytoplasmic/nuclear staining for S-100 protein, and nuclear staining for cyclin-D1, whereas HER-2/neu was absent. Analysis for the presence of the ETV6-NTRK3 fusion transcript revealed positivity in both HG and low-grade component of MASC in 2 of the 3 studied cases. The tumor in case 2 was negative in both its elements for the t(12;15) translocation, but ETV6 gene rearrangement was detected in both components in all 3 cases. Analysis of TP53 and CTNNB1 gene mutations in the HG component of MASCs as well as detection of copy number aberration of EGFR and CCND1 gene did not harbor any abnormalities. All 3 patients with HG-transformed MASC died of disseminated disease within 2 to 6 years after diagnosis. Recognizing HG-transformed MASC and testing for ETV6 rearrangement may be of potential value in patient treatment, because the presence of the ETV6-NTRK3 translocation may represent a therapeutic target in MASC.

  19. ETS Gene Fusions as Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer

    DTIC Science & Technology

    2013-08-01

    University of Michigan Ann Arbor, MI 48109 REPORT DATE: August 2013 TYPE OF REPORT: Annual ummary PREPARED FOR: U.S. Army Medical...2. REPORT TYPE Annual 3. DATES COVERED 15 July 2012 to 14 July 2013 4. TITLE AND SUBTITLE ETS Gene Fusions as Predictive Biomarkers of...wild- type prostate cancer cells and human prostate cancer samples (data not shown). Unfortunately, this level of homogenous diffuse expression, as well

  20. Inference of gene function based on gene fusion events: the rosetta-stone method.

    PubMed

    Suhre, Karsten

    2007-01-01

    The method described in this chapter can be used to infer putative functional links between two proteins. The basic idea is based on the principle of "guilt by association." It is assumed that two proteins, which are found to be transcribed by a single transcript in one (or several) genomes are likely to be functionally linked, for example by acting in a same metabolic pathway or by forming a multiprotein complex. This method is of particular interest for studying genes that exhibit no, or only remote, homologies with already well-characterized proteins. Combined with other non-homology based methods, gene fusion events may yield valuable information for hypothesis building on protein function, and may guide experimental characterization of the target protein, for example by suggesting potential ligands or binding partners. This chapter uses the FusionDB database (http://www.igs.cnrs-mrs.fr/FusionDB/) as source of information. FusionDB provides a characterization of a large number of gene fusion events at hand of multiple sequence alignments. Orthologous genes are included to yield a comprehensive view of the structure of a gene fusion event. Phylogenetic tree reconstruction is provided to evaluate the history of a gene fusion event, and three-dimensional protein structure information is used, where available, to further characterize the nature of the gene fusion. For genes that are not comprised in FusionDB, some instructions are given as how to generate a similar type of information, based solely on publicly available web tools that are listed here.

  1. InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

    PubMed Central

    Okonechnikov, Konstantin; Imai-Matsushima, Aki; Seitz, Alexander; Meyer, Thomas F.; Garcia-Alcalde, Fernando

    2016-01-01

    Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found. The ability to detect gene fusions of different types, including isoform fusions and fusions involving non-coding regions, has not been thoroughly studied yet. Here, we propose a novel computational toolkit called InFusion for fusion gene detection from RNA-seq data. InFusion introduces several unique features, such as discovery of fusions involving intergenic regions, and detection of anti-sense transcription in chimeric RNAs based on strand-specificity. Our approach demonstrates superior detection accuracy on simulated data and several public RNA-seq datasets. This improved performance was also evident when evaluating data from RNA deep-sequencing of two well-established prostate cancer cell lines. InFusion identified 26 novel fusion events that were validated in vitro, including alternatively spliced gene fusion isoforms and chimeric transcripts that include intergenic regions. The toolkit is freely available to download from http:/bitbucket.org/kokonech/infusion. PMID:27907167

  2. InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.

    PubMed

    Okonechnikov, Konstantin; Imai-Matsushima, Aki; Paul, Lukas; Seitz, Alexander; Meyer, Thomas F; Garcia-Alcalde, Fernando

    2016-01-01

    Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found. The ability to detect gene fusions of different types, including isoform fusions and fusions involving non-coding regions, has not been thoroughly studied yet. Here, we propose a novel computational toolkit called InFusion for fusion gene detection from RNA-seq data. InFusion introduces several unique features, such as discovery of fusions involving intergenic regions, and detection of anti-sense transcription in chimeric RNAs based on strand-specificity. Our approach demonstrates superior detection accuracy on simulated data and several public RNA-seq datasets. This improved performance was also evident when evaluating data from RNA deep-sequencing of two well-established prostate cancer cell lines. InFusion identified 26 novel fusion events that were validated in vitro, including alternatively spliced gene fusion isoforms and chimeric transcripts that include intergenic regions. The toolkit is freely available to download from http:/bitbucket.org/kokonech/infusion.

  3. Gene Prioritization by Compressive Data Fusion and Chaining

    PubMed Central

    Žitnik, Marinka; Nam, Edward A.; Dinh, Christopher; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaž

    2015-01-01

    Data integration procedures combine heterogeneous data sets into predictive models, but they are limited to data explicitly related to the target object type, such as genes. Collage is a new data fusion approach to gene prioritization. It considers data sets of various association levels with the prediction task, utilizes collective matrix factorization to compress the data, and chaining to relate different object types contained in a data compendium. Collage prioritizes genes based on their similarity to several seed genes. We tested Collage by prioritizing bacterial response genes in Dictyostelium as a novel model system for prokaryote-eukaryote interactions. Using 4 seed genes and 14 data sets, only one of which was directly related to the bacterial response, Collage proposed 8 candidate genes that were readily validated as necessary for the response of Dictyostelium to Gram-negative bacteria. These findings establish Collage as a method for inferring biological knowledge from the integration of heterogeneous and coarsely related data sets. PMID:26465776

  4. Fusion safety program Annual report, Fiscal year 1995

    SciTech Connect

    Longhurst, G.R.; Cadwallader, L.C.; Carmack, W.J.

    1995-12-01

    This report summarizes the major activities of the Fusion Safety Program in FY-95. The Idaho National Engineering Laboratory (INEL) is the designated lead laboratory, and Lockheed Idaho Technologies Company is the prime contractor for this program. The Fusion Safety Program was initiated in 1979. Activities are conducted at the INEL, at other DOE laboratories, and at other institutions. Among the technical areas covered in this report are tritium safety, beryllium safety, chemical reactions and activation product release, safety aspects of fusion magnet systems, plasma disruptions, risk assessment failure rate database development, and safety code development and application to fusion safety issues. Most of this work has been done in support of the International Thermonuclear Experimental Reactor (ITER). Also included in the report are summaries of the safety and environmental studies performed by the Fusion Safety Program for the Tokamak Physics Experiment and the Tokamak Fusion Test Reactor and the technical support for commercial fusion facility conceptual design studies. A final activity described is work to develop DOE Technical Standards for Safety of Fusion Test Facilities.

  5. Fusion Safety Program annual report, fiscal year 1994

    SciTech Connect

    Longhurst, G.R.; Cadwallader, L.C.; Dolan, T.J.; Herring, J.S.; McCarthy, K.A.; Merrill, B.J.; Motloch, C.G.; Petti, D.A.

    1995-03-01

    This report summarizes the major activities of the Fusion Safety Program in fiscal year 1994. The Idaho National Engineering Laboratory (INEL) is the designated lead laboratory and Lockheed Idaho Technologies Company is the prime contractor for this program. The Fusion Safety Program was initiated in 1979. Activities are conducted at the INEL, at other DOE laboratories, and at other institutions, including the University of Wisconsin. The technical areas covered in this report include tritium safety, beryllium safety, chemical reactions and activation product release, safety aspects of fusion magnet systems, plasma disruptions, risk assessment failure rate data base development, and thermalhydraulics code development and their application to fusion safety issues. Much of this work has been done in support of the International Thermonuclear Experimental Reactor (ITER). Also included in the report are summaries of the safety and environmental studies performed by the Fusion Safety Program for the Tokamak Physics Experiment and the Tokamak Fusion Test Reactor and of the technical support for commercial fusion facility conceptual design studies. A major activity this year has been work to develop a DOE Technical Standard for the safety of fusion test facilities.

  6. Fundamental studies of fusion plasmas. Final report

    SciTech Connect

    Aamodt, R.E.

    1998-01-30

    Lodestar has carried out a vigorous research program in the areas of rf, edge plasma and divertor physics, with emphasis largely geared towards improving the understanding and performance of ion-cyclotron heating and current drive (ICRF) systems. Additionally, a research program in the field of edge plasma and divertor modeling was initiated. Theoretical work on high power rf sheath formation for multi-strap rf arrays was developed and benchmarked against recent experimental data from the new JET A2 antennas. Sophisticated modeling tools were employed to understand the sheath formation taking into account realistic three-dimensional antenna geometry. A novel physics explanation of an observed anomaly in the low power loading of antennas was applied to qualitatively interpret data on DIII-D in terms of rf sheaths, and potential applications of the idea to develop a near-field sheath diagnostic were explored. Other rf-wave related topics were also investigated. Full wave ICRF modeling studies were carried out in support of ongoing and planned tokamaks experiments, including the investigation of low frequency plasma heating and current drive regimes for IGNITOR. In a cross-disciplinary study involving both MHD and ICRF physics, ponderomotive feedback stabilization by rf was investigated as a potential means of controlling external kink mode disruptions. In another study, the instability of the ion hybrid wave (IHW) in the presence of fusion alpha particles was studied. In the field of edge plasma and divertor modeling studies, Lodestar began the development of a theory of generalized ballooning and sheath instabilities in the scrape off layer (SOL) of divertor tokamaks. A detailed summary of the technical progress in these areas during the contract period is included, as well as where references to published work can be found. A separate listing of publications, meeting abstracts, and other presentations is also given at the end of this final report.

  7. Discovery of human-similar gene fusions in canine cancers.

    PubMed

    Ulvé, Ronan; Rault, Mélanie; Bahin, Mathieu; Lagoutte, Laetitia; Abadie, Jérôme; De Brito, Clotilde; Coindre, Jean-Michel; Botherel, Nadine; Rousseau, Audrey; Wucher, Valentin; Cadieu, Edouard; Thieblemont, Catherine; Hitte, Christophe; Cornevin, Laurence; Cabillic, Florian; Bachelot, Laura; Gilot, David; Hennuy, Benoit; Guillaudeux, Thierry; Le Goff, Arnaud; Derrien, Thomas; Hédan, Benoît; André, Catherine

    2017-09-07

    Canine cancers represent a tremendous natural resource due to their incidence and striking similarities to human cancers, sharing similar clinical and pathological features as well as oncogenic events including identical somatic mutations. Considering the importance of gene fusions as driver alterations, we explored their relevance in canine cancers. We focused on three distinct human-comparable canine cancers representing different tissues and embryonic origins. Through RNA-Seq, we discovered similar gene fusions as those found in their human counterparts: IGK-CCND3 in B-cell lymphoma, MPB-BRAF in glioma, and COL3A1-PDGFB in dermatofibrosarcoma protuberans-like. We showed not only similar partner genes but also identical breakpoints leading to oncogene overexpression. This study demonstrates similar gene fusion partners and mechanisms in human-dog corresponding tumors and allows for selection of targeted therapies in preclinical and clinical trials with pet dogs prior to human trials, within the framework of personalized medicine. Copyright ©2017, American Association for Cancer Research.

  8. The EWS–Oct-4 fusion gene encodes a transforming gene

    PubMed Central

    Lee, Jungwoon; Kim, Ja Young; Kang, In Young; Kim, Hye Kyoung; Han, Yong-Mahn; Kim, Jungho

    2007-01-01

    The t(6;22)(p21;q12) translocation associated with human bone and soft-tissue tumours results in a chimaeric molecule fusing the NTD (N-terminal domain) of the EWS (Ewing's sarcoma) gene to the CTD (C-terminal domain) of the Oct-4 (octamer-4) embryonic gene. Since the N-terminal domains of EWS and Oct-4 are structurally different, in the present study we have assessed the functional consequences of the EWS–Oct-4 fusion. We find that this chimaeric gene encodes a nuclear protein which binds DNA with the same sequence specificity as the parental Oct-4 protein. Comparison of the transactivation properties of EWS–Oct-4 and Oct-4 indicates that the former has higher transactivation activity for a known target reporter gene containing Oct-4 binding. Deletion analysis of the functional domains of EWS–Oct-4 indicates that the EWS (NTD), the POU domain and the CTD of EWS–Oct-4 are necessary for full transactivation potential. EWS–Oct-4 induced the expression of fgf-4 (fibroblast growth factor 4) and nanog, which are potent mitogens as well as Oct-4 downstream target genes whose promoters contain potential Oct-4-binding sites. Finally, ectopic expression of EWS–Oct-4 in Oct-4-null ZHBTc4 ES (embryonic stem) cells resulted in increased tumorigenic growth potential in nude mice. These results suggest that the oncogenic effect of the t(6;22) translocation is due to the EWS–Oct-4 chimaeric protein and that fusion of the EWS NTD to the Oct-4 DNA-binding domain produces a transforming chimaeric product. PMID:17564582

  9. Fusion Simulation Program Definition. Final report

    SciTech Connect

    Cary, John R.

    2012-09-05

    We have completed our contributions to the Fusion Simulation Program Definition Project. Our contributions were in the overall planning with concentration in the definition of the area of Software Integration and Support. We contributed to the planning of multiple meetings, and we contributed to multiple planning documents.

  10. Fusion safety program annual report fiscal year 1997

    SciTech Connect

    Longhurst, G.R.; Anderl, R.A.; Cadwallader, L.C.

    1998-01-01

    This report summarizes the major activities of the Fusion Safety Program in FY 1997. The Idaho National Engineering and Environmental Laboratory (INEEL) is the designated lead laboratory, and Lockheed Martin Idaho Technologies Company is the prime contractor for this program. The Fusion Safety Program was initiated in FY 1979 to perform research and develop data needed to ensure safety in fusion facilities. Activities include experiments, analysis, code development and application, and other forms of research. These activities are conducted at the INEEL, different DOE laboratories, and other institutions. The technical areas covered in this report include chemical reactions and activation product release, tritium safety, risk assessment failure rate database development, and safety code development and application to fusion safety issues. Most of this work has been done in support of the International Thermonuclear Experimental Reactor (ITER) project. Work done for ITER this year has focused on developing the needed information for the Non-site Specific Safety Report (NSSR-2).

  11. RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method.

    PubMed

    Zhao, Jianmei; Li, Xuecang; Yao, Qianlan; Li, Meng; Zhang, Jian; Ai, Bo; Liu, Wei; Wang, Qiuyu; Feng, Chenchen; Liu, Yuejuan; Bai, Xuefeng; Song, Chao; Li, Shang; Li, Enmin; Xu, Liyan; Li, Chunquan

    2016-09-20

    While gene fusions have been increasingly detected by next-generation sequencing (NGS) technologies based methods in human cancers, these methods have limitations in identifying driver fusions. In addition, the existing methods to identify driver gene fusions ignored the specificity among different cancers or only considered their local rather than global topology features in networks. Here, we proposed a novel network-based method, called RWCFusion, to identify phenotype-specific cancer driver gene fusions. To evaluate its performance, we used leave-one-out cross-validation in 35 cancers and achieved a high AUC value 0.925 for overall cancers and an average 0.929 for signal cancer. Furthermore, we classified 35 cancers into two classes: haematological and solid, of which the haematological got a highly AUC which is up to 0.968. Finally, we applied RWCFusion to breast cancer and found that top 13 gene fusions, such as BCAS3-BCAS4, NOTCH-NUP214, MED13-BCAS3 and CARM-SMARCA4, have been previously proved to be drivers for breast cancer. Additionally, 8 among the top 10 of the remaining candidate gene fusions, such as SULF2-ZNF217, MED1-ACSF2, and ACACA-STAC2, were inferred to be potential driver gene fusions of breast cancer by us.

  12. RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method

    PubMed Central

    Zhao, Jianmei; Li, Xuecang; Yao, Qianlan; Li, Meng; Zhang, Jian; Ai, Bo; Liu, Wei; Wang, Qiuyu; Feng, Chenchen; Liu, Yuejuan; Bai, Xuefeng; Song, Chao; Li, Shang; Li, Enmin; Xu, Liyan; Li, Chunquan

    2016-01-01

    While gene fusions have been increasingly detected by next-generation sequencing (NGS) technologies based methods in human cancers, these methods have limitations in identifying driver fusions. In addition, the existing methods to identify driver gene fusions ignored the specificity among different cancers or only considered their local rather than global topology features in networks. Here, we proposed a novel network-based method, called RWCFusion, to identify phenotype-specific cancer driver gene fusions. To evaluate its performance, we used leave-one-out cross-validation in 35 cancers and achieved a high AUC value 0.925 for overall cancers and an average 0.929 for signal cancer. Furthermore, we classified 35 cancers into two classes: haematological and solid, of which the haematological got a highly AUC which is up to 0.968. Finally, we applied RWCFusion to breast cancer and found that top 13 gene fusions, such as BCAS3-BCAS4, NOTCH-NUP214, MED13-BCAS3 and CARM-SMARCA4, have been previously proved to be drivers for breast cancer. Additionally, 8 among the top 10 of the remaining candidate gene fusions, such as SULF2-ZNF217, MED1-ACSF2, and ACACA-STAC2, were inferred to be potential driver gene fusions of breast cancer by us. PMID:27506935

  13. Recurrent fusion of the genes FN1 and ALK in gastrointestinal leiomyomas.

    PubMed

    Panagopoulos, Ioannis; Gorunova, Ludmila; Lund-Iversen, Marius; Lobmaier, Ingvild; Bjerkehagen, Bodil; Heim, Sverre

    2016-11-01

    Leiomyomas of the gastrointestinal tract are mostly found in the esophagus, stomach, and colon. Genetic information about them is very limited and no fusion genes have been described. We present herein cytogenetic and molecular genetic analyses of two gastrointestinal leiomyomas found in the esophagus and small intestine. The esophageal leiomyoma had the karyotype 45,Y,der(X)t(X;6)(p22;p21),inv(2)(p23q35),add(6)(p21),-11[cp6]/46,XY[7]. The intestinal leiomyoma karyotype was 46,X,add(X)(q2?),der(2)add(2)(p23)add(2)(q33),add(4)(p14),add(14)(q22)[10]/47,XX,+12[2]/46,XX[1]. RNA-sequencing detected FN1-ALK fusion transcripts in both tumors. RT-PCR together with Sanger sequencing verified the presence of the FN1-ALK fusion transcripts. Fluorescence in situ hybridization using an ALK breakapart probe further confirmed the rearrangement of the ALK gene. Immunohistochemical investigation of ALK in the leiomyoma of the small intestine revealed positivity with strong granular cytoplasmatic staining in the tumor cells. This is the first ever ALK fusion reported in gastrointestinal leiomyomas. Our results are of potential clinical importance because crizotinib, a selective ALK inhibitor, has demonstrated effect in patients whose tumors harbor ALK rearrangements. Thus, ALK emerges as a possible therapeutic target in patients whose tumors, including gastrointestinal leiomyomas, carry ALK fusions.

  14. Rooting the eukaryote tree by using a derived gene fusion.

    PubMed

    Stechmann, Alexandra; Cavalier-Smith, Thomas

    2002-07-05

    Single-gene trees have failed to locate the root of the eukaryote tree because of systematic biases in sequence evolution. Structural genetic data should yield more reliable insights into deep phylogenetic relationships. We searched major protist groups for the presence or absence of a gene fusion in order to locate the root of the eukaryote tree. In striking contrast to previous molecular studies, we show that all eukaryote groups ancestrally with two cilia (bikonts) are evolutionarily derived. The root lies between bikonts and opisthokonts (animals, Fungi, Choanozoa). Amoebozoa either diverged even earlier or are sister of bikonts or (less likely) opisthokonts.

  15. Mutation-associated fusion cancer genes in solid tumors.

    PubMed

    Kaye, Frederic J

    2009-06-01

    Chromosomal translocations and fusion oncogenes serve as the ultimate biomarker for clinicians as they show specificity for distinct histopathologic malignancies while simultaneously encoding an etiologic mutation and a therapeutic target. Previously considered a minor mutational event in epithelial solid tumors, new methodologies that do not rely on the detection of macroscopic cytogenetic alterations, as well as access to large series of annotated clinical material, are expanding the inventory of recurrent fusion oncogenes in both common and rare solid epithelial tumors. Unexpectedly, related assays are also revealing a high number of tandem or chimeric transcripts in normal tissues including, in one provocative case, a template for a known fusion oncogene. These observations may force us to reassess long-held views on the definition of a gene. They also raise the possibility that some rearrangements might represent constitutive forms of a physiological chimeric transcript. Defining the chimeric transcriptome in both health (transcription-induced chimerism and intergenic splicing) and disease (mutation-associated fusion oncogenes) will play an increasingly important role in the diagnosis, prognosis, and therapy of patients with cancer.

  16. Analysis of fusion gene expression in prostate tumors by using single-end reads.

    PubMed

    Xie, D D; Li, J Y; Wang, Y; Chen, L; Yu, D X

    2013-08-12

    Fusion gene expression, a kind of chromosome rearrangement mode, has been strongly linked to prostate cancer diagnosis and prognosis as well as to the Gleason score and the American Joint Committee on Cancer stage assessment. In combination with traditional methods for locating fusion genes and scoring their association with cancer cell growth, proliferation, and invasion through the basement membrane, the emerging high-throughput sequencing technologies offer a panorama of fusion genes in a genome and facilitate the discovery of new fusion modes. We describe here a method for using single-end reads to analyze fusion gene expression in prostate tumors. We obtained the fusion gene expression profiling of prostate tumors, clustered them into several biological pathways, highlighted three "rediscovered" fusion genes (TMPRSS2-ERG, KLK2, and KLK3) and proved the reliability of our method.

  17. CRAF gene fusions in pediatric low-grade gliomas define a distinct drug response based on dimerization profiles.

    PubMed

    Jain, P; Fierst, T M; Han, H J; Smith, T E; Vakil, A; Storm, P J; Resnick, A C; Waanders, A J

    2017-08-14

    Pediatric low-grade gliomas (PLGGs) are commonly associated with BRAF gene fusions that aberrantly activate the mitogen-activated protein kinase (MAPK) signaling pathway. This has led to PLGG clinical trials utilizing RAF- and MAPK pathway-targeted therapeutics. Whole-genome profiling of PLGGs has also identified rare gene fusions involving another RAF isoform, CRAF/RAF1, in PLGGs and cancers occuring in adults. Whereas BRAF fusions primarily dysregulate MAPK signaling, the CRAF fusions QKI-RAF1 and SRGAP3-RAF1 aberrantly activate both the MAPK and phosphoinositide-3 kinase/mammalian target of rapamycin (PI3K/mTOR) signaling pathways. Although ATP-competitive, first-generation RAF inhibitors (vemurafenib/PLX4720, RAFi) cause paradoxical activation of the MAPK pathway in BRAF-fusion tumors, inhibition can be achieved with 'paradox breaker' RAFi, such as PLX8394. Here we report that, unlike BRAF fusions, CRAF fusions are unresponsive to both generations of RAFi, vemurafenib and PLX8394, highlighting a distinct responsiveness of CRAF fusions to clinically relevant RAFi. Whereas PLX8394 decreased BRAF-fusion dimerization, CRAF-fusion dimerization is unaffected primarily because of robust protein-protein interactions mediated by the N-terminal non-kinase fusion partner, such as QKI. The pan-RAF dimer inhibitor, LY3009120, could suppress CRAF-fusion oncogenicity by inhibiting dimer-mediated signaling. In addition, as CRAF fusions activate both the MAPK and PI3K/mTOR signaling pathways, we identify combinatorial inhibition of the MAPK/mTOR pathway as a potential therapeutic strategy for CRAF-fusion-driven tumors. Overall, we define a mechanistic distinction between PLGG-associated BRAF- and CRAF/RAF1 fusions in response to RAFi, highlighting the importance of molecularly classifying PLGG patients for targeted therapy. Furthermore, our study uncovers an important contribution of the non-kinase fusion partner to oncogenesis and potential therapeutic strategies against PLGG

  18. [Construction and expression of the targeting super-antigen EGF-SEA fusion gene].

    PubMed

    Xie, Yang; Peng, Shaoping; Liao, Zhiying; Liu, Jiafeng; Liu, Xuemei; Chen, Weifeng

    2014-05-01

    To construct expression vector for the SEA-EGF fusion gene. Clone the SEA gene and the EGF gene segment with PCR and RT-PCR independently, and connect this two genes by the bridge PCR. Insert the fusion gene EGF-SEA into the expression vector PET-44. Induced the secretion of the fusion protein SEA-EGF by the antileptic. The gene fragment encoding EGF and SEA mature peptide was successfully cloned. The fusion gene EGF-SEA was successfully constructed and was inserted into expression vector. The new recombinant expression vector for fusion gene EGF-SEA is specific for head and neck cancer, laid the foundation for the further study of fusion protein SEA-EGF targeting immune therapy in head and neck tumors.

  19. Final Report on The Theory of Fusion Plasmas

    SciTech Connect

    Steven C. Cowley

    2008-06-17

    Report describes theoretical research in the theory of fusion plasmas funded under grant DE-FG02-04ER54737. This includes work on: explosive instabilities, plasma turbulence, Alfven wave cascades, high beta (pressure) tokamaks and magnetic reconnection. These studies have lead to abetter understanding of fusion plasmas and in particular the future behavior of ITER. More than ten young researchers were involved in this research -- some were funded under the grant.

  20. Gene expression profile of ewing sarcoma cell lines differing in their EWS-FLI1 fusion type.

    PubMed

    Bandrés, Eva; Malumbres, Raquel; Escalada, Alvaro; Cubedo, Elena; González, Iranzu; Honorato, Beatriz; Zarate, Ruth; García-Foncillas, Jesus; de Alava, Enrique

    2005-10-01

    The t(11;22)(q24;q12) translocation is present in up to 95% of Ewing tumor patients and results in the formation of an EWS-FLI-1 fusion gene that encodes a chimeric transcription factor. Many alternative forms of EWS-FLI-1 exist because of variations in the location of the EWS and FLI-1 genomic breakpoints. Previous reports have shown that the type 1 fusion is associated with a significantly better prognosis than the other fusion types. It has been suggested that the observed clinical discrepancies result from different transactivation potentials of the various EWS-FLI-1 fusion proteins. In an attempt to identify genes whose expression levels are differentially modulated by structurally different EWS-FLI-1 transcription factors, we have used microarray technology to interrogate 19,000 sequence genes to compare gene expression profile of type 1 or non-type 1 Ewing sarcoma cell lines. Data analysis showed few qualitative differences on gene expression; expression of only 41 genes (0.215% of possible sequences analyzed) differed significantly between Ewing tumor cell lines carrying EWS-FLI-1 fusion type 1 with respect to those with non-type 1 fusion.

  1. Anaerobically expressed Escherichia coli genes identified by operon fusion techniques.

    PubMed Central

    Choe, M; Reznikoff, W S

    1991-01-01

    Genes that are expressed under anaerobic conditions were identified by operon fusion techniques with a hybrid bacteriophage of lambda and Mu, lambda placMu53, which creates transcriptional fusions to lacZY. Cells were screened for anaerobic expression on XG medium. Nine strains were selected, and the insertion point of the hybrid phage in each strain was mapped on the Escherichia coli chromosome linkage map. The anaerobic and aerobic expression levels of these genes were measured by beta-galactosidase assays in different medium conditions and in the presence of three regulatory mutations (fnr, narL, and rpoN). The anaerobically expressed genes (aeg) located at minute 99 (aeg-99) and 75 (aeg-75) appeared to be partially regulated by fnr, and aeg-93 is tightly regulated by fnr. aeg-60 requires a functional rpoN gene for its anaerobic expression. aeg-46.5 is repressed by narL. aeg-65A and aeg-65C are partially controlled by fnr but only in media containing nitrate or fumarate. aeg-47.5 and aeg-48.5 were found to be anaerobically induced only in rich media. The effects of a narL mutation on aeg-46.5 expression were observed in all medium conditions regardless of the presence or absence of nitrate. This suggests that narL has a regulatory function in the absence of exogenously added nitrate. PMID:1917846

  2. Discovering and understanding oncogenic gene fusions through data intensive computational approaches

    PubMed Central

    Latysheva, Natasha S.; Babu, M. Madan

    2016-01-01

    Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different—yet highly complementary and symbiotic—approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation. PMID:27105842

  3. Status report on the fusion breeder

    SciTech Connect

    Moir, R.W.

    1980-12-12

    The rationale for hybrid fusion-fission reactors is the production of fissile fuel for fission reactors. A new class of reactor, the fission-suppressed hybrid promises unusually good safety features as well as the ability to support 25 light-water reactors of the same nuclear power rating, or even more high-conversion-ratio reactors such as the heavy-water type. One 4000-MW nuclear hybrid can produce 7200 kg of /sup 233/U per year. To obtain good economics, injector efficiency times plasma gain (eta/sub i/Q) should be greater than 2, the wall load should be greater than 1 MW m/sup -2/, and the hybrid should cost less than 6 times the cost of a light-water reactor. Introduction rates for the fission-suppressed hybrid are unusually rapid.

  4. Fusion Safety Program annual report, Fiscal Year 1993

    SciTech Connect

    Longhurst, G.R.; Cadwallader, L.C.; Dolan, T.J.; Herring, J.S.; McCarthy, K.A.; Merrill, B.J.; Motloch, C.G.; Petti, D.A.

    1993-12-01

    This report summarizes the major activities of the Fusion Safety Program in Fiscal Year 1993. The Idaho National Engineering Laboratory (INEL) has been designated by DOE as the lead laboratory for fusion safety, and EG&G Idaho, Inc., is the prime contractor for INEL operations. The Fusion Safety Program was initiated in 1979. Activities are conducted at the INEL and in participating organizations, including universities and private companies. Technical areas covered in the report include tritium safety, beryllium safety, activation product release, reactions involving potential plasma-facing materials, safety of fusion magnet systems, plasma disruptions and edge physics modeling, risk assessment failure rates, computer codes for reactor transient analysis, and regulatory support. These areas include work completed in support of the International Thermonuclear Experimental Reactor (ITER). Also included in the report are summaries of the safety and environmental studies performed at the INEL for the Tokamak Physics Experiment and the Tokamak Fusion Test Reactor projects at the Princeton Plasma Physics Laboratory and a summary of the technical support for the ARIES/PULSAR commercial reactor design studies.

  5. Fusion Safety Program Annual Report, Fiscal Year 1996

    SciTech Connect

    Longhurst, G.R.; Anderl, R.A.; Cadwallader, L.C.

    1996-12-01

    This report summarizes the major activities of the Fusion Safety Program in FY 1996. The Idaho National Engineering Laboratory (INEL) is the designated lead laboratory, and Lockheed Martin Idaho Technologies Company is the prime contractor for this program. The Fusion Safety Program was initiated in 1979. The objective is to perform research and develop data needed to ensure safety in fusion facilities. Activities include experiments, analysis, code development and application, and other forms of research. These activities are conducted at the INEL, at other DOE laboratories, and at other institutions. Among the technical areas covered in this report are tritium safety, chemical reactions and activation product release, risk assessment failure rate database development, and safety code development and application to fusion safety issues. Most of this work has been done in support of the International Thermonuclear Experimental Reactor (ITER). Work done for ITER this year has focused on developing the needed information for the Non- Site- Specific Safety Report (NSSR-1). A final area of activity described is development of the new DOE Technical Standards for Safety of Magnetic Fusion Facilities.

  6. Characterization of nif regulatory genes in Rhodopseudomonas capsulata using lac gene fusions.

    PubMed

    Kranz, R G; Haselkorn, R

    1985-01-01

    Translational fusions of the Escherichia coli lacZYA operon to Rhodopseudomonas capsulata nif genes were obtained by using mini-MudII1734 [Castilho et al., J. Bacteriol. 158 (1984) 488-495] inserts into cloned fragments of R. capsulata DNA. A lac fusion to the nifH gene, which encodes dinitrogenase reductase, was used to classify Nif- mutations occurring in regulatory genes. Nine mutations were unable to activate nifHDK transcription. The nine mutations define four nif regulatory genes. Three of these genes are located on the same R. capsulata 8.4-kb EcoRI fragment. Each is transcribed independently. One of these (complementing mutant J61) is partially homologous with the ntrC gene of Escherichia coli, based on Southern hybridization. The fourth nif regulatory gene (complementing mutants LJ1, AH1 and AH3) is unlinked to the others. Lac fusions to all four regulatory genes were constructed. Each regulatory gene is weakly expressed compared to derepressed nifH and partially repressed in the presence of ammonia.

  7. Rad51C-ATXN7 fusion gene expression in colorectal tumors.

    PubMed

    Kalvala, Arjun; Gao, Li; Aguila, Brittany; Dotts, Kathleen; Rahman, Mohammad; Nana-Sinkam, Serge P; Zhou, Xiaoping; Wang, Qi-En; Amann, Joseph; Otterson, Gregory A; Villalona-Calero, Miguel A; Duan, Wenrui

    2016-06-13

    Fusion proteins have unique oncogenic properties and their identification can be useful either as diagnostic or therapeutic targets. Next generation sequencing data have previously shown a fusion gene formed between Rad51C and ATXN7 genes in the MCF7 breast cancer cell line. However, the existence of this fusion gene in colorectal patient tumor tissues is largely still unknown. We evaluated for the presence of Rad51C-ATXN7 fusion gene in colorectal tumors and cells by RT-PCR, PCR, Topo TA cloning, Real time PCR, immunoprecipitation and immunoblotting techniques. We identified two forms of fusion mRNAs between Rad51C and ATXN7 in the colorectal tumors, including a Variant 1 (fusion transcript between Rad51C exons 1-7 and ATXN7 exons 6-13), and a Variant 2 (between Rad51C exons 1-6 and ATXN7 exons 6-13). In silico analysis showed that the Variant 1 produces a truncated protein, whereas the Variant 2 was predicted to produce a fusion protein with molecular weight of 110 KDa. Immunoprecipitation and Western blot analysis further showed a 110 KDa protein in colorectal tumors. 5-Azacytidine treatment of LS-174 T cells caused a 3.51-fold increase in expression of the fusion gene (Variant 2) as compared to no treatment controls evaluated by real time PCR. In conclusion we found a fusion gene between DNA repair gene Rad51C and neuro-cerebral ataxia Ataxin-7 gene in colorectal tumors. The in-frame fusion transcript of Variant 2 results in a fusion protein with molecular weight of 110 KDa. In addition, we found that expression of fusion gene is associated with functional impairment of Fanconi Anemia (FA) DNA repair pathway in colorectal tumors. The expression of Rad51C-ATXN7 in tumors warrants further investigation, as it suggests the potential of the fusion gene in treatment and predictive value in colorectal cancers.

  8. Protein functional links in Trypanosoma brucei, identified by gene fusion analysis

    PubMed Central

    2011-01-01

    Background Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit protein complex, or in a metabolic pathway. Gene fusion analysis has been used to identify protein functional links in prokaryotes as well as in eukaryotic model organisms, such as yeast and Drosophila. Results In this study we have extended this approach to include a number of recently sequenced protists, four of which are pathogenic, to identify fusion linked proteins in Trypanosoma brucei, the causative agent of African sleeping sickness. We have also examined the evolution of the gene fusion events identified, to determine whether they can be attributed to fusion or fission, by looking at the conservation of the fused genes and of the individual component genes across the major eukaryotic and prokaryotic lineages. We find relatively limited occurrence of gene fusions/fissions within the protist lineages examined. Our results point to two trypanosome-specific gene fissions, which have recently been experimentally confirmed, one fusion involving proteins involved in the same metabolic pathway, as well as two novel putative functional links between fusion-linked protein pairs. Conclusions This is the first study of protein functional links in T. brucei identified by gene fusion analysis. We have used strict thresholds and only discuss results which are highly likely to be genuine and which either have already been or can be experimentally verified. We discuss the possible impact of the identification of these novel putative protein-protein interactions, to the development of new trypanosome therapeutic drugs. PMID:21729286

  9. TMPRSS2-ERG gene fusion in small cell carcinoma of the prostate.

    PubMed

    Guo, Charles C; Dancer, Jane Y; Wang, Yan; Aparicio, Ana; Navone, Nora M; Troncoso, Patricia; Czerniak, Bogdan A

    2011-01-01

    Recent studies have shown that most prostate cancers carry the TMPRSS2-ERG gene fusion. Here we evaluated the TMPRSS2-ERG gene fusion in small cell carcinoma of the prostate (n = 12) in comparison with small cell carcinoma of the urinary bladder (n = 12) and lung (n = 11). Fluorescence in situ hybridization demonstrated rearrangement of the ERG gene in 8 cases of prostatic small cell carcinoma (67%), and the rearrangement was associated with deletion of the 5' ERG gene in 7 cases, but rearrangement of the ERG gene was not present in any small cell carcinoma of the urinary bladder or lung. Next we evaluated the TMPRSS2-ERG gene fusion in nude mouse xenografts that were derived from 2 prostatic small cell carcinomas carrying the TMPRSS2-ERG gene fusion. Two transcripts encoded by the TMPRSS2-ERG gene fusion were detected by reverse transcriptase polymerase chain reaction, and DNA sequencing demonstrated that the 2 transcripts were composed of fusions of exon 1 of the TMPRSS2 gene to exon 4 or 5 of the ERG gene. Our study demonstrates the specific presence of TMPRSS2-ERG gene fusion in prostatic small cell carcinoma, which may be helpful in distinguishing small cell carcinoma of prostatic origin from nonprostatic origins. The high prevalence of the TMPRSS2-ERG gene fusion in prostatic small cell carcinoma as well as adenocarcinoma implies that small cell carcinoma may share a common pathogenic pathway with adenocarcinoma in the prostate.

  10. Clinical Courses of Two Pediatric Patients with Acute Megakaryoblastic Leukemia Harboring the CBFA2T3-GLIS2 Fusion Gene

    PubMed Central

    Ishibashi, Mayu; Yokosuka, Tomoko; Yanagimachi, Masakatsu D.; Iwasaki, Fuminori; Tsujimoto, Shin-ichi; Sasaki, Koji; Takeuchi, Masanobu; Tanoshima, Reo; Kato, Hiromi; Kajiwara, Ryosuke; Tanaka, Fumiko; Goto, Hiroaki; Yokota, Shumpei

    2016-01-01

    Acute megakaryoblastic leukemia (AMKL) in children without Down syndrome (DS) has an extremely poor outcome with 3-year survival of less than 40%, whereas AMKL in children with DS has an excellent survival rate. Recently, a novel recurrent translocation involving CBFA2T3 and GLIS2 was identified in about 30% of children with non-DS AMKL, and the fusion gene was reported as a strong poor prognostic factor in pediatric AMKL. We report the difficult clinical courses of pediatric patients with AMKL harboring the CBFA2T3-GLIS2 fusion gene. PMID:27094503

  11. Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

    PubMed Central

    Parker, Brittany C.; Zhang, Wei

    2013-01-01

    Studies over the past decades have uncovered fusion genes, a class of oncogenes that provide immense diagnostic and therapeutic advantages because of their tumor-specific expression. Originally associated with hemotologic cancers, fusion genes have recently been discovered in a wide array of solid tumors, including sarcomas, carcinomas, and tumors of the central nervous system. Fusion genes are attractive as both therapeutic targets and diagnostic tools due to their inherent expression in tumor tissue alone. Therefore, the discovery and elucidation of fusion genes in various cancer types may provide more effective therapies in the future for cancer patients. PMID:24206917

  12. Structure and expression of the Drosophila ubiquitin-80-amino-acid fusion-protein gene.

    PubMed Central

    Barrio, R; del Arco, A; Cabrera, H L; Arribas, C

    1994-01-01

    In the fruitfly Drosophila, as in all eukaryotes examined so far, some ubiquitin-coding sequences appear fused to unrelated open reading frames. Two of these fusion genes have been previously described (the homologues of UBI1-UBI2 and UBI4 in yeast), and we report here the organization and expression of a third one, the DUb80 gene (the homologue of UBI3 in yeast). This gene encodes a ubiquitin monomer fused to an 80-amino-acid extension which is homologous with the ribosomal protein encoded by the UB13 gene. The 5' regulatory region of DUb80 shares common features with another ubiquitin fusion gene, DUb52, and with the ribosomal protein genes of Drosophila, Xenopus and mouse. We also find helix-loop-helix protein-binding sequences (E-boxes). The DUb80 gene is transcribed to a 0.9 kb mRNA which is particularly abundant under conditions of high protein synthesis, such as in ovaries and exponentially growing cells. Images Figure 3 Figure 4 PMID:8068011

  13. The yeast ubiquitin genes: a family of natural gene fusions.

    PubMed Central

    Ozkaynak, E; Finley, D; Solomon, M J; Varshavsky, A

    1987-01-01

    Ubiquitin is a 76-residue protein highly conserved among eukaryotes. Conjugation of ubiquitin to intracellular proteins mediates their selective degradation in vivo. We describe a family of four ubiquitin-coding loci in the yeast Saccharomyces cerevisiae. UB11, UB12 and UB13 encode hybrid proteins in which ubiquitin is fused to unrelated ('tail') amino acid sequences. The ubiquitin coding elements of UB11 and UB12 are interrupted at identical positions by non-homologous introns. UB11 and UB12 encode identical 52-residue tails, whereas UB13 encodes a different 76-residue tail. The tail amino acid sequences are highly conserved between yeast and mammals. Each tail contains a putative metal-binding, nucleic acid-binding domain of the form Cys-X2-4-Cys-X2-15-Cys-X2-4-Cys, suggesting that these proteins may function by binding to DNA. The fourth gene, UB14, encodes a polyubiquitin precursor protein containing five ubiquitin repeats in a head-to-tail, spacerless arrangement. All four ubiquitin genes are expressed in exponentially growing cells, while in stationary-phase cells the expression of UB11 and UB12 is repressed. The UB14 gene, which is strongly inducible by starvation, high temperatures and other stresses, contains in its upstream region strong homologies to the consensus 'heat shock box' nucleotide sequence. Elsewhere we show that the essential function of the UB14 gene is to provide ubiquitin to cells under stress. Images Fig. 1. Fig. 7. PMID:3038523

  14. Systematic identification and analysis of frequent gene fusion events in metabolic pathways

    DOE PAGES

    Henry, Christopher S.; Lerma-Ortiz, Claudia; Gerdes, Svetlana Y.; ...

    2016-06-24

    Here, gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. As a result, here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These setsmore » were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. In conclusion, customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.« less

  15. Systematic identification and analysis of frequent gene fusion events in metabolic pathways

    SciTech Connect

    Henry, Christopher S.; Lerma-Ortiz, Claudia; Gerdes, Svetlana Y.; Mullen, Jeffrey D.; Colasanti, Ric; Zhukov, Aleksey; Frelin, Oceane; Thiaville, Jennifer J.; Zallot, Remi; Niehaus, Thomas D.; Hasnain, Ghulam; Conrad, Neal; Hanson, Andrew D.; de Crecy-Lagard, Valerie

    2016-06-24

    Here, gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. As a result, here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. In conclusion, customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.

  16. Contribution to Fusion Materials Semiannual Report

    SciTech Connect

    Marian, J; Meier, W

    2012-02-24

    The objectives of this work are the following: (1) The application of micro and mesoscale modeling techniques to study dislocation properties in ferritic and W-based materials; and (2) The development of computational models and tools to study damage accumulation in >1 dpa (fusion-like) conditions, both for Fe and W-based alloys. The high-temperature strength of structural ferritic alloys (ferritic/martensitic steels, ODS steels, bcc refractory alloys) hinges on the thermal stability of second phase particles and their interactions with dislocations. Irradiation damage can modify the structure and stability of both the particles and dislocations, particularly by the introduction of gas atoms, point defects and point defect clusters. The three aspects of materials strength that we are studying are: (a) Computation of dislocation mobility functions (stress-velocity relations) as a function of temperature and dislocation character. This will be done via molecular dynamics (MD) simulations of single dislocation motion under applied shear stress. This is a fundamental input to dislocation dynamics (DD) simulations and also provides fundamental insights into the high-temperature plastic behavior of ferritic materials. (b) Simulations of dislocation-obstacle interactions using MD and DD. This subtask includes simulating the effect on dislocation glide of precipitates (e.g., {alpha}' Cr precipitates), ODS particles, and irradiation induced defect clusters (e.g. voids, dislocation loops, etc.). (c) Implementation of this information (dislocation mobilities and dislocation-defect interaction rules) into DD codes that will allow us to study plasticity of single crystals Fe alloys under relevant irradiation conditions.

  17. Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions.

    PubMed

    Shugay, Mikhail; Ortiz de Mendíbil, Iñigo; Vizmanos, José L; Novo, Francisco J

    2013-10-15

    Gene fusions resulting from chromosomal aberrations are an important cause of cancer. The complexity of genomic changes in certain cancer types has hampered the identification of gene fusions by molecular cytogenetic methods, especially in carcinomas. This is changing with the advent of next-generation sequencing, which is detecting a substantial number of new fusion transcripts in individual cancer genomes. However, this poses the challenge of identifying those fusions with greater oncogenic potential amid a background of 'passenger' fusion sequences. In the present work, we have used some recently identified genomic hallmarks of oncogenic fusion genes to develop a pipeline for the classification of fusion sequences, namely, Oncofuse. The pipeline predicts the oncogenic potential of novel fusion genes, calculating the probability that a fusion sequence behaves as 'driver' of the oncogenic process based on features present in known oncogenic fusions. Cross-validation and extensive validation tests on independent datasets suggest a robust behavior with good precision and recall rates. We believe that Oncofuse could become a useful tool to guide experimental validation studies of novel fusion sequences found during next-generation sequencing analysis of cancer transcriptomes. Oncofuse is a naive Bayes Network Classifier trained and tested using Weka machine learning package. The pipeline is executed by running a Java/Groovy script, available for download at www.unav.es/genetica/oncofuse.html.

  18. Recurrent and pathological gene fusions in breast cancer: current advances in genomic discovery and clinical implications.

    PubMed

    Veeraraghavan, Jamunarani; Ma, Jiacheng; Hu, Yiheng; Wang, Xiao-Song

    2016-07-01

    Gene fusions have long been considered principally as the oncogenic events of hematologic malignancies, but have recently gained wide attention in solid tumors due to several milestone discoveries and the advancement of deep sequencing technologies. With the progress in deep sequencing studies of breast cancer transcriptomes and genomes, the discovery of recurrent and pathological gene fusions in breast cancer is on the focus. Recently, driven by new deep sequencing studies, several recurrent or pathological gene fusions have been identified in breast cancer, including ESR1-CCDC170, SEC16A-NOTCH1, SEC22B-NOTCH2, and ESR1-YAP1 etc. More important, most of these gene fusions are preferentially identified in the more aggressive breast cancers, such as luminal B, basal-like, or endocrine-resistant breast cancer, suggesting recurrent gene fusions as additional key driver events in these tumors other than the known drivers such as the estrogen receptor. In this paper, we have comprehensively summarized the newly identified recurrent or pathological gene fusion events in breast cancer, reviewed the contributions of new genomic and deep sequencing technologies to new fusion discovery and the integrative bioinformatics tools to analyze these data, highlighted the biological relevance and clinical implications of these fusion discoveries, and discussed future directions of gene fusion research in breast cancer.

  19. Fusion breeder studies program: Final report

    SciTech Connect

    Berwald, D.H.

    1986-10-17

    This report is an assessment of technology related to hybrid reactors, especially the Fission-suppressed hybrid. A description of a typical fission-suppressed reactor is given. The economic advantages of the use of a hybrid reactor as part of a fuel cycle center are discussed at length. The inherent safety advantages of the hybrid reactor are analyzed. The report concludes with a proposed timetable for research and development. (JDH)

  20. Fusion Safety Program annual report, fiscal year 1992

    SciTech Connect

    Holland, D.F.; Cadwallader, L.C.; Herring, J.S.; Longhurst, G.R.; McCarthy, K.A.; Merrill, B.J.; Piet, S.J.

    1993-01-01

    This report summarizes the major activities of the Fusion Safety Program in fiscal year 1992. The Idaho National Engineering Laboratory (INEL) is the designated lead laboratory and EG G Idaho, Inc. is the prime contractor for this program. The Fusion Safety Program was initiated in 1979. Activities are conducted at the INEL and in participating organizations including the Westinghouse Hanford Company at the Hanford Engineering Development Laboratory, the Massachusetts Institute of Technology, and the University of Wisconsin. The technical areas covered in the report include tritium safety, activation product release, reactions involving beryllium, reactions involving lithium breeding materials, safety of fusion magnet systems, plasma disruptions, risk assessment failure rate data base, and computer code development for reactor transients. Also included in the report is a summary of the safety and environmental studies performed by the INEL for the Tokamak Physics Experiments and the Tokamak Fusion Test Reactor, the safety analysis for the International Thermonuclear Experimental Reactor design, and the technical support for the ARIES commercial reactor design study.

  1. Fusion Safety Program annual report, fiscal year 1992

    SciTech Connect

    Holland, D.F.; Cadwallader, L.C.; Herring, J.S.; Longhurst, G.R.; McCarthy, K.A.; Merrill, B.J.; Piet, S.J.

    1993-01-01

    This report summarizes the major activities of the Fusion Safety Program in fiscal year 1992. The Idaho National Engineering Laboratory (INEL) is the designated lead laboratory and EG&G Idaho, Inc. is the prime contractor for this program. The Fusion Safety Program was initiated in 1979. Activities are conducted at the INEL and in participating organizations including the Westinghouse Hanford Company at the Hanford Engineering Development Laboratory, the Massachusetts Institute of Technology, and the University of Wisconsin. The technical areas covered in the report include tritium safety, activation product release, reactions involving beryllium, reactions involving lithium breeding materials, safety of fusion magnet systems, plasma disruptions, risk assessment failure rate data base, and computer code development for reactor transients. Also included in the report is a summary of the safety and environmental studies performed by the INEL for the Tokamak Physics Experiments and the Tokamak Fusion Test Reactor, the safety analysis for the International Thermonuclear Experimental Reactor design, and the technical support for the ARIES commercial reactor design study.

  2. Colorimetric TMPRSS2-ERG Gene Fusion Detection in Prostate Cancer Urinary Samples via Recombinase Polymerase Amplification.

    PubMed

    Koo, Kevin M; Wee, Eugene J H; Trau, Matt

    2016-01-01

    TMPRSS2 (Exon 1)-ERG (Exon 4) is the most frequent gene fusion event in prostate cancer (PC), and is highly PC-specific unlike the current serum prostate specific antigen (PSA) biomarker. However, TMPRSS2-ERG levels are currently measured with quantitative reverse-transcription PCR (RT-qPCR) which is time-consuming and requires costly equipment, thus limiting its use in clinical diagnostics. Herein, we report a novel rapid, cost-efficient and minimal-equipment assay named "FusBLU" for detecting TMPRSS2-ERG gene fusions from urine. TMPRSS2-ERG mRNA was amplified by isothermal reverse transcription-recombinase polymerase amplification (RT-RPA), magnetically-isolated, and detected through horseradish peroxidase (HRP)-catalyzed colorimetric reaction. FusBLU was specific for TMPRSS2-ERG mRNA with a low visual detection limit of 10(5) copies. We also demonstrated assay readout versatility on 3 potentially useful platforms. The colorimetric readout was detectable by naked eye for a quick yes/no evaluation of gene fusion presence. On the other hand, a more quantitative TMPRSS2-ERG detection was achievable by absorbance/electrochemical measurements. FusBLU was successfully applied to 12 urinary samples and results were validated by gold-standard RT-qPCR. We also showed that sediment RNA was likely the main source of TMPRSS2-ERG mRNA in urinary samples. We believe that our assay is a potential clinical screening tool for PC and could also have wide applications for other disease-related fusion genes.

  3. Colorimetric TMPRSS2-ERG Gene Fusion Detection in Prostate Cancer Urinary Samples via Recombinase Polymerase Amplification

    PubMed Central

    Koo, Kevin M.; Wee, Eugene J.H.; Trau, Matt

    2016-01-01

    TMPRSS2 (Exon 1)-ERG (Exon 4) is the most frequent gene fusion event in prostate cancer (PC), and is highly PC-specific unlike the current serum prostate specific antigen (PSA) biomarker. However, TMPRSS2-ERG levels are currently measured with quantitative reverse-transcription PCR (RT-qPCR) which is time-consuming and requires costly equipment, thus limiting its use in clinical diagnostics. Herein, we report a novel rapid, cost-efficient and minimal-equipment assay named “FusBLU” for detecting TMPRSS2-ERG gene fusions from urine. TMPRSS2-ERG mRNA was amplified by isothermal reverse transcription-recombinase polymerase amplification (RT-RPA), magnetically-isolated, and detected through horseradish peroxidase (HRP)-catalyzed colorimetric reaction. FusBLU was specific for TMPRSS2-ERG mRNA with a low visual detection limit of 105 copies. We also demonstrated assay readout versatility on 3 potentially useful platforms. The colorimetric readout was detectable by naked eye for a quick yes/no evaluation of gene fusion presence. On the other hand, a more quantitative TMPRSS2-ERG detection was achievable by absorbance/electrochemical measurements. FusBLU was successfully applied to 12 urinary samples and results were validated by gold-standard RT-qPCR. We also showed that sediment RNA was likely the main source of TMPRSS2-ERG mRNA in urinary samples. We believe that our assay is a potential clinical screening tool for PC and could also have wide applications for other disease-related fusion genes. PMID:27375789

  4. High-speed biosensing strategy for non-invasive profiling of multiple cancer fusion genes in urine.

    PubMed

    Koo, Kevin M; Wee, Eugene J H; Trau, Matt

    2017-03-15

    Aberrant chromosal rearrangements, such as the multiple variants of TMPRSS2:ERG fusion gene mutations in prostate cancer (PCa), are promising diagnostic and prognostic biomarkers due to their specific expression in cancerous tissue only. Additionally, TMPRSS2:ERG variants are detectable in urine to provide non-invasive PCa diagnostic sampling as an attractive surrogate for needle biopsies. Therefore, rapid and simplistic assays for identifying multiple urinary TMPRSS2:ERG variants are potentially useful to aid in early cancer detection, immediate patient risk stratification, and prompt personalized treatment. However, current strategies for simultaneous detection of multiple gene fusions are limited by tedious and prolonged experimental protocols, thus limiting their use as rapid clinical screening tools. Herein, we report a simple and rapid gene fusion strategy which expliots the specificity of DNA ligase and the speed of isothermal amplification to simultaneously detect multiple fusion gene RNAs within a short sample-to-answer timeframe of 60min. The method has a low detection limit of 2 amol (1000 copies), and was successfully applied for non-invasive fusion gene profiling in patient urine samples with subsequent validation by a PCR-based gold standard approach. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Adenoid cystic carcinoma: emerging role of translocations and gene fusions

    PubMed Central

    Wysocki, Piotr T.; Izumchenko, Evgeny; Meir, Juliet; Ha, Patrick K.; Sidransky, David; Brait, Mariana

    2016-01-01

    Adenoid cystic carcinoma (ACC), the second most common salivary gland malignancy, is notorious for poor prognosis, which reflects the propensity of ACC to progress to clinically advanced metastatic disease. Due to high long-term mortality and lack of effective systemic treatment, the slow-growing but aggressive ACC poses a particular challenge in head and neck oncology. Despite the advancements in cancer genomics, up until recently relatively few genetic alterations critical to the ACC development have been recognized. Although the specific chromosomal translocations resulting in MYB-NFIB fusions provide insight into the ACC pathogenesis and represent attractive diagnostic and therapeutic targets, their clinical significance is unclear, and a substantial subset of ACCs do not harbor the MYB-NFIB translocation. Strategies based on detection of newly described genetic events (such as MYB activating super-enhancer translocations and alterations affecting another member of MYB transcription factor family-MYBL1) offer new hope for improved risk assessment, therapeutic intervention and tumor surveillance. However, the impact of these approaches is still limited by an incomplete understanding of the ACC biology, and the manner by which these alterations initiate and drive ACC remains to be delineated. This manuscript summarizes the current status of gene fusions and other driver genetic alterations in ACC pathogenesis and discusses new therapeutic strategies stemming from the current research. PMID:27533466

  6. Identification of target genes of synovial sarcoma-associated fusion oncoprotein using human pluripotent stem cells

    SciTech Connect

    Hayakawa, Kazuo; Ikeya, Makoto; Fukuta, Makoto; Woltjen, Knut; Tamaki, Sakura; Takahara, Naoko; Kato, Tomohisa; Sato, Shingo; Otsuka, Takanobu; Toguchida, Junya

    2013-03-22

    Highlights: ► We tried to identify targets of synovial sarcoma (SS)-associated SYT–SSX fusion gene. ► We established pluripotent stem cell (PSC) lines with inducible SYT–SSX gene. ► SYT–SSX responsive genes were identified by the induction of SYT–SSX in PSC. ► SS-related genes were selected from database by in silico analyses. ► 51 genes were finally identified among SS-related genes as targets of SYT–SSX in PSC. -- Abstract: Synovial sarcoma (SS) is a malignant soft tissue tumor harboring chromosomal translocation t(X; 18)(p11.2; q11.2), which produces SS-specific fusion gene, SYT–SSX. Although precise function of SYT–SSX remains to be investigated, accumulating evidences suggest its role in gene regulation via epigenetic mechanisms, and the product of SYT–SSX target genes may serve as biomarkers of SS. Lack of knowledge about the cell-of-origin of SS, however, has placed obstacle in the way of target identification. Here we report a novel approach to identify SYT–SSX2 target genes using human pluripotent stem cells (hPSCs) containing a doxycycline-inducible SYT–SSX2 gene. SYT–SSX2 was efficiently induced both at mRNA and protein levels within three hours after doxycycline administration, while no morphological change of hPSCs was observed until 24 h. Serial microarray analyses identified genes of which the expression level changed more than twofold within 24 h. Surprisingly, the majority (297/312, 95.2%) were up-regulated genes and a result inconsistent with the current concept of SYT–SSX as a transcriptional repressor. Comparing these genes with SS-related genes which were selected by a series of in silico analyses, 49 and 2 genes were finally identified as candidates of up- and down-regulated target of SYT–SSX, respectively. Association of these genes with SYT–SSX in SS cells was confirmed by knockdown experiments. Expression profiles of SS-related genes in hPSCs and human mesenchymal stem cells (hMSCs) were strikingly

  7. Realizing the Promise of Fusion Energy: Final Report of the Task Force on Fusion Energy, August 1999

    NASA Astrophysics Data System (ADS)

    Meserve, Richard A.; Bernstein, Ira; Frieman, Edward; Grunder, Hermann; Hanflin, Robert; Koonin, Steven; Papay, Lawrence; Prager, Stewart; Ripin, Barrett; Sessoms, Allen

    1999-06-01

    In December 1998, Secretary of Energy Bill Richardson asked the Secretary of Energy Advisory Board to form a Task Force on Fusion Energy to conduct a review of the Department's fusion energy technologies, both inertial and magnetic, and to provide recommendations as to the role of these technologies as part of a national fusion energy research program. This report reflects the Task Force's response to the request.

  8. Isolation of gene fusions (soi::lacZ) inducible by oxidative stress in Escherichia coli.

    PubMed Central

    Kogoma, T; Farr, S B; Joyce, K M; Natvig, D O

    1988-01-01

    Mu dX phage was used to isolate three gene fusions to the lacZ gene (soi::lacZ; soi for superoxide radical inducible) that were induced by treatment with superoxide radical anion generators such as paraquat and plumbagin. The induction of beta-galactosidase in these fusion strains with the superoxide radical generating agents required aerobic metabolism. Hyperoxygenation (i.e., bubbling of cultures with oxygen gas) also induced the fusions. On the other hand, hydrogen peroxide did not induce the fusions at concentrations that are known to invoke an adaptive response. Introduction of oxyR, htpR, or recA mutations did not affect the induction. Two of the fusion strains exhibited increased sensitivity to paraquat but not to hydrogen peroxide. The third fusion strain showed no increased sensitivity to either agent. All three fusions were located in the 45- to 61-min region of the Escherichia coli chromosome. PMID:2838846

  9. Inhibition of protein translation by the DISC1-Boymaw fusion gene from a Scottish family with major psychiatric disorders

    PubMed Central

    Ji, Baohu; Higa, Kerin K.; Kim, Minjung; Zhou, Lynn; Young, Jared W.; Geyer, Mark A.; Zhou, Xianjin

    2014-01-01

    The t(1; 11) translocation appears to be the causal genetic lesion with 70% penetrance for schizophrenia, major depression and other psychiatric disorders in a Scottish family. Molecular studies identified the disruption of the disrupted-in-schizophrenia 1 (DISC1) gene by chromosome translocation at chromosome 1q42. Our previous studies, however, revealed that the translocation also disrupted another gene, Boymaw (also termed DISC1FP1), on chromosome 11. After translocation, two fusion genes [the DISC1-Boymaw (DB7) and the Boymaw-DISC1 (BD13)] are generated between the DISC1 and Boymaw genes. In the present study, we report that expression of the DB7 fusion gene inhibits both intracellular NADH oxidoreductase activities and protein translation. We generated humanized DISC1-Boymaw mice with gene targeting to examine the in vivo functions of the fusion genes. Consistent with the in vitro studies on the DB7 fusion gene, protein translation activity is decreased in the hippocampus and in cultured primary neurons from the brains of the humanized mice. Expression of Gad67, Nmdar1 and Psd95 proteins are also reduced. The humanized mice display prolonged and increased responses to the NMDA receptor antagonist, ketamine, on various mouse genetic backgrounds. Abnormal information processing of acoustic startle and depressive-like behaviors are also observed. In addition, the humanized mice display abnormal erythropoiesis, which was reported to associate with depression in humans. Expression of the DB7 fusion gene may reduce protein translation to impair brain functions and thereby contribute to the pathogenesis of major psychiatric disorders. PMID:24908665

  10. Inhibition of protein translation by the DISC1-Boymaw fusion gene from a Scottish family with major psychiatric disorders.

    PubMed

    Ji, Baohu; Higa, Kerin K; Kim, Minjung; Zhou, Lynn; Young, Jared W; Geyer, Mark A; Zhou, Xianjin

    2014-11-01

    The t(1; 11) translocation appears to be the causal genetic lesion with 70% penetrance for schizophrenia, major depression and other psychiatric disorders in a Scottish family. Molecular studies identified the disruption of the disrupted-in-schizophrenia 1 (DISC1) gene by chromosome translocation at chromosome 1q42. Our previous studies, however, revealed that the translocation also disrupted another gene, Boymaw (also termed DISC1FP1), on chromosome 11. After translocation, two fusion genes [the DISC1-Boymaw (DB7) and the Boymaw-DISC1 (BD13)] are generated between the DISC1 and Boymaw genes. In the present study, we report that expression of the DB7 fusion gene inhibits both intracellular NADH oxidoreductase activities and protein translation. We generated humanized DISC1-Boymaw mice with gene targeting to examine the in vivo functions of the fusion genes. Consistent with the in vitro studies on the DB7 fusion gene, protein translation activity is decreased in the hippocampus and in cultured primary neurons from the brains of the humanized mice. Expression of Gad67, Nmdar1 and Psd95 proteins are also reduced. The humanized mice display prolonged and increased responses to the NMDA receptor antagonist, ketamine, on various mouse genetic backgrounds. Abnormal information processing of acoustic startle and depressive-like behaviors are also observed. In addition, the humanized mice display abnormal erythropoiesis, which was reported to associate with depression in humans. Expression of the DB7 fusion gene may reduce protein translation to impair brain functions and thereby contribute to the pathogenesis of major psychiatric disorders.

  11. Wnt signaling induces transcription, spatial proximity, and translocation of fusion gene partners in human hematopoietic cells.

    PubMed

    Ugarte, Giorgia D; Vargas, Macarena F; Medina, Matías A; León, Pablo; Necuñir, David; Elorza, Alvaro A; Gutiérrez, Soraya E; Moon, Randall T; Loyola, Alejandra; De Ferrari, Giancarlo V

    2015-10-08

    Chromosomal translocations are frequently associated with a wide variety of cancers, particularly hematologic malignancies. A recurrent chromosomal abnormality in acute myeloid leukemia is the reciprocal translocation t(8;21) that fuses RUNX1 and ETO genes. We report here that Wnt/β-catenin signaling increases the expression of ETO and RUNX1 genes in human hematopoietic progenitors. We found that β-catenin is rapidly recruited into RNA polymerase II transcription factories (RNAPII-Ser5) and that ETO and RUNX1 genes are brought into close spatial proximity upon Wnt3a induction. Notably, long-term treatment of cells with Wnt3a induces the generation a frequent RUNX1-ETO translocation event. Thus, Wnt/β-catenin signaling induces transcription and translocation of RUNX1 and ETO fusion gene partners, opening a novel window to understand the onset/development of leukemia.

  12. Inertial Fusion Program. Progress report, July 1-December 31, 1979

    SciTech Connect

    Skoberne, F.

    1981-10-01

    Progress in the development of high-energy short-pulse CO/sub 2/ laser systems for fusion research is reported. Improvements in the Los Alamos National Laboratory eight-beam Helios system are described. These improvements increased the reliability of the laser and permitted the firing of 290 shots, most of which delivered energies of approximately 8 kJ to the target. Modifications to Gemini are outlined, including the installation of a new target-insertion mechanism. The redirection of the Antares program is discussed in detail, which will achieve a total energy of approximatey 40 kJ with two beams. This redirection will bring Antares on-line almost two years earlier than was possible with the full six-beam system, although at a lower energy. Experiments with isentropically imploded Sirius-B targets are discussed, and x-ray radiation-loss data from gold microballoons are presented, which show that these results are essentially identical with those obtained at glass-laser wavelengths. Significant progress in characterizing laser fusion targets is reported. New processes for fabricating glass miroballoon x-ray diagnostic targets, the application of high-quality metallic coatings, and the deposition of thick plastic coatings are described. Results in the development of x-ray diagnostics are reported, and research in the Los Alamos heavy-ion fusion program is summarized. Results of investigations of phase-conjugation research of gaseous saturable absorbers and of the use of alkali-halide crystals in a new class of saturable absorbers are summarized. New containment-vessel concepts for Inertial Confinement Fusion reactors are discussed, and results of a scoping study of four fusion-fission hybrid concepts are presented.

  13. Identification of novel fusion genes with 28S ribosomal DNA in hematologic malignancies.

    PubMed

    Kobayashi, Satoru; Taki, Tomohiko; Nagoshi, Hisao; Chinen, Yoshiaki; Yokokawa, Yuichi; Kanegane, Hirokazu; Matsumoto, Yosuke; Kuroda, Junya; Horiike, Shigeo; Nishida, Kazuhiro; Taniwaki, Masafumi

    2014-04-01

    Fusion genes are frequently observed in hematologic malignancies and soft tissue sarcomas, and are usually associated with chromosome abnormalities. Many of these fusion genes create in-frame fusion transcripts that result in the production of fusion proteins, and some of which aid tumorigenesis. These fusion proteins are often associated with disease phenotype and clinical outcome, and act as markers for minimal residual disease and indicators of therapeutic targets. Here, we identified the 28S ribosomal DNA (RN28S1) gene as a novel fusion partner of the B-cell leukemia/lymphoma 11B gene (BCL11B), the immunoglobulin κ variable 3-20 gene (IGKV3-20) and the component of oligomeric Golgi complex 1 gene (COG1) in hematologic malignancies. The RN28S1-BCL11B fusion transcript was identified in a case with mixed-lineage (T/myeloid) acute leukemia having t(6;14)(q25;q32) by cDNA bubble PCR using BCL11B primers; however, the gene fused to BCL11B on 14q32 was not on 6q25. IGKV3-20-RN28S1 and COG1-RN28S1 fusion transcripts were identified in the Burkitt lymphoma cell line HBL-5, and the multiple myeloma cell line KMS-18. RN28S1 would not translate, and the breakpoints in partner genes of RN28S1 were within the coding exons, suggesting that disruption of fusion partners by fusion to RN28S1 is the possible mechanism of tumorigenesis. Although further analysis is needed to elucidate the mechanism(s) through which these RN28S1-related fusions play roles in tumorigenesis, our findings provide important insights into the role of rDNA function in human genomic architecture and tumorigenesis.

  14. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas

    PubMed Central

    Jones, David T. W.; Kocialkowski, Sylvia; Liu, Lu; Pearson, Danita M.; Bäcklund, L. Magnus; Ichimura, Koichi; Collins, V. Peter

    2008-01-01

    Brain tumours are the commonest solid tumours of childhood, and pilocytic astrocytomas (PAs) are the most common central nervous system tumour in 5-19 year-olds. Little is known about the genetic alterations underlying their development. Here we describe a tandem duplication of ∼2Mb at 7q34 occurring in 66% of pilocytic astrocytomas. This rearrangement, which was not observed in a series of 244 higher-grade astrocytomas, results in an in-frame fusion gene incorporating the kinase domain of the BRAF oncogene. We further show that the resulting fusion protein has constitutive BRAF kinase activity, and is able to transform NIH3T3 cells. This is the first report of BRAF activation through rearrangement as a frequent feature in a sporadic tumor. The frequency and specificity of this change underline its potential both as a therapeutic target and a diagnostic tool. PMID:18974108

  15. An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples.

    PubMed

    Scolnick, Jonathan A; Dimon, Michelle; Wang, I-Ching; Huelga, Stephanie C; Amorese, Douglas A

    2015-01-01

    Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET), for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue RNA in both normal tissue and cancer cells.

  16. An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

    PubMed Central

    Scolnick, Jonathan A.; Dimon, Michelle; Wang, I-Ching; Huelga, Stephanie C.; Amorese, Douglas A.

    2015-01-01

    Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET), for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue RNA in both normal tissue and cancer cells. PMID:26132974

  17. Inertial Confinement Fusion Annual Report 1999

    SciTech Connect

    Kauffman, Robert L.

    2001-07-01

    The ICF Program has undergone a significant change in 1999 with the decommissioning of the Nova laser and the transfer of much of the experimental program to the OMEGA laser at the University of Rochester. The Nova laser ended operations with the final experiment conducted on May 27, 1999. This marked the end to one of DOE's most successful experimental facilities. Since its commissioning in 1985, Nova performed 13,424 experiments supporting ICF, Defense Sciences, high-power laser research, and basic science research. At the time of its commissioning, Nova was the world's most powerful laser. Its early experiments demonstrated that 3ω light could produce high-drive, low-preheat environment required for indirect-drive ICE. In the early 1990s, the technical program on Nova for indirect drive ignition was defined by the Nova technical contract established by National Academy Review of ICF in 1990. Successful completion of this research program contributed significantly to the recommendation by the ICF Advisory Committee in 1995 to proceed with the construction of the National Ignition Facility? Nova experiments also demonstrated the utility of high-powered lasers for studying the physics of interest to Defense Sciences. Now, high-powered lasers along with pulsed-power machines are the principal facilities for studying high energy density science in DOE's Stockpile Stewardship Program (SSP). In 1997, one beam of Nova was converted to a short pulsed beam producing a petawatt of power in subpicosecond pulses. The petawatt beam was used for pioneering research in short-pulse laser-matter interactions relevant to fast ignitor ICF and short pulsed x-ray, electron, and particle production for use as probes. Nova is being disassembled and the space is being used to support NIF construction. Nova components are being distributed to a number of other laser laboratories around the world for reuse as determined by DOE. This report summarizes the research performed by the ICF

  18. ZNF384-related fusion genes define a subgroup of childhood B-cell precursor acute lymphoblastic leukemia with a characteristic immunotype

    PubMed Central

    Hirabayashi, Shinsuke; Ohki, Kentaro; Nakabayashi, Kazuhiko; Ichikawa, Hitoshi; Momozawa, Yukihide; Okamura, Kohji; Yaguchi, Akinori; Terada, Kazuki; Saito, Yuya; Yoshimi, Ai; Ogata-Kawata, Hiroko; Sakamoto, Hiromi; Kato, Motohiro; Fujimura, Junya; Hino, Moeko; Kinoshita, Akitoshi; Kakuda, Harumi; Kurosawa, Hidemitsu; Kato, Keisuke; Kajiwara, Ryosuke; Moriwaki, Koichi; Morimoto, Tsuyoshi; Nakamura, Kozue; Noguchi, Yasushi; Osumi, Tomoo; Sakashita, Kazuo; Takita, Junko; Yuza, Yuki; Matsuda, Koich; Yoshida, Teruhiko; Matsumoto, Kenji; Hata, Kenichiro; Kubo, Michiaki; Matsubara, Yoichi; Fukushima, Takashi; Koh, Katsuyoshi; Manabe, Atsushi; Ohara, Akira; Kiyokawa, Nobutaka

    2017-01-01

    Fusion genes involving ZNF384 have recently been identified in B-cell precursor acute lymphoblastic leukemia, and 7 fusion partners have been reported. We further characterized this type of fusion gene by whole transcriptome sequencing and/or polymerase chain reaction. In addition to previously reported genes, we identified BMP2K as a novel fusion partner for ZNF384. Including the EP300-ZNF384 that we reported recently, the total frequency of ZNF384-related fusion genes was 4.1% in 291 B-cell precursor acute lymphoblastic leukemia patients enrolled in a single clinical trial, and TCF3-ZNF384 was the most recurrent, with a frequency of 2.4%. The characteristic immunophenotype of weak CD10 and aberrant CD13 and/or CD33 expression was revealed to be a common feature of the leukemic cells harboring ZNF384-related fusion genes. The signature gene expression profile in TCF3-ZNF384-positive patients was enriched in hematopoietic stem cell features and related to that of EP300-ZNF384-positive patients, but was significantly distinct from that of TCF3-PBX1-positive and ZNF384-fusion-negative patients. However, clinical features of TCF3-ZNF384-positive patients are markedly different from those of EP300-ZNF384-positive patients, exhibiting higher cell counts and a younger age at presentation. TCF3-ZNF384-positive patients revealed a significantly poorer steroid response and a higher frequency of relapse, and the additional activating mutations in RAS signaling pathway genes were detected by whole exome analysis in some of the cases. Our observations indicate that ZNF384-related fusion genes consist of a distinct subgroup of B-cell precursor acute lymphoblastic leukemia with a characteristic immunophenotype, while the clinical features depend on the functional properties of individual fusion partners. PMID:27634205

  19. Inertial fusion program. Progress report, July 1-December 31, 1978

    SciTech Connect

    Perkins, R.B.

    1980-11-01

    Progress at Los Alamos Scientific Laboratory (LASL) in the development of high-energy short-pulse CO/sub 2/ laser systems for fusion research is reported. Improvements to LASL's two-beam system, Gemini, are outlined and experimental results are discussed. Our eight-beam system, Helios, was fired successfully on target for the first time, and became the world's most powerful gas laser for laser fusion studies. Work on Antares, our 100- to 200-TW target irradiation system, is summarized, indicating that design work and building construction are 70 and 48% complete, respectively. A baseline design for automatic centering of laser beams onto the various relay mirrors and the optical design of the Antares front end are discussed. The results of various fusion reactor studies are summarized, as well as investigations of synthetic-fuel production through application of fusion energy to hydrogen production by thermochemical water splitting. Studies on increased efficiency of energy extraction in CO/sub 2/ lasers and on lifetimes of cryogenic pellets in a reactor environment are summarized, as well as the results of studies on pellet injection, tracking, and beam synchronization.

  20. Cloning of alpha-beta fusion gene from Clostridium perfringens and its expression.

    PubMed

    Bai, Jia-Ning; Zhang, Yan; Zhao, Bao-Hua

    2006-02-28

    To study the cloning of alpha-beta fusion gene from Clostridium perfringens and the immunogenicity of alpha-beta fusion expression. Cloning was accomplished after PCR amplification from strains NCTC64609 and C58-1 of the protective antigen genes of alpha-toxin and beta-toxin. The fragment of the gene was cloned using plasmid pZCPAB. This fragment coded for the gene with the stable expression of alpha-beta fusion gene binding. In order to verify the exact location of the alpha-beta fusion gene, domain plasmids were constructed. The two genes were fused into expression vector pBV221. The expressed alpha-beta fusion protein was identified by ELISA, SDS-PAGE, Western blotting and neutralization assay. The protective alpha-toxin gene (cpa906) and the beta-toxin gene (cpb930) were obtained. The recombinant plasmid pZCPAB carrying alpha-beta fusion gene was constructed and transformed into BL21(DE3). The recombinant strain BL21(DE3)(pZCPAB) was obtained. After the recombinant strain BL21(DE3)(pZCPAB) was induced by 42 degC, its expressed product was about 22.14% of total cellular protein at SDS-PAGE and thin-layer gel scanning analysis. Neutralization assay indicated that the antibody induced by immunization with alpha-beta fusion protein could neutralize the toxicity of alpha-toxin and beta-toxin. The obtained alpha-toxin and beta-toxin genes are correct. The recombinant strain BL21(DE3)(pZCPAB) could produce alpha-beta fusion protein. This protein can be used for immunization and is immunogenic. The antibody induced by immunization with alpha-beta fusion protein could neutralize the toxicity of alpha-toxin and beta-toxin.

  1. Fusion

    NASA Astrophysics Data System (ADS)

    Herman, Robin

    1990-10-01

    The book abounds with fascinating anecdotes about fusion's rocky path: the spurious claim by Argentine dictator Juan Peron in 1951 that his country had built a working fusion reactor, the rush by the United States to drop secrecy and publicize its fusion work as a propaganda offensive after the Russian success with Sputnik; the fortune Penthouse magazine publisher Bob Guccione sank into an unconventional fusion device, the skepticism that met an assertion by two University of Utah chemists in 1989 that they had created "cold fusion" in a bottle. Aimed at a general audience, the book describes the scientific basis of controlled fusion--the fusing of atomic nuclei, under conditions hotter than the sun, to release energy. Using personal recollections of scientists involved, it traces the history of this little-known international race that began during the Cold War in secret laboratories in the United States, Great Britain and the Soviet Union, and evolved into an astonishingly open collaboration between East and West.

  2. Identification of the merR gene of R100 by using mer-lac gene and operon fusions.

    PubMed Central

    Foster, T J; Brown, N L

    1985-01-01

    Transcriptional (operon) and translational (gene) fusions between the R100 merR gene and lacZ were constructed in vitro in a pBR322 plasmid carrying the mer genes derived from plasmid R100. The translational fusions were oriented in the opposite direction to and divergently from the merTCAD genes. This shows that the reading frame previously thought to be merR was incorrect. Expression of the gene fusion was repressed in trans by a compatible plasmid carrying the R100 merR+ gene, as was a similarly oriented transcriptional fusion. In contrast, expression of beta-galactosidase by the lac fragment located at the same site but in the opposite orientation was at a lower level and was not repressed by merR+. Images PMID:2993235

  3. Studying Gene Expression: Database Searches and Promoter Fusions to Investigate Transcriptional Regulation in Bacteria†

    PubMed Central

    Martinez-Vaz, Betsy M.; Makarevitch, Irina; Stensland, Shane

    2010-01-01

    A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in Escherichia coli. The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students’ knowledge of databases, reporter genes and transcriptional regulation. PMID:23653697

  4. TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma | Office of Cancer Genomics

    Cancer.gov

    Recently, the landscape of single base mutations in diffuse large B-cell lymphoma (DLBCL) was described. Here we report the discovery of a gene fusion between TBL1XR1 and TP63, the only recurrent somatic novel gene fusion identified in our analysis of transcriptome data from 96 DLBCL cases. Based on this cohort and a further 157 DLBCL cases analyzed by FISH, the incidence in de novo germinal center B cell-like (GCB) DLBCL is 5% (6 of 115).

  5. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

    PubMed Central

    2014-01-01

    Background The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase template switching events, incorrect mapping, and other systematic errors. Such lists lack any indication of oncogenic relevance, and they are too large for exhaustive experimental validation. Results We have designed and implemented a pipeline, Pegasus, for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation. Conclusion We show the effectiveness of Pegasus in predicting new driver fusions in 176 RNA-Seq samples of glioblastoma multiforme (GBM) and 23 cases of anaplastic large cell lymphoma (ALCL). Contact: fa2306@columbia.edu. PMID:25183062

  6. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.

    PubMed

    Abate, Francesco; Zairis, Sakellarios; Ficarra, Elisa; Acquaviva, Andrea; Wiggins, Chris H; Frattini, Veronique; Lasorella, Anna; Iavarone, Antonio; Inghirami, Giorgio; Rabadan, Raul

    2014-09-04

    The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase template switching events, incorrect mapping, and other systematic errors. Such lists lack any indication of oncogenic relevance, and they are too large for exhaustive experimental validation. We have designed and implemented a pipeline, Pegasus, for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation. We show the effectiveness of Pegasus in predicting new driver fusions in 176 RNA-Seq samples of glioblastoma multiforme (GBM) and 23 cases of anaplastic large cell lymphoma (ALCL).

  7. SNAP-25 gene family members differentially support secretory vesicle fusion.

    PubMed

    Arora, Swati; Saarloos, Ingrid; Kooistra, Robbelien; van de Bospoort, Rhea; Verhage, Matthijs; Toonen, Ruud F

    2017-06-01

    Neuronal dense-core vesicles (DCVs) transport and secrete neuropeptides necessary for development, plasticity and survival, but little is known about their fusion mechanism. We show that Snap-25-null mutant (SNAP-25 KO) neurons, previously shown to degenerate after 4 days in vitro (DIV), contain fewer DCVs and have reduced DCV fusion probability in surviving neurons at DIV14. At DIV3, before degeneration, SNAP-25 KO neurons show normal DCV fusion, but one day later fusion is significantly reduced. To test if other SNAP homologs support DCV fusion, we expressed SNAP-23, SNAP-29 or SNAP-47 in SNAP-25 KO neurons. SNAP-23 and SNAP-29 rescued viability and supported DCV fusion in SNAP-25 KO neurons, but SNAP-23 did so more efficiently. SNAP-23 also rescued synaptic vesicle (SV) fusion while SNAP-29 did not. SNAP-47 failed to rescue viability and did not support DCV or SV fusion. These data demonstrate a developmental switch, in hippocampal neurons between DIV3 and DIV4, where DCV fusion becomes SNAP-25 dependent. Furthermore, SNAP-25 homologs support DCV and SV fusion and neuronal viability to variable extents - SNAP-23 most effectively, SNAP-29 less so and SNAP-47 ineffectively. © 2017. Published by The Company of Biologists Ltd.

  8. Inertial Fusion Program. Progress report, January-December 1980

    SciTech Connect

    Not Available

    1982-05-01

    This report summarizes research and development effort in support of the Inertial Confinement Fusion program, including absorption measurements with an integrating sphere, generation of high CO/sub 2/-laser harmonics in the backscattered light from laser plasmas, and the effects of hydrogen target contamination on the hot-electron temperature and transport. The development of new diagnostics is outlined and measurements taken with a proximity-focused x-ray streak camera are presented. High gain in phase conjugation using germanium was demonstrated, data were obtained on retropulse isolation by plasmas generated from metal shutters, damage thresholds for copper mirrors at high fluences were characterized, and phase conjugation in the ultraviolet was demonstrated. Significant progress in the characterization of targets, new techniques in target coating, and important advances in the development of low-density, small-cell-size plastic foam that permit highly accurate machining to any desired shape are presented. The results of various fusion reactor system studies are summarized.

  9. Mirror fusion. Quarterly report, April-June 1981

    SciTech Connect

    Not Available

    1981-09-11

    The information in each Quarterly is presented in the same sequence as in the Field Work Package Proposal and Authorization System (WPAS) submissions prepared for the U.S. Department of Energy; the main sections are Applied Plasma Physics, Confinement Systems, Development and Technology, and Mirror Fusion Test Facility (Planning and Projects). On occasion, we shall include information pertaining to the LLNL role as Lead Laboratory for the Open Systems Mirror Fusion Program. Each of these sections is introduced by an overall statement of the goals and purposes of the groups reporting in it. As appropriate within each section, statements of the goals of individual programs and projects are followed by articles containing summaries of significant recent activity and descriptive text.

  10. INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.

    PubMed

    Zhang, Jin; Mardis, Elaine R; Maher, Christopher A

    2017-02-15

    While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens. We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens. INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo . christophermaher@wustl.edu. Supplementary data are available at Bioinformatics online.

  11. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. | Office of Cancer Genomics

    Cancer.gov

    Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, BCR-ABL1, EML4-ALK, and ETV6-NTRK3, as well as 20 previously uncharacterized fusion genes identified in TCGA datasets.

  12. Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer.

    PubMed

    Latysheva, Natasha S; Oates, Matt E; Maddox, Louis; Flock, Tilman; Gough, Julian; Buljan, Marija; Weatheritt, Robert J; Babu, M Madan

    2016-08-18

    Gene fusions are common cancer-causing mutations, but the molecular principles by which fusion protein products affect interaction networks and cause disease are not well understood. Here, we perform an integrative analysis of the structural, interactomic, and regulatory properties of thousands of putative fusion proteins. We demonstrate that genes that form fusions (i.e., parent genes) tend to be highly connected hub genes, whose protein products are enriched in structured and disordered interaction-mediating features. Fusion often results in the loss of these parental features and the depletion of regulatory sites such as post-translational modifications. Fusion products disproportionately connect proteins that did not previously interact in the protein interaction network. In this manner, fusion products can escape cellular regulation and constitutively rewire protein interaction networks. We suggest that the deregulation of central, interaction-prone proteins may represent a widespread mechanism by which fusion proteins alter the topology of cellular signaling pathways and promote cancer. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Inertial Confinement Fusion: Quarterly report, April-June 1996

    SciTech Connect

    Correll, D.

    1996-06-01

    The lead article, `Ion-beam propagation in a low-density reactor chamber for heavy-ion inertial fusion` (p. 89), explores the ability of heavy-ion beams to be adequately transported and focused in an IFE reactor. The next article, `Efficient production and applications of 2- to 10-keV x rays by laser-heated underdense radiators` (p. 96), explores the ability of the NIF to produce sufficient high-energy x rays for diagnostic backlighting, target preheating, or uniform irradiation of large test objects for Nuclear Weapons Effects Testing. For capsule implosion experiments, the increasing energies and distances involved in the NIF compared to Nova require the development of new diagnostics methods. The article `Fusion reaction-rate measurements--Nova and NIF` (p. 115) first reviews the use of time-resolved neutron measurements on Nova to monitor fusion burn histories and then explores the limitations of that technique, principally Doppler broadening, for the proposed NIF. It also explores the use of gamma rays on Nova, thereby providing a proof-of-principle for using gamma rays for monitoring fusion burn histories on the NIF. The articles `The energetics of gas-filled hohlraums` (p. 110) and `Measurements of laser- speckle-induced perturbations in laser-driven foils` (p. 123) report measurements on Nova of two important aspects of implosion experiments. The first characterizes the amount of energy lost from a hohlraum by stimulated Brillouin and Raman scattering as a function of gas fill and laser-beam uniformity. The second of these articles shows that the growth of density nonuniformities implanted on smooth capsule surfaces by laser speckle can be correlated with the effects of physical surface roughness. The article `Laser-tissue interaction modeling with the LATIS computer program` (p. 103) explores the use of modeling to enhance the effectiveness--maximize desired effects and minimize collateral damage--of lasers for medical purposes.

  14. Multisource report-level simulator for fusion research

    NASA Astrophysics Data System (ADS)

    Carlotto, Mark J.; Kadar, Ivan

    2003-08-01

    The Multi-source Report-level Simulator (MRS) is a tool developed by Veridian Systems as part of its Model-adaptive Multi-source Track Fusion (MMTF) effort under DARPA's DTT program. MRS generates simulated multisensor contact reports for GMTI, HUMINT, IMINT, SIGINT, UGS, and video. It contains a spatial editor for creating ground tracks along which vehicles move over the terrain. Vehicles can start, stop, speed up, or slow down. The spatial editor is also used to define the locations of fixed sensors such as UGS and HUMINT observers on the ground, and flight paths of GMTI, IMINT, SIGINT, and video sensors in the air. Observation models characterize each sensor at the report level in terms of their operating characteristics (revisit rate, resolution, etc.) measurement errors, and detection/classification performance (i.e., Pd, Nfa, Pcc, and Pid). Contact reports are linked to ground truth data to facilitate the testing of track/fusion algorithms and the validation of associated performance models.

  15. Post-entrapment genome engineering: first exon size does not affect the expression of fusion transcripts generated by gene entrapment.

    PubMed

    Osipovich, Anna B; Singh, Aparna; Ruley, H Earl

    2005-03-01

    Gene trap mutagenesis in mouse embryonic stem cells has been widely used for genome-wide studies of mammalian gene function. However, while large numbers of genes can be disrupted, individual mutations may suffer from limitations due to the structure and/or placement of targeting vector. To extend the utility of gene trap mutagenesis, replaceable 3' [or poly(A)] gene trap vectors were developed that permit sequences inserted in individual entrapment clones to be engineered by Cre-mediated recombination. 3' traps incorporating different drug resistance genes could be readily exchanged, simply by selecting for the drug-resistance gene of the replacement vector. By substituting different 3' traps, we show that otherwise identical fusion genes containing a large first exon (804 nt) are not expressed at appreciably lower levels than genes expressing small first exons (384 and 151 nt). Thus, size appears to have less effect on the expression and processing of first exons than has been reported for internal exons. Finally, a retroviral poly(A) trap (consisting of a RNA polymerase II promoter, a neomycin-resistance gene, and 5'-splice site) typically produced mutagenized clones in which vector sequences spliced to the 3'-terminal exons of cellular transcription units, suggesting strong selection for fusion transcripts that evade nonsense-mediated decay. The efficient exchange of poly(A) traps should greatly extend the utility of mutant libraries generated by gene entrapment and provides new strategies to study the rules that govern the expression of exons inserted throughout the genome.

  16. [Recombination and fusion expression of porcine defensin gene PBD-I in E. coli].

    PubMed

    Luo, Gang; Wei, Hong

    2003-03-01

    The porcine defensin gene PBD-I was amplified by RT-PCR, then the gene was inserted into expression vector PinPoint(TM) Xa-3. Recombinant plasmid named as ppd-1 was transformed into E.Coli JM109, which could effectively produce fusion protein induced with IPTG. The positive clone of PBD-I gene expressed 17kDa fusion protein by SDS-PAGE electrophoresis. Expression of PBD-I gene didn't increase distinctly along with time. The expression of PBD-I gene lays a foundation in research on antimicrobial activities and its mechanism of the defensin.

  17. ETS Gene Fusions as Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer

    DTIC Science & Technology

    2016-05-01

    gene   fusion  product)  and  the   DNA  repair  protein   DNA -­PK,  and  3)  to  determine  if  ETS  gene  fusion  status  is  a  clinical  biomarker...established  this  axis  as  a  potential  therapeutic   target.         15. SUBJECT  TERMS Prostate cancer, ETS gene fusions, ERG, radiation resistance, DNA ...interaction  between  ERG   (the   predominant   ETS   gene   fusion   product)   and   the   DNA   repair   protein   DNA -­PK,   and   3)   to

  18. Emergence of FGFR family gene fusions as therapeutic targets in a wide spectrum of solid tumours.

    PubMed

    Parker, Brittany C; Engels, Manon; Annala, Matti; Zhang, Wei

    2014-01-01

    The emergence of fibroblast growth factor receptor (FGFR) family fusions across diverse cancers has brought attention to FGFR-derived cancer therapies. The discovery of the first recurrent FGFR fusion in glioblastoma was followed by discoveries of FGFR fusions in bladder, lung, breast, thyroid, oral, and prostate cancers. Drug targeting of FGFR fusions has shown promising results and should soon be translating into clinical trials. FGFR fusions form as a result of various mechanisms – predominantly deletion for FGFR1, translocation for FGFR2, and tandem duplication for FGFR3. The ability to exploit the unique targetability of FGFR fusions proves that FGFR-derived therapies could have a promising future in cancer therapeutics. Drug targeting of fusion genes has proven to be an extremely effective therapeutic approach for cancers such as the recurrent BCR–ABL1 fusion in chronic myeloid leukaemia. The recent discovery of recurrent FGFR family fusions in several cancer types has brought to attention the unique therapeutic potential for FGFR-positive patients. Understanding the diverse mechanisms of FGFR fusion formation and their oncogenic potential will shed light on the impact of FGFR-derived therapy in the future.

  19. Construction of hpaA gene from a clinical isolate of Helicobacter pylori and identification of fusion protein.

    PubMed

    Mao, Ya-Fei; Yan, Jie; Li, Li-Wei; Li, Shu-Ping

    2003-07-01

    To clone hpaA gene from a clinical strain of Helicobacter pylori and to construct the expression vector of the gene and to identify immunity of the fusion protein. The hpaA gene from a clinical isolate Y06 of H.pylori was amplified by high fidelity PCR. The nucleotide sequence of the target DNA amplification fragment was sequenced after T-A cloning. The recombinant expression vector inserted with hpaA gene was constructed. The expression of HpaA fusion protein in E.coli BL21DE3 induced by IPTG at different dosages was examined by SDS-PAGE. Western blot with commercial antibody against whole cell of H.pylori as well as immunodiffusion assay with self-prepared rabbit antiserum against HpaA fusion protein were applied to determine immunity of the fusion protein. ELISA was used to detect the antibody against HpaA in sera of 125 patients infected with H.pylori and to examine HpaA expression of 109 clinical isolates of H.pylori. In comparison with the reported corresponding sequences, the homologies of nucleotide and putative amino acid sequences of the cloned hpaA gene were from 94.25-97.32 % and 95.38-98.46 %, respectively. The output of HpaA fusion protein in its expression system of pET32a-hpaA-BL21DE3 was approximately 40 % of the total bacterial proteins. HpaA fusion protein was able to combine with the commercial antibody against whole cell of H.pylori and to induce rabbit producing specific antiserum with 1:4 immunodiffusion titer after the animal was immunized with the fusion protein. 81.6 % of the serum samples from 125 patients infected with H.pylori (102/125) were positive for HpaA antibody and all of the tested isolates of H.pylori (109/109) were detectable for HpaA. A prokaryotic expression system with high efficiency of H.pylori hpaA gene was successfully established. The HpaA expressing fusion protein showed satisfactory immunoreactivity and antigenicity. High frequencies of HpaA expression in different H.pylori clinical strains and specific antibody

  20. Construction of hpaA gene from a clinical isolate of Helicobacter pylori and identification of fusion protein

    PubMed Central

    Mao, Ya-Fei; Yan, Jie; Li, Li-Wei; Li, Shu-Ping

    2003-01-01

    AIM: To clone hpaA gene from a clinical strain of Helicobacter pylori and to construct the expression vector of the gene and to identify immunity of the fusion protein. METHODS: The hpaA gene from a clinical isolate Y06 of H. pylori was amplified by high fidelity PCR. The nucleotide sequence of the target DNA amplification fragment was sequenced after T-A cloning. The recombinant expression vector inserted with hpaA gene was constructed. The expression of HpaA fusion protein in E.coli BL21(DE3) induced by IPTG at different dosages was examined by SDS-PAGE. Western blot with commercial antibody against whole cell of H. pylori as well as immunodiffusion assay with self-prepared rabbit antiserum against HpaA fusion protein were applied to determine immunity of the fusion protein. ELISA was used to detect the antibody against HpaA in sera of 125 patients infected with H. pylori and to examine HpaA expression of 109 clinical isolates of H. pylori. RESULTS: In comparison with the reported corresponding sequences, the homologies of nucleotide and putative amino acid sequences of the cloned hpaA gene were from 94.25%-97.32% and 95.38%-98.46%, respectively. The output of HpaA fusion protein in its expression system of pET32a-hpaA-BL21(DE3) was approximately 40% of the total bacterial proteins. HpaA fusion protein was able to combine with the commercial antibody against whole cell of H. pylori and to induce rabbit producing specific antiserum with 1:4 immunodiffusion titer after the animal was immunized with the fusion protein. 81.6% of the serum samples from 125 patients infected with H. pylori (102/125) were positive for HpaA antibody and all of the tested isolates of H. pylori (109/109) were detectable for HpaA. CONCLUSION: A prokaryotic expression system with high efficiency of H. pylori hpaA gene was successfully established. The HpaA expressing fusion protein showed satisfactory immunoreactivity and antigenicity. High frequencies of HpaA expression in different H

  1. Highly Specific Targeting of the TMPRSS2/ERG Fusion Gene in Prostate Cancer Using Liposomal Nanotechnology

    DTIC Science & Technology

    2012-06-01

    time due to elimination by reticuloendothelial system. To increase stability and blood circulation half- life coating nanoparticles with polymers such...ERG fusion gene in prostate cancer using liposomal nanotechnology PRINCIPAL INVESTIGATOR: Bulent Ozpolat, M.D., Ph.D...fusion gene in prostate cancer using liposomal nanotechnology 5b. GRANT NUMBER W81XWH-09-1-0385 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

  2. Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species

    PubMed Central

    Potter, Sally; Moritz, Craig; Eldridge, Mark D. B.

    2015-01-01

    Complex Robertsonian rearrangements, with shared arms in different fusions, are expected to prevent gene flow between hybrids through missegregation during meiosis. Here, we estimate gene flow between recently diverged and chromosomally diverse rock-wallabies (Petrogale) to test for this form of chromosomal speciation. Contrary to expectations, we observe relatively high admixture among species with complex fusions. Our results reinforce the need to consider alternative roles of chromosome change, together with genic divergence, in driving speciation. PMID:26445985

  3. Construction and Expression of Sugar Kinase Transcriptional Gene Fusions by Using the Sinorhizobium meliloti ORFeome▿

    PubMed Central

    Humann, Jodi L.; Schroeder, Brenda K.; Mortimer, Michael W.; House, Brent L.; Yurgel, Svetlana N.; Maloney, Scott C.; Ward, Kristel L.; Fallquist, Heather M.; Ziemkiewicz, Hope T.; Kahn, Michael L.

    2008-01-01

    The Sinorhizobium meliloti ORFeome project cloned 6,314 open reading frames (ORFs) into a modified Gateway entry vector system from which the ORFs could be transferred to destination vectors in vivo via bacterial conjugation. In this work, a reporter gene destination vector, pMK2030, was constructed and used to generate ORF-specific transcriptional fusions to β-glucuronidase (gusA) and green fluorescent protein (gfp) reporter genes. A total of 6,290 ORFs were successfully transferred from the entry vector library into pMK2030. To demonstrate the utility of this system, reporter plasmids corresponding to 30 annotated sugar kinase genes were integrated into the S. meliloti SM1021 and/or SM8530 genome. Expression of these genes was measured using a high-throughput β-glucuronidase assay to track expression on nine different carbon sources. Six ORFs integrated into SM1021 and SM8530 had different basal levels of expression in the two strains. The annotated activities of three other sugar kinases were also confirmed. PMID:18791020

  4. Fusion Energy Division annual progress report, period ending December 31, 1989

    SciTech Connect

    Sheffield, J.; Baker, C.C.; Saltmarsh, M.J.

    1991-07-01

    The Fusion Program of Oak Ridge National Laboratory (ORNL) carries out research in most areas of magnetic confinement fusion. The program is directed toward the development of fusion as an energy source and is a strong and vital component of both the US fusion program and the international fusion community. Issued as the annual progress report of the ORNL Fusion Energy Division, this report also contains information from components of the Fusion Program that are carried out by other ORNL organizations (about 15% of the program effort). The areas addressed by the Fusion Program and discussed in this report include the following: Experimental and theoretical research on magnetic confinement concepts, engineering and physics of existing and planned devices, including remote handling, development and testing of diagnostic tools and techniques in support of experiments, assembly and distribution to the fusion community of databases on atomic physics and radiation effects, development and testing of technologies for heating and fueling fusion plasmas, development and testing of superconducting magnets for containing fusion plasmas, development and testing of materials for fusion devices, and exploration of opportunities to apply the unique skills, technology, and techniques developed in the course of this work to other areas. Highlights from program activities are included in this report.

  5. Fusion Energy Division annual progress report, period ending December 31, 1988

    SciTech Connect

    Sheffield, J.; Berry, L.A.; Saltmarsh, M.J.

    1990-02-01

    This report discusses the following topics on fusion research: toroidal confinement activities; atomic physics and plasma diagnostics development; fusion theory and computation; plasma technology; superconducting magnet development; advanced systems program; fusion materials research; neutron transport; and management services, quality assurance, and safety.

  6. Acute myeloid leukemia fusion proteins deregulate genes involved in stem cell maintenance and DNA repair

    PubMed Central

    Alcalay, Myriam; Meani, Natalia; Gelmetti, Vania; Fantozzi, Anna; Fagioli, Marta; Orleth, Annette; Riganelli, Daniela; Sebastiani, Carla; Cappelli, Enrico; Casciari, Cristina; Sciurpi, Maria Teresa; Mariano, Angela Rosa; Minardi, Simone Paolo; Luzi, Lucilla; Muller, Heiko; Di Fiore, Pier Paolo; Frosina, Guido; Pelicci, Pier Giuseppe

    2003-01-01

    Acute myelogenous leukemias (AMLs) are genetically heterogeneous and characterized by chromosomal rearrangements that produce fusion proteins with aberrant transcriptional regulatory activities. Expression of AML fusion proteins in transgenic mice increases the risk of myeloid leukemias, suggesting that they induce a preleukemic state. The underlying molecular and biological mechanisms are, however, unknown. To address this issue, we performed a systematic analysis of fusion protein transcriptional targets. We expressed AML1/ETO, PML/RAR, and PLZF/RAR in U937 hemopoietic precursor cells and measured global gene expression using oligonucleotide chips. We identified 1,555 genes regulated concordantly by at least two fusion proteins that were further validated in patient samples and finally classified according to available functional information. Strikingly, we found that AML fusion proteins induce genes involved in the maintenance of the stem cell phenotype and repress DNA repair genes, mainly of the base excision repair pathway. Functional studies confirmed that ectopic expression of fusion proteins constitutively activates pathways leading to increased stem cell renewal (e.g., the Jagged1/Notch pathway) and provokes accumulation of DNA damage. We propose that expansion of the stem cell compartment and induction of a mutator phenotype are relevant features underlying the leukemic potential of AML-associated fusion proteins. PMID:14660751

  7. In vivo topological analysis of Ste2, a yeast plasma membrane protein, by using beta-lactamase gene fusions.

    PubMed Central

    Cartwright, C P; Tipper, D J

    1991-01-01

    Gene fusions were constructed between Ste2, the receptor for the Saccharomyces cerevisiae alpha-factor, and beta la, the secreted form of beta-lactamase encoded by the bla gene of pBR322. The Ste2 and beta la components were linked by a processing fragment (P) from the yeast killer preprotoxin containing a C-terminal lysine-arginine site for cleavage by the Golgi-associated Kex2 protease. Ste2 is predicted to have a rhodopsinlike topology, with an external N terminus and seven transmembrane segments. Fusions to three of the four Ste2 domains predicted to be external resulted in beta la secretion from yeast cells. A fusion at a site just preceding the first transmembrane segment was an exception; the product was cell associated, indicating that the first 44 residues of Ste2 are insufficient to direct secretion of beta la; translocation of this domain presumably requires the downstream transmembrane segment. Expression of fusions located in two domains predicted to be cytoplasmic failed to result in beta la secretion. Following insertion of the preprotoxin signal peptide (S) between the Ste2 and P components of these cytoplasmic fusions, secretion of beta la activity occurred, which is consistent with inversion of the orientation of the beta la reporter. Conversely, insertion of S between Ste2 and P in an external fusion sharply reduced beta la secretion. Complementary information about both cytoplasmic and external domains of Ste2 was therefore provided, and most aspects of the predicted topology were confirmed. The steady-state levels of beta la detected were low, presumably because of efficient degradation of the fusions in the secretory pathway; levels, however, were easily detectable. This method should be valuable in the analysis of in vivo topologies of both homologous and foreign plasma membrane proteins expressed in yeast cells. Images PMID:2017168

  8. Fusion Energy Division: Annual progress report, period ending December 31, 1987

    SciTech Connect

    Morgan, O.B. Jr.; Berry, L.A.; Sheffield, J.

    1988-11-01

    The Fusion Program of Oak Ridge National Laboratory (ORNL), a major part of the national fusion program, carries out research in nearly all areas of magnetic fusion. Collaboration among staff from ORNL, Martin Marietta Energy Systems, Inc., private industry, the academic community, and other fusion laboratories, in the United States and abroad, is directed toward the development of fusion as an energy source. This report documents the program's achievements during 1987. Issued as the annual progress report of the ORNL Fusion Energy Division, it also contains information from components of the Fusion Program that are external to the division (about 15% of the program effort). The areas addressed by the Fusion Program include the following: experimental and theoretical research on magnetic confinement concepts, engineering and physics of existing and planned devices, development and testing of diagnostic tools and techniques in support of experiments, assembly and distribution to the fusion community of databases on atomic physics and radiation effects, development and testing of technologies for heating and fueling fusion plasmas, development and testing of superconducting magnets for containing fusion plasmas, and development and testing of materials for fusion devices. Highlights from program activities are included in this report. 126 figs., 15 tabs.

  9. Report of the Fusion Energy Sciences Advisory Committee. Panel on Integrated Simulation and Optimization of Magnetic Fusion Systems

    SciTech Connect

    Dahlburg, Jill; Corones, James; Batchelor, Donald; Bramley, Randall; Greenwald, Martin; Jardin, Stephen; Krasheninnikov, Sergei; Laub, Alan; Leboeuf, Jean-Noel; Lindl, John; Lokke, William; Rosenbluth, Marshall; Ross, David; Schnack, Dalton

    2002-11-01

    Fusion is potentially an inexhaustible energy source whose exploitation requires a basic understanding of high-temperature plasmas. The development of a science-based predictive capability for fusion-relevant plasmas is a challenge central to fusion energy science, in which numerical modeling has played a vital role for more than four decades. A combination of the very wide range in temporal and spatial scales, extreme anisotropy, the importance of geometric detail, and the requirement of causality which makes it impossible to parallelize over time, makes this problem one of the most challenging in computational physics. Sophisticated computational models are under development for many individual features of magnetically confined plasmas and increases in the scope and reliability of feasible simulations have been enabled by increased scientific understanding and improvements in computer technology. However, full predictive modeling of fusion plasmas will require qualitative improvements and innovations to enable cross coupling of a wider variety of physical processes and to allow solution over a larger range of space and time scales. The exponential growth of computer speed, coupled with the high cost of large-scale experimental facilities, makes an integrated fusion simulation initiative a timely and cost-effective opportunity. Worldwide progress in laboratory fusion experiments provides the basis for a recent FESAC recommendation to proceed with a burning plasma experiment (see FESAC Review of Burning Plasma Physics Report, September 2001). Such an experiment, at the frontier of the physics of complex systems, would be a huge step in establishing the potential of magnetic fusion energy to contribute to the world’s energy security. An integrated simulation capability would dramatically enhance the utilization of such a facility and lead to optimization of toroidal fusion plasmas in general. This science-based predictive capability, which was cited in the FESAC

  10. NUP98 gene fusions and hematopoietic malignancies: common themes and new biologic insights

    PubMed Central

    Gough, Sheryl M.; Slape, Christopher I.

    2011-01-01

    Structural chromosomal rearrangements of the Nucleoporin 98 gene (NUP98), primarily balanced translocations and inversions, are associated with a wide array of hematopoietic malignancies. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. NUP98 gene fusions typically encode a fusion protein that retains the amino terminus of NUP98; in this context, it is important to note that several recent studies have demonstrated that the amino-terminal portion of NUP98 exhibits transcription activation potential. Approximately half of the NUP98 fusion partners encode homeodomain proteins, and at least 5 NUP98 fusions involve known histone-modifying genes. Several of the NUP98 fusions, including NUP98-homeobox (HOX)A9, NUP98-HOXD13, and NUP98-JARID1A, have been used to generate animal models of both lymphoid and myeloid malignancy; these models typically up-regulate HOXA cluster genes, including HOXA5, HOXA7, HOXA9, and HOXA10. In addition, several of the NUP98 fusion proteins have been shown to inhibit differentiation of hematopoietic precursors and to increase self-renewal of hematopoietic stem or progenitor cells, providing a potential mechanism for malignant transformation. PMID:21948299

  11. Fission-Fusion Neutron Source Progress Report Sept 30, 2009

    SciTech Connect

    Chapline, G F; Daffin, F; Clark, R

    2010-02-19

    In this report the authors describe the progress made in FY09 in evaluating the feasibility of a new concept for using the DT fusion reaction to produce intense pulses of 14 MeV neutrons. In this new scheme the heating of the DT is accomplished using fission fragments rather than ion beams as in conventional magnet confinement fusion schemes or lasers in inertial confinement schemes. As a source of fission fragments they propose using a dust reactor concept introduced some time ago by one of us (RC). An attractive feature of this approach is that there is no need for a large auxiliary power source to heat the DT plasma to the point where self-sustaining fusion become possible. Their scheme does require pulsed magnetic fields, but generating these fields requires only a modest power source. The dust reactor that they propose using for their neutron source would use micron-sized UC pellets suspended in a vacuum as the reactor fuel. Surrounding the fuel with a moderator such as heavy water (D{sub 2}O) would allow the reactor to operate as a thermal reactor and require only modest amounts of HEU. The scheme for using fission fragments to generate intense pulses of 14 MeV neutrons is based on the fission fragment rocket idea. In the fission fragment rocket scheme it was contemplated that the fission fragments produced in a low density reactor core could be guided out of the reactor by large magnetic fields used to form a 'rocket exhaust'. Their adaptation of this idea for the purposes of making a neutron source involves using the fission fragments escaping from one side of a tandem magnet mirror to heat DT gas confined in the adjacent magnetic trap.

  12. Repair welding of fusion reactor components. Final technical report

    SciTech Connect

    Chin, B.A.; Wang, C.A.

    1997-09-30

    The exposure of metallic materials, such as structural components of the first wall and blanket of a fusion reactor, to neutron irradiation will induce changes in both the material composition and microstructure. Along with these changes can come a corresponding deterioration in mechanical properties resulting in premature failure. It is, therefore, essential to expect that the repair and replacement of the degraded components will be necessary. Such repairs may require the joining of irradiated materials through the use of fusion welding processes. The present ITER (International Thermonuclear Experimental Reactor) conceptual design is anticipated to have about 5 km of longitudinal welds and ten thousand pipe butt welds in the blanket structure. A recent study by Buende et al. predict that a failure is most likely to occur in a weld. The study is based on data from other large structures, particularly nuclear reactors. The data used also appear to be consistent with the operating experience of the Fast Flux Test Facility (FFTF). This reactor has a fuel pin area comparable with the area of the ITER first wall and has experienced one unanticipated fuel pin failure after two years of operation. The repair of irradiated structures using fusion welding will be difficult due to the entrapped helium. Due to its extremely low solubility in metals, helium will diffuse and agglomerate to form helium bubbles after being trapped at point defects, dislocations, and grain boundaries. Welding of neutron-irradiated type 304 stainless steels has been reported with varying degree of heat-affected zone cracking (HAZ). The objectives of this study were to determine the threshold helium concentrations required to cause HAZ cracking and to investigate techniques that might be used to eliminate the HAZ cracking in welding of helium-containing materials.

  13. Midline lumbar fusion using cortical bone trajectory screws. Preliminary report

    PubMed Central

    Bielecki, Mateusz; Prokopienko, Marek; Nowak, Arkadiusz; Czernicki, Tomasz; Marchel, Andrzej

    2016-01-01

    Introduction Midline lumbar fusion (MIDLF) using cortical bone trajectory is an alternative method of transpedicular spinal fusion for degenerative disease. The new entry points’ location and screwdriving direction allow the approach-related morbidity to be reduced. Aim To present our preliminary experience with the MIDLF technique on the first 5 patients with lumbar degenerative disease and with follow-up of at least 6 months. Material and methods Retrospective analysis was performed on the first 5 patients with foraminal (4) or central (1) stenosis operated on between December 2014 and February 2015. Three patients were fused at L4–L5 and two at the L5–S1 level. Results No intra- or post-operative complications occurred with this approach. An improvement regarding the leading symptom in the early postoperative period (sciatica 4/4, claudication 1/1) was achieved in all patients. The mean improvements in the visual analogue scale for low back and leg pain were 2.2 and 4.8 respectively. The mean Oswestry Disability Index scores were 52% (range: 16–82%) before surgery and 33% (range: 12–56%) at 3-month follow-up (mean improvement 19%). At the most recent follow-up, 4 patients reported the maintenance of the satisfactory result. The early standing and follow-up X-rays showed satisfactory screw placement in all patients. Conclusions In our initial experience, the MIDLF technique seems to be an encouraging alternative to traditional transpedicular trajectory screws when short level lumbar fusion is needed. Nevertheless, longer observations on larger groups of patients are needed to reliably evaluate the safety of the method and the sustainability of the results. PMID:27829938

  14. A rapid and efficient newly established method to detect COL1A1-PDGFB gene fusion in dermatofibrosarcoma protuberans

    SciTech Connect

    Yokoyama, Yoko; Shimizu, Akira; Okada, Etsuko; Ishikawa, Osamu; Motegi, Sei-ichiro

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer We developed new method to rapidly identify COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer New PCR method using a single primer pair detected COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer This is the first report of DFSP with a novel COL1A1 breakpoint in exon 5. -- Abstract: The detection of fusion transcripts of the collagen type 1{alpha}1 (COL1A1) and platelet-derived growth factor-BB (PDGFB) genes by genetic analysis has recognized as a reliable and valuable molecular tool for the diagnosis of dermatofibrosarcoma protuberans (DFSP). To detect the COL1A1-PDGFB fusion, almost previous reports performed reverse transcription polymerase chain reaction (RT-PCR) using multiplex forward primers from COL1A1. However, it has possible technical difficulties with respect to the handling of multiple primers and reagents in the procedure. The objective of this study is to establish a rapid, easy, and efficient one-step method of PCR using only a single primer pair to detect the fusion transcripts of the COL1A1 and PDGFB in DFSP. To validate new method, we compared the results of RT-PCR in five patients of DFSP between the previous method using multiplex primers and our established one-step RT-PCR using a single primer pair. In all cases of DFSP, the COL1A1-PDGFB fusion was detected by both previous method and newly established one-step PCR. Importantly, we detected a novel COL1A1 breakpoint in exon 5. The newly developed method is valuable to rapidly identify COL1A1-PDGFB fusion transcripts in DFSP.

  15. The birth of a human-specific neural gene by incomplete duplication and gene fusion.

    PubMed

    Dougherty, Max L; Nuttle, Xander; Penn, Osnat; Nelson, Bradley J; Huddleston, John; Baker, Carl; Harshman, Lana; Duyzend, Michael H; Ventura, Mario; Antonacci, Francesca; Sandstrom, Richard; Dennis, Megan Y; Eichler, Evan E

    2017-03-09

    Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.

  16. Assessment of the Fusion Energy Sciences Program. Final Report

    SciTech Connect

    2001-05-01

    An assessment of the Office of Fusion Energy Sciences (OFES) program with guidance for future program strategy. The overall objective of this study is to prepare an independent assessment of the scientific quality of the Office of Fusion Energy Sciences program at the Department of Energy. The Fusion Science Assessment Committee (FuSAC) has been appointed to conduct this study.

  17. Drosophila and mammalian models uncover a role for the myoblast fusion gene TANC1 in rhabdomyosarcoma

    PubMed Central

    Avirneni-Vadlamudi, Usha; Galindo, Kathleen A.; Endicott, Tiana R.; Paulson, Vera; Cameron, Scott; Galindo, Rene L.

    2011-01-01

    Rhabdomyosarcoma (RMS) is a malignancy of muscle myoblasts, which fail to exit the cell cycle, resist terminal differentiation, and are blocked from fusing into syncytial skeletal muscle. In some patients, RMS is caused by a translocation that generates the fusion oncoprotein PAX-FOXO1, but the underlying RMS pathogenetic mechanisms that impede differentiation and promote neoplastic transformation remain unclear. Using a Drosophila model of PAX-FOXO1–mediated transformation, we show here that mutation in the myoblast fusion gene rolling pebbles (rols) dominantly suppresses PAX-FOXO1 lethality. Further analysis indicated that PAX-FOXO1 expression caused upregulation of rols, which suggests that Rols acts downstream of PAX-FOXO1. In mammalian myoblasts, gene silencing of Tanc1, an ortholog of rols, revealed that it is essential for myoblast fusion, but is dispensable for terminal differentiation. Misexpression of PAX-FOXO1 in myoblasts upregulated Tanc1 and blocked differentiation, whereas subsequent reduction of Tanc1 expression to native levels by RNAi restored both fusion and differentiation. Furthermore, decreasing human TANC1 gene expression caused RMS cancer cells to lose their neoplastic state, undergo fusion, and form differentiated syncytial muscle. Taken together, these findings identify misregulated myoblast fusion caused by ectopic TANC1 expression as a RMS neoplasia mechanism and suggest fusion molecules as candidates for targeted RMS therapy. PMID:22182840

  18. Fusion Energy Division progress report, 1 January 1990--31 December 1991

    SciTech Connect

    Sheffield, J.; Baker, C.C.; Saltmarsh, M.J.

    1994-03-01

    The Fusion Program of the Oak Ridge National Laboratory (ORNL), a major part of the national fusion program, encompasses nearly all areas of magnetic fusion research. The program is directed toward the development of fusion as an economical and environmentally attractive energy source for the future. The program involves staff from ORNL, Martin Marietta Energy systems, Inc., private industry, the academic community, and other fusion laboratories, in the US and abroad. Achievements resulting from this collaboration are documented in this report, which is issued as the progress report of the ORNL Fusion Energy Division; it also contains information from components for the Fusion Program that are external to the division (about 15% of the program effort). The areas addressed by the Fusion Program include the following: experimental and theoretical research on magnetic confinement concepts; engineering and physics of existing and planned devices, including remote handling; development and testing of diagnostic tools and techniques in support of experiments; assembly and distribution to the fusion community of databases on atomic physics and radiation effects; development and testing of technologies for heating and fueling fusion plasmas; development and testing of superconducting magnets for containing fusion plasmas; development and testing of materials for fusion devices; and exploration of opportunities to apply the unique skills, technology, and techniques developed in the course of this work to other areas (about 15% of the Division`s activities). Highlights from program activities during 1990 and 1991 are presented.

  19. Fission-Fusion Neutron Source Progress Report July 31, 2009

    SciTech Connect

    Chapline, G; Daffin, F; Clarke, R

    2010-02-19

    In this report the authors describe progress in evaluating the feasibility of a novel concept for producing intense pulses of 14 MeV neutrons using the DT fusion reaction. In this new scheme the heating of the DT is accomplished using fission fragments rather than ion beams as in conventional magnet fusion schemes or lasers in ICF schemes. This has the great advantage that there is no need for any large auxiliary power source. The scheme does require large magnetic fields, but generating these fields, e.g. with superconducting magnets, requires only a modest power source. As a source of fission fragments they propose using a dusty reactor concept introduced some time ago by one of us (RC). The version of the dusty reactor that they propose using for our neutron source would operate as a thermal neutron reactor and use highly enriched uranium in the form of micron sized pellets of UC. Our scheme for using the fission fragments to produce intense pulses of 14 MeV neutrons is based on the fission fragment rocket idea. In the fission fragment rocket scheme it was contemplated that the fission fragments produced in a low density reactor core would then be guided out of the reactor by large magnetic fields. A simple version of this idea would be to use the fission fragments escaping from one side of a tandem magnet mirror to heat DT gas confined in the adjacent magnetic trap.

  20. Model year 2010 Ford Fusion Level-1 testing report.

    SciTech Connect

    Rask, E.; Bocci, D.; Duoba, M.; Lohse-Busch, H.; Energy Systems

    2010-11-23

    As a part of the US Department of Energy's Advanced Vehicle Testing Activity (AVTA), a model year 2010 Ford Fusion was procured by eTec (Phoenix, AZ) and sent to ANL's Advanced Powertrain Research Facility for the purposes of vehicle-level testing in support of the Advanced Vehicle Testing Activity. Data was acquired during testing using non-intrusive sensors, vehicle network information, and facilities equipment (emissions and dynamometer). Standard drive cycles, performance cycles, steady-state cycles, and A/C usage cycles were conducted. Much of this data is openly available for download in ANL's Downloadable Dynamometer Database. The major results are shown in this report. Given the benchmark nature of this assessment, the majority of the testing was done over standard regulatory cycles and sought to obtain a general overview of how the vehicle performs. These cycles include the US FTP cycle (Urban) and Highway Fuel Economy Test cycle as well as the US06, a more aggressive supplemental regulatory cycle. Data collection for this testing was kept at a fairly high level and includes emissions and fuel measurements from an exhaust emissions bench, high-voltage and accessory current/voltage from a DC power analyzer, and CAN bus data such as engine speed, engine load, and electric machine operation. The following sections will seek to explain some of the basic operating characteristics of the MY2010 Fusion and provide insight into unique features of its operation and design.

  1. Inertial fusion program. Progress report, January 1-June 30, 1978

    SciTech Connect

    Skoberne, F.

    1980-05-01

    Studies and experiments aimed at investigating the possibility of restoring wavefront quality in optical systems through phase conjugation are summarized, and work that could lead to the development of highly damage-resistant isolators is discussed. The effects of various parameters on pulse-energy uniformity and of multipass extraction on laser efficiency are reported. Results of equation-of-state, shock propagation, multiburst simulation, and opacity measurements are discussed. Target designs are described that should provide a smooth transition from the exploding-pusher regime of experiments to that of isentropic compression. Progress in target fabrication techniques toward creating a 20-times-liquid-density target are outlined, and efforts that led to the extension of our neutron detection capability to levels of less than 10/sup 3/ n are summarized. The results of various studies of laser fusion application, e.g., for producing ultrahigh-temperature process heat or hydrogen from water decomposition are presented, as well as investigations of fusion-fission hybrids for the production of /sup 233/U from /sup 232/Th.

  2. Monitoring of gene expression in bacteria during infections using an adaptable set of bioluminescent, fluorescent and colorigenic fusion vectors.

    PubMed

    Uliczka, Frank; Pisano, Fabio; Kochut, Annika; Opitz, Wiebke; Herbst, Katharina; Stolz, Tatjana; Dersch, Petra

    2011-01-01

    A family of versatile promoter-probe plasmids for gene expression analysis was developed based on a modular expression plasmid system (pZ). The vectors contain different replicons with exchangeable antibiotic cassettes to allow compatibility and expression analysis on a low-, midi- and high-copy number basis. Suicide vector variants also permit chromosomal integration of the reporter fusion and stable vector derivatives can be used for in vivo or in situ expression studies under non-selective conditions. Transcriptional and translational fusions to the reporter genes gfp(mut3.1), amCyan, dsRed2, luxCDABE, phoA or lacZ can be constructed, and presence of identical multiple cloning sites in the vector system facilitates the interchange of promoters or reporter genes between the plasmids of the series. The promoter of the constitutively expressed gapA gene of Escherichia coli was included to obtain fluorescent and bioluminescent expression constructs. A combination of the plasmids allows simultaneous detection and gene expression analysis in individual bacteria, e.g. in bacterial communities or during mouse infections. To test our vector system, we analyzed and quantified expression of Yersinia pseudotuberculosis virulence genes under laboratory conditions, in association with cells and during the infection process.

  3. A protein disulfide isomerase gene fusion expression system that increases the extracellular productivity of Bacillus brevis.

    PubMed

    Kajino, T; Ohto, C; Muramatsu, M; Obata, S; Udaka, S; Yamada, Y; Takahashi, H

    2000-02-01

    We have developed a versatile Bacillus brevis expression and secretion system based on the use of fungal protein disulfide isomerase (PDI) as a gene fusion partner. Fusion with PDI increased the extracellular production of heterologous proteins (light chain of immunoglobulin G, 8-fold; geranylgeranyl pyrophosphate synthase, 12-fold). Linkage to PDI prevented the aggregation of the secreted proteins, resulting in high-level accumulation of fusion proteins in soluble and biologically active forms. We also show that the disulfide isomerase activity of PDI in a fusion protein is responsible for the suppression of the aggregation of the protein with intradisulfide, whereas aggregation of the protein without intradisulfide was prevented even when the protein was fused to a mutant PDI whose two active sites were disrupted, suggesting that another PDI function, such as chaperone-like activity, synergistically prevented the aggregation of heterologous proteins in the PDI fusion expression system.

  4. Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

    PubMed

    Yao, Fei; Kausalya, Jaya P; Sia, Yee Yen; Teo, Audrey S M; Lee, Wah Heng; Ong, Alicia G M; Zhang, Zhenshui; Tan, Joanna H J; Li, Guoliang; Bertrand, Denis; Liu, Xingliang; Poh, Huay Mei; Guan, Peiyong; Zhu, Feng; Pathiraja, Thushangi Nadeera; Ariyaratne, Pramila N; Rao, Jaideepraj; Woo, Xing Yi; Cai, Shaojiang; Mulawadi, Fabianus H; Poh, Wan Ting; Veeravalli, Lavanya; Chan, Chee Seng; Lim, Seong Soo; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D; Chew, Elaine G Y; Nagarajan, Niranjan; Jacques, Pierre-Étienne; So, Jimmy B Y; Ruan, Xiaoan; Yeoh, Khay Guan; Tan, Patrick; Sung, Wing-Kin; Hunziker, Walter; Ruan, Yijun; Hillmer, Axel M

    2015-07-14

    Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed.

  5. Use of gene fusions to determine the orientation of gene phoA on the Escherichia coli chromosome.

    PubMed Central

    Sarthy, A; Michaelis, S; Beckwith, J

    1981-01-01

    We present genetic evidence which demonstrates that the phoA gene is transcribed in the clockwise direction on the Escherichia coli chromosome, in contrast to an earlier proposal. Our conclusion is based on analysis of various genetic fusions between the lac operon and the phoA gene. PMID:7007316

  6. Analysis of Expression of a Phenazine Biosynthesis Locus of Pseudomonas aureofaciens PGS12 on Seeds with a Mutant Carrying a Phenazine Biosynthesis Locus-Ice Nucleation Reporter Gene Fusion

    PubMed Central

    Georgakopoulos, Dimitrios G.; Hendson, Mavis; Panopoulos, Nickolas J.; Schroth, Milton N.

    1994-01-01

    A derivative of Pseudomonas aureofaciens PGS12 expressing a promoterless ice nucleation gene under the control of a phenazine biosynthesis locus was used to study the expression of a phenazine antibiotic locus (Phz) during bacterial seed colonization. Seeds of various plants were inoculated with wild-type PGS12 and a PGS12 ice nucleation-active phz:inaZ marker exchange derivative and planted in soil, and the expression of the reporter gene was monitored at different intervals for 48 h during seed germination. phz gene expression was first detected 12 h after planting, and the expression increased during the next 36-h period. Significant differences in expression of bacterial populations on different seeds were measured at 48 h. The highest expression level was recorded for wheat seeds (one ice nucleus per 4,000 cells), and the lowest expression level was recorded for cotton seeds (one ice nucleus per 12,000,000 cells). These values indicate that a small proportion of bacteria in a seed population expressed phenazine biosynthesis. Reporter gene expression levels and populations on individual seeds in a sample were lognormally distributed. There was greater variability in reporter gene expression than in population size among individual seeds in a sample. Expression on sugar beet and radish seeds was not affected by different inoculum levels or soil matric potentials of -10 and -40 J/kg; only small differences in expression on wheat and sugar beet seeds were detected when the seeds were planted in various soils. It is suggested that the nutrient level in seed exudates is the primary reason for the differences observed among seeds. The lognormal distribution of phenazine expression on seeds and the timing and difference in expression of phenazine biosynthesis on seeds have implications for the potential efficacy of biocontrol microorganisms against plant pathogens. PMID:16349467

  7. Geophysical data fusion for subsurface imaging. Final report

    SciTech Connect

    1995-10-01

    This report contains the results of a three year, three-phase project whose long-range goal has been to create a means for the more detailed and accurate definition of the near-surface (0--300 ft) geology beneath a site that had been subjected to environmental pollution. The two major areas of research and development have been: improved geophysical field data acquisition techniques; and analytical tools for providing the total integration (fusion) of all site data. The long-range goal of this project has been to mathematically, integrate the geophysical data that could be derived from multiple sensors with site geologic information and any other type of available site data, to provide a detailed characterization of thin clay layers and geological discontinuities at hazardous waste sites.

  8. Fusion research at General Atomics annual report, October 1, 1993-- September 30, 1994

    SciTech Connect

    1995-11-01

    In FY94, the General Atomics (GA) Fusion Group made significant contributions to the technology needs of the controlled fusion power program. The work was supported by the Office of Fusion Energy, Advanced Physics and Technology Division and ITER and Technology Division, of the US Department of Energy. The work is reported in the following sections on Fusion Power Plant Studies, Plasma Interactive Materials, RF Technology, and Diagnostics. Meetings attended and publications are listed in their respective sections. The overall objective of GA`s fusion technology research is to develop the technologies necessary for fusion to move successfully from present-day physics experiments to the next-generation fusion reactor experiments, Tokamak Physics Experiment (TPX) and ITER, and ultimately to fusion power plants. To achieve this overall objective, we carry out fusion systems design studies to evaluate the technologies needed for next-step experiments and power reactors, and we conduct research to develop basic knowledge about these technologies, including plasma technologies, fusion nuclear technologies, and fusion materials. We continue to be committed to the development of fusion power and its commercialization by US industry.

  9. Fusion Energy Division progress report, January 1, 1992--December 31, 1994

    SciTech Connect

    Sheffield, J.; Baker, C.C.; Saltmarsh, M.J.; Shannon, T.E.

    1995-09-01

    The report covers all elements of the ORNL Fusion Program, including those implemented outside the division. Non-fusion work within FED, much of which is based on the application of fusion technologies and techniques, is also discussed. The ORNL Fusion Program includes research and development in most areas of magnetic fusion research. The program is directed toward the development of fusion as an energy source and is a strong and vital component of both the US and international fusion efforts. The research discussed in this report includes: experimental and theoretical research on magnetic confinement concepts; engineering and physics of existing and planned devices; development and testing of plasma diagnostic tools and techniques; assembly and distribution of databases on atomic physics and radiation effects; development and testing of technologies for heating and fueling fusion plasmas; and development and testing of materials for fusion devices. The activities involving the use of fusion technologies and expertise for non-fusion applications ranged from semiconductor manufacturing to environmental management.

  10. RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.

    PubMed

    Sakarya, Onur; Breu, Heinz; Radovich, Milan; Chen, Yongzhi; Wang, Yulei N; Barbacioru, Catalin; Utiramerur, Sowmi; Whitley, Penn P; Brockman, Joel P; Vatta, Paolo; Zhang, Zheng; Popescu, Liviu; Muller, Matthew W; Kudlingar, Vidya; Garg, Nriti; Li, Chieh-Yuan; Kong, Benjamin S; Bodeau, John P; Nutter, Robert C; Gu, Jian; Bramlett, Kelli S; Ichikawa, Jeffrey K; Hyland, Fiona C; Siddiqui, Asim S

    2012-01-01

    High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions-particularly those expressed with low abundance- is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample.

  11. Development of RNA-FISH Assay for Detection of Oncogenic FGFR3-TACC3 Fusion Genes in FFPE Samples

    PubMed Central

    Kojima, Takahiro; Nishimura, Kouichi; Kandori, Shuya; Kawahara, Takashi; Yoshino, Takayuki; Ueno, Satoshi; Iizumi, Yuichi; Mitsuzuka, Koji; Arai, Yoichi; Tsuruta, Hiroshi; Habuchi, Tomonori; Kobayashi, Takashi; Matsui, Yoshiyuki; Ogawa, Osamu; Sugimoto, Mikio; Kakehi, Yoshiyuki; Nagumo, Yoshiyuki; Tsutsumi, Masakazu; Oikawa, Takehiro; Kikuchi, Koji; Nishiyama, Hiroyuki

    2016-01-01

    Introduction and Objectives Oncogenic FGFR3-TACC3 fusions and FGFR3 mutations are target candidates for small molecule inhibitors in bladder cancer (BC). Because FGFR3 and TACC3 genes are located very closely on chromosome 4p16.3, detection of the fusion by DNA-FISH (fluorescent in situ hybridization) is not a feasible option. In this study, we developed a novel RNA-FISH assay using branched DNA probe to detect FGFR3-TACC3 fusions in formaldehyde-fixed paraffin-embedded (FFPE) human BC samples. Materials and Methods The RNA-FISH assay was developed and validated using a mouse xenograft model with human BC cell lines. Next, we assessed the consistency of the RNA-FISH assay using 104 human BC samples. In this study, primary BC tissues were stored as frozen and FFPE tissues. FGFR3-TACC3 fusions were independently detected in FFPE sections by the RNA-FISH assay and in frozen tissues by RT-PCR. We also analyzed the presence of FGFR3 mutations by targeted sequencing of genomic DNA extracted from deparaffinized FFPE sections. Results FGFR3-TACC3 fusion transcripts were identified by RNA-FISH and RT-PCR in mouse xenograft FFPE tissues using the human BC cell lines RT112 and RT4. These cell lines have been reported to be fusion-positive. Signals for FGFR3-TACC3 fusions by RNA-FISH were positive in 2/60 (3%) of non-muscle-invasive BC (NMIBC) and 2/44 (5%) muscle-invasive BC (MIBC) patients. The results of RT-PCR of all 104 patients were identical to those of RNA-FISH. FGFR3 mutations were detected in 27/60 (45%) NMIBC and 8/44 (18%) MIBC patients. Except for one NMIBC patient, FGFR3 mutation and FGFR3-TACC3 fusion were mutually exclusive. Conclusions We developed an RNA-FISH assay for detection of the FGFR3-TACC3 fusion in FFPE samples of human BC tissues. Screening for not only FGFR3 mutations, but also for FGFR3-TACC3 fusion transcripts has the potential to identify additional patients that can be treated with FGFR inhibitors. PMID:27930669

  12. Discovery and characterization of a novel CCND1/MRCK gene fusion in mantle cell lymphoma.

    PubMed

    Masamha, Chioniso Patience; Albrecht, Todd R; Wagner, Eric J

    2016-03-29

    The t(11;14) translocation resulting in constitutive cyclin D1 expression is an early event in mantle cell lymphoma (MCL) transformation. Patients with a highly proliferative phenotype produce cyclin D1 transcripts with truncated 3'UTRs that evade miRNA regulation. Here, we report the recurrence of a novel gene fusion in MCL cell lines and MCL patient isolates that consists of the full protein coding region of cyclin D1 (CCND1) and a 3'UTR consisting of sequences from both the CCND1 3'UTR and myotonic dystrophy kinase-related Cdc42-binding kinase's (MRCK) intron one. The resulting CCND1/MRCK mRNA is resistant to CCND1-targeted miRNA regulation, and targeting the MRCK region of the chimeric 3'UTR with siRNA results in decreased CCND1 levels.

  13. ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma

    PubMed Central

    Green, Ann E.; Nielsen, Julie S.; Nelson, Brad H.; Drescher, Charles W.; Brown, Patrick O.

    2011-01-01

    Every year, ovarian cancer kills approximately 14,000 women in the United States and more than 140,000 women worldwide. Most of these deaths are caused by tumors of the serous histological type, which is rarely diagnosed before it has disseminated. By deep paired-end sequencing of mRNA from serous ovarian cancers, followed by deep sequencing of the corresponding genomic region, we identified a recurrent fusion transcript. The fusion transcript joins the 5′ exons of ESRRA, encoding a ligand-independent member of the nuclear-hormone receptor superfamily, to the 3′ exons of C11orf20, a conserved but uncharacterized gene located immediately upstream of ESRRA in the reference genome. To estimate the prevalence of the fusion, we tested 67 cases of serous ovarian cancer by RT-PCR and sequencing and confirmed its presence in 10 of these. Targeted resequencing of the corresponding genomic region from two fusion-positive tumor samples identified a nearly clonal chromosomal rearrangement positioning ESRRA upstream of C11orf20 in one tumor, and evidence of local copy number variation in the ESRRA locus in the second tumor. We hypothesize that the recurrent novel fusion transcript may play a role in pathogenesis of a substantial fraction of serous ovarian cancers and could provide a molecular marker for detection of the cancer. Gene fusions involving adjacent or nearby genes can readily escape detection but may play important roles in the development and progression of cancer. PMID:21949640

  14. EP300-ZNF384 fusion gene product up-regulates GATA3 gene expression and induces hematopoietic stem cell gene expression signature in B-cell precursor acute lymphoblastic leukemia cells.

    PubMed

    Yaguchi, Akinori; Ishibashi, Takeshi; Terada, Kazuki; Ueno-Yokohata, Hitomi; Saito, Yuya; Fujimura, Junya; Shimizu, Toshiaki; Ohki, Kentaro; Manabe, Atsushi; Kiyokawa, Nobutaka

    2017-04-04

    ZNF384-related fusion genes are associated with a distinct subgroup of B-cell precursor acute lymphoblastic leukemias in childhood, with a frequency of approximately 3-4%. We previously identified a novel EP300-ZNF384 fusion gene. Patients with the ZNF384-related fusion gene exhibit a hematopoietic stem cell (HSC) gene expression signature and characteristic immunophenotype with negative or low expression of CD10 and aberrant expression of myeloid antigens, such as CD33 and CD13. However, the molecular basis of this pathogenesis remains completely unknown. In the present study, we examined the biological effects of EP300-ZNF384 expression induced by retrovirus-mediated gene transduction in an REH B-cell precursor acute lymphoblastic leukemia cell line, and observed the acquisition of the HSC gene expression signature and an up-regulation of GATA3 gene expression, as assessed by microarray analysis. In contrast, the gene expression profile induced by wild-type ZNF384 in REH cells was significantly different from that by EP300-ZNF384 expression. Together with the results of reporter assays, which revealed the enhancement of GATA3-promoter activity by EP300-ZNF384 expression, these findings suggest that EP300-ZNF384 mediates GATA3 gene expression and may be involved in the acquisition of the HSC gene expression signature and characteristic immunophenotype in B-cell precursor acute lymphoblastic leukemia cells.

  15. Fusion gene and splice variant analyses in liquid biopsies of lung cancer patients

    PubMed Central

    Giménez-Capitán, Ana; Karachaliou, Niki; Pérez-Rosado, Ana; Viteri, Santiago; Morales-Espinosa, Daniela; Rosell, Rafael

    2016-01-01

    Obtaining a biopsy of solid tumors requires invasive procedures that strongly limit patient compliance. In contrast, a blood extraction is safe, can be performed at many time points during the course disease and encourages appropriate therapy modifications, potentially improving the patient’s clinical outcome and quality of life. Fusion of the tyrosine kinase genes anaplastic lymphoma kinase (ALK), C-ROS oncogen 1 (ROS 1), rearranged during transfection (RET) and neurotrophic tyrosine kinase 1 (NTRK1) occur in 1–5% of lung adenocarcinomas and constitute therapeutic targets for tyrosine kinase inhibitors. In addition, a MET splicing variant of exon 14, has been reported in 2–4% of lung adenocarcinoma and recent studies suggests that targeted therapies inhibiting MET signaling would be beneficial for patients with this alteration. In this review, we will summarize the new techniques recently developed to detect ALK, RET, ROS and NTRK1 fusions and MET exon 14 splicing variant in liquid biopsy using plasma, serum, circulating tumor cells (CTCs), platelets and exosomes as starting material. PMID:27826534

  16. Inertial confinement fusion target component fabrication and technology development report

    NASA Astrophysics Data System (ADS)

    Steinman, D.

    1994-03-01

    On December 30, 1990, the US Department of Energy entered into a contract with General Atomics (GA) to be the Inertial Confinement Fusion Target Component Fabrication and Technology Development Support contractor. This report documents the technical activities which took place under this contract during the period of October 1, 1992 through September 30, 1993. During this period, GA was assigned 18 tasks in support of the Inertial Confinement Fusion program and its laboratories. These tasks included 'Capabilities Activation' and 'Capabilities Demonstration' to enable us to begin production of glass and composite polymer capsules. Capsule delivery tasks included 'Small Glass Shell Deliveries' and 'Composite Polymer Capsules' for Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). We also were asked to provide direct 'Onsite Support' at LLNL and LANL. We continued planning for the transfer of 'Micromachining Equipment from Rocky Flats' and established 'Target Component Micromachining and Electroplating Facilities' at GA. We fabricated over 1100 films and filters of 11 types for Sandia National Laboratory and provided full-time onsite engineering support for target fabrication and characterization. We initiated development of methods to make targets for the Naval Research Laboratory. We investigated spherical interferometry, built an automated capsule sorter, and developed an apparatus for calorimetric measurement of fuel fill for LLNL. We assisted LANL in the 'Characterization of Opaque b-Layered Targets.' We developed deuterated and UV-opaque polymers for use by the University of Rochester's Laboratory for Laser Energetics (UR/LLE) and devised a triple-orifice droplet generator to demonstrate the controlled-mass nature of the microencapsulation process.

  17. Inertial Confinement Fusion quarterly report, April--June 1995. Volume 5, No. 3

    SciTech Connect

    1995-12-31

    The ICF Quarterly Reports is published four times each fiscal year by the Inertial Confinement Fusion Program at the Lawrence Livermore National Laboratory. The journal reports selected current research within the ICF Program. Major areas of investigation presented here include fusion target theory and design, target fabrication, target experiments, and laser and optical science and technology.

  18. Fusion technology development. Annual report, October 1, 1994--September 30, 1995

    SciTech Connect

    1996-08-01

    In FY95, the General Atomics (GA) Fusion Group made significant contributions to the technology needs of the magnetic fusion program. The work is reported in the following sections on Fusion Power Plant Studies (Section 2), DiMES (Section 3), SiC Composite Studies (Section 4), Magnetic Probe (Section 5) and RF Technology (Section 6). Meetings attended and publications are listed in their respective sections. The overall objective of GA`s fusion technology research is to develop the technologies necessary for fusion to move successfully from present-day physics experiments to ITER and other next-generation fusion experiments, and ultimately to fusion power plants. To achieve this overall objective, they carry out fusion systems design studies to evaluate the technologies needed for next-step experiments and power plants, and they conduct research to develop basic knowledge about these technologies, including plasma technologies, fusion nuclear technologies, and fusion materials. They continue to be committed to the development of fusion power and its commercialization by US industry.

  19. Fusion technology development annual report, October 1, 1995--September 30, 1996

    SciTech Connect

    1997-03-01

    In FY96, the General Atomics (GA) Fusion Group made significant contributions to the technology needs of the magnetic fusion program. The work is reported in the following sections on Fusion Power Plant Design Studies (Section 2), Plasma Interactive Materials (Section 3), SiC/SiC Composite Material Development (Section 4), Magnetic Diagnostic Probes (Section 5) and RF Technology (Section 6). Meetings attended and publications are listed in their respective sections. The overall objective of GA`s fusion technology research is to develop the technologies necessary for fusion to move successfully from present-day physics experiments to ITER and other next-generation fusion experiments, and ultimately to fusion power plants. To achieve this overall objective, the authors carry out fusion systems design studies to evaluate the technologies needed for next-step experiments and power plants, and they conduct research to develop basic knowledge about these technologies, including plasma technologies, fusion nuclear technologies, and fusion materials. They continue to be committed to the development of fusion power and its commercialization by US industry.

  20. Identification and Characterization of Genes Required for Cell-to-Cell Fusion in Neurospora crassa ▿ †

    PubMed Central

    Fu, Ci; Iyer, Priyadarshini; Herkal, Amrita; Abdullah, Julia; Stout, Angela; Free, Stephen J.

    2011-01-01

    A screening procedure was used to identify cell fusion (hyphal anastomosis) mutants in the Neurospora crassa single gene deletion library. Mutants with alterations in 24 cell fusion genes required for cell fusion between conidial anastomosis tubes (CATs) were identified and characterized. The cell fusion genes identified included 14 genes that are likely to function in signal transduction pathways needed for cell fusion to occur (mik-1, mek-1, mak-1, nrc-1, mek-2, mak-2, rac-1, pp2A, so/ham-1, ham-2, ham-3, ham-5, ham-9, and mob3). The screening experiments also identified four transcription factors that are required for cell fusion (adv-1, ada-3, rco-1, and snf5). Three genes encoding proteins likely to be involved in the process of vesicular trafficking were also identified as needed for cell fusion during the screening (amph-1, ham-10, pkr1). Three of the genes identified by the screening procedure, ham-6, ham-7, and ham-8, encode proteins that might function in mediating the plasma membrane fusion event. Three of the putative signal transduction proteins, three of the transcription factors, the three putative vesicular trafficking proteins, and the three proteins that might function in mediating cell fusion had not been identified previously as required for cell fusion. PMID:21666072

  1. Tunnelling effects on low-energy fusion cross sections. Special report, June-August 1989

    SciTech Connect

    Leakeas, C.L.

    1989-09-01

    Recently, the claim of discovery of cold fusion among the isotopes of hydrogen in a metal lattice has raised many questions as to the cross sections of some fusion reactions at low energies. This report investigates the quantum phenomenon of tunneling and its effects on the fusion process. Special attention is paid to penetrabilities in the Hulthen potential, which gives a reasonably accurate approximation of the potential inside the metal lattice. This report includes cross section data for the DD, DT and pD reactions. Also given are graphs showing the fusion cross section crossover point between the DD and DT reactions and the increased penetrabilities due to enhance tunneling effects.

  2. mPlum-IFP 1.4 fluorescent fusion protein may display Förster resonance energy transfer associated properties that can be used for near-infrared based reporter gene imaging.

    PubMed

    Lin, Liang-Ting; Wang, Bo-Sheng; Chen, Jyh-Cheng; Liu, Chi-Hsien; Chou, Chien; Chiu, Shu-Jun; Chang, Wen-Yi; Liu, Ren-Shyan; Allen Chang, C; Lee, Yi-Jang

    2013-12-01

    Bacteriophytochrome infrared fluorescent protein (IFP) has a long emission wavelength that is appropriate for detecting pathophysiological effects via near-infrared (NIR) based imaging. However, the brightness and photostability of IFP are suboptimal, although an exogenous supply of biliverdin (BV) IXα is able to enhance these properties. In this study, we fused a far red mPlum fluorescent protein to IFP 1.4 via a linker deoxyribonucleic acid (DNA) sequence encoding eight amino acids. The brightness of mPlum-IFP 1.4 fusion protein at the IFP emission channel was comparable to that of native IFP 1.4 protein when fusion protein and IFP 1.4 were excited by 543 and 633 nm using confocal microscopy, respectively. Visualization of IFP 1.4 fluorescence by excitation of mPlum in mPlum-IFP 1.4 fusion protein is likely to be associated with Förster resonance energy transfer (FRET). The FRET phenomenon was also predicted by acceptor photobleaching using confocal microscopy. Furthermore, the expression of mPlum-IFP 1.4 fusion protein could be detected in cell culture and in xenograft tumors in the absence of BV using in vivo imaging system, although the BV was still essential for detecting native IFP 1.4. Therefore, this innovative-fluorescent fusion protein would be useful for NIR-based imaging in vitro and in vivo.

  3. Nuclear fusion occurs during mating in Candida albicans and is dependent on the KAR3 gene.

    PubMed

    Bennett, Richard J; Miller, Mathew G; Chua, Penelope R; Maxon, Mary E; Johnson, Alexander D

    2005-02-01

    It is now well established that mating can occur between diploid a and alpha cells of Candida albicans. There is, however, controversy over when, and with what efficiency, nuclear fusion follows cell fusion to create stable tetraploid a/alpha cells. In this study, we have analysed the mating process between C. albicans strains using both cytological and genetic approaches. Using strains derived from SC5314, we used a number of techniques, including time-lapse microscopy, to demonstrate that efficient nuclear fusion occurs in the zygote before formation of the first daughter cell. Consistent with these observations, zygotes micromanipulated from mating mixes gave rise to mononuclear tetraploid cells, even when no selection for successful mating was applied to them. Mating between different clinical isolates of C. albicans revealed that while all isolates could undergo nuclear fusion, the efficiency of nuclear fusion varied in different crosses. We also show that nuclear fusion in C. albicans requires the Kar3 microtubule motor protein. Deletion of the CaKAR3 gene from both mating partners had little or no effect on zygote formation but reduced the formation of stable tetraploids more than 600-fold, as determined by quantitative mating assays. These findings demonstrate that nuclear fusion is an active process that can occur in C. albicans at high frequency to produce stable, mononucleate mating products.

  4. PML-RARalpha fusion gene transcripts and biological features in acute promyelocytic leukemia patients.

    PubMed

    Melo, R A M; de Vasconcellos, J F; Melo, F C B C; Machado, C G F; Lacerda, T M S; Souto, F R

    2006-04-01

    Acute promyelocytic leukemia (APL) is characterized by the presence of rearrangements involving the retinoic acid receptor alpha (RARalpha) gene and a variable incidence in different populations. The hybrid gene PML-RARalpha, present in 98% of cases, encodes a fusion protein essential to the pathogenesis of the disease. Depending of the PML's gene breakpoint in chromosome 15, the transcript subtypes bcr1, bcr2 and bcr3 may be formed. The correlation between these transcript subtypes and clinical parameters is still controversial. The objective of this study was to determine the frequencies of the PML-RARalpha transcripts and subtypes in a series of 32 APL patients from Northeast Brazil and to evaluate the association of these subtypes to different parameters. The method used was RT-PCR. The frequency of our APL cases is approximately 28% of the acute leukemias. The results showed the presence of PML-RARalpha isoform in all patients and a higher frequency of the bcr1/2 subtype. No significant statistical association was found between molecular subtypes and age, sex, French-American-British (FAB) classification, leukocyte and platelet count, hemoglobin level or coagulation tests. In conclusion, these data suggest similar molecular and biological features for our APL patients at diagnosis in comparison with those reported in current scientific literature.

  5. Cold fusion verification. Final report for period ending 1989

    SciTech Connect

    North, M.H.; Mastny, G.F.; Wesley, E.J.

    1991-03-01

    The objective of this work to verify and reproduce experimental observations of Cold Nuclear Fusion (CNF), as originally reported in 1989. The method was to start with the original report and add such additional information as became available to build a set of operational electrolytic CNF cells. Verification was to be achieved by first observing cells for neutron production, and for those cells that demonstrated a nuclear effect, careful calorimetric measurements were planned. The authors concluded, after laboratory experience, reading published work, talking with others in the field, and attending conferences, that CNF probably is chimera and will go the way of N-rays and polywater. The neutron detector used for these tests was a completely packaged unit built into a metal suitcase that afforded electrostatic shielding for the detectors and self-contained electronics. It was battery-powered, although it was on charge for most of the long tests. The sensor element consists of He detectors arranged in three independent layers in a solid moderating block. The count from each of the three layers as well as the sum of all the detectors were brought out and recorded separately. The neutron measurements were made with both the neutron detector and the sample tested in a cave made of thick moderating material that surrounded the two units on the sides and bottom.

  6. A human ESC model for MLL-AF4 leukemic fusion gene reveals an impaired early hematopoietic-endothelial specification

    PubMed Central

    Bueno, Clara; Montes, Rosa; Melen, Gustavo J; Ramos-Mejia, Verónica; Real, Pedro J; Ayllón, Verónica; Sanchez, Laura; Ligero, Gertrudis; Gutierrez-Aranda, Iván; Fernández, Agustín F; Fraga, Mario F; Moreno-Gimeno, Inmaculada; Burks, Deborah; del Carmen Plaza-Calonge, María; Rodríguez-Manzaneque, Juan C; Menendez, Pablo

    2012-01-01

    The MLL-AF4 fusion gene is a hallmark genomic aberration in high-risk acute lymphoblastic leukemia in infants. Although it is well established that MLL-AF4 arises prenatally during human development, its effects on hematopoietic development in utero remain unexplored. We have created a human-specific cellular system to study early hemato-endothelial development in MLL-AF4-expressing human embryonic stem cells (hESCs). Functional studies, clonal analysis and gene expression profiling reveal that expression of MLL-AF4 in hESCs has a phenotypic, functional and gene expression impact. MLL-AF4 acts as a global transcriptional activator and a positive regulator of homeobox gene expression in hESCs. Functionally, MLL-AF4 enhances the specification of hemogenic precursors from hESCs but strongly impairs further hematopoietic commitment in favor of an endothelial cell fate. MLL-AF4 hESCs are transcriptionally primed to differentiate towards hemogenic precursors prone to endothelial maturation, as reflected by the marked upregulation of master genes associated to vascular-endothelial functions and early hematopoiesis. Furthermore, we report that MLL-AF4 expression is not sufficient to transform hESC-derived hematopoietic cells. This work illustrates how hESCs may provide unique insights into human development and further our understanding of how leukemic fusion genes, known to arise prenatally, regulate human embryonic hematopoietic specification. PMID:22212479

  7. A human ESC model for MLL-AF4 leukemic fusion gene reveals an impaired early hematopoietic-endothelial specification.

    PubMed

    Bueno, Clara; Montes, Rosa; Melen, Gustavo J; Ramos-Mejia, Verónica; Real, Pedro J; Ayllón, Verónica; Sanchez, Laura; Ligero, Gertrudis; Gutierrez-Aranda, Iván; Fernández, Agustín F; Fraga, Mario F; Moreno-Gimeno, Inmaculada; Burks, Deborah; Plaza-Calonge, María del Carmen; Rodríguez-Manzaneque, Juan C; Menendez, Pablo

    2012-06-01

    The MLL-AF4 fusion gene is a hallmark genomic aberration in high-risk acute lymphoblastic leukemia in infants. Although it is well established that MLL-AF4 arises prenatally during human development, its effects on hematopoietic development in utero remain unexplored. We have created a human-specific cellular system to study early hemato-endothelial development in MLL-AF4-expressing human embryonic stem cells (hESCs). Functional studies, clonal analysis and gene expression profiling reveal that expression of MLL-AF4 in hESCs has a phenotypic, functional and gene expression impact. MLL-AF4 acts as a global transcriptional activator and a positive regulator of homeobox gene expression in hESCs. Functionally, MLL-AF4 enhances the specification of hemogenic precursors from hESCs but strongly impairs further hematopoietic commitment in favor of an endothelial cell fate. MLL-AF4 hESCs are transcriptionally primed to differentiate towards hemogenic precursors prone to endothelial maturation, as reflected by the marked upregulation of master genes associated to vascular-endothelial functions and early hematopoiesis. Furthermore, we report that MLL-AF4 expression is not sufficient to transform hESC-derived hematopoietic cells. This work illustrates how hESCs may provide unique insights into human development and further our understanding of how leukemic fusion genes, known to arise prenatally, regulate human embryonic hematopoietic specification.

  8. Spatiotemporal Changes of Calcitonin Gene-Related Peptide Innervation in Spinal Fusion

    PubMed Central

    Zhou, Xiao-Yi; Xu, Xi-Ming; Wu, Sui-Yi; Wang, Fei; Yang, Yi-Lin; Li, Ming

    2016-01-01

    Few studies have investigated the role calcitonin gene-related peptide (CGRP) plays in the process of spinal fusion. The aim of the present study is to observe the temporal and spatial changes of CGRP induced by experimental fusion surgery in rats and elucidate the role of CGRP in spinal fusion. Male Sprague-Dawley rats were used in the study and the specimens were collected on the 7th, 14th, 21st, and 28th day, respectively. Then, histological and immunohistochemical analysis were applied to evaluate the fusion mass and spatiotemporal changes of CGRP chronologically. The results demonstrated that density of CGRP reached peak on the 21st day after surgery and most of the CGRP expression located surrounding the interface of allograft and fibrous tissue where the cells differentiate into osteoblasts, indicating that CGRP might be involved in the process of bone formation and absorption. PMID:27990431

  9. Protein fusions with the kanamycin resistance gene from transposon Tn5.

    PubMed Central

    Reiss, B; Sprengel, R; Schaller, H

    1984-01-01

    The gene for the neomycin phosphotransferase II (NPT II) from transposon Tn5 was fused at the amino or carboxy terminus to foreign DNA sequences coding for 3-300 amino acids and the properties of the fused proteins were investigated. All amino-terminal fusions examined conferred kanamycin resistance to their host cell, but profound differences in their enzymatic activity and stability were detected. Short additions to the amino terminus of the NPT II resulted in highly enzymatically active fusion proteins whereas long amino-terminal fusions often had to be proteolytically degraded to release active proteins. Fusions at the carboxy-terminal end of the NPT II protein did not always induce kanamycin resistance and their enzymatic activity depended more stringently on the nature of the junction sequence. Images Fig. 4. PMID:6098471

  10. Inertial confinement fusion. Quarterly report, July--September 1993: Volume 3, No. 4

    SciTech Connect

    Sacks, R.A.; Murphy, P.W.; Schleich, D.P.

    1993-12-31

    This report discusses the following research: Diode-pumped solid- state-laser driver for inertial fusion energy power plants; Longitudinal beam dynamics in heavy ion fusion accelerators; Design of the ion sources for heavy ion fusion; Measurement of electron density in laser-produced plasma with a soft x-ray moire deflectometer; and Analysis of weakly nonlinear three-dimensional Rayleigh-Taylor instability growth.

  11. Post-entrapment genome engineering: First exon size does not affect the expression of fusion transcripts generated by gene entrapment

    PubMed Central

    Osipovich, Anna B.; Singh, Aparna; Ruley, H. Earl

    2005-01-01

    Gene trap mutagenesis in mouse embryonic stem cells has been widely used for genome-wide studies of mammalian gene function. However, while large numbers of genes can be disrupted, individual mutations may suffer from limitations due to the structure and/or placement of targeting vector. To extend the utility of gene trap mutagenesis, replaceable 3′ [or poly(A)] gene trap vectors were developed that permit sequences inserted in individual entrapment clones to be engineered by Cre-mediated recombination. 3′ traps incorporating different drug resistance genes could be readily exchanged, simply by selecting for the drug-resistance gene of the replacement vector. By substituting different 3′ traps, we show that otherwise identical fusion genes containing a large first exon (804 nt) are not expressed at appreciably lower levels than genes expressing small first exons (384 and 151 nt). Thus, size appears to have less effect on the expression and processing of first exons than has been reported for internal exons. Finally, a retroviral poly(A) trap (consisting of a RNA polymerase II promoter, a neomycin-resistance gene, and 5′-splice site) typically produced mutagenized clones in which vector sequences spliced to the 3′-terminal exons of cellular transcription units, suggesting strong selection for fusion transcripts that evade nonsense-mediated decay. The efficient exchange of poly(A) traps should greatly extend the utility of mutant libraries generated by gene entrapment and provides new strategies to study the rules that govern the expression of exons inserted throughout the genome. PMID:15741512

  12. Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions.

    PubMed

    Whoriskey, S K; Nghiem, V H; Leong, P M; Masson, J M; Miller, J H

    1987-05-01

    We describe gene fusions that result from genetic duplications of 5-20 kb, which are amplified 50- to 100-fold. Because one end point of the fusion lies within the sequenced lacI gene, the new junctures created by the duplications are readily identified. Using a procedure for dideoxy sequencing of double-stranded DNA, we show that the duplications occur almost exclusively at short sequence repeats (less than 15 bp), sometimes involving broken homologies, in the 30 cases examined. Most of the duplications place the lacI-Z encoded hybrid repressor-beta-galactosidase protein under the control of a downstream promoter, resulting in the production of a more complex hybrid protein with beta-galactosidase activity. In some cases the fusion occurs with the lacY or the lacA gene, which suggests that silent promoters can be uncovered by gene fusion and subsequent amplification. In some ways this system represents a bacterial analog to chromosomal rearrangements of oncogenes in higher cells, since here the expression of a silent gene is the result of a genetic rearrangement that is followed by amplification during selected growth.

  13. NAB2-STAT6 fusion gene analysis in two cases of meningeal solitary fibrous tumor/hemangiopericytoma with late distant metastases.

    PubMed

    Nakada, Satoko; Minato, Hiroshi; Takegami, Tsutomu; Kurose, Nozomu; Ikeda, Hiroko; Kobayashi, Masako; Sasagawa, Yasuo; Akai, Takuya; Kato, Takashi; Yamamoto, Norio; Nojima, Takayuki

    2015-10-01

    We present two cases of meningeal solitary fibrous tumor (SFT)/hemangiopericytoma (HPC) with immunohistochemistry of STAT6 and analysis of NAB2-STAT6 fusion genes. Case 1 was a 37-year-old male with a left middle fossa tumor; case 2 was a 68-year-old female with a cerebellar tumor. They showed late metastasis to the lung or bone 8 or 13 years, respectively, after the first surgery. Histology of both primary and metastatic tumors showed a cellular hemangiopericytomatous pattern with nuclear atypia. The primary tumors showed nuclear staining of STAT6, but both metastatic tumors showed nuclear and cytoplasmic STAT6. DNA sequencing revealed two kinds of NAB2-STAT6 fusion genes. One consisted of exon 6 of NAB2, intron 6 of NAB2, and the middle of exon 17 of STAT6 (observed in the primary and metastatic tumors of case 1); the other consisted of exon 6 of NAB2 and the beginning of exon 17 of STAT6 (observed in the metastatic tumor of case 2). The primary tumor of case 2 had both fusion genes. To the best of our knowledge, we are the first to report NAB2-STAT6 fusion gene analysis in primary and metastatic meningeal SFT/HPCs and a case showed different fusion gene status in the metastatic tumor.

  14. RELATIVE EXPRESSION AND STABILITY OF A CHROMOSOMALLY INTEGRATED AND PLASMID-BORNE MARKER GENE FUSION IN ENVIRONMENTALLY COMPETENT BACTERIA

    EPA Science Inventory

    A xyIE-iceC transcriptional fusion was created by ligating a DNA fragment harboring the cloned xyIE structural gene from the TOL plasmid of Pseudomonas putida mt-2 into the cloned iceC gene of Pseudomonas syringae Cit7. This fusion construct was integrated into chromosome of Pseu...

  15. RELATIVE EXPRESSION AND STABILITY OF A CHROMOSOMALLY INTEGRATED AND PLASMID-BORNE MARKER GENE FUSION IN ENVIRONMENTALLY COMPETENT BACTERIA

    EPA Science Inventory

    A xyIE-iceC transcriptional fusion was created by ligating a DNA fragment harboring the cloned xyIE structural gene from the TOL plasmid of Pseudomonas putida mt-2 into the cloned iceC gene of Pseudomonas syringae Cit7. This fusion construct was integrated into chromosome of Pseu...

  16. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining

    PubMed Central

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-01

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. PMID:27899563

  17. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

    PubMed

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-04

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Protein NCRII-18: the role of gene fusion in the molecular evolution of restriction endonucleases.

    PubMed

    Ibryashkina, Elena M; Solonin, Alexander S; Zakharova, Marina V

    2017-06-01

    This work first constructed the fusion protein NCRII-18 by fusing the restriction endonuclease Ecl18kI gene and part of the gene coding for the N-terminal domain of the endonuclease EcoRII. The fusion of the EcoRII N-terminal domain leads to a change in the properties of the recombinant protein. Unlike Ecl18kI, which made the basis of NCRII-18, the fusion protein predominantly recognizes the CCWGG sites, having lost the capability of interacting with the CCSGG sites. Experimental data support the hypothesis of a close evolutionary relationship between type IIE and IIP restriction endonucleases via a recombination between domains with active site structure and elements for recognition with domains responsible for recognition of DNA sequences. © 2017 Federation of European Biochemical Societies.

  19. Gene fusion vehicles for the analysis of gene expression in Rhizobium meliloti.

    PubMed Central

    Kahn, M L; Timblin, C R

    1984-01-01

    A set of plasmid cloning vehicles was developed to facilitate the construction of gene or operon fusions in Rhizobium meliloti. The vehicles also contain a broad-host-range replicon and could be introduced into bacteria either by transformation or by transduction, using bacteriophage P2. Insertion of foreign DNA into a unique restriction endonuclease cleavage site promotes the synthesis of either the Escherichia coli lactose operon or the kanamycin phosphotransferase gene from transposon Tn5. Expression of the lactose operon could be detected by observing the color of Rhizobium colonies on medium that contained a chromogenic indicator. We also determined the growth conditions that make it possible to select either for or against the expression of the E. coli lactose operon in R. meliloti. Recombinant plasmids were constructed by inserting MboI restriction fragments of R. meliloti DNA into one of the vehicles, pMK353 . Expression of beta-galactosidase by a number of these recombinants was measured in both R. meliloti and E. coli. PMID:6327625

  20. Fusion Energy Division annual progress report period ending December 31, 1986

    SciTech Connect

    Morgan, O.B. Jr.; Berry, L.A.; Sheffield, J.

    1987-10-01

    This annual report on fusion energy discusses the progress on work in the following main topics: toroidal confinement experiments; atomic physics and plasma diagnostics development; plasma theory and computing; plasma-materials interactions; plasma technology; superconducting magnet development; fusion engineering design center; materials research and development; and neutron transport. (LSP)

  1. Particle-beam-fusion progress report, July 1979 through December 1979

    SciTech Connect

    Not Available

    1981-01-01

    The following chapters are included in this semi-annual progress report: (1) fusion target studies, (2) target experiments, (3) particle-beam source developments, (4) particle beam experiments, (5) pulsed power, (6) pulsed power applications, and (7) electron beam fusion accelerator project. (MOW)

  2. Massachusetts Institute of Technology Plasma Fusion Center 1992--1993 report to the President

    SciTech Connect

    Not Available

    1993-07-01

    This report discusses research being conducted at MIT`s plasma fusion center. Some of the areas covered are: plasma diagnostics; rf plasma heating; gyrotron research; treatment of solid waste by arc plasma; divertor experiments; tokamak studies; and plasma and fusion theory.

  3. Bilateral fusion in primary mandibular teeth: a report of two cases.

    PubMed

    Tewari, N; Pandey, R K

    2011-01-01

    The rare anomaly of fusion in primary dentition has very little documentation in Indian population. Two rare cases of bilateral fusion between primary mandibular lateral incisors and canines and primary mandibular central incisors and lateral incisors have been presented in this report. A minimal intervention approach, preventive procedures, and a long-term follow-up have been discussed.

  4. TEL/AML-1 fusion gene. its frequency and prognostic significance in childhood acute lymphoblastic leukemia.

    PubMed

    Jamil, A; Theil, K S; Kahwash, S; Ruymann, F B; Klopfenstein, K J

    2000-10-15

    TEL gene rearrangement due to the 12;21 chromosome translocation is believed to be the most common molecular genetic abnormality in childhood acute lymphoblastic leukemia (ALL). A study was conducted to investigate the frequency and prognostic significance of TEL/AML-1 fusion gene resulting from a cryptic t(12;21)(p13;q22). Bone marrow samples from 86 patients diagnosed over the past 5 years at Columbus Children's Hospital were analyzed by fluorescence in situ hybridization (FISH) technique for TEL/AML-1 fusion gene, using LSI((R)) DNA probes. The positive cases were analyzed for clinical outcome. Patients in this study received treatment according to Children's Cancer Group (CCG) protocols. Fifteen of the 86 cases (17%) were positive for the fusion gene. All were B-cell lineage and except for one, all were CD10 positive. TEL/AML-1 was not found in any T-cell ALL. The mean overall survival (OS) following diagnosis for the TEL/AML-1-positive group was significantly longer than for the TEL/AML-1-negative group by log-rank = 7.84, P = 0.005. Similarly, the event-free survival (EFS) after remission for the positive group (median 94.5 months) was longer than the negative group (median 57 months) by log-rank = 7.19, P = 0.007. This study confirms that the TEL/AML-1 fusion gene may be the most common genetic event in childhood ALL, occurring in 17% of the patients. It appears restricted to the B-cell lineage. In this study, the presence of a TEL/AML-1 fusion gene was statistically significant in predicting both OS and EFS, indicating a favorable clinical outcome for these patients. Screening for TEL/AML-1 should become routine at diagnosis and a useful biological variable for risk stratification in future clinical trials.

  5. Prostate cancer of transition zone origin lacks TMPRSS2-ERG gene fusion.

    PubMed

    Guo, Charles C; Zuo, Geyan; Cao, Dongdong; Troncoso, Patricia; Czerniak, Bogdan A

    2009-07-01

    Recent studies have shown a unique chromosomal rearrangement that leads to the fusion of 5'-transmembrane protein serine proteinase-2 (TMPRSS2) with the EST-related gene (ERG) in prostate cancer. In this study, we used fluorescence in situ hybridization to evaluate TMPRSS2-ERG gene fusion in prostate cancer of different zonal origins. Radical prostatectomy specimens with multifocal prostate cancer were obtained from 30 patients who were treated at our institution. Two separate tumor foci in each specimen, one in the peripheral zone and the other in the transition zone, were selected for gene fusion analysis. The selected peripheral zone tumor foci had a mean Gleason score of 6.8 (range, 6-7) and a mean tumor volume of 1.2 cm(3) (range, 0.1-4.6 cm(3)). The selected transition zone tumor foci had a mean Gleason score of 6.7 (range, 5-8) and a mean tumor volume of 4.0 cm(3) (range, 0.5-9.0 cm(3)). ERG gene rearrangement was not observed in any transition zone tumors; however, it was found in the peripheral zone tumors in 13 cases (43%). In 10 cases, the rearrangement was associated with the deletion of the 5'-end of ERG. In conclusion, we found that TMPRSS2-ERG gene fusion is associated with the zonal origin of prostate cancer. This gene fusion is prevalent in prostate cancer arising from the peripheral zone, but is lacking in prostate cancer arising from the transition zone.

  6. Design and Characterization of Novel Recombinant Listeriolysin O–Protamine Fusion Proteins for Enhanced Gene Delivery

    PubMed Central

    2015-01-01

    To improve the efficiency of gene delivery for effective gene therapy, it is essential that the vector carries functional components that can promote overcoming barriers in various steps leading to the transport of DNA from extracellular to ultimately nuclear compartment. In this study, we designed genetically engineered fusion proteins as a platform to incorporate multiple functionalities in one chimeric protein. Prototypes of such a chimera tested here contain two domains: one that binds to DNA; the other that can facilitate endosomal escape of DNA. The fusion proteins are composed of listeriolysin O (LLO), the endosomolytic pore-forming protein from Listeria monocytogenes, and a 22 amino acid sequence of the DNA-condensing polypeptide protamine (PN), singly or as a pair: LLO-PN and LLO-PNPN. We demonstrate dramatic enhancement of the gene delivery efficiency of protamine-condensed DNA upon incorporation of a small amount of LLO-PN fusion protein and further improvement with LLO-PNPN in vitro using cultured cells. Additionally, the association of anionic liposomes with cationic LLO-PNPN/protamine/DNA complexes, yielding a net negative surface charge, resulted in better in vitro transfection efficiency in the presence of serum. An initial, small set of data in mice indicated that the observed enhancement in gene expression could also be applicable to in vivo gene delivery. This study suggests that incorporation of a recombinant fusion protein with multiple functional components, such as LLO–protamine fusion protein, in a nonviral vector is a promising strategy for various nonviral gene delivery systems. PMID:25521817

  7. Detection of PML/RARα Fusion Gene in Bone Marrow of Patients with Functionalized Graphene Oxide.

    PubMed

    Li, Ran; Tan, Yanhong; Chen, Xiuhua; Ren, Fanggang; Zhang, Yaofang; Wang, Hongwei

    2016-01-01

    Current diagnostic methods of acute promyelocytic leukemia (APL) have some inevitable shortcomings; therefore, further studies are needed to develop more effective diagnostic methods. We used functionalized graphene oxide (GO) to detect the promyelocytic leukemia/retinoic acid receptor, α fusion gene (PML/RARα fusion gene) in bone marrow of APL patients. This method was more convenient and time-saving, and we can obtain the detection results in 1 hour. Our group consists of 36 cases, among them are 16 cases which are PML-RARα positive, 20 cases which are PML-RARα negative. Firstly, samples were fixed, drilled, and incubated with antibody CD45. Secondly, GO, fluorescent probes, and buffer liquid were added. One hour later, samples were washed with PBS (1 x) buffer, centrifuged, and fluorescent signals were detected with flow cytometry. Using functional GO to carry the fluorescent probe we ascertained whether bone marrow samples contain the L type PML/RARα fusion gene. Using the probe, only cells which contain L type PML/RARα fusion gene will have fluorescent signals compared to no signals (p < 0.05). The GO detection method was accurate and has clinical diagnostic values (p < 0.05). The GO detection method has the advantages of accurate, time-saving, energy-saving simple operation, and no pollution.

  8. Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold.

    PubMed

    Zitnik, Marinka; Zupan, Blaž

    2014-01-01

    The development of effective methods for the characterization of gene functions that are able to combine diverse data sources in a sound and easily-extendible way is an important goal in computational biology. We have previously developed a general matrix factorization-based data fusion approach for gene function prediction. In this manuscript, we show that this data fusion approach can be applied to gene function prediction and that it can fuse various heterogeneous data sources, such as gene expression profiles, known protein annotations, interaction and literature data. The fusion is achieved by simultaneous matrix tri-factorization that shares matrix factors between sources. We demonstrate the effectiveness of the approach by evaluating its performance on predicting ontological annotations in slime mold D. discoideum and on recognizing proteins of baker's yeast S. cerevisiae that participate in the ribosome or are located in the cell membrane. Our approach achieves predictive performance comparable to that of the state-of-the-art kernel-based data fusion, but requires fewer data preprocessing steps.

  9. Dramatic growth of mice that develop from eggs microinjected with metallothionein–growth hormone fusion genes

    PubMed Central

    Palmiter, Richard D.; Brinster, Ralph L.; Hammer, Robert E.; Trumbauer, Myrna E.; Rosenfeld, Michael G.; Birnberg, Neal C.; Evans, Ronald M.

    2016-01-01

    A DNA fragment containing the promoter of the mouse metallothionein-I gene fused to the structural gene of rat growth hormone was microinjected into the pronuclei of fertilized mouse eggs. Of 21 mice that developed from these eggs, seven carried the fusion gene and six of these grew significantly larger than their littermates. Several of these transgenic mice had extraordinarily high levels of the fusion mRNA in their liver and growth hormone in their serum. This approach has implications for studying the biological effects of growth hormone, as a way to accelerate animal growth, as a model for gigantism, as a means of correcting genetic disease, and as a method of farming valuable gene products. PMID:6958982

  10. The brain expressed x-linked gene 1 (Bex1) regulates myoblast fusion

    PubMed Central

    Yue, Feng; Kuang, Shihuan

    2015-01-01

    Skeletal muscle development (myogenesis) is a complex but precisely orchestrated process involving spatiotemporal regulation of the proliferation, differentiation and fusion of myogenic progenitor cells (myoblasts). Here we identify brain expressed x-linked gene 1 (Bex1) as a transient, developmentally regulated gene involved in myoblast fusion. Bex1 expression is undetectable in adult muscles or in quiescent muscle stem cells (satellite cells). During embryonic myogenesis, however, Bex1 is robustly expressed by myogenin+ differentiating myoblasts, but not by Pax7+ proliferating myoblasts. Interestingly, Bex1 is initially localized in the cytoplasm and then translocates into the nucleus. During adult muscle regeneration, Bex1 is highly expressed in newly regenerated myofibers and the expression is rapidly downregulated during maturation. Consistently, in cultured myoblasts, Bex1 is not expressed at the proliferation stage but transiently expressed upon induction of myogenic differentiation, following a similar cytoplasm to nucleus translocation pattern as seen in vivo. Using gain- and loss-of-function studies, we found that overexpression of Bex1 promotes the fusion of primary myoblasts without affecting myogenic differentiation and myogenin expression. Conversely, Bex1 knockout myoblasts exhibit obvious fusion defects, even though they express normal levels of myogenin and differentiate normally. These results elucidate a novel role of Bex1 in myogenesis through regulating myoblast fusion. PMID:26586200

  11. Establishment of cells to monitor Microprocessor through fusion genes of microRNA and GFP.

    PubMed

    Tsutsui, Motomu; Hasegawa, Hitoki; Adachi, Koichi; Miyata, Maiko; Huang, Peng; Ishiguro, Naoki; Hamaguchi, Michinari; Iwamoto, Takashi

    2008-08-08

    Microprocessor, the complex of Drosha and DGCR8, promotes the processing of primary microRNA to precursor microRNA, which is a crucial step for microRNA maturation. So far, no convenient assay systems have been developed for observing this step in vivo. Here we report the establishment of highly sensitive cellular systems where we can visually monitor the function of Microprocessor. During a series of screening of transfectants with fusion genes of the EGFP cDNA and primary microRNA genes, we have obtained certain cell lines where introduction of siRNA against DGCR8 or Drosha strikingly augments GFP signals. In contrast, these cells have not responded to Dicer siRNA; thus they have a unique character that GFP signals should be negatively and specifically correlated to the action of Microprocessor among biogenesis of microRNA. These cell lines can be useful tools for real-time analysis of Microprocessor action in vivo and identifying its novel modulators.

  12. A novel candidate disease genes prioritization method based on module partition and rank fusion.

    PubMed

    Chen, Xing; Yan, Gui-Ying; Liao, Xiao-Ping

    2010-08-01

    Identifying disease genes is very important not only for better understanding of gene function and biological process but also for human medical improvement. Many computational methods have been proposed based on the similarity between all known disease genes (seed genes) and candidate genes in the entire gene interaction network. Under the hypothesis that potential disease-related genes should be near the seed genes in the network and only the seed genes that are located in the same module with the candidate genes will contribute to disease genes prediction, three modularized candidate disease gene prioritization algorithms (MCDGPAs) are proposed to identify disease-related genes. MCDGPA is divided into three steps: module partition, genes prioritization in each disease-associated module, and rank fusion for the global ranking. When applied to the prostate cancer and breast cancer network, MCDGPA significantly improves previous algorithms in terms of cross-validation and disease-related genes prediction. In addition, the improvement is robust to the selection of gene prioritization methods when implementing prioritization in each disease-associated module and module partition algorithms when implementing network partition. In this sense MCDGPA is a general framework that allows integrating many previous gene prioritization methods and improving predictive accuracy.

  13. Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast

    PubMed Central

    Natrajan, Rachael; Wilkerson, Paul M; Marchiò, Caterina; Piscuoglio, Salvatore; Ng, Charlotte KY; Wai, Patty; Lambros, Maryou B; Samartzis, Eleftherios P; Dedes, Konstantin J; Frankum, Jessica; Bajrami, Ilirjana; Kopec, Alicja; Mackay, Alan; A'hern, Roger; Fenwick, Kerry; Kozarewa, Iwanka; Hakas, Jarle; Mitsopoulos, Costas; Hardisson, David; Lord, Christopher J; Kumar-Sinha, Chandan; Ashworth, Alan; Weigelt, Britta; Sapino, Anna; Chinnaiyan, Arul M; Maher, Christopher A; Reis-Filho, Jorge S

    2014-01-01

    Micropapillary carcinoma (MPC) is a rare histological special type of breast cancer, characterized by an aggressive clinical behaviour and a pattern of copy number aberrations (CNAs) distinct from that of grade- and oestrogen receptor (ER)-matched invasive carcinomas of no special type (IC-NSTs). The aims of this study were to determine whether MPCs are underpinned by a recurrent fusion gene(s) or mutations in 273 genes recurrently mutated in breast cancer. Sixteen MPCs were subjected to microarray-based comparative genomic hybridization (aCGH) analysis and Sequenom OncoCarta mutation analysis. Eight and five MPCs were subjected to targeted capture and RNA sequencing, respectively. aCGH analysis confirmed our previous observations about the repertoire of CNAs of MPCs. Sequencing analysis revealed a spectrum of mutations similar to those of luminal B IC-NSTs, and recurrent mutations affecting mitogen-activated protein kinase family genes and NBPF10. RNA-sequencing analysis identified 17 high-confidence fusion genes, eight of which were validated and two of which were in-frame. No recurrent fusions were identified in an independent series of MPCs and IC-NSTs. Forced expression of in-frame fusion genes (SLC2A1–FAF1 and BCAS4–AURKA) resulted in increased viability of breast cancer cells. In addition, genomic disruption of CDK12 caused by out-of-frame rearrangements was found in one MPC and in 13% of HER2-positive breast cancers, identified through a re-analysis of publicly available massively parallel sequencing data. In vitro analyses revealed that CDK12 gene disruption results in sensitivity to PARP inhibition, and forced expression of wild-type CDK12 in a CDK12-null cell line model resulted in relative resistance to PARP inhibition. Our findings demonstrate that MPCs are neither defined by highly recurrent mutations in the 273 genes tested, nor underpinned by a recurrent fusion gene. Although seemingly private genetic events, some of the fusion transcripts found

  14. A gene fusion at a homeobox locus: alterations in leaf shape and implications for morphological evolution.

    PubMed Central

    Chen, J J; Janssen, B J; Williams, A; Sinha, N

    1997-01-01

    Compound leaves are seen in many angiosperm genera and are thought to be either fundamentally different from simple leaves or elaborations of simple leaves. The knotted1-like homeobox (knox) genes are known to regulate plant development. When overexpressed in homologous or heterologous species, this family of genes can cause changes in leaf morphology, including excessive leaf compounding in tomato. We describe here an instance of a spontaneously arisen fusion between a gene encoding a metabolic enzyme and a homeodomain protein. We show that the fusion results in overexpression of the homeodomain protein and a change in morphology that approximates the changes caused by overexpression of the same gene under the control of the cauliflower mosaic virus 35S promoter in transgenic plants. Exon-shuffling events can account for the modularity of proteins. If the shuffled exons are associated with altered promoters, changes in gene expression patterns can result. Our results show that gene fusions of this nature can cause changes in expression patterns that lead to altered morphology. We suggest that such phenomena may have played a role in the evolution of form. PMID:9286107

  15. Integrated genomic analyses identify frequent gene fusion events and VHL inactivation in gastrointestinal stromal tumors

    PubMed Central

    Sun, Choong-Hyun; Park, Inho; Lee, Seungmook; Kwon, Jekeun; Do, Ingu; Hong, Min Eui; Van Vrancken, Michael; Lee, Jeeyun; Park, Joon Oh; Cho, Jeonghee; Kim, Kyoung-Mee; Sohn, Tae Sung

    2016-01-01

    Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. We sequenced nine exomes and transcriptomes, and two genomes of GISTs for integrated analyses. We detected 306 somatic variants in nine GISTs and recurrent protein-altering mutations in 29 genes. Transcriptome sequencing revealed 328 gene fusions, and the most frequently involved fusion events were associated with IGF2 fused to several partner genes including CCND1, FUS, and LASP1. We additionally identified three recurrent read-through fusion transcripts: POLA2-CDC42EP2, C8orf42-FBXO25, and STX16-NPEPL1. Notably, we found intragenic deletions in one of three exons of the VHL gene and increased mRNAs of VEGF, PDGF-β, and IGF-1/2 in 56% of GISTs, suggesting a mechanistic link between VHL inactivation and overexpression of hypoxia-inducible factor target genes in the absence of hypoxia. We also identified copy number gain and increased mRNA expression of AMACR, CRIM1, SKP2, and CACNA1E. Mapping of copy number and gene expression results to the KEGG pathways revealed activation of the JAK-STAT pathway in small intestinal GISTs and the MAPK pathway in wild-type GISTs. These observations will allow us to determine the genetic basis of GISTs and will facilitate further investigation to develop new therapeutic options. PMID:25987131

  16. Integrated genomic analyses identify frequent gene fusion events and VHL inactivation in gastrointestinal stromal tumors.

    PubMed

    Kang, Guhyun; Yun, Hongseok; Sun, Choong-Hyun; Park, Inho; Lee, Seungmook; Kwon, Jekeun; Do, Ingu; Hong, Min Eui; Van Vrancken, Michael; Lee, Jeeyun; Park, Joon Oh; Cho, Jeonghee; Kim, Kyoung-Mee; Sohn, Tae Sung

    2016-02-09

    Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. We sequenced nine exomes and transcriptomes, and two genomes of GISTs for integrated analyses. We detected 306 somatic variants in nine GISTs and recurrent protein-altering mutations in 29 genes. Transcriptome sequencing revealed 328 gene fusions, and the most frequently involved fusion events were associated with IGF2 fused to several partner genes including CCND1, FUS, and LASP1. We additionally identified three recurrent read-through fusion transcripts: POLA2-CDC42EP2, C8orf42-FBXO25, and STX16-NPEPL1. Notably, we found intragenic deletions in one of three exons of the VHL gene and increased mRNAs of VEGF, PDGF-β, and IGF-1/2 in 56% of GISTs, suggesting a mechanistic link between VHL inactivation and overexpression of hypoxia-inducible factor target genes in the absence of hypoxia. We also identified copy number gain and increased mRNA expression of AMACR, CRIM1, SKP2, and CACNA1E. Mapping of copy number and gene expression results to the KEGG pathways revealed activation of the JAK-STAT pathway in small intestinal GISTs and the MAPK pathway in wild-type GISTs. These observations will allow us to determine the genetic basis of GISTs and will facilitate further investigation to develop new therapeutic options.

  17. Fusion reactor materials. Semiannual progress report for period ending September 30, 1993

    SciTech Connect

    Rowcliffe, A.F.; Burn, G.L.; Knee`, S.S.; Dowker, C.L.

    1994-02-01

    This is the fifteenth in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following progress reports: Alloy Development for Irradiation Performance; Damage Analysis and Fundamental Studies; Special purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials programs being conducted in support of the Magnetic Fusion Energy Program of the U.S. Department of Energy. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide.

  18. Frequency of the ETV6-RUNX1, BCR-ABL1, TCF3-PBX1, and MLL-AFF1 fusion genes in Guatemalan pediatric acute lymphoblastic leukemia patients and their ethnic associations.

    PubMed

    Carranza, Claudia; Granados, Lilian; Morales, Oneida; Jo, Wendy; Villagran, Swuanny; Tinti, Damaris; Villegas, Mauricio; Antillón, Federico; Torselli, Silvana; Silva, Gabriel

    2013-06-01

    Fusion genes involved in acute lymphoblastic leukemia (ALL) occur mostly due to genetic and environmental factors, and only a limited number of studies have reported any ethnic influence. This study assesses whether an ethnic influence has an effect on the frequency of any of the four fusion genes: BCR-ABL1, ETV6-RUNX1, TCF3-PBX1, and MLL-AFF1 found in ALL. To study this ethnic influence, mononuclear cells were obtained from bone marrow samples from 143 patients with ALL. We performed RNA extraction and reverse transcription, then assessed the quality of the cDNA by amplifying the ABL1 control gene, and finally evaluated the presence of the four transcripts by multiplex polymerase chain reaction. We found 10 patients who had the BCR-ABL1 fusion gene (7%); 3 patients (2%) were TCF3-PBX1 positive; and 6 patients (4.5%) were ETV6-RUNX1 positive. The incidence of this last fusion gene is quite low when compared to the values reported in most countries. The low incidence of the ETV6-RUNX1 fusion gene found in Guatemala matches the incidence rates that have been reported in Spain and Indian Romani. Since it is known that an ethnic resemblance exists among these three populations, as shown by ancestral marker studies, the ALL data suggests an ethnic influence on the occurrence and frequency of this particular fusion gene. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. TMPRSS2-ERG Fusion Gene Expression in Prostate Tumor Cells and Its Clinical and Biological Significance in Prostate Cancer Progression

    PubMed Central

    St. John, Jason; Powell, Katelyn; Conley-LaComb, M. Katie; Chinni, Sreenivasa R.

    2012-01-01

    TMPRSS2-Ets gene fusions were identified in prostate cancers where the promoter of transmembrane protease, serine 2 (TMPRSS2) fused with coding sequence of the erythroblastosis virus E26 (Ets) gene family members. TMPRSS2 is an androgen responsive transmembrane serine protease. Ets family members are oncogenic transcription factors that contain a highly conserved Ets DNA binding domain and an N-terminal regulatory domain. Fusion of these gene results in androgen dependent transcription of Ets factor in prostate tumor cells. The ERG is the most common fusion partner with TMPRSS2 promoter in prostate cancer patients. The high prevalence of these gene fusions, in particular TMPRSS2-ERG, makes them attractive as potential diagnostic and prognostic indicators, as well as making them a potential target for tailored therapies. This review focuses on the clinical and biological significance of TMPRSS2-ERG fusions and their role in PC development and progression. PMID:23264855

  20. Repeated Complication Following Atlantoaxial Fusion: A Case Report

    PubMed Central

    Oh, Chang Hyun; Ji, Gyu Yeul; Seo, Hyun Sung; Hyun, Dongkeun; Park, Hyeong-Chun

    2014-01-01

    A patients with atlantoaixial instability and osodontoideum underwent atlantoaixial fusion (Harms and Melcher technique) with demineralized bone matrix. But, unfortunately, the both pedicle screws in C2 were fractured within 9 weeks follow-up periods after several suspected episode of neck hyper-flexion. Fractured screws were not contact to occipital bone in several imaging studies, but it could irritate the occipital bone when neck extension because the relatively close distance between the occipital bone and C1 posterior arch. The patient underwent revision operation with translaminar screw fixation with autologus iliac bone graft. Postsurgical course were uneventful except donor site pain, but the bony fusion was not satisfied after 4 months follow-up. The patient re-underwent revision operation in other hospital. Continuous complication after atlantoaixial fusion is rare, but the clinical course could be unlucky to patients. Postoperative immobilization could be important to prevent the unintended clinical course of patients. PMID:24891865

  1. Repeated complication following atlantoaxial fusion: a case report.

    PubMed

    Oh, Chang Hyun; Ji, Gyu Yeul; Seo, Hyun Sung; Yoon, Seung Hwan; Hyun, Dongkeun; Park, Hyeong-Chun

    2014-03-01

    A patients with atlantoaixial instability and osodontoideum underwent atlantoaixial fusion (Harms and Melcher technique) with demineralized bone matrix. But, unfortunately, the both pedicle screws in C2 were fractured within 9 weeks follow-up periods after several suspected episode of neck hyper-flexion. Fractured screws were not contact to occipital bone in several imaging studies, but it could irritate the occipital bone when neck extension because the relatively close distance between the occipital bone and C1 posterior arch. The patient underwent revision operation with translaminar screw fixation with autologus iliac bone graft. Postsurgical course were uneventful except donor site pain, but the bony fusion was not satisfied after 4 months follow-up. The patient re-underwent revision operation in other hospital. Continuous complication after atlantoaixial fusion is rare, but the clinical course could be unlucky to patients. Postoperative immobilization could be important to prevent the unintended clinical course of patients.

  2. Laser fusion driven breeder design study. Final report

    SciTech Connect

    Berwald, D.H.; Massey, J.V.

    1980-12-01

    The results of the Laser Fusion Breeder Design Study are given. This information primarily relates to the conceptual design of an inertial confinement fusion (ICF) breeder reactor (or fusion-fission hybrid) based upon the HYLIFE liquid metal wall protection concept developed at Lawrence Livermore National Laboratory. The blanket design for this breeder is optimized to both reduce fissions and maximize the production of fissile fuel for subsequent use in conventional light water reactors (LWRs). When the suppressed fission blanket is compared with its fast fission counterparts, a minimal fission rate in the blanket results in a unique reactor safety advantage for this concept with respect to reduced radioactive inventory and reduced fission product decay afterheat in the event of a loss-of-coolant-accident.

  3. Report of the heavy-ion fusion task group

    SciTech Connect

    Sawyer, G.A.; Booth, L.A.; Henderson, D.B.; Jameson, R.A.; Kindel, J.M.; Knapp, E.A.; Pollock, R.; Talbert, W.L.; Thode, L.E.; Williams, J.M.

    1980-02-01

    An assessment of heavy-ion fusion has been completed. Energetic heavy ions, for example 10-GeV uranium, provided by an rf linac or an induction linac, are used as alternatives to laser light to drive inertial confinement fusion pellets. The assessment has covered accelerator technology, transport of heavy-ion beams, target interaction physics, civilian power issues, and military applications. It is concluded that particle accelerators promise to be efficient pellet drivers, but that there are formidable technical problems to be solved. It is recommended that a moderate level research program on heavy-ion fusion be pursued and that LASL should continue to work on critical issues in accelerator development, beam transport, reactor systems studies, and target physics over the next few years.

  4. Acute leukemias of different lineages have similar MLL gene fusions encoding related chimeric proteins resulting from chromosomal translocation

    SciTech Connect

    Corral, J.; Forster, A.; Thompson, S.; Rabbitts, T.H. ); Lampert, F. ); Kaneko, Y. ); Slater, R.; Kroes, W.G. ); Van Der Schoot, C.E. ); Ludwig, W.D. ); Karpas, A. ); Pocock, C.; Cotter, F. )

    1993-09-15

    The MLL gene, on human chromosome 11q23, undergoes chromosomal translocation in acute leukemias, resulting in gene fusion with AF4 (chromosome 4) and ENL (chromosome 19). The authors report here translocation of MLL with nine different chromosomes and two paracentric chromosome 11 deletions in early B cell, B- or T-cell lineage, or nonlymphocytic acute leukemias. The mRNA translocation junction from 22t(4;11) patients, including six adult leukemias, and nine t(11;19) tumors reveals a remarkable conservation of breakpoints within MLL, AF4, or ENL genes, irrespective of tumor phenotype. Typically, the breakpoints are upstream of the zinc-finger region of MLL, and deletion of this region can accompany translocation, supporting the der(11) chromosome as the important component in leukemogenesis. Partial sequence of a fusion between MLL and the AFX1 gene from chromosome X shows the latter to be rich in Ser/Pro codons, like the ENL mRNA. These data suggest that the heterogeneous 11q23 abnormalities might cause attachment of Ser/Pro-rich segments to the NH[sub 2] terminus of MLL, lacking the zinc-finger region, and that translocation occurs in early hematopoietic cells, before commitment to distinct lineages. 36 refs., 2 figs.

  5. Functional characterization of the 5' flanking region of human ubiquitin fusion degradation 1 like gene (UFD1L).

    PubMed

    Amati, Francesca; Conti, Emanuela; Botta, Annalisa; Amicucci, Paola; Dallapiccola, Bruno; Novelli, Giuseppe

    2002-06-01

    UFD1L (Ubiquitin Fusion Degradation 1 Like) gene encodes for a component of a multi-complex involved in the degradation of ubiquitin fusion proteins. The gene maps on chromosome 22q11, in a region commonly deleted in severe congenital disorders such as DiGeorge (DGS) and velo-cardio-facial (VCFS) syndromes. UFD1L is a single copy gene ubiquitously expressed in high levels in the pharyngeal pouches and fourth branchial arch artery during development. To understand the regulation of UFD1L expression we performed a functional analysis of its 5' regulatory region. 5'-RACE and primer extension analyses revealed the presence of different transcription start sites in adult and fetal tissues. UFD1L 5' flanking region contains a TATA-box motif and is also very GC-rich with a CpG island encompassing exon 1. Transcriptional activity of this region was examined by transfection experiments of promoter-GFP reporter gene constructs in a human epithelial cell line. These experiments revealed the importance of the region between -17 and -463 nt which contains the TATA-box. EMSA assay resulted in the detection of five functional consensus sequences respectively for the transcription complex TFIID and for the transcription factors AP-1 (one site), AP-2 (one) and Sp1 (two).

  6. FY-2013 FES (Fusion Energy Sciences) Joint Research Target Report

    SciTech Connect

    Fenstermacher, M. E.; Garofalo, A. M.; Gerhardt, S. P.; Hubbard, A.; Maingi, R.; Whyte, D.

    2013-09-30

    investigated. The research will strengthen the basis for extrapolation of stationary regimes which combine high energy confinement with good particle and impurity control, to ITER and other future fusion facilities for which avoidance of large ELMs is a critical issue. Data from the Alcator C-Mod tokamak (MIT), DIII-D tokamak (General Atomics), and NSTX spherical tokamak (PPPL) contribute to this report. Experiments specifically motivated by this research target were conducted on DIII-D, with a national team of researchers from GA, LLNL, PPPL, MIT and ORNL contributing. Both the Alcator C-Mod and NSTX-U teams contributed analysis of previously collected data, as those two facilities did not operate in FY2013. Within each of the three research groups, members from both the host institutions and collaborating institutions made critical contributions. Highlights from these research activities are provided, with additional details.

  7. [CCL21-CD40L fusion gene induce augmented antitumor activity in colon cancer].

    PubMed

    Gong, Ting; Zhou, Hong-Li; Ba, Yi

    2013-09-01

    To investigate the anti-tumor activity of CCL21-exCD40L eukaryotic expression vector. CCL21-exCD40L fusion gene were constructed by overlap PCR connecting CCL21 and exCD40L through a flexible linker (Gly3Ser)4, and then was cloned into expression vector pcDNA3.1(+). pcDNA3.1(+)/CCL21 and pcDNA3.1(+)/exCD were constructed as negative control. Wsestern blot was used to identify the fusion protein. CHO cells was transfected with pcDNA3.1(+)/CCL21-exCD, pcDNA3.1(+)/CCL21 and pcDNA3.1(+), respectively. The chemotatic function of the expressed product was detected by Transwell method and its anti-tumor activity was tested with vivo transfection. Gene sequencing and restrictive digestion proved the successful construction of pcDNA3.1(+)/CCL21-exCD40L,and its expression was conformed by western blot. The transfectant supernantes of pcDNA3.1(+)/CCL21-exCD40 group had a significant chmotactic function to DCs, of which the cell numbers passing through the film was 14.95 times of blank control every high power microscope visual field. After tumor orthotoic injection of plasmid carrying fusion gene in Balb/c mouse, the tumor mass reduced remarkablely, and all the mouse in fusion gene group survived after 4 weeks. CCL21-exCD40L fusion protein had a remarkable function to DCs and it can inhibit tumor growth and prolong the mouse survival time, which is more effective than all control group.

  8. Fusion gene profile of biphenotypic sinonasal sarcoma: an analysis of 44 cases.

    PubMed

    Fritchie, Karen J; Jin, Long; Wang, Xiaoke; Graham, Rondell P; Torbenson, Michael S; Lewis, Jean E; Rivera, Michael; Garcia, Joaquin J; Schembri-Wismayer, David J; Westendorf, Jennifer J; Chou, Margaret M; Dong, Jie; Oliveira, Andre M

    2016-12-01

    Biphenotypic sinonasal sarcoma (SNS) is a locally aggressive tumour that occurs in the sinonasal region. PAX3-MAML3 has recently been identified as a recurrent fusion gene event in this entity; however, a subset of tumours harbour alternative PAX3 rearrangement without the involvement of MAML3. In this study we sought to characterize the molecular profile of a large series of cases, with a special emphasis on tumours with alternative fusions. Forty-four examples of SNS were screened by fluorescence in-situ hybridization and reverse transcription polymerase chain reaction to better characterize its molecular profile and identify potential novel fusion genes. Twenty-four were positive for PAX3-MAML3 (55%), 15 showed rearrangements of PAX3 without MAML3 involvement (34%), one showed rearrangement of MAML3 without PAX3 involvement, and four were negative for the involvement of either gene (9%). Among 15 cases with PAX3 involvement only, three were found to harbour PAX3-FOXO1. Two of these cases arose in the nasal cavities of female patients (aged 31 and 47 years), and one showed bilateral involvement of the nasal cavities of a 35-year-old male. A fourth case involved the skull base of a 47-year-old male, and was positive for PAX3-NCOA1. Patients with fusion-negative tumours were slightly older. More than half of the SNSs in this series were positive for PAX3-MAML3. However, a subset of tumours may harbour alternative PAX3 fusion genes or show no involvement of PAX3. Except for a possible weak association between age and molecular profile, the overall morphological and immunophenotypic features of all cases seem to be similar. Because of the rarity of these tumours, the impact of the molecular profile on the clinical course of these tumours remains to be determined. © 2016 John Wiley & Sons Ltd.

  9. NTRK gene fusions as novel targets of cancer therapy across multiple tumour types

    PubMed Central

    Sartore-Bianchi, Andrea; Siena, Salvatore

    2016-01-01

    The tropomyosin receptor kinase (Trk) receptor family comprises 3 transmembrane proteins referred to as Trk A, B and C (TrkA, TrkB and TrkC) receptors that are encoded by the NTRK1, NTRK2 and NTRK3 genes, respectively. These receptor tyrosine kinases are expressed in human neuronal tissue and play an essential role in the physiology of development and function of the nervous system through activation by neurotrophins. Gene fusions involving NTRK genes lead to transcription of chimeric Trk proteins with constitutively activated or overexpressed kinase function conferring oncogenic potential. These genetic abnormalities have recently emerged as targets for cancer therapy, because novel compounds have been developed that are selective inhibitors of the constitutively active rearranged proteins. Developments in this field are being aided by next generation sequencing methods as tools for unbiased gene fusions discovery. In this article, we review the role of NTRK gene fusions across several tumour histologies, and the promises and challenges of targeting such genetic alterations for cancer therapy. PMID:27843590

  10. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.

    PubMed

    Promponas, Vasilis J; Ouzounis, Christos A; Iliopoulos, Ioannis

    2014-05-01

    More than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. This structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. Furthermore, this view has raised the real possibility to detect functional associations of genes and their corresponding proteins for any entire genome sequence. Yet, despite these exciting developments, there have been relatively few cases of real use of these methods outside the computational biology field, as reflected from citation analysis. These methods have the potential to be used in high-throughput experimental settings in functional genomics and proteomics to validate results with very high accuracy and good coverage. In this critical survey, we provide a comprehensive overview of 30 most prominent examples of single pairwise protein interaction cases in small-scale studies, where protein interactions have either been detected by gene fusion or yielded additional, corroborating evidence from biochemical observations. Our conclusion is that with the derivation of a validated gold-standard corpus and better data integration with big experiments, gene fusion detection can truly become a valuable tool for large-scale experimental biology.

  11. Gene fusion analysis of membrane protein topology: a direct comparison of alkaline phosphatase and beta-lactamase fusions.

    PubMed Central

    Prinz, W A; Beckwith, J

    1994-01-01

    To compare two approaches to analyzing membrane protein topology, a number of alkaline phosphatase fusions to membrane proteins were converted to beta-lactamase fusions. While some alkaline phosphatase fusions near the N terminus of cytoplasmic loops of membrane proteins have anomalously high levels of activity, the equivalent beta-lactamase fusions do not. This disparity may reflect differences in the folding of beta-lactamase and alkaline phosphatase in the cytoplasm. PMID:7929016

  12. Isolation and characterization of Escherichia coli strains containing new gene fusions (soi::lacZ) inducible by superoxide radicals.

    PubMed Central

    Mito, S; Zhang, Q M; Yonei, S

    1993-01-01

    Gene fusions in Escherichia coli that showed increased beta-galactosidase expression in response to treatment with a superoxide radical (O2-) generator, methyl viologen (MV), were obtained. These fusions were constructed by using a Mud(Ap lac) phage to insert the lactose structural genes randomly into the E. coli chromosome. Ampicillin-resistant colonies were screened for increased expression of beta-galactosidase on X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside) plates containing MV at 1.25 micrograms/ml. Other O2- generators, menadione and plumbagin, also induced beta-galactosidase activity in these fusion strains. The induction by these drugs occurred only under aerobic conditions. Hyperoxygenation also elicited an induction of the fusions. On the other hand, no significant induction was observed with hydrogen peroxide and cumene hydroperoxide. The induction of these fusions by MV was not dependent on the peroxide stress control mediated by the oxyR gene or on the recA-dependent SOS system. These fusions were named soi (superoxide inducible)::lacZ. The induction of beta-galactosidase was significantly reduced by introducing a soxS::Tn10 locus into the fusion strains, indicating that the soi genes are members of the soxRS regulon. Five of the fusions were located in 6 to 26 min of the E. coli genetic map, while three fusions were located in 26 to 36 min, indicating that these fusions are not related to genes already known to be inducible by O2- under the control of soxRS. At least five mutants containing the soi::lacZ fusion were more sensitive to MV and menadione than the wild-type strain, suggesting that the products of these soi genes play an important role in protection against oxidative stress. PMID:8386722

  13. Dissection of left iliac artery during anterior lumbar interspace fusion: Report of a case.

    PubMed

    Fischer, Uwe M; Davies, Mark G; El Sayed, Hosam

    2015-04-01

    Vascular injury is an uncommon complication of spine surgery. Among the different approaches, anterior lumbar interbody fusion has increased potential for vascular injuries, since the great vessels and their branches overly the disc spaces to be operated on, and retraction of these vessels is necessary to gain adequate surgical exposure. The reported incidence for anterior lumbar interbody fusion-associated vascular injuries ranges from 0% to 18.1%, with venous laceration as the most common type. We report a case of anterior lumbar interbody fusion-associated left common iliac artery dissection leading to delayed acute limb ischemia developing in early post-operative period.

  14. Two novel imatinib-responsive PDGFRA fusion genes in chronic eosinophilic leukaemia.

    PubMed

    Curtis, Claire E; Grand, Francis H; Musto, Pellegrino; Clark, Andrew; Murphy, John; Perla, Gianni; Minervini, Maria M; Stewart, Janet; Reiter, Andreas; Cross, Nicholas C P

    2007-07-01

    We identified two patients with a t(2;4)(p24;q12) and a t(4;12)(q2?3;p1?2), respectively, in association with BCR-ABL and FIP1L1-PDGFRA negative chronic eosinophilic leukaemia. Molecular analysis revealed a novel STRN-PDGFRA fusion for the t(2;4) and ETV6-PDGFRA for the t(4;12). The fusions were confirmed by specific amplification of the genomic breakpoints, reverse transcription polymerase chain reaction and fluorescence in situ hybridisation. Both patients were treated with imatinib and, following a rapid haematological response, achieved cytogenetic remission and a major molecular response. In conclusion, PDGFRA fuses to diverse partner genes in myeloid disorders. Identification of these fusions is important as they are particularly sensitive to imatinib.

  15. Recurrent MET fusion genes represent a drug target in pediatric glioblastoma.

    PubMed

    2016-11-01

    Pediatric glioblastoma is one of the most common and most deadly brain tumors in childhood. Using an integrative genetic analysis of 53 pediatric glioblastomas and five in vitro model systems, we identified previously unidentified gene fusions involving the MET oncogene in ∼10% of cases. These MET fusions activated mitogen-activated protein kinase (MAPK) signaling and, in cooperation with lesions compromising cell cycle regulation, induced aggressive glial tumors in vivo. MET inhibitors suppressed MET tumor growth in xenograft models. Finally, we treated a pediatric patient bearing a MET-fusion-expressing glioblastoma with the targeted inhibitor crizotinib. This therapy led to substantial tumor shrinkage and associated relief of symptoms, but new treatment-resistant lesions appeared, indicating that combination therapies are likely necessary to achieve a durable clinical response.

  16. A Search for Gene Fusions/Translocations in Breast Cancer

    DTIC Science & Technology

    2012-10-01

    pseudogenes derived from AURKA (kidney samples), RHOB (colon samples), and HMGB1 ( myeloproliferative neoplasms [MPNs]) (Figure 3A, top). Interestingly...key clusters are labeled with their corresponding parental gene symbols. MPN, myeloproliferative neoplasms . See also Table S6.transcripts in samples

  17. The distribution of BRAF gene fusions in solid tumors and response to targeted therapy.

    PubMed

    Ross, Jeffrey S; Wang, Kai; Chmielecki, Juliann; Gay, Laurie; Johnson, Adrienne; Chudnovsky, Jacob; Yelensky, Roman; Lipson, Doron; Ali, Siraj M; Elvin, Julia A; Vergilio, Jo-Anne; Roels, Steven; Miller, Vincent A; Nakamura, Brooke N; Gray, Adam; Wong, Michael K; Stephens, Philip J

    2016-02-15

    Although the BRAF V600E base substitution is an approved target for the BRAF inhibitors in melanoma, BRAF gene fusions have not been investigated as anticancer drug targets. In our study, a wide variety of tumors underwent comprehensive genomic profiling for hundreds of known cancer genes using the FoundationOne™ or FoundationOne Heme™ comprehensive genomic profiling assays. BRAF fusions involving the intact in-frame BRAF kinase domain were observed in 55 (0.3%) of 20,573 tumors, across 12 distinct tumor types, including 20 novel BRAF fusions. These comprised 29 unique 5' fusion partners, of which 31% (9) were known and 69% (20) were novel. BRAF fusions included 3% (14/531) of melanomas; 2% (15/701) of gliomas; 1.0% (3/294) of thyroid cancers; 0.3% (3/1,062) pancreatic carcinomas; 0.2% (8/4,013) nonsmall-cell lung cancers and 0.2% (4/2,154) of colorectal cancers, and were enriched in pilocytic (30%) vs. nonpilocytic gliomas (1%; p < 0.0001), Spitzoid (75%) vs. nonSpitzoid melanomas (1%; p = 0.0001), acinar (67%) vs. nonacinar pancreatic cancers (<1%; p < 0.0001) and papillary (3%) vs. nonpapillary thyroid cancers (0%; p < 0.03). Clinical responses to trametinib and sorafenib are presented. In conclusion, BRAF fusions are rare driver alterations in a wide variety of malignant neoplasms, but enriched in Spitzoid melanoma, pilocytic astrocytomas, pancreatic acinar and papillary thyroid cancers. © 2015 The Authors. Published by Wiley Periodicals, Inc. on behalf of UICC.

  18. Fusion of the TEL gene on 12p13 to the AML1 gene on 21q22 in acute lymphoblastic leukemia

    SciTech Connect

    Barker, G.F.; Golub, T.R.; Gilliland, D.G.; Bohlander, S.K.; Rowley, J.D.; Heibert, S.W.; Raimondi, S.C.; Ward, D.C.; Bray-Ward, P.; Morgan, E.

    1995-05-23

    Chromosomal rearrangements involving band 12p13 are found in a wide variety of human leukemias but are particularly common in childhood acute lymphoblastic leukemia. The genes involved in these rearrangements, however, have not been identified. We now report the cloning of a t(12;21) translocation breakpoint involving 12p13 and 21q22 in two cases of childhood pre-B acute lymphoblastic leukemia, in which t(12;21) rearrangements were not initially apparent. The consequence of the translocation is fusion of the helix-loop-helix domain of TEL, an ETS-like putative transcription factor, to the DNA-binding and transactivation domains of the transcription factor AML1. These data show that TEL, previously shown to be fused to the platelet-derived growth factor receptor {beta} in chronic myelomonocytic leukemia, can be implicated in the pathogenesis of leukemia through its fusion to either a receptor tyrosine kinase or a transcription factor. The TEL-AML1 fusion also indicates that translocations affecting the AML1 gene can be associated with lymphoid, as well as myeloid, malignancy. 23 refs., 5 figs.

  19. Final report on the Magnetized Target Fusion Collaboration

    SciTech Connect

    John Slough

    2009-09-08

    Nuclear fusion has the potential to satisfy the prodigious power that the world will demand in the future, but it has yet to be harnessed as a practical energy source. The entry of fusion as a viable, competitive source of power has been stymied by the challenge of finding an economical way to provide for the confinement and heating of the plasma fuel. It is the contention here that a simpler path to fusion can be achieved by creating fusion conditions in a different regime at small scale (~ a few cm). One such program now under study, referred to as Magnetized Target Fusion (MTF), is directed at obtaining fusion in this high energy density regime by rapidly compressing a compact toroidal plasmoid commonly referred to as a Field Reversed Configuration (FRC). To make fusion practical at this smaller scale, an efficient method for compressing the FRC to fusion gain conditions is required. In one variant of MTF a conducting metal shell is imploded electrically. This radially compresses and heats the FRC plasmoid to fusion conditions. The closed magnetic field in the target plasmoid suppresses the thermal transport to the confining shell, thus lowering the imploding power needed to compress the target. The undertaking to be described in this proposal is to provide a suitable target FRC, as well as a simple and robust method for inserting and stopping the FRC within the imploding liner. The timescale for testing and development can be rapidly accelerated by taking advantage of a new facility funded by the Department of Energy. At this facility, two inductive plasma accelerators (IPA) were constructed and tested. Recent experiments with these IPAs have demonstrated the ability to rapidly form, accelerate and merge two hypervelocity FRCs into a compression chamber. The resultant FRC that was formed was hot (T&ion ~ 400 eV), stationary, and stable with a configuration lifetime several times that necessary for the MTF liner experiments. The accelerator length was less than

  20. Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution.

    PubMed

    Ruiz-Herrera, Aurora; Farré, Marta; Ponsà, Montserrat; Robinson, Terence J

    2010-11-01

    Monobrachial homology resulting from Robertsonian (Rb) fusions is thought to contribute to chromosomal speciation through underdominance. Given the karyotypic diversity characterizing wild house mouse populations [Mus musculus domesticus, (MMU)], variation that results almost exclusively from Rb fusions (diploid numbers range from 22 to 40) and possibly whole arm reciprocal translocations (WARTs), this organism represents an excellent model for testing hypotheses of chromosomal evolution. Previous studies of chromosome size and recombination rates have failed to explain the bias for certain chromosomes to be involved more frequently than others in these rearrangements. Here, we show that the pericentromeric region of one such chromosome, MMU19, which is infrequently encountered as a fusion partner in wild populations, is significantly enriched for housekeeping genes when compared to other chromosomes in the genome. These data suggest that there is selection against breakpoints in the pericentromeric region and provide new insights into factors that constrain chromosomal reorganizations in house mice. Given the anticipated increase in vertebrate whole genome sequences, the examination of gene content and expression profiles of the pericentromeric regions of other mammalian lineages characterized by Rb fusions (i.e., other rodents, bats, and bovids, among others) is both achievable and crucial to developing broadly applicable models of chromosome evolution.

  1. Gene Fusion Analysis in the Battle against the African Endemic Sleeping Sickness

    PubMed Central

    Trimpalis, Philip; Koumandou, Vassiliki Lila; Pliakou, Evangelia; Anagnou, Nicholas P.; Kossida, Sophia

    2013-01-01

    The protozoan Trypanosoma brucei causes African Trypanosomiasis or sleeping sickness in humans, which can be lethal if untreated. Most available pharmacological treatments for the disease have severe side-effects. The purpose of this analysis was to detect novel protein-protein interactions (PPIs), vital for the parasite, which could lead to the development of drugs against this disease to block the specific interactions. In this work, the Domain Fusion Analysis (Rosetta Stone method) was used to identify novel PPIs, by comparing T. brucei to 19 organisms covering all major lineages of the tree of life. Overall, 49 possible protein-protein interactions were detected, and classified based on (a) statistical significance (BLAST e-value, domain length etc.), (b) their involvement in crucial metabolic pathways, and (c) their evolutionary history, particularly focusing on whether a protein pair is split in T. brucei and fused in the human host. We also evaluated fusion events including hypothetical proteins, and suggest a possible molecular function or involvement in a certain biological process. This work has produced valuable results which could be further studied through structural biology or other experimental approaches so as to validate the protein-protein interactions proposed here. The evolutionary analysis of the proteins involved showed that, gene fusion or gene fission events can happen in all organisms, while some protein domains are more prone to fusion and fission events and present complex evolutionary patterns. PMID:23874788

  2. Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guanche

    PubMed Central

    Jones, Corbin D.; Custer, Andrew W.; Begun, David J.

    2005-01-01

    An understanding of the mutational and evolutionary mechanisms underlying the emergence of novel genes is critical to studies of phenotypic and genomic evolution. Here we describe a new example of a recently formed chimeric fusion gene that occurs in Drosophila guanche, D. madeirensis, and D. subobscura. This new gene, which we name Adh-Twain, resulted from an Adh mRNA that retrotransposed into the Gapdh-like gene, CG9010. Adh-Twain is transcribed; its 5′ promoters and transcription patterns appear similar to those of CG9010. Population genetic and phylogenetic analyses suggest that the amino acid sequence of Adh-Twain evolved rapidly via directional selection shortly after it arose. Its more recent history, however, is characterized by slower evolution consistent with increasing functional constraints. We present a model for the origin of this new gene and discuss genetic and evolutionary factors affecting the evolution of new genes and functions. PMID:15781692

  3. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.

    PubMed

    Norton, Nadine; Sun, Zhifu; Asmann, Yan W; Serie, Daniel J; Necela, Brian M; Bhagwate, Aditya; Jen, Jin; Eckloff, Bruce W; Kalari, Krishna R; Thompson, Kevin J; Carr, Jennifer M; Kachergus, Jennifer M; Geiger, Xochiquetzal J; Perez, Edith A; Thompson, E Aubrey

    2013-01-01

    Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlations of >0.94 and >0.80 with NanoString and ScriptSeq protocols, respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes) and ScriptSeq whole transcriptome protocols respectively, p<2x10(-16). Specifically for lincRNAs, we observed superb Pearson correlation (0.988) between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads). Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transcriptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol performed

  4. The relationship of TMPRSS2-ERG gene fusion between primary and metastatic prostate cancers

    PubMed Central

    Guo, Charles C.; Wang, Yan; Xiao, Li; Troncoso, Patricia; Czerniak, Bogdan A.

    2013-01-01

    Recent studies have revealed the presence of TMPRSS2-ERG gene fusion in both primary and metastatic prostatic cancers (PCAs). However, the relationship between primary and corresponding metastatic PCAs with respect to the status of this gene fusion remains unclear. Using fluorescence in situ hybridization, we evaluated the rearrangement of the ERG gene in the radical prostatectomy (RP) specimens and corresponding lymph node metastases from 19 patients with PCA. The mean age of the patients was 61 years and the median Gleason score in the RP specimens was 7 (4+3). PCA was unifocal in 6 cases and multifocal in 13 cases, including 10 with 2 foci and 3 with 3 foci. In the primary PCAs, rearrangement of the ERG gene was observed in 13 cases and associated with deletion of the 5’ ERG gene in 8 cases. In the metastases, the ERG rearrangement was present in 10 cases and associated with deletion of the 5’ ERG gene in 6 cases. In unifocal PCAs, the status of the ERG rearrangement was concordant between the primary PCA and metastasis in 5 of 6 cases. In multifocal PCA, despite a significant interfocal discordance, the status of the ERG rearrangement was concordant between the index (largest) primary tumor focus and metastasis in all 13 cases. Our study demonstrates a close relationship of the TMPRSS2-ERG gene fusion status between primary and metastatic PCA. The concordance of the ERG gene rearrangement status between the index primary tumor focus and metastasis suggests that metastasis most likely arises from the index tumor focus in multifocal PCA. PMID:21937078

  5. The relationship of TMPRSS2-ERG gene fusion between primary and metastatic prostate cancers.

    PubMed

    Guo, Charles C; Wang, Yan; Xiao, Li; Troncoso, Patricia; Czerniak, Bogdan A

    2012-05-01

    Recent studies have revealed the presence of TMPRSS2-ERG gene fusion in both primary and metastatic prostate cancers. However, the relationship between primary and corresponding metastatic prostate cancers with respect to the status of this gene fusion remains unclear. Using fluorescence in situ hybridization, we evaluated the rearrangement of the ERG gene in the radical prostatectomy specimens and corresponding lymph node metastases from 19 patients with prostate cancer. The mean age of the patients was 61 years, and the median Gleason score in the radical prostatectomy specimens was 7 (4 + 3). Prostate cancer was unifocal in 6 cases and multifocal in 13 cases, including 10 with 2 foci and 3 with 3 foci. In the primary prostate cancers, rearrangement of the ERG gene was observed in 13 cases and associated with deletion of the 5' ERG gene in 8 cases. In the metastases, the ERG rearrangement was present in 10 cases and associated with deletion of the 5' ERG gene in 6 cases. In unifocal prostate cancers, the status of the ERG rearrangement was concordant between the primary prostate cancer and metastasis in 5 of 6 cases. In multifocal prostate cancer, despite a significant interfocal discordance, the status of the ERG rearrangement was concordant between the index (largest) primary tumor focus and metastasis in all 13 cases. Our study demonstrates a close relationship of the TMPRSS2-ERG gene fusion status between primary and metastatic prostate cancer. The concordance of the ERG gene rearrangement status between the index primary tumor focus and metastasis suggests that metastasis most likely arises from the index tumor focus in multifocal prostate cancer.

  6. Technical Letter Report - Preliminary Assessment of NDE Methods on Inspection of HDPE Butt Fusion Piping Joints for Lack of Fusion

    SciTech Connect

    Crawford, Susan L.; Cumblidge, Stephen E.; Doctor, Steven R.; Hall, Thomas E.; Anderson, Michael T.

    2008-05-29

    was conducted. Millimeter (mm) waves were also used to inspect these assemblies. Fluor and NDE Innovations, Inc. conducted TOFD inspections using their commercially available equipment on all 24 specimens. These NDE inspection results were reviewed and several of the specimens were selected for destructive evaluation using a microtome to slice small blocks of blank and fusion joint material. This interim report provides a status/summary of the work that has been conducted to date. In the areas selected for destructive testing where there were strong acoustic responses, LOF was verified. In areas where there were no NDE responses, no LOF was found. It needs to be noted that only a small amount of material has been destructively characterized at this point and further work is planned to determine if these trends hold up. Some of the material from three of the assemblies was sent off for mechanical testing but the results were not available to be included in this status report. The initial work shows that at least some of the LOF is providing NDE responses that have been verified through destructive testing. Thus, there is promise that a volumetric examination can be conducted on HDPE butt fusion joints. The future work will lead to quantifying what various NDE methods can detect, what they miss, and what they incorrectly characterize as defective.

  7. CONFERENCE REPORT: Summary of the 8th IAEA Technical Meeting on Fusion Power Plant Safety

    NASA Astrophysics Data System (ADS)

    Girard, J. Ph.; Gulden, W.; Kolbasov, B.; Louzeiro-Malaquias, A.-J.; Petti, D.; Rodriguez-Rodrigo, L.

    2008-01-01

    Reports were presented covering a selection of topics on the safety of fusion power plants. These included a review on licensing studies developed for ITER site preparation surveying common and non-common issues (i.e. site dependent) as lessons to a broader approach for fusion power plant safety. Several fusion power plant models, spanning from accessible technology to more advanced-materials based concepts, were discussed. On the topic related to fusion-specific technology, safety studies were reported on different concepts of breeding blanket modules, tritium handling and auxiliary systems under normal and accident scenarios' operation. The testing of power plant relevant technology in ITER was also assessed in terms of normal operation and accident scenarios, and occupational doses and radioactive releases under these testings have been determined. Other specific safety issues for fusion have also been discussed such as availability and reliability of fusion power plants, dust and tritium inventories and component failure databases. This study reveals that the environmental impact of fusion power plants can be minimized through a proper selection of low activation materials and using recycling technology helping to reduce waste volume and potentially open the route for its reutilization for the nuclear sector or even its clearance into the commercial circuit. Computational codes for fusion safety have been presented in support of the many studies reported. The on-going work on establishing validation approaches aiming at improving the prediction capability of fusion codes has been supported by experimental results and new directions for development have been identified. Fusion standards are not available and fission experience is mostly used as the framework basis for licensing and target design for safe operation and occupational and environmental constraints. It has been argued that fusion can benefit if a specific fusion approach is implemented, in particular

  8. SFM: A novel sequence-based fusion method for disease genes identification and prioritization.

    PubMed

    Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

    2015-10-21

    The identification of disease genes from human genome is of great importance to improve diagnosis and treatment of disease. Several machine learning methods have been introduced to identify disease genes. However, these methods mostly differ in the prior knowledge used to construct the feature vector for each instance (gene), the ways of selecting negative data (non-disease genes) where there is no investigational approach to find them and the classification methods used to make the final decision. In this work, a novel Sequence-based fusion method (SFM) is proposed to identify disease genes. In this regard, unlike existing methods, instead of using a noisy and incomplete prior-knowledge, the amino acid sequence of the proteins which is universal data has been carried out to present the genes (proteins) into four different feature vectors. To select more likely negative data from candidate genes, the intersection set of four negative sets which are generated using distance approach is considered. Then, Decision Tree (C4.5) has been applied as a fusion method to combine the results of four independent state-of the-art predictors based on support vector machine (SVM) algorithm, and to make the final decision. The experimental results of the proposed method have been evaluated by some standard measures. The results indicate the precision, recall and F-measure of 82.6%, 85.6% and 84, respectively. These results confirm the efficiency and validity of the proposed method.

  9. Adenoviral-Mediated Imaging of Gene Transfer Using a Somatostatin Receptor-Cytosine Deaminase Fusion Protein

    PubMed Central

    Lears, Kimberly A.; Parry, Jesse J.; Andrews, Rebecca; Nguyen, Kim; Wadas, Thaddeus J.; Rogers, Buck E.

    2015-01-01

    Suicide gene therapy is a process by which cells are administered a gene that encodes a protein capable of converting a nontoxic prodrug into an active toxin. Cytosine deaminase (CD) has been widely investigated as a means of suicide gene therapy due to the enzyme’s ability to convert the prodrug 5-fluorocytosine (5-FC) into the toxic compound 5-fluorouracil (5-FU). However, the extent of gene transfer is a limiting factor in predicting therapeutic outcome. The ability to monitor gene transfer, non-invasively, would strengthen the efficiency of therapy. In this regard, we have constructed and evaluated a replication-deficient adenovirus (Ad) containing the human somatostatin receptor subtype 2 (SSTR2) fused with a C-terminal yeast CD gene for the non-invasive monitoring of gene transfer and therapy. The resulting Ad (AdSSTR2-yCD) was evaluated in vitro in breast cancer cells to determine the function of the fusion protein. These studies demonstrated that the both the SSTR2 and yCD were functional in binding assays, conversion assays, and cytotoxicity assays. In vivo studies similarly demonstrated the functionality using conversion assays, biodistribution studies, and small animal positron-emission tomography (PET) imaging studies. In conclusion, the fusion protein has been validated as useful for the non-invasive imaging of yCD expression and will be evaluated in the future for monitoring yCD-based therapy. PMID:25837665

  10. Adenoviral-mediated imaging of gene transfer using a somatostatin receptor-cytosine deaminase fusion protein.

    PubMed

    Lears, K A; Parry, J J; Andrews, R; Nguyen, K; Wadas, T J; Rogers, B E

    2015-03-01

    Suicide gene therapy is a process by which cells are administered a gene that encodes a protein capable of converting a nontoxic prodrug into an active toxin. Cytosine deaminase (CD) has been widely investigated as a means of suicide gene therapy owing to the enzyme's ability to convert the prodrug 5-fluorocytosine (5-FC) into the toxic compound 5-fluorouracil (5-FU). However, the extent of gene transfer is a limiting factor in predicting therapeutic outcome. The ability to monitor gene transfer, non-invasively, would strengthen the efficiency of therapy. In this regard, we have constructed and evaluated a replication-deficient adenovirus (Ad) containing the human somatostatin receptor subtype 2 (SSTR2) fused with a C-terminal yeast CD gene for the non-invasive monitoring of gene transfer and therapy. The resulting Ad (AdSSTR2-yCD) was evaluated in vitro in breast cancer cells to determine the function of the fusion protein. These studies demonstrated that both the SSTR2 and yCD were functional in binding assays, conversion assays and cytotoxicity assays. In vivo studies similarly demonstrated the functionality using conversion assays, biodistribution studies and small animal positron-emission tomography (PET) imaging studies. In conclusion, the fusion protein has been validated as useful for the non-invasive imaging of yCD expression and will be evaluated in the future for monitoring yCD-based therapy.

  11. Inferring orthologous gene regulatory networks using interspecies data fusion

    PubMed Central

    Penfold, Christopher A.; Millar, Jonathan B. A.; Wild, David L.

    2015-01-01

    Motivation: The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. Examples include transferring information from Arabidopsis thaliana into related crop species for food security purposes, or from mice into humans for medical applications. Here we develop two related Bayesian approaches to network inference that allow GRNs to be jointly inferred in, or leveraged between, several related species: in one framework, network information is directly propagated between species; in the second hierarchical approach, network information is propagated via an unobserved ‘hypernetwork’. In both frameworks, information about network similarity is captured via graph kernels, with the networks additionally informed by species-specific time series gene expression data, when available, using Gaussian processes to model the dynamics of gene expression. Results: Results on in silico benchmarks demonstrate that joint inference, and leveraging of known networks between species, offers better accuracy than standalone inference. The direct propagation of network information via the non-hierarchical framework is more appropriate when there are relatively few species, while the hierarchical approach is better suited when there are many species. Both methods are robust to small amounts of mislabelling of orthologues. Finally, the use of Saccharomyces cerevisiae data and networks to inform inference of networks in the budding yeast Schizosaccharomyces pombe predicts a novel role in cell cycle regulation for Gas1 (SPAC19B12.02c), a 1,3-beta-glucanosyltransferase. Availability and implementation: MATLAB code is available from http://go.warwick.ac.uk/systemsbiology/software/. Contact: d.l.wild@warwick.ac.uk Supplementary information: Supplementary data are available at Bioinformatics

  12. Intrafocal heterogeneity of ERG protein expression and gene fusion pattern in prostate cancer.

    PubMed

    Suh, Ja Hee; Park, Jeong Hwan; Lee, Cheol; Moon, Kyung Chul

    2017-10-01

    Prostate cancer is considered to be highly heterogeneous, with various morphologic features and biologic behaviors. The TMPRSS2-ERG gene fusion is the most frequently observed genetic aberration in prostate cancer. The aim of this study was to elucidate the intrafocal heterogeneity of ERG gene fusion status. ERG immunohistochemistry (IHC) was performed in samples from 168 prostate cancer patients who had undergone radical prostatectomy, and 40 cases showing ERG-positive IHC staining were selected for tissue microarray (TMA) construction. Two to six representative cores were selected from each tumor focus. In the cases with heterogeneous ERG IHC staining intensity, the areas showing different intensities were separately selected. Using the TMA blocks, IHC and fluorescence in situ hybridization (FISH) were conducted to evaluate the heterogeneity of ERG protein expression and ERG fusion gene patterns, respectively, in a single tumor focus. Heterogeneity of ERG IHC staining was defined as the simultaneous presence of negative and positive cores in the same tumor focus. Heterogeneity of ERG FISH was defined by the presence of cores with positive and negative FISH signals or cores with break-apart and interstitial deletion FISH signals in the same tumor focus. A total of 202 TMA cores were isolated from 40 ERG-positive cases. Of the 202 total cores, 19 were negative for ERG IHC staining, and 46 showed 1+, 52 showed 2+, and 85 showed 3+ ERG staining intensity. Eleven cores were negative for ERG FISH signal, 119 cores showed ERG break-apart FISH signals, and the remaining 72 cores revealed interstitial deletion. Intrafocal heterogeneity of ERG IHC staining was found in 20% (8/40) of cases, and intrafocal heterogeneity of ERG gene fusion pattern was found in 32.5% (13/40) of cases. In summary, this study showed significantly frequent intrafocal heterogeneity of ERG protein expression, gene fusion status and fusion pattern. This heterogeneity can be caused by the development

  13. Improved Controls for Fusion RF Systems. Final technical report

    SciTech Connect

    Casey, Jeffrey A.

    2011-11-08

    We have addressed the specific requirements for the integrated systems controlling an array of klystrons used for Lower Hybrid Current Drive (LHCD). The immediate goal for our design was to modernize the transmitter protection system (TPS) for LHCD on the Alcator C-Mod tokamak at the MIT Plasma Science and Fusion Center (MIT-PSFC). Working with the Alcator C-Mod team, we have upgraded the design of these controls to retrofit for improvements in performance and safety, as well as to facilitate the upcoming expansion from 12 to 16 klystrons. The longer range goals to generalize the designs in such a way that they will be of benefit to other programs within the international fusion effort was met by designing a system which was flexible enough to address all the MIT system requirements, and modular enough to adapt to a large variety of other requirements with minimal reconfiguration.

  14. The role of FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1, in Ewing sarcoma.

    PubMed

    Elzi, David J; Song, Meihua; Houghton, Peter J; Chen, Yidong; Shiio, Yuzuru

    2015-11-01

    Ewing sarcoma is a cancer of bone and soft tissue in children that is characterized by a chromosomal translocation involving EWS and an Ets family transcription factor, most commonly FLI-1. The EWS-FLI-1 fusion oncogene is widely believed to play a central role in Ewing sarcoma. The EWS-FLI-1 gene product regulates the expression of a number of genes important for cancer progression, can transform mouse cells such as NIH3T3 and C3H10T1/2, and is necessary for proliferation and tumorigenicity of Ewing sarcoma cells, suggesting that EWS-FLI-1 is the causative oncogene. However, a variety of evidence also suggest that EWS-FLI-1 alone cannot fully explain the Ewing sarcomagenesis. Here we report that FLI-1-EWS, a fusion gene reciprocal to EWS-FLI-1, is frequently expressed in Ewing sarcoma. We present evidence suggesting that endogenous FLI-1-EWS is required for Ewing sarcoma growth and that FLI-1-EWS cooperates with EWS-FLI-1 in human mesenchymal stem cells, putative cells of origin of Ewing sarcoma, through abrogation of the proliferation arrest induced by EWS- FLI-1.

  15. C2-C3 Anterior Cervical Fusion: Technical Report.

    PubMed

    Finn, Michael A; MacDonald, Joel D

    2016-12-01

    Retrospective review of patients at a university hospital. To describe the anterior approach for cervical discectomy and fusion (ACDF) at C2-C3 level and evaluate its suitability for treatment of instability and degenerative disease in this region. The anterior approach is commonly used for ACDF in the lower cervical spine but is used less often in the high cervical spine. We retrospectively reviewed a database of consecutive cervical spine surgeries performed at our institution to identify patients who underwent ACDF at the C2-C3 level during a 10-year period. Demographic data, clinical indications, surgical technique, complications, and immediate results were evaluated. Of the 11 patients (7 female, 4 male; mean age 46 y) identified, 7 were treated for traumatic fractures and 4 for degenerative disk disease. Three patients treated for myelopathy showed improvement in mean Nurick grade from 3.6 to 1.3. Pain was significantly improved in all patients who had preoperative pain. Solid bony fusion was achieved in 5 of 7 patients at 3-month follow-up. Complications included dysphagia in 4 patients (which resolved in 3), aspiration pneumonia, mild persistent dysphonia, and construct failure at C2 requiring posterior fusion. One patient died of a pulmonary embolism 2 weeks postoperatively. ACDF at the C2-C3 level is an option for the treatment of high cervical disease or trauma but is associated with a higher rate of approach-related morbidity. Familiarity with local anatomy may help to reduce complications. ACDF at C2-C3 appears to have a fusion rate similar to ACDF performed at other levels.

  16. Determination of fusion cycles for polystyrene bead foam. Final report

    SciTech Connect

    Fossey, D.J.

    1982-06-01

    The fusion cycles required to encapsulate two electronic packages with 0.3 g/cm/sup 3/ polystyrene bead foam (PSBF) were developed. The encapsulation process for one unit included the uniform dispersion of desiccant beads in the PSBF. An epoxy coating was required to maintain the integrity of the PSBF surfaces in the cavity formed for a block of molded desiccant. A method to obtain adhesion of the PSBF to an aluminum substrate was developed.

  17. ETS Gene Fusions as Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer

    DTIC Science & Technology

    2015-10-01

    Award Number: W81XWH-10-1-0582 TITLE: ETS Gene Fusions as Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer PRINCIPAL...Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer 5b. GRANT NUMBER W81XWH-10-1-0582 5c. PROGRAM ELEMENT NUMBER 6... therapy , which represents a primary treatment modality for localized prostate cancer. In the fifth year of this grant period, we have accomplished

  18. Deciphering the Role of microRNAs in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma.

    PubMed

    Pathak, Ekta; Bhavya; Mishra, Divya; Atri, Neelam; Mishra, Rajeev

    2017-01-01

    NUT midline carcinoma (NMC) is a very aggressive and lethal type of squamous epithelial cell cancer caused due to fusion of BRD4 and NUT genes. The gene fusion results into a new fusion protein that promotes oncogenesis. The detailed molecular mechanisms underlying the NMC are still not clear and new findings are urgently required to complement the current efforts. Abnormal microRNAs (miRNA) expression promotes tumour formation by modulating the functional expression of critical genes other than the parent genes involved in tumour cell proliferation or survival. Here, using Insilco methods, miRNA targeting the transcripts of parent genes (BRD4 and NUT) and the BRD4-NUT fusion gene were predicted. We investigated a situation, wherein abnormal miRNA expression in malignant cells could arise due to deletion and fusion of genomic regions encompassing the target site of miRNA genes. A set of 48 dysregulated miRNAs targeting the critical genes other than the parent genes (BRD4 and NUT) was identified. Functional enrichment analysis of KEGG pathways of target genes of these Ex-miRNAs implicates their role in cancer pathways. Amplification in the expression level of these miRNAs can be used for NMC diagnosis and prognosis.

  19. SUPPRESSOR OF FRIGIDA (SUF4) Supports Gamete Fusion via Regulating Arabidopsis EC1 Gene Expression.

    PubMed

    Resentini, Francesca; Cyprys, Philipp; Steffen, Joshua G; Alter, Svenja; Morandini, Piero; Mizzotti, Chiara; Lloyd, Alan; Drews, Gary N; Dresselhaus, Thomas; Colombo, Lucia; Sprunck, Stefanie; Masiero, Simona

    2017-01-01

    The EGG CELL1 (EC1) gene family of Arabidopsis (Arabidopsis thaliana) comprises five members that are specifically expressed in the egg cell and redundantly control gamete fusion during double fertilization. We investigated the activity of all five EC1 promoters in promoter-deletion studies and identified SUF4 (SUPPRESSOR OF FRIGIDA4), a C2H2 transcription factor, as a direct regulator of the EC1 gene expression. In particular, we demonstrated that SUF4 binds to all five Arabidopsis EC1 promoters, thus regulating their expression. The down-regulation of SUF4 in homozygous suf4-1 ovules results in reduced EC1 expression and delayed sperm fusion, which can be rescued by expressing SUF4-β-glucuronidase under the control of the SUF4 promoter. To identify more gene products able to regulate EC1 expression together with SUF4, we performed coexpression studies that led to the identification of MOM1 (MORPHEUS' MOLECULE1), a component of a silencing mechanism that is independent of DNA methylation marks. In mom1-3 ovules, both SUF4 and EC1 genes are down-regulated, and EC1 genes show higher levels of histone 3 lysine-9 acetylation, suggesting that MOM1 contributes to the regulation of SUF4 and EC1 gene expression.

  20. Fusion Plasma Theory: Task 1, Magnetic confinement Fusion Plasma Theory. Annual progress report, November 16, 1992--November 15, 1993

    SciTech Connect

    Callen, J.D.

    1993-10-01

    The research performed under this grant during the current year has concentrated on few tokamak plasma confinement issues: applications of our new Chapman-Enskog-like approach for developing hybrid fluid/kinetic descriptions of tokamak plasmas; multi-faceted studies as part of our development of a new interacting island paradigm for the tokamak equilibrium`` and transport; investigations of the resolution power of BES and ECE diagnostics for measuring core plasma fluctuations; and studies of net transport in the presence of fluctuating surfaces. Recent progress and publications in these areas, and in the management of the NERSC node and the fusion theory workstations are summarized briefly in this report.

  1. A malignant inflammatory myofibroblastic tumor of the hypopharynx harboring the 3a/b variants of the EML4-ALK fusion gene

    PubMed Central

    Muscarella, Lucia Anna; Rossi, Giulio; Trombetta, Domenico; La Torre, Annamaria; Di Candia, Leonarda; Mengoli, Maria Cecilia; Sparaneo, Angelo; Fazio, Vito Michele; Graziano, Paolo

    2017-01-01

    Inflammatory myofibroblastic tumors (IMT) in the head and neck region are rare neoplasms that generally mimic benign/low-grade neoplasms. Overexpression of anaplastic lymphoma kinase (ALK) has been reported in 50% of IMT cases, secondary to ALK activation by structural rearrangements in the ALK gene, which results in a fusion protein with echinoderm microtubule associated protein like 4 (EML4) in ~20% of cases. The present study describes a case of a 74-year-old woman with a malignant IMT in the right posterior hypopharynx harboring a previously unreported chromosomal rearrangement resulting in EML4 and ALK gene fusion. Strong ALK immunoreactivity was observed in neoplastic cells, while fluorescent in situ hybridization combined with fluorescent fragment analysis and direct sequencing identified the first case of the 3a/b variants of the EML4-ALK fusion gene in IMT. The results of the current study highlight the uncommon occurrence of ALK-positive IMT in the head/neck region and demonstrate the importance of integrating different molecular methodologies to identify unequivocal gene fusion characterization. PMID:28356934

  2. Inertial Confinement Fusion quarterly report, January--March 1995. Volume 5, No. 2

    SciTech Connect

    1995-09-01

    The ICF quarterly report is published by the Inertial Confinement Fusion Program at the Lawrence Livermore National Laboratory. Topics included this quarter include: the role of the National Ignition Facility in the development of Inertial Confinement Fusion, laser-plasma interactions in large gas-filled hohlraums, evolution of solid-state induction modulators for a heavy-ion recirculator, the National Ignition Facility project, and terminal-level relaxation in Nd-doped laser material.

  3. CONFERENCE REPORT: 11th EU-US Transport Task Force workshop on transport in fusion plasmas

    NASA Astrophysics Data System (ADS)

    Connor, J. W.; Angioni, C.; Diamond, P. H.; Hammett, G. W.; Hidalgo, C.; Loarte, A.; Mantica, P.

    2007-04-01

    This report summarizes the contributions presented at the 11th EU-US Transport Task Force workshop on transport in fusion plasmas, held in Marseilles, France, 4-7 September, 20068The present workshop: http://www-fusion-magnetique.cea.fr/ttf2006.. There were sessions on momentum transport, multi-scale physics, electron transport, particle transport and transport in the scrape-off layer.

  4. Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.

    PubMed

    Kim, Pora; Jia, Peilin; Zhao, Zhongming

    2016-12-24

    Assessing the impact of kinase in gene fusion is essential for both identifying driver fusion genes (FGs) and developing molecular targeted therapies. Kinase domain retention is a crucial factor in kinase fusion genes (KFGs), but such a systematic investigation has not been done yet. To this end, we analyzed kinase domain retention (KDR) status in chimeric protein sequences of 914 KFGs covering 312 kinases across 13 major cancer types. Based on 171 kinase domain-retained KFGs including 101 kinases, we studied their recurrence, kinase groups, fusion partners, exon-based expression depth, short DNA motifs around the break points and networks. Our results, such as more KDR than 5'-kinase fusion genes, combinatorial effects between 3'-KDR kinases and their 5'-partners and a signal transduction-specific DNA sequence motif in the break point intronic sequences, supported positive selection on 3'-kinase fusion genes in cancer. We introduced a degree-of-frequency (DoF) score to measure the possible number of KFGs of a kinase. Interestingly, kinases with high DoF scores tended to undergo strong gene expression alteration at the break points. Furthermore, our KDR gene fusion network analysis revealed six of the seven kinases with the highest DoF scores (ALK, BRAF, MET, NTRK1, NTRK3 and RET) were all observed in thyroid carcinoma. Finally, we summarized common features of 'effective' (highly recurrent) kinases in gene fusions such as expression alteration at break point, redundant usage in multiple cancer types and 3'-location tendency. Collectively, our findings are useful for prioritizing driver kinases and FGs and provided insights into KFGs' clinical implications. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. [Construction of the plant expression vector with hepatitis a capsid protein fusion gene and genetic transformation of Citrus. Sinensis Osbeck].

    PubMed

    Hu, Rong; Wei, Hong; Chen, Shan-Chun; He, Yong-Rui

    2004-07-01

    The use of edible plants for the production and delivery of vaccine proteins could provide an economical alternative to fermentation systems. The construction of the plant expression vector pBI121-A was reported, which contained a fusion gene encoding hepatitis A capsid proteins. The gene was located between the left and right Ti border sequences under the control of CaMV35S promoter. The vector was identified via PCR and restriction enzyme analysis and was introduced into Agrobacterium tumerifacience LBA4404. The transgenic Citrus plants were produced by Agrobacterium-mediated transformation of epicotyl segments.13 putatively transformed plants through the kanamycin selection were micrografted onto the seedlings. The presence and integration of the transgene had been verified by PCR analysis. The result showed that five transformants were integrated and the transformation efficiency was 4.1%.

  6. The rationale of vectored gene-fusion vaccines against cancer: evolving strategies and latest evidence

    PubMed Central

    Ragonnaud, Emeline

    2013-01-01

    The development of vaccines that target tumor antigens in cancer has proven difficult. A major reason for this is that T cells specific for tumor self-antigens and neoantigens are eliminated or inactivated through mechanisms of tolerance. Antigen fusion strategies which increase the ability of vaccines to stimulate T cells that have escaped tolerance mechanisms, may have a particular potential as immunotherapies. This review highlights antigen fusion strategies that have been successful in stimulating the induction of T-cell immunity against cancer and counteracting tumor-associated tolerance. In preclinical studies, these strategies have shown to improve the potency of vectored vaccines through fusion of tumor antigen to proteins or protein domains that increase CD4+ T-cell help, CD8+ T-cell responses or both the CD4+ and CD8+ T-cell responses. However, in clinical trials such strategies seem to be less efficient when provided as a DNA vaccine. The first clinical trial using a viral vectored fusion-gene vaccine is expected to be tested as a partner in a heterologous prime-boost regimen directed against cervical cancer. PMID:24757514

  7. [Analysis of DEK-CAN fusion gene expression in acute myeloid leukemia patients with 6; 9 chromosome translocation].

    PubMed

    Wang, Ya-Lun; Wang, Tong; Xu, Feng; Gang, Yan; Wang, Jie

    2006-04-01

    This study was aimed to explore the relationship of 6; 9 chromosome translocation with DEK-CAN fusion gene expression in patients with acute myeloid leukemia (AML) and its clinical significance. Chromosome specimens were prepared by routine method after short-term culture of bone marrow cells; karyotype analysis was performed by R banding technique; the expression of fusion gene DEK-CAN was analyzed by RT-nested-PCR in mononuclear cells of bone marrow or peripheral blood of 4 AML patients, for 3 patients received allo-BMT out of 4 patients the dynamic follow-up was performed. The results indicated that t (6; 9) (p23; q34) was confirmed by chromosome karyotype analysis in the four AML patients. The DEK-CAN fusion gene was found during in all four de novo, relapsed and CR patients (100%). And the expression of DEK-CAN fusion gene enhanced apparently in de novo and relapsed patients, and weakened in CR patient. DEK-CAN mRNA was found in the three patients during 1-24 months after allo-BMT. Clinical data showed 2 patients relapsed and died after CR for 1-24 months; the other two patients received allo-BMT got CR and still survive. It is concluded that DEK-CAN fusion gene is the molecular basis in pathogenesis of AML. The detection of DEK-CAN fusion gene is significant for diagnosis of AML, evaluation of curative effect, and predication of prognosis.

  8. Mitochondrial genome dynamics in plants and animals: convergent gene fusions of a MutS homologue.

    PubMed

    Abdelnoor, Ricardo V; Christensen, Alan C; Mohammed, Saleem; Munoz-Castillo, Bryan; Moriyama, Hideaki; Mackenzie, Sally A

    2006-08-01

    Mitochondrial processes influence a broad spectrum of physiological and developmental events in higher eukaryotes, and their aberrant function can lead to several familiar disease phenotypes in mammals. In plants, mitochondrial genes directly influence pollen development and the occurrence of male sterility in natural plant populations. Likewise, in animal systems evidence accumulates to suggest important mitochondrial functions in spermatogenesis and reproduction. Here we present evidence for a convergent gene fusion involving a MutS-homologous gene functioning within the mitochondrion and designated Msh1. In only plants and soft corals, the MutS homologue has fused with a homing endonuclease sequence at the carboxy terminus of the protein. However, the endonuclease domains in the plants and the soft corals are members of different groups. In plants, Msh1 can influence mitochondrial genome organization and male sterility expression. Based on parallels in Msh1 gene structure shared by plants and corals, and their similarities in reproductive behavior, we postulate that this convergent gene fusion might have occurred in response to coincident adaptive pressures on reproduction.

  9. Report of the Integrated Program Planning Activity for the DOE Fusion Energy Sciences Program

    SciTech Connect

    2000-12-01

    This report of the Integrated Program Planning Activity (IPPA) has been prepared in response to a recommendation by the Secretary of Energy Advisory Board that, ''Given the complex nature of the fusion effort, an integrated program planning process is an absolute necessity.'' We, therefore, undertook this activity in order to integrate the various elements of the program, to improve communication and performance accountability across the program, and to show the inter-connectedness and inter-dependency of the diverse parts of the national fusion energy sciences program. This report is based on the September 1999 Fusion Energy Sciences Advisory Committee's (FESAC) report ''Priorities and Balance within the Fusion Energy Sciences Program''. In its December 5,2000, letter to the Director of the Office of Science, the FESAC has reaffirmed the validity of the September 1999 report and stated that the IPPA presents a framework and process to guide the achievement of the 5-year goals listed in the 1999 report. The National Research Council's (NRC) Fusion Assessment Committee draft final report ''An Assessment of the Department of Energy's Office of Fusion Energy Sciences Program'', reviewing the quality of the science in the program, was made available after the IPPA report had been completed. The IPPA report is, nevertheless, consistent with the recommendations in the NRC report. In addition to program goals and the related 5-year, 10-year, and 15-year objectives, this report elaborates on the scientific issues associated with each of these objectives. The report also makes clear the relationships among the various program elements, and cites these relationships as the reason why integrated program planning is essential. In particular, while focusing on the science conducted by the program, the report addresses the important balances between the science and energy goals of the program, between the MFE and IFE approaches, and between the domestic and international aspects

  10. An ice nucleation reporter gene system: identification of inducible pathogenicity genes in Pseudomonas syringae pv. phaseolicola.

    PubMed Central

    Lindgren, P B; Frederick, R; Govindarajan, A G; Panopoulos, N J; Staskawicz, B J; Lindow, S E

    1989-01-01

    We have constructed derivatives of the transposon Tn3 that allow an ice nucleation gene (inaZ) to be used as 'reporter' of the transcriptional activity of genes into which it is inserted. In these derivatives (Tn3-Ice and Tn3-Spice), the lacZYA sequences of transposon Tn3-HoHo1 were replaced with inaZ lacking its native promoter. The ice nucleation activity of virB::inaZ fusions in the correct transcriptional orientation was inducible by acetosyringone, a plant metabolite which activates the vir operon of Agrobacterium tumefaciens Ti plasmids, while fusions in the opposite orientation were unresponsive to the inducer. Tn3-Spice was also used to investigate the expression of a cluster of genes (hrp) which control pathogenicity and hypersensitivity elicited by Pseudomonas syringae pv. phaseolicola. An inducible region was identified which is expressed at low levels in vitro but becomes activated when the bacteria come into contact with the susceptible host, bean. Activation of this region occurred within 2 h post-inoculation and was nearly complete by the time the bacteria began to multiply in the leaf tissue. The inaZ reporter appears to be at least 10(5)-fold more sensitive than lacZ in P.s.phaseolicola. Thus, the inaZ fusion system provides a sensitive, convenient and inexpensive tool for the study of bacterial gene expression, particularly during plant pathogenesis, and should be generally useful as a reporter gene system in Gram-negative bacteria. PMID:2548841

  11. Innovative approaches to inertial confinement fusion reactors: Final report

    SciTech Connect

    Bourque, R.F.; Schultz, K.R.

    1986-11-01

    Three areas of innovative approaches to inertial confinement fusion (ICF) reactor design are given. First, issues pertaining to the Cascade reactor concept are discussed. Then, several innovative concepts are presented which attempt to directly recover the blast energy from a fusion target. Finally, the Turbostar concept for direct recovery of that energy is evaluated. The Cascade issues discussed are combustion of the carbon granules in the event of air ingress, the use of alternate granule materials, and the effect of changes in carbon flow on details of the heat exchanger. Carbon combustion turns out to be a minor problem. Four ICF innovative concepts were considered: a turbine with ablating surfaces, a liquid piston system, a wave generator, and a resonating pump. In the final analysis, none show any real promise. The Turbostar concept of direct recovery is a very interesting idea and appeared technically viable. However, it shows no efficiency gain or any decrease in capital cost compared to reactors with conventional thermal conversion systems. Attempts to improve it by placing a close-in lithium sphere around the target to increase gas generation increased efficiency only slightly. It is concluded that these direct conversion techniques require thermalization of the x-ray and debris energy, and are Carnot limited. They therefore offer no advantage over existing and proposed methods of thermal energy conversion or direct electrical conversion.

  12. Z-inertial fusion energy: power plant final report FY 2006.

    SciTech Connect

    Anderson, Mark; Kulcinski, Gerald; Zhao, Haihua; Cipiti, Benjamin B.; Olson, Craig Lee; Sierra, Dannelle P.; Meier, Wayne; McConnell, Paul E.; Ghiaasiaan, M. (Georgia Institute of Technology, Atlanta, GA); Kern, Brian (Georgia Institute of Technology, Atlanta, GA); Tajima, Yu (University of California, Los Angeles, CA); Campen, Chistopher (University of California, Berkeley, CA); Sketchley, Tomas (University of California, Los Angeles, CA); Moir, R (Lawrence Livermore National Laboratories); Bardet, Philippe M. (University of California, Berkeley, CA); Durbin, Samuel; Morrow, Charles W.; Vigil, Virginia L (University of Wisconsin, Madison, WI); Modesto-Beato, Marcos A.; Franklin, James Kenneth; Smith, James Dean; Ying, Alice; Cook, Jason T.; Schmitz, Lothar (University of California, Los Angeles, CA); Abdel-Khalik, S. (Georgia Institute of Technology, Atlanta, GA); Farnum, Cathy Ottinger; Abdou, Mohamed A.; Bonazza, Riccardo; Rodriguez, Salvador B.; Sridharan, Kumar (University of Wisconsin, Madison, WI); Rochau, Gary Eugene; Gudmundson, Jesse; Peterson, Per F.; Marriott, Ed; Oakley, Jason

    2006-10-01

    This report summarizes the work conducted for the Z-inertial fusion energy (Z-IFE) late start Laboratory Directed Research Project. A major area of focus was on creating a roadmap to a z-pinch driven fusion power plant. The roadmap ties ZIFE into the Global Nuclear Energy Partnership (GNEP) initiative through the use of high energy fusion neutrons to burn the actinides of spent fuel waste. Transmutation presents a near term use for Z-IFE technology and will aid in paving the path to fusion energy. The work this year continued to develop the science and engineering needed to support the Z-IFE roadmap. This included plant system and driver cost estimates, recyclable transmission line studies, flibe characterization, reaction chamber design, and shock mitigation techniques.

  13. Fusion Materials Semiannual Progress Report for the Period Ending June 30, 1999

    SciTech Connect

    Rowcliffe, A.F.

    1999-09-01

    This is the twenty-sixth in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and its reported separately.

  14. Fusion Materials Semiannual Progress Report for Period Ending December 31, 1998

    SciTech Connect

    Rowcliff, A.F.; Burn, G.

    1999-04-01

    This is the twenty-fifth in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the U.S. Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately.

  15. Fusion reactor materials: Semiannual progress report for the period ending March 31, 1987

    SciTech Connect

    none,

    1987-09-01

    This is the second in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities in the following areas: (1) Alloy Development for Irradiation Performance; (2) Damage Analysis and Fundamental Studies; and (3) Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. Separate analytics were prepared for the reports in this volume.

  16. Membrane fusion inducers, chloroquine and spermidine increase lipoplex-mediated gene transfection

    SciTech Connect

    Wong-Baeza, Carlos; Bustos, Israel; Serna, Manuel; Tescucano, Alonso; Alcantara-Farfan, Veronica; Ibanez, Miguel; Montanez, Cecilia; Wong, Carlos; Baeza, Isabel

    2010-05-28

    Gene transfection into mammalian cells can be achieved with viral and non-viral vectors. Non-viral vectors, such as cationic lipids that form lipoplexes with DNA, are safer and more stable than viral vectors, but their transfection efficiencies are lower. Here we describe that the simultaneous treatment with a membrane fusion inducer (chlorpromazine or procainamide) plus the lysosomotropic agent chloroquine increases lipoplex-mediated gene transfection in human (HEK293 and C-33 A) and rat (PC12) cell lines (up to 9.2-fold), as well as in situ in BALB/c mice spleens and livers (up to 6-fold); and that the polyamine spermidine increases lipoplex-mediated gene transfection and expression in cell cultures. The use of these four drugs provides a novel, safe and relatively inexpensive way to considerably increase lipoplex-mediated gene transfection efficiency.

  17. Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event

    PubMed Central

    Yang, Zefeng; Liu, Li; Fang, Huimin; Li, Pengcheng; Xu, Shuhui; Cao, Wei; Xu, Chenwu; Huang, Jinling; Zhou, Yong

    2016-01-01

    The Tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a direct inhibitor of ToMV RNA replication to protect tomato from infection. The plant Tm-1-like (Tm-1L) protein is predicted to contain an uncharacterized N-terminal UPF0261 domain and a C-terminal TIM-barrel signal transduction (TBST) domain. Homologous searches revealed that proteins containing both of these two domains are mainly present in charophyte green algae and land plants but absent from glaucophytes, red algae and chlorophyte green algae. Although Tm-1 homologs are widely present in bacteria, archaea and fungi, UPF0261- and TBST-domain-containing proteins are generally encoded by different genes in these linages. A co-evolution analysis also suggested a putative interaction between UPF0261- and TBST-domain-containing proteins. Phylogenetic analyses based on homologs of these two domains revealed that plants have acquired UPF0261- and TBST-domain-encoding genes through two independent horizontal gene transfer (HGT) events before the origin of land plants from charophytes. Subsequently, gene fusion occurred between these two horizontally acquired genes and resulted in the origin of the Tm-1L gene in streptophytes. Our results demonstrate a novel evolutionary mechanism through which the recipient organism may acquire genes with functional interaction through two different HGT events and further fuse them into one functional gene. PMID:27647002

  18. Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH

    PubMed Central

    Chen, Sonja; Deniz, Kemal; Sung, Yun-Shao; Zhang, Lei; Dry, Sarah; Antonescu, Cristina R.

    2016-01-01

    The genetics of Ewing sarcoma (ES) are characterized by a canonical fusion involving EWSR1 gene and a member of the ETS family of transcription factors, such as FLI1 and ERG. In fact, ERG gene rearrangements represent the second most common molecular alteration, with EWSR1-ERG being identified in 5–10% of cases, while only a handful of reports document a FUS-ERG fusion. In this study, we focus on ES with ERG gene abnormalities, specifically to investigate the prevalence and clinicopathologic features of FUS-ERG fusions in a large cohort of small blue round cell tumors (SBRCTs) and compare to the eight reported FUS-positive ES. Among the 85 SBRCTs tested, seven (8.2%) cases harbored FUS gene rearrangements; six fused to ERG and one with FEV. During this investigation we came across a number of ERG-rearranged ES lacking both EWSR1 and FUS abnormalities by FISH. In one case, RNA sequencing identified an EWSR1-ERG transcript despite the negative EWSR1 rearrangements by FISH. Additional 3-color FISH fusion assay demonstrated the fusion of EWSR1 and ERG signals in all four cases negative for break-apart EWSR1 FISH. These results emphasize a potential pitfall of relying on EWSR1 FISH assay alone for diagnosis of ES. In cases with classic morphology and/or strong CD99 and ERG immunoreactivity, additional molecular testing should be applied, such as ERG FISH or RT-PCR/next generation sequencing, for a more definitive diagnosis. Although our study group is small, there were no differences noted between the clinical, morphologic features and immunoprofile of the different subsets of ERG-rearranged SBRCTs. PMID:26690869

  19. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

    PubMed Central

    2011-01-01

    Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer

  20. Analysis of API2-MALT1 fusion, trisomies, and immunoglobulin VH genes in pulmonary mucosa-associated lymphoid tissue lymphoma.

    PubMed

    Xia, Hongjing; Nakayama, Takahisa; Sakuma, Hidenori; Yamada, Seiji; Sato, Fumihiko; Takino, Hisashi; Okabe, Mitsukuni; Fujiyoshi, Yukio; Hattori, Hideo; Inagaki, Hiroshi

    2011-09-01

    Pulmonary mucosa-associated lymphoid tissue lymphoma is unique in that chronic inflammation is rare and that API2-MALT1 fusion, resulting from t(11;18)(q21;q21), occurs frequently. In this study, we examined 20 cases for API2-MALT1 fusion using the multiplex reverse-transcription polymerase chain reaction and looked for trisomy 3, trisomy 18, and abnormalities of MALT1 and IGH genes using fluorescence in situ hybridization. In addition, we analyzed VH genes by subcloning of the monoclonal polymerase chain reaction products. Of 20 cases studied, we detected gene abnormalities in 16: API2-MALT1 fusion in 9, trisomy 3 in 5, trisomy 18 in 4, MALT1 abnormality in 13, and IGH abnormality in 1. MALT1 gene abnormalities were concordant with API2-MALT1 fusion or trisomy 18. One case showed API2-MALT1 fusion and trisomy 3. On detection of API2-MALT1 fusion and trisomies, we were able to divide our cases into 3 groups, API2-MALT1 positive, trisomy positive, and no detectable gene abnormality, suggesting that tumor development had processed along different genetic pathways. All 20 cases were analyzed for VH genes. Most of the VH genes selected by the lymphomas belonged to the VH3 family, but there was no restriction to any particular VH fragment. Of interest, VH genes were unmutated in 7 cases, suggesting that T-cell-independent extrafollicular B-cell maturation may be important in the development of this lymphoma. In addition, both mutated and unmutated tumor cases were found to carry the API2-MALT1 fusion and trisomy 3. This observation suggests that these gene abnormalities may occur in microenvironments found before or outside of follicular germinal centers.

  1. Anti-colorectal cancer effect of interleukin-2 and interferon-β fusion gene driven by carcinoembryonic antigen promoter

    PubMed Central

    Wang, Yan; Wang, Mengchun; Li, Yan

    2016-01-01

    This study was designed to investigate the antitumor effects of combined interleukin-2/interferon-β-based gene therapy in colorectal cancer. Transfection of the fusion gene expression plasmid induced significant apoptosis of Lovo cells. Additionally, the fusion gene exhibited strong inhibitory activity against tumor growth and apoptosis when being injected into the nude mice implanted with human colon cancer cells. Furthermore, the tail-vein injection showed a more notable effect than direct injection into tumor. These results suggest that the combined interleukin-2/interferon-β-based gene therapy with the carcinoembryonic antigen promoter might be an effective antitumor strategy. PMID:27313471

  2. Ethanol utilization regulatory protein: profile alignments give no evidence of origin through aldehyde and alcohol dehydrogenase gene fusion.

    PubMed Central

    Nicholas, H. B.; Persson, B.; Jörnvall, H.; Hempel, J.

    1995-01-01

    The suggestion that the ethanol regulatory protein from Aspergillus has its evolutionary origin in a gene fusion between aldehyde and alcohol dehydrogenase genes (Hawkins AR, Lamb HK, Radford A, Moore JD, 1994, Gene 146:145-158) has been tested by profile analysis with aldehyde and alcohol dehydrogenase family profiles. We show that the degree and kind of similarity observed between these profiles and the ethanol regulatory protein sequence is that expected from random sequences of the same composition. This level of similarity fails to support the suggested gene fusion. PMID:8580855

  3. Report on the 9th European Fusion Physics Workshop* Report on the 9th European Fusion Physics Workshop

    NASA Astrophysics Data System (ADS)

    Campbell, D. J.; Barabaschi, P.; Bécoulet, M.; Federici, G.; Hellsten, T.; Loarte, A.; Pautasso, G.; Wilson, H.

    2003-04-01

    The 9th EFPW took place in December 2001 at Saariselka in Finland, hosted by the Technical Research Centre of Finland (VTT) and the Helsinki University, and sponsored by the European Commission. Within an overall theme of `transient events, their mitigation and their implications for plasma facing components in ITER', four topics of importance to the future development of magnetically confined fusion were discussed in detail. In addition, the key issues for the ITER design which are associated with transient events and a review of the JET scientific and technical programme under EFDA were presented. The main issues discussed and the areas identified as requiring further study are summarized here.

  4. Fusion of a fork head domain gene to PAX3 in the solid tumour alveolar rhabdomyosarcoma.

    PubMed

    Galili, N; Davis, R J; Fredericks, W J; Mukhopadhyay, S; Rauscher, F J; Emanuel, B S; Rovera, G; Barr, F G

    1993-11-01

    We have examined the structure and expression of the products associated with the t(2;13)(q35;q14) translocation associated with alveolar rhabdomyosarcoma. The chromosome 13 gene (FKHR) is identified as a member of the fork head domain family of transcription factors characterized by a conserved DNA binding motif. Polymerase chain reaction analysis demonstrates that a 5'PAX3-3' FKHR chimaeric transcript is expressed in all eight alveolar rhabdomyosarcomas investigated. Immunoprecipitation experiments detect the predicted fusion protein. These findings indicate that the t(2;13) generates a potentially tumorigenic fusion transcription factor consisting of intact PAX3 DNA binding domains, a truncated fork head DNA binding domain and C-terminal FKHR regions.

  5. MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome

    PubMed Central

    Wang, Qian-fei; Wu, George; Mi, Shuangli; He, Fuhong; Wu, Jun; Dong, Jingfang; Luo, Roger T.; Mattison, Ryan; Kaberlein, Joseph J.; Prabhakar, Shyam; Ji, Hongkai

    2011-01-01

    MLL encodes a histone methyltransferase that is critical in maintaining gene expression during embryonic development and hematopoiesis. 11q23 translocations result in the formation of chimeric MLL fusion proteins that act as potent drivers of acute leukemia. However, it remains unclear what portion of the leukemic genome is under the direct control of MLL fusions. By comparing patient-derived leukemic cell lines, we find that MLL fusion-bound genes are a small subset of that recognized by wild-type MLL. In an inducible MLL-ENL model, MLL fusion protein binding and changes in H3K79 methylation are limited to a specific portion of the genome, whereas wild-type MLL distributes to a much larger set of gene loci. Surprisingly, among 223 MLL-ENL–bound genes, only 12 demonstrate a significant increase in mRNA expression on induction of the fusion protein. In addition to Hoxa9 and Meis1, this includes Eya1 and Six1, which comprise a heterodimeric transcription factor important in several developmental pathways. We show that Eya1 has the capacity to immortalize hematopoietic progenitor cells in vitro and collaborates with Six1 in hematopoietic transformation assays. Altogether, our data suggest that MLL fusions contribute to the development of acute leukemia through direct activation of a small set of target genes. PMID:21518926

  6. Fusion materials semiannual progress report for period ending December 31, 1999

    SciTech Connect

    Burn, G.

    2000-03-01

    This is the twenty-seventh in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components.

  7. Protein interaction maps for complete genomes based on gene fusion events

    NASA Astrophysics Data System (ADS)

    Enright, Anton J.; Iliopoulos, Ioannis; Kyrpides, Nikos C.; Ouzounis, Christos A.

    1999-11-01

    A large-scale effort to measure, detect and analyse protein-protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.

  8. Fusion and retrotransposition events in the evolution of the sea anemone Anemonia viridis neurotoxin genes.

    PubMed

    Moran, Yehu; Weinberger, Hagar; Lazarus, Nimrod; Gur, Maya; Kahn, Roy; Gordon, Dalia; Gurevitz, Michael

    2009-08-01

    Sea anemones are sessile predators that use a variety of toxins to paralyze prey and foe. Among these toxins, Types I, II and III are short peptides that affect voltage-gated sodium channels. Anemonia viridis is the only sea anemone species that produces both Types I and III neurotoxin. Although the two toxin types are unrelated in sequence and three-dimensional structure, cloning and comparative analysis of their loci revealed a highly similar sequence at the 5' region, which encodes a signal peptide. This similarity was likely generated by gene fusion and could be advantageous in transcript stability and intracellular trafficking and secretion. In addition, these analyses identified the processed pseudogenes of the two gene families in the genome of A. viridis, probably resulting from retrotransposition events. As presence of processed pseudogenes in the genome requires transcription in germ-line cells, we analyzed oocyte-rich ovaries and found that indeed they contain Types I and III transcripts. This result raises questions regarding the role of toxin transcripts in these tissues. Overall, the retrotransposition and gene fusion events suggest that the genes of both Types I and III neurotoxins evolved in a similar fashion and share a partial common ancestry.

  9. TMPRSS2:ERG fusion gene occurs less frequently in Chinese patients with prostate cancer.

    PubMed

    Jiang, Hui; Mao, Xueying; Huang, Xiaoyi; Zhao, Jing; Wang, Lumei; Xu, Jingjing; Zhang, Hongwei; Lu, Yongjie; Yu, Yongwei

    2016-09-01

    Prostate cancer is the commonest male malignancy in the Western world, but its morbidity is much lower in China. The principal aim of this study was to evaluate the frequency of TMPRSS2:ERG fusion in Chinese prostate cancer patients using immunohistochemistry and reverse transcription polymerase chain (RT-PCR). In addition, we compared the ERG protein expression with TMPRSS2:ERG fusion gene. The relationship between ERG expression and clinicopathologic features was also examined. Samples from patients who underwent radical prostatectomies in Changhai Hospital (Shanghai, China) were collected and stored in ethically approved tissue banks. One hundred seventy-four prostate cancer tissue samples and 10 normal tissues were marked on standard hematoxylin-eosin (HE) sections, punched out of the paraffin blocks and inserted into a recipient block using tissue arrayer instruments. Immunohistochemistry and RT-PCR were employed to detect TMPRSS2:ERG fusion gene. ERG was highly expressed in the nuclei of endothelial cells of vessels and weak cytoplasmic staining was occasionally observed. ERG positive staining was present in 14.9 % (26/174) of the tumor samples in microarray. All benign prostate samples were found to be negative. RT-PCR results revealed that 11.1 % (15/135) were TMPRSS2:ERG fusion positive. Altogether, there was a good agreement of ERG immunostaining with the presence of TMPRSS2:ERG. However, no correlation was observed between ERG expression and age, Gleason score, stage, surgical margin, and seminal vesicle involvement in Chinese patients. In the present study, we identified a high correlation between ERG expression and ERG TMPRSS2:ERG, with 100 % sensitivity and 88.9 % specificity. The expression level of ERG was unrelated to the age, Gleason score, stage, surgical margin, and seminal vesicle involvement. Therefore, the association between ERG expression and prostate cancer based on Chinese population should be further investigated in the future.

  10. Xp11.2 translocation renal cell carcinoma with NONO-TFE3 gene fusion: morphology, prognosis, and potential pitfall in detecting TFE3 gene rearrangement.

    PubMed

    Xia, Qiu-Yuan; Wang, Zhe; Chen, Ni; Gan, Hua-Lei; Teng, Xiao-Dong; Shi, Shan-Shan; Wang, Xuan; Wei, Xue; Ye, Sheng-Bing; Li, Rui; Ma, Heng-Hui; Lu, Zhen-Feng; Zhou, Xiao-Jun; Rao, Qiu

    2017-03-01

    Xp11 translocation renal cell carcinomas are characterized by several different translocations involving the TFE3 gene. Tumors with different specific gene fusions may have different clinicopathological manifestations. Fewer than 10 renal cell carcinoma cases with NONO-TFE3 have been described. Here we examined eight additional cases of this rare tumor using clinicopathological, immunohistochemical, and molecular analyses. The male-to-female ratio of our study cohort was 1:1, and the median age was 30 years. The most distinctive feature of the tumors was that they exhibited glandular/tubular or papillary architecture that was lined with small-to-medium cuboidal to high columnar cells with indistinct cell borders and an abundantly clear or flocculent eosinophilic cytoplasm. The nuclei were oriented toward the luminal surface and were round and uniform in shape, which resulted in the appearance of secretory endometrioid subnuclear vacuolization. The distinct glandular/tubular or papillary architecture was often accompanied by sheets of epithelial cells that presented a biphasic pattern. Immunohistochemically, all eight cases demonstrated moderate (2+) or strong (3+) positive staining for TFE3, CD10, RCC marker, and PAX-8. None of the tumors were immunoreactive for CK7, Cathepsin K, Melan-A, HMB45, Ksp-cadherin, Vimentin, CA9, 34βE12 or CD117. NONO-TFE3 fusion transcripts were identified in six cases by RT-PCR. All eight cases showed equivocal split signals with a distance of nearly 2 signal diameters and sometimes had false-negative results. Furthermore, we developed a fluorescence in situ hybridization (FISH) assay to serve as an adjunct diagnostic tool for the detection of the NONO-TFE3 fusion gene and used this method to detect the fusion gene in all eight cases. Long-term follow-up (range, 10-102 months) was available for 7 patients. All 7 patients were alive with no evidence of recurrent disease or disease progression after their initial resection. This report

  11. Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A.

    PubMed

    Kimura, Hirokazu; Nagasawa, Koo; Tsukagoshi, Hiroyuki; Matsushima, Yuki; Fujita, Kiyotaka; Yoshida, Lay Myint; Tanaka, Ryota; Ishii, Haruyuki; Shimojo, Naoki; Kuroda, Makoto; Ryo, Akihide

    2016-09-01

    We studied the molecular evolution of the fusion protein (F) gene in the human respiratory syncytial virus subgroup A (HRSV-A). We performed time-scaled phylogenetic analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. We also conducted genetic distance (p-distance), positive/negative selection, and Bayesian skyline plot analyses. Furthermore, we mapped the amino acid substitutions of the protein. The MCMC-constructed tree indicated that the HRSV F gene diverged from the bovine RSV (BRSV) gene approximately 550years ago and had a relatively low substitution rate (7.59×10(-4) substitutions/site/year). Moreover, a common ancestor of HRSV-A and -B diverged approximately 280years ago, which has since formed four distinct clusters. The present HRSV-A strains were assigned six genotypes based on F gene sequences and attachment glycoprotein gene sequences. The present strains exhibited high F gene sequence similarity values and low genetic divergence. No positive selection sites were identified; however, 50 negative selection sites were identified. F protein amino acid substitutions at 17 sites were distributed in the F protein. The effective population size of the gene has remained relatively constant, but the population size of the prevalent genotype (GA2) has increased in the last 10years. These results suggest that the HRSV-AF gene has evolved independently and formed some genotypes. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Fusion materials semiannual progress report for the period ending March 31, 1995

    SciTech Connect

    1995-07-01

    This is the eighteenth in a series of semiannual technical progress reports on fusion materials. This report combines research and development activities which were previously reported separately in the following progress reports: {sm_bullet} Alloy Development for Irradiation Performance. {sm_bullet} Damage Analysis and Fundamental Studies. {sm_bullet} Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials programs being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide. This report has been compiled and edited under the guidance of A.F. Rowcliffe by Gabrielle Burn, Oak Ridge National Laboratory. Their efforts, and the efforts of the many persons who made technical contributions, are gratefully acknowledged.

  13. A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication

    PubMed Central

    Zhong, Yan; Cheng, Zong-Ming (Max)

    2016-01-01

    Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs. PMID:27678195

  14. Fusion in the Era of Burning Plasma Studies: Workforce Planning for 2004 to 2014. Final report to FESA C

    SciTech Connect

    none,

    2004-03-29

    This report has been prepared in response to Dr. R. Orbach’s request of the Fusion Energy Sciences Advisory Committee (FESAC) to “address the issue of workforce development in the U.S. fusion program.” The report addresses three key questions: what is the current status of the fusion science, technology, and engineering workforce; what is the workforce that will be needed and when it will be needed to ensure that the U.S. is an effective partner in ITER and to enable the U.S. to successfully carry out the fusion program; and, what can be done to ensure a qualified, diversified, and sufficiently large workforce and a pipeline to maintain that workforce? In addressing the charge, the Panel considers a workforce that allows for a vigorous national program of fusion energy research that includes participation in magnetic fusion (ITER) and inertial fusion (NIF) burning plasma experiments.

  15. Development of GFP fusions for examination of the effects of the space environment on gene expression in Escherichia coli

    NASA Astrophysics Data System (ADS)

    Mancinelli, R.; Fahlen, T.

    The goal of the In situ Space Gene Expression on Nano-satillites (ISGEN) program is to be ready to fly technology that can support a fully automated experiment to quantify changes in model organisms in situ in low earth orbit in a free flyer platform in less than two years. A straightforward gene expression assay that meets the ISGEN flight objective for testing flight hardware as well as return data regarding the effects of microgravity on gene expression has been developed. Escherichia coli K-12, a bacterium that exhibits changes in its growth pattern when flown in micro-gravity on the Space Shuttle, was used. The scientific objective of this work is to determine if there is a discernable change in metabolic and stress pathway gene expression due to growth in the space environment. To that end, we have linked the green fluorescent protein (GFP) reporter gfp to phoP, a gene that responds to extracellular Mg2+ levels, and pykF, a gene involved in the glycolytic pathway that responds to changes in intracellular pyruvate. These genes respond to the metabolic needs of the cell and may be altered in the micro-gravity environment. E. coli cells containing a plasmid encoding the phoP-gfp-mut3 reporter construct were grown with or without MgSO_4. The effect of the added MgSO_4 is the repression of the expression of GFP. This is the expected result if GFP expression were under the control of a magnesium-regulated promoter such as phoP. Consistent with the negative feedback loop, we observe repression of GFP production in cells containing our pykF-gfp plasmid construct, when grown in the presence of excess glucose. Thus, the pykF-gfp fusion functions as a glucose sensor.

  16. A Preliminary Report on the CO2 Laser for Lumbar Fusion: Safety, Efficacy and Technical Considerations.

    PubMed

    Villavicencio, Alan T; Burneikiene, Sigita; Babuska, Jason M; Nelson, Ewell L; Mason, Alexander; Rajpal, Sharad

    2015-04-01

    The purpose of this study was to evaluate potential technical advantages of the CO2 laser technology in mini-open transforaminal lumbar interbody fusion (TLIF) surgeries and report our preliminary clinical data on the safety and clinical outcomes. There is currently no literature discussing the recently redeveloped CO2 laser technology application for lumbar fusion. Safety and clinical outcomes were compared between two groups: 24 patients that underwent CO2 laser-assisted one-level TLIF surgeries and 30 patients that underwent standard one-level TLIF surgeries without the laser. There were no neural thermal injuries or other intraoperative laser-related complications encountered in this cohort of patients. At a mean follow-up of 17.4 months, significantly reduced lower back pain scores (P=0.013) were reported in the laser-assisted patient group compared to a standard fusion patient group. Lower extremity radicular pain intensity scores were similar in both groups. Laser-assisted TLIF surgeries showed a tendency (P = 0.07) of shorter operative times that was not statistically significant. Based on this preliminary clinical report, the safety of the CO2 laser device for lumbar fusion surgeries was assessed. There were no neural thermal injuries or other intraoperative laser-related complications encountered in this cohort of patients. Further investigation of CO2 laser-assisted lumbar fusion procedures is warranted in order to evaluate its effect on clinical outcomes.

  17. Fusion reactor materials semiannual progress report for the period ending March 31, 1993

    SciTech Connect

    Not Available

    1993-07-01

    This is the fourteenth in a series of semiannual technical progress reports on fusion reactor materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials programs being conducted in support of the Magnetic Fusion Energy Program of the US Depart of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. Separate abstracts were prepared for each individual section.

  18. Fusion materials semiannual progress report for the period ending June 30, 1998

    SciTech Connect

    Burn, G.

    1998-09-01

    This is the twenty-fourth in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the US Department of Energy. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.

  19. Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.

    PubMed

    Panagopoulos, Ioannis; Thorsen, Jim; Gorunova, Ludmila; Micci, Francesca; Heim, Sverre

    2014-08-01

    Cancer-specific fusion genes are often caused by cytogenetically visible chromosomal rearrangements such as translocations, inversions, deletions or insertions, they can be the targets of molecular therapy, they play a key role in the accurate diagnosis and classification of neoplasms, and they are of prognostic impact. The identification of novel fusion genes in various neoplasms therefore not only has obvious research importance, but is also potentially of major clinical significance. The "traditional" methodology to detect them began with cytogenetic analysis to find the chromosomal rearrangement, followed by utilization of fluorescence in situ hybridization techniques to find the probe which spans the chromosomal breakpoint, and finally molecular cloning to localize the breakpoint more precisely and identify the genes fused by the chromosomal rearrangement. Although laborious, the above-mentioned sequential approach is robust and reliable and a number of fusion genes have been cloned by such means. Next generation sequencing (NGS), mainly RNA sequencing (RNA-Seq), has opened up new possibilities to detect fusion genes even when cytogenetic aberrations are cryptic or information about them is unknown. However, NGS suffers from the shortcoming of identifying as "fusion genes" also many technical, biological and, perhaps in particular, clinical "false positives," thus making the assessment of which fusions are important and which are noise extremely difficult. The best way to overcome this risk of information overflow is, whenever reliable cytogenetic information is at hand, to compare karyotyping and sequencing data and concentrate exclusively on those suggested fusion genes that are found in chromosomal breakpoints. This article is part of a Directed Issue entitled: Rare Cancers. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Construction and characterization of Escherichia coli polA-lacZ gene fusions.

    PubMed Central

    Ward, D F; Murray, N E

    1980-01-01

    The promoter of the polA gene of Escherichia coli K-12 was fused to the lacZ gene by selecting deletions within a lambda lacZ polA transducing phage. Four fusions, deleting varying amounts of the polA gene, were characterized. The polA promoter was found to be approximately 3% as active as the fully induced lac promoter. This figure is compatible with the normal intracellular level of deoxyribonucleic acid polymerase I. No evidence was found for outogenous regulation of transcription from the polA promoter. Expression from this promoter was influenced by neither recA nor mitomycin C, but uvrD and uvrE mutations reduced expression slightly. Images PMID:6445899

  1. Fusion reactor materials semiannual progress report for period ending September 30, 1990

    SciTech Connect

    Not Available

    1991-04-01

    This is the ninth in series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following technical progress reports: Alloy Development of Irradiation Performance; Damage Analysis and Fundamental Studies; and Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide.

  2. Fusion reactor materials semiannual progress report for the period ending September 30, 1989

    SciTech Connect

    none,

    1989-01-01

    This is the seventh in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following technical progress reports: alloy development for irradiation performance, damage analysis and fundamental studies, and special purpose materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide.

  3. Fusion reactor materials: Semiannual progress report for period ending September 30, 1987

    SciTech Connect

    none,

    1988-03-01

    This is the third in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following technical progress reports: Alloy Development for Irradiation Performances; Damage Analysis and Fundamental Studies; Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide.

  4. Fusion materials semiannual progress report for the period ending September 30, 1994

    SciTech Connect

    1995-04-01

    This is the sixteenth in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following Progress reports: Alloy Development for Irradiation Performance; Damage Analysis and Fundamental Studies; and Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials programs being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide. The individual papers in this paper have been cataloged separately elsewhere.

  5. Fusion reactor materials semiannual progress report for the period ending March 31, 1991

    SciTech Connect

    none,

    1991-07-01

    This is the tenth in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following progress reports: alloy development for irradiation performance; damage analysis and fundamental studies; special purpose materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of program participants, and to provide a means of communicating the efforts of materials scientists to the test of the fusion community, both nationally and worldwide.

  6. Fusion Reactor Materials semiannual progress report for the period ending March 31, 1992

    SciTech Connect

    Not Available

    1992-07-01

    This is the twelfth in a series of semiannual technical progress reports on fusion reactor materials. This report combines research and development activities which were previously reported separately in the following progress reports: Alloy Development for Irradiation Performance; Damage Analysis and Fundamental Studies; and Special Purpose Materials. These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials programs being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Reactor Materials Program is a national effort involving several national laboratories, universities, and industries. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide.

  7. Fusion technology development. Annual report to the US Department of Energy, October 1, 1996--September 30, 1997

    SciTech Connect

    1998-03-01

    In FY97, the General Atomics (GA) Fusion Group made significant contributions to the technology needs of the magnetic fusion program. The work was supported by the Office of Fusion Energy Sciences, International and Technology Division, of the US Department of Energy. The work is reported in the following sections on Fusion Power Plant Studies (Section 2), Plasma Interactive Materials (Section 3), Magnetic Diagnostic Probes (Section 4) and RF Technology (Section 5). Meetings attended and publications are listed in their respective sections. The overall objective of GA`s fusion technology research is to develop the technologies necessary for fusion to move successfully from present-day physics experiments to ITER and other next-generation fusion experiments, and ultimately to fusion power plants. To achieve this overall objective, we carry out fusion systems design studies to evaluate the technologies needed for next-step experiments and power plants, and we conduct research to develop basic knowledge about these technologies, including plasma technologies, fusion nuclear technologies, and fusion materials. We continue to be committed to the development of fusion power and its commercialization by US industry.

  8. Isolation of ara-lac gene fusions in Salmonella typhimurium LT2 by using transducing bacteriophage Mu d (Apr lac).

    PubMed

    Lee, J H; Heffernan, L; Wilcox, G

    1980-09-01

    A specialized Mu transducing phage containing a gene encoding ampicillin resistance and the lac structural genes without the lac promotor [Mu d(apr lac)] has been constructed and used to create gene fusions in Escherichia coli (M. J. Cadadaban and S. N. Cohen, Proc. Natl. Acad. Sci. U.S.A. 76:4530--4533, 1979). Transposition of the Mu d(Apr lac) phage to chromosomal sites can result in lac expression being controlled by a chromosomal promoter. We have constructed an Escherichia coli K-12 strain in which the Mu d(Apr lac) phage is integrated into an F factor. The F+::Mu d(Apr lac) was then transferred by conjugation into a Salmonella typhimurium strain that was sensitive to L-arabinose. Strains containing gene fusions were selected as L-arabinose-resistant colonies after partial induction of the phage. Two classes of ara-lac fusion strains were isolated: (i) araC-lac fusions in which the expression of beta-galactosidase synthesis was constitutuve and not inducible by L-arabinose; and ((ii) fusion of the lac genes to the ara structural genes in which the expression of beta-galatosidase synthesis was induced 263-fold by L-arabinose.

  9. Obesity and Prostate Cancer Risk According to Tumor TMPRSS2:ERG Gene Fusion Status.

    PubMed

    Egbers, Lieke; Luedeke, Manuel; Rinckleb, Antje; Kolb, Suzanne; Wright, Jonathan L; Maier, Christiane; Neuhouser, Marian L; Stanford, Janet L

    2015-05-01

    The T2E gene fusion, formed by fusion of the transmembrane protease, serine 2, gene (TMPRSS2) with the erythroblast transformation-specific (ETS)-related gene (ERG), is found in approximately 50% of prostate cancers and may characterize distinct molecular subtypes of prostate cancer with different etiologies. We investigated the relationship between body mass index (BMI; weight (kg)/height (m)(2)) and prostate cancer risk by T2E status. Study participants were residents of King County, Washington, recruited for 2 population-based case-control studies conducted in 1993-1996 and 2002-2005. Tumor T2E status was determined for 563 prostate cancer patients who underwent radical prostatectomy. Information on weight, height, and covariables was obtained through in-person interviews. We performed polytomous logistic regression to calculate odds ratios and 95% confidence intervals for T2E-positive and -negative prostate cancer. Comparing the highest BMI quartile with the lowest, inverse associations were observed between recent (≥29.7 vs. <24.5: odds ratio = 0.66, 95% confidence interval: 0.45, 0.97) and maximum (≥31.8 vs. <25.9: odds ratio = 0.69, 95% confidence interval: 0.47, 1.02) BMI and the risk of T2E-positive prostate cancer. No significant associations were seen for men with T2E-negative tumors. This study provides evidence that obesity is specifically associated with reduced risk of developing androgen-responsive T2E fusion-positive tumors. The altered steroid hormone profile in obese men may contribute to this inverse association. © The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. [Cloning of CTB-PROIN fusion gene and its expression in Escherichia coli].

    PubMed

    Chen, Li; Ouyang, Feng-Xiu; Qian, Bing-Jun; Ren, Hong; Wang, Qiang; Jiang, Qing-Wu; Wang, Yu-Jiong; Liu, Jing-Bo; Liang, Wan-Qi; Zhang, Da-Bing

    2005-03-01

    A fusion gene CTB-PROIN, in which Proinsulin gene was fused to the 3' end of CTB gene by a hinge peptide 'GPGP', was constructed and cloned into pET-30a(+) to obtain a prokaryotic expression vector pETCPI. Subsequently the recombinant plasmid pETCPI was transformed into E. coli stain BL21 (DE3). After induced by IPTG, the expression product was analyzed by sodium dodecyl sulphate-polyacrylamide gel (15%) electrophoresis (SDS-PAGE), and its result indicated that the recombinant protein CTB-PROIN was expressed and accumulated as inclusion bodies. The recombinant CTB-PROIN protein accumulated to the level of 25% of total bacterial proteins. After inclusion bodies was denaturalized and refolded in vitro, significant assembly of monomers had occurred, and the recombinant protein represented assembled pentamers. The results of western blotting analysis also demonstrated that the fusion protein could be recognized by the anti-CT and anti-insulin antibody, respectively. In addition, the result of the CTB-PROIN-GM1 binding assay, that the protein could bind to monosialoganglioside specifically, showed it possesed biological activity in vitro. These results provided the possibility of developing a cheaper and more efficient oral vaccine for type I diabetes using such constructs.

  11. Nodular fasciitis: a novel model of transient neoplasia induced by MYH9-USP6 gene fusion.

    PubMed

    Erickson-Johnson, Michele R; Chou, Margaret M; Evers, Barbara R; Roth, Christopher W; Seys, Amber R; Jin, Long; Ye, Ying; Lau, Alan W; Wang, Xiaoke; Oliveira, Andre M

    2011-10-01

    Nodular fasciitis (NF) is a relatively common mass-forming and self-limited subcutaneous pseudosarcomatous myofibroblastic proliferation of unknown pathogenesis. Due to its rapid growth and high mitotic activity, NF is often misdiagnosed as a sarcoma. While studying the USP6 biology in aneurysmal bone cyst and other mesenchymal tumors, we identified high expression levels of USP6 mRNA in two examples of NF. This finding led us to further examine the mechanisms underlying USP6 overexpression in these lesions. Upon subsequent investigation, genomic rearrangements of the USP6 locus were found in 92% (44 of 48) of NF. Rapid amplification of 5'-cDNA ends identified MYH9 as the translocation partner. RT-PCR and direct sequencing revealed the fusion of the MYH9 promoter region to the entire coding region of USP6. Control tumors and tissues were negative for this fusion. Xenografts of cells overexpressing USP6 in nude mice exhibited clinical and histological features similar to human NF. The identification of a sensitive and specific abnormality in NF holds the potential to be used diagnostically. Considering the self-limited nature of the lesion, NF may represent a model of 'transient neoplasia', as it is, to our knowledge, the first example of a self-limited human disease characterized by a recurrent somatic gene fusion event. © 2011 USCAP, Inc All rights reserved

  12. Fetal origins of the TEL-AML1 fusion gene in identical twins with leukemia

    PubMed Central

    Ford, Anthony M.; Bennett, Caroline A.; Price, Cathy M.; Bruin, M. C. A.; Van Wering, Elisabeth R.; Greaves, Mel

    1998-01-01

    The TEL (ETV6)−AML1 (CBFA2) gene fusion is the most common reciprocal chromosomal rearrangement in childhood cancer occurring in ≈25% of the most predominant subtype of leukemia— common acute lymphoblastic leukemia. The TEL-AML1 genomic sequence has been characterized in a pair of monozygotic twins diagnosed at ages 3 years, 6 months and 4 years, 10 months with common acute lymphoblastic leukemia. The twin leukemic DNA shared the same unique (or clonotypic) but nonconstitutive TEL-AML1 fusion sequence. The most plausible explanation for this finding is a single cell origin of the TEL-AML fusion in one fetus in utero, probably as a leukemia-initiating mutation, followed by intraplacental metastasis of clonal progeny to the other twin. Clonal identity is further supported by the finding that the leukemic cells in the two twins shared an identical rearranged IGH allele. These data have implications for the etiology and natural history of childhood leukemia. PMID:9539781

  13. MODELLING THERMODYNAMICS OF ALLOYS FOR FUSION APPLICATION . Semi annual report for the Fusion Program

    SciTech Connect

    Caro, J A

    2007-07-31

    This research has two main objectives: (1) The development of computational tools to evaluate alloy properties, using the information contained in thermodynamic functions. We aim at improving the ability of classical potentials to account for complex alloy behavior; and (2) The application of these tools to predict properties of alloys under irradiation. Atomistic simulations of alloys at the empirical level face the challenge of correctly modeling basic thermodynamic properties. In the periods reported previously we develop a methodology to generalize many-body classic potentials to incorporate complex formation energy curves. Application to Fe-Cr allows us to predict the implications of the ab initio results of formation energy on the phase diagram of this alloy and to get a detailed insight into the processes leading to precipitation of {alpha}{prime} phase under irradiation. In particular in this period we report on the consequences of the negative heat of formation at low Cr composition on the short range order SRO existing in the {alpha} phase. We elaborate a simple description of SRO on a two phase alloy and compare the predictions with experiments. We provide a key to rationalize a diversity of experiments on SRO versus annealing time or irradiation dose.

  14. Decoding of exon splicing patterns in the human RUNX1-RUNX1T1 fusion gene.

    PubMed

    Grinev, Vasily V; Migas, Alexandr A; Kirsanava, Aksana D; Mishkova, Olga A; Siomava, Natalia; Ramanouskaya, Tatiana V; Vaitsiankova, Alina V; Ilyushonak, Ilia M; Nazarov, Petr V; Vallar, Laurent; Aleinikova, Olga V

    2015-11-01

    The t(8;21) translocation is the most widespread genetic defect found in human acute myeloid leukemia. This translocation results in the RUNX1-RUNX1T1 fusion gene that produces a wide variety of alternative transcripts and influences the course of the disease. The rules of combinatorics and splicing of exons in the RUNX1-RUNX1T1 transcripts are not known. To address this issue, we developed an exon graph model of the fusion gene organization and evaluated its local exon combinatorics by the exon combinatorial index (ECI). Here we show that the local exon combinatorics of the RUNX1-RUNX1T1 gene follows a power-law behavior and (i) the vast majority of exons has a low ECI, (ii) only a small part is represented by "exons-hubs" of splicing with very high ECI values, and (iii) it is scale-free and very sensitive to targeted skipping of "exons-hubs". Stochasticity of the splicing machinery and preferred usage of exons in alternative splicing can explain such behavior of the system. Stochasticity may explain up to 12% of the ECI variance and results in a number of non-coding and unproductive transcripts that can be considered as a noise. Half-life of these transcripts is increased due to the deregulation of some key genes of the nonsense-mediated decay system in leukemia cells. On the other hand, preferred usage of exons may explain up to 75% of the ECI variability. Our analysis revealed a set of splicing-related cis-regulatory motifs that can explain "attractiveness" of exons in alternative splicing but only when they are considered together. Cis-regulatory motifs are guides for splicing trans-factors and we observed a leukemia-specific profile of expression of the splicing genes in t(8;21)-positive blasts. Altogether, our results show that alternative splicing of the RUNX1-RUNX1T1 transcripts follows strict rules and that the power-law component of the fusion gene organization confers a high flexibility to this process. Copyright © 2015 Elsevier Ltd. All rights

  15. Targetable kinase gene fusions in high risk B-ALL: a study from the Children's Oncology Group.

    PubMed

    Reshmi, Shalini C; Harvey, Richard C; Roberts, Kathryn G; Stonerock, Eileen; Smith, Amy; Jenkins, Heather; Chen, I-Ming; Valentine, Marc; Liu, Yu; Li, Yongjin; Shao, Ying; Easton, John; Payne-Turner, Debbie; Gu, Zhaohui; Tran, Thai Hoa; Nguyen, Jonathan V; Devidas, Meenakshi; Dai, Yunfeng; Heerema, Nyla A; Carroll, Andrew J; Raetz, Elizabeth A; Borowitz, Michael J; Wood, Brent L; Angiolillo, Anne L; Burke, Michael J; Salzer, Wanda L; Zweidler-McKay, Patrick A; Rabin, Karen R; Carroll, William L; Zhang, Jinghui; Loh, Mignon L; Mullighan, Charles G; Willman, Cheryl L; Gastier-Foster, Julie M; Hunger, Stephen P

    2017-04-13

    Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a high-risk subtype characterized by genomic alterations that activate cytokine receptor and kinase signaling. We examined the frequency and spectrum of targetable genetic lesions in a retrospective cohort of 1389 consecutively diagnosed childhood B-ALL patients with high-risk clinical features and/or elevated minimal residual disease at the end of remission induction therapy. The Ph-like gene expression profile was identified in 341 of 1389 patients, 57 of which were excluded from additional analysis because of the presence of BCR-ABL1 (n=46) or ETV6-RUNX1 (n=11). Among the remaining 284 (20.4%) patients, overexpression and rearrangement of CRLF2 (IGH-CRLF2 or P2RY8-CRLF2) were identified in 124 (43.7%), with concomitant genomic alterations activating the JAK-STAT pathway (JAK1, JAK2, IL7R) identified in 63 patients (50.8% of CRLF2-rearranged cases). Of the remaining patients, using RT-PCR or transcriptome sequencing, we identified targetable ABL-class fusions (ABL1, ABL2, CSF1R and PDGFRB) in 14.1% of Ph-like ALL cases, EPOR rearrangements or JAK2 fusions (8.8%), alterations activating other JAK-STAT signaling genes (IL7R, SH2B3, JAK1; 6.3%) and other kinases (FLT3, NTRK3, LYN; 4.6%), and mutations involving the Ras pathway (KRAS, NRAS, NF1, PTPN11; 6%). We identified eight new rearrangement partners for four kinase genes previously reported to be rearranged in Ph-like ALL. The current findings provide support for the precision-medicine testing and treatment approach for Ph-like ALL that has been implemented in Children's Oncology Group ALL trials.

  16. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites

    PubMed Central

    Djuika, Carine F.; Huerta-Cepas, Jaime; Przyborski, Jude M.; Deil, Sophia; Sanchez, Cecilia P.; Doerks, Tobias; Bork, Peer; Lanzer, Michael; Deponte, Marcel

    2015-01-01

    Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones. PMID:28357258

  17. Pandemic H1N1 influenza A directly induces a robust and acute inflammatory gene signature in primary human bronchial epithelial cells downstream of membrane fusion.

    PubMed

    Paquette, Stéphane G; Banner, David; Chi, Le Thi Bao; Leόn, Alberto J; Xu, Luoling; Ran, Longsi; Huang, Stephen S H; Farooqui, Amber; Kelvin, David J; Kelvin, Alyson A

    2014-01-05

    Pandemic H1N1 influenza A (H1N1pdm) elicits stronger pulmonary inflammation than previously circulating seasonal H1N1 influenza A (sH1N1), yet mechanisms of inflammatory activation in respiratory epithelial cells during H1N1pdm infection are unclear. We investigated host responses to H1N1pdm/sH1N1 infection and virus entry mechanisms in primary human bronchial epithelial cells in vitro. H1N1pdm infection rapidly initiated a robust inflammatory gene signature (3 h post-infection) not elicited by sH1N1 infection. Protein secretion inhibition had no effect on gene induction. Infection with membrane fusion deficient H1N1pdm failed to induce robust inflammatory gene expression which was rescued with restoration of fusion ability, suggesting H1N1pdm directly triggered the inflammatory signature downstream of membrane fusion. Investigation of intra-virion components revealed H1N1pdm viral RNA (vRNA) triggered a stronger inflammatory phenotype than sH1N1 vRNA. Thus, our study is first to report H1N1pdm induces greater inflammatory gene expression than sH1N1 in vitro due to direct virus-epithelial cell interaction.

  18. Sequence-specific electrochemical detection of double-strand PCR amplicons of PML/RARα fusion gene in acute promyelocytic leukemia.

    PubMed

    Lei, Yun; Feng, Mei-juan; Wang, Kun; Lin, Li-qing; Chen, Yuan-zhong; Lin, Xin-hua

    2013-01-01

    A novel electrochemical method for the sequence-specific detection of double-stranded polymerase chain reaction (PCR) products of PML/RARα fusion gene in acute promyelocytic leukemia (APL) was described in detail. Based on a "sandwich" sensing mode involving a pair of locked nucleic acids probes (capture probe and reporter probe), this DNA sensor exhibited excellent selectivity and specificity. The direct and quantitative analysis of double-stranded complementary was firstly performed by our sensor without the use of alkali, helicase enzymes, or denaturants. Finally, combining PCR technique with electrochemical detection scheme, PCR amplicons (191 bp) of the PML/RARα fusion gene were obtained and rapidly identified with a low detection limit of 79 fmol in the 100-μL hybridization system. The results clearly showed the power of sensor as a promising tool for the sensitive, specific, and portable detection of APL and other diseases.

  19. A new microcolumn-type microchip for examining the expression of chimeric fusion genes using a nucleic acid sandwich hybridization technique.

    PubMed

    Ohnishi, Michihiro; Sasaki, Naoyuki; Kishimoto, Takuya; Watanabe, Hidetoshi; Takagi, Masatoshi; Mizutani, Shuki; Kishii, Noriyuki; Yasuda, Akio

    2014-11-01

    We report a new type of microcolumn installed in a microchip. The architecture allows use of a nucleic acid sandwich hybridization technique to detect a messenger RNA (mRNA) chain as a target. Data are presented that demonstrate that the expression of a chimeric fusion gene can be detected. The microcolumn was filled with semi-transparent microbeads made of agarose gel that acted as carriers, allowing increased efficiency of the optical detection of fluorescence from the microcolumn. The hybrid between the target trapped on the microbeads and a probe DNA labeled with a fluorescent dye was detected by measuring the intensity of the fluorescence from the microcolumn directly. These results demonstrate an easy and simple method for determining the expression of chimeric fusion genes with no preamplification. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Progress report on muon catalyzed fusion studies in H2+D2 and HD gaseous targets

    NASA Astrophysics Data System (ADS)

    Aniol, K. A.; Margaziotis, D. J.; Noble, A. J.; Stanislaus, S.; Virtue, C. J.; Measday, D. F.; Horvath, D.; Robertson, B. C.; Salomon, M.; Jones, S. E.

    1988-12-01

    Gamma yields from the decay of the muonic molecule pdμ produced in muon-catalyzed fusion studies in H2+D2 and HD gaseous targets have been measured. The experiments have been performed at TRIUMF and the data is presented in this report. (AIP)

  1. Lymphocele formation after anterior lumbar interbody fusion at L4-5. Case report.

    PubMed

    Pee, Yong Hun; Kim, Ki Joon; Choi, Young-Geun; Jeon, Sang Hyeop; Park, Jong Dae; Lee, Sang-Ho

    2007-11-01

    In this report, the authors present the case of patient with a lymphocele in the retroperitoneal area following anterior lumbar interbody fusion at L4-5. A lymphocele is a rare complication of spinal operations, especially lower lumbar spinal surgeries. The authors discuss this complicating factor and describe its features and treatments.

  2. Fusion materials semiannual progress report for the period ending December 31, 1997

    SciTech Connect

    Burn, G.

    1998-03-01

    This is the twenty-third in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The Fusion Materials Program is a national effort involving several national laboratories, universities, and industries. A large fraction of this work, particularly in relation to fission reactor experiments, is carried out collaboratively with their partners in Japan, Russia, and the European Union. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.

  3. Institute for Fusion Studies, Final Technical Report, December 1, 1995 - February 29, 2004

    SciTech Connect

    Dr. James Van Dam

    2005-02-14

    During the 2001-2003 grant period, Institute for Fusion Studies (IFS) scientist made notable progress in a number of research areas. This report summarizes the work that has been accomplished in the following areas: (1) Magnetohydrodynamics; (2) Burning plasma and energetic particle physics; (3) Turbulent transport; (4) Computational physics; (5) Fundamental Theory; (6) Innovative confinement concepts; and (7) Plasma applications.

  4. CONFERENCE REPORT: 13th EU-US Transport Task Force Workshop on transport in fusion plasmas

    NASA Astrophysics Data System (ADS)

    Connor, J. W.; Fasoli, A.; Hidalgo, C.; Kirk, A.; Naulin, V.; Peeters, A. G.; Tala, T.

    2009-04-01

    This report summarizes the contributions presented at the 13th EU-US Transport Task Force Workshop on transport in fusion plasmas, held in Copenhagen, Denmark, 1-4 September 2008. There were sessions on core heat and particle transport; core and edge momentum transport; edge and scrape-off-layer transport and MHD and fast particle interaction with transport.

  5. Bilateral Supernumerary Deciduous Maxillary Lateral Incisors with Fusion: Report of a Rare Case

    PubMed Central

    Ghaderi, Faezeh; Rafiee, Azade

    2016-01-01

    Dental anomaly in number, size and shape might be due to excessive activation of dental lamina during the morpho-differentiation stage. Fusion is one of the most unusual and rare anomalies of shape of the teeth. It frequently involves the supernumerary teeth resulting in a challenging differential diagnosis with gemination. Dental anomalies may result in different problems such as delayed eruption and crowding; thus, early diagnosis is required for effective intervention and proper in-time treatment. The case reported here is a 4-year-old girl with bilateral supernumerary primary maxillary lateral incisors associated with fusion between primary maxillary left lateral incisor and supernumerary lateral tooth. PMID:26966712

  6. Phase 1 report on sensor technology, data fusion and data interpretation for site characterization

    SciTech Connect

    Beckerman, M.

    1991-10-01

    In this report we discuss sensor technology, data fusion and data interpretation approaches of possible maximal usefulness for subsurface imaging and characterization of land-fill waste sites. Two sensor technologies, terrain conductivity using electromagnetic induction and ground penetrating radar, are described and the literature on the subject is reviewed. We identify the maximum entropy stochastic method as one providing a rigorously justifiable framework for fusing the sensor data, briefly summarize work done by us in this area, and examine some of the outstanding issues with regard to data fusion and interpretation. 25 refs., 17 figs.

  7. Fusion research at General Atomics. Annual report, October 1, 1992--September 30, 1993. General Atomics Project 3469

    SciTech Connect

    Not Available

    1994-05-01

    This report is the General Atomics Fusion Physics annual report for the period October 1992 thru September 1993. It highlights major activities and projects in four areas: fusion technology development overview; reactor design studies; RF technology; plasma facing components. A listing of publications for the period is also enclosed.

  8. Proteus mirabilis urease: operon fusion and linker insertion analysis of ure gene organization, regulation, and function.

    PubMed Central

    Island, M D; Mobley, H L

    1995-01-01

    Urease is an inducible virulence factor of uropathogenic Proteus mirabilis. Although eight contiguous genes necessary for urease activity have been cloned and sequenced, the transcriptional organization and regulation of specific genes within the Proteus gene cluster has not been investigated in detail. The first gene, ureR, is located 400 bp upstream and is oriented in the direction opposite the other seven genes, ureDABCEFG. The structural subunits of urease are encoded by ureABC. Previously, UreR was shown to contain a putative helix-turn-helix DNA-binding motif 30 residues upstream of a consensus sequence which is a signature for the AraC family of positive regulators; this polypeptide is homologous to other DNA-binding regulatory proteins. Nested deletions of ureR linked to either ureD-lacZ or ureA-lacZ operon fusions demonstrated that an intact ureR is required for urea-induced synthesis of LacZ from either ureA or ureD and identified a urea-regulated promoter in the ureR-ureD intergenic region. However, lacZ operon fusions to fragments encompassing putative promoter regions upstream of ureA and ureF demonstrated that no urea-regulated promoters occur upstream of these open reading frames; regions upstream of ureR, ureE, and ureG were not tested. These data suggest that UreR acts as a positive regulator in the presence of urea, activating transcription of urease structural and accessory genes via sequences upstream of ureD. To address the role of the nonstructural regulatory and accessory genes, we constructed deletion, cassette, and linker insertion mutations throughout the ure gene cluster and determined the effect of these mutations on production and regulation of urease activity in Escherichia coli. Mutations were obtained, with locations determine by DNA sequencing, in all genes except ureA and ureE. In each case, the mutation resulted in a urease-negative phenotype. PMID:7559355

  9. Definition of the ovalbumin gene promoter by transfer of an ovalglobin fusion gene into cultured cells.

    PubMed Central

    Knoll, B J; Zarucki-Schulz, T; Dean, D C; O'Malley, B W

    1983-01-01

    In order to study the initiation of transcription from the ovalbumin gene promoter, we constructed a hybrid gene (ovalglobin) in which 753 bps of ovalbumin gene 5'-flanking sequence were joined to the chicken adult beta-globin gene. When transfected into HeLa S3 cells, ovalglobin gene transcription initiated at the ovalbumin gene cap site, as measured by S1 nuclease and primer extension analysis. Deletion of 5'-flanking sequences to position -95 had little effect on transcription; deletion to -77 reduced transcription to about 20% of the wild type level and deletion to -48 reduced the level to about 2%. A deletion to -24, removing the sequence TATATAT, abolished transcription entirely. Hormonal regulation of the ovalglobin gene was observed when primary oviduct cells were used as recipients for DNA transfection. Under these conditions, addition of progesterone increased the level of ovalglobin transcripts to more than 10 times the uninduced level. Images PMID:6314256

  10. Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay.

    PubMed

    Lyu, Xiaodong; Wang, Xianwei; Zhang, Lina; Chen, Zhenzhu; Zhao, Yu; Hu, Jieying; Fan, Ruihua; Song, Yongping

    2017-07-25

    Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management. We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization. Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL). We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an

  11. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences.

    PubMed

    Feng, Weiguo; Leach, Sonia M; Tipney, Hannah; Phang, Tzulip; Geraci, Mark; Spritz, Richard A; Hunter, Lawrence E; Williams, Trevor

    2009-12-16

    Orofacial malformations resulting from genetic and/or environmental causes are frequent human birth defects yet their etiology is often unclear because of insufficient information concerning the molecular, cellular and morphogenetic processes responsible for normal facial development. We have, therefore, derived a comprehensive expression dataset for mouse orofacial development, interrogating three distinct regions - the mandibular, maxillary and frontonasal prominences. To capture the dynamic changes in the transcriptome during face formation, we sampled five time points between E10.5-E12.5, spanning the developmental period from establishment of the prominences to their fusion to form the mature facial platform. Seven independent biological replicates were used for each sample ensuring robustness and quality of the dataset. Here, we provide a general overview of the dataset, characterizing aspects of gene expression changes at both the spatial and temporal level. Considerable coordinate regulation occurs across the three prominences during this period of facial growth and morphogenesis, with a switch from expression of genes involved in cell proliferation to those associated with differentiation. An accompanying shift in the expression of polycomb and trithorax genes presumably maintains appropriate patterns of gene expression in precursor or differentiated cells, respectively. Superimposed on the many coordinated changes are prominence-specific differences in the expression of genes encoding transcription factors, extracellular matrix components, and signaling molecules. Thus, the elaboration of each prominence will be driven by particular combinations of transcription factors coupled with specific cell:cell and cell:matrix interactions. The dataset also reveals several prominence-specific genes not previously associated with orofacial development, a subset of which we externally validate. Several of these latter genes are components of bidirectional

  12. Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences

    PubMed Central

    Feng, Weiguo; Leach, Sonia M.; Tipney, Hannah; Phang, Tzulip; Geraci, Mark; Spritz, Richard A.; Hunter, Lawrence E.; Williams, Trevor

    2009-01-01

    Orofacial malformations resulting from genetic and/or environmental causes are frequent human birth defects yet their etiology is often unclear because of insufficient information concerning the molecular, cellular and morphogenetic processes responsible for normal facial development. We have, therefore, derived a comprehensive expression dataset for mouse orofacial development, interrogating three distinct regions – the mandibular, maxillary and frontonasal prominences. To capture the dynamic changes in the transcriptome during face formation, we sampled five time points between E10.5–E12.5, spanning the developmental period from establishment of the prominences to their fusion to form the mature facial platform. Seven independent biological replicates were used for each sample ensuring robustness and quality of the dataset. Here, we provide a general overview of the dataset, characterizing aspects of gene expression changes at both the spatial and temporal level. Considerable coordinate regulation occurs across the three prominences during this period of facial growth and morphogenesis, with a switch from expression of genes involved in cell proliferation to those associated with differentiation. An accompanying shift in the expression of polycomb and trithorax genes presumably maintains appropriate patterns of gene expression in precursor or differentiated cells, respectively. Superimposed on the many coordinated changes are prominence-specific differences in the expression of genes encoding transcription factors, extracellular matrix components, and signaling molecules. Thus, the elaboration of each prominence will be driven by particular combinations of transcription factors coupled with specific cell:cell and cell:matrix interactions. The dataset also reveals several prominence-specific genes not previously associated with orofacial development, a subset of which we externally validate. Several of these latter genes are components of bidirectional

  13. Pyosalpinx as a sequela of labial fusion in a post-menopausal woman: a case report

    PubMed Central

    2011-01-01

    Introduction Complete labia fusion is a rare clinical entity in post-menopausal women. The most common complications of this presentation are infections of the urinary tract and retention of urine in the vagina. We present the case of a post-menopausal woman with adnexal mass and abdominal pain due to fusion of the labia majora. To the best of our knowledge this is the first report in the literature of this complication. Case presentation A 78-year-old Caucasian woman was admitted to our hospital due to abdominal pain and urination difficulty, along with fever and leucocytosis. On examination the labial majora were fused. Computed tomography of the abdomen revealed a cystic formation in the anatomical area of the right adnexa. Our patient had developed a pyosalpinx as a Sequela of labial fusion. At laparoscopy the right pyosalpinx was identified and resected, whereas the labia majora were reconstructed via dissection and separation. Conclusions Labial fusion is a rare clinical entity in post-menopausal women and can have serious and unexpected complications. Though this presentation is rare, a clinical examination must be performed in detail in order to gain valuable information for an accurate diagnosis. Post-operational instruction must be given to patients in order to prevent the re-occurrence of the fusion and its complications. PMID:22054217

  14. Establishment of an Institute for Fusion Studies. Technical progress report, November 1, 1994--October 31, 1995

    SciTech Connect

    1995-07-01

    The Institute for Fusion Studies is a national center for theoretical fusion plasma physics research. Its purposes are to (1) conduct research on theoretical questions concerning the achievement of controlled fusion energy by means of magnetic confinement--including both fundamental problems of long-range significance, as well as shorter-term issues; (2) serve as a national and international center for information exchange by hosting exchange visits, conferences, and workshops; and (3) train students and postdoctoral research personnel for the fusion energy program and plasma physics research areas. During FY 1995, a number of significant scientific advances were achieved at the IFS, both in long-range fundamental problems as well as in near-term strategic issues, consistent with the Institute`s mandate. Examples of these achievements include, for example, tokamak edge physics, analytical and computational studies of ion-temperature-gradient-driven turbulent transport, alpha-particle-excited toroidal Alfven eigenmode nonlinear behavior, sophisticated simulations for the Numerical Tokamak Project, and a variety of non-tokamak and non-fusion basic plasma physics applications. Many of these projects were done in collaboration with scientists from other institutions. Research discoveries are briefly described in this report.

  15. Methods of economic analysis applied to fusion research. Fourth annual report

    SciTech Connect

    Hazelrigg, Jr, G A

    1980-12-31

    The current study reported here has involved three separate tasks. The first task deals with the development of expected utility analysis techniques for economic evaluation of fusion research. A decision analytic model is developed for the incorporation of market uncertainties, as well as technological uncertainties in an economic evaluation of long-range energy research. The model is applied to the case of fusion research. The second task deals with the potential effects of long-range energy RD and D on fossil fuel prices. ECON's previous fossil fuel price model is extended to incorporate a dynamic demand function. The dynamic demand function supports price fluctuations such as those observed in the marketplace. The third task examines alternative uses of fusion technologies, specifically superconducting technologies and first wall materials to determine the potential for alternative, nonfusion use of these technologies. In both cases, numerous alternative uses are found.

  16. Melanotic Translocation Renal Cell Carcinoma With a Novel ARID1B-TFE3 Gene Fusion.

    PubMed

    Antic, Tatjana; Taxy, Jerome B; Alikhan, Mir; Segal, Jeremy

    2017-09-04

    A 36-year-old male was found to have a 7.0 cm left upper pole renal mass on renal ultrasound. Following nephrectomy, the mass was grossly ill-demarcated, friable and red-brown, invading renal parenchyma, hilar fat and the renal vein. Microscopically, the tumor had a nested and papillary architecture. The cells demonstrated abundant clear and eosinophilic cytoplasm and focal intracytoplasmic melanin pigment. Nucleoli were prominent. By immunohistochemistry, the tumor was positive for TFE3; HMB-45 stained approximately 5% of tumor cells corresponding to the histologic melanin pigment, which was confirmed with Fontana-Masson stain with bleach. Immunostains for PAX8, CD10, MiTF, and CAIX were negative; keratins Cam 5.2 and AE1/AE3 were focally positive. Targeted next-generation sequencing revealed an ARID1B-TFE3 gene fusion. Melanotic Xp11 renal cell carcinoma is a rare, pigment containing translocation variant demonstrating overlapping features with melanoma and is usually associated with an SFPQ-TFE3 gene fusion. The patient is alive and without evidence of disease 7 years after his diagnosis. The combination of high grade histopathology, the presence of melanin, absent PAX8, keratin positivity, and relatively indolent clinical behavior with a unique translocation may warrant recognition as a distinct renal cell carcinoma translocation subtype.

  17. On the origin of protein synthesis factors: a gene duplication/fusion model.

    PubMed

    Cousineau, B; Leclerc, F; Cedergren, R

    1997-12-01

    Sequence similarity has given rise to the proposal that IF-2, EF-G, and EF-Tu are related through a common ancestor. We evaluate this proposition and whether the relationship can be extended to other factors of protein synthesis. Analysis of amino acid sequence similarity gives statistical support for an evolutionary affiliation among IF-1, IF-2, IF-3, EF-Tu, EF-Ts, and EF-G and suggests further that this association is a result of gene duplication/fusion events. In support of this mechanism, the three-dimensional structures of IF-3, EF-Tu, and EF-G display a predictable domain structure and overall conformational similarity. The model that we propose consists of three consecutives duplication/fusion events which would have taken place before the divergence of the three superkingdoms: eubacteria, archaea, and eukaryotes. The root of this protein superfamily tree would be an ancestor of the modern IF-1 gene sequence. The repeated fundamental motif of this protein superfamily is a small RNA binding domain composed of two alpha-helices packed along side of an antiparallel beta-sheet.

  18. A Rhodopsin-Guanylyl Cyclase Gene Fusion Functions in Visual Perception in a Fungus

    PubMed Central

    Avelar, Gabriela M.; Schumacher, Robert I.; Zaini, Paulo A.; Leonard, Guy; Richards, Thomas A.; Gomes, Suely L.

    2014-01-01

    Summary Sensing light is the fundamental property of visual systems, with vision in animals being based almost exclusively on opsin photopigments [1]. Rhodopsin also acts as a photoreceptor linked to phototaxis in green algae [2, 3] and has been implicated by chemical means as a light sensor in the flagellated swimming zoospores of the fungus Allomyces reticulatus [4]; however, the signaling mechanism in these fungi remains unknown. Here we use a combination of genome sequencing and molecular inhibition experiments with light-sensing phenotype studies to examine the signaling pathway involved in visual perception in the closely related fungus Blastocladiella emersonii. Our data show that in these fungi, light perception is accomplished by the function of a novel gene fusion (BeGC1) of a type I (microbial) rhodopsin domain and guanylyl cyclase catalytic domain. Photobleaching of rhodopsin function prevents accumulation of cGMP levels and phototaxis of fungal zoospores exposed to green light, whereas inhibition of guanylyl cyclase activity negatively affects fungal phototaxis. Immunofluorescence microscopy localizes the BeGC1 protein to the external surface of the zoospore eyespot positioned close to the base of the swimming flagellum [4, 5], demonstrating this is a photoreceptive organelle composed of lipid droplets. Taken together, these data indicate that Blastocladiomycota fungi have a cGMP signaling pathway involved in phototaxis similar to the vertebrate vision-signaling cascade but composed of protein domain components arranged as a novel gene fusion architecture and of distant evolutionary ancestry to type II rhodopsins of animals. PMID:24835457

  19. Expression pattern of the RAR alpha-PML fusion gene in acute promyelocytic leukemia.

    PubMed Central

    Alcalay, M; Zangrilli, D; Fagioli, M; Pandolfi, P P; Mencarelli, A; Lo Coco, F; Biondi, A; Grignani, F; Pelicci, P G

    1992-01-01

    Two chimeric genes, PML-RAR alpha and RAR alpha-PML, are formed as a consequence of the acute promyelocytic leukemia (APL)-specific reciprocal translocation of chromosomes 15 and 17 [t(15;17)]. PML-RAR alpha is expressed as a fusion protein. We investigated the organization and expression pattern of the RAR alpha-PML gene in a series of APL patients representative of the molecular heterogeneity of the t(15;17) and found (i) two types of RAR alpha-PML mRNA junctions (RAR alpha exon 2/PML exon 4 or RAR alpha exon 2/PML exon 7) that maintain the RAR alpha and PML longest open reading frames aligned and are the result of chromosome 15 breaking at two different sites; and (ii) 10 different RAR alpha-PML fusion transcripts that differ for the assembly of their PML coding exons. A RAR alpha-PML transcript was present in most, but not all, APL patients. Images PMID:1317574

  20. PL1 fusion gene: a novel visual selectable marker gene that confers tolerance to multiple abiotic stresses in transgenic tomato.

    PubMed

    Jin, Feng; Li, Shu; Dang, Lijie; Chai, Wenting; Li, Pengli; Wang, Ning Ning

    2012-10-01

    Visual selectable markers, including the purple color caused by the accumulation of anthocyanins, have been proposed for use as antibiotic-free alternatives. However, the excessive accumulation of anthocyanins seriously inhibits the growth and development of transgenic plants. In our study, the AtDWF4 promoter from Arabidopsis and the tomato LeANT1 gene, encoding a MYB transcription factor, were used to construct the PL1 fusion gene to test whether it could be used as a visual selectable marker gene for tomato transformation. All the PL1 transgenic shoots exhibited intense purple color on shoot induction medium. In the transgenic tomato plants, PL1 was highly expressed in the cotyledons, but expressed only slightly in the true leaves and other organs. The expression of PL1 had no significantly adverse effects on the growth or development of the transgenic tomato plants, and conferred tolerance to multiple abiotic stresses in them. With the “cut off green shoots” method, multiple independent 35S::GFP transgenic tomato lines were successfully obtained using PL1 as the selectable marker gene. These results suggest that PL1 has potential application of visual selectable marker gene for tomato transformation.

  1. Horizontal gene transfers and cell fusions in microbiology, immunology and oncology (Review).

    PubMed

    Sinkovics, Joseph G

    2009-09-01

    Evolving young genomes of archaea, prokaryota and unicellular eukaryota were wide open for the acceptance of alien genomic sequences, which they often preserved and vertically transferred to their descendants throughout three billion years of evolution. Established complex large genomes, although seeded with ancestral retroelements, have come to regulate strictly their integrity. However, intruding retroelements, especially the descendents of Ty3/Gypsy, the chromoviruses, continue to find their ways into even the most established genomes. The simian and hominoid-Homo genomes preserved and accommodated a large number of endogenous retroviral genomic segments. These retroelements may mature into exogenous retroviruses, or into functional new genes. Phages and viruses have been instrumental in incorporating and transferring host cell genes. These events profoundly influenced and altered the course of evolution. Horizontal (lateral) gene transfers (HGT) overwhelmed the genomes of the ancient protocells and the evolving unicellular microorganisms, actually leading to their Cambrian explosion. While the rigidly organized genomes of multicellular organisms increasingly resist H/LGT, de-differentiated cells assuming the metabolism of their onto- or phylogenetic ancestors, open up widely to the practice of H/LGT by direct transfer, or to transfers mediated by viruses, or by cell fusions. This activity is intensified in malignantly transformed cells, thus rendering these subjects receptive to therapy with oncolytic viruses and with viral vectors of tumor-suppressive or immunogenic genetic materials. Naturally formed hybrids of dendritic and tumor cells are often tolerogenic, whereas laboratory products of these unisons may be immunogenic in the hosts of origin. As human breast cancer stem cells are induced by a treacherous class of CD8+ T cells to undergo epithelial to mesenchymal (ETM) transition and to yield to malignant transformation by the omnipresent proto

  2. In vitro expression of a Tn9-derived chloramphenicol acetyltransferase gene fusion by using a Bacillus subtilis system.

    PubMed Central

    Zaghloul, T I; Doi, R H

    1987-01-01

    A coupled in vitro protein-synthesizing system has been developed with components derived totally from Bacillus subtilis. The system synthesized specific gene products from various exogenous DNA templates, including B. subtilis phage phi 29, plasmid pUB110, and a heterologous B. subtilis-Escherichia coli gene fusion containing the transposon Tn9-derived chloramphenicol acetyltransferase (cat) gene. The gene fusion product was able to show CAT activity, bind specifically to a Sephacryl-chloramphenicol column, and react immunologically against anti-CAT antiserum. The fidelity of this in vitro system was demonstrated by the synthesis of gene products identical to that made in vivo. We suggest that this system may be used to study the regulation of gene expression in vitro. Images PMID:3102458

  3. Use of gene fusions to study outer membrane protein localization in Escherichia coli.

    PubMed Central

    Silhavy, T J; Shuman, H A; Beckwith, J; Schwartz, M

    1977-01-01

    Escherichia coli strains have been isolated that produce hybrid proteins comprised of an NH2-terminal sequence from the lamB gene product (an outer membrane protein) and a major portion of the COOH-terminal sequence of beta-galactosidase (beta-D-galactoside galactohydrolase, EC 3.2.1.23; a cytoplasmic protein). These proteins exhibit beta-galactosidase activity. One such strain, pop 3105, produces a hybrid protein containing very little of the lamB gene protein; the protein is found in the cytoplasm. The protein found in a second strain, pop 3186, contains much more of the lamB gene protein; a substantial fraction of the beta-galactosidase activity is found in the outer membrane, probably facing outward. These results indicate that information necessary to direct the lamB gene product to its outer membrane location is located within the lamB gene itself. The properties of such fusion strains open up the prospect of a precise genetic analysis of the genetic components involved in protein transport. Images PMID:414221

  4. Variations for susceptibilities to ultraviolet induced cellular inactivation and gene segregation among protoplast fusion hybrids of Candida albicans.

    PubMed

    Sarachek, A; Henderson, L A

    1988-01-01

    Hybrids of the naturally diploid, asexual and opportunistically pathogenic yeast, Candida albicans, can be obtained artificially by protoplast fusion. Evidence is presented that gene conversion and reciprocal recombination contribute to ultraviolet (UV)-induced segregations of heterozygous markers from both diploid and hybrid strains, and that hybrids also segregate through induced chromosome loss. Heterozygous diploid strains independently derived from the same wild-type diploid stock were alike in post-UV survival and segregational responses, and the organization of a four gene linkage group identified in diploids from the segregant products of reciprocal recombinations was transmitted intact to all hybrids from fusions between diploids of isogenic or nonisogenic backgrounds. However, hybrids arising independently from a given fusion cross differed significantly from each other in post-UV survival, absolute ability to segregate some parental markers, frequency of gene segregation, and proclivities for each of the three mechanisms of gene segregation. The bearings of the genetic backgrounds of parental strains and of growth temperatures during hybrid formation on each of these variables are described. The findings emphasize that awareness of the intrinsic heterogeneities of fusion hybrids is essential for reliable application of the protoplast fusion procedure to genetic analysis of C. albicans.

  5. Clinical Significance of EML4-ALK Fusion Gene and Association with EGFR and KRAS Gene Mutations in 208 Chinese Patients with Non-Small Cell Lung Cancer

    PubMed Central

    Wei, Sen; Wang, Jing; Wang, Min; Wang, Yuli; Zhou, Qinghua; Liu, Hongyu; Chen, Jun

    2013-01-01

    The EML4-ALK fusion gene has been recently identified in a small subset of non-small cell lung cancer (NSCLC) patients who respond positively to ALK inhibitors. The characteristics of the EML4-ALK fusion gene in Chinese patients with NSCLC are poorly understood. Here, we report on the prevalence of EML4-ALK, EGFR status and KRAS mutations in 208 Chinese patients with NSCLC. EGFR mutations were found in 24.5% (51/208) of patients. In concordance with previous reports, these mutations were identified at high frequencies in females (47.5% vs 15.0% in males; P<0.05); never-smokers (42.3% vs 13.9% in smokers; P<0.05), and adenocarcinoma patients (44.2% vs 8.0% in non-adenocarcinoma patients; P<0.05). There were only 2.88% (6/208) patients with KRAS mutations in our study group. We identified 7 patients who harbored the EML4-ALK fusion gene (3.37%, 7/208), including 4 cases with variant 3 (57.1%), 2 with variant 1, and 1 with variant 2. All positive cases corresponded to female patients (11.5%, 7/61). Six of the positive cases were non-smokers (7.69%, 6/78). The incidence of EML4-ALK translocation in female, non-smoking adenocarcinoma patients was as high as 15.2% (5/33). No EGFR/KRAS mutations were detected among the EML4-ALK positive patients. Pathological analysis showed no difference between solid signet-ring cell pattern (4/7) and mucinous cribriform pattern (3/7) in ALK-positive patients. Immunostaining showed intratumor heterogeneity of ALK rearrangement in primary carcinomas and 50% (3/6) of metastatic tumors with ALK-negative staining. Meta-analysis demonstrated that EML4-ALK translocation occurred in 4.84% (125/2580) of unselected patients with NSCLC, and was also predominant in non-smoking patients with adenocarcinoma. Taken together, EML4-ALK translocations were infrequent in the entire NSCLC patient population, but were frequent in the NSCLC subgroup of female, non-smoker, adenocarcinoma patients. There was intratumor heterogeneity of ALK rearrangement in

  6. Inertial confinement fusion quarterly report, October-December 1996

    SciTech Connect

    Hammer, J.

    1997-01-01

    The articles in this issue report progress on: Supernova Hydrodynamics Experiments on the Nova Laser; Characterization of Laser-Driven Shock Waves Using Interferometry; Absolute Equation of State Measurements of Compressed Liquid Deuterium Using Nova; Low-Density-Foam Shells; Tetrahedral Hohlraums; The Rosseland Mean Opacity of a Composite Material at High Temperatures.

  7. A novel BCR-ABL1 fusion gene identified by next-generation sequencing in chronic myeloid leukemia.

    PubMed

    Lyu, Xiaodong; Yang, Jingke; Wang, Xianwei; Hu, Jieying; Liu, Bing; Zhao, Yu; Guo, Zhen; Liu, Bingshan; Fan, Ruihua; Song, Yongping

    2016-01-01

    BCR-ABL1 fusion proteins contain constitutively active tyrosine kinases that are potential candidates for targeted therapy with tyrosine kinase inhibitors such as imatinib in chronic myeloid leukemia (CML). However, uncharacterized BCR-ABL1 fusion genes can be missed by quantitative RT-PCR (qRT-PCR)-based routine screening methods, causing adverse effect on drug selection and treatment outcome. In this study, we demonstrated that the next-generation sequencing (NGS) can be employed to overcome this obstacle. Through NGS, we identified a novel BCR-ABL1 fusion gene with breakpoints in the BCR intron 14 and the ABL1 intron 2, respectively, in a rare case of CML. Its mRNA with an e14a3 junction was then detected using customized RT-PCR followed by Sanger sequencing. Subsequently, the patient received targeted medicine imatinib initially at 400 mg/day, and later 300 mg/day due to intolerance reactions. With this personalized treatment, the patient's condition was significantly improved. Interestingly, this novel fusion gene encodes a fusion protein containing a compromised SH3 domain, which is usually intact in the majority of CML cases, suggesting that dysfunctional SH3 domain may be associated with altered drug response and unique clinicopathological manifestations observed in this patient. We identified a novel BCR-ABL1 fusion gene using NGS in a rare case of CML while routine laboratory procedures were challenged, demonstrating the power of NGS as a diagnostic tool for detecting novel genetic mutations. Moreover, our new finding regarding the novel fusion variant will provide useful insights to improve the spectrum of the genomic abnormalities recognizable by routine molecular screening.

  8. In vivo characterization of a reporter gene system for imaging hypoxia-induced gene expression.

    PubMed

    Carlin, Sean; Pugachev, Andrei; Sun, Xiaorong; Burke, Sean; Claus, Filip; O'Donoghue, Joseph; Ling, C Clifton; Humm, John L

    2009-10-01

    To characterize a tumor model containing a hypoxia-inducible reporter gene and to demonstrate utility by comparison of reporter gene expression to the uptake and distribution of the hypoxia tracer (18)F-fluoromisonidazole ((18)F-FMISO). Three tumors derived from the rat prostate cancer cell line R3327-AT were grown in each of two rats as follows: (1) parental R3327-AT, (2) positive control R3327-AT/PC in which the HSV1-tkeGFP fusion reporter gene was expressed constitutively, (3) R3327-AT/HRE in which the reporter gene was placed under the control of a hypoxia-inducible factor-responsive promoter sequence (HRE). Animals were coadministered a hypoxia-specific marker (pimonidazole) and the reporter gene probe (124)I-2'-fluoro-2'-deoxy-1-beta-d-arabinofuranosyl-5-iodouracil ((124)I-FIAU) 3 h prior to sacrifice. Statistical analysis of the spatial association between (124)I-FIAU uptake and pimonidazole fluorescent staining intensity was then performed on a pixel-by-pixel basis. Utility of this system was demonstrated by assessment of reporter gene expression versus the exogenous hypoxia probe (18)F-FMISO. Two rats, each bearing a single R3327-AT/HRE tumor, were injected with (124)I-FIAU (3 h before sacrifice) and (18)F-FMISO (2 h before sacrifice). Statistical analysis of the spatial association between (18)F-FMISO and (124)I-FIAU on a pixel-by-pixel basis was performed. Correlation coefficients between (124)I-FIAU uptake and pimonidazole staining intensity were: 0.11 in R3327-AT tumors, -0.66 in R3327-AT/PC and 0.76 in R3327-AT/HRE, confirming that only in the R3327-AT/HRE tumor was HSV1-tkeGFP gene expression associated with hypoxia. Correlation coefficients between (18)F-FMISO and (124)I-FIAU uptakes in R3327-AT/HRE tumors were r=0.56, demonstrating good spatial correspondence between the two tracers. We have confirmed hypoxia-specific expression of the HSV1-tkeGFP fusion gene in the R3327-AT/HRE tumor model and demonstrated the utility of this model for the

  9. Cold fusion, Alchemist's dream

    SciTech Connect

    Clayton, E.D.

    1989-09-01

    In this report the following topics relating to cold fusion are discussed: muon catalysed cold fusion; piezonuclear fusion; sundry explanations pertaining to cold fusion; cosmic ray muon catalysed cold fusion; vibrational mechanisms in excited states of D{sub 2} molecules; barrier penetration probabilities within the hydrogenated metal lattice/piezonuclear fusion; branching ratios of D{sub 2} fusion at low energies; fusion of deuterons into {sup 4}He; secondary D+T fusion within the hydrogenated metal lattice; {sup 3}He to {sup 4}He ratio within the metal lattice; shock induced fusion; and anomalously high isotopic ratios of {sup 3}He/{sup 4}He.

  10. Lateral transpsoas interbody fusion (LTIF) with plate fixation and unilateral pedicle screws: a preliminary report.

    PubMed

    Kepler, Christopher K; Sharma, Amit K; Huang, Russel C

    2011-08-01

    Retrospective cohort study. We present the radiographic and clinical outcomes of 13 patients who underwent lateral transpsoas interbody fusion (LTIF) stabilized by unilateral pedicle screw instrumentation and anterior instrumentation. LTIF is a surgical technique that permits anterior column lumbar interbody fusion via a direct lateral transpsoas approach. Because of the inherent stability of the implants used and the minimal disruption of stabilizing ligaments associated with LTIF, this technique may allow use of less invasive adjunctive fixation methods including unilateral pedicle screw fixation. Information from medical records included patient demographics, medical comorbidities, clinical assessment, surgical time, blood loss, implant information, and complications. Oswestry Disability Index, Short Form-12, and visual analog pain scale scores were obtained. Postoperative imaging allowed assessment of fusion, subsidence, and alignment. Estimated blood loss averaged 225 mL and operative time averaged 261 minutes. No patients received a transfusion. Average length of hospital stay was 4.6 days. Oswestry Disability Index, Short Form-12, and visual analog pain scores demonstrated significant improvement. All patients with available 1 year postoperative imaging demonstrated solid fusion with average cranial and caudal subsidence of 1.8 and 0.8 mm, respectively. Two patients developed postoperative nondisplaced vertebral fractures through the anterior fixation screw tracts. Three patients developed transient postoperative hip flexion weakness and one also developed transient hypoesthesia in the anterior thigh, likely approach related. We report a series of patients treated with unilateral pedicle screw fixation with LTIF. Although the patient cohort is small, validated outcomes instruments were used and fusion was assessed by computed tomography scan in most cases. The data suggest that unilateral pedicle screw fixation may be adequate to achieve high fusion rates

  11. Use of hupS::lacZ gene fusion to study regulation of hydrogenase expression in Rhodobacter capsulatus: stimulation by H2.

    PubMed Central

    Colbeau, A; Vignais, P M

    1992-01-01

    The Escherichia coli beta-galactosidase enzyme was used as a reporter molecule for genetic fusions in Rhodobacter capsulatus. DNA fragments that were from the upstream region of the hydrogenase structural operon hupSLM and contained 5' hupS sequences were fused in frame to a promoterless lacZ gene, yielding fusion proteins comprising the putative signal sequence and the first 22 amino acids of the HupS protein joined to the eight amino acid of beta-galactosidase. We demonstrate the usefulness of the hupS::lacZ fusion in monitoring regulation of hydrogenase gene expression. The activities of plasmid-determined beta-galactosidase and chromosome-encoded hydrogenase changed in parallel in response to various growth conditions (light or dark, aerobiosis or anaerobiosis, and presence or absence of ammonia or of H2), showing that changes in hydrogenase activity were due to changes in enzyme synthesis. Molecular hydrogen stimulated hydrogenase synthesis in dark, aerobic cultures and in illuminated, anaerobic cultures. Analysis of hupS::lacZ expression in various mutants indicated that neither the hydrogenase structural genes nor NifR4 (sigma 54) was essential for hydrogen regulation of hydrogenase synthesis. PMID:1624420

  12. Obesity and Prostate Cancer Risk According to Tumor TMPRSS2:ERG Gene Fusion Status

    PubMed Central

    Egbers, Lieke; Luedeke, Manuel; Rinckleb, Antje; Kolb, Suzanne; Wright, Jonathan L.; Maier, Christiane; Neuhouser, Marian L.; Stanford, Janet L.

    2015-01-01

    The T2E gene fusion, formed by fusion of the transmembrane protease, serine 2, gene (TMPRSS2) with the erythroblast transformation-specific (ETS)-related gene (ERG), is found in approximately 50% of prostate cancers and may characterize distinct molecular subtypes of prostate cancer with different etiologies. We investigated the relationship between body mass index (BMI; weight (kg)/height (m)2) and prostate cancer risk by T2E status. Study participants were residents of King County, Washington, recruited for 2 population-based case-control studies conducted in 1993–1996 and 2002–2005. Tumor T2E status was determined for 563 prostate cancer patients who underwent radical prostatectomy. Information on weight, height, and covariables was obtained through in-person interviews. We performed polytomous logistic regression to calculate odds ratios and 95% confidence intervals for T2E-positive and -negative prostate cancer. Comparing the highest BMI quartile with the lowest, inverse associations were observed between recent (≥29.7 vs. <24.5: odds ratio = 0.66, 95% confidence interval: 0.45, 0.97) and maximum (≥31.8 vs. <25.9: odds ratio = 0.69, 95% confidence interval: 0.47, 1.02) BMI and the risk of T2E-positive prostate cancer. No significant associations were seen for men with T2E-negative tumors. This study provides evidence that obesity is specifically associated with reduced risk of developing androgen-responsive T2E fusion–positive tumors. The altered steroid hormone profile in obese men may contribute to this inverse association. PMID:25852077

  13. Fusion materials semiannual progress report for period ending June 30, 1997

    SciTech Connect

    1997-08-01

    This is the twenty-second in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. Topics covered here are: vanadium alloys; silicon carbide composites; ferritic/martensitic steels; austenitic stainless steels; insulating ceramics and optical materials; solid breeding materials; radiation effects mechanistic studies and experimental methods; dosimetry damage parameters; activation calculations; materials engineering and design requirements; irradiation facilities; test matrices; and experimental methods.

  14. Identification and assembly of V genes as idiotype-specific DNA fusion vaccines in multiple myeloma.

    PubMed

    Sahota, Surinder S; Townsend, Mark; Stevenson, Freda K

    2005-01-01

    Tumor-specific markers are important in identifying and tracking malignant cells. In this regard, functionally rearranged immunoglobulin variable (V) region genes in B-cell tumors fulfill and extend these criteria. V genes provide signature motifs in tumor cells and can delineate critical features of the clonal history of the cell of origin. They also define a tumor-specific antigen, which can be targeted for immunotherapy. Our focus has been on using novel DNA fusion vaccines to induce antitumor immunity. Here, we describe in detail the methods for identifying tumor-derived V genes at the nucleotide level in the malignant plasma cells of multiple myeloma. We further present the methodology for assembly of tumor V genes as single-chain variable region fragments (scFv), fused in frame with an immunopotentiating nontoxic bacterial sequence, Fragment C (FrC) of tetanus toxin. These scFv.FrC DNA vaccines provide protection in myeloma models and are currently in clinical trials. The vaccines are patient specific and can be rapidly assembled for clinical use.

  15. Paediatric and adult soft tissue sarcomas with NTRK1 gene fusions: a subset of spindle cell sarcomas unified by a prominent myopericytic/haemangiopericytic pattern.

    PubMed

    Haller, Florian; Knopf, Jasmin; Ackermann, Anne; Bieg, Matthias; Kleinheinz, Kortine; Schlesner, Matthias; Moskalev, Evgeny A; Will, Rainer; Satir, Ali Abdel; Abdelmagid, Ibtihalat E; Giedl, Johannes; Carbon, Roman; Rompel, Oliver; Hartmann, Arndt; Wiemann, Stefan; Metzler, Markus; Agaimy, Abbas

    2016-04-01

    Neoplasms with a myopericytomatous pattern represent a morphological spectrum of lesions encompassing myopericytoma of the skin and soft tissue, angioleiomyoma, myofibromatosis/infantile haemangiopericytoma and putative neoplasms reported as malignant myopericytoma. Lack of reproducible phenotypic and genetic features of malignant myopericytic neoplasms have prevented the establishment of myopericytic sarcoma as an acceptable diagnostic category. Following detection of a LMNA-NTRK1 gene fusion in an index case of paediatric haemangiopericytoma-like sarcoma by combined whole-genome and RNA sequencing, we identified three additional sarcomas harbouring NTRK1 gene fusions, termed 'spindle cell sarcoma, NOS with myo/haemangiopericytic growth pattern'. The patients were two children aged 11 months and 2 years and two adults aged 51 and 80 years. While the tumours of the adults were strikingly myopericytoma-like, but with clear-cut atypical features, the paediatric cases were more akin to infantile myofibromatosis/haemangiopericytoma. All cases contained numerous thick-walled dysplastic-like vessels with segmental or diffuse nodular myxohyaline myo-intimal proliferations of smooth muscle actin-positive cells, occasionally associated with thrombosis. Immunohistochemistry showed variable expression of smooth muscle actin and CD34, but other mesenchymal markers, including STAT6, were negative. This study showed a novel variant of myo/haemangiopericytic sarcoma with recurrent NTRK1 gene fusions. Given the recent introduction of a novel therapeutic approach targeting NTRK fusion-positive neoplasms, recognition of this rare but likely under-reported sarcoma variant is strongly encouraged. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  16. Analysis of the fusion protein gene of the porcine rubulavirus LPMV: comparative analysis of paramyxovirus F proteins.

    PubMed

    Berg, M; Bergvall, A C; Svenda, M; Sundqvist, A; Moreno-López, J; Linné, T

    1997-01-01

    Complementary DNA clones representing the fusion (F) protein gene of the porcine rubulavirus LPMV were isolated and sequenced. The F gene was found to be 1,845 nucleotides long containing one long open reading frame capable of encoding a protein of 541 amino acids. The cleavage motif for F0 into F1 and F2 is His-Arg-Lys-Lys-Arg. A sequence comparison and a phylogenetic analysis was performed in order to identify possible functional domains of paramyxovirus fusion proteins and also to classify the porcine rubulavirus. The F gene of LPMV is most closely related to the human mumps virus and simian virus type 5 F genes, and is therefore classified into the rubulavirus genus. A coding region for a small hydrophobic protein was however not found between the F and hemagglutinin-neuraminidase (HN) genes as previously found in both SV5 and mumps.

  17. Simultaneous detection of 45 fusion genes in leukemia by dual-color fluorescence real-time PCR.

    PubMed

    Zheng, Z; Zhang, P; He, G; Liao, K; Wang, Z; Pan, J; Du, K; Du, J; Li, B-A

    2017-04-01

    Detection of recurrent genetic abnormalities is of great significance for a refined diagnosis and assessment of prognosis in leukemia. Conventional nested reverse transcription PCR is labor intensive and time-consuming. We have developed a novel dual-color TaqMan probe-based real-time PCR method for the simultaneous screening of 45 fusion transcripts in 12 parallel reactions. The method was tested and validated with cell lines carrying known fusion transcripts and patient samples. A multiplex real-time PCR method was successfully developed for rapid detection of 45 fusion genes and validated for 15 of the more commonly detected fusion genes. Intra-assay reproducibility assessed for the most frequent rearrangements ranged from 0.41% to 0.74% for the coefficient of variation (CV) of cycle threshold (Ct) and the interassay reproducibility ranged from 1.62% to 2.83% in five separate experiments. The lowest detection limit for the translocations tested ranged between 1 : 16 000 and 1 : 32 000. Validation of the method with 213 patient samples showed 100% specificity and excellent consistence with conventional nested RT-PCR. Overall, we believe that this method is easily applicable, cost-effective, and clinically useful for a rapid screening of fusion genes in the initial diagnostic phase of leukemia. Its use can also be extended to the monitoring of minimal residual disease. © 2017 John Wiley & Sons Ltd.

  18. Long Term Non-Invasive Imaging of Embryonic Stem Cells Using Reporter Genes

    PubMed Central

    Sun, Ning; Lee, Andrew; Wu, Joseph C.

    2013-01-01

    Development of non-invasive and accurate methods to track cell fate following delivery will greatly expedite transition of embryonic stem (ES) cell therapy to the clinic. Here we describe a protocol for the in vivo monitoring of stem cell survival, proliferation, and migration using reporter genes. We established stable ES cell lines constitutively expressing double fusion (DF; enhanced green fluorescent protein and firefly luciferase) or triple fusion (TF; monomeric red fluorescent protein, firefly luciferase, and herpes simplex virus thymidine kinase) reporter genes using lentiviral transduction. We used fluorescence activated cell sorting to purify these populations in vitro, bioluminescence imaging and positron emission tomography imaging to track them in vivo, and fluorescence immunostaining to confirm the results ex vivo. Unlike other methods of cell tracking such as iron particle and radionuclide labeling, reporter genes are inherited genetically and can be used to monitor cell proliferation and survival for the lifetime of transplanted cells and their progeny. PMID:19617890

  19. Ionic solid hydrogen fuel: Experimental investigation of cluster-impact fusion. Final report 1 Jul-30 Sep 90

    SciTech Connect

    Bae, Y.K.; Lorents, D.C.; Young, S.; Staider, K.

    1991-01-24

    This report discusses the investigation of a new novel fusion method: the use of deuterium-containing clusters for igniting fusion (cluster-impact fusion, CIF). If CIF becomes practical, the energy density that can be achieved with the DT fuel is 3.4 X 10 to the 14 power J/kg, which is eight orders of magnitude larger than the energy density of LO{sub X}/H{sub 2} (1,600,000 j/kg). For missions with specific impulse less than 100,000 s, the CIF rocket performance will be essentially identical to that of antimatter. Under the current project, we have successfully built and demonstrated a new cluster-impact fusion facility by extending the existing hydrogen cluster facility. We are confident that the new fusion method discovered at Brookhaven is very promising; thus, we are ready to investigate means of increasing the fusion yield to a practical level for rocket propulsion applications.

  20. Gemini, a Bifunctional Enzymatic and Fluorescent Reporter of Gene Expression

    PubMed Central

    Endy, Drew

    2009-01-01

    Background The development of collections of quantitatively characterized standard biological parts should facilitate the engineering of increasingly complex and novel biological systems. The existing enzymatic and fluorescent reporters that are used to characterize biological part functions exhibit strengths and limitations. Combining both enzymatic and fluorescence activities within a single reporter protein would provide a useful tool for biological part characterization. Methodology/Principal Findings Here, we describe the construction and quantitative characterization of Gemini, a fusion between the β-galactosidase (β-gal) α-fragment and the N-terminus of full-length green fluorescent protein (GFP). We show that Gemini exhibits functional β-gal activity, which we assay with plates and fluorometry, and functional GFP activity, which we assay with fluorometry and microscopy. We show that the protein fusion increases the sensitivity of β-gal activity and decreases the sensitivity of GFP. Conclusions/Significance Gemini is therefore a bifunctional reporter with a wider dynamic range than the β-gal α-fragment or GFP alone. Gemini enables the characterization of gene expression, screening assays via enzymatic activity, and quantitative single-cell microscopy or FACS via fluorescence activity. The analytical flexibility afforded by Gemini will likely increase the efficiency of research, particularly for screening and characterization of libraries of standard biological parts. PMID:19888458

  1. Assessing the efficacy of vesicle fusion with planar membrane arrays using a mitochondrial porin as reporter

    SciTech Connect

    Pszon-Bartosz, Kamila; Hansen, Jesper S.; Stibius, Karin B.; Groth, Jesper S.; Helix-Nielsen, Claus

    2011-03-04

    Research highlights: {yields} We have established a vesicle fusion efficacy assay based on the major non-specific porin of Fusobacterium nucleatum (FomA). {yields} Maximal fusion obtained was almost 150,000 porin insertions during 20 min. {yields} Incorporation can be either first order or exponential kinetics which has implications for establishing protein delivery to biomimetic membranes. -- Abstract: Reconstitution of functionally active membrane protein into artificially made lipid bilayers is a challenge that must be overcome to create a membrane-based biomimetic sensor and separation device. In this study we address the efficacy of proteoliposome fusion with planar membrane arrays. We establish a protein incorporation efficacy assay using the major non-specific porin of Fusobacterium nucleatum (FomA) as reporter. We use electrical conductance measurements and fluorescence microscopy to characterize proteoliposome fusion with an array of planar membranes. We show that protein reconstitution in biomimetic membrane arrays may be quantified using the developed FomA assay. Specifically, we show that FomA vesicles are inherently fusigenic. Optimal FomA incorporation is obtained with a proteoliposome lipid-to-protein molar ratio (LPR) = 50 more than 10{sup 5} FomA proteins could be incorporated in a bilayer array with a total membrane area of 2 mm{sup 2} within 20 min. This novel assay for quantifying protein delivery into lipid bilayers may be a useful tool in developing biomimetic membrane applications.

  2. Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion.

    PubMed

    Cheng, Gong; Hu, Yongfei; Yin, Yeshi; Yang, Xi; Xiang, Chunsheng; Wang, Baohong; Chen, Yanfei; Yang, Fengling; Lei, Fang; Wu, Na; Lu, Na; Li, Jing; Chen, Quanze; Li, Lanjuan; Zhu, Baoli

    2012-11-01

    The human gut microbiota has a high density of bacteria that are considered a reservoir for antibiotic resistance genes (ARGs). In this study, one fosmid metagenomic library generated from the gut microbiota of four healthy humans was used to screen for ARGs against seven antibiotics. Eight new ARGs were obtained: one against amoxicillin, six against d-cycloserine, and one against kanamycin. The new amoxicillin resistance gene encodes a protein with 53% identity to a class D β-lactamase from Riemerella anatipestifer RA-GD. The six new d-cycloserine resistance genes encode proteins with 73-81% identity to known d-alanine-d-alanine ligases. The new kanamycin resistance gene encodes a protein of 274 amino acids with an N-terminus (amino acids 1-189) that has 42% identity to the 6'-aminoglycoside acetyltransferase [AAC(6')] from Enterococcus hirae and a C-terminus (amino acids 190-274) with 35% identity to a hypothetical protein from Clostridiales sp. SSC/2. A functional study on the novel kanamycin resistance gene showed that only the N-terminus conferred kanamycin resistance. Our results showed that functional metagenomics is a useful tool for the identification of new ARGs.

  3. Synthesis of Fusion Genes for Cloning by Megaprimer-Based PCR.

    PubMed

    Aguiar, Tatiana Q; Oliveira, Carla; Domingues, Lucília

    2017-01-01

    The polymerase chain reaction (PCR) is the technique of choice used to obtain DNA for cloning, because it rapidly provides high amounts of desired DNA fragments and allows the easy introduction of extremities adequate for enzyme restriction or homologous recombination, and of artificial, native, or modified sequence elements for specific applications. In this context, the use of megaprimer-based PCR strategies allows the versatile and fast assembly and amplification of tailor-made DNA sequences readily available for cloning.In this chapter, we describe the design and use of a megaprimer-based PCR protocol to construct customized fusion genes ready for cloning into commercial expression plasmids by restriction digestion and ligation.

  4. Annual report of the Summit Members' Working Group on Controlled Thermonuclear Fusion (Fusin Working Group (FWG))

    SciTech Connect

    none,

    1987-04-01

    The Summit Members' Working Group on Controlled Thermonuclear Fusion (Fusion Working Group (FWG)) was established in 1983 in response to the Declaration of the Heads of State and Government at the Versailles Economic Summit meeting of 1982, and in response to the subsequent report of the Working Group in Technology, Growth and Employment (TGE) as endorsed at the Williamsburg Summit meeting, 1983. This document contains the complete written record of each of the three FWG meetings which include the minutes, lists of attendees, agendas, statements, and summary conclusions as well as the full reports of the Technical Working Party. In addition, there is a pertinent exchange of correspondence between FWG members on the role of the Technical Working Party and a requested background paper on the modalities associated with a possible future ETR project.

  5. Genetic diversity of fusion gene (ORF 117), an analogue of vaccinia virus A27L gene of capripox virus isolates.

    PubMed

    Dashprakash, M; Venkatesan, Gnanavel; Ramakrishnan, Muthannan Andavar; Muthuchelvan, Dhanavelu; Sankar, Muthu; Pandey, Awadh Bihari; Mondal, Bimelendu

    2015-04-01

    The fusion gene (ORF 117) sequences of twelve (n = 12) capripox virus isolates namely sheeppox (SPPV) and goatpox (GTPV) viruses from India were demonstrated for their genetic and phylogenetic relationship among them. All the isolates were confirmed for their identity by routine PCR before targeting ORF 117 gene for sequence analysis. The designed primers specifically amplified ORF 117 gene as 447 bp fragment from total genomic DNA extracted from all the isolates. Sequence analysis revealed a significant percentage of identity among GTPV, SPPV and between them at both nucleotide and amino acid levels. The topology of the phylogenetic tree revealed that three distinct clusters corresponding to SPPV, GTPV and lumpy skin disease virus was formed. However, SPPV Pune/08 and SPPV Roumanian Fanar isolates were clustered into GTPV group as these two isolates showed a 100 and 99.3 % identity with GTPV isolates of India at nt and aa levels, respectively. Protein secondary structure and 3D view was predicted and found that it has high antigenic index and surface probability with low hydrophobicity, and it can be targeted for expression and its evaluation to explore its diagnostic potential in epidemiological investigation in future.

  6. Codon-Optimized NADH Oxidase Gene Expression and Gene Fusion with Glycerol Dehydrogenase for Bienzyme System with Cofactor Regeneration

    PubMed Central

    Zhou, Qiang; Wang, Shizhen

    2015-01-01

    NADH oxidases (NOXs) play an important role in maintaining balance of NAD+/NADH by catalyzing cofactors regeneration. The expression of nox gene from Lactobacillus brevis in Escherichia coli BL21 (BL21 (DE3)) was studied. Two strategies, the high AT-content in the region adjacent to the initiation codon and codon usage of the whole gene sequence consistent with the host, obtained the NOX activity of 59.9 U/mg and 73.3 U/mg (crude enzyme), with enhanced expression level of 2.0 and 2.5-folds, respectively. Purified NOX activity was 213.8 U/mg. Gene fusion of glycerol dehydrogenase (GDH) and NOX formed bifuctional multi-enzymes for bioconversion of glycerol coupled with coenzyme regeneration. Kinetic parameters of the GDH-NOX for each substrate, glycerol and NADH, were calculated as Vmax(Glycerol) 20 μM/min, Km(Glycerol) 19.4 mM, Vmax (NADH) 12.5 μM/min and Km (NADH) 51.3 μM, respectively, which indicated the potential application of GDH-NOX for quick glycerol analysis and dioxyacetone biosynthesis. PMID:26115038

  7. Effects of an adenoviral vector containing a suicide gene fusion on growth characteristics of breast cancer cells.

    PubMed

    Kong, Heng; Liu, Chunli; Zhu, Ting; Huang, Zonghai; Yang, Liucheng; Li, Qiang

    2014-12-01

    The herpes simplex virus thymidine kinase/ganciclovir (HSV‑TK/GCV) and the cytosine deaminase/5‑fluorocytosine (CD/5‑FC) systems have been widely applied in suicide gene therapy for cancer. Although suicide gene therapy has been successfully used in vitro and in vivo studies, the number of studies on the effects of recombinant adenoviruses (Ads) containing suicide genes on target cancer cells is limited. The aim of this study was to examine whether recombinant Ads containing the CD/TK fusion gene affect cell proliferation of breast cancer cells in vitro. In the present study, we explored the use of a recombinant adenoviral vector to deliver the CD/TK fusion gene to the breast cancer cell line MCF‑7. We found that the recombinant adenoviral vector efficiently infected MCF‑7 cells. Western blot analysis revealed that CD and TK proteins are expressed in the infected cells. The infected breast cancer cells did not show any significant changes in morphology, ultrastructure, cell growth, and cell‑cycle distribution compared to the uninfected cells. This study revealed that the Ad‑vascular endothelial growth factor promoter (VEGFp)‑CD/TK vector is non‑toxic to MCF‑7 cells at the appropriate titer. Our results indicate that it is feasible to use a recombinant adenoviral vector containing the CD/TK fusion gene in suicide gene therapy to target breast cancer cells.

  8. Antitumor activities of the targeted multi-tyrosine kinase inhibitor lenvatinib (E7080) against RET gene fusion-driven tumor models.

    PubMed

    Okamoto, Kiyoshi; Kodama, Kotaro; Takase, Kazuma; Sugi, Naoko Hata; Yamamoto, Yuji; Iwata, Masao; Tsuruoka, Akihiko

    2013-10-28

    RET gene fusions are recurrent oncogenes identified in thyroid and lung carcinomas. Lenvatinib is a multi-tyrosine kinase inhibitor currently under evaluation in several clinical trials. Here we evaluated lenvatinib in RET gene fusion-driven preclinical models. In cellular assays, lenvatinib inhibited auto-phosphorylation of KIF5B-RET, CCDC6-RET, and NcoA4-RET. Lenvatinib suppressed the growth of CCDC6-RET human thyroid and lung cancer cell lines, and as well, suppressed anchorage-independent growth and tumorigenicity of RET gene fusion-transformed NIH3T3 cells. These results demonstrate that lenvatinib can exert antitumor activity against RET gene fusion-driven tumor models by inhibiting oncogenic RET gene fusion signaling.

  9. Noninvasive molecular imaging using reporter genes.

    PubMed

    Brader, Peter; Serganova, Inna; Blasberg, Ronald G

    2013-02-01

    Noninvasive reporter gene imaging is a component of molecular imaging. Reporter imaging can provide noninvasive assessments of endogenous biologic processes in living subjects and can be performed using different imaging modalities. This review will focus on radionuclide-based reporter gene imaging as developed and applied in preclinical and clinical studies. Examples of different reporter systems are presented, with a focus on human reporter systems. Selected applications are discussed, including adoptive cell therapies, gene and oncoviral therapies, oncogenesis, signal pathway monitoring, and imaging drug treatment. Molecular imaging, and noninvasive reporter gene imaging in particular, are making important contributions to our understanding of disease development, progression, and treatment in our current era of molecular medicine and individualized patient care.

  10. Inducible expression of a fusion gene encoding two proteinase inhibitors leads to insect and pathogen resistance in transgenic rice.

    PubMed

    Quilis, Jordi; López-García, Belén; Meynard, Donaldo; Guiderdoni, Emmanuel; San Segundo, Blanca

    2014-04-01

    Plant proteinase inhibitors (PIs) are considered as candidates for increased insect resistance in transgenic plants. Insect adaptation to PI ingestion might, however, compromise the benefits received by transgenic expression of PIs. In this study, the maize proteinase inhibitor (MPI), an inhibitor of insect serine proteinases, and the potato carboxypeptidase inhibitor (PCI) were fused into a single open reading frame and introduced into rice plants. The two PIs were linked using either the processing site of the Bacillus thuringiensis Cry1B precursor protein or the 2A sequence from the foot-and-mouth disease virus (FMDV). Expression of each fusion gene was driven by the wound- and pathogen-inducible mpi promoter. The mpi-pci fusion gene was stably inherited for at least three generations with no penalty on plant phenotype. An important reduction in larval weight of Chilo suppressalis fed on mpi-pci rice, compared with larvae fed on wild-type plants, was observed. Expression of the mpi-pci fusion gene confers resistance to C. suppressalis (striped stem borer), one of the most important insect pest of rice. The mpi-pci expression systems described may represent a suitable strategy for insect pest control, better than strategies based on the use of single PI genes, by preventing insect adaptive responses. The rice plants expressing the mpi-pci fusion gene also showed enhanced resistance to infection by the fungus Magnaporthe oryzae, the causal agent of the rice blast disease. Our results illustrate the usefulness of the inducible expression of the mpi-pci fusion gene for dual resistance against insects and pathogens in rice plants.

  11. Inertial confinement fusion quarterly report, October--December 1992. Volume 3, No. 1

    SciTech Connect

    Dixit, S.N.

    1992-12-31

    This report contains papers on the following topics: The Beamlet Front End: Prototype of a new pulse generation system;imaging biological objects with x-ray lasers; coherent XUV generation via high-order harmonic generation in rare gases; theory of high-order harmonic generation; two-dimensional computer simulations of ultra- intense, short-pulse laser-plasma interactions; neutron detectors for measuring the fusion burn history of ICF targets; the recirculator; and lasnex evolves to exploit computer industry advances.

  12. Fusion development and technology. Technical progress report, October 15, 1990--October 14, 1993

    SciTech Connect

    Montgomery, D.B.

    1992-06-01

    This report discusses the following: superconducting magnet technology; high field superconductors; advanced magnetic system and divertor development; poloidal field coils; gyrotron development; commercial reactor studies--aries; ITER physics: alpha physics and alcator R&D for ITER; lower hybrid current drive and heating in the ITER device; ITER superconducting PF scenario and magnet analysis; ITER systems studies; and safety, environmental and economic factors in fusion development.

  13. Inertial Confinement Fusion quarterly report, October--December 1994. Volume 5, No. 1

    SciTech Connect

    1995-09-01

    The ICF quarterly report is published by the Inertial Confinement Fusion Program at the Lawrence Livermore National Laboratory. Topics included in this issue include: system description and initial performance results for beamlet, design and performance of the beamlet amplifiers and optical switch, beamlet pulse-generation and wavefront-control system, large-aperture, high- damage-threshold optics for beamlet, beamlet pulsed power system, beamlet laser diagnostics, and beam propagation and frequency conversion modeling for the beamlet laser.

  14. Low-density hydrocarbon foams for laser fusion targets: Progress report, 1987

    SciTech Connect

    Haendler, B.L.; Buckley, S.R.; Chen, C.; Cook, A.R.; Cook, R.C.; Hair, L.M.; Kong, F.M.; Kramer, H.D.; Letts, S.A.; Overturf, G.E. III

    1988-06-01

    This report describes progress made in the development of direct-drive hydrocarbon foam targets for laser inertial confinement fusion during 1987. The foam materials are polystyrene, resorcinol-formaldehyde, carbonized resorcinol-formaldehyde, and cellulose acetate. The processes for making the foams, their properties, characterization techniques, and the relationship of their properties to target specifications are presented. Progress in the creation and testing of prototype targets is also described.

  15. MATRIX FACTORIZATION-BASED DATA FUSION FOR GENE FUNCTION PREDICTION IN BAKER’S YEAST AND SLIME MOLD

    PubMed Central

    ŽITNIK, MARINKA; ZUPAN, BLAŽ

    2014-01-01

    The development of effective methods for the characterization of gene functions that are able to combine diverse data sources in a sound and easily-extendible way is an important goal in computational biology. We have previously developed a general matrix factorization-based data fusion approach for gene function prediction. In this manuscript, we show that this data fusion approach can be applied to gene function prediction and that it can fuse various heterogeneous data sources, such as gene expression profiles, known protein annotations, interaction and literature data. The fusion is achieved by simultaneous matrix tri-factorization that shares matrix factors between sources. We demonstrate the effectiveness of the approach by evaluating its performance on predicting ontological annotations in slime mold D. discoideum and on recognizing proteins of baker’s yeast S. cerevisiae that participate in the ribosome or are located in the cell membrane. Our approach achieves predictive performance comparable to that of the state-of-the-art kernel-based data fusion, but requires fewer data preprocessing steps. PMID:24297565

  16. Segregation of myoblast fusion and muscle-specific gene expression by distinct ligand-dependent inactivation of GSK-3β

    PubMed Central

    Pansters, N. A. M.; van der Velden, J. L. J.; Kelders, M. C. J. M.; Laeremans, H.; Schols, A. M. W. J.

    2010-01-01

    Myogenic differentiation involves myoblast fusion and induction of muscle-specific gene expression, which are both stimulated by pharmacological (LiCl), genetic, or IGF-I-mediated GSK-3β inactivation. To assess whether stimulation of myogenic differentiation is common to ligand-mediated GSK-3β inactivation, myoblast fusion and muscle-specific gene expression were investigated in response to Wnt-3a. Moreover, crosstalk between IGF-I/GSK-3β/NFATc3 and Wnt/GSK-3β/β-catenin signaling was assessed. While both Wnt-3a and LiCl promoted myoblast fusion, muscle-specific gene expression was increased by LiCl, but not by Wnt-3a or β-catenin over-expression. Furthermore, LiCl and IGF-I, but not Wnt-3a, increased NFATc3 transcriptional activity. In contrast, β-catenin-dependent transcriptional activity was increased by Wnt-3a and LiCl, but not IGF-I. These results for the first time reveal a segregated regulation of myoblast fusion and muscle-specific gene expression following stimulation of myogenic differentiation in response to distinct ligand-specific signaling routes of GSK-3β inactivation. Electronic supplementary material The online version of this article (doi:10.1007/s00018-010-0467-7) contains supplementary material, which is available to authorized users. PMID:20694829

  17. Drosophila Erect wing (Ewg) controls mitochondrial fusion during muscle growth and maintenance by regulation of the Opa1-like gene.

    PubMed

    Rai, Mamta; Katti, Prasanna; Nongthomba, Upendra

    2014-01-01

    Mitochondrial biogenesis and morphological changes are associated with tissue-specific functional demand, but the factors and pathways that regulate these processes have not been completely identified. A lack of mitochondrial fusion has been implicated in various developmental and pathological defects. The spatiotemporal regulation of mitochondrial fusion in a tissue such as muscle is not well understood. Here, we show in Drosophila indirect flight muscles (IFMs) that the nuclear-encoded mitochondrial inner membrane fusion gene, Opa1-like, is regulated in a spatiotemporal fashion by the transcription factor/co-activator Erect wing (Ewg). In IFMs null for Ewg, mitochondria undergo mitophagy and/or autophagy accompanied by reduced mitochondrial functioning and muscle degeneration. By following the dynamics of mitochondrial growth and shape in IFMs, we found that mitochondria grow extensively and fuse during late pupal development to form the large tubular mitochondria. Our evidence shows that Ewg expression during early IFM development is sufficient to upregulate Opa1-like, which itself is a requisite for both late pupal mitochondrial fusion and muscle maintenance. Concomitantly, by knocking down Opa1-like during early muscle development, we show that it is important for mitochondrial fusion, muscle differentiation and muscle organization. However, knocking down Opa1-like, after the expression window of Ewg did not cause mitochondrial or muscle defects. This study identifies a mechanism by which mitochondrial fusion is regulated spatiotemporally by Ewg through Opa1-like during IFM differentiation and growth.

  18. Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B.

    PubMed

    Kimura, Hirokazu; Nagasawa, Koo; Kimura, Ryusuke; Tsukagoshi, Hiroyuki; Matsushima, Yuki; Fujita, Kiyotaka; Hirano, Eiko; Ishiwada, Naruhiko; Misaki, Takako; Oishi, Kazunori; Kuroda, Makoto; Ryo, Akihide

    2017-08-01

    In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10(-4)substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. High prostate cancer gene 3 (PCA3) scores are associated with elevated Prostate Imaging Reporting and Data System (PI-RADS) grade and biopsy Gleason score, at magnetic resonance imaging/ultrasonography fusion software-based targeted prostate biopsy after a previous negative standard biopsy.

    PubMed

    De Luca, Stefano; Passera, Roberto; Cattaneo, Giovanni; Manfredi, Matteo; Mele, Fabrizio; Fiori, Cristian; Bollito, Enrico; Cirillo, Stefano; Porpiglia, Francesco

    2016-11-01

    To determine the association among prostate cancer gene 3 (PCA3) score, Prostate Imaging Reporting and Data System (PI-RADS) grade and Gleason score, in a cohort of patients with elevated prostate-specific antigen (PSA), undergoing magnetic resonance imaging/ultrasonography fusion software-based targeted prostate biopsy (TBx) after a previous negative randomised 'standard' biopsy (SBx). In all, 282 patients who underwent TBx after previous negative SBx and a PCA3 urine assay, were enrolled. The associations between PCA3 score/PI-RADS and PCA3 score/Gleason score were investigated by K-means clustering, a receiver operating characteristic analysis and binary logistic regression. The PCA3 score difference for the negative vs positive TBx cohorts was highly statistically significant. A 1-unit increase in the PCA3 score was associated to a 2.4% increased risk of having a positive TBx result. A PCA3 score of >80 and a PI-RADS grade of ≥4 were independent predictors of a positive TBx. The association between the PCA3 score and PI-RADS grade was statistically significant (the median PCA3 score for PI-RADS grade groups 3, 4, and 5 was 58, 104, and 146, respectively; P = 0.006). A similar pattern was detected for the relationship between the PCA3 score and Gleason score; an increasing PCA3 score was associated with a worsening Gleason score (median PCA3 score equal to 62, 105, 132, 153, 203, and 322 for Gleason Score 3+4, 4+3, 4+4, 4+5, 5+4, and 5+5, respectively; P < 0.001). TBx improved PCA3 score diagnostic and prognostic performance for prostate cancer. The PCA3 score was directly associated both with biopsy Gleason score and PI-RADS grade: notably, in the 'indeterminate' PI-RADS grade 3 subgroup. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

  20. Overexpression of Recombinant Human Teriparatide, rhPTH (1–34) in Escherichia coli : An Innovative Gene Fusion Approach

    PubMed Central

    Bakhtiari, Nahid; Amini Bayat, Zahra; Sagharidouz, Sepideh; Vaez, Mohsen

    2017-01-01

    Background: Parathyroid hormone is an 84-amino acid peptide secreted by the parathyroid glands. Its physiological role is maintenance of normal serum calcium level and bone remodeling. Biological activity of this hormone is related to N-terminal 1–34 amino acids. The recombinant form of hormone (1–34) has been approved for treatment of osteoporosis from 2002. In this study, a novel fusion partner has been developed for preparation of high yield recombinant 1–34 amino acids of hPTH. Methods: Novel nucleotide cassette designed encoding a chimeric fusion protein comprising of a fusion partner consisting of a His-tag in N-terminal, 53 amino acids belong to Escherichia coli (E. coli) β-galactosidase (LacZ) gene, a linker sequence for increasing of expression and protection of target peptide structure from fusion tag effect, an Enteropeptidase cleavage site, rhPTH (1–34) gene fragment. Optimized fusion gene was synthesized and ligated into pET-28a vector under control of T7 promoter, and then transformed in E. coli (DH5α) cells. Positive clones containing this gene were double digested with NcoI and-BamHI and also approved by sequencing. Gene overexpression was observed in SDS-PAGE after induction with 0.2 mM IPTG. Confirmation of gene expression was performed by western blotting using anti-His-tag antibody conjugated with peroxidase. Results: By this fusion gene design approach, we achieved a high level expression of the rhPTH, where it represented at least 43.7% of the total protein as determined by SDS-PAGE and confirmed by western blotting. Conclusion: In addition to high level expression of the designed gene in this work, specific amino acid sequence of bacterial β-galactosidase was selected as major part of carrier tag for protection of this hormone as important step of recombinant rhPTH with relevant isoelectronic point (pI). This innovation resulted in recombinant production of hPTH very well and the gene construct could be applied as a pattern for

  1. Fusion of the FUS and CREB3L2 genes in a supernumerary ring chromosome in low-grade fibromyxoid sarcoma.

    PubMed

    Bartuma, Hammurabi; Möller, Emely; Collin, Anna; Domanski, Henryk A; Von Steyern, Fredrik Vult; Mandahl, Nils; Mertens, Fredrik

    2010-06-01

    Low-grade fibromyxoid sarcoma (LGFMS) is a rare, low-grade malignant soft tissue tumor that is often mistaken for either benign or more malignant tumor types. Commonly, this tumor affects young adults and typically arises in the deep proximal extremities or trunk with frequent recurrences and can metastasize to the lungs many years later. Most cases have a recurrent balanced translocation involving chromosomes 7 and 16, t(7;16)(q32-34;p11), which leads to the fusion of the FUS and CREB3L2 genes. However, supernumerary ring chromosomes have been identified in a subset of FUS/CREB3L2-positive LGFMS, but it has not yet been formally demonstrated that such ring chromosomes harbor the FUS/CREB3L2 fusion gene. Here, we report the genetic findings of a supernumerary ring chromosome from an LGFMS from a 77-year-old man. Chromosome banding analysis revealed a supernumerary ring chromosome, and further studies with fluorescence in situ hybridization and reverse transcriptase-polymerase chain reaction (RT-PCR) showed that the ring contained material from chromosomes 7 and 16, that the FUS gene was present in two rearranged copies, and that it expressed the FUS/CREB3L2 fusion gene. Moreover, an assessment of previously reported cases showed that tumors with ring chromosomes relapsed more often than tumors with a balanced t(7;16), suggesting that ring formation in LGFMS is correlated with tumor progression. Copyright 2010 Elsevier Inc. All rights reserved.

  2. Pandemic H1N1 influenza A directly induces a robust and acute inflammatory gene signature in primary human bronchial epithelial cells downstream of membrane fusion

    SciTech Connect

    Paquette, Stéphane G.; Banner, David; Chi, Le Thi Bao; Leon, Alberto J.; Xu, Luoling; Ran, Longsi; Huang, Stephen S.H.; Farooqui, Amber; and others

    2014-01-05

    Pandemic H1N1 influenza A (H1N1pdm) elicits stronger pulmonary inflammation than previously circulating seasonal H1N1 influenza A (sH1N1), yet mechanisms of inflammatory activation in respiratory epithelial cells during H1N1pdm infection are unclear. We investigated host responses to H1N1pdm/sH1N1 infection and virus entry mechanisms in primary human bronchial epithelial cells in vitro. H1N1pdm infection rapidly initiated a robust inflammatory gene signature (3 h post-infection) not elicited by sH1N1 infection. Protein secretion inhibition had no effect on gene induction. Infection with membrane fusion deficient H1N1pdm failed to induce robust inflammatory gene expression which was rescued with restoration of fusion ability, suggesting H1N1pdm directly triggered the inflammatory signature downstream of membrane fusion. Investigation of intra-virion components revealed H1N1pdm viral RNA (vRNA) triggered a stronger inflammatory phenotype than sH1N1 vRNA. Thus, our study is first to report H1N1pdm induces greater inflammatory gene expression than sH1N1 in vitro due to direct virus–epithelial cell interaction. - Highlights: • We investigated H1N1pdm/sH1N1 infection in primary epithelial cells. • H1N1pdm directly initiated a robust inflammatory gene signature, sH1N1 did not. • H1N1pdm viral RNA triggered a stronger response than sH1N1. • H1N1pdm induces greater response due to direct virus–cell interaction. • These results have potential to impact vaccine and therapeutic development.

  3. Synovial Sarcoma Microvesicles Harbor the SYT-SSX Fusion Gene Transcript: Comparison of Different Methods of Detection and Implications in Biomarker Research

    PubMed Central

    Fricke, A.; Ullrich, P. V.; Cimniak, A. F. V.; Follo, M.; Nestel, S.; Heimrich, B.; Nazarenko, I.; Stark, G. B.; Bannasch, H.; Braig, D.; Eisenhardt, S. U.

    2016-01-01

    Background. Synovial sarcoma is an aggressive soft-tissue malignancy. This study examines the presence of the SYT-SSX fusion transcript in synovial sarcoma microvesicles as well as its potential role as a biomarker for synovial sarcoma. Patients and Methods. Microvesicle release of synovial sarcoma cells was examined by transmission electron microscopy. RNA-content was analyzed by qPCR, nested PCR, nested qPCR, and droplet digital PCR to compare their sensitivity for detection of the SYT-SSX fusion gene transcript. Whole blood RNA, RNA of mononuclear cells, and microvesicle RNA of synovial sarcoma patients were analyzed for the presence of the fusion gene transcripts. Results. Electron microscopic analysis revealed synovial sarcoma cells releasing membrane-enclosed microvesicles. In vitro, the SYT-SSX fusion gene transcript was detected in both synovial sarcoma cells and microvesicles. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA. In contrast, the fusion gene transcript was not detected in peripheral blood cells and microvesicles of synovial sarcoma patients. Conclusion. Synovial sarcoma cells release microvesicles harboring the SYT-SSX fusion transcript. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA; however, more sensitive assays are needed to detect cancer-specific microvesicles in the peripheral blood of cancer patients. PMID:27069481

  4. Synovial Sarcoma Microvesicles Harbor the SYT-SSX Fusion Gene Transcript: Comparison of Different Methods of Detection and Implications in Biomarker Research.

    PubMed

    Fricke, A; Ullrich, P V; Cimniak, A F V; Follo, M; Nestel, S; Heimrich, B; Nazarenko, I; Stark, G B; Bannasch, H; Braig, D; Eisenhardt, S U

    2016-01-01

    Background. Synovial sarcoma is an aggressive soft-tissue malignancy. This study examines the presence of the SYT-SSX fusion transcript in synovial sarcoma microvesicles as well as its potential role as a biomarker for synovial sarcoma. Patients and Methods. Microvesicle release of synovial sarcoma cells was examined by transmission electron microscopy. RNA-content was analyzed by qPCR, nested PCR, nested qPCR, and droplet digital PCR to compare their sensitivity for detection of the SYT-SSX fusion gene transcript. Whole blood RNA, RNA of mononuclear cells, and microvesicle RNA of synovial sarcoma patients were analyzed for the presence of the fusion gene transcripts. Results. Electron microscopic analysis revealed synovial sarcoma cells releasing membrane-enclosed microvesicles. In vitro, the SYT-SSX fusion gene transcript was detected in both synovial sarcoma cells and microvesicles. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA. In contrast, the fusion gene transcript was not detected in peripheral blood cells and microvesicles of synovial sarcoma patients. Conclusion. Synovial sarcoma cells release microvesicles harboring the SYT-SSX fusion transcript. Nested qPCR proved to be the most sensitive in detecting the SYT-SSX fusion gene mRNA; however, more sensitive assays are needed to detect cancer-specific microvesicles in the peripheral blood of cancer patients.

  5. Fusion materials semiannual progress report for the period ending December 31, 1995

    SciTech Connect

    1996-04-01

    This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The Fusion Materials Program is a national effort involving several national laboratories, universities, and industries. A large fraction of this work, particularly in relation to fission reactor experiments, is carried out collaboratively with partners in Japan, Russian, and the European Union. The purpose of this series of reports is to provide a working technical record for the use of the program participants, and to provide a means of communicating the efforts of materials scientists to the rest of the fusion community, both nationally and worldwide. The following subjects are covered: vanadium alloys; silicon carbide composite materials; ferritic/martensitic steels; copper alloys and high heat flux materials; austenitic stainless steels; insulating ceramics and optical materials; solid breeding materials; radiation effects; mechanistic studies and experimental methods dosimetry, damage parameters, and activation calculations; materials engineering and design requirements; and irradiation facilities, test matrices and experimental methods. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  6. Hh/Gli antagonist in acute myeloid leukemia with CBFA2T3-GLIS2 fusion gene.

    PubMed

    Masetti, Riccardo; Bertuccio, Salvatore Nicola; Astolfi, Annalisa; Chiarini, Francesca; Lonetti, Annalisa; Indio, Valentina; De Luca, Matilde; Bandini, Jessica; Serravalle, Salvatore; Franzoni, Monica; Pigazzi, Martina; Martelli, Alberto Maria; Basso, Giuseppe; Locatelli, Franco; Pession, Andrea

    2017-01-21

    CBFA2T3-GLIS2 is a fusion gene found in 17% of non-Down syndrome acute megakaryoblastic leukemia (non-DS AMKL, FAB M7) and in 8% of pediatric cytogenetically normal acute myeloid leukemia (CN-AML, in association with several French-American-British (FAB) subtypes). Children with AML harboring this aberration have a poor outcome, regardless of the FAB subtype. This fusion gene drives a peculiar expression pattern and leads to overexpression of some of Hedgehog-related genes. GLI-similar protein 2 (GLIS2) is closely related to the GLI family, the final effectors of classic Hedgehog pathway. These observations lend compelling support to the application of GLI inhibitors in the treatment of AML with the aberration CBFA2T3-GLIS2. GANT61 is, nowadays, the most potent inhibitor of GLI family proteins. We exposed to GANT61 AML cell lines and primary cells positive and negative for CBFA2T3-GLIS2 and analyzed the effect on cellular viability, induction of apoptosis, cell cycle, and expression profile. As compared to AML cells without GLIS2 fusion, GANT61 exposure resulted in higher sensitivity of both cell lines and primary AML cells carrying CBFA2T3-GLIS2 to undergo apoptosis and G1 cell cycle arrest. Remarkably, gene expression studies demonstrated downregulation of GLIS2-specific signature genes in both treated cell lines and primary cells, in comparison with untreated cells. Moreover, chromatin immunoprecipitation analysis revealed direct regulation by GLIS2 chimeric protein of DNMT1 and DNMT3B, two genes implicated in important epigenetic functions. Our findings indicate that the GLI inhibitor GANT61 may be used to specifically target the CBFA2T3-GLIS2 fusion gene in pediatric AML.

  7. Code development incorporating environmental, safety, and economic aspects of fusion reactors (FY 89--91). Final report

    SciTech Connect

    Ho, S.K.; Fowler, T.K.; Holdren, J.P.

    1991-11-01

    This report discusses the following aspects of Fusion reactors.: Activation Analysis; Tritium Inventory; Environmental and Safety Indices and Their Graphical Representation; Probabilistic Risk Assessment (PRA) and Decision Analysis; Plasma Burn Control -- Application to ITER; and Other Applications.

  8. Laser-Fusion Studies at NRL. A Report to AEC for the Period July 1973 to June 1974,

    DTIC Science & Technology

    This report summarizes work done at NRL on laser fusion related problems during FY 1974. Included are sections related to laser development , and to experimental and theoretical studies of laser plasma interaction.

  9. Laser-Fusion Studies at NRL. A Report to ERDA for the Period July 1974 to June 1975.

    DTIC Science & Technology

    This report summarizes work done at NRL on laser fusion related to problems during FY 1975. Included are sections related to laser development and to experimental studies of laser plasma interaction. (Author)

  10. Microwave generation for magnetic fusion energy applications. Progress report, September 15, 1991--July 15, 1992

    SciTech Connect

    Antonsen, T.M. Jr.; Destler, W.W.; Granatstein, V.L.; Levush, B.

    1992-01-01

    This progress report encompasses work on two separate projects, both related to developing sources for electron cyclotron resonance heating of magnetic fusion plasmas. The report is therefore divided into two parts as follows: Free electron laser with small period wigglers; and theory and modeling of high frequency, high power gryotron operation. Task A is experimental and eventually aims at developing continuously tunable, cw sources for ECRH with power per unit as high as 5 megawatts. Task B provides gryotron theory and modeling in support of the gryotron development programs at MIT and Varian.

  11. Fusion reactor materials: Semiannual progress report for period ending September 30, 1986

    SciTech Connect

    none,

    1987-09-01

    These activities are concerned principally with the effects of the neutronic and chemical environment on the properties and performance of reactor materials; together they form one element of the overall materials program being conducted in support of the Magnetic Fusion Energy Program of the US Department of Energy. The major areas of concern covered in this report are irradiation facilities, test matrices, and experimental methods; dosimetry, damage parameters and activation calculations; materials engineering and design requirements; radiation effects; development of structural alloys; solid breeding materials; ceramics and superconducting magnet materials. There are 61 reports cataloged separately. (LSP)

  12. EWS-Oct-4B, an alternative EWS-Oct-4 fusion gene, is a potent oncogene linked to human epithelial tumours

    PubMed Central

    Kim, S; Lim, B; Kim, J

    2010-01-01

    Background: Characterisation of EWS-Oct-4 translocation fusion product in bone and soft-tissue tumours revealed a chimeric gene resulting from an in-frame fusion between EWS (Ewing's sarcoma gene) exons 1–6 and Oct-4 exons 1–4. Recently, an alternative form of the fusion protein between the EWS and Oct-4 genes, named EWS-Oct-4B, was reported in two types of epithelial tumours, a hidradenoma of the skin and a mucoepidermoid carcinoma of the salivary glands. As the N-terminal and POU domains of the EWS-Oct-4 and EWS-Oct-4B proteins are not structurally identical, we decided to investigate the functional consequences of the EWS-Oct-4B fusion. Methods: In this report, we have characterised the EWS-Oct-4B fusion protein. To investigate how the EWS-Oct-4B protein contributes to tumourigenesis in human cancers, we analysed its DNA-binding activity, subcellular localisation, transcriptional activation behaviour, and oncogenic properties. Results: We found that this new chimeric gene encodes a nuclear protein that binds DNA with the same sequence specificity as the parental Oct-4 protein or the fusion EWS-Oct-4 protein. We show that the nuclear localisation signal of EWS-Oct-4B is dependent on the POU DNA-binding domain, and we identified a cluster of basic amino acids, 269RKRKR273, in the POU domain that specifically mediates the nuclear localisation of EWS-Oct-4B. Comparison of the properties of EWS-Oct-4B and EWS-Oct-4 indicated that EWS-Oct-4B is a less-potent transcriptional activator of a reporter construct carrying the Oct-4-binding sites. Deletion analysis of the functional domains of EWS-Oct-4B revealed that the EWS N-terminal domain (NTD)B, POU, and C-terminal domain (CTD) are necessary for its full transactivation potential. Despite its reduced activity as a transcriptional activator, EWS-Oct-4B regulated the expression of fgf-4 (fibroblast growth factor-4) and nanog, which are potent mitogens, as well as of Oct-4 downstream target genes, the promoters of

  13. Long-Term Endurance Exercise in Humans Stimulates Cell Fusion of Myoblasts along with Fusogenic Endogenous Retroviral Genes In Vivo.

    PubMed

    Frese, Sebastian; Ruebner, Matthias; Suhr, Frank; Konou, Thierry M; Tappe, Kim A; Toigo, Marco; Jung, Hans H; Henke, Christine; Steigleder, Ruth; Strissel, Pamela L; Huebner, Hanna; Beckmann, Matthias W; van der Keylen, Piet; Schoser, Benedikt; Schiffer, Thorsten; Frese, Laura; Bloch, Wilhelm; Strick, Reiner

    2015-01-01

    Myogenesis is defined as growth, differentiation and repair of muscles where cell fusion of myoblasts to multinucleated myofibers is one major characteristic. Other cell fusion events in humans are found with bone resorbing osteoclasts and placental syncytiotrophoblasts. No unifying gene regulation for natural cell fusions has been found. We analyzed skeletal muscle biopsies of competitive cyclists for muscle-specific attributes and expression of human endogenous retrovirus (ERV) envelope genes due to their involvement in cell fusion of osteoclasts and syncytiotrophoblasts. Comparing muscle biopsies from post- with the pre-competitive seasons a significant 2.25-fold increase of myonuclei/mm fiber, a 2.38-fold decrease of fiber area/nucleus and a 3.1-fold decrease of satellite cells (SCs) occurred. We propose that during the pre-competitive season SC proliferation occurred following with increased cell fusion during the competitive season. Expression of twenty-two envelope genes of muscle biopsies demonstrated a significant increase of putative muscle-cell fusogenic genes Syncytin-1 and Syncytin-3, but also for the non-fusogenic erv3. Immunohistochemistry analyses showed that Syncytin-1 mainly localized to the sarcolemma of myofibers positive for myosin heavy-chain isotypes. Cellular receptors SLC1A4 and SLC1A5 of Syncytin-1 showed significant decrease of expression in post-competitive muscles compared with the pre-competitive season, but only SLC1A4 protein expression localized throughout the myofiber. Erv3 protein was strongly expressed throughout the myofiber, whereas envK1-7 localized to SC nuclei and myonuclei. Syncytin-1 transcription factors, PPARγ and RXRα, showed no protein expression in the myofiber, whereas the pCREB-Ser133 activator of Syncytin-1 was enriched to SC nuclei and myonuclei. Syncytin-1, Syncytin-3, SLC1A4 and PAX7 gene regulations along with MyoD1 and myogenin were verified during proliferating or actively-fusing human primary myoblast cell

  14. Long-Term Endurance Exercise in Humans Stimulates Cell Fusion of Myoblasts along with Fusogenic Endogenous Retroviral Genes In Vivo

    PubMed Central

    Suhr, Frank; Konou, Thierry M.; Tappe, Kim A.; Toigo, Marco; Jung, Hans H.; Henke, Christine; Steigleder, Ruth; Strissel, Pamela L.; Huebner, Hanna; Beckmann, Matthias W.; van der Keylen, Piet; Schoser, Benedikt; Schiffer, Thorsten; Frese, Laura; Bloch, Wilhelm; Strick, Reiner

    2015-01-01

    Myogenesis is defined as growth, differentiation and repair of muscles where cell fusion of myoblasts to multinucleated myofibers is one major characteristic. Other cell fusion events in humans are found with bone resorbing osteoclasts and placental syncytiotrophoblasts. No unifying gene regulation for natural cell fusions has been found. We analyzed skeletal muscle biopsies of competitive cyclists for muscle-specific attributes and expression of human endogenous retrovirus (ERV) envelope genes due to their involvement in cell fusion of osteoclasts and syncytiotrophoblasts. Comparing muscle biopsies from post- with the pre-competitive seasons a significant 2.25-fold increase of myonuclei/mm fiber, a 2.38-fold decrease of fiber area/nucleus and a 3.1-fold decrease of satellite cells (SCs) occurred. We propose that during the pre-competitive season SC proliferation occurred following with increased cell fusion during the competitive season. Expression of twenty-two envelope genes of muscle biopsies demonstrated a significant increase of putative muscle-cell fusogenic genes Syncytin-1 and Syncytin-3, but also for the non-fusogenic erv3. Immunohistochemistry analyses showed that Syncytin-1 mainly localized to the sarcolemma of myofibers positive for myosin heavy-chain isotypes. Cellular receptors SLC1A4 and SLC1A5 of Syncytin-1 showed significant decrease of expression in post-competitive muscles compared with the pre-competitive season, but only SLC1A4 protein expression localized throughout the myofiber. Erv3 protein was strongly expressed throughout the myofiber, whereas envK1-7 localized to SC nuclei and myonuclei. Syncytin-1 transcription factors, PPARγ and RXRα, showed no protein expression in the myofiber, whereas the pCREB-Ser133 activator of Syncytin-1 was enriched to SC nuclei and myonuclei. Syncytin-1, Syncytin-3, SLC1A4 and PAX7 gene regulations along with MyoD1 and myogenin were verified during proliferating or actively-fusing human primary myoblast cell

  15. A novel type of EWS-CHOP fusion gene in myxoid liposarcoma

    SciTech Connect

    Matsui, Yoshito . E-mail: ymatsui@sb4.so-net.ne.jp; Ueda, Takafumi; Kubo, Takahiro; Hasegawa, Tadashi; Tomita, Yasuhiko; Okamoto, Mina; Myoui, Akira; Kakunaga, Shigeki; Yasui, Natsuo; Yoshikawa, Hideki

    2006-09-22

    The cytogenetic hallmark of myxoid type and round cell type liposarcoma consists of reciprocal translocation of t(12;16)(q13;p11) and t(12;22)(q13;q12), which results in fusion of TLS/FUS and CHOP, and EWS and CHOP, respectively. Nine structural variations of the TLS/FUS-CHOP chimeric transcript have been reported, however, only two types of EWS-CHOP have been described. We describe here a case of myxoid liposarcoma containing a novel EWS-CHOP chimeric transcript and identified the breakpoint occurring in intron 13 of EWS. Reverse transcription-polymerase chain reaction and direct sequence showed that exon 13 of EWS was in-frame fused to exon 2 of CHOP. Genomic analysis revealed that the breaks were located in intron 13 of EWS and intron 1 of CHOP.

  16. Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors.

    PubMed

    Geybels, Milan S; Alumkal, Joshi J; Luedeke, Manuel; Rinckleb, Antje; Zhao, Shanshan; Shui, Irene M; Bibikova, Marina; Klotzle, Brandy; van den Brandt, Piet A; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Maier, Christiane; Stanford, Janet L

    2015-01-01

    About half of all prostate cancers harbor the TMPRSS2:ERG (T2E) gene fusion. While T2E-positive and T2E-negative tumors represent specific molecular subtypes of prostate cancer (PCa), previous studies have not yet comprehensively investigated how these tumor subtypes differ at the epigenetic level. We therefore investigated epigenome-wide DNA methylation profiles of PCa stratified by T2E status. The study included 496 patients with clinically localized PCa who had a radical prostatectomy as primary treatment for PCa. Fluorescence in situ hybridization (FISH) "break-apart" assays were used to determine tumor T2E-fusion status, which showed that 266 patients (53.6 %) had T2E-positive PCa. The study showed global DNA methylation differences between tumor subtypes. A large number of differentially methylated CpG sites were identified (false-discovery rate [FDR] Q-value <0.00001; n = 27,876) and DNA methylation profiles accurately distinguished between tumor T2E subgroups. A number of top-ranked differentially methylated CpGs in genes (FDR Q-values ≤1.53E-29) were identified: C3orf14, CACNA1D, GREM1, KLK10, NT5C, PDE4D, RAB40C, SEPT9, and TRIB2, several of which had a corresponding alteration in mRNA expression. These genes may have various roles in the pathogenesis of PCa, and the calcium-channel gene CACNA1D is a known ERG-target. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. This study identified substantial differences in DNA methylation profiles of T2E-positive and T2E-negative tumors, thereby providing further evidence that different underlying oncogenic pathways characterize these molecular subtypes.

  17. Fusion reactor systems studies. Progress report, November 1, 1992--October 31, 1993

    SciTech Connect

    Not Available

    1993-09-09

    Fusion Technology Institute personnel actively participated in the ARIES/PULSAR project during the present contract period. Numerous presentations were made at PULSAR project meetings, major contributions were written for the ARIES-II/IV Final Report presentations and papers were given at technical conferences contributions were written for the ARIES Lessons Learned report and a very large number of electronic-mail and regular-mail communications were sent. The remaining sections of this progress report win summarize the work accomplished and in progress for the PULSAR project during the contract period. The main areas of effort are: PULSAR Research; ARIES-II/IV Report Contributions; ARIES Lessons Learned Report Contributions; and Stellarator Study.

  18. Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis.

    PubMed

    Pozsgai, Eric R; Blair, Kris M; Kearns, Daniel B

    2012-02-01

    Transposons are mobile genetic elements bounded by insertion sequences that are recognized by a specific mobilizing transposase enzyme. The transposase may mobilize not only the insertion sequences but also intervening DNA. mariner is a particularly efficient transposon for the random chromosomal integration of genes and insertional mutagenesis. Here, we modify an existing mariner transposon, TnYLB, such that it can easily be genetically manipulated and introduced into Bacillus subtilis. We generate a series of three new mariner derivatives that mobilize spectinomycin, chloramphenicol, and kanamycin antibiotic resistance cassettes. Furthermore, we generate a series of transposons with a strong, outward-oriented, optionally isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible promoter for the random overexpression of neighboring genes and a series of transposons with a promoterless lacZ gene for the random generation of transcriptional reporter fusions. We note that the modification of the base transposon is not restricted to B. subtilis and should be applicable to any mariner-compatible host organism, provided that in vitro mutagenesis or an in vivo species-specific delivery vector is employed.

  19. Inertial confinement fusion reaction chamber and power conversion system study. Final report

    SciTech Connect

    Maya, I.; Schultz, K.R.; Bourque, R.F.; Cheng, E.T.; Creedon, R.L.; Norman, J.H.; Price, R.J.; Porter, J.; Schuster, H.L.; Simnad, M.J.

    1985-10-01

    This report summarizes the results of the second year of a two-year study on the design and evaluation of the Cascade concept as a commercial inertial confinement fusion (ICF) reactor. We developed a reactor design based on the Cascade reaction chamber concept that would be competitive in terms of both capital and operating costs, safe and environmentally acceptable in terms of hazard to the public, occupational exposure and radioactive waste production, and highly efficient. The Cascade reaction chamber is a double-cone-shaped rotating drum. The granulated solid blanket materials inside the rotating chamber are held against the walls by centrifugal force. The fusion energy is captured in a blanket of solid carbon, BeO, and LiAlO/sub 2/ granules. These granules are circulated to the primary side of a ceramic heat exchanger. Primary-side granule temperatures range from 1285 K at the LiAlO/sub 2/ granule heat exchanger outlet to 1600 K at the carbon granule heat exchanger inlet. The secondary side consists of a closed-cycle gas turbine power conversion system with helium working fluid, operating at 1300 K peak outlet temperature and achieving a thermal power conversion efficiency of 55%. The net plant efficiency is 49%. The reference design is a plant producing 1500 MW of D-T fusion power and delivering 815 MW of electrical power for sale to the utility grid. 88 refs., 44 figs., 47 tabs.

  20. THE GENERAL ATOMICS FUSION THEORY PROGRAM ANNUAL REPORT FOR GRANT YEAR 2004

    SciTech Connect

    PROJECT STAFF

    2004-12-01

    The dual objective of the fusion theory program at General Atomics (GA) is to significantly advance our scientific understanding of the physics of fusion plasmas and to support the DIII-D and other tokamak experiments. The program plan is aimed at contributing significantly to the Fusion Energy Science and the Tokamak Concept Improvement goals of the Office of Fusion Energy Sciences (OFES).

  1. The TITAN Reversed-Field Pinch fusion reactor study: Scoping phase report

    SciTech Connect

    Not Available

    1987-01-01

    The TITAN research program is a multi-institutional effort to determine the potential of the Reversed-Field Pinch (RFP) magnetic fusion concept as a compact, high-power-density, and ''attractive'' fusion energy system from economic (cost of electricity, COE), environmental, and operational viewpoints. In particular, a high neutron wall loading design (18 MW/m/sup 2/) has been chosen as the reference case in order to quantify the issue of engineering practicality, to determine the physics requirements and plasma operating mode, to assess significant benefits of compact systems, and to illuminate the main drawbacks. The program has been divided into two phases, each roughly one year in length: the Scoping Phase and the Design Phase. During the scoping phase, the TITAN design team has defined the parameter space for a high mass power density (MPD) RFP reactor, and explored a variety of approaches to the design of major subsystems. Two major design approaches consistent with high MPD and low COE, the lithium-vanadium blanket design and aqueous loop-in-pool design, have been selected for more detailed engineering evaluation in the design phase. The program has retained a balance in its approach to investigating high MPD systems. On the one hand, parametric investigations of both subsystems and overall system performance are carried out. On the other hand, more detailed analysis and engineering design and integration are performed, appropriate to determining the technical feasibility of the high MPD approach to RFP fusion reactors. This report describes the work of the scoping phase activities of the TITAN program. A synopsis of the principal technical findings and a brief description of the TITAN multiple-design approach is given. The individual chapters on Plasma Physics and Engineering, Parameter Systems Studies, Divertor, Reactor Engineering, and Fusion Power Core Engineering have been cataloged separately.

  2. Accelerator and Fusion Research Division annual report, October 1981-September 1982. Fiscal year 1982

    SciTech Connect

    Johnson, R.K.; Bouret, C.

    1983-05-01

    This report covers the activities of LBL's Accelerator and Fusion Research Division (AFRD) during 1982. In nuclear physics, the Uranium Beams Improvement Project was concluded early in the year, and experimentation to exploit the new capabilities began in earnest. Technical improvement of the Bevalac during the year centered on a heavy-ion radiofrequency quadrupole (RFQ) as part of the local injector upgrade, and we collaborated in studies of high-energy heavy-ion collision facilities. The Division continued its collaboration with Fermilab to design a beam-cooling system for the Tevatron I proton-antiprotron collider and to engineer the needed cooling components for the antiproton. The high-field magnet program set yet another record for field strength in an accelerator-type dipole magnet (9.2 T at 1.8 K). The Division developed the design for the Advanced Light Source (ALS), a 1.3-GeV electron storage ring designed explicitly (with low beam emittance and 12 long straight sections) to generate high-brilliance synchrotron light from insertion devices. The Division's Magnetic Fusion Energy group continued to support major experiments at the Princeton Plasma Physics Laboratory, the Lawrence Livermore National Laboratory (LLNL), and General Atomic Co. by developing positive-ion-based neutral-beam injectors. Progress was made toward converting our major source-test facility into a long-pulse national facility, the Neutral Beam Engineering Test Facility, which was completed on schedule and within budget in 1983. Heavy Ion Fusion research focused on planning, theoretical studies, and beam-transport experiments leading toward a High Temperature Experiment - a major test of this promising backup approach to fusion energy.

  3. Is the use of minimally invasive fusion technologies associated with improved outcomes after elective interbody lumbar fusion? Analysis of a nationwide prospective patient-reported outcomes registry.

    PubMed

    McGirt, Matthew J; Parker, Scott L; Mummaneni, Praveen; Knightly, John; Pfortmiller, Deborah; Foley, Kevin; Asher, Anthony L

    2017-07-01

    Over the last decade, clinical investigators and biomedical industry groups have used significant resources to develop advanced technologies that enable less invasive spine fusions. These minimally invasive surgery (MIS) technologies often require increased expenditures by hospitals and payers. Although several small single center studies have suggested MIS technologies decrease surgical morbidity and reduce hospital stay, evidence documenting benefit from a patient perspective remains limited. Furthermore, MIS outcomes have yet to be evaluated from the perspective of multiple practice types representing the broad spectrum of US spine surgery. This study aimed to examine a population of patients who underwent one- or two-level interbody lumbar fusion diagnosed with lumbar stenosis or Grade 1 spondylolisthesis in an observational, prospective national registry for the purposes of determining how MIS and traditional open technologies affect postsurgical and patient-reported outcomes (PROs). This study used observational analysis of prospectively collected data. The sample consisted of cases from the National Neurosurgery Quality and Outcomes Database (N(2)QOD). Numeric rating scale for back and leg pain, Oswestry Disability Index, EuroQol-5D, return to work, and perioperative morbidity were the outcome measures. The N(2)QOD is a prospective PROs registry enrolling patients undergoing elective spine surgery from 60 hospitals in 27 US states via representative sampling. We analyzed the N(2)QOD aggregate dataset (2010-2014) to identify one- and two-level lumbar interbody fusion procedures performed for lumbar stenosis or Grade 1 spondylolisthesis with 12 months' follow-up where surgical instrumentation and implant types were clearly identified. Perioperative and 1-year outcomes were compared between cases performed with MIS enabling technologies versus traditional open technologies before and after propensity matching. There were 467 (24%) patients who underwent

  4. Gene Content and Function of the Ancestral Chromosome Fusion Site in Human Chromosome 2q13–2q14.1 and Paralogous Regions

    PubMed Central

    Fan, Yuxin; Newman, Tera; Linardopoulou, Elena; Trask, Barbara J.

    2002-01-01

    Various portions of the region surrounding the site where two ancestral chromosomes fused to form human chromosome 2 are duplicated elsewhere in the human genome, primarily in subtelomeric and pericentromeric locations. At least 24 potentially functional genes and 16 pseudogenes reside in the 614-kb of sequence surrounding the fusion site and paralogous segments on other chromosomes. By comparing the sequences of genomic copies and transcripts, we show that at least 18 of the genes in these paralogous regions are transcriptionally active. Among these genes are new members of the cobalamin synthetase W domain (CBWD) and forkhead domain FOXD4 gene families. Copies of RPL23A and SNRPA1 on chromosome 2 are retrotransposed-processed pseudogenes that were included in segmental duplications; we find 53 RPL23A pseudogenes in the human genome and map the functional copy of SNRPA1 to 15qter. The draft sequence of the human genome also provides new information on the location and intron–exon structure of functional copies of other 2q-fusion genes (PGM5, retina-specific F379, helicase CHLR1, and acrosin). This study illustrates that the duplication and rearrangement of subtelomeric and pericentromeric regions have functional relevance to human biology; these processes can change gene dosage and/or generate genes with new functions. [Supplemental material is available online at http://www.genome.org. Sequence data reported in this paper have been deposited in GenBank and assigned the following accession nos.: AF452722, AF452723, and AF452724.] PMID:12421752

  5. Differential transactivation by orphan nuclear receptor NOR1 and its fusion gene product EWS/NOR1: possible involvement of poly(ADP-ribose) polymerase I, PARP-1.

    PubMed

    Ohkura, Naganari; Nagamura, Yuko; Tsukada, Toshihiko

    2008-10-15

    In extraskeletal myxoid chondrosarcoma, a chromosomal translocation creates a gene fusion between EWS and an orphan nuclear receptor, NOR1. The resulting fusion protein EWS/NOR1 has been believed to lead to malignant transformation by functioning as a transactivator for NOR1-target genes. By comparing the gene expression profiles of NOR1- and EWS/NOR1-overexpressing cells, we found that they largely shared up-regulated genes, but no significant correlation was observed with respect to the transactivation levels of each gene. In addition, the proteins associated with NOR1 and EWS/NOR1 were mostly the same in these cells. The results suggest that these proteins differentially transactivate overlapping target genes through a similar transcriptional machinery. To clarify the mechanisms underlying the transcriptional divergence between NOR1 and EWS/NOR1, we searched for alternatively associated proteins, and identified poly(ADP-ribose) polymerase I (PARP-1) as an NOR1-specific binding protein. Consistent with its binding properties, PARP-1 acted as a transcriptional repressor of NOR1, but not EWS/NOR1, in a luciferase reporter assay employing PARP-1(-/-) fibroblasts. Interestingly, suppressive activity of PARP-1 was observed in a DNA response element-specific manner, and in a subtype-specific manner toward the NR4A family (Nur77, Nurr1, and NOR1), suggesting that PARP-1 plays a role in the diversity of transcriptional regulation mediated by the NR4A family in normal cells. Altogether, our findings suggest that NOR1 and EWS/NOR1 regulate overlapping target genes differently by utilizing associated proteins, including PARP-1; and that EWS/NOR1 may acquire oncogenic activities by avoiding (or gaining) transcription factor-specific modulation by the associated proteins. (c) 2008 Wiley-Liss, Inc.

  6. Fusion materials semiannual progress report for the period ending December 31, 1996

    SciTech Connect

    1997-04-01

    This is the twenty-first in a series of semiannual technical progress reports on fusion materials. This report combines the full spectrum of research and development activities on both metallic and non-metallic materials with primary emphasis on the effects of the neutronic and chemical environment on the properties and performance of materials for in-vessel components. This effort forms one element of the materials program being conducted in support of the Fusion Energy Sciences Program of the US Department of Energy. The other major element of the program is concerned with the interactions between reactor materials and the plasma and is reported separately. The report covers the following topics: vanadium alloys; silicon carbide composite materials; ferritic/martensitic steels; copper alloys and high heat flux materials; austenitic stainless steels; insulating ceramics and optical materials; solid breeding materials; radiation effects, mechanistic studies and experimental methods; dosimetry, damage parameters, and activation calculations; materials engineering and design requirements; and irradiation facilities, test matrices, and experimental methods.

  7. Final Report: Establishment of an Institute for Fusion Studies, June 1, 1980 - March 1, 1998

    SciTech Connect

    Hazeltine, Richard D.

    1999-12-03

    The mission of the Institute for Fusion Studies has been to serve as a national center for theoretical fusion and plasma physics research. As an independent scientific group of critical size, its objectives were to conduct research on fundamental phenomena important to fusion; to serve as a center for fusion theory exchange activities with other countries; to exchange scientific developments with other academic disciplines; and to train students and postdoctoral fellows in fusion and plasma physics research.

  8. Importance of NAB2-STAT6 Fusion in the Diagnosis of Pancreatic Solitary Fibrous Tumor with Hamartoma-Like Features: A Case Report and Review of the Literature

    PubMed Central

    Tanaka, Kei; Kishimoto, Takashi; Ohtsuka, Masayuki; Nakatani, Yukio; Miyazaki, Masaru

    2015-01-01

    We report a case of pancreatic hamartoma-like solitary fibrous tumor which was differentiated from pancreatic hamartoma with the detection of NAB2-STAT6 fusion, a specific mutation for solitary fibrous tumors. A pancreatic well-demarcated solid nodule, 21 × 17 mm, of 82-year-old man was surgically enucleated. Microscopic findings were close to a pancreatic hamartoma that consisted of sparsely distributed pancreatic ducts and acini in heavily collagenized fibrous stroma. Neither islet nor peripheral nerve existed in the tumor. The fibroblastic cells in the stroma were immune-positive for CD34, CD99, and bcl-2. But these expressions were not decisive in the differentiation between solitary fibrous tumor and pancreatic hamartoma, because CD34 was positive for both tumors, and CD99 and bcl-2 expressions were not elucidated in the previous cases of pancreatic hamartomas. Thus, we evaluated NAB2-STAT6 fusion. The fibroblastic cells were positive for STAT6 and sequencing analysis revealed the gene fusion between NAB2 exon 4 and STAT6 exon 2, with which the final diagnos is of solitary fibrous tumor was achieved. In conclusion, detection of NAB2-STAT6 fusion has a great diagnostic value for pancreatic solitary fibrous tumors with hamartoma-like features. PMID:26425382

  9. Glioma stem cells targeted by oncolytic virus carrying endostatin-angiostatin fusion gene and the expression of its exogenous gene in vitro.

    PubMed

    Zhu, Guidong; Su, Wei; Jin, Guishan; Xu, Fujian; Hao, Shuyu; Guan, Fangxia; Jia, William; Liu, Fusheng

    2011-05-16

    The development of the cancer stem cell (CSCs) niche theory has provided a new target for the treatment of gliomas. Gene therapy using oncolytic viral vectors has shown great potential for the therapeutic targeting of CSCs. To explore whether a viral vector carrying an exogenous Endo-Angio fusion gene (VAE) can infect and kill glioma stem cells (GSCs), as well as inhibit their vascular niche in vitro, we have collected surgical specimens of human high-grade glioma (world health organization, WHO Classes III-VI) from which we isolated and cultured GSCs under conditions originally designed for the selective expansion of neural stem cells. Our results demonstrate the following: (1) Four lines of GSCs (isolated from 20 surgical specimens) could grow in suspension, were multipotent, had the ability to self-renew and expressed the neural stem cell markers, CD133 and nestin. (2) VAE could infect GSCs and significantly inhibit their viability. (3) The Endo-Angio fusion gene was expressed in GSCs 48 h after VAE infection and could inhibit the proliferation of human brain microvascular endothelial cells (HBMEC). (4) Residual viable cells lose the ability of self-renewal and adherent differentiation. In conclusion, VAE can significantly inhibit the activity of GSCs in vitro and the expression of exogenous Endo-Angio fusion gene can inhibit HBMEC proliferation. VAE can be used as a novel virus-gene therapy strategy for glioma. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Bony fusion of the maxilla and mandible as a sequelae of noma: A rare case report

    PubMed Central

    Awasthi, Ujjwala Rastogi; Mody, Bharat M.; Suma, Gundareddy N.; Garg, Shruti

    2015-01-01

    Noma is a gangrenous disease of the orofacial region that leads to severe facial tissue destruction and is a significant cause of death among children. With the advent of modern antibiotics and improved nutrition, children with noma may survive into adulthood, but must face the challenge of undergoing repair of the sequelae of noma. This report describes a case of bony fusion of the maxilla and mandible in a 28-year-old female patient, which was a sequelae of a childhood case of noma. PMID:26389063

  11. Heavy Ion Fusion Accelerator Research (HIFAR) year-end report, April 1, 1989--September 30, 1989

    SciTech Connect

    Not Available

    1989-12-01

    This report contains the following topics on heavy ion fusion: MBE-4 drifting beam quadrupole operating range; transverse emittance growth in MBE-4; an improved ion source for MBE-4; drifting beam studies on MBE-4; 2-MV injector; improvements in lifetime of the C{sup +} source; injector control system; Maxwell spark gap test update; ILSE cosine 2{theta} quadrupole magnet development; electrostatic quadrupole prototype development activity; induction accelerator cell development; effect of a spread in beamlet currents on longitudinal stability; and heavy ion linac driver analysis.

  12. Condylar joint fusion and stabilization (by screws & plates) in nontraumatic atlanto-occipital dislocation (AOD). Technical report of two cases.

    PubMed

    Chowdhury, Forhad H; Haque, Mohammod Raziul; Alam, Sarwar Murshed; Chowdhury, Noman Khaled; Khan, Shamsul Islam; Goel, Atul

    2017-07-29

    Nontraumatic spontaneous atlanto-occipital dislocation (AOD) is very rare. In this report, we discuss the technical steps of condylar joint fusion and stabilization (by screws & plates) in nontraumatic AOD. So far our knowledge it is probably the first report of such techniques. A young girl and a young man with progressive quadriparesis due to non traumatic spontaneous atlanto-occipital dislocation were managed by microsurgical reduction, fusion and stabilization of the joint by occipital condylar and C1 lateral mass screw and plate fixation after mobilization of vertebral artery. In both cases condylar joints fixation and fusion were done successfully. Condylar joints stabilization and fusion may be a good /or alternative option for AOD. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1

    PubMed Central

    Langer, Simon M.; Hopfensperger, Kristina; Iyer, Shilpa S.; Kreider, Edward F.; Learn, Gerald H.; Lee, Lan-Hui; Hahn, Beatrice H.; Sauter, Daniel

    2015-01-01

    Background Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown. Results Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-кB activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time. Conclusions Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype. PMID:26554585

  14. Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L).

    PubMed

    Botta, A; Tandoi, C; Fini, G; Calabrese, G; Dallapiccola, B; Novelli, G

    2001-09-05

    The ubiquitin fusion-degradation gene (UFD1L) encodes the human homologue of the yeast ubiquitin fusion-degradation 1 protein, an essential component of the ubiquitin-dependent proteolytic turnover and mRNA processing. Although the UFD1L gene has been mapped in the region commonly deleted in patients with DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), correlation between its haploinsufficiency and the phenotype has not yet been established. The only functional data available about mammalian Ufd1p is the ability to form a complex with the rat Npl4 protein, a component of the nuclear pore complex. In this paper we report the cloning and molecular characterization of the human NPL4 gene. This gene encodes for a protein 96% homologous to the rat Npl4, and 44 and 34% homologous to the C. elegans and S. cerevisiae Npl4 gene products, respectively. Fluorescence in situ hybridization experiments on human metaphases localized the NPL4 gene on the most telomeric region of chromosome 17q. Northern blots analysis on foetal and adult human tissues revealed a major approximately 4.5 kb transcript most abundant in heart, brain, kidney and skeletal muscle. In order to test a potential relationship between nuclear transport defects and some aspect of the DGS/VCFS phenotype, we also exclude the presence of mutations in the NPL4 coding sequence in a subset of patients with DGS/VCFS and no detectable 22q11 deletion or mutations at the UFD1L locus.

  15. A mass spectrometry assay to simultaneously analyze ROS1 and RET fusion gene expression in non-small-cell lung cancer.

    PubMed

    Wijesinghe, Priyanga; Bepler, Gerold; Bollig-Fischer, Aliccia

    2015-02-01

    ROS1 and RET gene fusions were recently discovered in non-small-cell lung cancer (NSCLC) as potential therapeutic targets with small-molecule kinase inhibitors. The conventional screening methods of these fusions are time-consuming and require samples of high quality and quantity. Here, we describe a novel and efficient method by coupling the power of multiplexing polymerase chain reaction and the sensitivity of mass spectrometry. The multiplex mass spectrometry platform simultaneously tests samples for the expression of nine ROS1 and six RET fusion genes. The assay incorporates detection of wild-type exon junctions immediately upstream and downstream of the fusion junction to exclude false-negative results. To flag false-positives, the system also comprises two independent assays for each fusion gene junction. The characteristic mass spectrometric peaks of the gene fusions were obtained using engineered plasmid constructs. Specific assays targeting the wild-type gene exon junctions were validated using complimentary DNA from lung tissue of healthy individuals. The system was further validated using complimentary DNA derived from NSCLC cell lines that express endogenous fusion genes. The expressed ROS1-SLC34A2 and CCDC6-RET gene fusions from the NSCLC cell lines HCC78 and LC-2/ad, respectively, were accurately detected by the novel assay. The assay is extremely sensitive, capable of detecting an event in test specimens containing 0.5% positive tumors. The novel multiplexed assay is robustly capable of detecting 15 different clinically relevant RET and ROS1 fusion variants. The benefits of this detection method include exceptionally low sample input, high cost efficiency, flexibility, and rapid turnover.

  16. Cervicothoracic junction arthroplasty after previous fusion surgery for adjacent segment degeneration: case report.

    PubMed

    Sekhon, Lali

    2005-01-01

    This is the first reported case of cervical arthroplasty using the Bryan Cervical Disc Prosthesis System (Medtronic Sofamor Danek, Inc., Memphis, TN) in the management of adjacent segment degeneration associated with previous fusion surgery and surgery at the cervicothoracic junction. This case report describes a 25-year-old woman who initially underwent a two-level anterior cervical fusion in 1998, 2 years after being involved in a motor vehicle accident. She was well until 18 months before presentation, when she developed bilateral shoulder pain, mechanical neck pain worse on flexion, and bilateral C8 distribution arm pain and paresthesia. On clinical examination, no focal deficits were found, although the range of motion was reduced. Preoperative cervical spine x-rays and magnetic resonance scanning confirmed accelerated degeneration of the C4-C5 and C7-T1 disc spaces, with evidence of neural compression at those levels. After careful consideration of various treatment options and failure of all conservative measures, the patient underwent an anterior C4-C5 and C7-T1 decompression with removal of the anterior cervical plate and placement of two artificial disc prostheses. After surgery, her course was uncomplicated and she was discharged from hospital well. There was complete resolution of the arm symptoms and reduction of the neck pain, with a reduction in the amount of analgesia she was taking. Seven months after surgery, she remains well with repeat x-rays confirming motion at the operated levels. This case demonstrates that cervical arthroplasty is a reasonable treatment option for patients who have had previous surgery in which interbody fusion has been performed and who have developed degeneration of adjacent levels. Despite the altered biomechanics at the cervicothoracic junction, no adverse features were noted with arthroplasty at this level.

  17. Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.

    PubMed

    Ma, Yuanjun; Miao, Yali; Peng, Zhuochun; Sandgren, Johanna; De Ståhl, Teresita Díaz; Huss, Mikael; Lennartsson, Lena; Liu, Yanling; Nistér, Monica; Nilsson, Sten; Li, Chunde

    2016-01-01

    Docetaxel has been the standard first-line therapy in metastatic castration resistant prostate cancer. The survival benefit is, however, limited by either primary or acquired resistance. In this study, Du145 prostate cancer cells were converted to docetaxel-resistant cells Du145-R and Du145-RB by in vitro culturing. Next generation RNAseq was employed to analyze these cell lines. Forty-two genes were identified to have acquired mutations after the resistance development, of which thirty-four were found to have mutations in published sequencing studies using prostate cancer samples from patients. Fourteen novel and 2 previously known fusion genes were inferred from the RNA-seq data, and 13 of these were validated by RT-PCR and/or re-sequencing. Four in-frame fusion transcripts could be transcribed into fusion proteins in stably transfected HEK293 cells, including MYH9-EIF3D and LDLR-RPL31P11, which were specific identified or up-regulated in the docetaxel resistant DU145 cells. A panel of 615 gene transcripts was identified to have significantly changed expression profile in the docetaxel resistant cells. These transcriptional changes have potential for further study as predictive biomarkers and as targets of docetaxel treatment.

  18. ETS Gene Fusions as Predictive Biomarkers of Resistance to Radiation Therapy for Prostate Cancer

    DTIC Science & Technology

    2011-08-01

    prostate, breast, melanoma, and Ew - ing’s sarcoma (Jané-Valbuena et al., 2010; Jeon et al., 1995; Shurtleff et al., 1995; Sorensen et al., 1994; Tognon...Shapiro, D.N. (1995). A variant Ewing’s sarcoma translocation (7;22) fuses the EWS gene to the ETS gene ETV1. Oncogene 10, 1229–1234. Kim, J., Yu, W...public release; distribution unlimited The views, opinions and/or findings contained in this report are those of the author( s ) and should not be

  19. Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma.

    PubMed

    Clark, J; Lu, Y J; Sidhar, S K; Parker, C; Gill, S; Smedley, D; Hamoudi, R; Linehan, W M; Shipley, J; Cooper, C S

    1997-10-01

    We demonstrate that the cytogenetically defined translocation t(X;1)(p11.2;p34) observed in papillary renal cell carcinomas results in the fusion of the splicing factor gene PSF located at 1p34 to the TFE3 helix-loop-helix transcription factor gene at Xp11.2. In addition we define an X chromosome inversion inv(X)(p11.2;q12) that results in the fusion of the NonO (p54nrb) gene to TFE3. NonO (p54nrb), the human homologue of the Drosophila gene NonAdiss which controls the male courtship song, is closely related to PSF and also believed to be involved in RNA splicing. In each case the rearrangement results in the fusion of almost the entire splicing factor protein to the TFE3 DNA-binding domain. These observations suggest the possibility of intriguing links between the processes of RNA splicing, DNA transcription and oncogenesis.

  20. Regulation of fos-lacZ fusion gene expression in primary mouse epidermal keratinocytes isolated from transgenic mice.

    PubMed Central

    Bollag, W B; Xiong, Y; Ducote, J; Harmon, C S

    1994-01-01

    The expression of a fos-lacZ fusion gene was studied in primary mouse epidermal keratinocytes obtained from transgenic mice. This gene construct contains the entire upstream regulatory sequence of c-fos, and expression of the endogenous and fusion gene was shown by Northern analysis to correlate upon induction with the phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA). Using a chromogenic substrate of beta-galactosidase, we also demonstrated that expression of the fusion gene product, like that of Fos, was localized to the cell nucleus. In addition, we showed that epidermal keratinocytes responded to dialysed fetal bovine serum (FBS), TPA and high-calcium medium with enhanced Fos-lacZ expression and an inhibition of proliferation. The time course of induction of Fos-lacZ expression was similar for dialysed FBS and TPA, with a peak approximately 2 h after exposure. Exposure for approximately 24 h to an elevated extracellular calcium concentration was required to elicit an increase in Fos-lacZ expression. The lack of an immediate effect of raising medium calcium levels on Fos-lacZ expression contrasted with the rapidity of its effect on DNA synthesis, which was significantly inhibited within 6-8 h. In addition, we found that the protein kinase C inhibitor Ro 31-7549 blocked Fos-lacZ expression induced by TPA but had little or no effect on that elicited by high calcium levels. Thus, although our results indicate that the fos gene product may be involved in mediating epidermal keratinocyte growth arrest in response to differentiative agents such as FBS, TPA and high medium calcium levels, the exact role of this gene product remains unclear. Images Figure 1 Figure 2 PMID:8198544

  1. Regulation of fos-lacZ fusion gene expression in primary mouse epidermal keratinocytes isolated from transgenic mice.

    PubMed

    Bollag, W B; Xiong, Y; Ducote, J; Harmon, C S

    1994-05-15

    The expression of a fos-lacZ fusion gene was studied in primary mouse epidermal keratinocytes obtained from transgenic mice. This gene construct contains the entire upstream regulatory sequence of c-fos, and expression of the endogenous and fusion gene was shown by Northern analysis to correlate upon induction with the phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA). Using a chromogenic substrate of beta-galactosidase, we also demonstrated that expression of the fusion gene product, like that of Fos, was localized to the cell nucleus. In addition, we showed that epidermal keratinocytes responded to dialysed fetal bovine serum (FBS), TPA and high-calcium medium with enhanced Fos-lacZ expression and an inhibition of proliferation. The time course of induction of Fos-lacZ expression was similar for dialysed FBS and TPA, with a peak approximately 2 h after exposure. Exposure for approximately 24 h to an elevated extracellular calcium concentration was required to elicit an increase in Fos-lacZ expression. The lack of an immediate effect of raising medium calcium levels on Fos-lacZ expression contrasted with the rapidity of its effect on DNA synthesis, which was significantly inhibited within 6-8 h. In addition, we found that the protein kinase C inhibitor Ro 31-7549 blocked Fos-lacZ expression induced by TPA but had little or no effect on that elicited by high calcium levels. Thus, although our results indicate that the fos gene product may be involved in mediating epidermal keratinocyte growth arrest in response to differentiative agents such as FBS, TPA and high medium calcium levels, the exact role of this gene product remains unclear.

  2. SOX2 expression is associated with FGFR fusion genes and predicts favorable outcome in lung squamous cell carcinomas.

    PubMed

    Zheng, Shanbo; Pan, Yunjian; Wang, Rui; Li, Yuan; Cheng, Chao; Shen, Xuxia; Li, Bin; Zheng, Difan; Sun, Yihua; Chen, Haiquan

    2015-01-01

    SOX2 is a gene that encodes for a transcription factor, which functions as an activator or suppressor of gene transcription. SOX2 amplification and overexpression have been found in various types of tumors and play important roles in cancer cells. The aim of the study was to evaluate SOX2 expression and amplification in lung squamous cell carcinomas (SCCs) and to determine the relationship with main clinicopathologic features, patient prognosis, and common driver mutations. SOX2 protein levels were measured by immunohistochemistry, while SOX2 copy numbers were measured by fluorescence in situ hybridization in resected samples from 162 Chinese lung SCC patients. All patients were also analyzed for mutations in EGFR, HER2, BRAF, PIK3CA, NFE2L2, and FGFR fusion genes. Clinical characteristics, including age, sex, smoking status, stage, relapse-free survival (RFS), and overall survival (OS), were collected. SOX2 overexpression and amplification were observed in 58.6% and 45.9% of lung SCCs. Lung SCC patients with SOX2 overexpression were significantly associated with absence of malignant tumor family history (P=0.021), FGFR fusion gene (P=0.046), longer RFS (P=0.041), and OS (P=0.025). No correlation was found between SOX2 gene amplification and main clinicopathologic features, patient prognosis, or common driver mutations. SOX2 overexpression and amplification are common in lung SCCs. SOX2 over-expression was associated with FGFR fusion genes and predicted favorable outcome in lung SCCs. The underlying relationship of SOX2 and FGFR still needs further investigation.

  3. Schinzel-Giedion syndrome: report of splenopancreatic fusion and proposed diagnostic criteria.

    PubMed

    Lehman, Anna M; McFadden, Deborah; Pugash, Denise; Sangha, Karan; Gibson, William T; Patel, Millan S

    2008-05-15

    We report on the 46th patient with Schinzel-Giedion syndrome (SGS) and the first observation of splenopancreatic fusion in this syndrome. In the antenatal period, a male fetus was found to have bilateral hydronephrosis. Postnatally, in keeping with a diagnosis of SGS, there were large fontanelles, ocular hypertelorism, a wide, broad forehead, midface retraction, a short, upturned nose, macroglossia, and a short neck. Other anomalies included cardiac defects, widened and dense long bone cortices, cerebral ventriculomegaly, and abnormal fundi. Splenopancreatic fusion, usually encountered in trisomy 13, was found on autopsy. Schinzel-Giedion syndrome is likely a monogenic condition for which neither the heritability pattern nor pathogenesis has yet been determined. A clinical diagnosis may be made by identifying the facial phenotype, including prominent forehead, midface retraction, and short, upturned nose, plus one of either of the two other major distinguishing features: typical skeletal abnormalities or hydronephrosis. Typical skeletal anomalies include a sclerotic skull base, wide supraoccipital-exoccipital synchondrosis, increased cortical density or thickness, and broad ribs. Other highly supportive features include neuroepithelial tumors (found in 17%), hypertrichosis, and brain abnormalities. Severe developmental delay and poor survival are constant features in reported patients.

  4. Role of starvation genes in the survival of deep subsurface bacterial communities. Final report

    SciTech Connect

    Matin, A.; Schmidt, T.; Caldwell, D.

    1998-11-01

    The investigation dealt with several aspects of subsurface bacterial survival and their nature. Mutants of Pseudomonas putida, a common environmental bacterium with counterparts in the subsurface, were isolated by transposon mutagenesis. These mutants were highly sensitive to starvation stress. Reporter gene fusions also showed that these genes were starvation genes since they were induced several fold when the cultures were started. Since the regulatory religions (promoters) of starvation genes are of interest in bioremediation and in experiments designed to understand the roles of starvation genes in the maintenance of microbial community structure, the promoter of one of these genes (pstarv1, contained in strain MK107) was characterized in detail. As a preliminary to these studies, the growth characteristics of Pseudomonas putida MK1 and MK107 were compared for cells growing in batch cultures or as an attached monolayer in microstat cultures.

  5. Increased gene copy number of ERG on chromosome 21 but not TMPRSS2–ERG fusion predicts outcome in prostatic adenocarcinomas

    PubMed Central

    Toubaji, Antoun; Albadine, Roula; Meeker, Alan K; Isaacs, William B; Lotan, Tamara; Haffner, Michael C; Chaux, Alcides; Epstein, Jonathan I; Han, Misop; Walsh, Patrick C; Partin, Alan W; De Marzo, Angelo M; Platz, Elizabeth A; Netto, George J

    2012-01-01

    The role of TMPRSS2–ERG gene fusion in prostate cancer prognostication remains controversial. We evaluated the prognostic role of TMPRSS2–ERG fusion using fluorescence in situ hybridization analysis in a case–control study nested in The Johns Hopkins retropubic radical prostatectomy cohort. In all, 10 tissue microarrays containing paired tumors and normal tissues obtained from 172 cases (recurrence) and 172 controls (non-recurrence) matched on pathological grade, stage, race/ethnicity, and age at the time of surgery were analyzed. All radical prostatectomies were performed at our institution between 1993 and 2004. Recurrence was defined as biochemical recurrence, development of clinical evidence of metastasis, or death from prostate carcinoma. Each tissue microarray spot was scored for the presence of TMPRSS2–ERG gene fusion and for ERG gene copy number gains. The odds ratio of recurrence and 95% confidence intervals were estimated from conditional logistic regression. Although the percentage of cases with fusion was slightly lower in cases than in controls (50 vs 57%), the difference was not statistically significant (P=0.20). The presence of fusion due to either deletion or split event was not associated with recurrence. Similarly, the presence of duplicated ERG deletion, duplicated ERG split, or ERG gene copy number gain with a single ERG fusion was not associated with recurrence. ERG gene polysomy without fusion was significantly associated with recurrence (odds ratio 2.0, 95% confidence interval 1.17–3.42). In summary, TMPRSS2–ERG fusion was not prognostic for recurrence after retropubic radical prostatectomy for clinically localized prostate cancer, although men with ERG gene copy number gain without fusion were twice more likely to recur. PMID:21743434

  6. A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report.

    PubMed

    Barnes, David J; Hookway, Edward; Athanasou, Nick; Kashima, Takeshi; Oppermann, Udo; Hughes, Simon; Swan, Daniel; Lueerssen, Dietrich; Anson, John; Hassan, A Bassim

    2016-08-12

    Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8 % cases). The patient reported here is only the eighth case of MNTI presenting in an extremity, and the first reported in the fibula. A 2-month-old female presented with a mass arising in the fibula. Exhaustive genomic, transcriptomic, epigenetic and pathological characterization was performed on the excised primary tumor and a derived cell line. Whole-exome analysis of genomic DNA from both the tumor and blood indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16(INK4A), D74A). SNP-array CGH on DNA samples revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. A derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators. In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by

  7. The Use of Bone Morphogenetic Protein in Pediatric Cervical Spine Fusion Surgery: Case Reports and Review of the Literature

    PubMed Central

    Molinari, Robert W.; Molinari, Christine

    2015-01-01

    Study Design Case report. Objective There is a paucity of literature describing the use of bone graft substitutes to achieve fusion in the pediatric cervical spine. The outcomes and complications involving the off-label use of bone morphogenetic protein (BMP)-2 in the pediatric cervical spine are not clearly defined. The purpose of this article is to report successful fusion without complications in two pediatric patients who had instrumented occipitocervical fusion using low-dose BMP-2. Methods A retrospective review of the medical records was performed, and the patients were followed for 5 years. Two patients under 10 years of age with upper cervical instability were treated with occipitocervical instrumented fusion using rigid occipitocervical fixation techniques along with conventionally available low-dose BMP-2. A Medline and PubMed literature search was conducted using the terms “bone morphogenetic protein,” “BMP,” “rh-BMP2,” “bone graft substitutes,” and “pediatric cervical spine.” Results Solid occipitocervical fusion was achieved in both pediatric patients. There were no reported perioperative or follow-up complications. At 5-year follow-up, radiographs in both patients showed successful occipital cervical fusion without evidence of instrumentation failure or changes in the occipitocervical alignment. To date, there are few published reports on this topic. Complications and the appropriate dosage application in the pediatric posterior cervical spine remain unknown. Conclusions We describe two pediatric patients with upper cervical instability who achieved successful occipital cervical fusion without complication using off-label BMP-2. This report underscores the potential for BMP-2 to achieve successful arthrodesis of the posterior occipitocervical junction in pediatric patients. Use should be judicious as complications and long-term outcomes of pediatric BMP-2 use remain undefined in the existing literature. PMID:26835215

  8. Fusion Energy Postdoctoral Research Program, Professional Development Program: FY 1987 annual report

    SciTech Connect

    Not Available

    1988-01-01

    In FY 1986, Oak Ridge Associated Universities (ORAU) initiated two programs for the US Department of Energy (DOE), Office of Fusion Energy (OFE): the Fusion Energy Postdoctoral Research Program and the Fusion Energy Professional Development Program. These programs provide opportunities to conduct collaborative research in magnetic fusion energy research and development programs at DOE laboratories and contractor sites. Participants become trained in advanced fusion energy research, interact with outstanding professionals, and become familiar with energy-related national issues while making personal contributions to the search for solutions to scientific problems. Both programs enhance the national fusion energy research and development effort by providing channels for the exchange of scientists and engineers, the diffusion of ideas and knowledge, and the transfer of relevant technologies. These programs, along with the Magnetic Fusion Energy Science and Technology Fellowship Programs, compose the fusion energy manpower development programs administered by ORAU for DOE/OFE.

  9. Usefulness of a non-invasive reporter system for monitoring reprogramming state in pig cells: results of a cell fusion experiment.

    PubMed

    Ozawa, Akio; Akasaka, Eri; Watanabe, Satoshi; Yoshida, Mitsutoshi; Miyoshi, Kazuchika; Sato, Masahiro

    2010-08-01

    Dedifferentiation of differentiated cells such as fibroblasts into pluripotent stem cells, so-called iPS cells, was first reported by Yamanaka et al., who successfully employed retroviral gene delivery of four stem-cell-specific transcription factors (Oct-3/4, Klf4, Sox2 and c-myc). Despite the mouse system in which an Oct-3/4 or Nanog promoter-based reporter system has already been established, there is no useful system in pigs for reporting the reprogramming state of gene-engineered cells. In this study, we constructed a pOEIN plasmid carrying a ca. 5.4-kb mouse Oct-3/4 promoter linked to the EGFP cDNA and neomycin expression unit and produced a porcine embryonic cell line stably incorporating it in the genome. Cell fusion with mouse embryonal carcinoma cell line F9 resulted in generation of colonies with distinct EGFP-derived fluorescence around 14 days after fusion. RT-PCR using these colonies also confirmed expression of endogenous porcine pluripotency-specific Oct-3/4, Sox2 and Stat3 mRNA. These findings suggest that mouse-derived components are sufficient to induce dedifferentiation of differentiated pig cells and also that reprogramming proceeds gradually. The present non-invasive reporter system will be useful to better define the reprogramming mechanism and/or to identify novel reprogramming molecules in the pig.

  10. Antitumor effects and radiosensitization of cytosine deaminase and thymidine kinase fusion suicide gene on colorectal carcinoma cells

    PubMed Central

    Wu, De-Hua; Liu, Li; Chen, Long-Hua

    2005-01-01

    AIM: To investigate the killing effect and radiosensitization of double suicide gene mediated by adenovirus on colorectal carcinoma cells. METHODS: Colorectal carcinoma cell line SW480 was transfected with adenovirus expression vector containing cytosine deaminase (CD) and thymidine kinase (TK) fusion gene. The expression of CD-TK fusion gene was detected by reverse transcriptase-polymerase chain reaction. The toxic effect of ganciclovir (GCV) and 5-fluorocytosine (5-FC) on infected cells was determined by MTT assay. The radiosensitization of double suicide gene was evaluated by clonogenic assay. RESULTS: After prodrugs were used, the survival rate of colorectal carcinoma cells was markedly decreased. When GCV and 5-FC were used in combination, the cytotoxicity and bystander effect were markedly superior to a single prodrug (χ2 = 30.371, P<0.01). Both GCV and 5-FC could sensitize colorectal carcinoma cells to the toxic effect of radiation, and greater radiosensitization was achieved when both prodrug were used in combination. CONCLUSION: CD-TK double suicide gene can kill and radiosensitize colorectal carcinoma cells. PMID:15918188

  11. A simple and universal ligation mediated fusion of genes based on hetero-staggered PCR for generating immunodominant chimeric proteins.

    PubMed

    Reddy, Prakash K; Ramlal, Shylaja; Sripathy, Murali H; Batra, Harshvardhan

    2012-11-01

    We developed a simple T4 DNA ligase mediated strategy for inframe splicing of two or more cohesive genes generated by hetero-staggered PCR and directionally cloning the spliced product bearing sticky overhangs in to a correspondingly cut vector. For this, two pairs of primers are used in two different parallel PCRs, for generation of each cohesive gene product. We exemplified this strategy by splicing two major super-antigen genes of Staphylococcus aureus, namely, staphylococcal enterotoxin A (sea), and toxic shock syndrome toxin (tsst-1) followed by its directional cloning into pre-digested pRSET A vector. The fusion gene encoding chimeric recombinant SEA-TSST protein (32kDa) was expressed in E. coli BL21(DE3) host strain. The recombinant chimeric protein retained the antigenicity of both toxins as observed by the strong immunoreactivity with commercial antibodies against both SEA and TSST-1 toxin components by Western blot analysis. We observed that the present method for gene splicing with cohesive ends is simple since it does not require elaborate standardization and a single fusion product is obtained consistently during nested PCR with forward primer of first gene and reverse primer of second gene. For comparison, we fused the same genes using splicing by overlap extension PCR (SOE-PCR) and consistently obtained DNA smearing and multiple non-specific bands even after several rounds of PCRs from gel excised product. Moreover, the newly described method requires only two to six complimentary sticky ends between the genes to be spliced, in contrast to long stretch of overlapping nucleotides in case of SOE-PCR. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion.

    PubMed

    Nikolaidis, Nikolas; Doran, Nicole; Cosgrove, Daniel J

    2014-02-01

    Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbial-plant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.

  13. Structure and expression of the Drosophila ubiquitin-52-amino-acid fusion-protein gene.

    PubMed Central

    Cabrera, H L; Barrio, R; Arribas, C

    1992-01-01

    Ubiquitin belongs to a multigene family. In Drosophila two members of this family have been previously described. We report here the organization and expression of a third member, the DUb52 gene, isolated by screening a Drosophila melanogaster genomic library. This gene encodes an ubiquitin monomer fused to a 52-amino acid extension protein. There are no introns interrupting the coding sequence. Recently, it has been described that this extension encodes a ribosomal protein in Saccharomyces, Dictyostelium, and Arabidopsis. The present results show that the 5' regulatory region of DUb52 shares common features with the ribosomal protein genes of Drosophila, Xenopus and mouse, including GC- and pyrimidine-rich regions. Moreover, sequences similar to the consensus Ribo-box in Neurospora crassa have been identified. Furthermore, a sequence has been found that is similar to the binding site for the TFIIIA distal element factor from Xenopus laevis. The DUb52 gene is transcribed to a 0.9 kb mRNA that is expressed constitutively throughout development and is particularly abundant in ovaries. In addition, the DUb52 gene has been found to be preferentially transcribed in exponentially growing Drosophila cells. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:1381584

  14. Incidental finding of two rare developmental anomalies: Fusion and dilaceration: A case report and literature review

    PubMed Central

    Sultan, Nishat

    2015-01-01

    A number of developmental anomalies of morphology are there. However, as compared to the more common oral diseases like caries or periodontal problems, they account for a relatively lower number. When present, they may pose various problems of esthetic, function, malocclusion, or possible disposition to other oral problems. Hence, though rare, their timely diagnosis is very vital in proper treatment planning to avoid unseen complications during extractions, endodontic or orthodontic treatment. The present case is of a patient reporting with two very rare developmental anomalies, that is, fusion and root dilaceration, in contralateral sides of the same patient. To the knowledge of the author, reportedly it is the first such case. The terminologies, etiology, and epidemiology of both these anomalies are also discussed. PMID:26604610

  15. EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer

    PubMed Central

    Koivunen, Jussi P.; Mermel, Craig; Zejnullahu, Kreshnik; Murphy, Carly; Lifshits, Eugene; Holmes, Alison J.; Choi, Hwan Geun; Kim, Jhingook; Chiang, Derek; Thomas, Roman; Lee, Jinseon; Richards, William G.; Sugarbaker, David J.; Ducko, Christopher; Lindeman, Neal; Marcoux, J. Paul; Engelman, Jeffrey A.; Gray, Nathanael S.; Lee, Charles; Meyerson, Matthew; Jänne, Pasi A.

    2011-01-01

    Purpose The EML4-ALK fusion gene has been detected in ~7% of Japanese non-small cell lung cancers (NSCLC). We determined the frequency of EML4-ALK in Caucasian NSCLCs and in NSCLC cell lines. We also determined whether TAE684, a specific ALK kinase inhibitor, would inhibit the growth of EML4-ALK containing cell lines in vitro and in vivo. Experimental Design We screened 305 primary NSCLCs (both US (n=138) and Korean (n=167) patients) and 83 NSCLC cell lines using RT-PCR and by exon array analyses. We evaluated the efficacy of TAE684 against NSCLC cell lines in vitro and in vivo. Results We detected 4 different variants, including two novel variants, of EML4-ALK using RT-PCR in 8/305 tumors (3%) and in 3/83 (3.6%) NSCLC cell lines. All EML4-ALK containing tumors and cell lines were adenocarcinomas. EML4-ALK was detected more frequently in NSCLC patients who were never or light (< 10 pack years) cigarette smokers compared to current/former smokers (6% vs. 1%; p=0.049). TAE684 inhibited the growth of 1 of 3 (H3122) EML4-ALK containing cell lines in vitro and in vivo, inhibited Akt phosphorylation and caused apoptosis. In another EML4-ALK cell line, DFCI032, TAE684 was ineffective due to co-activation of EGFR and ERBB2. The combination of TAE684 and CL-387,785 (EGFR/ERBB2 kinase inhibitor), inhibited growth and Akt phosphorylation and led to apoptosis in the DFCI032 cell line. Conclusions EML4-ALK is found in the minority of NSCLCs. ALK kinase inhibitors alone or in combination may nevertheless be clinically effective treatments for NSCLC patients whose tumors contain EML4-ALK. PMID:18594010

  16. Targeted endostatin-cytosine deaminase fusion gene therapy plus 5-fluorocytosine suppresses ovarian tumor growth.

    PubMed

    Sher, Y-P; Chang, C-M; Juo, C-G; Chen, C-T; Hsu, J L; Lin, C-Y; Han, Z; Shiah, S-G; Hung, M-C

    2013-02-28

    There are currently no effective therapies for cancer patients with advanced ovarian cancer, therefore developing an efficient and safe strategy is urgent. To ensure cancer-specific targeting, efficient delivery, and efficacy, we developed an ovarian cancer-specific construct (Survivin-VISA-hEndoyCD) composed of the cancer specific promoter survivin in a transgene amplification vector (VISA; VP16-GAL4-WPRE integrated systemic amplifier) to express a secreted human endostatin-yeast cytosine deaminase fusion protein (hEndoyCD) for advanced ovarian cancer treatment. hEndoyCD contains an endostatin domain that has tumor-targeting ability for anti-angiogenesis and a cytosine deaminase domain that converts the prodrug 5-fluorocytosine (5-FC) into the chemotherapeutic drug, 5-fluorouracil. Survivin-VISA-hEndoyCD was found to be highly specific, selectively express secreted hEndoyCD from ovarian cancer cells, and induce cancer-cell killing in vitro and in vivo in the presence of 5-FC without affecting normal cells. In addition, Survivin-VISA-hEndoyCD plus 5-FC showed strong synergistic effects in combination with cisplatin in ovarian cancer cell lines. Intraperitoneal (i.p.) treatment with Survivin-VISA-hEndoyCD coupled with liposome attenuated tumor growth and prolonged survival in mice bearing advanced ovarian tumors. Importantly, there was virtually no severe toxicity when hEndoyCD is expressed by Survivin-VISA plus 5-FC compared with CMV plus 5-FC. Thus, the current study demonstrates an effective cancer-targeted gene therapy that is worthy of development in clinical trials for treating advanced ovarian cancer.

  17. [Construction of eukaryotic recombinant vector and expression in COS7 cell of LipL32-HlyX fusion gene from Leptospira serovar Lai].

    PubMed

    Huang, Bi; Bao, Lang; Zhong, Qi; Zhang, Huidong; Zhang, Ying

    2009-04-01

    This study was conducted to construct eukaryotic recombinant vector of LipL32-HlyX fusion gene from Leptospira serovar Lai and express it in mammalian cell. Both of LipL32 gene and HlyX gene were amplified from Leptospira strain O17 genomic DNA by PCR. Then with the two genes as template, LipL32-HlyX fusion gene was obtained by SOE PCR (gene splicing by overlap extension PCR). The fusion gene was then cloned into pcDNA3.1 by restriction nuclease digestion. Having been transformed into E. coli DH5alpha, the recombiant plasmid was identified by restriction nuclease digestion, PCR analysis and sequencing. The recombinant plasmid was then transfected into COS7 cell whose expression was detected by RT-PCR and Western blotting analysis. RT-PCR amplified a fragment about 2000 bp and Western blotting analysis found a specific band about 75 KD which was consistent with the expected fusion protein size. In conclusion, the successful construction of eukaryotic recombinant vector containing LipL32-HlyX fusion gene and the effective expression in mammalian have laid a foundation for the application of Leptospira DNA vaccine.

  18. Characterization of foot-and-mouth disease virus gene products with antisera against bacterially synthesized fusion proteins

    SciTech Connect

    Strebel, K.; Beck, E.; Strohmaier, K.; Schaller, H.

    1986-03-01

    Defined segments of the cloned foot-and-mouth disease virus genome corresponding to all parts of the coding region were expressed in Escherichia coli as fusions to the N-terminal part of the MS2-polymerase gene under the control of the inducible lambdaPL promoter. All constructs yielded large amounts of proteins, which were purified and used to raise sequence-specific antisera in rabbits. These antisera were used to identify the corresponding viral gene products in /sup 35/S-labeled extracts from foot-and-mouth disease virus-infected BHK cells. This allowed us to locate unequivocally all mature foot-and-mouth disease virus gene products in the nucleotide sequence, to identify precursor-product relationships, and to detect several foot-and mouth disease virus gene products not previously identified in vivo or in vitro.

  19. Dominant negative selection of vaccinia virus using a thymidine kinase/thymidylate kinase fusion gene and the prodrug azidothymidine

    SciTech Connect

    Holzer, Georg W. . E-mail: falknef@baxter.com

    2005-07-05

    The Escherichia coli thymidine kinase/thymidylate kinase (tk/tmk) fusion gene encodes an enzyme that efficiently converts the prodrug 3'-azido-2',3'-dideoxythymidine (AZT) into its toxic triphosphate derivative, a substance which stops DNA chain elongation. Integration of this marker gene into vaccinia virus that normally is not inhibited by AZT allowed the establishment of a powerful selection procedure for recombinant viruses. In contrast to the conventional vaccinia thymidine kinase (tk) selection that is performed in tk-negative cell lines, AZT selection can be performed in normal (tk-positive) cell lines. The technique is especially useful for the generation of replication-deficient vaccinia viruses and may also be used for gene knock-out studies of essential vaccinia genes.

  20. Overexpression of HMGA2-LPP fusion transcripts promotes expression of the {alpha} 2 type XI collagen gene

    SciTech Connect

    Kubo, Takahiro; Matsui, Yoshito . E-mail: ymatsui@sb4.so-net.ne.jp; Goto, Tomohiro; Yukata, Kiminori; Yasui, Natsuo

    2006-02-10

    In a subset of human lipomas, a specific t (3; 12) chromosome translocation gives rise to HMGA2-LPP fusion protein, containing the amino (N)-terminal DNA binding domains of HMGA2 fused to the carboxyl (C)-terminal LIM domains of LPP. In addition to its role in adipogenesis, several observations suggest that HMGA2-LPP is linked to chondrogenesis. Here, we analyzed whether HMGA2-LPP promotes chondrogenic differentiation, a marker of which is transactivation of the {alpha} 2 type XI collagen gene (Col11a2). Real-time PCR analysis showed that HMGA2-LPP and COL11A2 were co-expressed. Luciferase assay demonstrated that either of HMGA2-LPP, wild-type HMGA2 or the N-terminal HMGA2 transactivated the Col11a2 promoter in HeLa cells, while the C-terminal LPP did not. RT-PCR analysis revealed that HMGA2-LPP transcripts in lipomas with the fusion were 591-fold of full-length HMGA2 transcripts in lipomas without the fusion. These results indicate that in vivo overexpression of HMGA2-LPP promotes chondrogenesis by upregulating cartilage-specific collagen gene expression through the N-terminal DNA binding domains.

  1. Multilevel anterior thoracic discectomies and anterior interbody fusion using a microsurgical thoracoscopic approach. Case report.

    PubMed

    Dickman, C A; Mican, C A

    1996-01-01

    A video-assisted thoracoscopic microsurgical approach was performed to treat a myelopathic patient with a severe kyphotic deformity caused by chronic nonunion of compression fractures of the T7-9 vertebrae. The kyphotic deformity was treated by combined operative procedures. First, an anterior release was performed using a thoracoscopic technique, sectioning the anterior longitudinal ligament and performing multilevel thoracic discectomies. Next, a posterior reduction and internal fixation of the deformity was achieved using hook-rod instrumentation. Finally, bone graft harvested during the posterior approach was used for interbody fusion via a thoracoscopic approach. Microsurgical thoracoscopic techniques potentially can be used in a variety of spinal surgeries. Compared to transthoracic and posterolateral approaches, this technique presents distinct advantages to treatment of anterior spinal pathology. The small incisions made into the intercostal spaces without retracting the ribs may reduce postoperative pain, shorten the length of hospitalization, and allow early return to activity. The operative techniques used in this case are described in detail. This report demonstrates that thoracoscopic discectomies and interbody fusion are technically feasible and can be effectively performed with acceptable results.

  2. Investigation of electromagnetic launcher behavior for impact fusion. Annual report, July 1, 1983-May 1, 1984

    SciTech Connect

    Thio, Y.C.

    1984-06-01

    A program to develop an ultrahigh velocity accelerator (SUVAC), based on the electromagnetic railgun accelerator concept and sponsored by the US Department of Energy, has been initiated at Westinghouse R and D Center. The program involves the construction over a 4-year period (July 1983 to June 1987) of a multi-stage railgun accelerator which has the potential of accelerating a 1-g projectile to about 30 km/s (Mach 100). The scientific objective of the program is to use the accelerator so built as the experimental apparatus to investigate the potential technical problems of accelerating macroparticles to velocity presently thought to be required to produce impact fusion. The program is part of a joint program with the University of Washington to develop the scientific and technological basis to achieve controlled thermonuclear fusion by hypervelocity impact. This report summarizes the progress made in the first year of the program. It covers work done for the period July 1, 1983 to May 1, 1984.

  3. Comprehensive therapy of a fusion between a mandibular lateral incisor and supernumerary tooth: case report.

    PubMed

    Onçag, Ozant; Candan, Umit; Arikan, Fatih

    2005-08-01

    The term fusion is used to define a developmental anomaly characterised by the union of two adjacent teeth. In the case reported here, clinical and radiographic examinations suggested a unilateral fusion between the mandibular left permanent incisor and a super-numerary tooth. Radiographs showed that the fused teeth had two distinct pulp chambers and canals. A diagnosis of chronic periapical abscess of the supernumerary tooth was made. Before root canal therapy, a periodontal surgical procedure was performed to section the central incisor and its fused supernumerary. Also, odontoplasty was performed on the roots, to establish an anatomy consistent with a normal central incisor. Later, the chronic apical abscess on the supernumerary tooth was instrumented chemo-mechanically, root canal filling was performed and an anterior composite resin restoration was placed. The patient was evaluated for one year after root canal therapy. The tooth was asymptomatic, not exhibiting any pathological root resorption or alveolar resorption, and the anterior composite restoration was intact. Instead of extracting the supernumerary tooth, the application of endodontic, periodontal, and restorative procedures proved to be an alternative treatment.

  4. Heavy ion fusion accelerator research (HIFAR) year-end report, April 1, 1987-September 30, 1987

    SciTech Connect

    Not Available

    1987-12-01

    The basic objective of the Heavy Ion Fusion Accelerator Research (HIFAR) program is to access the suitabilty of heavy ion accelerators as iginiters for Inertial Confinement Fusion (ICF). A specific accerelator techonolgy, the induction linac, has been studied at the Lawerence Berkeley Laboratory and has reached the point at which its viability for ICF applications can be assessed over the next few years. The HIFAR program addresses the generation of high-power, high-brightness beams of heavy ions, the understanding of the scaling laws in this novel physics regime, and the vadidation of new accelerator strategies, to cut costs. The papers in this report that address these goals are: MBE-4 mechanical progress, alignment of MBE-4, a compact energy analyzer for MBE-4, Cs/sup +/ injector modeling with the EGUN code, an improved emittance scanning system for HIFAR, 2-MV injector, carbon arc source development, beam combining in ILSE, emittance growth due to transverse beam combining in ILSE - particle simulation results, achromatic beam combiner for ILSE, additional elements for beam merging, quadrupole magnet design for ILSE, and waveforms and longitudinal beam-parameters for ILSE.

  5. Cold fusion research

    SciTech Connect

    1989-11-01

    I am pleased to forward to you the Final Report of the Cold Fusion Panel. This report reviews the current status of cold fusion and includes major chapters on Calorimetry and Excess Heat, Fusion Products and Materials Characterization. In addition, the report makes a number of conclusions and recommendations, as requested by the Secretary of Energy.

  6. Making genes green: creating green fluorescent protein (GFP) fusions with blunt-end PCR products.

    PubMed

    Lo, W; Rodgers, W; Hughes, T

    1998-07-01

    The jellyfish green fluorescent protein (GFP) has proven to be a useful tool in protein localization and trafficking studies. Fused to GFP, a protein of interest can be visualized and tracked in vivo through fluorescence microscopy. However, the process of making these fusion proteins is often tedious and painstaking. Here, we describe a simple and quick method for creating GFP fusion proteins using blunt-end PCR product ligation.

  7. Design of a sandwich-mode amperometric biosensor for detection of PML/RARα fusion gene using locked nucleic acids on gold electrode.

    PubMed

    Wang, Kun; Sun, Zhouliang; Feng, Meijuan; Liu, Ailin; Yang, Shuyu; Chen, Yuanzhong; Lin, Xinhua

    2011-02-15

    In this study, a novel DNA electrochemical probe (locked nucleic acid, LNA) was designed and involved in constructing an electrochemical DNA biosensor for detection of promyelocytic leukemia/retinoic acid receptor alpha (PML/RARα) fusion gene in acute promyelocytic leukemia for the first time. This biosensor was based on a 'sandwich' sensing mode, which involved a pair of LNA probes (capture probe immobilized at electrode surface and biotinyl reporter probe as an affinity tag for streptavidin-horseradish peroxidase (streptavidin-HRP). Since biotin can be connected with streptavidin-HRP, this biosensor offered an enzymatically amplified electrochemical current signal for the detection of target DNA. In the simple hybridization system, DNA fragment with its complementary DNA fragment was evidenced by amperometric detection, with a detection limit of 74 fM and a linear response range of 0.1-10 pM for synthetic PML/RARα fusion gene in acute promyelocytic leukemia (APL). Otherwise, the biosensor showed an excellent specificity to distinguish the complementary sequence and different mismatch sequences. The new pattern also exhibited high sensitivity and selectivity in mixed hybridization system. Copyright © 2010 Elsevier B.V. All rights reserved.

  8. The Chicken Gene Nomenclature Committee report.

    PubMed

    Burt, David W; Carrë, Wilfrid; Fell, Mark; Law, Andy S; Antin, Parker B; Maglott, Donna R; Weber, Janet A; Schmidt, Carl J; Burgess, Shane C; McCarthy, Fiona M

    2009-07-14

    Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its unique evolutionary niche, the chicken genome can be used to understand evolution of functional elements and gene regulation in mammalian species. However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs. This problem is compounded as different databases and sequence repositories proliferate and the names they assign to functional elements proliferate along with them. Currently, genes can be published under more than one name and one name sometimes refers to unrelated genes. Standardized gene nomenclature is necessary to facilitate communication between scientists and genomic resources. Moreover, it is important that this nomenclature be based on existing nomenclature efforts where possible to truly facilitate studies between different species. We report here the formation of the Chicken Gene Nomenclature Committee (CGNC), an international and centralized effort to provide standardized nomenclature for chicken genes. The CGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees for human and mouse. The CGNC will develop standardized nomenclature in consultation with the research community and relies on the support of the research community to ensure that the nomenclature facilitates comparative and genomic studies.

  9. Fusion Energy Postdoctoral Research Program and Professional Development Program: FY 1986 annual report

    SciTech Connect

    Not Available

    1987-01-01

    During FY 1986, Oak Ridge Associated Universities (ORAU) initiated two new programs for the US Department of Energy (DOE), Office of Fusion Energy (OFE). The Fusion Energy Postdoctoral Research Program and the Fusion Energy Professional Development Program provide opportunities to conduct collaborative research in magnetic fusion energy research and development programs at DOE laboratories and contractor sites. Participants become trained in advanced fusion energy research, interact with outstanding professionals, and become familiar with energy-related national issues while making personal contributions to the search for solutions. Both programs enhance the national fusion energy research and development effort by providing channels for the exchange of scientists and engineers, the diffusion of ideas and knowledge, and the transfer of relevant technologies. These programs complement the Magnetic Fusion Energy Science and Technology Fellowship Programs already administered by ORAU for DOE/OFE.

  10. Analysis of NAB2-STAT6 Gene Fusion in 17 Cases of Meningeal Solitary Fibrous Tumor/Hemangiopericytoma: Review of the Literature.

    PubMed

    Yuzawa, Sayaka; Nishihara, Hiroshi; Wang, Lei; Tsuda, Masumi; Kimura, Taichi; Tanino, Mishie; Tanaka, Shinya

    2016-08-01

    Solitary fibrous tumor/hemangiopericytoma (SFT/HPC) is a mesenchymal tumor that can affect virtually any region of the body. SFT/HPC of the thoracic cavity and soft tissue has been histologically considered a single biological entity termed SFT; in fact, NAB2-STAT6 gene fusion was recently identified in both diseases. In contrast, meningeal SFT and HPC still need to be investigated in detail with regard to gene fusion variants. The aim of this study was to verify the frequency of NAB2-STAT6 fusion and the relationship between fusion variants and clinicopathologic findings of SFT/HPC, especially meningeal SFT/HPC. We examined the NAB2-STAT6 fusion by reverse transcription polymerase chain reaction with 4 cases of meningeal SFT and 13 cases of meningeal HPC. NAB2-STAT6 fusion transcripts were identified in 12 of 17 cases, including NAB2ex6-STAT6ex17 (4/17, 24%), NAB2ex6-STAT6ex16 and NAB2ex4-STAT6ex2 (3/17, 18%, respectively), and NAB2ex5-STAT6ex16 (2/17, 12%). Three cases showed a pseudopapillary pattern, and 2 of them carried NAB2ex6-STAT6ex17. In addition, our meta-analysis revealed that the major fusion variant in meningeal SFT/HPC was NAB2ex6-STAT6ex16/17 (29/54, 54%), which was also common in soft tissue and intraperitoneum/retroperitoneum but rare in thoracic SFT. Fusion variant significantly correlated with age and histologic diagnosis in meningeal SFT/HPC but not with prognosis. Our results represented that meningeal SFT and HPC were in a single biological spectrum with NAB2-STAT6 gene fusion as was nonmeningeal SFT and further confirmed the organ-specific tumorigenic process and morphologic differences on the basis of fusion variants in meningeal SFT/HPC.

  11. The EWSR1/NR4A3 fusion protein of extraskeletal myxoid chondrosarcoma activates the PPARG nuclear receptor gene.

    PubMed

    Filion, C; Motoi, T; Olshen, A B; Laé, M; Emnett, R J; Gutmann, D H; Perry, A; Ladanyi, M; Labelle, Y

    2009-01-01

    The NR4A3 nuclear receptor is implicated in the development of extraskeletal myxoid chondrosarcoma (EMC), primitive sarcoma unrelated to conventional chondrosarcomas, through a specific fusion with EWSR1 resulting in an aberrant fusion protein that is thought to disrupt the transcriptional regulation of specific target genes. We performed an expression microarray analysis of EMC tumours expressing the EWSR1/NR4A3 fusion protein, comparing their expression profiles to those of other sarcoma types. We thereby identified a set of genes significantly overexpressed in EMC relative to other sarcomas, including PPARG and NDRG2. Western blot or immunohistochemical analyses confirm that PPARG and NDRG2 are expressed in tumours positive for EWSR1/NR4A3. Bioinformatic analysis identified a DNA response element for EWSR1/NR4A3 in the PPARG promoter, and band-shift experiments and transient transfections indicate that EWSR1/NR4A3 can activate transcription through this element. Western blots further show that an isoform of the native NR4A3 receptor lacking the C-terminal domain is very highly expressed in tumours positive for EWSR1/NR4A3, and co-transfections of this isoform along with EWSR1/NR4A3 indicate that it may negatively regulate the activity of the fusion protein on the PPARG promoter. These results suggest that the overall expression of PPARG in EMC may be regulated in part by the balance between EWSR1/NR4A3 and NR4A3, and that PPARG may play a crucial role in the development of these tumours. The specific up-regulation of PPARG by EWSR1/NR4A3 may also have potential therapeutic implications.

  12. EDITORIAL: Special issue: overview reports from the Fusion Energy Conference (FEC) (Daejeon, South Korea, 2010) Special issue: overview reports from the Fusion Energy Conference (FEC) (Daejeon, South Korea, 2010)

    NASA Astrophysics Data System (ADS)

    Thomas, Paul

    2011-09-01

    The group of 27 papers published in this special issue of Nuclear Fusion aims to monitor the worldwide progress made in the period 2008-2010 in the field of thermonuclear fusion. Of these papers, 22 are based on overview reports presented at the 23rd Fusion Energy Conference (FEC 2010) and five are summary reports. The conference was hosted by the Republic of Korea and organized by the IAEA in cooperation with the National Fusion Research Institute and the Daejeon Metropolitan City. It took place in Daejeon on 11-16 October 2010. The overviews presented at the conference have been rewritten and extended for the purpose of this special issue and submitted to the standard double-referee peer-review of Nuclear Fusion. The articles are placed in the following sequence: Conference summaries of the sessions devoted to: Tokamak and stellarator experiments, experimental divertor physics and plasma wall interaction experiments, stability experiments and waves and fast particles; ITER activities, fusion technology, safety and economics; Magnetic confinement theory and modelling; Inertial confinement fusion; Innovative confinement concepts, operational scenarios and confinement. Overview articles, presented in programme order, are as follows: Tokamaks Overview of KSTAR initial experiments; Recent progress in RF heating and long-pulse experiments on EAST; Overview of JET results; DIII-D contributions toward the scientific basis for sustained burning plasmas; Overview of JT-60U results toward the resolution of key physics and engineering issues in ITER and JT-60SA; Overview of physics results from NSTX; Overview of ASDEX Upgrade results; Overview of physics results from MAST; Contribution of Tore Supra in preparation of ITER; Overview of FTU results; Overview of experimental results on the HL-2A tokamak; Progress and scientific results in the TCV tokamak; Overview of the JT-60SA project; Recent results of the T-10 tokamak; The reconstruction and research progress of the TEXT

  13. NAB2-STAT6 Gene Fusion in Meningeal Hemangiopericytoma and Solitary Fibrous Tumor.

    PubMed

    Fritchie, Karen J; Jin, Long; Rubin, Brian P; Burger, Peter C; Jenkins, Sarah M; Barthelmeß, Sarah; Moskalev, Evgeny A; Haller, Florian; Oliveira, Andre M; Giannini, Caterina

    2016-03-01

    Meningeal solitary fibrous tumor (SFT) and hemangiopericytoma (HPC) are considered to be distinct entities in the WHO Classification of CNS Tumours (2007). They harbor NAB2-STAT6 fusions similar to their soft tissue counterparts, supporting the view that they are part of a tumor continuum. We examined 30 meningeal-based tumors originally diagnosed as either SFT or HPC. These showed a spectrum of morphologic features and were diagnosed as SFTs, malignant SFTs, HPCs, or tumors with "intermediate" features. All of the tumors showed nuclear expression of STAT6. SFTs consistently expressed diffuse CD34, while HPCs and intermediate tumors had heterogeneous staining. NAB2-STAT6 fusions were identified in 20 cases, including 7 with exon 4-exon 3, 9 with exon 6-exon 17, and 4 with exon 6-exon 18 fusions. NAB2 exon 4-STAT6 exon 3 fusion correlated with classic SFT morphology and older age and showed a trend toward less mitotic activity; there was also a trend toward more aggressive behavior in tumors lacking NAB2 exon 4-STAT6 exon 3. Thus, despite their clinical and morphologic differences, meningeal-based SFTs, HPCs, and tumors with intermediate features, similar to their soft tissue counterparts, form a histopathologic spectrum unified by STAT6 immunoexpression and NAB2-STAT6 fusion.

  14. Visualizing Presynaptic Calcium Dynamics and Vesicle Fusion with a Single Genetically Encoded Reporter at Individual Synapses.

    PubMed

    Jackson, Rachel E; Burrone, Juan

    2016-01-01

    Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs) that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses.

  15. Visualizing Presynaptic Calcium Dynamics and Vesicle Fusion with a Single Genetically Encoded Reporter at Individual Synapses

    PubMed Central

    Jackson, Rachel E.; Burrone, Juan

    2016-01-01

    Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs) that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses. PMID:27507942

  16. Leukemogenic MLL-ENL Fusions Induce Alternative Chromatin States to Drive a Functionally Dichotomous Group of Target Genes.

    PubMed

    Garcia-Cuellar, Maria-Paz; Büttner, Christian; Bartenhagen, Christoph; Dugas, Martin; Slany, Robert K

    2016-04-12

    MLL fusions are leukemogenic transcription factors that enhance transcriptional elongation through modification of chromatin and RNA Pol II. Global transcription rates and chromatin changes accompanying the transformation process induced by MLL-ENL were monitored by nascent RNA-seq and ChIP-seq, revealing 165 direct target genes separated into two distinct clades. ME5 genes bound MLL-ENL at the promoter, relied on DOT1L-mediated histone methylation, and coded preferentially for transcription factors, including many homeobox genes. A distinct ME3 group accumulated MLL-ENL beyond the termination site, was dependent on P-TEFb-mediated phosphorylation of RNA Pol II for transcription, and translated mainly into proteins involved in RNA biology and ribosome assembly. This dichotomy was reflected by a differential sensitivity toward small molecule inhibitors, suggesting the possibility of a combinatorial strategy for treatment of MLL-induced leukemia. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Bioluminescent reporters for catabolic gene expression and pollutant bioavailability

    SciTech Connect

    Heitzer, A.; DiGrazia, P.M.; Sayler, G.S. . Center for Environmental Biotechnology); Burlage, R.S. )

    1991-01-01

    The application of visualized catabolic nah-gene expression using a luxCDABE gene fusion provides a valuable method to measure quantitatively and specifically naphthalene and salicylate bioavailability. It has been demonstrated that the physiological state of the test culture together with the intrinsic regulation mechanisms of the naphthalene degradation pathway as well as the physiological aspects of the lux gene fusion have to be taken into account. The method presented provides a high potential for in situ bioprocess monitoring. In addition, the results obtained with immobilized cells provide a basis for the development of biosensors for environmental applications in specific pollutant monitoring in waste streams and soil slurry systems but, as a general method, also for more conventional biotechnological process control. 8 refs., 2 figs., 1 tab.