Science.gov

Sample records for reporter gene fusion

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

    DOEpatents

    Gambhir, Sanjiv; Pritha, Ray

    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.

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

    DOEpatents

    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.

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

    DOEpatents

    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.

  4. 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.

  5. 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.

  6. Fusion genes in solid tumors.

    PubMed

    Aman, P

    1999-08-01

    Tumor development in different cell types and tissue locations involves many pathways, distinct genes and exogenous factors. Tumor type-specific chromosome rearrangements resulting in fusion genes or promoter swapping are believed to be involved in the early development of many tumor types. They are present in almost all cases of a particular tumor type and cases have been described that carry only tumor type-specific translocations without any signs of other cytogenetic changes. The mechanisms behind chromosome rearrangements in solid tumors are largely unknown. Radiation is an important factor in thyroid carcinomas but no com-$bmon sequence motifs are made out in the break points of solid tumors. The fusion genes found in sarcomas are dominated by the transcription factor type of genes with the TLS/FUS and EWS series of fusion genes as the largest group. More than 50% of papillary thyroid carcinomas carry fusion proteins with tyrosine kinase activity. Rearrangements involving HMGIC, HMGIY, and PLAG1 are common in benign mesenchymal tumors and salivary gland adenomas. Many recurrent tumor translocations show a strict specificity for tumor type. This specificity can most likely be explained by the specific sets of target genes that are deregulated by the fusion gene products. Identification of the downstream target genes is currently the object of intense research and may provide us with information that will help design better diagnostic tools and eventually find a cure for these diseases.

  7. Inactivation of encapsulated cells and their therapeutic effects by means of TGL triple-fusion reporter/biosafety gene.

    PubMed

    Santos, Edorta; Larzabal, Leyre; Calvo, Alfonso; Orive, Gorka; Pedraz, José Luis; Hernández, Rosa Ma

    2013-01-01

    The immobilization of cells within alginate-poly-l-lysine-alginate (APA) microcapsules has been demonstrated to be an effective technology design for long term delivery of therapeutic products. Despite promising advances, biosafety aspects still remain to be improved. Here, we describe a complete characterization of the strategy based on TGL triple-fusion reporter gene--which codifies for Herpes Simplex virus type 1 thymidine-kinase (HSV1-TK), green fluorescent protein (GFP) and Firefly Luciferase--(SFG(NES)TGL) to inactivate encapsulated cells and their therapeutic effects. Myoblasts genetically engineered to secrete erythropoietin (EPO) were retroviraly transduced with the SFG(NES)TGL plasmid to further characterize their ganciclovir (GCV)-mediated inactivation process. GCV sensitivity of encapsulated cells was 100-fold lower when compared to cells plated onto 2D surfaces. However, the number of cells per capsule and EPO secretion decayed to less than 15% at the same time that proliferation was arrested after 14 days of GCV treatment in vitro. In vivo, ten days of GCV treatment was enough to restore the increased hematocrit levels of mice implanted with encapsulated TGL-expressing and EPO-secreting cells. Altogether, these results show that TGL triple-fusion reporter gene may be a good starting point in the search of a suitable biosafety strategy to inactivate encapsulated cells and control their therapeutic effects. PMID:23174140

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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. PMID:26040699

  15. 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

  16. 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. PMID:26492182

  17. 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.

  18. Primary Renal Sclerosing Epithelioid Fibrosarcoma: Report of Two Cases with EWSR1-CREB3L1 Gene Fusion

    PubMed Central

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

    2014-01-01

    We report the first two genetically confirmed cases of primary renal sclerosing epithelioid fibrosarcoma (SEF), occurring in a 17 year-old male and a 61 year-old female. 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 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. PMID:25353281

  19. Fusion of platelet-derived growth factor receptor β to CEV14 gene in chronic myelomonocytic leukemia: A case report and review of the literature

    PubMed Central

    GONG, SHENG-LAN; GUO, MENG-QIAO; TANG, GU-SHENG; ZHANG, CHUN-LING; QIU, HUI-YING; HU, XIAO-XIA; YANG, JIAN-MIN

    2016-01-01

    Myeloid tumor possessing platelet-derived growth factor receptor β (PDGFRβ) gene rearrangement is a rare hematological malignancy, which presents with typical characteristics of myeloid proliferation disorders and eosinophilia. In the present study, an elderly chronic myelomonocytic leukemia patient was diagnosed with chromosome rearrangement. Fluorescence in situ hybridization (FISH) was conducted with a PDGFRβ isolate probe, and gene translocation between PDGFRβ on chromosome 5 and genes on the chromosomes of group D (13–15) was detected. Karyotype analysis revealed a chromosome 5 break, and PDGFRβ-thyroid hormone receptor interactor 11 (CEV14) gene fusion was confirmed via reverse transcription-polymerase chain reaction (RT-PCR), which additionally revealed the chromosome rearrangement t(5;14)(q33;q32). Due to the correlation between PDGFRβ-CEV14 expression and effectiveness of treatment with tyrosine kinase inhibitors, this fusion gene is considered to be an oncogene. In the present study, an elderly patient was diagnosed with a myeloid tumor associated with the fusion gene PDGFRβ-CEV14, using the methods of FISH and RT-PCR. These methods were confirmed to be of significant value in improving diagnosis, guiding treatment and increasing the cure rate of patients, due to their ability to detect multiple rearrangement genes associated with PDGFRβ in myelodysplastic and myeloproliferative neoplasms. PMID:26870282

  20. 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.

  1. Parallel evolution of chimeric fusion genes.

    PubMed

    Jones, Corbin D; Begun, David J

    2005-08-01

    To understand how novel functions arise, we must identify common patterns and mechanisms shaping the evolution of new genes. Here, we take advantage of data from three Drosophila genes, jingwei, Adh-Finnegan, and Adh-Twain, to find evolutionary patterns and mechanisms governing the evolution of new genes. All three of these genes are independently derived from Adh, which enabled us to use the extensive literature on Adh in Drosophila to guide our analyses. We discovered a fundamental similarity in the temporal, spatial, and types of amino acid changes that occurred. All three genes underwent rapid adaptive amino acid evolution shortly after they were formed, followed by later quiescence and functional constraint. These genes also show striking parallels in which amino acids change in the Adh region. We showed that these early changes tend to occur at amino acid residues that seldom, if ever, evolve in Drosophila Adh. Changes at these slowly evolving sites are usually associated with loss of function or hypomorphic mutations in Drosophila melanogaster. Our data indicate that shifting away from ancestral functions may be a critical step early in the evolution of chimeric fusion genes. We suggest that the patterns we observed are both general and predictive.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. FusionDB: a database for in-depth analysis of prokaryotic gene fusion events.

    PubMed

    Suhre, Karsten; Claverie, Jean-Michel

    2004-01-01

    FusionDB (http://igs-server.cnrs-mrs.fr/FusionDB/) constitutes a resource dedicated to in-depth analysis of bacterial and archaeal gene fusion events. Such events can provide the 'Rosetta stone' in the search for potential protein-protein interactions, as well as metabolic and regulatory networks. However, the false positive rate of this approach may be quite high, prompting a detailed scrutiny of putative gene fusion events. FusionDB readily provides much of the information required for that task. Moreover, FusionDB extends the notion of gene fusion from that of a single gene to that of a family of genes by assembling pairs of genes from different genomes that belong to the same Cluster of Orthogonal Groups (COG). Multiple sequence alignments and phylogenetic tree reconstruction for the N- and C-terminal parts of these 'COG fusion' events are provided to distinguish single and multiple fusion events from cases of gene fission, pseudogenes and other false positives. Finally, gene fusion events with matches to known structures of heterodimers in the Protein Data Bank (PDB) are identified and may be visualized. FusionDB is fully searchable with access to sequence and alignment data at all levels. A number of different scores are provided to easily differentiate 'real' from 'questionable' cases, especially when larger database searches are performed. FusionDB is cross-linked with the 'Phylogenomic Display of Bacterial Genes' (PhydBac) online web server. Together, these servers provide the complete set of information required for in-depth analysis of non-homology-based gene function attribution. PMID:14681411

  7. FusionDB: a database for in-depth analysis of prokaryotic gene fusion events.

    PubMed

    Suhre, Karsten; Claverie, Jean-Michel

    2004-01-01

    FusionDB (http://igs-server.cnrs-mrs.fr/FusionDB/) constitutes a resource dedicated to in-depth analysis of bacterial and archaeal gene fusion events. Such events can provide the 'Rosetta stone' in the search for potential protein-protein interactions, as well as metabolic and regulatory networks. However, the false positive rate of this approach may be quite high, prompting a detailed scrutiny of putative gene fusion events. FusionDB readily provides much of the information required for that task. Moreover, FusionDB extends the notion of gene fusion from that of a single gene to that of a family of genes by assembling pairs of genes from different genomes that belong to the same Cluster of Orthogonal Groups (COG). Multiple sequence alignments and phylogenetic tree reconstruction for the N- and C-terminal parts of these 'COG fusion' events are provided to distinguish single and multiple fusion events from cases of gene fission, pseudogenes and other false positives. Finally, gene fusion events with matches to known structures of heterodimers in the Protein Data Bank (PDB) are identified and may be visualized. FusionDB is fully searchable with access to sequence and alignment data at all levels. A number of different scores are provided to easily differentiate 'real' from 'questionable' cases, especially when larger database searches are performed. FusionDB is cross-linked with the 'Phylogenomic Display of Bacterial Genes' (PhydBac) online web server. Together, these servers provide the complete set of information required for in-depth analysis of non-homology-based gene function attribution.

  8. Intraparenchymal mesenchymal chondrosarcoma of the frontal lobe--a case report and molecular detection of specific gene fusions from archival FFPE sample.

    PubMed

    Sajjad, Emir Ahmed; Sikora, Katarzyna; Paciejewski, Tomasz; Garbicz, Filip; Paskal, Wiktor; Szacht, Milena; Grajkowska, Wieslawa; Włodarski, Pawel Krzysztof

    2015-01-01

    Mesenchymal chondrosarcoma is a rare tumor of cartilaginous origin characterized by its bimorphic pattern composed of highly undifferentiated small round cells separated by islands of well-differentiated hyaline cartilage. It exhibits higher malignancy and earlier occurrence in comparison to classic chondrosarcomas. Recently identified HEY1-NCOA2 and IRF2BP2-CDX1 gene fusions confirm their distinct molecular origin and pose a promising diagnostic marker. The majority of cases arise from craniofacial bones. In this study, we present a rare case of mesenchymal chondrosarcoma encompassed within the brain parenchyma of the frontal lobe without any dural or bone attachment. We demonstrate histopathological findings and confirm the HEY1-NCOA2 gene fusion in a formalin-fixed paraffin-embedded archival sample using simple reverse transcription polymerase chain reaction (RT-PCR) method. IRF2BP2-CDX1 gene fusion was absent in the analyzed sample. The clinical follow-up is also presented with a review of treatment modalities for this entity.

  9. 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

  10. Evolution of gene fusions: horizontal transfer versus independent events

    PubMed Central

    Yanai, Itai; Wolf, Yuri I; Koonin, Eugene V

    2002-01-01

    Background Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution. Results The evolutionary history of gene fusions was studied by phylogenetic analysis of the domains in the fused proteins and the orthologous domains that form stand-alone proteins. Clustering of fusion components from phylogenetically distant species was construed as evidence of dissemination of the fused genes by horizontal transfer. Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms. On many occasions, the evolutionary scenario also involves one or more secondary fissions of the fusion gene. For approximately half of the fusions, stand-alone forms of the fusion components are encoded by juxtaposed genes, which are known or predicted to belong to the same operon in some of the prokaryotic genomes. This indicates that evolution of gene fusions often, if not always, involves an intermediate stage, during which the future fusion components exist as juxtaposed and co-regulated, but still distinct, genes within operons. Conclusion These findings suggest a major role for horizontal transfer of gene fusions in the evolution of protein-domain architectures, but also indicate that independent fusions of the same pair of domains in distant species is not uncommon, which suggests positive selection for the multidomain architectures. PMID:12049665

  11. Fusion of the HMGA2 and NFIB genes in lipoma.

    PubMed

    Nilsson, M; Panagopoulos, I; Mertens, F; Mandahl, N

    2005-11-01

    The major cytogenetic subgroup of lipomas is characterized by aberrations of chromosome segment 12q13-15, which recombines with a large number of other chromosomal regions. The gene HMGA2 is the main target in these aberrations. For some recurrent rearrangements, chimeric transcripts, including the 5' part of HMGA2, have been described. The 3' partners identified are LPP, LHFP, CMKOR1, and EBF. In addition, subsets of other benign solid tumors show aberrations of 12q13-15. Among pleomorphic adenomas of the salivary glands, where the preferred recombination partner with 12q13-15 is 9p22-24, an HMGA2/NFIB fusion gene has been reported. In the present study, two cases of lipoma with rearrangements of 9p22-24 and 12q15 were analyzed by reverse transcription polymerase chain reaction to find out if HMGA2/NFIB was also present in lipoma. An in-frame fusion transcript, combining the four first exons of HMGA2 with exon 8 of NFIB, was detected in one case. It was identical to a transcript that was previously described in salivary gland adenoma and contained a stop codon shortly 3' of the fusion point. The finding of the same fusion gene in different tumors is not unique. For example, HMGA2/LPP has been reported in lipoma, pulmonary chondroid hamartoma, and soft tissue chondroma. Since similar 9;12 translocations have been described also in rare cases of hamartoma and uterine leiomyoma, the occurrence of HMGA2/NFIB could be postulated in these tumors as well.

  12. 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

  13. 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

  14. 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

  15. JAZF1/SUZ12 gene fusion in endometrial stromal sarcomas.

    PubMed

    Hrzenjak, Andelko

    2016-01-01

    Endometrial stromal sarcomas (ESSs) belong to the rarest uterine malignancies (prevalence category <1-9/1,000,000). According to the new 2014 World Health Organisation (WHO) classification, they are separated into four categories; benign endometrial stromal nodules (ESNs), low grade endometrial stromal sarcomas (LG-ESSs), high-grade endometrial stromal sarcomas (HG-ESSs) and undifferentiated uterine sarcomas (UUSs). Due to heterogeneous histopathologic appearance these tumors still represent diagnostic challenge, even for experienced pathologists. ESSs are genetically very heterogeneous and several chromosomal translocations and gene fusions have so far been identified in these malignancies. To date the JAZF1/SUZ12 gene fusion is by far the most frequent and seems to be the cytogenetic hallmark of ESN and LG-ESS. Based on present literature data this gene fusion is present in approximately 75% of ESN, 50% of LG-ESS and 15% of HG-ESS cases. The frequency of JAZF1/SUZ12 appearance varies between classic ESS and different morphologic variants. This gene fusion is suggested to become a specific diagnostic tool, especially in difficult borderline cases. In combination with the recently described YWHAE/FAM22 gene fusion the JAZF1/SUZ12 fusion could be used to differentiate between LG-ESS and HG-ESS. The purpose of this review is to summarize literature data published in last two and a half decades about this gene fusion, as a contribution to our understanding of ESS genetics and pathogenesis. PMID:26879382

  16. 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.

  17. MLL-SEPTIN gene fusions in hematological malignancies.

    PubMed

    Cerveira, Nuno; Bizarro, Susana; Teixeira, Manuel R

    2011-08-01

    The mixed lineage leukemia (MLL) locus is involved in more than 60 different rearrangements with a remarkably diverse group of fusion partners in approximately 10% of human leukemias. MLL rearrangements include chromosomal translocations, gene internal duplications, chromosome 11q deletions or inversions and MLL gene insertions into other chromosomes, or vice versa. MLL fusion partners can be classified into four distinct categories: nuclear proteins, cytoplasmatic proteins, histone acetyltransferases and septins. Five different septin genes (SEPT2, SEPT5, SEPT6, SEPT9, and SEPT11) have been identified as MLL fusion partners, giving rise to chimeric fusion proteins in which the N terminus of MLL is fused, in frame, to almost the entire open reading frame of the septin partner gene. The rearranged alleles result from heterogeneous breaks in distinct introns of both MLL and its septin fusion partner, originating distinct gene fusion variants. MLL-SEPTIN rearrangements have been repeatedly identified in de novo and therapy related myeloid neoplasia in both children and adults, and some clinicopathogenetic associations are being uncovered. The fundamental roles of septins in cytokinesis, membrane remodeling and compartmentalization can provide some clues on how abnormalities in the septin cytoskeleton and MLL deregulation could be involved in the pathogenesis of hematological malignancies. PMID:21714766

  18. Reproducible, Scalable Fusion Gene Detection from RNA-Seq.

    PubMed

    Arsenijevic, Vladan; Davis-Dusenbery, Brandi N

    2016-01-01

    Chromosomal rearrangements resulting in the creation of novel gene products, termed fusion genes, have been identified as driving events in the development of multiple types of cancer. As these gene products typically do not exist in normal cells, they represent valuable prognostic and therapeutic targets. Advances in next-generation sequencing and computational approaches have greatly improved our ability to detect and identify fusion genes. Nevertheless, these approaches require significant computational resources. Here we describe an approach which leverages cloud computing technologies to perform fusion gene detection from RNA sequencing data at any scale. We additionally highlight methods to enhance reproducibility of bioinformatics analyses which may be applied to any next-generation sequencing experiment. PMID:26667464

  19. CEST MRI reporter genes.

    PubMed

    Liu, Guanshu; Bulte, Jeff W M; Gilad, Assaf A

    2011-01-01

    In recent years, several reporter genes have been developed that can serve as a beacon for non-invasive magnetic resonance imaging (MRI). Here, we provide a brief summary of recent advances in MRI reporter gene technology, as well as detailed "hands-on" protocols for cloning, expression, and imaging of reporter genes based on chemical exchange saturation transfer (CEST).

  20. 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

  1. Activation of Developmentally Mutated Human Globin Genes by Cell Fusion

    NASA Astrophysics Data System (ADS)

    Papayannopoulou, Thalia; Enver, Tariq; Takegawa, Susumu; Anagnou, Nicholas P.; Stamatoyannopoulos, George

    1988-11-01

    Human fetal globin genes are not expressed in hybrid cells produced by the fusion of normal human lymphocytes with mouse erythroleukemia cells. In contrast, when lymphocytes from persons with globin gene developmental mutations (hereditary persistence of fetal hemoglobin) are used for these fusions, fetal globin is expressed in the hybrid cells. Thus, mutations of developmental origin can be reconstituted in vitro by fusing mutant lymphoid cells with differentiated cell lines of the proper lineage. This system can readily be used for analyses, such as globin gene methylation, that normally require large numbers of pure nucleated erythroid cells, which are difficult to obtain.

  2. Low frequency of ESRRA-C11orf20 fusion gene in ovarian carcinomas.

    PubMed

    Micci, Francesca; Panagopoulos, Ioannis; Thorsen, Jim; Davidson, Ben; Tropé, Claes Gøran; Heim, Sverre

    2014-02-01

    The identification of recurrent gene fusions in common epithelial cancers--for example, TMPRSS2/ERG in prostate cancer and EML4/ALK in nonsmall cell lung carcinomas--has raised the question of whether fusion genes are pathogenetically important also in ovarian carcinomas. The first recurrent fusion transcript in serous ovarian carcinomas was reported by Salzman et al. in 2011, who used deep paired-end sequencing to detect the fusion gene ESRRA-C11orf20 in 10 out of 67 (15%) serous ovarian carcinomas examined, a finding that holds great promise for our understanding of ovarian tumorigenesis as well as, potentially, for new treatment strategies. We wanted to test how frequent the ESRRA/C11orf20 fusion is in ovarian carcinomas of all subtypes, and therefore examined a series of 230 ovarian carcinomas of which 197 were of the serous subtype and 163 of the 197 were of stages III and IV--that is, the very same carcinoma subset where the fusion transcript had been found. We performed PCR and high-throughput sequencing analyses in search of the fusion transcript. We used the same primers described previously for the detection of the fusion and the same primer combination, but found no ESRRA/C11orf20 fusion in our series. A synthetic DNA plasmid containing the reported ESRRA/C11orf20 fusion was included as a positive control for our PCR experiments. Data from high-throughput sequencing of 23 ovarian carcinomas were screened in search of alternative partner(s) for the ESRRA and/or C11orf20 gene, but none was found. We conclude that the frequency of the ESRRA/C11orf20 gene fusion in serous ovarian carcinomas of stages III and IV must be considerable less than that reported previously (0/163 in our experience compared with 10/67 in the previous study). At the very least, it seems clear that the said fusion cannot be a common pathogenetic event in this tumor type.

  3. 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

  4. Identification of novel fusion genes in testicular germ cell tumors

    PubMed Central

    Hoff, Andreas M.; Alagaratnam, Sharmini; Zhao, Sen; Bruun, Jarle; Andrews, Peter W.; Lothe, Ragnhild A.; Skotheim, Rolf I.

    2015-01-01

    Testicular germ cell tumors (TGCT) are the most frequently diagnosed solid tumors in young men ages 15 to 44 years. Embryonal carcinomas (EC) comprise a subset of TGCTs that exhibit pluripotent characteristics similar to embryonic stem (ES) cells, but the genetic drivers underlying malignant transformation of ECs are unknown. To elucidate the abnormal genetic events potentially contributing to TGCT malignancy, such as the existence of fusion genes or aberrant fusion transcript expression, we performed RNA sequencing of EC cell lines and their non-malignant ES cell line counterparts. We identified eight novel fusion transcripts and one gene with alternative promoter usage, ETV6. Four out of nine transcripts were found recurrently expressed in an extended panel of primary TGCTs and additional EC cell lines, but not in normal parenchyma of the testis, implying tumor-specific expression. Two of the recurrent transcripts involved an intrachromosomal fusion between RCC1 and HENMT1 located 80 Mbp apart and an interchromosomal fusion between RCC1 and ABHD12B. RCC1-ABHD12B and the ETV6 transcript variant were found to be preferentially expressed in the more undifferentiated TGCT subtypes. In vitro differentiation of the NTERA2 EC cell line resulted in significantly reduced expression of both fusion transcripts involving RCC1 and the ETV6 transcript variant, indicating that they are markers of pluripotency in a malignant setting. In conclusion, we identified eight novel fusion transcripts that, to our knowledge, are the first fusion genes described in TGCT and may therefore potentially serve as genomic biomarkers of malignant progression. PMID:26659575

  5. Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ

    PubMed Central

    Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, Mona

    2014-01-01

    Double-stranded DNA breaks occur on a regular basis in the human genome as a consequence of genotoxic stress and errors during replication. Usually these breaks are rapidly and faithfully repaired, but occasionally different chromosomes, or different regions of the same chromosome, are fused to each other. Some of these aberrant chromosomal translocations yield functional recombinant genes, which have been implicated as the cause of a number of lymphomas, leukemias, sarcomas, and solid tumors. Reliable methods are needed for the in situ detection of the transcripts encoded by these recombinant genes. We have developed just such a method, utilizing single-molecule fluorescence in situ hybridization (sm-FISH), in which approximately 50 short fluorescent probes bind to adjacent sites on the same mRNA molecule, rendering each target mRNA molecule visible as a diffraction-limited spot in a fluorescence microscope. Utilizing this method, gene fusion transcripts are detected with two differently colored probe sets, each specific for one of the two recombinant segments of a target mRNA; enabling the fusion transcripts to be seen in the microscope as distinct spots that fluoresce in both colors. We demonstrate this method by detecting the BCR-ABL fusion transcripts that occur in chronic myeloid leukemia cells, and by detecting the EWSR1-FLI1 fusion transcripts that occur in Ewing's sarcoma cells. This technology should pave the way for accurate in situ typing of many cancers that are associated with, or caused by, fusion transcripts. PMID:24675777

  6. [The progress of TMPRSS2-ETS gene fusions and their mechanism in prostate cancer].

    PubMed

    Guo, Xiao-Qiang; Gui, Yao-Ting; Cai, Zhi-Ming

    2011-02-01

    The gene fusions between transmembrane protease serine 2 (TMPRSS2) and E26 (ETS) transcription factors are present in over 50% of patients with prostate cancer. TMPRSS2-ERG is the most common gene fusion type. The ERG overexpression induced by TMPRSS2-ERG gene fusion contributes to the development of prostate cancer. Both androgen receptor binding and genotoxic stress induce chromosomal proximity and TMPRSS2-ETS gene fusions. TMPRSS2-ERG gene fusion functions as a biomarker for prostate cancer, which can be easily detected in urine. This review focuses on the characteristics, oncogenic and rearranged mechanism, and clinical application of TMPRSS2-ETS gene fusions.

  7. 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)

  8. 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.

  9. Characterization of vir-activated TnphoA gene fusions in Bordetella pertussis.

    PubMed Central

    Finn, T M; Shahin, R; Mekalanos, J J

    1991-01-01

    The expression of many of the known virulence determinants of Bordetella pertussis is coordinately regulated by the vir regulatory locus and reduced in response to environmental signals called modulators. We have previously identified eight TnphoA gene fusions in B. pertussis in which the expression of alkaline phosphatase was maximal in the absence of the modulators nicotinic acid and MgSO4. We have termed the genes identified by these fusions vir-activated genes. Here we report the characterization of these TnphoA mutant strains. Four fusion strains were defective in known virulence determinants. For one of these, fusion strain SK39, Southern blot hybridization demonstrated that TnphoA was inserted in the S1 subunit gene of pertussis toxin. Hemagglutination assays, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunoblots identified three fusions strains, SK16, SK75, and SK91, that were defective in filamentous hemagglutinin. Whereas all three filamentous hemagglutinin-defective mutants showed either normal or enhanced colonization, the pertussis toxin-defective mutant showed a marked defect in pulmonary persistence. Of the four other fusion strains, two were deficient in outer membrane proteins. One of these, strain SK8, was defective in a major outer membrane protein of 95 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This strain colonized mouse lungs less well and did not induce lymphocytosis after aerosol challenge. The other strain, SK34, was defective in four outer membrane proteins, three of which were detectable only on a Western blot with polyclonal sera against B. pertussis. Two of our gene fusion strains did not show any defect in identifiable vir-regulated proteins. Images PMID:1652562

  10. 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. PMID:24145651

  11. 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.

  12. 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

  13. 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.

  14. Mesenchymal chondrosarcoma diagnosed on FISH for HEY1-NCOA2 fusion gene.

    PubMed

    Moriya, Kunihiko; Katayama, Saori; Onuma, Masaei; Rikiishi, Takeshi; Hosaka, Masami; Watanabe, Mika; Hasegawa, Tadashi; Sasahara, Yoji; Kure, Shigeo

    2014-10-01

    Mesenchymal chondrosarcoma (MC) is an extremely rare subtype of chondrosarcoma that has a small round-cell sarcoma with focal cartilaginous differentiation, often with a pericytomatous vascular pattern. The non-cartilaginous components are usually dominant, and such lesions might be confused with other small round-cell tumors. Recently, a tumor-specific HEY1-NCOA2 fusion gene was identified in MC. Here we report the case of a 9-year-old boy who was diagnosed with MC by detection of HEY1-NCOA2 fusion signals in almost 50% of tumor cells in tissue sections on fluorescence in situ hybridization (FISH). In this way, the tumor was definitively diagnosed as MC. This case suggests that the detection of the HEY1-NCOA2 fusion gene on FISH is of diagnostic value for MC.

  15. Hematopoietic stem cell transplantation for pediatric mature B-cell acute lymphoblastic leukemia with non-L3 morphology and MLL-AF9 gene fusion: three case reports and review of the literature.

    PubMed

    Sarashina, Takeo; Iwabuchi, Haruko; Miyagawa, Naoyuki; Sekimizu, Masahiro; Yokosuka, Tomoko; Fukuda, Kunio; Hamanoue, Satoshi; Iwasaki, Fuminori; Goto, Shoko; Shiomi, Masae; Imai, Chihaya; Goto, Hiroaki

    2016-07-01

    Mature B-cell acute lymphoblastic leukemia (B-ALL) is typically associated with French-American-British (FAB)-L3 morphology and MYC gene rearrangement. However, rare cases of mature B-ALL with non-L3 morphology and MLL-AF9 fusion have been reported, and such cases are characterized by a rapid and aggressive clinical course. We here report three such cases of pediatric mature B-ALL in female patients respectively aged 15 months, 4 years, and 4 months. Bone marrow smears at diagnosis showed FAB-L1 morphology in all patients. Immunophenotypically, they were positive for cluster of differentiation (CD)10, CD19, CD20 (or CD22), Human Leukocyte Antigen-DR, and surface immunoglobulin λ. No evidence of MYC rearrangement was detected in any of the cases by fluorescent in situ hybridization (FISH) analysis. However, MLL rearrangement was detected by FISH, and MLL-AF9 fusion was confirmed by reverse transcriptase-polymerase chain reaction. All patients achieved complete remission after conventional chemotherapy and subsequently underwent hematopoietic stem cell transplantation as high-risk ALL; patient 3 for infantile ALL with MLL rearrangement and the others for ALL with MLL rearrangement and hyperleukocytosis (white blood cell count at diagnosis >50 × 10(9)/L). At the latest follow-up for each case (12-98 months post-transplantation), complete remission was maintained. Moreover, we discuss the clinical, genetic, and immunophenotypic features of this rare disease. PMID:27084248

  16. Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements†

    PubMed Central

    Richards, Thomas A.; Dacks, Joel B.; Campbell, Samantha A.; Blanchard, Jeffrey L.; Foster, Peter G.; McLeod, Rima; Roberts, Craig W.

    2006-01-01

    Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been

  17. FUS-ERG gene fusion in isolated myeloid sarcoma showing uncommon clinical features.

    PubMed

    Ueda, Ryosuke; Maruyama, Dai; Nomoto, Junko; Maeshima, Akiko M; Fukuhara, Suguru; Kitahara, Hideaki; Miyamoto, Ken-Ichi; Munakata, Wataru; Suzuki, Tatsuya; Taniguchi, Hirokazu; Kobayashi, Yukio; Tobinai, Kensei

    2016-01-01

    FUS-ERG gene fusion has not been reported in cases of myeloid sarcoma (MS), a subtype of acute myeloid leukemia involving extramedullary anatomic sites. Here, we report a case of a 48-year-old man with primary isolated MS of the anterior mediastinum, who later developed multiple extramedullary recurrences without bone marrow infiltration throughout the course. G-banding analysis of the cells in pericardial effusion at recurrence showed complex karyotypic abnormalities including t(16;21)(p11.2;q22). FUS break-apart fluorescent in situ hybridization analysis showed split signals in biopsy sections at initial diagnosis and recurrence. Reverse transcriptase polymerase chain reaction and direct sequencing demonstrated the presence of the FUS-ERG chimeric gene transcript. The patient underwent cord blood transplantation, but died of pneumonia on day 64. To our knowledge, this is the first report of isolated MS carrying FUS-ERG gene fusion. In future study, relationship between the fusion gene and uncommon clinical features should be investigated in isolated MS. PMID:26770812

  18. 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.

  19. 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.

  20. Criteria for practical fusion power systems: Report from the EPRI fusion panel

    NASA Astrophysics Data System (ADS)

    Kaslow, J.; Brown, M.; Hirsch, R.; izzo, R.; McCann, J.; McCloud, D.; Muston, B.; Peterson, A.; Rosen, S.; Schneider, T.; Skrgic, P.; Snow, B.

    1994-09-01

    Electric utilities are keenly interested in the promise of fusion: large-scale electricity production anywhere, with virtually no natural resource depletion or environmental pollution. To expedite development of commercially viable fusion systems, the Electric Power Research Institute (EPRI)—the R&D wing of the U.S. electric utility industry—recently convened a panel of top utility R&D managers and executive officers to identify the key criteria that must be met by fusion plants in order to be acceptable to utilities. The panel's findings, summarized in this report, emphasize competitive economics, positive public perception, and regulatory simplicity.

  1. 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. PMID:27540857

  2. 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.

  3. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.

    PubMed

    Giacomini, Craig P; Sun, Steven; Varma, Sushama; Shain, A Hunter; Giacomini, Marilyn M; Balagtas, Jay; Sweeney, Robert T; Lai, Everett; Del Vecchio, Catherine A; Forster, Andrew D; Clarke, Nicole; Montgomery, Kelli D; Zhu, Shirley; Wong, Albert J; van de Rijn, Matt; West, Robert B; Pollack, Jonathan R

    2013-04-01

    Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis. PMID:23637631

  4. Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma

    PubMed Central

    Kannan, Kalpana; Coarfa, Cristian; Chao, Pei-Wen; Luo, Liming; Wang, Yan; Brinegar, Amy E.; Hawkins, Shannon M.; Milosavljevic, Aleksandar; Matzuk, Martin M.; Yen, Laising

    2015-01-01

    High-grade serous ovarian cancer (HGSC) is among the most lethal forms of cancer in women. Excessive genomic rearrangements, which are expected to create fusion oncogenes, are the hallmark of this cancer. Here we report a cancer-specific gene fusion between BCAM, a membrane adhesion molecule, and AKT2, a key kinase in the PI3K signaling pathway. This fusion is present in 7% of the 60 patient cancers tested, a significant frequency considering the highly heterogeneous nature of this malignancy. Further, we provide direct evidence that BCAM-AKT2 is translated into an in-frame fusion protein in the patient’s tumor. The resulting AKT2 fusion kinase is membrane-associated, constitutively phosphorylated, and activated as a functional kinase in cells. Unlike endogenous AKT2, whose activity is tightly regulated by external stimuli, BCAM-AKT2 escapes the regulation from external stimuli. Moreover, a BCAM-AKT2 fusion gene generated via chromosomal translocation using the CRISPR/Cas9 system leads to focus formation in both OVCAR8 and HEK-293T cell lines, suggesting that BCAM-AKT2 is oncogenic. Together, the results indicate that BCAM-AKT2 expression is a new mechanism of AKT2 kinase activation in HGSC. BCAM-AKT2 is the only fusion gene in HGSC that is proven to translate an aberrant yet functional kinase fusion protein with oncogenic properties. This recurrent genomic alteration is a potential therapeutic target and marker of a clinically relevant subtype for tailored therapy of HGSC. PMID:25733895

  5. 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

  6. Incidence of preleukemic fusion genes in healthy subjects.

    PubMed

    Kosik, P; Skorvaga, M; Belyaev, I

    2016-01-01

    The diagnostics of leukemia relies upon multi-parametric approach involving a number of different pathology disciplines such as flow cytometry, histopathology, cytogenetics and molecular genetics [fluorescent in situ hybridization (FISH) and polymerase chain reaction (PCR)]. Childhood leukemia is often determined by the presence of specific chromosomal translocation that entails the generation of preleukemic fusion genes (PFG). In the last two decades, several studies have reported observations that PFG are present in healthy population and not necessarily result in leukemia. The first such study by Limpens and colleagues on t(14/18)/ BCL2-JH [1] and next in line [2, 3] led to many questions regarding the significance of these chromosomal translocations in leukemogenesis. However, the data on the incidence of PFG are contradictive. This review aims to highlight the molecular genetic approaches used by various studies with regard to differences in diagnostics and incidence of PFG in healthy subjects. The focus is on the incidence and prevalence of the most common PFG such as TEL-AML1, MLL-AF4, BCR-ABL (p190), AML1-ETO, PML-RARA, and CBFB-MYH11 detected in umbilical cord blood, in neonatal blood spots (Guthrie cards (GC)), bone marrow, peripheral blood and tissues of amortized fetuses. We conclude that the incidence of PFG is significantly higher than incidence of leukemia and more sophisticated analysis of PFG in leukemogenic cell populations is warranted to relate the occurrence of PFG with leukemia. The emerging notion is that only those PFG may contribute to development of leukemia which arise in stem cells at specific time windows during development. Thus, screening of PFG in subpopulations of stem cells may be a challenge for assessment of predisposition to leukemia and for validation of cell transplant to minimize donor cell-derived leukemia. PMID:27468869

  7. 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

  8. 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.

  9. 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).

  10. Detection of EML4-ALK fusion gene and features associated with EGFR mutations in Chinese patients with non-small-cell lung cancer

    PubMed Central

    Wen, Miaomiao; Wang, Xuejiao; Sun, Ying; Xia, Jinghua; Fan, Liangbo; Xing, Hao; Zhang, Zhipei; Li, Xiaofei

    2016-01-01

    Purpose Echinoderm microtubule-associated protein-like 4–anaplastic lymphoma kinase (EML4-ALK) and epidermal growth factor receptor (EGFR) define specific molecular subsets of lung cancer with distinct clinical features. We aimed at revealing the clinical features of EML4-ALK fusion gene and EGFR mutation in non-small-cell lung cancer (NSCLC). Methods We enrolled 694 Chinese patients with NSCLC for analysis. EML4-ALK fusion gene was analyzed by real-time polymerase chain reaction, and EGFR mutations were analyzed by amplified refractory mutation system. Results Among the 694 patients, 60 (8.65%) patients had EML4-ALK fusions. In continuity correction χ2 test analysis, EML4-ALK fusion gene was correlated with sex, age, smoking status, and histology, but no significant association was observed between EML4-ALK fusion gene and clinical stage. A total of 147 (21.18%) patients had EGFR mutations. In concordance with previous reports, EGFR mutation was correlated with age, smoking status, histology, and clinical stage, whereas patient age was not significantly associated with EGFR mutation. Meanwhile, to our surprise, six (0.86%) patients had coexisting EML4-ALK fusions and EGFR mutations. Conclusion EML4-ALK fusion gene defines a new molecular subset in patients with NSCLC. Six patients who harbored both EML4-ALK fusion genes and EGFR mutations were identified in our study. The EGFR mutations and the EML4-ALK fusion genes are coexistent. PMID:27103824

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

    PubMed

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

    1987-05-01

    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. PMID:3038523

  12. FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells

    PubMed Central

    Semrau, Stefan; Crosetto, Nicola; Bienko, Magda; Boni, Marina; Bernasconi, Bernasconi; Chiarle, Roberto; van Oudenaarden, Alexander

    2014-01-01

    SUMMARY Transcribed gene fusions are key biomarkers in many hematologic and solid tumors, often representing the primary oncogenic driver mutation. Here, we report an experimental and computational pipeline for detecting fusion transcripts using single-molecule RNA FISH and unbiased correlation analysis (FuseFISH). We constructed a genome-wide database of optimal oligonucleotide sequences, enabling quick design of FuseFISH probes against known and novel fusions. We implemented FuseFISH in cell lines, tissue sections, and purified RNA, reliably detecting one BCR-ABL1 positive in 10,000 negative cells. In 34 hematologic samples, we detected BCR-ABL1 transcripts with high specificity and sensitivity. Finally, we measured BCR-ABL1 expression heterogeneity and dynamics in single CML cells exposed to the kinase inhibitor Nilotinib. Our resource and methods are ideal for streamlined validation of fusions newly identified by next-generation sequencing, and pave the way to studying the impact of fusion expression variability on clinical outcome. PMID:24373969

  13. 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

  14. MLL-MLLT10 fusion gene in pediatric acute megakaryoblastic leukemia.

    PubMed

    Morerio, Cristina; Rapella, Annamaria; Tassano, Elisa; Rosanda, Cristina; Panarello, Claudio

    2005-10-01

    The occurrence of MLL gene rearrangement in acute megakaryoblastic leukemia (AML-M7, acute myeloid leukemia, French-American-British type M7) is very rare and limited to pediatric age: in particular, MLL-MLLT10 fusion, previously reported as characteristic of monocytic leukemia, has been reported in only one case of pediatric megakaryoblastic leukemia. We describe the second case with this association in light of the few reported cases of AML-M7 with MLL and/or 11q23 involvement.

  15. 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.

  16. Fusion of the Saccharomyces cerevisiae leu2 gene to an Escherichia coli beta-galactosidase gene.

    PubMed Central

    Martinez-Arias, A E; Casadaban, M J

    1983-01-01

    The promoter and translation initiation region of the Saccharomyces cerevisiae leu2 gene was fused to the Escherichia coli beta-galactosidase gene. This fusion located the control region of the leu gene and orientated its direction of expression. When the fusion was placed into yeast cells, beta-galactosidase was expressed under the same regulatory pattern as the original leu2 gene product: its synthesis was repressed in the presence of leucine and threonine. Sensitive chromogenic substrates for beta-galactosidase were used to detect expression in isolated colonies growing on agar medium. Mutant yeast cells with increased beta-galactosidase activity were identified by the color of the colonies they formed. One class of mutants obtained appeared to affect ars1 plasmid maintenance, and another class appeared to affect beta-galactoside uptake. PMID:6406836

  17. A New Type of Fusion Analysis Applicable to Many Organisms: Protein Fusions to the URA3 Gene of Yeast

    PubMed Central

    Alani, Eric; Kleckner, Nancy

    1987-01-01

    We have made constructs that join the promoter sequences and a portion of the coding region of the Saccharomyces cerevisiae HIS4 and GAL1 genes and the E. coli lacZ gene to the sixth codon of the S. cerevisiae URA3 gene (encodes orotidine-5'-phosphate (OMP) decarboxylase) to form three in frame protein fusions. In each case the fusion protein has OMP decarboxylase activity as assayed by complementation tests and this activity is properly regulated. A convenient cassette consisting of the URA3 segment plus some immediately proximal amino acids of HIS4C is available for making URA3 fusions to other proteins of interest. URA3 fusions offer several advantages over other systems for gene fusion analysis: the URA3 specified protein is small and cytosolic; genetic selections exist to identify mutants with either increased or decreased URA3 function in both yeast (S. cerevisiae and Schizosaccharomyces pombe) and bacteria (Escherichia coli and Salmonella typhimurium); and a sensitive OMP decarboxylase enzyme assay is available. Also, OMP decarboxylase activity is present in mammals, Drosophila and plants, so URA3 fusions may eventually be applicable in these other organisms as well. PMID:3311876

  18. 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

  19. 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. PMID:27375789

  20. 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

  1. 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.

  2. 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. PMID:27372070

  3. Characterization of a ubiquitin-fusion gene from the tobacco hawkmoth, Manduca sexta.

    PubMed Central

    Bishoff, S T; Schwartz, L M

    1990-01-01

    A gene encoding a ubiquitin-fusion protein was isolated from a cDNA library made from the intersegmental muscles (ISM) of the moth, Manduca sexta. The predicted amino acid sequence of this fusion protein is highly conserved when compared to the sequence of homologous proteins from diverse species. The Manduca clone encoding this ubiquitin fusion gene hybridized with a single, abundantly expressed transcript in all tissues examined. In the ISM, the transcript was present at high levels, independent of the developmental stage or hormonal treatment of these muscles. Data from other species indicate that ubiquitin-fusion genes participate in ribosome biogenesis. Images PMID:1700368

  4. Expression of the Escherichia coli ftsZ gene: trials and tribulations of gene fusion studies.

    PubMed

    Robin, A; D'Ari, R

    1993-02-01

    The ftsZ gene of Escherichia coli, which codes for an essential cell division protein, is subjected to multiple regulation, as shown in part with studies using an ftsZ::lacZ operon fusion located on phage lambda JFL100. Using this same fusion, we sought to isolate regulatory mutants overexpressing ftsZ by selecting mutants able to grow on lactose. One Lac+ mutant was obtained which overexpressed the ftsZ::lacZ fusion 70-fold. The mutation responsible for the overexpression lies in a new gene, cot, located near 56 min on the E. coli genetic map. The cot mutation probably affects the transcription of a chromosomal open reading frame, ORF1, lying downstream of the bioA gene and adjacent to the ftzZ::lacZ fusion of the lambda JFL100 prophage integrated at att lambda. Using an ftsZ84(Ts) strain, in which there was a double selection for overexpression of both ftsZ::lacZ and ftsZ+, no Lac+Tr mutants were obtained from 3.6 x 10(10) bacteria; the introduction of a mutL allele, increasing spontaneous base substitution mutation rates 75-fold, did not permit us to isolate such a mutant. We conclude that Lac+ ftsZ-constitutive mutations cannot be obtained in lambda JFL100 lysogens by a single base substitution. PMID:8468005

  5. 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

  6. Interactions between genes involved in exocytotic membrane fusion in paramecium.

    PubMed

    Bonnemain, H; Gulik-Krzywicki, T; Grandchamp, C; Cohen, J

    1992-03-01

    Crosses between members of two independent collections of Paramecium tetraurelia mutants blocked in the final membrane fusion step of trichocyst release (nd mutants) allowed us to define 13 complementation groups comprising 23 alleles. The mutant nd9a was then used as a target in a mutagenesis experiment designed to screen both revertants and new mutants in order to identify interacting genes. This mutant was chosen because it is the best known of its class to date and seems to be altered in assembly of the material connecting the trichocyst membrane to the plasma membrane and in assembly of the "rosette," a complex array of intramembranous particles in the plasma membrane at the trichocyst insertion sites. No revertants were obtained but two new mutants deficient for rosette assembly were identified, nd16b and nd18, whose gene products appear to interact with that of nd9. Indeed, the double mutants grown at 18 degrees, a permissive temperature for each of the single mutants, are characterized by a deficiency in exocytosis and in rosette assembly, as are also double mutants combining other allelic forms of the same genes. Moreover, aberrant dominance relationships among alleles of nd9 and of nd16 indicate the existence of interactions between identical subunits, which most likely assemble into multimeric structures. The nd16 gene product was shown by microinjection experiments to be a cytosolic factor, as is the nd9 gene product. It is therefore tempting to propose that the nd16 gene product also belongs to the connecting material and is involved in rosette assembly, in cooperation with nd9 and nd18.

  7. 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.

  8. 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. PMID:26132974

  9. A simple system for converting lacZ to gfp reporter fusions in diverse bacteria.

    PubMed

    Goulian, Mark; van der Woude, Marjan

    2006-05-10

    We describe new plasmids that facilitate the rapid conversion of lacZ fusions to gfp transcriptional fusions in bacteria. The exchange is based on a double recombination between lacZ sequences in a suicide vector and the recipient chromosome. The suicide vector is a mobilizable, conditionally replicative plasmid that contains the gene for gfp with flanking lacZ homology and is derived from a broad host range plasmid that has been successfully used in a wide range of bacterial species. The technique was used to convert lacZ reporter fusions to gfp fusions in Escherichia coli, Bordetella bronchiseptica and Agrobacterium tumefaciens. Green fluorescent protein expression in the new recombinants reflected the beta galactosidase expression in the parent strains. GFP is particularly useful for rapid quantification of gene expression in real time and in single cells. As a demonstration of an application of this system, we studied the induction of virE transcription by the VirA/VirG two-component system in A. tumefaciens in response to various levels of phenolic inducer. Analysis of GFP fluorescence in single cells revealed that at intermediate levels of inducer the population of cells was remarkably heterogeneous. The tools described here will be useful for general studies of transcriptional regulation as well as for applications that require spatial and temporal identification of gene expression, such as in the study of biofilms, and interactions between bacteria and their environment. PMID:16500039

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. A Double-Switch Cell Fusion-Inducible Transgene Expression System for Neural Stem Cell-Based Antiglioma Gene Therapy

    PubMed Central

    Luo, Yumei; Lam, Dang Hoang; Huang, Juan; Tang, Yi; Luo, Xitu; Wang, Shu

    2015-01-01

    Recent progress in neural stem cell- (NSC-) based tumor-targeted gene therapy showed that NSC vectors expressing an artificially engineered viral fusogenic protein, VSV-G H162R, could cause tumor cell death specifically under acidic tumor microenvironment by syncytia formation; however, the killing efficiency still had much room to improve. In the view that coexpression of another antitumoral gene with VSV-G can augment the bystander effect, a synthetic regulatory system that triggers transgene expression in a cell fusion-inducible manner has been proposed. Here we have developed a double-switch cell fusion-inducible transgene expression system (DoFIT) to drive transgene expression upon VSV-G-mediated NSC-glioma cell fusion. In this binary system, transgene expression is coregulated by a glioma-specific promoter and targeting sequences of a microRNA (miR) that is highly expressed in NSCs but lowly expressed in glioma cells. Thus, transgene expression is “switched off” by the miR in NSC vectors, but after cell fusion with glioma cells, the miR is diluted and loses its suppressive effect. Meanwhile, in the syncytia, transgene expression is “switched on” by the glioma-specific promoter. Our in vitro and in vivo experimental data show that DoFIT successfully abolishes luciferase reporter gene expression in NSC vectors but activates it specifically after VSV-G-mediated NSC-glioma cell fusion. PMID:26074975

  15. 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.

  16. t(9;11)(p22;p15) with NUP98-LEDGF fusion gene in pediatric acute myeloid leukemia.

    PubMed

    Morerio, Cristina; Acquila, Maura; Rosanda, Cristina; Rapella, Annamaria; Tassano, Elisa; Micalizzi, Concetta; Panarello, Claudio

    2005-04-01

    The rare t(9;11)(p22;p15) translocation is associated with adult acute myeloid leukemia (AML) with immature forms. We report a novel fusion of the NUP98 and LEDGF genes in a pediatric AML with intermediate characteristics between M2-M3 French-American-British (FAB) subtypes exhibiting the same chromosomal rearrangement. Fluorescence in situ hybridization (FISH) and reverse transcriptase-PCR (RT-PCR) studies identified the chimeric transcript product of in-frame fusion of NUP98 exon 8 to LEDGF exon 4.

  17. Clinicopathological differences between variants of the NAB2-STAT6 fusion gene in solitary fibrous tumors of the meninges and extra-central nervous system.

    PubMed

    Nakada, Satoko; Minato, Hiroshi; Nojima, Takayuki

    2016-07-01

    Investigations on the NAB2-STAT6 fusion gene in solitary fibrous tumors (SFTs) and hemangiopericytomas (HPCs) have increased since its discovery in 2013. Although several SFTs reported without NAB2-STAT6 fusion gene analysis, we reviewed 546 SFTs/HPCs with NAB2-STAT6 fusion gene analysis in this study and investigated differences between the gene variants. In total, 452 cases tested positive for the NAB2-STAT6 fusion gene, with more than 40 variants being detected. The most frequent of these were NAB2 exon 6-STAT6 exon 16/17/18 and NAB2 exon 4-STAT6 exon 2/3, with the former occurring most frequently in SFTs in meninges, soft tissues, and head and neck; the latter predominated in SFTs in the pleura and lung. There was no difference between the histology of SFTs and fusion gene variants. A follow-up analysis of SFTs showed that 51 of 202 cases had a recurrence, with 18 of 53 meningeal SFTs having a local recurrence and/or metastasis within 0-19 years. In meninges and soft tissue, SFTs with the NAB2 exon 6-STAT6 exon 16/17/18 tended to recur more frequently than SFTs with the NAB2 exon 4-STAT6 exon 2/3. Clinicopathological data, including yearly follow-ups, are required for meningeal SFTs/HPCs to define the correlation of variants of NAB2-STAT6 fusion gene.

  18. Frequent CTLA4-CD28 gene fusion in diverse types of T-cell lymphoma.

    PubMed

    Yoo, Hae Yong; Kim, Pora; Kim, Won Seog; Lee, Seung Ho; Kim, Sangok; Kang, So Young; Jang, Hye Yoon; Lee, Jong-Eun; Kim, Jaesang; Kim, Seok Jin; Ko, Young Hyeh; Lee, Sanghyuk

    2016-06-01

    CTLA4 and CD28 are co-regulatory receptors with opposite roles in T-cell signaling. By RNA sequencing, we identified a fusion between the two genes from partial gene duplication in a case of angioimmunoblastic T-cell lymphoma. The fusion gene, which codes for the extracellular domain of CTLA4 and the cytoplasmic region of CD28, is likely capable of transforming inhibitory signals into stimulatory signals for T-cell activation. Ectopic expression of the fusion transcript in Jurkat and H9 cells resulted in enhanced proliferation and AKT and ERK phosphorylation, indicating activation of downstream oncogenic pathways. To estimate the frequency of this gene fusion in mature T-cell lymphomas, we examined 115 T-cell lymphoma samples of diverse subtypes using reverse transcriptase polymerase chain reaction analysis and Sanger sequencing. We identified the fusion in 26 of 45 cases of angioimmunoblastic T-cell lymphomas (58%), nine of 39 peripheral T-cell lymphomas, not otherwise specified (23%), and nine of 31 extranodal NK/T cell lymphomas (29%). We further investigated the mutation status of 70 lymphoma-associated genes using ultra-deep targeted resequencing for 74 mature T-cell lymphoma samples. The mutational landscape we obtained suggests that T-cell lymphoma results from diverse combinations of multiple gene mutations. The CTLA4-CD28 gene fusion is likely a major contributor to the pathogenesis of T-cell lymphomas and represents a potential target for anti-CTLA4 cancer immunotherapy. PMID:26819049

  19. Frequent CTLA4-CD28 gene fusion in diverse types of T-cell lymphoma

    PubMed Central

    Yoo, Hae Yong; Kim, Pora; Kim, Won Seog; Lee, Seung Ho; Kim, Sangok; Kang, So Young; Jang, Hye Yoon; Lee, Jong-Eun; Kim, Jaesang; Kim, Seok Jin; Ko, Young Hyeh; Lee, Sanghyuk

    2016-01-01

    CTLA4 and CD28 are co-regulatory receptors with opposite roles in T-cell signaling. By RNA sequencing, we identified a fusion between the two genes from partial gene duplication in a case of angioimmunoblastic T-cell lymphoma. The fusion gene, which codes for the extracellular domain of CTLA4 and the cytoplasmic region of CD28, is likely capable of transforming inhibitory signals into stimulatory signals for T-cell activation. Ectopic expression of the fusion transcript in Jurkat and H9 cells resulted in enhanced proliferation and AKT and ERK phosphorylation, indicating activation of downstream oncogenic pathways. To estimate the frequency of this gene fusion in mature T-cell lymphomas, we examined 115 T-cell lymphoma samples of diverse subtypes using reverse transcriptase polymerase chain reaction analysis and Sanger sequencing. We identified the fusion in 26 of 45 cases of angioimmunoblastic T-cell lymphomas (58%), nine of 39 peripheral T-cell lymphomas, not otherwise specified (23%), and nine of 31 extranodal NK/T cell lymphomas (29%). We further investigated the mutation status of 70 lymphoma-associated genes using ultra-deep targeted resequencing for 74 mature T-cell lymphoma samples. The mutational landscape we obtained suggests that T-cell lymphoma results from diverse combinations of multiple gene mutations. The CTLA4-CD28 gene fusion is likely a major contributor to the pathogenesis of T-cell lymphomas and represents a potential target for anti-CTLA4 cancer immunotherapy. PMID:26819049

  20. Inertial Confinement Fusion Annual Report 1999

    SciTech Connect

    Kauffman, R

    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 3{omega} 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

  1. 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.

  2. 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

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

    PubMed

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

    2015-10-01

    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.

  4. 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. PMID:24588013

  5. 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.

  6. Status report of the fusion alpha confinement test, March 1980

    SciTech Connect

    Grisham, L.R.; Post, D.E.; Weisheit, J.C.; Eubank, H.P.; Mikkelsen, D.R.; Stewart, L.D.

    1980-05-01

    The Fusion Alpha Confinement Test (FACT) investigates the ability of tokamaks and other magnetic devices to confine fusion-produced alpha particles and be heated by them. This report summarizes the progress made since the initial conception, and lists and discusses the remaining unresolved issues. Preliminary results are given for two experiments at the Lawrence Berkeley Laboratory (LBL) in which He/sup -/ currents of 30 mA and 69 mA, respectively, were obtained from two different ion sources. A number of atomic physics issues relevant to the utility of He/sup -/ as a source for He/sup 0/ are discussed, and a review of considerations for HeH/sup +/ and Li/sup -/ accelerators is presented.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing.

    PubMed

    Robinson, Dan R; Wu, Yi-Mi; Kalyana-Sundaram, Shanker; Cao, Xuhong; Lonigro, Robert J; Sung, Yun-Shao; Chen, Chun-Liang; Zhang, Lei; Wang, Rui; Su, Fengyun; Iyer, Matthew K; Roychowdhury, Sameek; Siddiqui, Javed; Pienta, Kenneth J; Kunju, Lakshmi P; Talpaz, Moshe; Mosquera, Juan Miguel; Singer, Samuel; Schuetze, Scott M; Antonescu, Cristina R; Chinnaiyan, Arul M

    2013-02-01

    A 44-year old woman with recurrent solitary fibrous tumor (SFT)/hemangiopericytoma was enrolled in a clinical sequencing program including whole-exome and transcriptome sequencing. A gene fusion of the transcriptional repressor NAB2 with the transcriptional activator STAT6 was detected. Transcriptome sequencing of 27 additional SFTs identified the presence of a NAB2-STAT6 gene fusion in all tumors. Using RT-PCR and sequencing, we detected this fusion in all 51 SFTs, indicating high levels of recurrence. Expression of NAB2-STAT6 fusion proteins was confirmed in SFT, and the predicted fusion products harbor the early growth response (EGR)-binding domain of NAB2 fused to the activation domain of STAT6. Overexpression of the NAB2-STAT6 gene fusion induced proliferation in cultured cells and activated the expression of EGR-responsive genes. These studies establish NAB2-STAT6 as the defining driver mutation of SFT and provide an example of how neoplasia can be initiated by converting a transcriptional repressor of mitogenic pathways into a transcriptional activator.

  13. 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

  14. 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

    Georgakopoulos, D G; Hendson, M; Panopoulos, N J; Schroth, M N

    1994-12-01

    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

  15. 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.

  16. 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.

  17. ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma.

    PubMed

    Salzman, Julia; Marinelli, Robert J; Wang, Peter L; Green, Ann E; Nielsen, Julie S; Nelson, Brad H; Drescher, Charles W; Brown, Patrick O

    2011-09-01

    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.

  18. Gene expression profiling and candidate gene resequencing identifies pathways and mutations important for malignant transformation caused by leukemogenic fusion genes.

    PubMed

    Novak, Rachel L; Harper, David P; Caudell, David; Slape, Christopher; Beachy, Sarah H; Aplan, Peter D

    2012-12-01

    NUP98-HOXD13 (NHD13) and CALM-AF10 (CA10) are oncogenic fusion proteins produced by recurrent chromosomal translocations in patients with acute myeloid leukemia (AML). Transgenic mice that express these fusions develop AML with a long latency and incomplete penetrance, suggesting that collaborating genetic events are required for leukemic transformation. We employed genetic techniques to identify both preleukemic abnormalities in healthy transgenic mice as well as collaborating events leading to leukemic transformation. Candidate gene resequencing revealed that 6 of 27 (22%) CA10 AMLs spontaneously acquired a Ras pathway mutation and 8 of 27 (30%) acquired an Flt3 mutation. Two CA10 AMLs acquired an Flt3 internal-tandem duplication, demonstrating that these mutations can be acquired in murine as well as human AML. Gene expression profiles revealed a marked upregulation of Hox genes, particularly Hoxa5, Hoxa9, and Hoxa10 in both NHD13 and CA10 mice. Furthermore, mir196b, which is embedded within the Hoxa locus, was overexpressed in both CA10 and NHD13 samples. In contrast, the Hox cofactors Meis1 and Pbx3 were differentially expressed; Meis1 was increased in CA10 AMLs but not NHD13 AMLs, whereas Pbx3 was consistently increased in NHD13 but not CA10 AMLs. Silencing of Pbx3 in NHD13 cells led to decreased proliferation, increased apoptosis, and decreased colony formation in vitro, suggesting a previously unexpected role for Pbx3 in leukemic transformation.

  19. 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.

  20. Gene fusions for the directed modification of the carotenoid biosynthesis pathway in Mucor circinelloides.

    PubMed

    Iturriaga, Enrique A; Papp, Tamás; Alvarez, María Isabel; Eslava, Arturo P

    2012-01-01

    Several fungal species, particularly some included in the Mucorales, have been used to develop fermentation processes for the production of β-carotene. Oxygenated derivatives of β-carotene are more valuable products, and the preference by the market of carotenoids from biological sources has increased the research in different carotenoid-producing organisms. We currently use Mucor circinelloides as a model organism to develop strains able to produce new, more valuable, and with an increased content of carotenoids. In this chapter we describe part of our efforts to construct active gene fusions which could advance in the diversification of carotenoid production by this fungus. The main carotenoid accumulated by M. circinelloides is β-carotene, although it has some hydroxylase activity and produces low amounts of zeaxanthin. Two enzymatic activities are required for the production of astaxanthin from β-carotene: a hydroxylase and a ketolase. We used the ctrW gene of Paracoccus sp. N81106, encoding a bacterial β-carotene ketolase, to construct gene fusions with two fungal genes essential for the modification of the pathway in M. circinelloides. First we fused it to the carRP gene of M. circinelloides, which is responsible for the phytoene synthase and lycopene cyclase activities in this fungus. The expected activity of this fusion gene would be the accumulation by M. circinelloides of canthaxanthin and probably some astaxanthin. A second construction was the fusion of the crtW gene of Paracoccus sp. to the crtS gene of Xanthophyllomyces dendrorhous, responsible for the synthesis of astaxanthin from β-carotene in this fungus, but which was shown to have only hydroxylase activity in M. circinelloides. The expected result in M. circinelloides transformants was the accumulation of astaxanthin. Here we describe a detailed and empirically tested protocol for the construction of these gene fusions. PMID:22711120

  1. 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

  2. Altered Notch signaling resulting from expression of a WAMTP1-MAML2 gene fusion in mucoepidermoid carcinomas and benign Warthin's tumors.

    PubMed

    Enlund, Fredrik; Behboudi, Afrouz; Andrén, Ywonne; Oberg, Camilla; Lendahl, Urban; Mark, Joachim; Stenman, Göran

    2004-01-01

    Chromosome translocations in neoplasia commonly result in fusion genes that may encode either novel fusion proteins or normal, but ectopically expressed proteins. Here we report the cloning of a novel fusion gene in a common type of salivary and bronchial gland tumor, mucoepidermoid carcinomas (MEC), as well as in benign Warthin's tumors (WATs). The fusion, which results from a t(11;19)(q21-22;p13) translocation, creates a chimeric gene in which exon 1 of a novel gene of unknown function, designated WAMTP1, is linked to exons 2-5 of the recently identified Mastermind-like Notch coactivator MAML2. In the fusion protein, the N-terminal basic domain of MAML2, which is required for binding to intracellular Notch (Notch ICD), is replaced by an unrelated N-terminal sequence from WAMTP1. Mutation analysis of the N-terminus of WAMTP1-MAML2 identified two regions of importance for nuclear localization (amino acids 11-20) and for colocalization with MAML2 and Notch1 ICD in nuclear granules (amino acids 21-42). Analyses of the Notch target genes HES5 and MASH1 in MEC tumors with and without the WAMTP1-MAML2 fusion revealed upregulation of HES5 and downregulation of MASH1 in fusion positive MECs compared to normal salivary gland tissue and MECs lacking the fusion. These findings suggest that altered Notch signaling plays an important role in the genesis of benign and malignant neoplasms of salivary and bronchial gland origin.

  3. 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.

  4. 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.

  5. SYT-SSX fusion genes and prognosis in synovial sarcoma

    PubMed Central

    Mezzelani, A; Mariani, L; Tamborini, E; Agus, V; Riva, C; Lo Vullo, S; Fabbri, A; Stumbo, M; Azzarelli, A; Casali, P G; Gronchi, A; Sozzi, G; Pierotti, M A; Pilotti, S

    2001-01-01

    A case series of 64 synovial sarcomas was characterized for the SYT-SSX fusion transcripts and statistically analysed in order to correlate molecular data with prognosis and morphology. SYT-SSX1 fusion transcript appeared to be an independent, though not reaching statistical significance (P = 0.183), prognostic factor clearly associated with a reduced metastasis-free survival. Regarding the association between transcript type and histologic subtype we found, a borderline P value (P = 0.067) between the SYT-SSX1 transcript and the biphasic subtype which, subsequently expanding the analysis to 70 cases, turned out to be significant. However, we could not confirm the prediction value of the biphasic subtype for the presence of the SYT-SSX1 transcript since in our hands 6 out 33 (18%) biphasic tumours carried the SYT-SSX2 transcript.© 2001 Cancer Research Campaign  http://www.bjcancer.com PMID:11720441

  6. Prostate cancer genes associated with TMPRSS2–ERG gene fusion and prognostic of biochemical recurrence in multiple cohorts

    PubMed Central

    Barwick, B G; Abramovitz, M; Kodani, M; Moreno, C S; Nam, R; Tang, W; Bouzyk, M; Seth, A; Leyland-Jones, B

    2010-01-01

    Background: Recent studies have indicated that prostate cancer patients with the TMPRSS2–ERG gene fusion have a higher risk of recurrence. To identify markers associated with TMPRSS2–ERG fusion and prognostic of biochemical recurrence, we analysed a cohort of 139 men with prostate cancer for 502 molecular markers. Methods: RNA from radical prostatectomy tumour specimens was analysed using cDNA-mediated, annealing, selection, extension and ligation (DASL) to determine mRNAs associated with TMPRSS2–ERG T1/E4 fusion and prognostic of biochemical recurrence. Differentially expressed mRNAs in T1/E4-positive tumours were determined using significance analysis of microarrays (false discovery rate (FDR) <5%). Univariate and multivariate Cox regression determined genes, gene signatures and clinical factors prognostic of recurrence (P-value <0.05, log–rank test). Analysis of two prostate microarray studies (GSE1065 and GSE8402) validated the findings. Results: In the 139 patients from this study and from a 455-patient Swedish cohort, 15 genes in common were differentially regulated in T1/E4 fusion-positive tumours (FDR <0.05). The most significant mRNAs in both cohorts coded ERG. Nine genes were found prognostic of recurrence in this study and in a 596-patient Minnesota cohort. A molecular recurrence score was significant in prognosticating recurrence (P-value 0.000167) and remained significant in multivariate analysis of a mixed clinical model considering Gleason score and TMPRSS2–ERG fusion status. Conclusions: TMPRSS2–ERG T1/E4 fusion-positive tumours had differentially regulated mRNAs observed in multiple studies, the most significant one coded for ERG. Several mRNAs were consistently associated with biochemical recurrence and have potential clinical utility but will require further validation for successful translation. PMID:20068566

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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. PMID:26314551

  12. 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.

  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. PMID:25893823

  14. 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.

  15. RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

    PubMed Central

    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. PMID:22496636

  16. Functional analysis of the TMPRSS2:ERG fusion gene in cisplatin‑induced cell death.

    PubMed

    Wu, Junqi; Chi, Linfeng; Chen, Zhanghui; Lu, Xianghong; Xiao, Suping; Zhang, Guanglin; Luo, Jindan; Chen, Ge-Ming; Yang, Jun

    2016-04-01

    The TMPRSS2:E‑twenty‑six (ETS) gene fusion occurs frequently in a high proportion of patients with prostate cancer (PCa) in Western countries, and the aberrant expression of TMPRSS2: v‑ETS avian erythroblastosis virus E26 oncogene homolog (ERG), the most common form of the corresponding protein, can regulate cell migration and contribute to tumor invasion and metastasis. However, its association with other cellular events, and in particular, cell death, remain unknown. To examine the function of such fusion genes, an expression plasmid containing the TMPRSS2:ERG (T1/E5) sequence (ΔERG) from a patient sample was constructed and transiently transfected into DU145 cells, which do not express the fusion gene. It was found that the overexpression of ΔERG significantly inhibited the ability of cisplatin to induce apoptosis in DU145 cells. By contrast, VCaP cells, which do contain TMPRSS2:ERG, were sensitized to cisplatin‑induced apoptosis through siRNA inhibition of the fusion gene. To elucidate the underlying mechanism, a stable cell line expressing the ΔERG gene was constructed. Expression of ΔERG did not affect cell migration, but did protect cells from DNA damage and apoptosis induced by cisplatin. Furthermore, knockdown of ΔERG by short interfering RNA resulted in cells regaining their sensitivity to cisplatin. Finally, the gene coding for activating transcription factor 5, which is important for cell survival, may be upregulated by ΔERG. Taken together, these data point to a new function of the TMPRSS2:ERG fusion gene in regulating the apoptotic pathway. PMID:26935606

  17. 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

    NASA Astrophysics Data System (ADS)

    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 innovativefluorescent fusion protein would be useful for NIR-based imaging in vitro and in vivo.

  18. 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.

  19. 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...

  20. 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.

  1. Design and characterization of novel recombinant listeriolysin O-protamine fusion proteins for enhanced gene delivery.

    PubMed

    Kim, Na Hyung; Provoda, Chester; Lee, Kyung-Dall

    2015-02-01

    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.

  2. The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

    PubMed Central

    Panagopoulos, Ioannis; Gorunova, Ludmila; Bjerkehagen, Bodil; Heim, Sverre

    2014-01-01

    Whole transcriptome sequencing was used to study a small round cell tumor in which a t(4;19)(q35;q13) was part of the complex karyotype but where the initial reverse transcriptase PCR (RT-PCR) examination did not detect a CIC-DUX4 fusion transcript previously described as the crucial gene-level outcome of this specific translocation. The RNA sequencing data were analysed using the FusionMap, FusionFinder, and ChimeraScan programs which are specifically designed to identify fusion genes. FusionMap, FusionFinder, and ChimeraScan identified 1017, 102, and 101 fusion transcripts, respectively, but CIC-DUX4 was not among them. Since the RNA sequencing data are in the fastq text-based format, we searched the files using the “grep” command-line utility. The “grep” command searches the text for specific expressions and displays, by default, the lines where matches occur. The “specific expression” was a sequence of 20 nucleotides from the coding part of the last exon 20 of CIC (Reference Sequence: NM_015125.3) chosen since all the so far reported CIC breakpoints have occurred here. Fifteen chimeric CIC-DUX4 cDNA sequences were captured and the fusion between the CIC and DUX4 genes was mapped precisely. New primer combinations were constructed based on these findings and were used together with a polymerase suitable for amplification of GC-rich DNA templates to amplify CIC-DUX4 cDNA fragments which had the same fusion point found with “grep”. In conclusion, FusionMap, FusionFinder, and ChimeraScan generated a plethora of fusion transcripts but did not detect the biologically important CIC-DUX4 chimeric transcript; they are generally useful but evidently suffer from imperfect both sensitivity and specificity. The “grep” command is an excellent tool to capture chimeric transcripts from RNA sequencing data when the pathological and/or cytogenetic information strongly indicates the presence of a specific fusion gene. PMID:24950227

  3. 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

    2008-08-01

    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.

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

    SciTech Connect

    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.

  5. Frequent fusion of the CRTC1 and MAML2 genes in clear cell variants of cutaneous hidradenomas.

    PubMed

    Winnes, Marta; Mölne, Lena; Suurküla, Mart; Andrén, Ywonne; Persson, Fredrik; Enlund, Fredrik; Stenman, Göran

    2007-06-01

    Fusion of the CREB regulated transcription coactivator CRTC1 (a.k.a. MECT1, TORC1, or WAMTP1) to the Notch coactivator MAML2 is a characteristic feature of low-grade mucoepidermoid carcinomas of salivary and bronchial glands. The CRTC1-MAML2 fusion protein acts by inducing transcription of cAMP/CREB target genes, and this activity is crucial for the transforming properties of the protein. Here we show that the CRTC1-MAML2 gene fusion is also frequent in benign hidradenomas of the skin. FISH and RT-PCR analyses revealed that hidradenomas are genetically heterogeneous, and that 10 of the 20 tumors analyzed (50%) contained the CRTC1-MAML2 gene fusion and expressed the resulting fusion transcript. Immunohistochemical analysis demonstrated expression of the fusion protein in the majority of tumor cells, including clear cells, poroid cells, and cells with epidermoid and ductal differentiation. In addition, we could show that all fusion-positive tumors were morphologically distinguished by the presence of more or less abundant areas of clear cells whereas all fusion-negative tumors lacked clear cells. Our findings thus demonstrate that the CRTC1-MAML2 gene fusion is frequent in hidradenomas and is associated with clear cell variants of this tumor. Taken together, the present and previous observations indicate that the CRTC1-MAML2 fusion is etiologically linked to benign and low-grade malignant tumors originating from diverse exocrine glands rather than being linked to a separate tumor entity.

  6. 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.

  7. 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. PMID:24297565

  8. Expression pattern of the septin gene family in acute myeloid leukemias with and without MLL-SEPT fusion genes.

    PubMed

    Santos, Joana; Cerveira, Nuno; Bizarro, Susana; Ribeiro, Franclim R; Correia, Cecília; Torres, Lurdes; Lisboa, Susana; Vieira, Joana; Mariz, José M; Norton, Lucília; Snijder, Simone; Mellink, Clemens H; Buijs, Arjan; Shih, Lee-Yung; Strehl, Sabine; Micci, Francesca; Heim, Sverre; Teixeira, Manuel R

    2010-05-01

    Septins are proteins associated with crucial steps in cell division and cellular integrity. In humans, 14 septin genes have been identified, of which five (SEPT2, SEPT5, SEPT6, SEPT9, and SEPT11) are known to participate in reciprocal translocations with the MLL gene in myeloid neoplasias. We have recently shown a significant down-regulation of both SEPT2 and MLL in myeloid neoplasias with the MLL-SEPT2 fusion gene. In this study, we examined the expression pattern of the other 13 known septin genes in altogether 67 cases of myeloid neoplasia, including three patients with the MLL-SEPT2 fusion gene, four with MLL-SEPT6 fusion, and three patients with the MLL-SEPT9 fusion gene. When compared with normal controls, a statistically significant down-regulation was observed for the expression of both MLL (6.4-fold; p=0.008) and SEPT6 (1.7-fold; p=0.002) in MLL-SEPT6 leukemia. Significant down-regulation of MLL was also found in MLL-MLLT3 leukemias. In addition, there was a trend for SEPT9 down-regulation in MLL-SEPT9 leukemias (4.6-fold; p=0.077). Using hierarchical clustering analysis to compare acute myeloid leukemia genetic subgroups based on their similarity of septin expression changes, we found that MLL-SEPT2 and MLL-SEPT6 neoplasias cluster together apart from the remaining subgroups and that PML-RARA leukemia presents under-expression of most septin family genes. PMID:19748670

  9. 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.

  10. Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts

    PubMed Central

    Yeager, Meredith; Im, Kate; Gold, Bert; Schneider, Thomas D.; Fraumeni, Joseph F.; Chanock, Stephen J.; Anderson, Stephen K.; Dean, Michael

    2012-01-01

    Beta-microseminoprotein (MSP)/MSMB is an immunoglobulin superfamily protein synthesized by prostate epithelial cells and secreted into seminal plasma. Variants in the promoter of the MSMB gene have been associated with the risk of prostate cancer (PCa) in several independent genome-wide association studies. Both MSMB and an adjacent gene, NCOA4, are subjected to transcriptional control via androgen response elements. The gene product of NCOA4 interacts directly with the androgen receptor as a co-activator to enhance AR transcriptional activity. Here, we provide evidence for the expression of full-length MSMB-NCOA4 fusion transcripts regulated by the MSMB promoter. The predominant MSMB-NCOA4 transcript arises by fusion of the 5′UTR and exons 1–2 of the MSMB pre-mRNA, with exons 2–10 of the NCOA4 premRNA, producing a stable fusion protein, comprising the essential domains of NCOA4. Analysis of the splice sites of this transcript shows an unusually strong splice acceptor at NCOA4 exon 2 and the presence of Alu repeats flanking the exons potentially involved in the splicing event. Transfection experiments using deletion clones of the promoter coupled with luciferase reporter assays define a core MSMB promoter element located between –27 and –236 of the gene, and a negative regulatory element immediately upstream of the start codon. Computational network analysis reveals that the MSMB gene is functionally connected to NCOA4 and the androgen receptor signaling pathway. The data provide an example of how GWAS-associated variants may have multiple genetic and epigenetic effects. PMID:22661295

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

    PubMed

    Natrajan, Rachael; Wilkerson, Paul M; Marchiò, Caterina; Piscuoglio, Salvatore; Ng, Charlotte K Y; 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

    2014-04-01

    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 in

  12. 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.

  13. 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.

  14. 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.

  15. A gold nanoparticle pentapeptide: gene fusion to induce therapeutic gene expression in mesenchymal stem cells.

    PubMed

    Muroski, Megan E; Morgan, Thomas J; Levenson, Cathy W; Strouse, Geoffrey F

    2014-10-22

    Mesenchymal stem cells (MSC) have been identified as having great potential as autologous cell therapeutics to treat traumatic brain injury and spinal injury as well as neuronal and cardiac ischemic events. All future clinical applications of MSC cell therapies must allow the MSC to be harvested, transfected, and induced to express a desired protein or selection of proteins to have medical benefit. For the full potential of MSC cell therapy to be realized, it is desirable to systematically alter the protein expression of therapeutically beneficial biomolecules in harvested MSC cells with high fidelity in a single transfection event. We have developed a delivery platform on the basis of the use of a solid gold nanoparticle that has been surface modified to produce a fusion containing a zwitterionic, pentapeptide designed from Bax inhibiting peptide (Ku70) to enhance cellular uptake and a linearized expression vector to induce enhanced expression of brain-derived neurotrophic factor (BDNF) in rat-derived MSCs. Ku70 is observed to effect >80% transfection following a single treatment of femur bone marrow isolated rat MSCs with efficiencies for the delivery of a 6.6 kbp gene on either a Au nanoparticle (NP) or CdSe/ZnS quantum dot (QD). Gene expression is observed within 4 d by optical measurements, and secretion is observed within 10 d by Western Blot analysis. The combination of being able to selectively engineer the NP, to colocalize biological agents, and to enhance the stability of those agents has provided the strong impetus to utilize this novel class of materials to engineer primary MSCs. PMID:25198921

  16. 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.

  17. 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.

  18. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

    PubMed

    Maeder, Morgan L; Angstman, James F; Richardson, Marcy E; Linder, Samantha J; Cascio, Vincent M; Tsai, Shengdar Q; Ho, Quan H; Sander, Jeffry D; Reyon, Deepak; Bernstein, Bradley E; Costello, Joseph F; Wilkinson, Miles F; Joung, J Keith

    2013-12-01

    Genome-wide studies have defined cell type-specific patterns of DNA methylation that are important for regulating gene expression in both normal development and disease. However, determining the functional significance of specific methylation events remains challenging, owing to the lack of methods for removing such modifications in a targeted manner. Here we describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator-like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, we demonstrate that modification of critical methylated promoter CpG positions can lead to substantial increases in the expression of endogenous human genes. Our results delineate a strategy for understanding the functional significance of specific CpG methylation marks in the context of endogenous gene loci and validate programmable DNA demethylation reagents with potential utility for research and therapeutic applications.

  19. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:23220349

  1. Registered report: Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukemia

    PubMed Central

    Fung, Juan José; Kosaka, Alan; Shan, Xiaochuan; Danet-Desnoyers, Gwenn; Gormally, Michael; Owen, Kate; Iorns, Elizabeth

    2015-01-01

    The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered report describes the proposed replication plan of key experiments from ‘Inhibition of bromodomain and extra terminal (BET) recruitment to chromatin as an effective treatment for mixed-lineage leukemia (MLL)-fusion leukemia’ by Dawson and colleagues, published in Nature in 2011 (Dawson et al., 2011). The experiments to be replicated are those reported in Figures 2A, 3D, 4B, 4D and Supplementary Figures 11A-B and 16A. In this study, BET proteins were demonstrated as potential therapeutic targets for modulating aberrant gene expression programs associated with MLL-fusion leukemia. In Figure 2A, the BET bromodomain inhibitor I-BET151 was reported to suppress growth of cells harboring MLL-fusions compared to those with alternate oncogenic drivers. In Figure 3D, treatment of MLL-fusion leukemia cells with I-BET151 resulted in transcriptional suppression of the anti-apoptotic gene BCL2. Figures 4B and 4D tested the therapeutic efficacy of I-BET151 in vivo using mice injected with human MLL-fusion leukemia cells and evaluated disease progression following I-BET151 treatment. The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published in eLife. DOI: http://dx.doi.org/10.7554/eLife.08997.001 PMID:26327698

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

    PubMed Central

    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

    2016-01-01

    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. PMID:26314551

  3. 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)

  4. 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.

  5. 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)

  6. 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

  7. 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. PMID:25837665

  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. 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

  11. 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.

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

    PubMed

    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.

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

    PubMed

    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

  14. 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

  15. FGFR3-TACC3: A novel gene fusion in cervical cancer.

    PubMed

    Carneiro, Benedito A; Elvin, Julia A; Kamath, Suneel D; Ali, Siraj M; Paintal, Ajit S; Restrepo, Alvaro; Berry, Emily; Giles, Francis J; Johnson, Melissa L

    2015-08-01

    Cervical cancer epitomizes the success of cancer prevention through the human papillomavirus (HPV) vaccine, but significant challenges remain in the treatment of advanced disease. We report the first three cases of cervical carcinoma harboring an FGFR3-TACC3 fusion, which serves as a novel therapeutic target. The fusion, identified by comprehensive genomic profiling, activates the FGFR pathway that has been implicated in HPV-driven carcinogenesis. One of the patients whose tumor contained the FGFR3-TACC3 fusion was treated with an investigational FGFR tyrosine kinase inhibitor. Concomitant molecular alterations involving the PI3K/AKT/mTOR and RAF/MEK pathways were also identified and suggest other treatment strategies that deserve investigation. This case series highlights the role of comprehensive genomic profiling in the identification of new therapeutic targets and in targeted therapy selection for patients with cervical cancer. PMID:26425723

  16. FGFR3–TACC3: A novel gene fusion in cervical cancer

    PubMed Central

    Carneiro, Benedito A.; Elvin, Julia A.; Kamath, Suneel D.; Ali, Siraj M.; Paintal, Ajit S.; Restrepo, Alvaro; Berry, Emily; Giles, Francis J.; Johnson, Melissa L.

    2015-01-01

    Cervical cancer epitomizes the success of cancer prevention through the human papillomavirus (HPV) vaccine, but significant challenges remain in the treatment of advanced disease. We report the first three cases of cervical carcinoma harboring an FGFR3–TACC3 fusion, which serves as a novel therapeutic target. The fusion, identified by comprehensive genomic profiling, activates the FGFR pathway that has been implicated in HPV-driven carcinogenesis. One of the patients whose tumor contained the FGFR3–TACC3 fusion was treated with an investigational FGFR tyrosine kinase inhibitor. Concomitant molecular alterations involving the PI3K/AKT/mTOR and RAF/MEK pathways were also identified and suggest other treatment strategies that deserve investigation. This case series highlights the role of comprehensive genomic profiling in the identification of new therapeutic targets and in targeted therapy selection for patients with cervical cancer. PMID:26425723

  17. 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.

  18. Molecular Characterization of Inflammatory Myofibroblastic Tumors with Frequent ALK and ROS1 Fusions and Rare Novel RET Gene Rearrangement

    PubMed Central

    Antonescu, Cristina R; Suurmeijer, Albert JH; Zhang, Lei; Sung, Yun-Shao; Jungbluth, Achim A; Travis, William D; Al-Ahmadie, Hikmat; Fletcher, Christopher DM; Alaggio, Rita

    2015-01-01

    Approximately 50% of conventional IMTs harbor ALK gene rearrangement and overexpress ALK. Recently gene fusions involving other kinases have been implicated in the pathogenesis of IMT, including ROS1 and in one patient PDGFRB. However, it remains uncertain if the emerging genotypes correlate with clinicopathologic characteristics of IMT. In this study we expand the molecular investigation of IMT in a large cohort of different clinical presentations and analyze for potential genotype-phenotype associations. Criteria for inclusion in the study were typical morphology and tissue availability for molecular studies. The lack of ALK immunoreactivity was not an excluding factor. As overlapping gene fusions involving actionable kinases are emerging in both IMT and lung cancer, we set out to evaluate abnormalities in ALK, ROS1, PDGFRB, NTRK1 and RET by FISH. Additionally, next generation paired-end RNA sequencing and FusionSeq algorithm was applied in 4 cases, which identified EML4-ALK fusions in 2 cases. Of the 62 IMTs (25 children and 37 adults), 35 (56%) showed ALK gene rearrangement. Of note, EML4-ALK inversion was noted in 7 (20%) cases, seen mainly in the lung and soft tissue of young children including 2 lesions from newborns. There were 6 (10%) ROS1 rearranged IMTs, all except one presenting in children, mainly in the lung and intra-abdominal and showed a distinctive fascicular growth of spindle cells with long cell processes, often positive for ROS1 IHC. Two of the cases showed TFG-ROS1 fusions. Interestingly, one adult IMT revealed a RET gene rearrangement, a previously unreported finding. Our results show that 42/62 (68%) of IMTs are characterized by kinase fusions, offering a rationale for targeted therapeutic strategies. Interestingly 90% of fusion negative IMT were seen in adults, while >90% of pediatric IMT showed gene rearrangements.EML4-ALK inversion and ROS1 fusions emerge as common fusion abnormalities in IMT, closely recapitulating the pattern seen in

  19. 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.

  20. Transposon assisted gene insertion technology (TAGIT): a tool for generating fluorescent fusion proteins.

    PubMed

    Gregory, James A; Becker, Eric C; Jung, James; Tuwatananurak, Ida; Pogliano, Kit

    2010-01-01

    We constructed a transposon (transposon assisted gene insertion technology, or TAGIT) that allows the random insertion of gfp (or other genes) into chromosomal loci without disrupting operon structure or regulation. TAGIT is a modified Tn5 transposon that uses Kan(R) to select for insertions on the chromosome or plasmid, beta-galactosidase to identify in-frame gene fusions, and Cre recombinase to excise the kan and lacZ genes in vivo. The resulting gfp insertions maintain target gene reading frame (to the 5' and 3' of gfp) and are integrated at the native chromosomal locus, thereby maintaining native expression signals. Libraries can be screened to identify GFP insertions that maintain target protein function at native expression levels, allowing more trustworthy localization studies. We here use TAGIT to generate a library of GFP insertions in the Escherichia coli lactose repressor (LacI). We identified fully functional GFP insertions and partially functional insertions that bind DNA but fail to repress the lacZ operon. Several of these latter GFP insertions localize to lacO arrays integrated in the E. coli chromosome without producing the elongated cells frequently observed when functional LacI-GFP fusions are used in chromosome tagging experiments. TAGIT thereby faciliates the isolation of fully functional insertions of fluorescent proteins into target proteins expressed from the native chromosomal locus as well as potentially useful partially functional proteins. PMID:20090956

  1. 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

  2. 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

  3. A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.

    PubMed

    Pierron, Gaëlle; Tirode, Franck; Lucchesi, Carlo; Reynaud, Stéphanie; Ballet, Stelly; Cohen-Gogo, Sarah; Perrin, Virginie; Coindre, Jean-Michel; Delattre, Olivier

    2012-04-01

    The identification of subtype-specific translocations has revolutionized the diagnostics of sarcoma and has provided new insight into oncogenesis. We used RNA-seq to investigate samples from individuals diagnosed with small round cell tumors of bone, possibly Ewing sarcoma, but which lacked the canonical EWSR1-ETS translocation. A new fusion was observed between BCOR (encoding the BCL6 co-repressor) and CCNB3 (encoding the testis-specific cyclin B3) on the X chromosome. RNA-seq results were confirmed by RT-PCR and through cloning of the tumor-specific genomic translocation breakpoints. In total, 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcoma cases. Gene profiling experiments indicated that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this subgroup of sarcoma and that overexpression of BCOR-CCNB3 or of truncated CCNB3 activates S phase in NIH3T3 cells. Thus, the intrachromosomal X-chromosome fusion described here represents a new subtype of bone sarcoma caused by a newly identified gene fusion mechanism. PMID:22387997

  4. [Fusion expression of O type foot-and-mouth diseases virus VP1 gene and HSP70 gene and induction of immune responses in mice].

    PubMed

    Su, Chun-Xia; Duan, Xiang-Guo; Wang, Xiu-Qing; Ren, Xue-Feng; Cao, Rui-Bing; Zhou, Bin; Chen, Pu-Yan

    2006-09-01

    Vp1 gene of O type foot-and-mouth diseases virus and M. tuberculosis HSP70 were expressed in methylotrophic yeast Pichia pastoris expression system. The results of cellular immune responses and humoral immune response were examined after BALB/c mice were immunized with fusion protein expressed in methylotrophic yeast Pichia pastoris. The genes was cloned into the vector pPICZalpha-A by routine molecular technique. The plasmid fusion (pPICZalphaA-vp1-HSP70) was created that HSP70 located downstream of VP1 gene of O type foot-and-mouth disease virus. Vp1 was expressed by fusing to the amino terminus of M. tuberculosis hsp70 in yeast Pichia pastoris. The recombined fusion plasmid was transformed into methylotrophic yeast Pichia pastoris X-33 by electrophoration. The recombinant transformants were selected by Zeocin and induced by the addition of methanol every 24h. The expressived product analyzed by SDS-PAGE and Western blotting. The result indicated that the fusion protein(vp1-HSP70) has specific antigenicity. Mice were inoculated transcutaneous three times at a two-weeks interval with fusion protein, PBS and conventional inactivated vaccines. To evaluate the prophylaxtic efficacy of fusion protein, Titers of antibodies was detected by ELISA and proliferation of lymphocytes were determined by MTT. The results indicated that fusion protein could elicit specific humoral immune and cellular immune responses. Compared with conventional inactivated vaccines, fusion protein elicited slightly lower FMDV antibody level but stronger T cell proliferation.

  5. 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.

  6. 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. PMID:27291709

  7. Genetic Analysis of Fusion Recombinants in Bacillus Subtilis: Function of the Rece Gene

    PubMed Central

    Ftouhi, N.; Guillen, N.

    1990-01-01

    Bacillus subtilis protoplast fusion allows the study of the genetic recombination of an entire procaryotic genome. Protoplasts from bacterial strains marked genetically by chromosomal mutations were fused using polyethylene glycol and the regenerated cells analyzed. Recombinants represent 19.3% of heterozygotic cells; they are haploids. Individual characterization of clones show a unique particular phenotype in each colony suggesting that recombination takes place immediately after fusion, probably before the first cellular division. Recombination occurs in the whole chromosome; in one-third of the cases both reciprocal recombinants could be shown in the colony. The genetic interval that includes the chromosome replication origin shows the highest recombination level. Our results suggest that the RecE protein accounts for most of the fused protoplast recombination; however, some ``replication origin-specific'' recombination events were independent of the recE gene product. PMID:2123461

  8. 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.

  9. 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

  10. 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.

  11. A GRIA2 and PAX8-positive renal solitary fibrous tumor with NAB2-STAT6 gene fusion.

    PubMed

    Ichiyanagi, Osamu; Ito, Hiromi; Takai, Satoshi; Naito, Sei; Kato, Tomoyuki; Nagaoka, Akira; Yamakawa, Mitsunori

    2015-01-01

    Solitary fibrous tumor (SFT) is a rare neoplasm composed of mesenchymal-derived spindle cells. Although SFT occurs anywhere in the body, they most frequently affects the thoracic region. Here, we reported an extremely rare case of an extrathoracic SFT occurring primarily in the kidney. To our knowledge, little information has been described on the immunohistochemistry (IHC) and genetics of renal SFT.A 41-year old Japanese female came to our hospital for further examination of a left kidney mass detected incidentally with ultrasound. Extensive investigation of the tumor, including physical, laboratory, and image examinations led to a clinical diagnosis of renal cancer (cT1aN0M0), which were in most parts imbedded in the lower polar parenchyma. The patient underwent laparoscopic radical nephrectomy. The mass was diagnosed pathologically as SFT originating from the kidney, but not as renal carcinoma. Microscopically, the tumor was composed of spindle-shape cells distributed variably in dense collagenous stroma and had a focal hemangiopericytomatous staghorn-like vascular pattern. Mitotic figures, atypical structures, necrosis and hemorrhage were not identified. No adjuvant therapies were given postoperatively. The patient has been free of tumor recurrence for 25 months since the surgery. IHC revealed that the tumor diffusely expressed CD34, CD99, Bcl2, PAX8, NAB2, STAT6, and GRIA2. The tumor stained negatively for desmin, S-100, c-Kit, CK-AE1/AE3, CDK4 and MDM2. A NAB2-SATA6 gene fusion was detected in tumor cells by reverse transcription-polymerase chain reaction, direct sequencing, and an in situ proximity ligation brightfield assay. The gene fusion occurred as an 831 bp truncation of exon 2 in NAB2 connected to the beginning of exon 3 in STAT6. We have reported a case of GRIA2 and PAX8-positive SFT occurring primarily in the kidney with such NAB2-STAT6 gene fusion for the first time. Diffuse expression of PAX8 in the tumor might present with a renal origin

  12. A GRIA2 and PAX8-positive renal solitary fibrous tumor with NAB2-STAT6 gene fusion.

    PubMed

    Ichiyanagi, Osamu; Ito, Hiromi; Takai, Satoshi; Naito, Sei; Kato, Tomoyuki; Nagaoka, Akira; Yamakawa, Mitsunori

    2015-09-04

    Solitary fibrous tumor (SFT) is a rare neoplasm composed of mesenchymal-derived spindle cells. Although SFT occurs anywhere in the body, they most frequently affects the thoracic region. Here, we reported an extremely rare case of an extrathoracic SFT occurring primarily in the kidney. To our knowledge, little information has been described on the immunohistochemistry (IHC) and genetics of renal SFT.A 41-year old Japanese female came to our hospital for further examination of a left kidney mass detected incidentally with ultrasound. Extensive investigation of the tumor, including physical, laboratory, and image examinations led to a clinical diagnosis of renal cancer (cT1aN0M0), which were in most parts imbedded in the lower polar parenchyma. The patient underwent laparoscopic radical nephrectomy. The mass was diagnosed pathologically as SFT originating from the kidney, but not as renal carcinoma. Microscopically, the tumor was composed of spindle-shape cells distributed variably in dense collagenous stroma and had a focal hemangiopericytomatous staghorn-like vascular pattern. Mitotic figures, atypical structures, necrosis and hemorrhage were not identified. No adjuvant therapies were given postoperatively. The patient has been free of tumor recurrence for 25 months since the surgery. IHC revealed that the tumor diffusely expressed CD34, CD99, Bcl2, PAX8, NAB2, STAT6, and GRIA2. The tumor stained negatively for desmin, S-100, c-Kit, CK-AE1/AE3, CDK4 and MDM2. A NAB2-SATA6 gene fusion was detected in tumor cells by reverse transcription-polymerase chain reaction, direct sequencing, and an in situ proximity ligation brightfield assay. The gene fusion occurred as an 831 bp truncation of exon 2 in NAB2 connected to the beginning of exon 3 in STAT6. We have reported a case of GRIA2 and PAX8-positive SFT occurring primarily in the kidney with such NAB2-STAT6 gene fusion for the first time. Diffuse expression of PAX8 in the tumor might present with a renal origin

  13. 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.

  14. Identification of Oncogenic Mutations and Gene Fusions in the Follicular Variant of Papillary Thyroid Carcinoma

    PubMed Central

    Dias-Santagata, Dora; Sadow, Peter M.; Lynch, Kerry D.; Lubitz, Carrie; Donovan, Samuel E.; Zheng, Zongli; Le, Long; Iafrate, A. J.; Daniels, Gilbert H.

    2014-01-01

    Background: The diagnosis of the follicular variant of papillary thyroid carcinoma (FVPTC) is increasingly common. Recent studies have suggested that FVPTC is heterogeneous and comprises multiple tumor types with distinct biological behaviors and underlying genetics. Objectives: The purpose of this work was to identify the prevalence of mutations and gene fusions in known oncogenes in a panel representative of the common spectrum of FVPTC diagnosed at an academic medical center and correlate the clinical and pathological features obtained at the initial diagnosis with the tumor genotype. Materials and Methods: We performed SNaPshot genotyping on a panel of 129 FVPTCs of ≥1 cm for 90 point mutations or small deletions in known oncogenes and tumor suppressors and identified gene fusions using an anchored multiplex PCR assay targeting a panel of rearranged oncogenes. Results: We identified a mutation or gene fusion in 70% (89 of 127) of cases. Mutations targeting the RAS family of oncogenes were the most frequently observed class of alterations, present in 36% (46 of 127) of cases, followed by BRAF mutation, present in 30% (38 of 127). We also detected oncogenic rearrangements not previously associated with FVPTC, including TFG-ALK and CREB3L2-PPARγ. BRAF mutation was significantly associated with unencapsulated tumor status. Conclusions: These data support the hypothesis that FVPTC is composed of distinct biological entities, with one class being identified by BRAF mutation and support the use of clinical genotyping assays that detect a diverse array of rearrangements involving ALK and PPARγ. Additional studies are necessary to identify genetic drivers in the 30% of FVPTCs with no known oncogenic alteration and to better predict behavior in tumors with known genotypes. PMID:25148236

  15. 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

  16. 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

  17. KIAA1549: BRAF Gene Fusion and FGFR1 Hotspot Mutations Are Prognostic Factors in Pilocytic Astrocytomas.

    PubMed

    Becker, Aline Paixão; Scapulatempo-Neto, Cristovam; Carloni, Adriana C; Paulino, Alessandra; Sheren, Jamie; Aisner, Dara L; Musselwhite, Evelyn; Clara, Carlos; Machado, Hélio R; Oliveira, Ricardo S; Neder, Luciano; Varella-Garcia, Marileila; Reis, Rui M

    2015-07-01

    Up to 20% of patients with pilocytic astrocytoma (PA) experience a poor outcome. BRAF alterations and Fibroblast growth factor receptor 1 (FGFR1) point mutations are key molecular alterations in Pas, but their clinical implications are not established. We aimed to determine the frequency and prognostic role of these alterations in a cohort of 69 patients with PAs. We assessed KIAA1549:BRAF fusion by fluorescence in situ hybridization and BRAF (exon 15) mutations by capillary sequencing. In addition, FGFR1 expression was analyzed using immunohistochemistry, and this was compared with gene amplification and hotspot mutations (exons 12 and 14) assessed by fluorescence in situ hybridization and capillary sequencing. KIAA1549:BRAF fusion was identified in almost 60% of cases. Two tumors harbored mutated BRAF. Despite high FGFR1 expression overall, no cases had FGFR1 amplifications. Three cases harbored a FGFR1 p.K656E point mutation. No correlation was observed between BRAF and FGFR1 alterations. The cases were predominantly pediatric (87%), and no statistical differences were observed in molecular alterations-related patient ages. In summary, we confirmed the high frequency of KIAA1549:BRAF fusion in PAs and its association with a better outcome. Oncogenic mutations of FGFR1, although rare, occurred in a subset of patients with worse outcome. These molecular alterations may constitute alternative targets for novel clinical approaches, when radical surgical resection is unachievable. PMID:26083571

  18. 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

    2014-01-01

    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.

  19. 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.

  20. 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. PMID:26320575

  1. 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.

  2. 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.

  3. 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.

  4. Penile pseudomyogenic hemangioendothelioma/epithelioid sarcoma-like hemangioendothelioma with a novel pattern of SERPINE1-FOSB fusion detected by RT-PCR--report of a case.

    PubMed

    Ide, Yoshi-Hiro; Tsukamoto, Yoshitane; Ito, Takaaki; Watanabe, Takahiro; Nakagawa, Noboru; Haneda, Takashi; Nagai, Makoto; Yamanishi, Kiyofumi; Hirota, Seiichi

    2015-05-01

    We experienced a rare case of penile mesenchymal tumor in a 43-year-old Japanese man. At least three nodules were observed around the penis. The tumors were composed of spindle- to oval-shaped atypical cells with and without prominent nucleoli. These cells were like myogenic cells, but negative for myogenic markers. They were positive for endothelial markers, such as ERG, Fli1 and CD31. They were also positive for nuclear and cytoplasmic FOSB which are not expressed in epithelioid hemangioendothelioma or epithelioid sarcoma. These pathological and immunohistochemical findings strongly suggested pseudomyogenic hemangioendothelioma/epithelioid sarcoma-like hemangioendothelioma (PHE/ES-HE). Since a recent report directly proved that two cases of PHE/ES-HE have SERPINE1-FOSB fusion gene by reverse transcription-polymerase chain reaction (RT-PCR), we examined whether the fusion gene is present or not in the present case by RT-PCR using fresh frozen surgical material. Sequencing of the PCR product revealed that this case has SERPINE1-FOSB fusion. The fusion pattern of our case was different from those of two previously reported cases. In our case, 86 nucleotides of SERPINE1 intron 1 were inserted between SERPINE1 exon 1 and the middle portion of FOSB exon 1, and a putative translation start codon was identified in SERPINE1 intron 1. Thus, this is the third case of PHE/ES-HE with SERPINE1-FOSB fusion proved by RT-PCR.

  5. 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.

  6. 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.

  7. 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

  8. Ferritin reporter used for gene expression imaging by magnetic resonance

    SciTech Connect

    Ono, Kenji; Fuma, Kazuya; Tabata, Kaori; Sawada, Makoto

    2009-10-23

    Magnetic resonance imaging (MRI) is a minimally invasive way to provide high spatial resolution tomograms. However, MRI has been considered to be useless for gene expression imaging compared to optical imaging. In this study, we used a ferritin reporter, binding with biogenic iron, to make it a powerful tool for gene expression imaging in MRI studies. GL261 mouse glioma cells were over-expressed with dual-reporter ferritin-DsRed under {beta}-actin promoter, then gene expression was observed by optical imaging and MRI in a brain tumor model. GL261 cells expressing ferritin-DsRed fusion protein showed enhanced visualizing effect by reducing T2-weighted signal intensity for in vitro and in vivo MRI studies, as well as DsRed fluorescence for optical imaging. Furthermore, a higher contrast was achieved on T2-weighted images when permeating the plasma membrane of ferritin-DsRed-expressing GL261. Thus, a ferritin expression vector can be used as an MRI reporter to monitor in vivo gene expression.

  9. 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.

  10. Superior protective and therapeutic effects of IL-12 and IL-18 gene-transduced dendritic neuroblastoma fusion cells on liver metastasis of murine neuroblastoma.

    PubMed

    Iinuma, Hisae; Okinaga, Kota; Fukushima, Ryoji; Inaba, Tsuyoshi; Iwasaki, Kota; Okinaga, Akira; Takahashi, Ichiro; Kaneko, Michio

    2006-03-15

    Fusion vaccine of dendritic cells (DCs) and tumor cells has the advantage of inducing an immune response against multiple tumor Ags, including unknown tumor Ags. Using the liver metastasis model of C1300 neuroblastoma cells, we assessed the protective and therapeutic effects of fusion cells transduced with the IL-12 gene and/or the IL-18 gene. Improving the fusion method by combining polyethylene glycol and electroporation increased loading efficiency. In the A/J mice vaccinated with fusion cells modified with the LacZ gene (fusion/LacZ), IFN-gamma production and CTL activity increased significantly compared with that of DCs/LacZ, C1300/LacZ, or a mixture of the two (mixture/LacZ). With the transduction of IL-12 and IL-18 genes into the fusion cells (fusion/IL-12/IL-18), the level of IFN-gamma increased more than five times that of other fusion groups. In addition, NK cell activity and CTL activity increased significantly compared with that of mixture/LacZ, fusion/LacZ, DC/LacZ, or C1300/LacZ. In the protective and therapeutic studies of fusion cell vaccine, mice vaccinated with fusion/LacZ, fusion/IL-12, fusion/IL-18, or fusion/IL-12/IL-18 showed a significant decrease in liver metastasis and a significant increase in survival compared with mice given a mixture/LacZ, DCs/LacZ, or C1300/LacZ. In particular, the mice receiving fusion/IL-12/IL-18 vaccine showed a complete protective effect and the highest therapeutic effects. The present study investigates the improved loading efficiency of fusion cells and suggests that the introduction of IL-12 and IL-18 genes can induce extremely strong protective and therapeutic effects on liver metastasis of neuroblastoma.

  11. A case of PSF-TFE3 gene fusion in Xp11.2 renal cell carcinoma with melanotic features.

    PubMed

    Zhan, He-Qin; Chen, Hong; Wang, Chao-Fu; Zhu, Xiong-Zeng

    2015-03-01

    Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) with PSF-TFE3 gene fusion is a rare neoplasm. Only 22 cases of Xp11.2 RCCs with PSF-TFE3 have been reported to date. We describe an additional case of Xp11.2 RCC with PSF-TFE3 showing melanotic features. Microscopically, the histologic features mimic clear cell renal cell carcinoma. However, the dark-brown pigments were identified and could be demonstrated as melanins. Immunohistochemically, the tumor cells were widely positive for CD10, human melanoma black 45, and TFE3 but negative for cytokeratins, vimentin, Melan-A, microphthalmia-associated transcription factor, smooth muscle actin, and S-100 protein. Genetically, we demonstrated PSF-TFE3 fusion between exon 9 of PSF and exon 5 of TFE3. The patient was free of disease with 50 months of follow-up. The prognosis of this type of tumor requires more cases because of limited number of cases and follow-up period. Xp11.2 RCC with PSF-TFE3 inevitably requires differentiation from other kidney neoplasms. Immunohistochemical and molecular genetic analyses are essential for accurate diagnosis. PMID:25582502

  12. 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.

  13. Evolutionary analysis of synteny and gene fusion for pyrimidine biosynthetic enzymes in Euglenozoa: an extraordinary gap between kinetoplastids and diplonemids.

    PubMed

    Makiuchi, Takashi; Annoura, Takeshi; Hashimoto, Tetsuo; Murata, Eri; Aoki, Takashi; Nara, Takeshi

    2008-07-01

    A unique feature of the genome architecture in the parasitic trypanosomatid protists is large-scale synteny. We addressed the evolutionary trait of synteny in the eukaryotic group, Euglenozoa, which consists of euglenoids (earliest branching), diplonemids, and kinetoplastids (trypanosomatids and bodonids). Synteny of the pyrimidine biosynthetic (pyr) gene cluster, which constitutes part of a large syntenic cluster in trypanosomatids and includes four separate genes (pyr1-pyr4) and one fused gene (pyr6/pyr5 fusion), was conserved in the bodonid, Parabodo caudatus. In the diplonemid, Diplonema papillatum, we identified pyr4 and pyr6 genes. Phylogenetic analyses of pyr4 and pyr6 showed the separate origin of each in kinetoplastids and euglenoids/diplonemids and suggested that kinetoplastids have acquired these genes via lateral gene transfer (LGT). Because replacement of genes by non-orthologs within the syntenic cluster is highly unlikely, we concluded that, after separation of the line leading to diplonemids, the syntenic pyr gene cluster was established in the common ancestor of kinetoplastids, preceded by their acquisition via LGT. Notably, we found that diplonemid pyr6 is a stand-alone gene, inconsistent with both euglenoid pyr5/pyr6 and kinetoplastid pyr6/pyr5 fusions. Our findings provide insights into the evolutionary gaps within Euglenozoa and the evolutionary trait of rearrangement of gene fusion in this lineage.

  14. Production of geranylgeraniol on overexpression of a prenyl diphosphate synthase fusion gene in Saccharomyces cerevisiae.

    PubMed

    Ohto, Chikara; Muramatsu, Masayoshi; Obata, Shusei; Sakuradani, Eiji; Shimizu, Sakayu

    2010-07-01

    An acyclic diterpene alcohol, (E,E,E)-geranylgeraniol (GGOH), is one of the important compounds used as perfume and pharmacological agents. A deficiency of squalene (SQ) synthase activity allows yeasts to accumulate an acyclic sesquiterpene alcohol, (E,E)-farnesol, in their cells. Since sterols are essential for the growth of yeasts, a deficiency of SQ synthase activity makes the addition of supplemental sterols to the culture media necessary. To develop a GGOH production method not requiring any supplemental sterols, we overexpressed HMG1 encoding hydroxymethylglutaryl-CoA reductase and the genes of two prenyl diphosphate synthases, ERG20 and BTS1, in Saccharomyces cerevisiae. A prototrophic diploid coexpressing HMG1 and the ERG20-BTS1 fusion accumulated GGOH with neither disruption of the SQ synthase gene nor the addition of any supplemental sterols. The GGOH content on the diploid cultivation in a 5-l jar fermenter reached 138.8 mg/l under optimal conditions.

  15. Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.

    PubMed

    Mohajeri, Arezoo; Tayebwa, Johnbosco; Collin, Anna; Nilsson, Jenny; Magnusson, Linda; von Steyern, Fredrik Vult; Brosjö, Otte; Domanski, Henryk A; Larsson, Olle; Sciot, Raf; Debiec-Rychter, Maria; Hornick, Jason L; Mandahl, Nils; Nord, Karolin H; Mertens, Fredrik

    2013-10-01

    Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2--a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither chromosome banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level.

  16. 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

  17. 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.

  18. Fusion materials high energy-neutron studies. A status report

    SciTech Connect

    Doran, D.G.; Guinan, M.W.

    1980-01-01

    The objectives of this paper are (1) to provide background information on the US Magnetic Fusion Reactor Materials Program, (2) to provide a framework for evaluating nuclear data needs associated with high energy neutron irradiations, and (3) to show the current status of relevant high energy neutron studies. Since the last symposium, the greatest strides in cross section development have been taken in those areas providing FMIT design data, e.g., source description, shielding, and activation. In addition, many dosimetry cross sections have been tentatively extrapolated to 40 MeV and integral testing begun. Extensive total helium measurements have been made in a variety of neutron spectra. Additional calculations are needed to assist in determining energy dependent cross sections.

  19. 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.

  20. 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.

  1. 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.

  2. Identification of PML/RARalpha fusion gene transcripts that showed no t(15;17) with conventional karyotyping and fluorescent in situ hybridization.

    PubMed

    Choughule, A; Polampalli, S; Amre, P; Shinde, S; Banavali, S; Prabhash, K; Nair, R; Subramanian, P G; Gujral, S; Parikh, P M

    2009-01-01

    Acute promyelocytic leukemia (APL) is characterized by a reciprocal translocation, t(15;17)(q22;q11-21), resulting in the fusion of the promyelocytic leukemia (PML) and retinoic acid receptor alpha (RARalpha) genes. Using conventional cytogenetic methods, these translocations are normally detected in about 70-90% of patients; most negative results are due to technical problems or cryptic variants. These masked PML/RARalpha fusions can be identified by molecular analyses, such as reverse transcriptase-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization (FISH). Approximately 5 to 10% of all APL cases reported do not show PML/RARalpha fusion transcripts, even with dual-colored FISH. We report three of 40 diagnosed APL cases that showed morphological, cytochemical, and immunophenotypic features of hypergranular APL, but did not show a PML/RARalpha fusion signal or any of its variants, on FISH. All cases were identified by RT-PCR, which was further confirmed by cDNA sequencing. Conventional karyotyping showed other clonal aberrations in these cases, but failed to show t(15;17) or any other variants or complex translocations. PMID:19224461

  3. 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

  4. Detection of Rare Variant of SS18-SSX1 Fusion Gene and Mutations of Important Cancer-Related Genes in Synovial Sarcoma of the Lip: Gene Analyses of a Case and Literature Review.

    PubMed

    Mikami, Toshinari; Kurose, Akira; Javed, Fawad; Takeda, Yasunori

    2015-08-01

    Synovial sarcoma (SS) accounts for 5 to 10% of soft tissue sarcomas; however, intraoral SS is rare. Histopathologically, SS shows a biphasic pattern with epithelial and spindle cell components or a monophasic pattern with only spindle cells. The precise diagnosis of SS, especially at an unusual site, is often a challenge to pathologists and clinical oncologists, because the differential diagnosis of SS includes a broad range of tumors, such as soft tissue sarcomas and carcinomas. In the present case, the patient was a 50-year-old woman who presented with the chief complaint of swelling and a slowly enlarging mass of the lower lip in the mucolabial fold region. The mass was covered with intact mucosa and intraoral examination showed no malignant findings. The clinical diagnosis was a benign tumor and a probable salivary gland tumor. Macroscopically, the excised mass also indicated a benign tumor; however, histopathologic findings suggested the diagnosis of SS. For definitive diagnosis, genetic analyses were performed with conventional polymerase chain reaction and next-generation sequencing. As a result, a rare variant of the SS18-SSX1 fusion transcript, which could not be identified by routine procedures for genetic diagnosis, was detected. In addition, 8 missense mutations of cancer-related genes were confirmed. Detection of the fusion transcript is widely used in the diagnosis of SS; however, reported cases of transcript variants of each fusion gene type are limited. Reports of mutational analysis of cancer-related genes on SS also are rare. The accumulation of rare transcript variants and the cytogenetic characters of SS are suggested to be necessary for assuming a genetic diagnosis of SS.

  5. Acquiring transgenic tobacco plants with insect resistance and glyphosate tolerance by fusion gene transformation.

    PubMed

    Sun, He; Lang, Zhihong; Zhu, Li; Huang, Dafang

    2012-10-01

    The advantages of gene 'stacking' or 'pyramiding' are obvious in genetically modified (GM) crops, and several different multi-transgene-stacking methods are available. Using linker peptides for multiple gene transformation is considered to be a good method to meet a variety of needs. In our experiment, the Bt cry1Ah gene, which encodes the insect-resistance protein, and the mG ( 2 ) -epsps gene, which encodes the glyphosate-tolerance protein, were connected by a 2A or LP4/2A linker. Linker 2A is a peptide from the foot-and-mouth disease virus (FMDV) that has self-cleavage activity. LP4 is a peptide from Raphanus sativus seeds that has a recognition site and is cleaved by a protease. LP4/2A is a hybrid peptide that contains the first 9 amino acids of LP4 and 20 amino acids from 2A. We used the linker peptide to construct four coordinated expression vectors: pHAG, pHLAG, pGAH and pGLAH. Two single gene expression vectors, pSAh and pSmG(2), were used as controls. The six expression vectors and the pCAMBIA2301 vector were transferred into tobacco by Agrobacterium tumefaciens-mediated transformation, and 529 transformants were obtained. Molecular detection and bioassay detection data demonstrated that the transgenic tobaccos possessed good pest resistance and glyphosate tolerance. The two genes in the fusion vector were expressed simultaneously. The plants with the genes linked by the LP4/2A peptide showed better pest resistance and glyphosate tolerance than the plants with the genes linked by 2A. The expression level of the two genes linked by LP4/2A was not significantly different from the single gene vector. Key message The expression level of the two genes linked by LP4/2A was higher than those linked by 2A and was not significantly different from the single gene vector.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Acute promyelocytic leukaemia in patients originating in Latin America is associated with an increased frequency of the bcr1 subtype of the PML/RARalpha fusion gene.

    PubMed

    Douer, Dan; Santillana, Sergio; Ramezani, Laleh; Samanez, Cesar; Slovak, Marilyn L; Lee, Ming S; Watkins, Kristy; Williams, Tony; Vallejos, Carlos

    2003-08-01

    The PML/RARalpha fusion gene in acute promyelocytic leukaemia (APL) has three subtypes based on the breakpoint site of the PML gene: long (bcr1), short (bcr3) and variable (bcr2) subtypes. The PML/RARalpha fusion protein is involved in the pathogenesis of APL and the breakpoint site of the PML gene might be associated with aetiological factor(s). Because APL is over-represented in patients that originate in Latin America (Latinos), we evaluated whether the distribution of the PML/RARalpha fusion mRNA in this population is different to that reported in non-Latinos. Among 52 APL patients (28 from Mexico and Central America diagnosed in Los Angeles and 24 from Peru, South America), bcr1, bcr2 and bcr3 expression was 75%, 10% and 15% respectively. However, bcr1 breakpoints were significantly higher compared with non-Latino patients (340/654, 52%) reported in four studies. Often bcr1 and bcr2 are reported together; 862 (60%) of 1429 non-Latino APL patients reported in nine studies were either bcr1 or bcr2, compared with 44 (85%) in our 52 Latino patients. This difference was also statistically significant when our patients were compared to each of the individual studies from USA and Europe, but not for a small series from China and Japan. These results suggest that the overrepresentation of APL among Latin American patients can be accounted for by an increase of a single subtype--bcr1, and the breakage sites in the PML gene may not be random but possibly influenced by genetic and/or environmental factor(s).

  12. Insertion of a GFP reporter gene in influenza virus.

    PubMed

    Perez, Jasmine T; García-Sastre, Adolfo; Manicassamy, Balaji

    2013-01-01

    The incorporation of a fluorescent reporter gene into a replication-competent influenza A virus (IAV) has made it possible to trace IAV infection in vivo. This protocol describes the process of inserting a green fluorescent protein (GFP) reporter into the IAV genome using the established reverse genetics system. The strategy begins with the reorganization of segment eight of the IAV genome, during which the open reading frames of nonstructural protein 1 (NS1) and the nuclear export protein (NEP) are separated to allow for GFP fusion to the NS1 protein. The NS1, GFP, and NEP open reading frames (ORF) are then cloned into the IAV rescue system backbone. Upon construction of the GFP-encoding segment eight rescue plasmid, recombinant NS1-GFP influenza virus can be rescued via co-transfection with the remaining seven rescue plasmids. The generated NS1-GFP IAV can subsequently be used to visualize infected cells, both in vitro and in vivo.

  13. Expression of a preproinsulin-beta-galactosidase gene fusion in mammalian cells.

    PubMed Central

    Nielsen, D A; Chou, J; MacKrell, A J; Casadaban, M J; Steiner, D F

    1983-01-01

    As an approach to the study of mammalian gene expression, the promoters and translation initiation regions of the rat preproinsulin II and the simian virus 40 early genes were fused to the structural gene of Escherichia coli beta-galactosidase, a sensitive probe for gene expression. These fusions were introduced into COS-7 cells, a simian virus 40 large tumor-antigen-producing monkey kidney cell line, where they directed the synthesis of enzymatically active hybrid beta-galactosidase proteins. Conditions for transfection were varied to optimize the expression of beta-galactosidase activity in the transfected cells. The pH optimum of this activity was found to be 7.0, the same as that of native E. coli beta-galactosidase and distinct from the major lysosomal "acid" beta-galactosidase. The fused preproinsulin-beta-galactosidase was further characterized by gel electrophoresis of nondenatured cell extracts stained by a fluorogenic substrate and by immunoprecipitation and gel electrophoresis of 3H-labeled cell proteins. These results all indicate that fully active tetrameric beta-galactosidase hybrids can be produced in mammalian cells. The expression of preproinsulin-beta-galactosidase activity was measured in the presence of high glucose, insulin, dexamethasone, or epidermal growth factor but no regulatory changes were observed. Images PMID:6310564

  14. 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

  15. The Role of Plastids in the Expression of Nuclear Genes for Thylakoid Proteins Studied with Chimeric [beta]-Glucuronidase Gene Fusions.

    PubMed Central

    Bolle, C.; Sopory, S.; Lubberstedt, T.; Klosgen, R. B.; Herrmann, R. G.; Oelmuller, R.

    1994-01-01

    We have analyzed plastid and nuclear gene expression in tobacco seedlings using the carotenoid biosynthesis inhibitor nor-flurazon. mRNA levels for three nuclear-encoded chlorophyll-binding proteins of photosystem I and photosystem II (CAB I and II and the CP 24 apoprotein) are no longer detectable in photobleached seedlings, whereas those for other components of the thylakoid membrane (the 33- and 23-kD polypeptides and Rieske Fe/S polypeptide) accumulate to some extent. Transgenic tobacco seedlings with promoter fusions from genes for thylakoid membrane proteins exhibit a similar expression behavior: a CAB-[beta]-glucuronidase (GUS) gene fusion is not expressed in herbicide-treated seedlings, whereas PC-, FNR-, PSAF-, and ATPC-promoter fusions are expressed, although at reduced levels. All identified segments in nuclear promoters analyzed that have been shown to respond to light also respond to photodamage to the plastids. Thus, the regulatory signal pathways either merge prior to gene regulation or interact with closely neighboring cis elements. These results indicate that plastids control nuclear gene expression via different and gene-specific cis-regulatory elements and that CAB gene expression is different from the expression of the other genes tested. Finally, a plastid-directing import sequence from the maize Waxy gene is capable of directing the GUS protein into the photodamaged organelle. Therefore, plastid import seems to be functional in photobleached organelles. PMID:12232290

  16. Far-red fluorescence gene reporter tomography for determination of placement and viability of cell-based gene therapies.

    PubMed

    Lu, Yujie; Darne, Chinmay D; Tan, I-Chih; Zhu, Banghe; Hall, Mary A; Lazard, Zawaunyka W; Davis, Alan R; Simpson, Lashan; Sevick-Muraca, Eva M; Olmsted-Davis, Elizabeth A

    2013-10-01

    Non-invasive injectable cellular therapeutic strategies based on sustained delivery of physiological levels of BMP-2 for spinal fusion are emerging as promising alternatives, which could provide sufficient fusion without the associated surgical risks. However, these injectable therapies are dependent on bone formation occurring only at the specific target region. In this study, we developed and deployed fluorescence gene reporter tomography (FGRT) to provide information on in vivo cell localization and viability. This information is sought to confirm the ideal placement of the materials with respect to the area where early bone reaction is required, ultimately providing three dimensional data about the future fusion. However, because almost all conventional fluorescence gene reporters require visible excitation wavelengths, current in vivo imaging of fluorescent proteins is limited by high tissue absorption and confounding autofluorescence. We previously administered fibroblasts engineered to produce BMP-2, but is difficult to determine 3-D information of placement prior to bone formation. Herein we used the far-red fluorescence gene reporter, IFP1.4 to report the position and viability of fibroblasts and developed 3-D tomography to provide placement information. A custom small animal, far-red fluorescence tomography system integrated into a commercial CT scanner was used to assess IFP1.4 fluorescence and to demark 3-D placement of encapsulated fibroblasts with respect to the vertebrae and early bone formation as assessed from CT. The results from three experiments showed that the placement of the materials within the spine could be detected. This work shows that in vivo fluorescence gene reporter tomography of cell-based gene therapy is feasible and could help guide cell-based therapies in preclinical models.

  17. The human ubiquitin-52 amino acid fusion protein gene shares several structural features with mammalian ribosomal protein genes.

    PubMed Central

    Baker, R T; Board, P G

    1991-01-01

    Complementary DNA clones encoding ubiquitin fused to a 52 amino acid tail protein were isolated from human placental and adrenal gland cDNA libraries. The deduced human 52 amino acid tail protein is very similar to the homologous protein from other species, including the conservation of the putative metal-binding, nucleic acid-binding domain observed in these proteins. Northern blot analysis with a tail-specific probe indicated that the previously identified UbA mRNA species most likely represents comigrating transcripts of the 52 amino acid tail (UbA52) and 80 amino acid tail (UbA80) ubiquitin fusion genes. The UbA52 gene was isolated from a human genomic library and consists of five exons distributed over 3400 base pairs. One intron is in the 5' non-coding region, two interrupt the single ubiquitin coding unit, and the fourth intron is within the tail coding region. Several members of the Alu family of repetitive DNA are associated with the gene. The UbA52 promoter has several features in common with mammalian ribosomal protein genes, including its location in a CpG-rich island, initiation of transcription within a polypyrimidine tract, the lack of a consensus TATA motif, and the presence of Sp1 binding sites, observations that are consistent with the recent identification of the ubiquitin-free tail proteins as ribosomal proteins. Thus, in spite of its unusual feature of being translationally fused to ubiquitin, the 52 amino acid tail ribosomal protein is expressed from a structurally typical ribosomal protein gene. Images PMID:1850507

  18. Hawaiian skirt: an F-box gene that regulates organ fusion and growth in Arabidopsis.

    PubMed

    González-Carranza, Zinnia H; Rompa, Unchalee; Peters, Janny L; Bhatt, Anuj M; Wagstaff, Carol; Stead, Anthony D; Roberts, Jeremy A

    2007-07-01

    A fast neutron-mutagenized population of Arabidopsis (Arabidopsis thaliana) Columbia-0 wild-type plants was screened for floral phenotypes and a novel mutant, termed hawaiian skirt (hws), was identified that failed to shed its reproductive organs. The mutation is the consequence of a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a putative F-box protein (At3g61590). The most striking anatomical characteristic of hws plants is seen in flowers where individual sepals are fused along the lower part of their margins. Crossing of the abscission marker, Pro(PGAZAT):beta-glucuronidase, into the mutant reveals that while floral organs are retained it is not the consequence of a failure of abscission zone cells to differentiate. Anatomical analysis indicates that the fusion of sepal margins precludes shedding even though abscission, albeit delayed, does occur. Spatial and temporal characterization, using Pro(HWS):beta-glucuronidase or Pro(HWS):green fluorescent protein fusions, has identified HWS expression to be restricted to the stele and lateral root cap, cotyledonary margins, tip of the stigma, pollen, abscission zones, and developing seeds. Comparative phenotypic analyses performed on the hws mutant, Columbia-0 wild type, and Pro(35S):HWS ectopically expressing lines has revealed that loss of HWS results in greater growth of both aerial and below-ground organs while overexpressing the gene brings about a converse effect. These observations are consistent with HWS playing an important role in regulating plant growth and development.

  19. 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.

  20. 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.

  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. Final report SI 08-SI-004: Fusion application targets

    SciTech Connect

    Biener, J; Kucheyev, S O; Wang, M Y; Dawedeit, C; Worsley, M A; Kim, S H; Walton, C; Gilmer, G; Zepeda-Ruiz, L; Chernov, A A; Lee, J I; Willey, T M; Biener, M M; van Buuren, T; Wu, K J; Satcher, J H; Hamza, A V

    2010-12-03

    Complex target structures are necessary to take full advantage of the unique laboratory environment created by inertial confinement fusion experiments. For example, uses-of-ignition targets that contain a thin layer of a low density nanoporous material inside a spherical ablator shell allow placing dopants in direct contact with the DT fuel. The ideal foam for this application is a low-density hydrocarbon foam that is strong enough to survive wetting with cryogenic hydrogen, and low enough in density (density less than {approx}30 mg/cc) to not reduce the yield of the target. Here, we discuss the fabrication foam-lined uses-of-ignition targets, and the development of low-density foams that can be used for this application. Much effort has been directed over the last 20 years toward the development of spherical foam targets for direct-drive and fast-ignition experiments. In these targets, the spherical foam shell is used to define the shape of the cryogenic DT fuel layer, or acts as a surrogate to simulate the cryogenic fuel layer. These targets are fabricated from relatively high-density aerogels (>100 mg/cc) and coated with a few micron thick permeation barrier. With exception of the above mentioned fast ignition targets, the wall of these targets is typically larger than 100 microns. In contrast, the fusion application targets for indirect-drive experiments on NIF will require a much thinner foam shell surrounded by a much thicker ablator shell. The design requirements for both types of targets are compared in Table 1. The foam shell targets for direct-drive experiments can be made in large quantities and with reasonably high yields using an encapsulation technique pioneered by Takagi et al. in the early 90's. In this approach, targets are made by first generating unsupported foam shells using a triple-orifice droplet generator, followed by coating the dried foam shells with a thin permeation barrier. However, this approach is difficult, if not impossible, to

  3. 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. PMID:25323393

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. The MYB-NFIB gene fusion-a novel genetic link between adenoid cystic carcinoma and dermal cylindroma.

    PubMed

    Fehr, A; Kovács, A; Löning, T; Frierson, Hf; van den Oord, Jj; Stenman, G

    2011-07-01

    We have recently shown that the recurrent t(6;9)(q22 ∼ 23;p23 ∼ 24) translocation in adenoid cystic carcinoma (ACC) of the breast and head and neck results in a fusion of the two transcription factor genes MYB and NFIB. Here we demonstrate, for the first time, that benign sporadic, dermal cylindromas also express the MYB-NFIB gene fusion. RT-PCR and immunohistochemical analyses revealed that eight of 12 analysed tumours (67%) expressed MYB-NFIB fusion transcripts and/or stained positive for MYB protein. Nucleotide sequence analyses confirmed that the composition of the chimeric transcript variants identified was identical to that in ACC, suggesting a similar molecular mechanism of activation of MYB in cylindroma as in ACC. In contrast, no evidence for the presence of the MYB-NFIB fusion was found in other types of basaloid skin and salivary gland tumours, indicating that the fusion indeed has a restricted expression pattern. Our findings broaden the spectrum of neoplasms associated with MYB oncogene activation and reveal a novel genetic link between ACC and dermal cylindroma. These results, together with our previous observations, further strengthen the evidence for common molecular pathways of importance for the development of both benign and malignant breast, salivary and adnexal tumours.

  11. 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.

  12. 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.

  13. Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.

    PubMed

    Walther, Charles; Hofvander, Jakob; Nilsson, Jenny; Magnusson, Linda; Domanski, Henryk A; Gisselsson, David; Tayebwa, Johnbosco; Doyle, Leona A; Fletcher, Christopher D M; Mertens, Fredrik

    2015-09-01

    Benign fibrous histiocytomas (FH) can be subdivided into several morphological and clinical subgroups. Recently, gene fusions involving either one of two protein kinase C genes (PRKCB and PRKCD) or the ALK gene were described in FH. We here wanted to evaluate the frequency of PRKCB and PRKCD gene fusions in FH. Using interphase fluorescence in situ hybridization on sections from formalin-fixed paraffin-embedded (FFPE) tumors, 36 cases could be analyzed. PRKCB or PRKCD rearrangements were seen in five tumors: 1/7 regular, 0/3 aneurysmal, 0/6 cellular, 2/7 epithelioid, 0/1 atypical, 2/10 deep, and 0/2 metastatic lesions. We also evaluated the status of the ALK gene in selected cases, finding rearrangements in 3/7 epithelioid and 0/1 atypical lesions. To assess the gene fusion status of FH further, deep sequencing of RNA (RNA-Seq) was performed on FFPE tissue from eight cases with unknown gene fusion status, as well as on two FH and six soft tissue sarcomas with known gene fusions; of the latter eight positive controls, the expected fusion transcript was found in all but one, while 2/8 FH with unknown genetic status showed fusion transcripts, including a novel KIRREL/PRKCA chimera. Thus, also a third member of the PRKC family is involved in FH tumorigenesis. We conclude that gene fusions involving PRKC genes occur in several morphological (regular, cellular, aneurysmal, epithelioid) and clinical (cutaneous, deep) subsets of FH, but they seem to account for only a minority of the cases. In epithelioid lesions, however, rearrangements of PRKC or ALK were seen, as mutually exclusive events, in the majority (5/7) of cases. Finally, the study also shows that RNA-Seq is a promising tool for identifying gene fusions in FFPE tissues.

  14. Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.

    PubMed

    Walther, Charles; Hofvander, Jakob; Nilsson, Jenny; Magnusson, Linda; Domanski, Henryk A; Gisselsson, David; Tayebwa, Johnbosco; Doyle, Leona A; Fletcher, Christopher D M; Mertens, Fredrik

    2015-09-01

    Benign fibrous histiocytomas (FH) can be subdivided into several morphological and clinical subgroups. Recently, gene fusions involving either one of two protein kinase C genes (PRKCB and PRKCD) or the ALK gene were described in FH. We here wanted to evaluate the frequency of PRKCB and PRKCD gene fusions in FH. Using interphase fluorescence in situ hybridization on sections from formalin-fixed paraffin-embedded (FFPE) tumors, 36 cases could be analyzed. PRKCB or PRKCD rearrangements were seen in five tumors: 1/7 regular, 0/3 aneurysmal, 0/6 cellular, 2/7 epithelioid, 0/1 atypical, 2/10 deep, and 0/2 metastatic lesions. We also evaluated the status of the ALK gene in selected cases, finding rearrangements in 3/7 epithelioid and 0/1 atypical lesions. To assess the gene fusion status of FH further, deep sequencing of RNA (RNA-Seq) was performed on FFPE tissue from eight cases with unknown gene fusion status, as well as on two FH and six soft tissue sarcomas with known gene fusions; of the latter eight positive controls, the expected fusion transcript was found in all but one, while 2/8 FH with unknown genetic status showed fusion transcripts, including a novel KIRREL/PRKCA chimera. Thus, also a third member of the PRKC family is involved in FH tumorigenesis. We conclude that gene fusions involving PRKC genes occur in several morphological (regular, cellular, aneurysmal, epithelioid) and clinical (cutaneous, deep) subsets of FH, but they seem to account for only a minority of the cases. In epithelioid lesions, however, rearrangements of PRKC or ALK were seen, as mutually exclusive events, in the majority (5/7) of cases. Finally, the study also shows that RNA-Seq is a promising tool for identifying gene fusions in FFPE tissues. PMID:26121314

  15. LAMTOR1-PRKCD and NUMA1-SFMBT1 fusion genes identified by RNA sequencing in aneurysmal benign fibrous histiocytoma with t(3;11)(p21;q13).

    PubMed

    Panagopoulos, Ioannis; Gorunova, Ludmila; Bjerkehagen, Bodil; Lobmaier, Ingvild; Heim, Sverre

    2015-11-01

    RNA sequencing of an aneurysmal benign fibrous histiocytoma with the karyotype 46,XY,t(3;11)(p21;q13),del(6)(p23)[17]/46,XY[2] showed that the t(3;11) generated two fusion genes: LAMTOR1-PRKCD and NUMA1-SFMBT1. RT-PCR together with Sanger sequencing verified the presence of fusion transcripts from both fusion genes. In the LAMTOR1-PRKCD fusion, the part of the PRKCD gene coding for the catalytic domain of the serine/threonine kinase is under control of the LAMTOR1 promoter. In the NUMA1-SFMBT1 fusion, the part of the SFMBT1 gene coding for two of four malignant brain tumor domains and the sterile alpha motif domain is controlled by the NUMA1 promoter. The data support a neoplastic genesis of aneurysmal benign fibrous histiocytoma and indicate a pathogenetic role for LAMTOR1-PRKCD and NUMA1-SFMBT1.

  16. The Schizosaccharomyces pombe fusion gene hal3 encodes three distinct activities.

    PubMed

    Molero, Cristina; Petrényi, Katalin; González, Asier; Carmona, Mercè; Gelis, Samuel; Abrie, J Albert; Strauss, Erick; Ramos, José; Dombradi, Viktor; Hidalgo, Elena; Ariño, Joaquín

    2013-10-01

    Saccharomyces cerevisiae Hal3 and Vhs3 are moonlighting proteins, forming an atypical heterotrimeric decarboxylase (PPCDC) required for CoA biosynthesis, and regulating cation homeostasis by inhibition of the Ppz1 phosphatase. The Schizosaccharomyces pombe ORF SPAC15E1.04 (renamed as Sp hal3) encodes a protein whose amino-terminal half is similar to Sc Hal3 whereas its carboxyl-terminal half is related to thymidylate synthase (TS). We show that Sp Hal3 and/or its N-terminal domain retain the ability to bind to and modestly inhibit in vitro S. cerevisiae Ppz1 as well as its S. pombe homolog Pzh1, and also exhibit PPCDC activity in vitro and provide PPCDC function in vivo, indicating that Sp Hal3 is a monogenic PPCDC in fission yeast. Whereas the Sp Hal3 N-terminal domain partially mimics Sc Hal3 functions, the entire protein and its carboxyl-terminal domain rescue the S. cerevisiae cdc21 mutant, thus proving TS function. Additionally, we show that the 70 kDa Sp Hal3 protein is not proteolytically processed under diverse forms of stress and that, as predicted, Sp hal3 is an essential gene. Therefore, Sp hal3 represents a fusion event that joined three different functional activities in the same gene. The possible advantage derived from this surprising combination of essential proteins is discussed. PMID:23962284

  17. Hawaiian skirt: an F-box gene that regulates organ fusion and growth in Arabidopsis.

    PubMed

    González-Carranza, Zinnia H; Rompa, Unchalee; Peters, Janny L; Bhatt, Anuj M; Wagstaff, Carol; Stead, Anthony D; Roberts, Jeremy A

    2007-07-01

    A fast neutron-mutagenized population of Arabidopsis (Arabidopsis thaliana) Columbia-0 wild-type plants was screened for floral phenotypes and a novel mutant, termed hawaiian skirt (hws), was identified that failed to shed its reproductive organs. The mutation is the consequence of a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a putative F-box protein (At3g61590). The most striking anatomical characteristic of hws plants is seen in flowers where individual sepals are fused along the lower part of their margins. Crossing of the abscission marker, Pro(PGAZAT):beta-glucuronidase, into the mutant reveals that while floral organs are retained it is not the consequence of a failure of abscission zone cells to differentiate. Anatomical analysis indicates that the fusion of sepal margins precludes shedding even though abscission, albeit delayed, does occur. Spatial and temporal characterization, using Pro(HWS):beta-glucuronidase or Pro(HWS):green fluorescent protein fusions, has identified HWS expression to be restricted to the stele and lateral root cap, cotyledonary margins, tip of the stigma, pollen, abscission zones, and developing seeds. Comparative phenotypic analyses performed on the hws mutant, Columbia-0 wild type, and Pro(35S):HWS ectopically expressing lines has revealed that loss of HWS results in greater growth of both aerial and below-ground organs while overexpressing the gene brings about a converse effect. These observations are consistent with HWS playing an important role in regulating plant growth and development. PMID:17496113

  18. 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.

  19. Evidence that the lung adenocarcinoma EML4-ALK fusion gene is not caused by exposure to secondhand tobacco smoke during childhood

    PubMed Central

    Jen, Jin; Yi, Eunhee S.; Olivo-Marston, Susan; Yang, Ping; Harris, Curtis C.

    2014-01-01

    Background The EML4-ALK fusion gene is more frequently found in younger, never smoking, lung cancer patients. Meanwhile, never smokers exposed to secondhand tobacco smoke (SHS) during childhood are diagnosed at a younger age compared with never smoking lung cancer patients that are not exposed. We therefore hypothesized that SHS, which can induce DNA damage, is associated with the EML4-ALK fusion gene. Methods We compared the frequency of the EML4-ALK fusion gene among 197 never smoker lung cancer patients with and without a history of exposure to SHS during childhood at Mayo Clinic. Results The EML4-ALK fusion gene was detected in 33% of cases from never smokers with a history of SHS exposure during childhood, while 47% of never smoking lung cancer cases without a history of childhood SHS exposure tested positive for the fusion gene. Conclusions The EML4-ALK fusion gene is not enriched in tumors from individuals exposed to SHS during childhood. Impact These data suggest that childhood exposure to SHS is not a significant etiologic cause of the EML4-ALK fusion gene in lung cancer. PMID:24755712

  20. 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.

  1. Molecular characterization of the MLL-SEPT6 fusion gene in acute myeloid leukemia: identification of novel fusion transcripts and cloning of genomic breakpoint junctions.

    PubMed

    Cerveira, Nuno; Micci, Francesca; Santos, Joana; Pinheiro, Manuela; Correia, Cecília; Lisboa, Susana; Bizarro, Susana; Norton, Lucília; Glomstein, Anders; Asberg, Ann E; Heim, Sverre; Teixeira, Manuel R

    2008-07-01

    One of the MLL fusion partners in leukemia is the SEPT6 gene, which belongs to the evolutionarily conserved family of genes of septins. In this work we aimed to characterize at both the RNA and DNA levels three acute myeloid leukemias with cytogenetic evidence of a rearrangement between 11q23 and Xq24. Molecular analysis led to the identification of several MLL-SEPT6 fusion transcripts in all cases, including a novel MLL-SEPT6 rearrangement (MLL exon 6 fused with SEPT6 exon 2). Genomic DNA breakpoints were found inside or near Alu or LINE repeats in the MLL breakpoint cluster region, whereas the breakpoint junctions in the SEPT6 intron 1 mapped to the vicinity of GC-rich low-complexity repeats, Alu repeats, and a topoisomerase II consensus cleavage site. These data suggest that a non-homologous end-joining repair mechanism may be involved in the generation of MLL-SEPT6 rearrangements in acute myeloid leukemia. PMID:18492691

  2. 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.

  3. Spine fusion cross-link causing delayed dural erosion and CSF leak: case report.

    PubMed

    Rahmathulla, Gazanfar; Deen, H Gordon

    2015-04-01

    The past 2 decades have seen a considerable increase in the number of lumbar spinal fusion surgeries. To enhance spinal stabilization and fusion, make the construct resistant to or stiffer for axial stress loading, lateral bending, and torsional stresses, cross-links and connectors were designed and included in a rod-screw construct. The authors present the case of a 49-year-old woman who presented 11 years after undergoing an L4-5 decompression and fusion in which a pedicle screw-rod construct with an integrated cross-link was designed to attach onto the pedicle screws. The patient's response at the time to the initial surgery was excellent; however, at the time of presentation 11 years later, she had significant postural headaches, severe neurogenic claudication, and radiculopathy. Imaging revealed canal compression across the instrumented levels and a possible thickened adherent filum terminale. Reexploration of the level revealed a large erosive dural defect with a CSF leak, spinal canal compression, and a thickened filum at the level of the cross-link. To the author's knowledge, such complications have not been reported in literature. The authors discuss this rare complication of spinal fusion and the need to avoid dural compression when cross-links are used. PMID:25635637

  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. The NAB2-STAT6 gene fusion in solitary fibrous tumor can be reliably detected by anchored multiplexed PCR for targeted next-generation sequencing.

    PubMed

    Guseva, Natalya V; Tanas, Munir R; Stence, Aaron A; Sompallae, Ramakrishna; Schade, Jenna C; Bossler, Aaron D; Bellizzi, Andrew M; Ma, Deqin

    2016-01-01

    Solitary fibrous tumor (SFT) is a mesenchymal tumor of fibroblastic origin, which can affect any region of the body. 10-15% of SFTs metastasize and metastatic tumors are uniformly lethal with no effective therapies. The behavior of SFT is difficult to predict based on morphology. Recently, an intrachromosomal gene fusion between NAB2 and STAT6 was identified as the defining driving genetic event of SFT and different fusion types correlated with tumor histology and behavior. Due to the proximity of NAB2 and STAT6 on chromosome 12, this fusion may be missed by fluorescence in-situ hybridization. We evaluated 12 SFTs from 10 patients. All tumors showed strong nuclear staining for STAT6 by immunohistochemistry (IHC). The same formalin-fixed, paraffin-embedded blocks for IHC were used for gene fusion detection by a next-generation sequencing (NGS)-based assay. Targeted RNA fusion sequencing for gene fusions was performed using the Universal RNA Fusion Detection Kit, the Archer(™) FusionPlex(™) Sarcoma Panel and the Ion Torrent PGM, and data were analyzed using the Archer Analysis Pipeline 3.3. All tumors were positive for NAB2-STAT6 fusion. Six types of fusions were detected: NAB2ex4-STAT6ex2, NAB2ex2-STAT6ex5, NAB2ex6-STAT6ex16, NAB2ex6-STAT6ex17, NAB2ex3-STAT6ex18 and NAB2intron6-STAT6Ex17. The NGS findings were confirmed by RT-PCR followed by Sanger sequencing. No STAT6 fusion was detected in selected morphologic mimics of SFT. The assay also allows for detection of novel fusions and can detect NAB2-STAT6 fusions at a single-base resolution. PMID:27292373

  6. The NAB2-STAT6 gene fusion in solitary fibrous tumor can be reliably detected by anchored multiplexed PCR for targeted next-generation sequencing.

    PubMed

    Guseva, Natalya V; Tanas, Munir R; Stence, Aaron A; Sompallae, Ramakrishna; Schade, Jenna C; Bossler, Aaron D; Bellizzi, Andrew M; Ma, Deqin

    2016-01-01

    Solitary fibrous tumor (SFT) is a mesenchymal tumor of fibroblastic origin, which can affect any region of the body. 10-15% of SFTs metastasize and metastatic tumors are uniformly lethal with no effective therapies. The behavior of SFT is difficult to predict based on morphology. Recently, an intrachromosomal gene fusion between NAB2 and STAT6 was identified as the defining driving genetic event of SFT and different fusion types correlated with tumor histology and behavior. Due to the proximity of NAB2 and STAT6 on chromosome 12, this fusion may be missed by fluorescence in-situ hybridization. We evaluated 12 SFTs from 10 patients. All tumors showed strong nuclear staining for STAT6 by immunohistochemistry (IHC). The same formalin-fixed, paraffin-embedded blocks for IHC were used for gene fusion detection by a next-generation sequencing (NGS)-based assay. Targeted RNA fusion sequencing for gene fusions was performed using the Universal RNA Fusion Detection Kit, the Archer(™) FusionPlex(™) Sarcoma Panel and the Ion Torrent PGM, and data were analyzed using the Archer Analysis Pipeline 3.3. All tumors were positive for NAB2-STAT6 fusion. Six types of fusions were detected: NAB2ex4-STAT6ex2, NAB2ex2-STAT6ex5, NAB2ex6-STAT6ex16, NAB2ex6-STAT6ex17, NAB2ex3-STAT6ex18 and NAB2intron6-STAT6Ex17. The NGS findings were confirmed by RT-PCR followed by Sanger sequencing. No STAT6 fusion was detected in selected morphologic mimics of SFT. The assay also allows for detection of novel fusions and can detect NAB2-STAT6 fusions at a single-base resolution.

  7. 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.

  8. 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.

  9. 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.

  10. [Bilateral congenital fusion of the scaphoid and the trapezium. A case report].

    PubMed

    Moreel, P; Wilson, S M; Descamps, S; Roulot, E

    2008-02-01

    Congenital synostosis has been described between nearly all of the carpal bones. It can occur in an isolated form or most commonly in relation between the lunatum and the triquetrum. It can also occur in a multiple form and be associated with other malformations. We report a rare case of scaphoid-trapezium fusion observed bilaterally in a nearly asymptomatic 63-year-old patient.

  11. 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.

  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. Prevention of adverse events of interferon γ gene therapy by gene delivery of interferon γ-heparin-binding domain fusion protein in mice.

    PubMed

    Ando, Mitsuru; Takahashi, Yuki; Yamashita, Takuma; Fujimoto, Mai; Nishikawa, Makiya; Watanabe, Yoshihiko; Takakura, Yoshinobu

    2014-01-01

    Sustained gene delivery of interferon (IFN) γ can be an effective treatment, but our previous study showed high levels of IFNγ-induced adverse events, including the loss of body weight. These unwanted events could be reduced by target-specific delivery of IFNγ after in vivo gene transfer. To achieve this, we selected the heparin-binding domain (HBD) of extracellular superoxide dismutase as a molecule to anchor IFNγ to the cell surface. We designed three IFNγ derivatives, IFNγ-HBD1, IFNγ-HBD2, and IFNγ-HBD3, each of which had 1, 2, or 3 HBDs, respectively. Each plasmid-encoding fusion proteins was delivered to the liver, a model target in this study, by hydrodynamic tail vein injection. The serum concentration of IFNγ-HBD2 and IFNγ-HBD3 after gene delivery was lower than that of IFNγ or IFNγ-HBD1. Gene delivery of IFNγ-HBD2, but not of IFNγ-HBD3, effectively increased the mRNA expression of IFNγ-inducible genes in the liver, suggesting liver-specific distribution of IFNγ-HBD2. Gene delivery of IFNγ-HBD2-suppressed tumor growth in the liver as efficiently as that of IFNγ with much less symptoms of adverse effects. These results indicate that the adverse events of IFNγ gene transfer can be prevented by gene delivery of IFNγ-HBD2, a fusion protein with high cell surface affinity. PMID:26015966

  14. A transgenic insertion on mouse chromosome 17 inactivates a novel immunoglobulin superfamily gene potentially involved in sperm-egg fusion.

    PubMed

    Lorenzetti, Diego; Poirier, Christophe; Zhao, Ming; Overbeek, Paul A; Harrison, Wilbur; Bishop, Colin E

    2014-04-01

    Fertilization is the process that leads to the formation of a diploid zygote from two haploid gametes. This is achieved through a complex series of cell-to-cell interactions between a sperm and an egg. The final event of fertilization is the fusion of the gametes' membranes, which allows the delivery of the sperm genetic material into the egg cytoplasm. In vivo studies in the laboratory mouse have led to the discovery of membrane proteins that are essential for the fusion process in both the sperm and egg. Specifically, the sperm protein Izumo1 was shown to be necessary for normal fertility. Izumo1-deficient spermatozoa fail to fuse with the egg plasma membrane. Izumo1 is a member of the Immunoglobulin Superfamily of proteins, which are known to be involved in cell adhesion. Here, we describe BART97b, a new mouse line with a recessive mutation that displays a fertilization block associated with a failure of sperm fusion. BART97b mutants carry a deletion that inactivates Spaca6, a previously uncharacterized gene expressed in testis. Similar to Izumo1, Spaca6 encodes an immunoglobulin-like protein. We propose that the Spaca6 gene product may, together with Izumo1, mediate sperm fusion by binding an as yet unidentified egg membrane receptor.

  15. A case of 8p11 myeloproliferative syndrome with BCR-FGFR1 gene fusion presenting with trilineage acute leukemia/lymphoma, successfully treated by cord blood transplantation.

    PubMed

    Morishige, Satoshi; Oku, Eijiro; Takata, Yuka; Kimura, Yoshizo; Arakawa, Fumiko; Seki, Ritsuko; Imamura, Rie; Osaki, Koichi; Hashiguchi, Michitoshi; Yakushiji, Kazuaki; Mizuno, Shinichi; Yoshimoto, Koji; Nagafuji, Koji; Ohshima, Koichi; Okamura, Takashi

    2013-01-01

    The 8p11 myeloproliferative syndrome is a rare neoplasm associated with chromosomal translocations involving the fibroblast growth factor receptor 1 (FGFR1) gene located at chromosome 8p11-12. FGFR1 encodes a transmembrane receptor tyrosine kinase. The resultant fusion proteins are constitutively active tyrosine kinases that drive the proliferation of hematopoietic cells, whose uncontrolled growth can present as a myeloproliferative neoplasm. We report here the case of a 50-year-old man harboring the t(8;22)(p12;q11) chromosomal translocation in cells from both bone marrow and lymph nodes. He presented with acute leukemia and lymphoma with trilineage features. A novel mRNA in-frame fusion between exon 4 of the breakpoint cluster region (BCR) gene at chromosome 22q11 and exon 9 of FGFR1 gene on chromosome 8p11-12 was identified by reverse transcription polymerase chain reaction analysis and was confirmed by DNA sequencing. Because the patient was refractory to chemotherapy, cord blood transplantation was performed in progressive disease. It resulted in a successful outcome in which cytogenetic complete remission has been maintained for 2 years till date. PMID:23171834

  16. 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

  17. PCR-mediated gene modification strategy for construction of fluorescent protein fusions in Candida parapsilosis.

    PubMed

    Gonia, Sara; Larson, Britta; Gale, Cheryl A

    2016-02-01

    Candida parapsilosis is a common cause of invasive candidiasis, especially in premature infants, even surpassing Candida albicans as the most frequently identified Candida species in some newborn intensive care units. Whereas many molecular tools are available to facilitate the study of C. albicans, relatively few have been developed for C. parapsilosis. In this study, we show that plasmids harbouring green, yellow and mCherry fluorescent protein sequences, previously developed for expression in C. albicans, can be used to construct fluorescent fusion proteins in C. parapsilosis by PCR-mediated gene modification. Further, the strategy can be used in clinical isolates of C. parapsilosis, which are typically prototrophic, because the plasmids include NAT1, a dominant selectable trait that confers resistance to the antibiotic nourseothricin. Overall, these tools will be useful to yeast researchers who require the ability to visualize C. parapsilosis directly, e.g. in in vitro and in vivo infection models. In addition, this strategy can be used to generate fluorescence in other C. parapsilosis clinical isolates and to tag sequences of interest for protein localization studies. Lastly, the ability to express up to three different fluorescent proteins will allow researchers to visualize and differentiate C. parapsilosis and/or C. albicans clinical isolates from each other in mixed infection models.

  18. 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.

  19. [Expression of SET-NUP214 fusion gene in patients with T-cell acute lymphoblastic leukemia and its clinical significance].

    PubMed

    Dai, Hai-Ping; Wang, Qian; Wu, Li-Li; Ping, Na-Na; Wu, Chun-Xiao; Xie, Jun-Dan; Pan, Jin-Lan; Xue, Yong-Quan; Wu, De-Pei; Chen, Su-Ning

    2012-10-01

    This study was aimed to investigate the occurrence and clinical significance of the SET-NUP214 fusion gene in patients with T-cell acute lymphoblastic leukemia (T-ALL), analyse clinical and biological characteristics in this disease. RT-PCR was used to detect the expression of SET-NUP214 fusion gene in 58 T-ALL cases. Interphase FISH and Array-CGH were used to detect the deletion of 9q34. Direct sequencing was applied to detect mutations of PHF6 and NOTCH1. The results showed that 6 out of 58 T-ALL cases (10.3%) were detected to have the SET-NUP214 fusion gene by RT-PCR. Besides T-lineage antigens, expression of CD13 and(or) CD33 were detected in all the 6 cases. Deletions of 9q34 were detected in 4 out of the 6 patients by FISH. Array-CGH results of 3 SET-NUP214 positive T-ALL patients confirmed that this fusion gene was resulted from a cryptic deletion of 9q34.11q34.13. PHF6 and NOTCH1 gene mutations were found in 4 and 5 out of 6 SET-NUP214 positive T-ALL patients, respectively. It is concluded that SET-NUP214 fusion gene is often resulted from del(9)(q34). PHF6 and NOTCH1 mutations may be potential leukemogenic event in SET-NUP214 fusion gene.

  20. 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)

  1. Biological Sensor for Sucrose Availability: Relative Sensitivities of Various Reporter Genes

    PubMed Central

    Miller, William G.; Brandl, Maria T.; Quiñones, Beatriz; Lindow, Steven E.

    2001-01-01

    A set of three sucrose-regulated transcriptional fusions was constructed. Fusions p61RYTIR, p61RYlac, and p61RYice contain the scrR sucrose repressor gene and the promoterless gfp, lacZ, and inaZ reporter genes, respectively, fused to the scrY promoter from Salmonella enterica serovar Typhimurium. Cells of Erwinia herbicola containing these fusions are induced only in media amended with sucrose, fructose, or sorbose. While a large variation in sucrose-dependent reporter gene activity was observed in cells harboring all gene fusions, fusions to the inaZ reporter gene yielded a much wider range of activity and were responsive to lower levels of sucrose than either lacZ or gfp. The lacZ reporter gene was found to be more efficient than gfp, requiring approximately 300-fold fewer cells for a detectable response over all concentrations of sucrose. Similarly, inaZ was found to be more efficient than lacZ, requiring 30-fold fewer cells at 1.45 μM sucrose and 6,100-fold fewer cells at 29 mM sucrose for a quantifiable response. The fluorescence of individual cells containing p61RYTIR was quantified following epifluorescence microscopy in order to relate the fluorescence exhibited by populations of cells in batch cultures with that of individual cells in such cultures. While the mean fluorescence intensity of a population of individual cells increased with increasing concentrations of sucrose, a wide range of fluorescence intensity was seen among individual cells. For most cultures the distribution of fluorescence intensity among individual cells was log-normally distributed, but cells grown in intermediate concentrations of sucrose exhibited two distinct populations of cells, one having relatively low fluorescence and another with much higher fluorescence. When cells were inoculated onto bean leaves, whole-cell ice nucleation and gfp-based biological sensors for sucrose each indicated that the average concentration of sucrose on moist leaf surfaces was about 20

  2. 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

  3. A series of vectors to construct lacZ fusions for the study of gene expression in Schizosaccharomyces pombe.

    PubMed

    Lafuente, M J; Petit, T; Gancedo, C

    1997-12-22

    We have constructed a series of plasmids to facilitate the fusion of promoters with or without coding regions of genes of Schizosaccharomyces pombe to the lacZ gene of Escherichia coli. These vectors carry a multiple cloning region in which fission yeast DNA may be inserted in three different reading frames with respect to the coding region of lacZ. The plasmids were constructed with the ura4+ or the his3+ marker of S. pombe. Functionality of the plasmids was tested measuring in parallel the expression of fructose 1,6-bisphosphatase and beta-galactosidase under the control of the fbp1+ promoter in different conditions.

  4. The tigA gene is a transcriptional fusion of glycolytic genes encoding triose-phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase in oomycota.

    PubMed Central

    Unkles, S E; Logsdon, J M; Robison, K; Kinghorn, J R; Duncan, J M

    1997-01-01

    Genes encoding triose-phosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are fused and form a single transcriptional unit (tigA) in Phytophthora species, members of the order Pythiales in the phylum Oomycota. This is the first demonstration of glycolytic gene fusion in eukaryotes and the first case of a TPI-GAPDH fusion in any organism. The tigA gene from Phytophthora infestans has a typical Oomycota transcriptional start point consensus sequence and, in common with most Phytophthora genes, has no introns. Furthermore, Southern and PCR analyses suggest that the same organization exists in other closely related genera, such as Pythium, from the same order (Oomycota), as well as more distantly related genera, Saprolegnia and Achlya, in the order Saprolegniales. Evidence is provided that in P. infestans, there is at least one other discrete copy of a GAPDH-encoding gene but not of a TPI-encoding gene. Finally, a phylogenetic analysis of TPI does not place Phytophthora within the assemblage of crown eukaryotes and suggests TPI may not be particularly useful for resolving relationships among major eukaryotic groups. PMID:9352934

  5. Colorado School of Mines fusion gamma ray diagnostic project. Technical progress report

    SciTech Connect

    Cecil, F.E.

    1992-02-14

    This report summarizes the 1991 calendar year activities of the fusion gamma ray diagnostics project in the Physics Department at the Colorado School of Mines. Considerable progress has been realized in the fusion gamma ray diagnostic project in the last year. Specifically we have achieved the two major goals of the project as outlined in last year`s proposed work statement to the Office of Applied Plasma Physics in the DOE Division of Magnetic Fusion Energy. The two major goals were: (1) Solution of the severe interference problem encountered during the operation of the gamma ray spectrometer concurrent with high power levels of the neutral beam injectors (NBI) and the ICRH antenae. (2) Experimental determination of the absolute detection efficiency of the gamma ray spectrometer. This detection efficiency will allow the measured yields of the gamma rays to be converted to a total reaction rate. In addition to these two major accomplishments, we have continued, as permitted by the TFTR operating schedule, the observation of high energy gamma rays from the 3He(D,{gamma})5Li reaction during deuterium NBI heating of 3He plasmas.

  6. Expression of a mouse metallothionein-Escherichia coli. beta. -galactosidase fusion gene (MT-. beta. gal) in early mouse embryos

    SciTech Connect

    Stevens, M.E.; Meneses, J.J.; Pedersen, R.A. )

    1989-08-01

    The authors have microinjected DNA containing the inducible mouse metallothionein-I (MT-I) promoter, coupled to the structural gene for Escherichia coli {beta}-galactosidase (lacZ), into the pronuclei of one-cell mouse embryos. A qualitative histochemical assay, with 5-bromo-4-chloro-3-indolyl {beta}-D-galactopyranoside (X-Gal) as a substrate, was used to detect expression of lacZ at several preimplantation stages. They observed staining indicative of exogenous {beta}-galactosidase activity in 5-17% of DNA-injected embryos assayed at preimplantation stages after 16-24 h treatment with ZnSO{sub 4}. Thus, lacZ can be used as an indicator gene for promoter function during early mouse embryogenesis, and the incorporation of the MT-I promoter into fusion genes can be a useful means of controlling the expression of exogenous genes in preimplantation mouse embryos.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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).

  13. 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.

  14. 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.

  15. 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

  16. Bony fusion of the maxilla and mandible as a sequelae of noma: A rare case report.

    PubMed

    Bagewadi, Shivanand B; Awasthi, Ujjwala Rastogi; Mody, Bharat M; Suma, Gundareddy N; Garg, Shruti

    2015-09-01

    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.

  17. 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.

  18. A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins.

    PubMed

    Kleinlogel, Sonja; Terpitz, Ulrich; Legrum, Barbara; Gökbuget, Deniz; Boyden, Edward S; Bamann, Christian; Wood, Phillip G; Bamberg, Ernst

    2011-12-01

    The precise co-localization and stoichiometric expression of two different light-gated membrane proteins can vastly improve the physiological usefulness of optogenetics for the modulation of cell excitability with light. Here we present a gene-fusion strategy for the stable 1:1 expression of any two microbial rhodopsins in a single polypeptide chain. By joining the excitatory channelrhodopsin-2 with the inhibitory ion pumps halorhodopsin or bacteriorhodopsin, we demonstrate light-regulated quantitative bi-directional control of the membrane potential in HEK293 cells and neurons in vitro. We also present synergistic rhodopsin combinations of channelrhodopsin-2 with Volvox carteri channelrhodopsin-1 or slow channelrhodopsin-2 mutants, to achieve enhanced spectral or kinetic properties, respectively. Finally, we demonstrate the utility of our fusion strategy to determine ion-turnovers of as yet uncharacterized rhodopsins, exemplified for archaerhodopsin and CatCh, or to correct pump cycles, exemplified for halorhodopsin. PMID:22056675

  19. 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.

  20. 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. PMID:26927892

  1. 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.

  2. 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.

  3. 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. PMID:26883114

  4. Secretory breast carcinomas with ETV6-NTRK3 fusion gene belong to the basal-like carcinoma spectrum.

    PubMed

    Laé, Marick; Fréneaux, Paul; Sastre-Garau, Xavier; Chouchane, Olfa; Sigal-Zafrani, Brigitte; Vincent-Salomon, Anne

    2009-02-01

    Secretory breast carcinomas (<0.15% of breast tumors) are associated with a characteristic morphology and a favorable prognosis. Remarkably, this entity is the only epithelial tumor of the breast with a balanced translocation, t(12;15), that creates an ETV6-NTRK3 gene fusion encoding chimeric tyrosine kinase also encountered in cellular mesoblastic nephroma and infantile fibrosarcoma. The aim of this study was to determine the phenotypic class (ie luminal A/B, ERBB2, basal-like) of secretory breast carcinoma. A series of six secretory breast carcinomas were identified in our files. The ETV6 rearrangement was confirmed in all cases by fluorescence in situ hybridization. Immunophenotype was assessed with anti-ER, PR, ERBB2, KIT, EGFR, E-cadherin, vimentin, PS100, smooth muscle actin, basal (CK5/6 and 14), luminal cytokeratins (CK8/18) and p63 antibodies. In situ and invasive components shared the same immunoprofile and were ER, PR, ERBB2 negative with expression of basal cytokeratins. ETV6 gene alterations were present in both in situ and invasive components, highlighting their genetic similarities. The immunoprofile data (triple-negative with expression of basal markers) showed that secretory breast carcinomas with ETV6-NTRK3 fusion gene belong to the phenotypic basal-like spectrum of breast carcinomas. These results support the hypothesis that secretory breast carcinomas have immunohistochemical and genetic features that distinguish them from other basal-like tumors of the breast.

  5. New derivatives of transposon Tn5 suitable for mobilization of replicons, generation of operon fusions and induction of genes in gram-negative bacteria.

    PubMed

    Simon, R; Quandt, J; Klipp, W

    1989-08-01

    Three types of new variants of the broad-host-range transposon Tn5 are described. (i) Tn5-mob derivatives with the new selective resistance (R) markers GmR, SpR and TcR facilitate the efficient mobilization of replicons within a wide range of Gram-negative bacteria. (ii) Promoter probe transposons carry the promoterless reporter genes lacZ, nptII, or luc, and NmR, GmR or TcR as selective markers. These transposons can be used to generate transcriptional fusions upon insertion, thus facilitating accurate determinations of gene expression. (iii) Tn5-P-out derivatives carry the npt- or tac-promoter reading out from the transposon, and TcR, NmR or GmR genes. These variants allow the constitutive expression of downstream genes. The new Tn5 variants are available on mobilizable Escherichia coli vectors suitable as suicidal carriers for transposon mutagenesis of non-E. coli recipients and some on a phage lambda mutant to be used for transposon mutagenesis in E. coli. PMID:2551782

  6. Fusion protein Isl1-Lhx3 specifies motor neuron fate by inducing motor neuron genes and concomitantly suppressing the interneuron programs.

    PubMed

    Lee, Seunghee; Cuvillier, James M; Lee, Bora; Shen, Rongkun; Lee, Jae W; Lee, Soo-Kyung

    2012-02-28

    Combinatorial transcription codes generate the myriad of cell types during development and thus likely provide crucial insights into directed differentiation of stem cells to a specific cell type. The LIM complex composed of Isl1 and Lhx3 directs the specification of spinal motor neurons (MNs) in embryos. Here, we report that Isl1-Lhx3, a LIM-complex mimicking fusion, induces a signature of MN transcriptome and concomitantly suppresses interneuron differentiation programs, thereby serving as a potent and specific inducer of MNs in stem cells. We show that an equimolar ratio of Isl1 and Lhx3 and the LIM domain of Lhx3 are crucial for generating MNs without up-regulating interneuron genes. These led us to design Isl1-Lhx3, which maintains the desirable 1:1 ratio of Isl1 and Lhx3 and the LIM domain of Lhx3. Isl1-Lhx3 drives MN differentiation with high specificity and efficiency in the spinal cord and embryonic stem cells, bypassing the need for sonic hedgehog (Shh). RNA-seq analysis revealed that Isl1-Lhx3 induces the expression of a battery of MN genes that control various functional aspects of MNs, while suppressing key interneuron genes. Our studies uncover a highly efficient method for directed MN generation and MN gene networks. Our results also demonstrate a general strategy of using embryonic transcription complexes for producing specific cell types from stem cells. PMID:22343290

  7. 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

  8. Estradiol induces gene proximity and MLL-MLLT3 fusion in an activation-induced cytidine deaminase-mediated pathway.

    PubMed

    Wright, Rebecca L; Slemmons, Katherine K; Vaughan, Andrew T M

    2015-05-01

    Epidemiological data have linked birth control formulations to an increased risk of infant acute leukemia involving MLL rearrangements. Reverse transcription polymerase chain reaction (RT-PCR) studies showed that 10 nM estradiol enhanced MLL transcription in addition to its common translocation partners, MLLT2 (AF4) and MLLT3 (AF9). The same concentration of estradiol triggered MLL and MLLT3 co-localization without affecting the interaction of genes located on the same chromosomes. Estradiol also stimulated the generation of MLL-MLLT3 fusion transcripts as seen by RT-PCR. RNAi knockdown of activation-induced cytidine deaminase (AICDA) suppressed the induction of MLL-MLLT3 fusion transcript formation observed with estradiol. Additionally, chromatin immunoprecipitation (ChIP) analysis showed estradiol dependent localization of AICDA in MLL intron 11, upstream of a hotspot for both DNA cleavage and rearrangement, but not downstream within intron 12. Combined, these studies show that levels of estradiol consistent with that observed during pregnancy have the potential to initiate MLL fusions through an AICDA-mediated mechanism.

  9. The promoter region of the arg3 gene in Saccharomyces cerevisiae: nucleotide sequence and regulation in an arg3-lacZ gene fusion.

    PubMed

    Crabeel, M; Huygen, R; Cunin, R; Glansdorff, N

    1983-01-01

    We have determined the DNA sequence for the 5' end of the arg3 gene of Saccharomyces cerevisiae, including part of the coding region and the 200 nucleotides immediately upstream. A promoter-deletion mutant was found to have lost all of the sequence lying normally in front of the gene except for the 33 nucleotides preceding the AUG codon. The role of the 5' domain in initiation and regulation of arg3 transcription was assessed by a gene fusion experiment. The Escherichia coli lacZ gene, was truncated of the eight amino-terminal codons substituted in vitro, on a 2mu plasmid, for the carboxy-terminal and 3'-flanking regions of arg3, leaving only the first 19 proximal codons and approximately 1600 nucleotides of the region preceding arg3 on the yeast chromosome. The fused gene was expressed in phase and was still submitted to the two mechanisms regulating the wild-type arg3 gene: the general, probably transcriptional control of amino acid biosynthesis and the specific, apparently post-transcriptional control mediated by the products of the argR genes. These results suggest a determining role for the 5' end portion of the arg3 messenger in the specific arginine-mediated control mechanism. PMID:11894927

  10. Recurrent NTRK1 Gene Fusions Define a Novel Subset of Locally Aggressive Lipofibromatosis-like Neural Tumors.

    PubMed

    Agaram, Narasimhan P; Zhang, Lei; Sung, Yun-Shao; Chen, Chun-Liang; Chung, Catherine T; Antonescu, Cristina R; Fletcher, Christopher Dm

    2016-10-01

    The family of pediatric fibroblastic and myofibroblastic proliferations encompasses a wide spectrum of pathologic entities with overlapping morphologies and ill-defined genetic abnormalities. Among the superficial lesions, lipofibromatosis (LPF), composed of an admixture of adipose tissue and fibroblastic elements, in the past has been variously classified as infantile fibromatosis or fibrous hamartoma of infancy. In this regard, we have encountered a group of superficial soft tissue tumors occurring in children and young adults, with a notably infiltrative growth pattern reminiscent of LPF, variable cytologic atypia, and a distinct immunoprofile of S100 protein and CD34 reactivity, suggestive of neural differentiation. SOX10 and melanocytic markers were negative in all cases tested. In contrast, a control group of classic LPF displayed bland, monomorphic histology and lacked S100 protein immunoreactivity. To define the pathogenetic abnormalities in these seemingly distinctive groups, we performed RNA sequencing for fusion gene discovery in 2 cases each, followed by screening for any novel alterations identified in a larger cohort representing both entities. The 2 index LPF-like neural tumors (LPF-NT) showed TPR-NTRK1 and TPM3-NTRK1 gene fusions, which were further validated by fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction. Subsequent FISH screening of 14 LPF-NT identified recurrent NTRK1 gene rearrangements in 10 (71%) cases. Of the NTRK1-negative LPF-NT cases, 1 case each showed ROS1 and ALK gene rearrangements. In contrast, none of the 25 classic LPFs showed NTRK1 gene rearrangements, although regional abnormalities were noted in the 1q21-22 region by FISH in a majority of cases. Furthermore, NTRK1 immunostaining was positive only in NTRK1-rearranged S100-positive LPF-NT but negative in classic LPF. These results suggest that NTRK1 oncogenic activation through gene fusion defines a novel and distinct subset of soft

  11. Recurrent NTRK1 Gene Fusions Define a Novel Subset of Locally Aggressive Lipofibromatosis-like Neural Tumors.

    PubMed

    Agaram, Narasimhan P; Zhang, Lei; Sung, Yun-Shao; Chen, Chun-Liang; Chung, Catherine T; Antonescu, Cristina R; Fletcher, Christopher Dm

    2016-10-01

    The family of pediatric fibroblastic and myofibroblastic proliferations encompasses a wide spectrum of pathologic entities with overlapping morphologies and ill-defined genetic abnormalities. Among the superficial lesions, lipofibromatosis (LPF), composed of an admixture of adipose tissue and fibroblastic elements, in the past has been variously classified as infantile fibromatosis or fibrous hamartoma of infancy. In this regard, we have encountered a group of superficial soft tissue tumors occurring in children and young adults, with a notably infiltrative growth pattern reminiscent of LPF, variable cytologic atypia, and a distinct immunoprofile of S100 protein and CD34 reactivity, suggestive of neural differentiation. SOX10 and melanocytic markers were negative in all cases tested. In contrast, a control group of classic LPF displayed bland, monomorphic histology and lacked S100 protein immunoreactivity. To define the pathogenetic abnormalities in these seemingly distinctive groups, we performed RNA sequencing for fusion gene discovery in 2 cases each, followed by screening for any novel alterations identified in a larger cohort representing both entities. The 2 index LPF-like neural tumors (LPF-NT) showed TPR-NTRK1 and TPM3-NTRK1 gene fusions, which were further validated by fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction. Subsequent FISH screening of 14 LPF-NT identified recurrent NTRK1 gene rearrangements in 10 (71%) cases. Of the NTRK1-negative LPF-NT cases, 1 case each showed ROS1 and ALK gene rearrangements. In contrast, none of the 25 classic LPFs showed NTRK1 gene rearrangements, although regional abnormalities were noted in the 1q21-22 region by FISH in a majority of cases. Furthermore, NTRK1 immunostaining was positive only in NTRK1-rearranged S100-positive LPF-NT but negative in classic LPF. These results suggest that NTRK1 oncogenic activation through gene fusion defines a novel and distinct subset of soft

  12. Differential gene expression in nematode-induced feeding structures of transgenic plants harbouring promoter-gusA fusion constructs.

    PubMed

    Goddijn, O J; Lindsey, K; van der Lee, F M; Klap, J C; Sijmons, P C

    1993-11-01

    Sedentary plant-parasitic nematodes are able to induce specialized feeding structures in the root system of their host plants by triggering a series of dramatic cellular responses. These changes presumably are accompanied by a reprogramming of gene expression. To monitor such changes, a variety of promoter-gusA fusion constructs were introduced into Arabidopsis and tobacco. Transgenic plants were analysed histochemically for GUS activity in the nematode feeding structures after infection with either Heterodera schachtii or Meloidogyne incognita. Promoters of the Cauliflower Mosaic Virus 35S gene, the bacterial nopaline synthase, rooting loci (rol) and T-cyt genes and the plant-derived phenylalanine ammonia-lyase I gene, which are highly active in non-infected roots, were all downregulated in the feeding structures as indicated by the strong decrease of GUS activity inside these structures. Less stringent downregulation was observed with chimeric gusA fusion constructs harbouring truncated rolB and rolC promoter sequences. Similar observations were made with transgenic Arabidopsis lines that carried randomly integrated promoterless gusA constructs to identify regulatory sequences in the plant genome. Most of the lines that were selected for expression in the root vascular cylinder demonstrated local downregulation in feeding structures after infection with H. schachtii. The reverse pattern of GUS activity, a blue feeding structure amidst unstained root cells, was also found in several lines. However, GUS activity that was entirely specific for the feeding structures was not observed. Our data show that the expression of a large number of genes is influenced during the development of the nematode feeding structures.

  13. 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.

  14. 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.

  15. Sequence analysis of the fusion protein gene from infectious salmon anemia virus isolates: evidence of recombination and reassortment.

    PubMed

    Devold, M; Karlsen, M; Nylund, A

    2006-07-01

    Studies of infectious salmon anemia virus (ISAV; genus Isavirus, family Orthomyxoviridae) haemagglutinin-esterase (HE) gene sequences have shown that this gene provides a tool for genotyping and, hence, a tool to follow the dissemination of ISAV. The problem with using only the HE gene is that ISAV has a segmented genome and one segment may not tell the whole story about the origin and history of ISAV from outbreaks. To achieve a better genotyping system, the present study has focused on segment 5, the fusion (F) protein gene, which contains sequence variation at about the same level as the HE gene. The substitution rates of the HE and F gene sequences, based on 54 Norwegian ISAV isolates, are 6.1(+/-0.3)x10(-6) and 8.6(+/-5.0)x10(-5) nt per site per year, respectively. The results of phylogenetic analysis of the two gene segments have been compared and, with the exception of a few cases of reassortment, they tell the same story about the ISAV isolates. A combination of the two segments is recommended as a tool for future genotyping of ISAV. Inserts (INs) of 8-11 aa may occur close to the cleavage site of the precursor F(0) protein in some ISAV isolates. The nucleotide sequence of two of these INs shows 100% sequence identity to parts of the 5' end of the F protein gene, whilst the third IN is identical to a part of the nucleoprotein gene. This shows that recombination is one of the evolutionary mechanisms shaping the genome of ISAV. The possible importance of the INs with respect to virulence remains uncertain. PMID:16760406

  16. Protein-protein fusion catalyzed by sortase A.

    PubMed

    Levary, David A; Parthasarathy, Ranganath; Boder, Eric T; Ackerman, Margaret E

    2011-04-06

    Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.

  17. Protein-Protein Fusion Catalyzed by Sortase A

    PubMed Central

    Levary, David A.; Parthasarathy, Ranganath; Boder, Eric T.; Ackerman, Margaret E.

    2011-01-01

    Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality — demonstrating the robust and facile nature of this reaction. PMID:21494692

  18. Analysis of a MULE-cyanide hydratase gene fusion in Verticillium dahliae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the phytopathogenic fungus Verticillium dahliae encodes numerous Class II “cut-and-paste” transposable elements, including those of a small group of MULE transposons. We have previously identified a fusion event between a MULE transposon sequence and sequence encoding a cyanide hydrata...

  19. An MSC2 Promoter-lacZ Fusion Gene Reveals Zinc-Responsive Changes in Sites of Transcription Initiation That Occur across the Yeast Genome

    PubMed Central

    Wu, Yi-Hsuan; Taggart, Janet; Song, Pamela Xiyao; MacDiarmid, Colin; Eide, David J.

    2016-01-01

    The Msc2 and Zrg17 proteins of Saccharomyces cerevisiae form a complex to transport zinc into the endoplasmic reticulum. ZRG17 is transcriptionally induced in zinc-limited cells by the Zap1 transcription factor. In this report, we show that MSC2 mRNA also increases (~1.5 fold) in zinc-limited cells. The MSC2 gene has two in-frame ATG codons at its 5’ end, ATG1 and ATG2; ATG2 is the predicted initiation codon. When the MSC2 promoter was fused at ATG2 to the lacZ gene, we found that unlike the chromosomal gene this reporter showed a 4-fold decrease in lacZ mRNA in zinc-limited cells. Surprisingly, β-galactosidase activity generated by this fusion gene increased ~7 fold during zinc deficiency suggesting the influence of post-transcriptional factors. Transcription of MSC2ATG2-lacZ was found to start upstream of ATG1 in zinc-replete cells. In zinc-limited cells, transcription initiation shifted to sites just upstream of ATG2. From the results of mutational and polysome profile analyses, we propose the following explanation for these effects. In zinc-replete cells, MSC2ATG2-lacZ mRNA with long 5’ UTRs fold into secondary structures that inhibit translation. In zinc-limited cells, transcripts with shorter unstructured 5’ UTRs are generated that are more efficiently translated. Surprisingly, chromosomal MSC2 did not show start site shifts in response to zinc status and only shorter 5’ UTRs were observed. However, the shifts that occur in the MSC2ATG2-lacZ construct led us to identify significant transcription start site changes affecting the expression of ~3% of all genes. Therefore, zinc status can profoundly alter transcription initiation across the yeast genome. PMID:27657924

  20. EWSR1-POU5F1 fusion in soft tissue myoepithelial tumors. A molecular analysis of sixty-six cases, including soft tissue, bone, and visceral lesions, showing common involvement of the EWSR1 gene.

    PubMed

    Antonescu, Cristina R; Zhang, Lei; Chang, Ning-En; Pawel, Bruce R; Travis, William; Katabi, Nora; Edelman, Morris; Rosenberg, Andrew E; Nielsen, G Petur; Dal Cin, Paola; Fletcher, Christopher D M

    2010-12-01

    The diagnosis of myoepithelial (ME) tumors outside salivary glands remains challenging, especially in unusual clinical presentations, such as bone or visceral locations. A few reports have indicated EWSR1 gene rearrangement in soft tissue ME tumors, and, in one case each, the fusion partner was identified as either PBX1 or ZNF444. However, larger studies to investigate whether these genetic abnormalities are recurrent or restricted to tumors in soft tissue locations are lacking. Sixty-six ME tumors mainly from soft tissue (71%), but also from skin, bone, and visceral locations, characterized by classic morphological features and supporting immunoprofile were studied. Gene rearrangements in EWSR1, FUS, PBX1, and ZNF444 were investigated by fluorescence in situ hybridization. EWSR1 gene rearrangement was detected in 45% of the cases. A EWSR1-POU5F1 fusion was identified in a pediatric soft tissue tumor by 3'Rapid Amplification of cDNA Euds (RACE) and subsequently confirmed in four additional soft tissue tumors in children and young adults. An EWSR1-PBX1 fusion was seen in five cases, whereas EWSR1-ZNF444 and FUS gene rearrangement was noted in one pulmonary tumor each. In conclusion, EWSR1 gene rearrangement is a common event in ME tumors arising outside salivary glands, irrespective of anatomical location. EWSR1-negative tumors were more often benign, superficially located, and showed ductal differentiation, suggesting the possibility of genetically distinct groups. A subset of soft tissue ME tumors with clear cell morphology harbor an EWSR1-POU5F1 fusion, which can be used as a molecular diagnostic test in difficult cases. These findings do not support a pathogenetic relationship between soft tissue ME tumors and their salivary gland counterparts.

  1. Synergistic antitumor effect of a human papillomavirus DNA vaccine harboring E6E7 fusion gene and vascular endothelial growth factor receptor 2 gene.

    PubMed

    Gao, Jie; Fan, Lei; Ma, Wei; Xiao, Huan

    2016-09-01

    Human papillomavirus (HPV) has been identified as the primary etiological factor in cervical cancer as well as in subsets of anogenital and oropharyngeal cancers. The two HPV viral oncoproteins, E6 and E7, are uniquely and consistently expressed in all HPV-infected cells and are therefore promising targets for therapeutic vaccination. In order to achieve a synergistic antitumor and anti-angiogenesis effect, we designed and constructed a novel DNA vaccine that can express the HPV 16 E6E7 fusion protein and VEGFR2 in the same reading frame. A series of DNA plasmids encoding E6E7, VEGFR2 and their conjugates were constructed and injected into mice. The resultant humoral and cellular immune responses were detected by ELISA and enzyme-linked immunospot (ELISPOT), respectively. To evaluate the antitumor efficacy of these plasmids, tumor-bearing mice expressing the E6E7 fusion protein were constructed. After injection into the tumor-bearing mouse model, the plasmid harboring the E6E7 fusion gene and VEGFR2 showed stronger inhibition of tumor growth than the plasmid expressing E6E7 or VEGFR2 alone, which indicated that the combination of E6E7 and VEGFR2 could exert a synergistic antitumor effect. These observations emphasize the potential of a synergistic antitumor and anti-angiogenesis strategy using a DNA vaccine, which could be a promising approach for tumor immunotherapy. PMID:27515281

  2. Biosensing of BCR/ABL fusion gene using an intensity-interrogation surface plasmon resonance imaging system

    NASA Astrophysics Data System (ADS)

    Wu, Jiangling; Huang, Yu; Bian, Xintong; Li, DanDan; Cheng, Quan; Ding, Shijia

    2016-10-01

    In this work, a custom-made intensity-interrogation surface plasmon resonance imaging (SPRi) system has been developed to directly detect a specific sequence of BCR/ABL fusion gene in chronic myelogenous leukemia (CML). The variation in the reflected light intensity detected from the sensor chip composed of gold islands array is proportional to the change of refractive index due to the selective hybridization of surface-bound DNA probes with target ssDNA. SPRi measurements were performed with different concentrations of synthetic target DNA sequence. The calibration curve of synthetic target sequence shows a good relationship between the concentration of synthetic target and the change of reflected light intensity. The detection limit of this SPRi measurement could approach 10.29 nM. By comparing SPRi images, the target ssDNA and non-complementary DNA sequence are able to be distinguished. This SPRi system has been applied for assay of BCR/ABL fusion gene extracted from real samples. This nucleic acid-based SPRi biosensor therefore offers an alternative high-effective, high-throughput label-free tool for DNA detection in biomedical research and molecular diagnosis.

  3. Amplification-Free Detection of Gene Fusions in Prostate Cancer Urinary Samples Using mRNA-Gold Affinity Interactions.

    PubMed

    Koo, Kevin M; Carrascosa, Laura G; Shiddiky, Muhammad J A; Trau, Matt

    2016-07-01

    A crucial issue in present-day prostate cancer (PCa) detection is the lack of specific biomarkers for accurately distinguishing between benign and malignant cancer forms. This is causing a high degree of overdiagnosis and overtreatment of otherwise clinically insignificant cases. As around half of all malignant PCa cases display a detectable gene fusion mutation between the TMPRSS2 promoter sequence and the ERG coding sequence (TMPRSS2:ERG) in urine, noninvasive screening of TMPRSS2:ERG mRNA in patient urine samples could improve the specificity of current PCa diagnosis. However, current gene fusion detection methodologies are largely dependent on RNA enzymatic amplification, which requires extensive sample manipulation, costly labels for detection, and is prone to bias/artifacts. Herein we introduce the first successful amplification-free electrochemical assay for direct detection of TMPRSS2:ERG mRNA in PCa urinary samples by selectively isolating and adsorbing TMPRSS2:ERG mRNA onto bare gold electrodes without requiring any surface modification. We demonstrated excellent limit-of-detection (10 cells) and specificity using PCa cell line models, and showcased clinical utility by accurately detecting TMPRSS2:ERG in a collection of 17 urinary samples obtained from PCa patients. Furthermore, these results were validated with the current gold standard reverse transcription (RT)-PCR approach with 100% concordance. PMID:27299694

  4. 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

  5. Use of the promoter fusion transposon Tn5 lac to identify mutations in Bordetella pertussis vir-regulated genes.

    PubMed

    Weiss, A A; Melton, A R; Walker, K E; Andraos-Selim, C; Meidl, J J

    1989-09-01

    Mutants of Bordetella pertussis deficient in virulence-associated factors were identified by using the transposon Tn5 lac. Tn5 lac is a derivative of Tn5 which generates promoter fusions for beta-galactosidase. Tn5 lac insertions in the vir-regulated genes of B. pertussis were identified by selecting for kanamycin-resistant mutants that expressed beta-galactosidase when the vir-regulated genes were expressed but not when the vir-regulated genes were turned off. Fourteen different mutations in vir-regulated genes were identified. Two mutants were deficient in the production of the filamentous hemagglutinin, two mutants were deficient in the production of adenylate cyclase toxin and hemolysin, and one mutant was deficient in the production of dermonecrotic toxin. One insertion mapped adjacent to the pertussis toxin gene, but the mutant produced pertussis toxin. The phenotypes of the remaining eight mutants were not determined, but the mutants did not appear to be deficient in the production of the 69,000-dalton outer membrane protein (agglutinogen 3) or the capsule. Screening for mutations in either of the fimbrial genes proved to be problematic since the parental strain was found to switch from a fimbriated to a nonfimbriated state at a high frequency, which was suggestive of the metastable expression of pili in other bacteria. We used Southern blot analysis with a 30-mer specific for the fimbrial sequences. No bands with the predicted increase in size due to the 12 kilobases from Tn5 lac were observed, which suggests that none of these genes were mutated. Southern blot analysis also revealed that seven of the eight unidentified mutations mapped to different restriction fragments, which suggests that they could be deficient in as many as seven different genes. PMID:2569447

  6. Use of the promoter fusion transposon Tn5 lac to identify mutations in Bordetella pertussis vir-regulated genes.

    PubMed Central

    Weiss, A A; Melton, A R; Walker, K E; Andraos-Selim, C; Meidl, J J

    1989-01-01

    Mutants of Bordetella pertussis deficient in virulence-associated factors were identified by using the transposon Tn5 lac. Tn5 lac is a derivative of Tn5 which generates promoter fusions for beta-galactosidase. Tn5 lac insertions in the vir-regulated genes of B. pertussis were identified by selecting for kanamycin-resistant mutants that expressed beta-galactosidase when the vir-regulated genes were expressed but not when the vir-regulated genes were turned off. Fourteen different mutations in vir-regulated genes were identified. Two mutants were deficient in the production of the filamentous hemagglutinin, two mutants were deficient in the production of adenylate cyclase toxin and hemolysin, and one mutant was deficient in the production of dermonecrotic toxin. One insertion mapped adjacent to the pertussis toxin gene, but the mutant produced pertussis toxin. The phenotypes of the remaining eight mutants were not determined, but the mutants did not appear to be deficient in the production of the 69,000-dalton outer membrane protein (agglutinogen 3) or the capsule. Screening for mutations in either of the fimbrial genes proved to be problematic since the parental strain was found to switch from a fimbriated to a nonfimbriated state at a high frequency, which was suggestive of the metastable expression of pili in other bacteria. We used Southern blot analysis with a 30-mer specific for the fimbrial sequences. No bands with the predicted increase in size due to the 12 kilobases from Tn5 lac were observed, which suggests that none of these genes were mutated. Southern blot analysis also revealed that seven of the eight unidentified mutations mapped to different restriction fragments, which suggests that they could be deficient in as many as seven different genes. Images PMID:2569447

  7. Genes encoding Cher-TPR fusion proteins are predominantly found in gene clusters encoding chemosensory pathways with alternative cellular functions.

    PubMed

    Muñoz-Martínez, Francisco; García-Fontana, Cristina; Rico-Jiménez, Miriam; Alfonso, Carlos; Krell, Tino

    2012-01-01

    Chemosensory pathways correspond to major signal transduction mechanisms and can be classified into the functional families flagellum-mediated taxis, type four pili-mediated taxis or pathways with alternative cellular functions (ACF). CheR methyltransferases are core enzymes in all of these families. CheR proteins fused to tetratricopeptide repeat (TPR) domains have been reported and we present an analysis of this uncharacterized family. We show that CheR-TPRs are widely distributed in GRAM-negative but almost absent from GRAM-positive bacteria. Most strains contain a single CheR-TPR and its abundance does not correlate with the number of chemoreceptors. The TPR domain fused to CheR is comparatively short and frequently composed of 2 repeats. The majority of CheR-TPR genes were found in gene clusters that harbor multidomain response regulators in which the REC domain is fused to different output domains like HK, GGDEF, EAL, HPT, AAA, PAS, GAF, additional REC, HTH, phosphatase or combinations thereof. The response regulator architectures coincide with those reported for the ACF family of pathways. Since the presence of multidomain response regulators is a distinctive feature of this pathway family, we conclude that CheR-TPR proteins form part of ACF type pathways. The diversity of response regulator output domains suggests that the ACF pathways form a superfamily which regroups many different regulatory mechanisms, in which all CheR-TPR proteins appear to participate. In the second part we characterize WspC of Pseudomonas putida, a representative example of CheR-TPR. The affinities of WspC-Pp for S-adenosylmethionine and S-adenosylhomocysteine were comparable to those of prototypal CheR, indicating that WspC-Pp activity is in analogy to prototypal CheRs controlled by product feed-back inhibition. The removal of the TPR domain did not impact significantly on the binding constants and consequently not on the product feed-back inhibition. WspC-Pp was found to be

  8. 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

  9. 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. PMID:27507942

  10. Enhanced green fluorescent protein fusion proteins of herpes simplex virus type 1 thymidine kinase and cytochrome P450 4B1: applications for prodrug-activating gene therapy.

    PubMed

    Steffens, S; Frank, S; Fischer, U; Heuser, C; Meyer, K L; Dobberstein, K U; Rainov, N G; Kramm, C M

    2000-05-01

    To monitor therapeutic transgene expression, we developed fusion genes of enhanced green fluorescent protein (EGFP) with two different prodrug-activating enzyme genes: herpes simplex virus type 1 thymidine kinase (HSV-tk) and rabbit cytochrome P450 4B1 (cyp4b1). Expression of the resulting fusion proteins, TK-EGFP and 4B1-EGFP, rendered transduced human and rodent glioma cells sensitive to cytotoxic treatment with the corresponding prodrugs ganciclovir and 4-ipomeanol. Ganciclovir and 4-ipomeanol sensitivity was comparable with that achieved with the native HSV-TK and CYP4B1 proteins. As shown by fluorescence microscopy, TK-EGFP was expressed predominantly intranuclearly, whereas 4B1-EGFP was detectable in the cytoplasm, thereby displaying the orthotopic subcellular distribution of the corresponding native enzymes. The fluorescence intensity correlated well with the corresponding prodrug sensitivity, as shown by fluorescence-activated cell sorter analysis. EGFP expression was also used for the selection of stably HSV-tk-transduced cells by flow cytometric cell sorting. Resulting cell populations showed a homogeneity of fluorescence intensity similar to single-cell clones after antibiotic selection. In conclusion, tk-egfp and 4b1-egfp fusion genes are valuable tools for monitoring prodrug-activating gene therapy in living cells. EGFP fusion genes/proteins provide a simple and reproducible means for the detection, selection, and characterization of cells expressing enzyme genes for prodrug activation.

  11. Adverse Event Recording and Reporting in Clinical Trials Comparing Lumbar Disk Replacement with Lumbar Fusion: A Systematic Review.

    PubMed

    Hiratzka, Jayme; Rastegar, Farbod; Contag, Alec G; Norvell, Daniel C; Anderson, Paul A; Hart, Robert A

    2015-12-01

    Study Design Systematic review. Objectives (1) To compare the quality of adverse event (AE) methodology and reporting among randomized trials comparing lumbar fusion with lumbar total disk replacement (TDR) using established AE reporting systems; (2) to compare the AEs and reoperations of lumbar spinal fusion with those from lumbar TDR; (3) to make recommendations on how to report AEs in randomized controlled trials (RCTs) so that surgeons and patients have more-detailed and comprehensive information when making treatment decisions. Methods A systematic search of PubMed, the Cochrane collaboration database, and the National Guideline Clearinghouse through May 2015 was conducted. Randomized controlled trials with at least 2 years of follow-up comparing lumbar artificial disk replacement with lumbar fusion were included. Patients were required to have axial or mechanical low back pain of ≥3 months' duration due to degenerative joint disease defined as degenerative disk disease, facet joint disease, or spondylosis. Outcomes included the quality of AE acquisition methodology and results reporting, and AEs were defined as those secondary to the procedure and reoperations. Individual and pooled relative risks and their 95% confidence intervals comparing lumbar TDR with fusion were calculated. Results RCTs demonstrated a generally poor description of methods for assessing AEs. There was a consistent lack of clear definition or grading for these events. Furthermore, there was a high degree of variation in reporting of surgery-related AEs. Most studies lacked adequate reporting of the timing of AEs, and there were no clear distinctions between acute or chronic AEs. Meta-analysis of the pooled data demonstrated a twofold increased risk of AEs in patients having lumbar fusion compared with patients having lumbar TDR at 2-year follow-up, and this relative risk was maintained at 5 years. Furthermore, the pooled data demonstrated a 1.7 times greater relative risk of

  12. Gene identification and analysis: an application of neural network-based information fusion

    SciTech Connect

    Matis, S.; Xu, Y.; Shah, M.B.; Mural, R.J.; Einstein, J.R.; Uberbacher, E.C.

    1996-10-01

    Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. We describe a gene localization and modeling system called GRAIL. GRAIL is a multiple sensor-neural network based system. It localizes genes in anonymous DNA sequence by recognizing gene features related to protein-coding slice sites, and then combines the recognized features using a neural network system. Localized coding regions are then optimally parsed into a gene mode. RNA polymerase II promoters can also be predicted. Through years of extensive testing, GRAIL consistently localizes about 90 percent of coding portions of test genes with a false positive rate of about 10 percent. A number of genes for major genetic diseases have been located through the use of GRAIL, and over 1000 research laboratories worldwide use GRAIL on regular bases for localization of genes on their newly sequenced DNA.

  13. Spinal fusion

    MedlinePlus

    ... Anterior spinal fusion; Spine surgery - spinal fusion; Low back pain - fusion; Herniated disk - fusion ... If you had chronic back pain before surgery, you will likely still have some pain afterward. Spinal fusion is unlikely to take away all your pain ...

  14. Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment.

    PubMed Central

    Menzel, R; Gellert, M

    1987-01-01

    We have previously shown that the genes encoding the two subunits of Escherichia coli DNA gyrase are regulated in a manner which is dependent on DNA conformation. When the DNA encoding the gyrA and gyrB genes is relaxed, both genes are expressed at a high level; in negatively supercoiled DNA they are expressed at a low level. In this paper we describe fusions of both the gyrA and gyrB 5' sequences to the E. coli galactokinase gene. In such fusions we found that galactokinase can be induced by treating the cells with coumermycin A1, an inhibitor of DNA gyrase. Our results suggest that the regulation occurs at the transcriptional level and that only a small region of DNA is necessary for coumermycin-induced gene expression. PMID:3029031

  15. Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.

    PubMed

    Gawryluk, Ryan M R; Eme, Laura; Roger, Andrew J

    2015-10-01

    ATP citrate lyase (ACL) is an enzyme critical to the generation of cytosolic acetyl-CoA in eukaryotes. In most studied organisms, ACL activity is conferred in combination by two proteins, ACLA and ACLB (dsACL); however, animals encode a single-subunit ACL (ssACL) - the result of a gene fusion event. Through phylogenetic analyses, we investigated the evolution of ACL in a broad range of eukaryotes, including numerous microbes (protists). We show that the fused form is not restricted to animals, and is instead widely distributed among eukaryotes. Furthermore, ssACL and dsACL are patchily distributed and appear to be mutually exclusive; both types arose early in eukaryotic evolution. Finally, we present several compelling hypotheses of lateral gene transfer and gene loss, along with the secondary gene fission of ssACL in Ascomycota. Collectively, our in-depth analyses suggest that a complex suite of evolutionary events, usually considered rare, has shaped the evolution of ACL in eukaryotes.

  16. Posterior spinal instrumented fusion for idiopathic scoliosis in patients with multisystemic neurodegenerative disorder: a report of two cases.

    PubMed

    Loh, K W; Chan, C Yw; Chiu, C K; Bin Hasan, M S; Kwan, M K

    2016-08-01

    Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke (MELAS) syndrome is a progressive multisystemic neurodegenerative disorder. MELAS syndrome impairs oxidative phosphorylation and predisposes patients to lactic acidosis, particularly under metabolic stress. We report 2 siblings with MELAS-associated idiopathic scoliosis who underwent posterior spinal instrumented fusion with measures taken to minimise anaesthetic and surgical stress, blood loss, and operating time. PMID:27574278

  17. LLE 1998 annual report, October 1997--September 1998. Inertial fusion program and National Laser Users` Facility program

    SciTech Connect

    1999-01-01

    This report summarizes research at the Laboratory for Laser Energetics (LLE), the operation of the National Laser Users` Facility (NLUF), and programs involving the education of high school, undergraduate, and graduate students for FY98. Research summaries cover: progress in laser fusion; diagnostic development; laser and optical technology; and advanced technology for laser targets.

  18. Code development incorporating environmental, safety, and economic aspects of fusion reactors (FY 92--94). Final report

    SciTech Connect

    Ho, S.K.; Fowler, T.K.; Holdren, J.P.

    1994-11-01

    This is the Final Report for a three-year (FY 92--94) study of the Environmental, Safety, and Economic (ESE) aspects of fusion energy systems, emphasizing development of computerized approaches suitable for incorporation as modules in fusion system design codes. First, as is reported in Section 2, the authors now have operating a simplified but complete environment and safety evaluation code, BESAFE. The first tests of BESAFE as a module of the SUPERCODE, a design optimization systems code at LLNL, are reported in Section 3. Secondly, as reported in Section 4, the authors have maintained a strong effort in developing fast calculational schemes for activation inventory evaluation. In addition to these major accomplishments, considerable progress has been made on research on specific topics as follows. A tritium modeling code TRIDYN was developed in collaboration with the TSTA group at LANL and the Fusion Nuclear Technology group at UCLA. A simplified algorithm has been derived to calculate the transient temperature profiles in the blanket during accidents. The scheme solves iteratively a system of non-linear ordinary differential equations describing about 10 regions of the blanket by preserving energy balance. The authors have studied the physics and engineering aspects of divertor modeling for safety applications. Several modifications in the automation and characterization of environmental and safety indices have been made. They have applied this work to the environmental and safety comparisons of stainless steel with alternative structural materials for fusion reactors. A methodology in decision analysis utilizing influence and decision diagrams has been developed to model fusion reactor design problems. Most of the work during this funding period has been reported in 26 publications including theses, journal publications, conference papers, and technical reports, as listed in Section 11.

  19. Workshop on Accelerators for Heavy Ion Fusion: Summary Report of the Workshop

    SciTech Connect

    Seidl, P.A.; Barnard, J.J.

    2011-04-29

    The Workshop on Accelerators for Heavy Ion Fusion was held at Lawrence Berkeley National Laboratory May 23-26, 2011. The workshop began with plenary sessions to review the state of the art in HIF (heavy ion fusion), followed by parallel working groups, and concluded with a plenary session to review the results. There were five working groups: IFE (inertial fusion energy) targets, RF approach to HIF, induction accelerator approach to HIF, chamber and driver interface, ion sources and injectors.

  20. Inertial confinement fusion. ICF quarterly report, October 1993--December 1993, Volume 4, Number 1

    SciTech Connect

    Powell, H.T.; Schleich, D.P.; Murphy, P.W.

    1994-05-01

    In the 1990 National Academy of Sciences (NAS) report of its review of the U.S. Inertial Confinement Fusion (ICF) Program, it was recommended that a high priority be placed on completing the Precision Nova Project and its associated experimental campaign. Since fiscal year 1990, the lab has therefore campaigned vigorously on Nova and in its supporting laboratories to develop the Precision Nova capabilities needed to perform the stressful target experiments recommended in the 1990 NAS report. The activities to enable these experiments have been directed at improvements in three areas - the Nova laser, target fabrication capabilities, and target diagnostics. As summarized in the five articles in this report, the Precision Nova improvements have been successfully completed. These improvements have had a positive impact on target performance and on the ability to diagnose the results, as evidenced by the HEP-1 experimental results. The five articles generally concentrate on improvements to the capabilities rather than on the associated target physics experiments. Separate abstracts are included for each paper.

  1. Inertial Confinement Fusion quarterly report, January-March 1998, volume 8, number 2

    SciTech Connect

    Kruer, W

    1998-03-31

    The coupling of laser light with plasmas is one of the key physics issues for the use of high-power lasers for inertial fusion, high-energy-density physics, and scientific stockpile stewardship. The coupling physics is extremely rich and challenging, particularly in the large plasmas to be accessed on the National Ignition Facility (NIF). The coupling mechanisms span the gamut from classical inverse bremsstrahlung absorption to a variety of nonlinear optical processes. These include stimulated Raman scattering (SRS) from electron plasma waves, stimulated Brillouin scattering (SBS) from ion sound waves, resonant decay into electron plasma and ion sound waves, and laser beam filamentation. These processes depend on laser intensity and produce effects such as changes in the efficiency and location of the energy deposition or generation of a component of very energetic electrons, which can preheat capsules. Coupling physics issues have an extremely high leverage. The coupling models are clearly very important ingredients for detailed calculations of laser-irradiated target behavior. Improved understanding and models enable a more efficient use of laser facilities, which becomes even more important as these facilities become larger and more expensive. Advances in the understanding also allow a more timely and cost-effective identification of new applications of high-power lasers, such as for generation of high-temperature hohlraums and compact x-ray sources, or for discovery of advanced fusion schemes. Finally, the interaction of intense electromagnetic waves with ionized media is a fundamental topic of interest to numerous areas of applied science and is an excellent test bed for advancing plasma science and computational modeling of complex phenomena. This issue of the ICF Quarterly Report is dedicated to laser--plasma interactions. The eight articles present a cross section of the broad progress in understanding the key interaction issues, such as laser beam bending

  2. Celastrol Suppresses Tumor Cell Growth through Targeting an AR-ERG-NF-κB Pathway in TMPRSS2/ERG Fusion Gene Expressing Prostate Cancer

    PubMed Central

    Cai, Yi; Castro, Patricia; Dakhov, Olga; Shi, Ping; Bai, Yaoxia; Ji, Huixiang; Shen, Wenhao; Wang, Jianghua

    2013-01-01

    The TMPRSS2/ERG (T/E) fusion gene is present in the majority of all prostate cancers (PCa). We have shown previously that NF-kB signaling is highly activated in these T/E fusion expressing cells via phosphorylation of NF-kB p65 Ser536 (p536). We therefore hypothesize that targeting NF-kB signaling may be an efficacious approach for the subgroup of PCas that carry T/E fusions. Celastrol is a well known NF-kB inhibitor, and thus may inhibit T/E fusion expressing PCa cell growth. We therefore evaluated Celastrol’s effects in vitro and in vivo in VCaP cells, which express the T/E fusion gene. VCaP cells were treated with different concentrations of Celastrol and growth inhibition and target expression were evaluated. To test its ability to inhibit growth in vivo, 0.5 mg/kg Celastrol was used to treat mice bearing subcutaneous VCaP xenograft tumors. Our results show Celastrol can significantly inhibit the growth of T/E fusion expressing PCa cells both in vitro and in vivo through targeting three critical signaling pathways: AR, ERG and NF-kB in these cells. When mice received 0.5 mg/kg Celastrol for 4 times/week, significant growth inhibition was seen with no obvious toxicity or significant weight loss. Therefore, Celastrol is a promising candidate drug for T/E fusion expressing PCa. Our findings provide a novel strategy for the targeted therapy which may benefit the more than half of PCa patients who have T/E fusion expressing PCas. PMID:23554889

  3. The t(10;11)(p13;q14) in the U937 cell line results in the fusion of the AF10 gene and CALM, encoding a new member of the AP-3 clathrin assembly protein family.

    PubMed Central

    Dreyling, M H; Martinez-Climent, J A; Zheng, M; Mao, J; Rowley, J D; Bohlander, S K

    1996-01-01

    The translocation t(10;11)(p13;q14) is a recurring chromosomal abnormality that has been observed in patients with acute lymphoblastic leukemia as well as acute myeloid leukemia. We have recently reported that the monocytic cell line U937 has a t(10;11)(p13;q14) translocation. Using a combination of positional cloning and candidate gene approach, we cloned the breakpoint and were able to show that AF10 is fused to a novel gene that we named CALM (Clathrin Assembly Lymphoid Myeloid leukemia gene) located at 11q14. AF10, a putative transcription factor, had recently been cloned as one of the fusion partners of MLL. CALM has a very high homology in its N-terminal third to the murine ap-3 gene which is one of the clathrin assembly proteins. The N-terminal region of ap-3 has been shown to bind to clathrin and to have a high-affinity binding site for phosphoinositols. The identification of the CALM/AF10 fusion gene in the widely used U937 cell line will contribute to our understanding of the malignant phenotype of this line. Images Fig. 1 Fig. 3 PMID:8643484

  4. IFMIF, International Fusion Materials Irradiation Facility conceptual design activity cost report

    SciTech Connect

    Rennich, M.J.

    1996-12-01

    This report documents the cost estimate for the International Fusion Materials Irradiation Facility (IFMIF) at the completion of the Conceptual Design Activity (CDA). The estimate corresponds to the design documented in the Final IFMIF CDA Report. In order to effectively involve all the collaborating parties in the development of the estimate, a preparatory meeting was held at Oak Ridge National Laboratory in March 1996 to jointly establish guidelines to insure that the estimate was uniformly prepared while still permitting each country to use customary costing techniques. These guidelines are described in Section 4. A preliminary cost estimate was issued in July 1996 based on the results of the Second Design Integration Meeting, May 20--27, 1996 at JAERI, Tokai, Japan. This document served as the basis for the final costing and review efforts culminating in a final review during the Third IFMIF Design Integration Meeting, October 14--25, 1996, ENEA, Frascati, Italy. The present estimate is a baseline cost estimate which does not apply to a specific site. A revised cost estimate will be prepared following the assignment of both the site and all the facility responsibilities.

  5. Inertial Confinement Fusion Target Component Fabrication and Technology Development report. Annual report, October 1, 1992--September 30, 1993

    SciTech Connect

    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.

  6. Construction, expression and immunoassay detection of recombinant plasmid encoding fusion protein of Roman chicken complement C3d and Newcastle disease virus F gene.

    PubMed

    Liu, D; Niu, Z-X

    2008-12-01

    The terminal degradation product (C3d) of mammalian complement component C3 plays an important role in modulation of the adaptive immune response through the interaction with complement receptor type 2 (CR2) on B cells. In this study, the gene fragment coding for the complement protein C3d (chC3d) from Roman chicken was cloned and expressed as a fusion protein for its application in the vaccine study of chicken, and for in vitro experiments. The chC3d fragment strengthened B-cell responses when complexed with antigen. Three potential vaccine construct units were engineered to contain two, four and six copies of chC3d coding gene linked to the F gene of Newcastle disease virus (NDV), an economically important pathogen of chicken that is classified as a list A contagious disease of poultry by the Office International des Epizooties. The cloned chC3d protein and different repeats of C3d proteins in addition to the F gene of NDV were generated separately in Escherichia coli and chicken embryo fibroblast cells with the help of expression vectors. All recombinant proteins were analysed by SDS-PAGE and Western blotting. Analysis of the immunogenicity of different repeats of C3d revealed that chC3d had an enhancing effect on the immunogenicity of antigens, and that six or more repeats of C3d may be necessary for efficient enhancement of antigen-specific immune responses. To date, published research into the adjuvant activities of C3d has been limited to experiments in mice, rabbits and cattle. The adjuvant properties of C3d have not been assessed in poultry using homologous C3d in association with antigens relevant to the target species. The Roman chicken C3d fusion proteins described in this study is the first report and will provide a basis for immunization trials in chicken, studies of receptor binding and cell activation of chicken lymphocytes, and investigations of new types of vaccines, including recombinant vaccines and DNA vaccines for future use against other

  7. Use of the Aspergillus oryzae actin gene promoter in a novel reporter system for exploring antifungal compounds and their target genes.

    PubMed

    Marui, Junichiro; Yoshimi, Akira; Hagiwara, Daisuke; Fujii-Watanabe, Yoshimi; Oda, Ken; Koike, Hideaki; Tamano, Koichi; Ishii, Tomoko; Sano, Motoaki; Machida, Masayuki; Abe, Keietsu

    2010-08-01

    Demand for novel antifungal drugs for medical and agricultural uses has been increasing because of the diversity of pathogenic fungi and the emergence of drug-resistant strains. Genomic resources for various living species, including pathogenic fungi, can be utilized to develop novel and effective antifungal compounds. We used Aspergillus oryzae as a model to construct a reporter system for exploring novel antifungal compounds and their target genes. The comprehensive gene expression analysis showed that the actin-encoding actB gene was transcriptionally highly induced by benomyl treatment. We therefore used the actB gene to construct a novel reporter system for monitoring responses to cytoskeletal stress in A. oryzae by introducing the actB promoter::EGFP fusion gene. Distinct fluorescence was observed in the reporter strain with minimum background noise in response to not only benomyl but also compounds inhibiting lipid metabolism that is closely related to cell membrane integrity. The fluorescent responses indicated that the reporter strain can be used to screen for lead compounds affecting fungal microtubule and cell membrane integrity, both of which are attractive antifungal targets. Furthermore, the reporter strain was shown to be technically applicable for identifying novel target genes of antifungal drugs triggering perturbation of fungal microtubules or membrane integrity.

  8. TALE-PvuII fusion proteins--novel tools for gene targeting.

    PubMed

    Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

    2013-01-01

    Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.

  9. Investigation of parameters critical to muon-catalyzed fusion: Annual performance report, 1986-1987

    SciTech Connect

    Jones, S.E.; Palmer, E.P.; Thorne, J.M.; Mueller, B.; Rafelski, J.; Anderson, A.N.

    1987-05-19

    It has been demonstrated (in conjunction with our colleagues) that muon catalysis cycling rates increase rapidly with increasing deuterium-tritium gas temperatures and densities. Furthermore, muon-capture losses are significantly smaller than predicted before the experiments began, although recent theoretical work narrows the gap between theory and observation. As a result of these effects, it was possible to achieve muon-catalyzed fusion yields of 150 fusions/muon (average). The fusion energy thereby released, nearly 3 GeV/muon, significantly exceeds theoretical expectations, and still higher yields are expected. Therefore, the limits of muon-catalyzed fusion are being explored to provide answers to questions regarding energy applications of muon-catalyzed fusion.

  10. Robust expression of heterologous genes by selection marker fusion system in improved Chlamydomonas strains.

    PubMed

    Kong, Fantao; Yamasaki, Tomohito; Kurniasih, Sari Dewi; Hou, Liyuan; Li, Xiaobo; Ivanova, Nina; Okada, Shigeru; Ohama, Takeshi

    2015-09-01

    Chlamydomonas is a very attractive candidate plant cell factory. However, its main drawback is the difficulty to find the transformants that robustly express heterologous genes randomly inserted in the nuclear genome. We previously showed that domestic squalene synthase (SQS) gene of Chlamydomonas was much more efficiently overexpressed in a mutant strain [UV-mediated mutant (UVM) 4] than in wild type. In this study, we evaluated the possibility of a new mutant strain, met1, which contains a tag in the maintenance type methyltransferase gene that is expected to play a key role in the maintenance of transcriptional gene silencing. The versatile usefulness of the UVM4 strain to express heterologous genes was also analyzed. We failed to overexpress CrSSL3 cDNA, which is the codon-adjusted squalene synthase-like gene originated from Botryococcus braunii, using the common expression cassette in the wild-type CC-1690 and UVM4 strains. However, we succeeded in isolating western blot-positive transformants through the combinational use of the UVM4 strain and ble2A expression system of which expression cassette bears a fused ORF of the target gene and the antibiotic resistance gene ble via the foot-and-mouth disease virus (FMDV) self-cleaving 2A sequence. It is noteworthy that even with this system, huge deviations in the accumulated protein levels were still observed among the UVM4 transformants. PMID:25660568

  11. Secretory Breast Carcinoma: A Histopathologic and Genomic Spectrum Characterized by a Joint Specific ETV6-NTRK3 Gene Fusion.

    PubMed

    Del Castillo, Marie; Chibon, Frédéric; Arnould, Laurent; Croce, Sabrina; Ribeiro, Agnès; Perot, Gaëlle; Hostein, Isabelle; Geha, Sameh; Bozon, Catherine; Garnier, Agnès; Lae, Marick; Vincent-Salomon, Anne; MacGrogan, Gaëtan

    2015-11-01

    Secretory breast carcinoma (SBC) is a rare breast carcinoma with distinctive morphologic features and a recurrent specific chromosomal translocation t(12;15)(p13;q25), usually of low histologic grade and favorable prognosis. We describe the morphologic and genetic characteristics of 11 cases of SBC from 10 patients. Histologic and immunohistochemical analyses, fluorescence in situ hybridization using break-apart probes specific to ETV6 on 12p13, reverse transcription polymerase chain reaction with in-house probes specific to the ETV6-NTRK3 gene fusion, and DNA copy number variation by array comparative genomic hybridization analyses were performed on all cases. Seven cases were of low histologic grade, 3 were intermediate, and 1 had high-grade nuclear atypia, necrosis, and numerous mitoses. This patient had a fatal outcome. Five cases displayed low hormonal receptor expression, whereas the rest had basal-type immunoprofiles. All interpretable cases harbored an ETV6-NTRK3 gene fusion by reverse transcription polymerase chain reaction and/or an ETV6 rearrangement by fluorescence in situ hybridization, with duplication of the oncogenic derivative in 2 cases. Array comparative genomic hybridization analysis showed simplex genomic profiles. The 2 cases with ETV6-NTRK3 duplication included a gain of 12p starting from the ETV6 locus to the telomere, associated with a gain of the 15q from the centromere to NTRK3 in 1 case, and in the other a normal profile up to NTRK3 on 15q, and then a loss up to the telomere, suggesting loss of corresponding normal chromosome 15. These findings provide a novel insight into the morphologic and genetic spectrum of SBC, ranging from low-grade to high-grade histology, with occasional low hormonal receptor expression, simplex genomic profiles, and possible unfavorable course.

  12. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes

    SciTech Connect

    Rizk, Mazen; Antranikian, Garabed; Elleuche, Skander

    2012-11-09

    Highlights: Black-Right-Pointing-Pointer Multifunctional enzymes offer an interesting approach for biomass degradation. Black-Right-Pointing-Pointer Size and conformation of separate constructs play a role in the effectiveness of chimeras. Black-Right-Pointing-Pointer A connecting linker allows for maximal flexibility and increased thermostability. Black-Right-Pointing-Pointer Genes with functional similarities are the best choice for fusion candidates. -- Abstract: The reduction of fossil fuels, coupled with its increase in price, has made the search for alternative energy resources more plausible. One of the topics gaining fast interest is the utilization of lignocellulose, the main component of plants. Its primary constituents, cellulose and hemicellulose, can be degraded by a series of enzymes present in microorganisms, into simple sugars, later used for bioethanol production. Thermophilic bacteria have proven to be an interesting source of enzymes required for hydrolysis since they can withstand high and denaturing temperatures, which are usually required for processes involving biomass degradation. However, the cost associated with the whole enzymatic process is staggering. A solution for cost effective and highly active production is through the construction of multifunctional enzyme complexes harboring the function of more than one enzyme needed for the hydrolysis process. There are various strategies for the degradation of complex biomass ranging from the regulation of the enzymes involved, to cellulosomes, and proteins harboring more than one enzymatic activity. In this review, the construction of multifunctional biomass degrading enzymes through end-to-end gene fusions, and its impact on production and activity by choosing the enzymes and linkers is assessed.

  13. Characterization of the telomere complex, TERF1 and TERF2 genes in muntjac species with fusion karyotypes

    SciTech Connect

    Hartmann, Nils; Scherthan, Harry . E-mail: scherth@web.de

    2005-05-15

    The telomere binding proteins TRF1 and TRF2 maintain and protect chromosome ends and confer karyotypic stability. Chromosome evolution in the genus Muntiacus is characterized by numerous tandem (end-to-end) fusions. To study TRF1 and TRF2 telomere binding proteins in Muntiacus species, we isolated and characterized the TERF1 and -2 genes from Indian muntjac (Muntiacus muntjak vaginalis; 2n = 6 female) and from Chinese muntjac (Muntiacus reveesi; 2n = 46). Expression analysis revealed that both genes are ubiquitously expressed and sequence analysis identified several transcript variants of both TERF genes. Control experiments disclosed a novel testis-specific splice variant of TERF1 in human testes. Amino acid sequence comparisons demonstrate that Muntiacus TRF1 and in particular TRF2 are highly conserved between muntjac and human. In vivo TRF2-GFP and immuno-staining studies in muntjac cell lines revealed telomeric TRF2 localization, while deletion of the DNA binding domain abrogated this localization, suggesting muntjac TRF2 represents a functional telomere protein. Finally, expression analysis of a set of telomere-related genes revealed their presence in muntjac fibroblasts and testis tissue, which suggests the presence of a conserved telomere complex in muntjacs. However, a deviation from the common theme was noted for the TERT gene, encoding the catalytic subunit of telomerase; TERT expression could not be detected in Indian or Chinese muntjac cDNA or genomic DNA using a series of conserved primers, while TRAP assay revealed functional telomerase in Chinese muntjac testis tissues. This suggests muntjacs may harbor a diverged telomerase sequence.

  14. Proteome-wide identification of novel binding partners to the oncogenic fusion gene protein, NPM-ALK, using tandem affinity purification and mass spectrometry.

    PubMed

    Wu, Fang; Wang, Peng; Young, Leah C; Lai, Raymond; Li, Liang

    2009-02-01

    Nucleophosmin-anaplastic lymphoma kinase (NPM-ALK), an oncogenic fusion gene protein that is characteristically found in a subset of anaplastic large cell lymphomas, promotes tumorigenesis through its functional and physical interactions with various biologically important proteins. The identification of these interacting proteins has proven to be useful to further our understanding of NPM-ALK-mediated tumorigenesis. For the first time, we performed a proteome-wide identification of NPM-ALK-binding proteins using tandem affinity purification and a highly sensitive mass spectrometric technique. Tandem affinity purification is a recently developed method that carries a lower background and higher sensitivity compared with the conventional immunoprecipitation-based protein purification protocols. The NPM-ALK gene was cloned into an HB-tagged vector and expressed in GP293 cells. Three independent experiments were performed and the reproducibility of the data was 68%. The vast majority of the previously reported NPM-ALK-binding proteins were detected. We also identified proteins that are involved in various cellular processes that were not previously described in association with NPM-ALK, such as MCM6 and MSH2 (DNA repair), Nup98 and importin 8 (subcellular protein transport), Stim1 (calcium signaling), 82Fip (RNA regulation), and BAG2 (proteosome degradation). We believe that these data highlight the functional diversity of NPM-ALK and provide new research directions for the study of the biology of this oncoprotein.

  15. A lacZ Reporter-Based Strategy for Rapid Expression Analysis and Target Validation of Mycobacterium tuberculosis Latent Infection Genes.

    PubMed

    Sood, Shivani; Kaur, Satinder; Shrivastava, Rahul

    2016-02-01

    We report a novel lacZ fusion vector and demonstrate its utility for expression analysis of genes associated with Mycobacterium tuberculosis latent infection. The vector contains E. coli (oriE) and mycobacterial (oriM) origins of replication, a kanamycin resistance gene (Km(r)) as selection marker, and a lacZ reporter gene in fusion with MCS for cloning of upstream regulatory sequence of the desired genes. β-galactosidase activity of the vector was standardized for expression analysis under latent mycobacterial conditions using Phsp60, a constitutive mycobacterial promoter, utilizing Mycobacterium smegmatis as model organism. Validation of the vector was done by cloning and expression analysis of PhspX (alpha crystalline) and Picl (isocitrate lyase), promoters from two of the genes shown to be involved in M. tuberculosis persistence. Both genes showed appreciable levels of β-galactosidase expression under hypoxia-induced persistent conditions in comparison to their actively replicating state. Expression analysis of a set of hypothetical genes was also done, of which Rv0628c showed increased expression under persistent conditions. The reported fusion vector and the strategy can be effectively used for short listing and validation of drug targets deduced from various non-conclusive approaches such as bioinformatics and microarray analysis against latent/persistent form of mycobacterial infection. PMID:26597215

  16. CONFERENCE REPORT: Summary of the 16th IAEA Technical Meeting on 'Research using Small Fusion Devices'

    NASA Astrophysics Data System (ADS)

    Gribkov, V.; Van Oost, G.; Malaquias, A.; Herrera, J.

    2006-10-01

    Common research topics that are being studied in small, medium and large devices such as H-mode like or improved confinement, turbulence and transport are reported. These included modelling and diagnostic developments for edge and core, to characterize plasma density, temperature, electric potential, plasma flows, turbulence scale, etc. Innovative diagnostic methods were designed and implemented which could be used to develop experiments in small devices (in some cases not possible in large devices due to higher power deposition) to allow a better understanding of plasma edge and core properties. Reports are given addressing research in linear devices that can be used to study particular plasma physics topics relevant for other magnetic confinement devices such as the radial transport and the modelling of self-organized plasma jets involved in spheromak-like plasma formation. Some aspects of the work presented are of interest to the astrophysics community since they are believed to shed light on the basis of the physics of stellar jets. On the dense magnetized plasmas (DMP) topic, the present status of research, operation of new devices, plasma dynamics modelling and diagnostic developments is reported. The main devices presented belong to the class of Z-pinches, mostly plasma foci, and several papers were presented under this topic. The physics of DMP is important both for the main-stream fusion investigations as well as for providing the basis for elaboration of new concepts. New high-current technology introduced in the DMP devices design and construction make these devices nowadays more reliably fitted to various applications and give the possibility to widen the energy range used by them in both directions—to the multi-MJ level facilities and down to miniature plasma focus devices with energy of just a few J.

  17. Fusion Energy Division annual progress report period ending December 31, 1983

    SciTech Connect

    Not Available

    1984-09-01

    The Fusion Program carries out work in a number of areas: (1) experimental and theoretical research on two magnetic confinement concepts - the ELMO Bumpy Torus (EBT) and the tokamak, (2) theoretical and engineering studies on a third concept - the stellarator, (3) engineering and physics of present-generation fusion devices, (4) development and testing of diagnostic tools and techniques, (5) development and testing of materials for fusion devices, (6) development and testing of the essential technologies for heating and fueling fusion plasmas, (7) development and testing of the superconducting magnets that will be needed to confine these plasmas, (8) design of future devices, (9) assessment of the environmental impact of fusion energy, and (10) assembly and distribution to the fusion community of data bases on atomic physics and radiation effects. The interactions between these activities and their integration into a unified program are major factors in the success of the individual activities, and the ORNL Fusion Program strives to maintain a balance among these activities that will lead to continued growth.

  18. Establishment of an Institute for Fusion Studies. Technical progress report, November 1, 1991--October 31, 1992

    SciTech Connect

    Hazeltine, R.D.

    1992-07-01

    The Institute for Fusion Studies is a national center for theoretical fusion plasma physics research. Its purposes are: (1) to 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) to serve as a center for information exchange, nationally and internationally, by hosting exchange visits, conferences, and workshops; (3) and to train students and postdoctoral research personnel for the fusion energy program and plasma physics research areas. The theoretical research results that are obtained by the Institute contribute mainly to the progress of national and international efforts in nuclear fusion research, whose goal is the development of fusion power.as a basic energy source. In addition to its primary focus on fusion physics, the Institute is also involved with research in related fields, such as advanced computing techniques, nonlinear dynamics, plasma astrophysics, and accelerator physics. The work of EFS scientists continued to receive national and international recognition. Numerous invited papers were given during the past year at workshops, conferences, and scientific meetings. Last year IFS scientists published 95 scientific articles in technical journals and monographs.

  19. Solitary fibrous tumors/hemangiopericytomas with different variants of the NAB2-STAT6 gene fusion are characterized by specific histomorphology and distinct clinicopathological features.

    PubMed

    Barthelmeß, Sarah; Geddert, Helene; Boltze, Carsten; Moskalev, Evgeny A; Bieg, Matthias; Sirbu, Horia; Brors, Benedikt; Wiemann, Stefan; Hartmann, Arndt; Agaimy, Abbas; Haller, Florian

    2014-04-01

    Recurrent somatic fusions of the two genes, NGFI-A-binding protein 2 (NAB2) and STAT6, located at chromosomal region 12q13, have been recently identified to be presumable tumor-initiating events in solitary fibrous tumors (SFT). Herein, we evaluated a cohort of 52 SFTs/hemangiopericytomas (HPCs) by whole-exome sequencing (one case) and multiplex RT-PCR (all 52 cases), and identified 12 different NAB2-STAT6 fusion variants in 48 cases (92%). All 52 cases showed strong and diffuse nuclear positivity for STAT6 by IHC. We categorized the fusion variants according to their potential functional effects within the predicted fusion protein and found strong correlations with relevant clinicopathological features. Tumors with the most common fusion variant, NAB2ex4-STAT6ex2/3, corresponded to classic pleuropulmonary SFTs with diffuse fibrosis and mostly benign behavior and occurred in older patients (median age, 69 years). In contrast, tumors with the second most common fusion variant, NAB2ex6-STAT6ex16/17, were found in much younger patients (median age, 47 years) and represented typical HPCs from deep soft tissue with a more aggressive phenotype and clinical behavior. In summary, these molecular genetic findings support the concept that classic pleuropulmonary SFT and deep-seated HPC are separate entities that share common features but correlate to different clinical outcome.

  20. Single-cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion.

    PubMed

    Freeman, Brian T; Jung, Jangwook P; Ogle, Brenda M

    2016-01-01

    Fusion of donor mesenchymal stem cells with parenchymal cells of the recipient can occur in the brain, liver, intestine and heart following transplantation. The therapeutic benefit or detriment of resultant hybrids is unknown. Here we sought a global view of phenotypic diversification of mesenchymal stem cell-cardiomyocyte hybrids and associated time course. Using single-cell RNA-seq, we found hybrids consistently increase ribosome components and decrease genes associated with the cell cycle suggesting an increase in protein production and decrease in proliferation to accommodate the fused state. But in the case of most other gene groups, hybrids were individually distinct. In fact, though hybrids can express a transcriptome similar to individual fusion partners, approximately one-third acquired distinct expression profiles in a single day. Some hybrids underwent reprogramming, expressing pluripotency and cardiac precursor genes latent in parental cells and associated with developmental and morphogenic gene groups. Other hybrids expressed genes associated with ontologic cancer sets and two hybrids of separate experimental replicates clustered with breast cancer cells, expressing critical oncogenes and lacking tumor suppressor genes. Rapid transcriptional diversification of this type garners consideration in the context of cellular transplantation to damaged tissues, those with viral infection or other microenvironmental conditions that might promote fusion. PMID:26997336

  1. Single-cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion.

    PubMed

    Freeman, Brian T; Jung, Jangwook P; Ogle, Brenda M

    2016-03-21

    Fusion of donor mesenchymal stem cells with parenchymal cells of the recipient can occur in the brain, liver, intestine and heart following transplantation. The therapeutic benefit or detriment of resultant hybrids is unknown. Here we sought a global view of phenotypic diversification of mesenchymal stem cell-cardiomyocyte hybrids and associated time course. Using single-cell RNA-seq, we found hybrids consistently increase ribosome components and decrease genes associated with the cell cycle suggesting an increase in protein production and decrease in proliferation to accommodate the fused state. But in the case of most other gene groups, hybrids were individually distinct. In fact, though hybrids can express a transcriptome similar to individual fusion partners, approximately one-third acquired distinct expression profiles in a single day. Some hybrids underwent reprogramming, expressing pluripotency and cardiac precursor genes latent in parental cells and associated with developmental and morphogenic gene groups. Other hybrids expressed genes associated with ontologic cancer sets and two hybrids of separate experimental replicates clustered with breast cancer cells, expressing critical oncogenes and lacking tumor suppressor genes. Rapid transcriptional diversification of this type garners consideration in the context of cellular transplantation to damaged tissues, those with viral infection or other microenvironmental conditions that might promote fusion.

  2. Investigation of parameters critical to muon-catalyzed fusion: Performance report, May 19-August 31, 1987: (Final technical report)

    SciTech Connect

    Jones, S.E.; Palmer, E.P.; Thorne, J.M.; Mueller, B.; Rafelski, J.; Anderson, A.N.

    1987-11-20

    We have demonstrated (in conjunction with our colleagues) that muon catalysis cycling rates increase rapidly with increasing deuterium-tritium gas temperatures and densities. Furthermore, muon-capture losses are significantly smaller than predicted before the experiments began, although recent theoretical work narrows the gap between theory and observation. As a result of these effects, we have been able to achieve muon-catalyzed fusion yields of 150 fusions/muon (average). The fusion energy thereby released, nearly 3 GeV/muon, significantly exceeds theoretical expectations, and still higher yields are expected. Therefore, we are exploring the limits of muon-catalyzed fusion, to provide answers to questions regarding energy applications of muon-catalyzed fusion.

  3. Enhancing potency of siRNA targeting fusion genes by optimization outside of target sequence

    PubMed Central

    Gavrilov, Kseniya; Seo, Young-Eun; Tietjen, Gregory T.; Cui, Jiajia; Cheng, Christopher J.; Saltzman, W. Mark

    2015-01-01

    Canonical siRNA design algorithms have become remarkably effective at predicting favorable binding regions within a target mRNA, but in some cases (e.g., a fusion junction site) region choice is restricted. In these instances, alternative approaches are necessary to obtain a highly potent silencing molecule. Here we focus on strategies for rational optimization of two siRNAs that target the junction sites of fusion oncogenes BCR-ABL and TMPRSS2-ERG. We demonstrate that modifying the termini of these siRNAs with a terminal G-U wobble pair or a carefully selected pair of terminal asymmetry-enhancing mismatches can result in an increase in potency at low doses. Importantly, we observed that improvements in silencing at the mRNA level do not necessarily translate to reductions in protein level and/or cell death. Decline in protein level is also heavily influenced by targeted protein half-life, and delivery vehicle toxicity can confound measures of cell death due to silencing. Therefore, for BCR-ABL, which has a long protein half-life that is difficult to overcome using siRNA, we also developed a nontoxic transfection vector: poly(lactic-coglycolic acid) nanoparticles that release siRNA over many days. We show that this system can achieve effective killing of leukemic cells. These findings provide insights into the implications of siRNA sequence for potency and suggest strategies for the design of more effective therapeutic siRNA molecules. Furthermore, this work points to the importance of integrating studies of siRNA design and delivery, while heeding and addressing potential limitations such as restricted targetable mRNA regions, long protein half-lives, and nonspecific toxicities. PMID:26627251

  4. Fusion of the Dhfr/Mtx and IR/MAR gene amplification methods produces a rapid and efficient method for stable recombinant protein production.

    PubMed

    Noguchi, Chiemi; Araki, Yoshio; Miki, Daisuke; Shimizu, Noriaki

    2012-01-01

    Amplification of the dihydrofolate reductase gene (Dhfr) by methotrexate (Mtx) exposure is commonly used for recombinant protein expression in Chinese hamster ovary (CHO) cells. However, this method is both time- and labor-intensive, and the high-producing cells that are generated are frequently unstable in culture. Another gene amplification method is based on using a plasmid bearing a mammalian replication initiation region (IR) and a matrix attachment region (MAR), which result in the spontaneous initiation of gene amplification in transfected cells. The IR/MAR and Dhfr/Mtx methods of gene amplification are based on entirely different principles. In this study, we combine these two methods to yield a novel method, termed the IR/MAR-Dhfr fusion method, which was used to express three proteins, the Fc receptor, GFP, and recombinant antibody. The fusion method resulted in a dramatic increase in expression of all three proteins in two CHO sub-lines, DXB-11, and DG44. The IR/MAR-Dhfr fusion amplified the genes rapidly and efficiently, and produced larger amounts of antibody than the Dhfr/Mtx or IR/MAR methods alone. While the amplified structure produced by the Dhfr/Mtx method was highly unstable, and the antibody production rate rapidly decreased with the culture time of the cells, the IR/MAR-Dhfr fusion method resulted in stable amplification and generated clonal cells that produced large amounts of antibody protein over a long period of time. In summary, the novel IR/MAR-Dhfr fusion method enables isolation of stable cells that produce larger amounts of a target recombinant protein more rapidly and easily than either the Dhfr/Mtx or IR/MAR methods alone.

  5. Fusion of the Dhfr/Mtx and IR/MAR Gene Amplification Methods Produces a Rapid and Efficient Method for Stable Recombinant Protein Production

    PubMed Central

    Miki, Daisuke; Shimizu, Noriaki

    2012-01-01

    Amplification of the dihydrofolate reductase gene (Dhfr) by methotrexate (Mtx) exposure is commonly used for recombinant protein expression in Chinese hamster ovary (CHO) cells. However, this method is both time- and labor-intensive, and the high-producing cells that are generated are frequently unstable in culture. Another gene amplification method is based on using a plasmid bearing a mammalian replication initiation region (IR) and a matrix attachment region (MAR), which result in the spontaneous initiation of gene amplification in transfected cells. The IR/MAR and Dhfr/Mtx methods of gene amplification are based on entirely different principles. In this study, we combine these two methods to yield a novel method, termed the IR/MAR-Dhfr fusion method, which was used to express three proteins, the Fc receptor, GFP, and recombinant antibody. The fusion method resulted in a dramatic increase in expression of all three proteins in two CHO sub-lines, DXB-11, and DG44. The IR/MAR-Dhfr fusion amplified the genes rapidly and efficiently, and produced larger amounts of antibody than the Dhfr/Mtx or IR/MAR methods alone. While the amplified structure produced by the Dhfr/Mtx method was highly unstable, and the antibody production rate rapidly decreased with the culture time of the cells, the IR/MAR-Dhfr fusion method resulted in stable amplification and generated clonal cells that produced large amounts of antibody protein over a long period of time. In summary, the novel IR/MAR-Dhfr fusion method enables isolation of stable cells that produce larger amounts of a target recombinant protein more rapidly and easily than either the Dhfr/Mtx or IR/MAR methods alone. PMID:23300841

  6. Energy storage as heat-of-fusion in containerized salts. Report on energy storage boiler tank

    NASA Astrophysics Data System (ADS)

    Chubb, T. A.; Nemecek, J. J.; Simmons, D. E.

    1980-06-01

    This report is concerned with energy storage based on heat-of-fusion in containerized salt. The 'energy storage boiler tank' uses evaporation and condensation of a heat transfer fluid to provide heat transfer into and out of stacked cans of salt. The 'energy storage superheater tank' uses a network of alkali metal heat pipes to distribute heat throughout a building filled with salt cans. It uses a radiation to transfer energy to and from stacked cans of salt. The paper summarizes the rationale for energy storage in containerized salt, it discusses salt availability, salt processing, container requirements, can technology and heat transfer fluid degradation problems. These discussions lead to estimates of energy storage system costs. The Naval Research Laboratory is building a 2 MWht proof-of-concept energy storage boiler tank. Laboratory investigations studying the compatibility of the heat transfer fluid with the molten storage salt are described, along with measurements of temperature drops associated with the energy input process. An assessment of the current status of the energy storage boiler tank is presented.

  7. Fluctuations and transport in fusion plasmas. Final report, October 1, 1981-December 31, 1983

    SciTech Connect

    Gould, R.W.

    1983-01-01

    This report describes continuing research on fluctuations and anomalous transport in fusion plasmas. The research has an experimental task and a theoretical task. The primary objective is to characterize the properties of the fluctuations observed in tokamaks and to try to develop an understanding of the fluctuation-induced anomalous transport of particles and heat. The experimental and theoretical activities are closely related. The main thrust of the experimental activity has been to measure and to characterize, in some detail, the main properties of the electric and magnetic fluctuations through various measurements, with emphasis on those properties which appear to relate to transport. The temporal and spatial distribution, spectral characteristics, and cross correlation of various fluctuating quantities are observed. Recently probe arrays (Langmuir probes and photodiodes) have been introduced to permit imaging of the fluctuations. The theoretical activity has emphasized the comparison of experimental results on both turbulence and anomalous transport from various machines with existing theories, including numerical computation and extension of existing theories where necessary. The theoretical activity also provided valuable guidance to the Caltech experimental program.

  8. A Luciferase Reporter Gene System for High-Throughput Screening of γ-Globin Gene Activators.

    PubMed

    Xie, Wensheng; Silvers, Robert; Ouellette, Michael; Wu, Zining; Lu, Quinn; Li, Hu; Gallagher, Kathleen; Johnson, Kathy; Montoute, Monica

    2016-01-01

    Luciferase reporter gene assays have long been used for drug discovery due to their high sensitivity and robust signal. A dual reporter gene system contains a gene of interest and a control gene to monitor non-specific effects on gene expression. In our dual luciferase reporter gene system, a synthetic promoter of γ-globin gene was constructed immediately upstream of the firefly luciferase gene, followed downstream by a synthetic β-globin gene promoter in front of the Renilla luciferase gene. A stable cell line with the dual reporter gene was cloned and used for all assay development and HTS work. Due to the low activity of the control Renilla luciferase, only the firefly luciferase activity was further optimized for HTS. Several critical factors, such as cell density, serum concentration, and miniaturization, were optimized using tool compounds to achieve maximum robustness and sensitivity. Using the optimized reporter assay, the HTS campaign was successfully completed and approximately 1000 hits were identified. In this chapter, we also describe strategies to triage hits that non-specifically interfere with firefly luciferase. PMID:27316998

  9. Right Congenital Diaphragmatic Hernia Associated With Hepatic Pulmonary Fusion: A Case Report

    PubMed Central

    Laamiri, Rachida; Belhassen, Samia; Ksia, Amine; Ben Salem, Amina; Kechiche, Nahla; Mosbahi, Sana; Sahnoun, Lassaad; Mekki, Mongi; Belghith, Mohsen; Nouri, Abdellatif

    2016-01-01

    We present a case of male newborn presented with respiratory distress at 21 hours of life. The patient was operated for right congenital diaphragmatic hernia (CDH). Hepatic pulmonary fusion (HPF) was found at surgery. PMID:27433453

  10. Fusion energy division annual progress report, period ending December 31, 1980

    SciTech Connect

    Not Available

    1981-11-01

    The ORNL Program encompasses most aspects of magnetic fusion research including research on two magnetic confinement programs (tokamaks and ELMO bumpy tori); the development of the essential technologies for plasma heating, fueling, superconducting magnets, and materials; the development of diagnostics; the development of atomic physics and radiation effect data bases; the assessment of the environmental impact of magnetic fusion; the physics and engineering of present-generation devices; and the design of future devices. The integration of all of these activities into one program is a major factor in the success of each activity. An excellent example of this integration is the extremely successful application of neutral injection heating systems developed at ORNL to tokamaks both in the Fusion Energy Division and at Princeton Plasma Physics Laboratory (PPPL). The goal of the ORNL Fusion Program is to maintain this balance between plasma confinement, technology, and engineering activities.

  11. Laboratory evaluation of fusion-bonded epoxy coatings for civil works applications. Final report

    SciTech Connect

    Race, T.D.; Boy, J.H.

    1995-01-01

    This study investigates safer, more cost-effective alternatives to U.S. Army Corps of Engineers paint specification C-200A, Coal Tar Epoxy Coating, which is used to protect steel sheet piling. Fusion-bonded epoxy, a nonpolluting shop-applied coating, was evaluated in laboratory tests as a potential replacement for C-200A. Laboratory tests that included salt and fresh water immersion, cyclic salt fog/ultraviolet (UV) condensation, impact resistance, and cathodic disbondment were conducted on four fusion-bonded epoxy and two control coating systems. Fusion-bonded epoxy coatings have excellent resistance to impact and cathodic disbondment. Resistance to corrosion in fresh and salt water immersion and in cyclic salt fog/UV-condensation exposures was comparable to the control coating systems. Based on the results of the laboratory tests, a field evaluation of fusion-bonded epoxy is recommended.

  12. Fusion driver study. Final technical report, April 1, 1978-March 31, 1980

    SciTech Connect

    Friedman, H.W.

    1980-04-01

    A conceptual design of a multi-megajoule, repetitively pulsed CO/sub 2/ laser system for Inertial Confinement Fusion is presented. System configurations consisting of 50 to 100 kJ modules operating at subatmospheric pressures with multiple pass optical extraction appear feasible with present or near term technology. Overall laser system efficiencies of greater than 10% at repetition rates in excess of 10 Hz are possible with the state-of-the-art pulsed power technology. The synthesis of all the laser subsystems into a specific configuration for a Laser Fusion Driver depends upon the reactor chamber(s) layout, subsystem reliability and restrictions on overall dimensions of the fusion driver. A design is presented which stacks power amplifier modules in series in a large torus with centrally located reactor chamber. Cost estimates of the overall Laser Fusion Driver are also presented.

  13. Accelerator and Fusion Research Division annual report, fiscal year 1980, October 1979-September 1980

    SciTech Connect

    Not Available

    1981-03-01

    Research during October 1979 to September 1980 is summarized. Areas covered include: accelerator operations; positron-electron project; stochastic beam cooling; high-field superconducting magnets; accelerator theory; neutral beam sources; and heavy ion fusion. (GHT)

  14. SECAD-- a Schema-based Environment for Configuring, Analyzing and Documenting Integrated Fusion Simulations. Final report

    SciTech Connect

    Shasharina, Svetlana

    2012-05-23

    SECAD is a project that developed a GUI for running integrated fusion simulations as implemented in FACETS and SWIM SciDAC projects. Using the GUI users can submit simulations locally and remotely and visualize the simulation results.

  15. Optimizing expression and purification of an ATP-binding gene gsiA from Escherichia coli k-12 by using GFP fusion

    PubMed Central

    Wang, Zhongshan; Xiang, Quanju; Wang, Guangjun; Wang, Haiyan; Zhang, Yizheng

    2011-01-01

    The cloning, expression and purification of the glutathione (sulfur) import system ATP-binding protein (gsiA) was carried out. The coding sequence of Escherichia coli gsiA, which encodes the ATP-binding protein of a glutathione importer, was amplified by PCR, and then inserted into a prokaryotic expression vector pWaldo-GFPe harboring green fluorescent protein (GFP) reporter gene. The resulting recombinant plasmid pWaldo-GFP-GsiA was transformed into various E. coli strains, and expression conditions were optimized. The effect of five E. coli expression strains on the production of the recombinant gsiA protein was evaluated. E. coli BL21 (DE3) was found to be the most productive strain for GsiA-GFP fusion-protein expression, most of which was insoluble fraction. However, results from in-gel and Western blot analysis suggested that expression of recombinant GsiA in Rosetta (DE3) provides an efficient source in soluble form. By using GFP as reporter, the most suitable host strain was conveniently obtained, whereby optimizing conditions for overexpression and purification of the proteins for further functional and structural studies, became, not only less laborious, but also time-saving. PMID:22215971

  16. Rho GTPase activity modulates paramyxovirus fusion protein-mediated cell-cell fusion

    SciTech Connect

    Schowalter, Rachel M.; Wurth, Mark A.; Aguilar, Hector C.; Lee, Benhur; Moncman, Carole L.; McCann, Richard O.; Dutch, Rebecca Ellis . E-mail: rdutc2@uky.edu

    2006-07-05

    The paramyxovirus fusion protein (F) promotes fusion of the viral envelope with the plasma membrane of target cells as well as cell-cell fusion. The plasma membrane is closely associated with the actin cytoskeleton, but the role of actin dynamics in paramyxovirus F-mediated membrane fusion is unclear. We examined cell-cell fusion promoted by two different paramyxovirus F proteins in three cell types in the presence of constitutively active Rho family GTPases, major cellular coordinators of actin dynamics. Reporter gene and syncytia assays demonstrated that expression of either Rac1{sup V12} or Cdc42{sup V12} could increase cell-cell fusion promoted by the Hendra or SV5 glycoproteins, though the effect was dependent on the cell type expressing the viral glycoproteins. In contrast, RhoA{sup L63} decreased cell-cell fusion promoted by Hendra glycoproteins but had little affect on SV5 F-mediated fusion. Also, data suggested that GTPase activation in the viral glycoprotein-containing cell was primarily responsible for changes in fusion. Additionally, we found that activated Cdc42 promoted nuclear rearrangement in syncytia.

  17. Internet and web projects for fusion plasma science and education. Final technical report

    SciTech Connect

    Eastman, Timothy E.

    1999-08-30

    The plasma web site at http://www.plasmas.org provides comprehensive coverage of all plasma science and technology with site links worldwide. Prepared to serve the general public, students, educators, researchers, and decision-makers, the site covers basic plasma physics, fusion energy, magnetic confinement fusion, high energy density physics include ICF, space physics and astrophysics, pulsed-power, lighting, waste treatment, plasma technology, plasma theory, simulations and modeling.

  18. FRAG1, a gene that potently activates fibroblast growth factor receptor by C-terminal fusion through chromosomal rearrangement.

    PubMed Central

    Lorenzi, M V; Horii, Y; Yamanaka, R; Sakaguchi, K; Miki, T

    1996-01-01

    A constitutively active form of fibroblast growth factor 2 (FGFR2) was identified in rat osteosarcoma (ROS) cells by an expression cloning strategy. Unlike other tyrosine kinase receptors activated by N-terminal truncation in tumors, this receptor, FGFR2-ROS, contains an altered C terminus generated from chromosomal rearrangement with a novel gene, designated FGFR activating gene 1 (FRAG1). While the removal of the C terminus slightly activates FGFR2, the presence of the FRAG1 sequence drastically stimulates the transforming activity and autophosphorylation of the receptor. FGFR2-ROS is expressed as a unusually large protein and is highly phosphorylated in NIH 3T3 transfectants. FRAG1 is ubiquitously expressed and encodes a predicted protein of 28 kDa lacking significant structural similarity to known proteins. Epitope-tagged FRAG1 protein showed a perinuclear localization by immunofluorescence staining. The highly activated state of FGFR2-ROS appears to be attributed to constitutive dimer formation and higher phosphorylation level as well as possibly altered subcellular localization. These results indicate a unique mechanism of receptor activation by a C terminus alteration through a chromosomal fusion with FRAG1. Images Fig. 1 Fig. 2 Fig. 3 Fig. 5 Fig. 6 PMID:8799135

  19. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

    PubMed Central

    Ren, Shancheng; Peng, Zhiyu; Mao, Jian-Hua; Yu, Yongwei; Yin, Changjun; Gao, Xin; Cui, Zilian; Zhang, Jibin; Yi, Kang; Xu, Weidong; Chen, Chao; Wang, Fubo; Guo, Xinwu; Lu, Ji; Yang, Jun; Wei, Min; Tian, Zhijian; Guan, Yinghui; Tang, Liang; Xu, Chuanliang; Wang, Linhui; Gao, Xu; Tian, Wei; Wang, Jian; Yang, Huanming; Wang, Jun; Sun, Yinghao

    2012-01-01

    There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations. Three of the 14 tumors (21.4%) harbored a TMPRSS2-ERG fusion, and the low prevalence of this fusion in Chinese patients was further confirmed in an additional tumor set (10/54=18.5%). Notably, two novel gene fusions, CTAGE5-KHDRBS3 (20/54=37%) and USP9Y-TTTY15 (19/54=35.2%), occurred frequently in our patient cohort. Further systematic transcriptional profiling identified numerous long ncRNAs that were differentially expressed in the tumors. An analysis of the correlation between expression of long ncRNA and genes suggested that long ncRNAs may have functions beyond transcriptional regulation. This study yielded new insights into the pathogenesis of prostate cancer in the Chinese population. PMID:22349460

  20. Epidermal Growth Factor Receptor Mutation and Anaplastic Lymphoma Kinase Gene Fusion: Detection in Malignant Pleural Effusion by RNA or PNA Analysis

    PubMed Central

    Chen, Yi-Lin; Lee, Chung-Ta; Lu, Cheng-Chan; Yang, Shu-Ching; Chen, Wan-Li; Lee, Yang-Cheng; Yang, Chung-Hsien; Peng, Shu-Ling; Su, Wu-Chou; Chow, Nan-Haw; Ho, Chung-Liang

    2016-01-01

    Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis. The percentage of tumor cells in the pleural effusion may be low; therefore, mutant enrichment is required for a successful analysis. The EGFR mutation status in MPE was determined using three methods: (1) PCR sequencing of genomic DNA (direct sequencing), (2) mutant-enriched PCR sequencing of genomic DNA using peptide nucleic acid (PNA-sequencing), and (3) PCR sequencing of cDNA after reverse transcription for cellular RNA (RNA-sequencing). RT-PCR was also used to test cases for ALK gene fusion. PNA-sequencing and RNA-sequencing had similar analytical sensitivities (< 1%), which indicates similar enrichment capabilities. The clinical sensitivity in 133 cases when detecting the common EGFR exon 19 and exon 21 mutations was 56.4% (75/133) for direct sequencing, 63.2% (84/133) for PNA-sequencing, and 65.4% (87/133) for RNA-sequencing. RT-PCR and sequencing showed 5 cases (3.8%) with ALK gene fusion. All had wild-type EGFR. For EGFR analysis of MPE, RNA-sequencing is at least as sensitive as PNA-sequencing but not limited to specific mutations. Detecting ALK fusion can be incorporated in the same RNA workflow. Therefore, RNA is a better source for comprehensive molecular diagnoses in MPE. PMID:27352172

  1. Inertial confinement fusion research and development studies. Final report, October 1979-August 1980

    SciTech Connect

    Bullis, R.; Finkelman, M.; Leng, J.; Luzzi, T.; Ojalvo, I.; Powell, E.; Sedgley, D.

    1980-08-01

    These Inertial Confinement Fusion (ICF) research and development studies were selected for structural, thermal, and vacuum pumping analyses in support of the High Yield Lithium Injection Fusion Energy (HYLIFE) concept development. An additional task provided an outlined program plan for an ICF Engineering Test Facility, using the HYLIFE concept as a model, although the plan is generally applicable to other ICF concepts. The HYLIFE is one promising type of ICF concept which features a falling array of liquid lithium jets. These jets surround the fusion reaction to protect the first structural wall (FSW) of the vacuum chamber by absorbing the fusion energy, and to act as the tritium breeder. The fusion energy source is a deuterium-tritium pellet injected into the chamber every second and driven by laser or heavy ion beams. The studies performed by Grumman have considered the capabilities of specific HYLIFE features to meet life requirements and the requirement to recover to preshot conditions prior to each subsequent shot. The components under investigation were the FSW which restrains the outward motion of the liquid lithium, the nozzle plate which forms the falling jet array, the graphite shield which is in direct top view of the fusion pellet, and the vacuum pumping system. The FSW studies included structural analysis, and definition of an experimental program to validate computer codes describing lithium motion and the resulting impact on the wall.

  2. Transgenic mouse model harboring the transcriptional fusion ccl20-luciferase as a novel reporter of pro-inflammatory response.

    PubMed

    Crispo, Martina; Van Maele, Laurye; Tabareau, Julien; Cayet, Delphine; Errea, Agustina; Ferreira, Ana María; Rumbo, Martin; Sirard, Jean Claude

    2013-01-01

    The chemokine CCL20, the unique ligand of CCR6 functions as an attractant of immune cells. Expression of CCL20 is induced by Toll-like Receptor (TLR) signaling or proinflammatory cytokine stimulation. However CCL20 is also constitutively produced at specific epithelial sites of mucosa. This expression profile is achieved by transcriptional regulation. In the present work we characterized regulatory features of mouse Ccl20 gene. Transcriptional fusions between the mouse Ccl20 promoter and the firefly luciferase (luc) encoding gene were constructed and assessed in in vitro and in vivo assays. We found that liver CCL20 expression and luciferase activity were upregulated by systemic administration of the TLR5 agonist flagellin. Using shRNA and dominant negative form specific for mouse TLR5, we showed that this expression was controlled by TLR5. To address in situ the regulation of gene activity, a transgenic mouse line harboring a functional Ccl20-luc fusion was generated. The luciferase expression was highly concordant with Ccl20 expression in different tissues. Our data indicate that the transgenic mouse model can be used to monitor activation of innate response in vivo.

  3. Transgenic Mouse Model Harboring the Transcriptional Fusion Ccl20-Luciferase as a Novel Reporter of Pro-Inflammatory Response

    PubMed Central

    Crispo, Martina; Van Maele, Laurye; Tabareau, Julien; Cayet, Delphine; Errea, Agustina; Ferreira, Ana María; Rumbo, Martin; Sirard, Jean Claude

    2013-01-01

    The chemokine CCL20, the unique ligand of CCR6 functions as an attractant of immune cells. Expression of CCL20 is induced by Toll-like Receptor (TLR) signaling or proinflammatory cytokine stimulation. However CCL20 is also constitutively produced at specific epithelial sites of mucosa. This expression profile is achieved by transcriptional regulation. In the present work we characterized regulatory features of mouse Ccl20 gene. Transcriptional fusions between the mouse Ccl20 promoter and the firefly luciferase (luc) encoding gene were constructed and assessed in in vitro and in vivo assays. We found that liver CCL20 expression and luciferase activity were upregulated by systemic administration of the TLR5 agonist flagellin. Using shRNA and dominant negative form specific for mouse TLR5, we showed that this expression was controlled by TLR5. To address in situ the regulation of gene activity, a transgenic mouse line harboring a functional Ccl20-luc fusion was generated. The luciferase expression was highly concordant with Ccl20 expression in different tissues. Our data indicate that the transgenic mouse model can be used to monitor activation of innate response in vivo. PMID:24265691

  4. Heterogeneous breakpoints on the immunoglobulin genes are involved in fusion with the 5' region of BCL2 in B-cell tumors.

    PubMed

    Yonetani, N; Ueda, C; Akasaka, T; Nishikori, M; Uchiyama, T; Ohno, H

    2001-09-01

    The 5' flanking region of the BCL2 gene (5'-BCL2) is a breakpoint cluster of rearrangements with immunoglobulin genes (IGs). In contrast to t(14;18)(q32;q21) affecting the 3' region of BCL2, 5'-BCL2 can fuse to not only the heavy chain gene (IGH), but also two light chain gene (IGL) loci. We report here cloning and sequencing of a total of eleven 5'-BCL2 / IGs junctional areas of B-cell tumors, which were amplified by long-distance polymerase chain reaction-based assays. The breakpoints on 5'-BCL2 were distributed from 378 to 2312 bp upstream of the translational initiation site and, reflecting the alteration of regulatory sequences of BCL2, 5'-BCL2 / IGs-positive cells showed markedly higher levels of BCL2 expression than those of t(14;18)-positive cells. In contrast, the breakpoints on the IGs were variable. Two 5'-BCL2 / IGH and two 5'-BCL2 / IGLkappa junctions occurred 5' of the joining (J) segments, suggesting operation of an erroneous variable (V) / diversity (D) / J and V / J rearrangement mechanism. However, two other 5'-BCL2 / IGH junctions affected switch regions, and the kappa-deleting element, which is located 24 kb downstream of the constant region of IGLkappa, followed the 5'-BCL2 in another case. One 5'-BCL2 / IGLkappa and two 5'-BCL2 / IGLlambda junctions involved intronic regions where the normal recombination process does not occur. In the remaining one case, the 5'-BCL2 fused 3' of a Vlambda gene that was upstream of another Vlambda / Jlambda complex carrying a non-producing configuration, indicating that the receptor editing mechanism was likely involved in this rearrangement. Our study revealed heterogeneous anatomy of the 5'-BCL2 / IGs fusion gene leading to transcriptional activation of BCL2, and suggested that the mechanisms underlying the formation of this particular oncogene / IGs recombination are not identical to those of t(14;18).

  5. Osiris and SOMBRERO inertial confinement fusion power plant designs. Volume 1, Executive summary and overview, Final report

    SciTech Connect

    Meier, W.R.; Bieri, R.L.; Monsler, M.J.

    1992-03-01

    Conceptual designs and assessments have been completed for two inertial fusion energy (IFE) electric power plants. The detailed designs and results of the assessment studies are presented in this report. Osiris is a heavy-ion-beam (HIB) driven power plant and SOMBRERO is a Krypton-Fluoride (KrF) laser-driven power plant. Both plants are sized for a net electric power of 1000 MWe.

  6. NAB2-STAT6 gene fusion and STAT6 immunoexpression in extrathoracic solitary fibrous tumors: the association between fusion variants and locations.

    PubMed

    Chuang, I-Chieh; Liao, Kuan-Cho; Huang, Hsuan-Ying; Kao, Yu-Chien; Li, Chien-Feng; Huang, Shih-Chiang; Tsai, Jen-Wei; Chen, Ko-Chin; Lan, Jui; Lin, Po-Chun

    2016-05-01

    Solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm harboring NAB2-STAT6 fusion, which drives STAT6 nuclear relocation. For extrathoracic SFTs, the clinical relevance of this molecular hallmark remains obscure. We assessed STAT6 immunoexpression for 61 extrathoracic SFTs exclusive of the meninges and head and neck, and 25 had analyzable RNAs to distinguish fusion variants by RT-PCR. The immunohistochemical and molecular findings were correlated with clincopathological features and disease-free survival (DFS). Twenty-eight males and 33 females had SFTs in the body cavities (n = 31), extremities (n = 17), and trunk (n = 13), categorized into 53 non-malignant and 8 malignant tumors. The vast majority (n = 57, 93%) exhibited distinctive STAT6 nuclear expression, including malignant ones. The common fusion variants were NAB2ex6-STAT6ex16/17 in 13 SFTs and NAB2ex4-STAT6ex2 in 8, while miscellaneous variants were detected only in 4 SFTs in the limbs and trunk but not in any body cavity-based cases (P = 0.026). The worse DFS was univariately associated with malignant histology (P = 0.04) but unrelated to tumor size, location, or fusion variant. Conclusively, extrathoracic SFTs mostly harbor NAB2ex6-STAT6ex16/17, followed by NAB2ex4-STAT6ex2. Miscellaneous variants are significantly rare in SFTs within the body cavities. The clinical aggressiveness of extrathoraic SFTs is associated with malignant histology but unrelated to the NAB2-STAT6 fusion variants. PMID:27039712

  7. NAB2-STAT6 gene fusion and STAT6 immunoexpression in extrathoracic solitary fibrous tumors: the association between fusion variants and locations.

    PubMed

    Chuang, I-Chieh; Liao, Kuan-Cho; Huang, Hsuan-Ying; Kao, Yu-Chien; Li, Chien-Feng; Huang, Shih-Chiang; Tsai, Jen-Wei; Chen, Ko-Chin; Lan, Jui; Lin, Po-Chun

    2016-05-01

    Solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm harboring NAB2-STAT6 fusion, which drives STAT6 nuclear relocation. For extrathoracic SFTs, the clinical relevance of this molecular hallmark remains obscure. We assessed STAT6 immunoexpression for 61 extrathoracic SFTs exclusive of the meninges and head and neck, and 25 had analyzable RNAs to distinguish fusion variants by RT-PCR. The immunohistochemical and molecular findings were correlated with clincopathological features and disease-free survival (DFS). Twenty-eight males and 33 females had SFTs in the body cavities (n = 31), extremities (n = 17), and trunk (n = 13), categorized into 53 non-malignant and 8 malignant tumors. The vast majority (n = 57, 93%) exhibited distinctive STAT6 nuclear expression, including malignant ones. The common fusion variants were NAB2ex6-STAT6ex16/17 in 13 SFTs and NAB2ex4-STAT6ex2 in 8, while miscellaneous variants were detected only in 4 SFTs in the limbs and trunk but not in any body cavity-based cases (P = 0.026). The worse DFS was univariately associated with malignant histology (P = 0.04) but unrelated to tumor size, location, or fusion variant. Conclusively, extrathoracic SFTs mostly harbor NAB2ex6-STAT6ex16/17, followed by NAB2ex4-STAT6ex2. Miscellaneous variants are significantly rare in SFTs within the body cavities. The clinical aggressiveness of extrathoraic SFTs is associated with malignant histology but unrelated to the NAB2-STAT6 fusion variants.

  8. Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript.

    PubMed

    Puig, Marta; Castellano, David; Pantano, Lorena; Giner-Delgado, Carla; Izquierdo, David; Gayà-Vidal, Magdalena; Lucas-Lledó, José Ignacio; Esko, Tõnu; Terao, Chikashi; Matsuda, Fumihiko; Cáceres, Mario

    2015-10-01

    Despite many years of study into inversions, very little is known about their functional consequences, especially in humans. A common hypothesis is that the selective value of inversions stems in part from their effects on nearby genes, although evidence of this in natural populations is almost nonexistent. Here we present a global analysis of a new 415-kb polymorphic inversion that is among the longest ones found in humans and is the first with clear position effects. This inversion is located in chromosome 19 and has been generated by non-homologous end joining between blocks of transposable elements with low identity. PCR genotyping in 541 individuals from eight different human populations allowed the detection of tag SNPs and inversion genotyping in multiple populations worldwide, showing that the inverted allele is mainly found in East Asia with an average frequency of 4.7%. Interestingly, one of the breakpoints disrupts the transcription factor gene ZNF257, causing a significant reduction in the total expression level of this gene in lymphoblastoid cell lines. RNA-Seq analysis of the effects of this expression change in standard homozygotes and inversion heterozygotes revealed distinct expression patterns that were validated by quantitative RT-PCR. Moreover, we have found a new fusion transcript that is generated exclusively from inverted chromosomes around one of the breakpoints. Finally, by the analysis of the associated nucleotide variation, we have estimated that the inversion was generated ~40,000-50,000 years ago and, while a neutral evolution cannot be ruled out, its current frequencies are more consistent with those expected for a deleterious variant, although no significant association with phenotypic traits has been found so far.

  9. A t(16;21)(p11;q22) in Acute Myeloid Leukemia (AML) Resulting in Fusion of the FUS/TLS and ERG Genes: A Review of the Literature.

    PubMed

    Buchanan, Justin; Tirado, Carlos A

    2016-01-01

    The t(16;21)(p11;q22) is a rare chromosomal abnormality that appears in approximately 1% of acute myeloid leukemia (AML) cases. Previously, between 50 and 60 cases have been reported. In this review, we will discuss the literature regarding t(16;21) as well as cases published. We compiled 68 cases from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer as well as 10 additional cases in the literature, for a total of 78 cases. The t(16;21) results in the TLS(FUS)-ERG fusion protein, which is believed to function as a transcriptional activator in leukemogenesis and has been demonstrated to interfere in normal pre-mRNA splicing functions of FUS/TLS. Reverse-transcriptase polymerase chain reaction of fusion transcripts in patients, has been demonstrated to have diagnostic significance in monitoring for minimal residual disease. Cytogenetically, about half of the cases had secondary chromosomal abnormalities; we found that trisomy 8 and 10 were the most common abnormalities, occurring in 9.1% of the otal cases for each. t(16;21) in AML has been described with various morphological features, such as phagocytosis and vacuolation, and is present in multiple FAB types. Immunophenotypic characteristics such as CD33 and CD34 expression have also been noted, and several studies have examined the relation between CD56 receptor expression and t(16;21) AML. In general, t(16;21) in AML is associated with a poor prognosis and this abnormality could serve as cytogenetic indicator in determining diagnosis and prognosis. Herein, we summarize the cytogenetic features found in the the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer for t(16;21) in AML, as well as review the current literature associated with t(16;21), AML and its features. PMID:27183148

  10. A sensitive HIV-1 envelope induced fusion assay identifies fusion enhancement of thrombin

    SciTech Connect

    Cheng, De-Chun; Zhong, Guo-Cai; Su, Ju-Xiang; Liu, Yan-Hong; Li, Yan; Wang, Jia-Ye; Hattori, Toshio; Ling, Hong; Zhang, Feng-Min

    2010-01-22

    To evaluate the interaction between HIV-1 envelope glycoprotein (Env) and target cell receptors, various cell-cell-fusion assays have been developed. In the present study, we established a novel fusion system. In this system, the expression of the sensitive reporter gene, firefly luciferase (FL) gene, in the target cells was used to evaluate cell fusion event. Simultaneously, constitutively expressed Renilla luciferase (RL) gene was used to monitor effector cell number and viability. FL gave a wider dynamic range than other known reporters and the introduction of RL made the assay accurate and reproducible. This system is especially beneficial for investigation of potential entry-influencing agents, for its power of ruling out the false inhibition or enhancement caused by the artificial cell-number variation. As a case study, we applied this fusion system to observe the effect of a serine protease, thrombin, on HIV Env-mediated cell-cell fusion and have found the fusion enhancement activity of thrombin over two R5-tropic HIV strains.

  11. Inertial Confinement Fusion. Annual report 10/1/98 through 9/30/99

    SciTech Connect

    Gibson, Jane

    1999-12-01

    General Atomics (GA) has served as the Inertial Confinement Fusion (ICF) Target Component Fabrication and Technology Development Support contractor for the U.S. Department of Energy since December 30, 1990. This report documents the technical activities of the period October 1, 1998 through September 30, 1999. During this period, GA and our partner Schafer Corporation were assigned 17 formal tasks in support of the ICF program and its five laboratories. A portion of the effort on these tasks included providing direct ''Onsite Support'' at Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), and Sandia National Laboratory (SNL). We fabricated and delivered over 1790 hohlraum mandrels and numerous other micromachined components to LLNL, LANL, and SNL. We produced more than 1380 glass and plastic target capsules over a wide range of sizes and designs (plus over 300 near target-quality capsules) for LLNL, LANL, SNL, and University of Rochester/Laboratory for Laser Energetic (UR/LLE). We also delivered various target foils and films for Naval Research Lab (NRL) and UWLLE in FY99. We fabricated a device to polish NIF-sized beryllium shells and prepared a laboratory for the safe operation of beryllium polishing activities. This report describes these target fabrication activities and the target fabrication and characterization development activities that made the deliveries possible. During FY99, the GA/Schafer portion of the GA/Schafer-UR/LLE-LANL team effort for design, procurement, installation, and testing of the OMEGA Cryogenic Target System (OCTS) that will field cryogenic targets on OMEGA was completed. All components of the OCTS were procured, fabricated, assembled, tested, and shipped to UR/LLE. Only minor documentation tasks remain to be done in FY00. The ICF program is anticipating experiments at the OMEGA laser and the National Ignition Facility (NIF) which will require targets containing cryogenic layered D2 or deuterium

  12. FY2014 FES (Fusion Energy Sciences) Theory & Simulation Performance Target, Final Report

    SciTech Connect

    Fu, Guoyong; Budny, Robert; Gorelenkov, Nikolai; Poli, Francesca; Chen, Yang; McClenaghan, Joseph; Lin, Zhihong; Spong, Don; Bass, Eric; Waltz, Ron

    2014-10-14

    We report here the work done for the FY14 OFES Theory Performance Target as given below: "Understanding alpha particle confinement in ITER, the world's first burning plasma experiment, is a key priority for the fusion program. In FY 2014, determine linear instability trends and thresholds of energetic particle-driven shear Alfven eigenmodes in ITER for a range of parameters and profiles using a set of complementary simulation models (gyrokinetic, hybrid, and gyrofluid). Carry out initial nonlinear simulations to assess the effects of the unstable modes on energetic particle transport". In the past year (FY14), a systematic study of the alpha-driven Alfven modes in ITER has been carried out jointly by researchers from six institutions involving seven codes including the transport simulation code TRANSP (R. Budny and F. Poli, PPPL), three gyrokinetic codes: GEM (Y. Chen, Univ. of Colorado), GTC (J. McClenaghan, Z. Lin, UCI), and GYRO (E. Bass, R. Waltz, UCSD/GA), the hybrid code M3D-K (G.Y. Fu, PPPL), the gyro-fluid code TAEFL (D. Spong, ORNL), and the linear kinetic stability code NOVA-K (N. Gorelenkov, PPPL). A range of ITER parameters and profiles are specified by TRANSP simulation of a hybrid scenario case and a steady-state scenario case. Based on the specified ITER equilibria linear stability calculations are done to determine the stability boundary of alpha-driven high-n TAEs using the five initial value codes (GEM, GTC, GYRO, M3D-K, and TAEFL) and the kinetic stability code (NOVA-K). Both the effects of alpha particles and beam ions have been considered. Finally, the effects of the unstable modes on energetic particle transport have been explored using GEM and M3D-K.

  13. CORSICA: A comprehensive simulation of toroidal magnetic-fusion devices. Final report to the LDRD Program

    SciTech Connect

    Crotinger, J.A.; LoDestro, L.; Pearlstein, L.D.; Tarditi, A.; Casper, T.A.; Hooper, E.B.

    1997-03-21

    In 1992, our group began exploring the requirements for a comprehensive simulation code for toroidal magnetic fusion experiments. There were several motivations for taking this step. First, the new machines being designed were much larger and more expensive than current experiments. Second, these new designs called for much more sophisticated control of the plasma shape and position, as well as the distributions of energy, mass, and current within the plasma. These factors alone made it clear that a comprehensive simulation capability would be an extremely valuable tool for machine design. The final motivating factor was that the national Numerical Tokamak Project (NTP) had recently received High Performance Computing and Communications (HPCC) Grand Challenge funding to model turbulent transport in tokamaks, raising the possibility that first-principles simulations of this process might be practical in the near future. We felt that the best way to capitalize on this development was to integrate the resulting turbulence simulation codes into a comprehensive simulation. Such simulations must include the effects of many microscopic length- and time-scales. In order to do a comprehensive simulation efficiently, the length- and time- scale disparities must be exploited. We proposed to do this by coupling the average or quasistatic effects from the fast time-scales to a slow-time-scale transport code for the macroscopic plasma evolution. In FY93-FY96 we received funding to investigate algorithms for computationally coupling such disparate-scale simulations and to implement these algorithms in a prototype simulation code, dubbed CORSICA. Work on algorithms and test cases proceeded in parallel, with the algorithms being incorporated into CORSICA as they became mature. In this report we discuss the methods and algorithms, the CORSICA code, its applications, and our plans for the future.

  14. Simultaneous gene inactivation and promoter reporting in cyanobacteria.

    PubMed

    Chen, Kangming; Xu, Xinyi; Gu, Liping; Hildreth, Michael; Zhou, Ruanbao

    2015-02-01

    Determining spatiotemporal gene expression and analyzing knockout mutant phenotypes have become powerful tools in elucidating the function of genes; however, genetic approaches for simultaneously inactivating a gene and monitoring its expression have not been reported in the literature. In this study, we designed a dual-functional gene knockout vector pZR606 that contains a multiple cloning site (MCS) for inserting the internal fragment of a target gene, with a gfp gene as its transcriptional marker located immediately downstream of the MCS. By using this gene knockout system, we inactivated ava_2679 from Anabaena variabilis ATCC 29413, as well as all2508, alr2887, alr3608, and all4388 from Anabaena sp. strain PCC 7120. The ava_2679 knockout mutant fails to grow diazotrophically. Morphological analysis of ava_2679 knockout mutant after nitrogen step-down revealed defective junctions between heterocysts and adjacent vegetative cells, and the heterocyst was 1.53-fold longer compared to wild-type heterocysts. The alr2887, all4388, and alr3608 mutant colonies turned yellow and showed lack of protracted growth when deprived of fixed nitrogen, consistent with the previous reports that alr2887, all4388, and alr3608 are Fox genes. The all2508 encodes a GTP-binding elongation factor (EF4/LepA), and its knockout mutant exhibited reduced diazotrophic growth. The heterocyst development of all2508 knockout was significantly delayed, and only about 4.0 % of vegetative cells differentiated to heterocysts after nitrogen deprivation for 72 h, decreased 49.6 % compared to wild-type. Thus, we discovered that All2508 may regulate heterocyst development spatiotemporally. Concurrently, the GFP reporter revealed that all five target gene expressions were up-regulated in response to nitrogen deprivation. We demonstrated that the pZR606-based specific gene knockout approach worked effectively for the five selected genes, including four previously identified Fox genes or Fox gene

  15. Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22-translocation.

    PubMed

    Panagopoulos, Ioannis; Thorsen, Jim; Gorunova, Ludmila; Haugom, Lisbeth; Bjerkehagen, Bodil; Davidson, Ben; Heim, Sverre; Micci, Francesca

    2013-07-01

    Endometrial stromal sarcomas (ESS) are genetically heterogeneous uterine tumors in which a JAZF1-SUZ12 chimeric gene resulting from the chromosomal translocation t(7;17)(p15;q21) as well as PHF1 rearrangements (in chromosomal band 6p21) with formation of JAZF1-PHF1, EPC1-PHF1, and MEAF6-PHF1 chimeras have been described. Here, we investigated two ESS characterized cytogenetically by the presence of a der(22)t(X;22)(p11;q13). Whole transcriptome sequencing one of the tumors identified a ZC3H7-BCOR chimeric transcript. Reverse transciptase-PCR with the ZC3H7B forward and BCOR reverse primer combinations confirmed the presence of a ZC3H7-BCOR chimeric transcript in both ESS carrying a der(22)t(X;22) but not in a control ESS with t(1;6) and the MEAF6-PHF1 fusion. Sequencing of the amplified cDNA fragments showed that in both cases ESS exon 10 of ZC3H7B (from 22q13; accession number NM_017590 version 4) was fused to exon 8 of BCOR (from Xp11; accession number NM_001123385 version 1). Reciprocal multiple BCOR-ZC3H7B cDNA fragments were amplified in only one case suggesting that ZC3H7B-BCOR, on the der(22)t(X;22), is the pathogenetically important fusion gene. The putative ZC3H7B-BCOR protein would contain the tetratricopeptide repeats and LD motif from ZC3H7B and the AF9 binding site (1093-1233aa), the 3 ankyrin repeats (1410-1509 aa), and the NSPC1 binding site of BCOR. Although the presence of these motifs suggests various functions of the chimeric protein, it is possible that its most important role may be in epigenetic regulation. Whether or not the (patho)genetic subsets JAZF1-SUZ12, PHF1 rearrangements, and ZC3H7B-BCOR correspond to any phenotypic, let alone clinically important, differences in ESS remain unknown. PMID:23580382

  16. Conference Report on the 3rd International Symposium on Lithium Application for Fusion Devices

    NASA Astrophysics Data System (ADS)

    Mazzitelli, G.; Hirooka, Y.; Hu, J. S.; Mirnov, S. V.; Nygren, R.; Shimada, M.; Ono, M.; Tabares, F. L.

    2015-02-01

    The third International Symposium on Lithium Application for Fusion Device (ISLA-2013) was held on 9-11 October 2013 at ENEA Frascati Centre with growing participation and interest from the community working on more general aspect of liquid metal research for fusion energy development. ISLA-2013 has been confirmed to be the largest and the most important meeting dedicated to liquid metal application for the magnetic fusion research. Overall, 45 presentation plus 5 posters were given, representing 28 institutions from 11 countries. The latest experimental results from nine magnetic fusion devices were presented in 16 presentations from NSTX (PPPL, USA), FTU (ENEA, Italy), T-11M (Trinity, RF), T-10 (Kurchatov Institute, RF), TJ-II (CIEMAT, Spain), EAST(ASIPP, China), HT-7 (ASIPP, China), RFX (Padova, Italy), KTM (NNC RK, Kazakhstan). Sessions were devoted to the following: (I) lithium in magnetic confinement experiments (facility overviews), (II) lithium in magnetic confinement experiments (topical issues), (III) special session on liquid lithium technology, (IV) lithium laboratory test stands, (V) Lithium theory/modelling/comments, (VI) innovative lithium applications and (VII) special Session on lithium-safety and lithium handling. There was a wide participation from the fusion technology communities, including IFMIF and TBM communities providing productive exchange with the physics oriented magnetic confinement liquid metal research groups. This international workshop will continue on a biennial basis (alternating with the Plasma-Surface Interactions (PSI) Conference) and the next workshop will be held at CIEMAT, Madrid, Spain, in 2015.

  17. Conference report on the 3rd International Symposium on Lithium Application for Fusion Devices

    SciTech Connect

    Mazzitelli, Guiseppe; Hirooka, Y.; Hu, J. S.; Mirnov, S. V.; Nygren, R.; Shimada, M.; Ono, M.; Tabares, F. L.

    2015-01-14

    The third International Symposium on Lithium Application for Fusion Device (ISLA-2013) was held on 9-11 October 2013 at ENEA Frascati Centre with growing participation and interest from the community working on more general aspect of liquid metal research for fusion energy development. ISLA-2013 has been confirmed to be the largest and the most important meeting dedicated to liquid metal application for the magnetic fusion research. Overall, 45 presentation plus 5 posters were given, representing 28 institutions from 11 countries. The latest experimental results from nine magnetic fusion devices were presented in 16 presentations from NSTX (PPPL, USA), FTU (ENEA, Italy), T-11M (Trinity, RF), T-10 (Kurchatov Institute, RF), TJ-II (CIEMAT, Spain), EAST(ASIPP, China), HT-7 (ASIPP, China), RFX (Padova, Italy), KTM (NNC RK, Kazakhstan). Sessions were devoted to the following: (I) lithium in magnetic confinement experiments (facility overviews), (II) lithium in magnetic confinement experiments (topical issues), (III) special session on liquid lithium technology, (IV) lithium laboratory test stands, (V) Lithium theory/modelling/comments, (VI) innovative lithium applications and (VII) special Session on lithium-safety and lithium handling. There was a wide participation from the fusion technology communities, including IFMIF and TBM communities providing productive exchange with the physics oriented magnetic confinement liquid metal research groups. Furthermore, this international workshop will continue on a biennial basis (alternating with the Plasma-Surface Interactions (PSI) Conference) and the next workshop will be held at CIEMAT, Madrid, Spain, in 2015.

  18. Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers.

    PubMed

    Andersson, Jan O; Roger, Andrew J

    2002-04-01

    Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes--the diplomonads--while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.

  19. Research Needs for Magnetic Fusion Energy Sciences. Report of the Research Needs Workshop (ReNeW) Bethesda, Maryland, June 8-12, 2009

    SciTech Connect

    2009-06-08

    Nuclear fusion - the process that powers the sun - offers an environmentally benign, intrinsically safe energy source with an abundant supply of low-cost fuel. It is the focus of an international research program, including the ITE R fusion collaboration, which involves seven parties representing half the world's population. The realization of fusion power would change the economics and ecology of energy production as profoundly as petroleum exploitation did two centuries ago. The 21st century finds fusion research in a transformed landscape. The worldwide fusion community broadly agrees that the science has advanced to the point where an aggressive action plan, aimed at the remaining barriers to practical fusion energy, is warranted. At the same time, and largely because of its scientific advance, the program faces new challenges; above all it is challenged to demonstrate the timeliness of its promised benefits. In response to this changed landscape, the Office of Fusion Energy Sciences (OFES ) in the US Department of Energy commissioned a number of community-based studies of the key scientific and technical foci of magnetic fusion research. The Research Needs Workshop (ReNeW) for Magnetic Fusion Energy Sciences is a capstone to these studies. In the context of magnetic fusion energy, ReNeW surveyed the issues identified in previous studies, and used them as a starting point to define and characterize the research activities that the advance of fusion as a practical energy source will require. Thus, ReNeW's task was to identify (1) the scientific and technological research frontiers of the fusion program, and, especially, (2) a set of activities that will most effectively advance those frontiers. (Note that ReNeW was not charged with developing a strategic plan or timeline for the implementation of fusion power.) This Report presents a portfolio of research activities for US research in magnetic fusion for the next two decades. It is intended to provide a

  20. Luciferase as a reporter of gene activity in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Since their development and introduction in the early days of plant genetic engineering, reporter genes have established a proven track record as effective tools for exploring the molecular underpinnings of gene regulation. When driven by appropriate genetic control systems (e.g. transcriptional pr...

  1. Fusion of the TBL1XR1 and HMGA1 genes in splenic hemangioma with t(3;6)(q26;p21).

    PubMed

    Panagopoulos, Ioannis; Gorunova, Ludmila; Bjerkehagen, Bodil; Lobmaier, Ingvild; Heim, Sverre

    2016-03-01

    RNA-sequencing of a splenic hemangioma with the karyotype 45~47,XX,t(3;6)(q26;p21) showed that this translocation generated a chimeric TBL1XR1-HMGA1 gene. This is the first time that this tumor has been subjected to genetic analysis, but the finding of an acquired clonal chromosome abnormality in cells cultured from the lesion and the presence of the TBL1XR1-HMGA1 fusion in them strongly favor the conclusion that splenic hemangiomas are of a neoplastic nature. Genomic PCR confirmed the presence of the TBL1XR1-HMGA1 fusion gene, and RT-PCR together with Sanger sequencing verified the presence of the fusion transcripts. The molecular consequences of the t(3;6) would be substantial. The cells carrying the translocation would retain only one functional copy of the wild-type TBL1XR1 gene while the other, rearranged allele could produce a putative truncated form of TBL1XR1 protein containing the LiSH and F-box-like domains. In the TBL1XR1-HMGA1 fusion transcript, furthermore, untranslated exons of HMGA1 are replaced by the first 5 exons of the TBL1XR1 gene. The result is that the entire coding region of HMGA1 comes under the control of the TBL1XR1 promoter, bringing about dysregulation of HMGA1. This is reminiscent of similar pathogenetic mechanisms involving high mobility genes in benign connective tissue tumors such as lipomas and leiomyomas.

  2. Fusion of the TBL1XR1 and HMGA1 genes in splenic hemangioma with t(3;6)(q26;p21)

    PubMed Central

    PANAGOPOULOS, IOANNIS; GORUNOVA, LUDMILA; BJERKEHAGEN, BODIL; LOBMAIER, INGVILD; HEIM, SVERRE

    2016-01-01

    RNA-sequencing of a splenic hemangioma with the karyotype 45~47,XX,t(3;6)(q26;p21) showed that this translocation generated a chimeric TBL1XR1-HMGA1 gene. This is the first time that this tumor has been subjected to genetic analysis, but the finding of an acquired clonal chromosome abnormality in cells cultured from the lesion and the presence of the TBL1XR1-HMGA1 fusion in them strongly favor the conclusion that splenic hemangiomas are of a neoplastic nature. Genomic PCR confirmed the presence of the TBL1XR1-HMGA1 fusion gene, and RT-PCR together with Sanger sequencing verified the presence of the fusion transcripts. The molecular consequences of the t(3;6) would be substantial. The cells carrying the translocation would retain only one functional copy of the wild-type TBL1XR1 gene while the other, rearranged allele could produce a putative truncated form of TBL1XR1 protein containing the LiSH and F-box-like domains. In the TBL1XR1-HMGA1 fusion transcript, furthermore, untranslated exons of HMGA1 are replaced by the first 5 exons of the TBL1XR1 gene. The result is that the entire coding region of HMGA1 comes under the control of the TBL1XR1 promoter, bringing about dysregulation of HMGA1. This is reminiscent of similar pathogenetic mechanisms involving high mobility genes in benign connective tissue tumors such as lipomas and leiomyomas. PMID:26708416

  3. Cloning-free regulated monitoring of reporter and gene expression

    PubMed Central

    al-Haj, Latifa; Al-Ahmadi, Wijdan; Al-Saif, Maher; Demirkaya, Omer; Khabar, Khalid SA

    2009-01-01

    Background The majority of the promoters, their regulatory elements, and their variations in the human genome remain unknown. Reporter gene technology for transcriptional activity is a widely used tool for the study of promoter structure, gene regulation, and signaling pathways. Construction of transcriptional reporter vectors, including use of cis-acting sequences, requires cloning and time-demanding manipulations, particularly with introduced mutations. Results In this report, we describe a cloning-free strategy to generate transcriptionally-controllable linear reporter constructs. This approach was applied in common transcriptional models of inflammatory response and the interferon system. In addition, it was used to delineate minimal transcriptional activity of selected ribosomal protein promoters. The approach was tested for conversion of genes into TetO-inducible/repressible expression cassettes. Conclusion The simple introduction and tuning of any transcriptional control in the linear DNA product renders promoter activation and regulated gene studies simple and versatile. PMID:19267938

  4. Final technical report. 1998 HU CFRT summer fusion high school workshop

    SciTech Connect

    Ali, Halima; Punjabi, Alkesh

    1999-07-01

    The center conducted its third High School Summer Fusion Science Workshop in Summer 1998. The center had only three faculty mentors available only for a part of Summer 1998, The center accepted four scholars in this workshop, Prof. Halima Ali coordinated this workshop. Each student was assigned to a research mentor according to the student's interest in a specific research area and problem. In the workshop in the center, the students received instructions and training in the basics of energy, plasma and fusion sciences. They also received one-on-one instructions and training by their mentors to further their understanding of the subject and to introduce to relevant concepts such as magnetic confinement fusion, tokamaks, diverters and area-preserving maps.

  5. Recurrence of cervical myelopathy secondary to a strut graft fracture 20 years after anterior decompression and fusion: a case report.

    PubMed

    Kida, Kazunobu; Takaya, Shogo; Tadokoro, Nobuaki; Kumon, Masashi; Kiyasu, Katsuhito; Kato, Tomonari; Takemasa, Ryuichi; Ikeuchi, Masahiko; Tani, Toshikazu

    2015-08-01

    This study reports on a 70-year-old man with recurrent cervical myelopathy 20 years after anterior decompression and fusion of C4-7 using a free vascularised strut graft. The recurrent myelopathy was secondary to a kyphotic deformity of a fractured graft and residual ossification of the posterior longitudinal ligament with stenosis at C3/4. Intraoperative spinal cord-evoked potentials indicated that spinal cord traction secondary to progressive kyphosis of the cervical spine after the graft fracture was the cause. The patient underwent laminoplasty at C3 and laminectomy at C4 to decompress the stenosis at C3/4 as well as posterior cervical spinal fusion at C3-7 with pedicle screws and a lateral mass screw and a bone graft to prevent further progression of the kyphosis. At postoperative 18 months, the patient's Japanese Orthopaedic Association score had improved to 14 from 8, and he could walk without support. PMID:26321562

  6. Summary of progress in laser fusion; advanced technology developments: National Laser Users Facility news; and a laser system report

    NASA Astrophysics Data System (ADS)

    1993-01-01

    This is an annual report covering research progress on laser fusion and the OMEGA Upgrade design and development. In laser fusion, line-spectroscopy methods were demonstrated to be useful in diagnosing the core temperature and densities of polymer-shell targets; a theoretical analysis of nonlocal heat transport effects on filamentation of light in plasmas confirms that the principle mechanism driving filamentation is kinetic thermal rather than ponderomotive; a new method (spatial beam deflection) to produce laser pulses of arbitrary shape was developed; laser-plasma x-ray emission was measured using photodiode arrays; experiments on long-scale-length plasmas have shown that smoothing by spectral dispersion has proven effective in reducing Raman scattering; a method for increasing the gas-retention time of polymer shell targets was developed by overcoating them with aluminum. Experiments relating to the OMEGA Upgrade are described.

  7. Transformation of tobacco plants by Yali PPO-GFP fusion gene and observation of subcellular localization.

    PubMed

    Qi, Jing; Li, Gui-Qin; Dong, Zhen; Zhou, Wei

    2016-01-01

    To explore the subcellular localization of Polyphenol oxidase (PPO) from Pyrus bretschneideri, the 1779 bp cDNA of PPO gene excluding the termination codon TAA was cloned and fused with GFP to construct a binary vector pBI121-PPO-GFP. Then, the binary vector was transformed into Nicotiana tabacum by the tumefanciens-mediated method. Using confocal laser scanning microscopy, green fluorescent signals were localized in chloroplasts of the transformed Nicotiana tabacum cell, suggesting that the Polyphenol oxidase from Pyrus bretschneideri was a chloroplast protein. PMID:27158362

  8. Distributed bosonic states and condensed-matter fusion. Final report, April-September 1989

    SciTech Connect

    Chubb, S.R.; Chubb, T.A.

    1990-02-01

    The article explains how it is possible for deuterons separated by macroscopic distances to interact in a nuclear fashion through the formation of a Bose Bloch Condensate (BBC) within a solid. Under suitable conditions, the formation of a BBC may lead to nuclear fusion and a variety of heretofore unobserved nuclear processes. The application of these ideas is used to explain the anomalous heating of Pd through the electrolysis of D{sub 2}O and LiOD and conclude that only a small concentration of BBC deutrons is required. Various experiments associated with condensed matter fusion are suggested that may provide a test of our theory.

  9. The GUS gene fusion system (Escherichia coli beta-D-glucuronidase gene), a useful tool in studies of root colonization by Fusarium oxysporum.

    PubMed Central

    Couteaudier, Y; Daboussi, M J; Eparvier, A; Langin, T; Orcival, J

    1993-01-01

    The plant-pathogenic fungus Fusarium oxysporum was successfully transformed with the beta-D-glucuronidase gene from Escherichia coli (gusA) (GUS system) in combination with the gene for nitrate reductase (niaD) as the selectable marker. The frequency of cotransformation, as determined by GUS expression on plates containing medium supplemented with 5-bromo-4-chloro-3-indolyl glucuronide (GUS+), was very high (up to 75%). Southern hybridization analyses of GUS+ transformants revealed that single or multiple copies of the gusA gene were integrated into the genomes. High levels of GUS activity are expressed in some transformants, but activity in F. oxysporum does not appear to be correlated with the copy number of the gusA gene. Since the highest activity was found in a transformant with a single copy, it can be assumed that sequence elements of F. oxysporum integrated upstream of the gene can act as a promoter or enhancer. Expression of the gusA gene was also detected during growth of the fungus in plants, indicating that the GUS system can be used as a sensitive and easy reporter gene assay in F. oxysporum. Images PMID:8328800

  10. Mutations in the Drosophila pushover gene confer increased neuronal excitability and spontaneous synaptic vesicle fusion

    SciTech Connect

    Richards, S.; Hillman, T.; Stern, M.

    1996-04-01

    We describe the identification of a gene called pushover (push), which affects both behavior and synaptic transmission at the neuromuscular junction. Adults carrying either of two mutations in push exhibit sluggishness, uncoordination, a defective escape response, and male sterility. Larvae defective in push exhibit increased release of transmitter at the neuromuscular junction. In particular, the frequency of spontaneous transmitter release and the amount of transmitter release evoked by nerve stimulation are each increased two- to threefold in push mutants at the lowest external [(Ca{sup 2+})] tested (0.15 mM). Furthermore, these mutants are more sensitive than wild type to application of the potassium channel-blocking drug quinidine: following quinidine application, push mutants, but not wild-type, display repetitive firing of the motor axon, leading to repetitive muscle postsynaptic potentials. The push gene thus might affect both neuronal excitability and the transmitter release process. Complementation tests and recombinational mapping suggest that the push mutations are allelic to a previously identified P-element-induced mutation, which also causes behavorial abnormalities and male sterility. 43 refs., 5 figs., 1 tab.

  11. Expression of metallothionein-human growth hormone fusion genes in transgenic mice results in disproportionate skeletal gigantism.

    PubMed

    Wolf, E; Rapp, K; Brem, G

    1991-01-01

    Transgenic mice harbouring mouse metallothionein I-human growth hormone (MT-hGH) fusion genes were produced using the microinjection technique. The bones of adult MT-hGH transgenic mice, which continuously expressed high levels of hGH in their serum, and age-matched controls lacking detectable concentrations of hGH were measured microscopically. In addition to analyzing absolute skeletal dimensions, measurements were related to the cube root of the maximum body weight of the same animal. Absolute values obtained from transgenic mice were significantly higher than those obtained from controls for most of the defined measurements. However, the increase in skeletal dimensions was mostly not as pronounced as the increase in body weight and all bones were not affected to the same extent. There was no significant correlation between the serum GH concentration in individual mice and their degree of bony overgrowth. A disproportionate skeletal gigantism in MT-hGH transgenic mice may result from time differences in epiphyseal union of various bones of both sexes as well as differences in mechanical bone loading due to a drastically increased body weight. Individual concentrations of locally produced tissue insulin-like growth factor I (IGF I) might also play a role. Possible effects of these factors are discussed. The results presented in this study show that MT-hGH transgenic mice provide a powerful tool for the investigation of hormonal regulation of bone growth. PMID:1938045

  12. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes.

    PubMed

    Rizk, Mazen; Antranikian, Garabed; Elleuche, Skander

    2012-11-01

    The reduction of fossil fuels, coupled with its increase in price, has made the search for alternative energy resources more plausible. One of the topics gaining fast interest is the utilization of lignocellulose, the main component of plants. Its primary constituents, cellulose and hemicellulose, can be degraded by a series of enzymes present in microorganisms, into simple sugars, later used for bioethanol production. Thermophilic bacteria have proven to be an interesting source of enzymes required for hydrolysis since they can withstand high and denaturing temperatures, which are usually required for processes involving biomass degradation. However, the cost associated with the whole enzymatic process is staggering. A solution for cost effective and highly active production is through the construction of multifunctional enzyme complexes harboring the function of more than one enzyme needed for the hydrolysis process. There are various strategies for the degradation of complex biomass ranging from the regulation of the enzymes involved, to cellulosomes, and proteins harboring more than one enzymatic activity. In this review, the construction of multifunctional biomass degrading enzymes through end-to-end gene fusions, and its impact on production and activity by choosing the enzymes and linkers is assessed.

  13. A simple, rapid, low-cost technique for naked-eye detection of urine-isolated TMPRSS2:ERG gene fusion RNA.

    PubMed

    Koo, Kevin M; Wee, Eugene J H; Mainwaring, Paul N; Trau, Matt

    2016-01-01

    The TMPRSS2:ERG gene fusion is one of a series of highly promising prostate cancer (PCa) biomarker alternatives to the controversial serum PSA. Current methods for detecting TMPRSS2:ERG are limited in terms of long processing time, high cost and the need for specialized equipment. Thus, there is an unmet need for less complex, faster, and cheaper methods to enable gene fusion detection in the clinic. We describe herein a simple, rapid and inexpensive assay which combines robust isothermal amplification technique with a novel visualization method for evaluating urinary TMPRSS2:ERG status at less than USD 5 and with minimal equipment. The assay is sensitive, and rapidly detects as low as 10(5) copies of TMPRSS2:ERG transcripts while maintaining high levels of specificity. PMID:27470540

  14. A simple, rapid, low-cost technique for naked-eye detection of urine-isolated TMPRSS2:ERG gene fusion RNA

    PubMed Central

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

    2016-01-01

    The TMPRSS2:ERG gene fusion is one of a series of highly promising prostate cancer (PCa) biomarker alternatives to the controversial serum PSA. Current methods for detecting TMPRSS2:ERG are limited in terms of long processing time, high cost and the need for specialized equipment. Thus, there is an unmet need for less complex, faster, and cheaper methods to enable gene fusion detection in the clinic. We describe herein a simple, rapid and inexpensive assay which combines robust isothermal amplification technique with a novel visualization method for evaluating urinary TMPRSS2:ERG status at less than USD 5 and with minimal equipment. The assay is sensitive, and rapidly detects as low as 105 copies of TMPRSS2:ERG transcripts while maintaining high levels of specificity. PMID:27470540

  15. Molecular cytogenetic findings in a three-way novel variant of t(1;8;21)(p35;q22;q22): a unique relocation of the AML1/ETO fusion gene 1p35 in AML-M2.

    PubMed

    Ahmad, Firoz; Kokate, Prajakta; Chheda, Pratiksha; Dalvi, Rupa; Das, Bibhu Ranjan; Mandava, Swarna

    2008-01-15

    Acute myeloid leukemia (AML) is a malignant neoplasm of hematopoietic stem cells characterized by an abnormal proliferation of myeloid precursors, a reduced rate of apoptosis, and an arrest in cellular differentiation. The present report deals with the results of hematologic, immunophenotypic, cytogenetic, fluorescence in situ hybridization (FISH), and molecular analyses of a 53-year-old female patient diagnosed with AML-M2. Cytogenetic and FISH analysis revealed a complex translocation involving three chromosomes showing t(1;8;21)(p35;q22;q22). The observation of breakpoints at 8q22 and 21q22 suggests a rearrangement of the ETO and AML1 genes, respectively. Using a dual-color FISH test with ETO and AML1 probes, an AML1/ETO fusion signal on the derivative 1p35 instead of der(8) was demonstrated. To the best of our knowledge, this is the first report about the relocation of the AML1/ETO fusion gene to the 1p35 rather than der(8), suggesting the presence of a novel variant of t(8;21)(q22;q22) in the observed patient. PMID:18206543

  16. LDRD final report on confinement of cluster fusion plasmas with magnetic fields.

    SciTech Connect

    Argo, Jeffrey W.; Kellogg, Jeffrey W.; Headley, Daniel Ignacio; Stoltzfus, Brian Scott; Waugh, Caleb J.; Lewis, Sean M.; Porter, John Larry, Jr.; Wisher, Matthew; Struve, Kenneth William; Savage, Mark Edward; Quevedo, Hernan J.; Bengtson, Roger

    2011-11-01

    Two versions of a current driver for single-turn, single-use 1-cm diameter magnetic field coils have been built and tested at the Sandia National Laboratories for use with cluster fusion experiments at the University of Texas in Austin. These coils are used to provide axial magnetic fields to slow radial loss of electrons from laser-produced deuterium plasmas. Typical peak field strength achievable for the two-capacitor system is 50 T, and 200 T for the ten-capacitor system. Current rise time for both systems is about 1.7 {mu}s, with peak current of 500 kA and 2 MA, respectively. Because the coil must be brought to the laser, the driver needs to be portable and drive currents in vacuum. The drivers are complete but laser-plasma experiments are still in progress. Therefore, in this report, we focus on system design, initial tests, and performance characteristics of the two-capacitor and ten-capacitors systems. The questions of whether a 200 T magnetic field can retard the breakup of a cluster-fusion plasma, and whether this field can enhance neutron production have not yet been answered. However, tools have been developed that will enable producing the magnetic fields needed to answer these questions. These are a two-capacitor, 400-kA system that was delivered to the University of Texas in 2010, and a 2-MA ten-capacitor system delivered this year. The first system allowed initial testing, and the second system will be able to produce the 200 T magnetic fields needed for cluster fusion experiments with a petawatt laser. The prototype 400-kA magnetic field driver system was designed and built to test the design concept for the system, and to verify that a portable driver system could be built that delivers current to a magnetic field coil in vacuum. This system was built copying a design from a fixed-facility, high-field machine at LANL, but made to be portable and to use a Z-machine-like vacuum insulator and vacuum transmission line. This system was sent to the

  17. Inertial confinement fusion quarterly report, July--September 1994. Volume 4, Number 4

    SciTech Connect

    Honea, E.

    1994-09-01

    The ICF Quarterly continues with six articles in this issue describing recent developments in the Inertial Confinement Fusion (ICF) Program at Lawrence Livermore National Laboratory. The topics include plasma characterization, production of millimeter scale-length plasmas for studying laser-plasma instabilities, hohlraum physics, three-dimensional hydrodynamic modeling, crystal growth, and laser-beam smoothing.

  18. Fusion reactor materials semiannual progress report for the period ending September 30, 1988

    SciTech Connect

    none,

    1989-04-01

    This paper discusses the following topics on fusion reactor materials: irradiation, facilities, test matrices, and experimental methods; dosimetry, damage parameters, and activation calculations; materials engineering and design requirements; fundamental mechanical behavior; radiation effects; development of structural alloys; solid breeding materials; and ceramics.

  19. A burning plasma program strategy to advance fusion energy. Report of the Fusion Energy Sciences Advisory Committee, Burning Plasma Strategy Panel

    SciTech Connect

    None, None

    2002-09-01

    Fusion energy shows great promise to contribute to securing the energy future of humanity. The risk of conflicts arising from energy shortages and supply cutoffs, as well as the risk of severe environmental impacts from existing methods of energy production, are strong reasons to pursue fusion energy now. The world effort to develop fusion energy is at the threshold of a new stage in its research: the investigation of burning plasmas. This investigation, 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. The defining feature of a burning plasma is that it is self-heated: the 100 million degree temperature of the plasma is maintained mainly by the heat generated by the fusion reactions themselves, as occurs in burning stars. The fusion-generated alpha particles produce new physical phenomena that are strongly coupled together as a nonlinear complex system. Understanding all elements of this system poses a major challenge to fundamental plasma physics. The technology needed to produce and control a burning plasma presents challenges in engineering science similarly essential to the development of fusion energy.

  20. Reporter genes for embryogenesis research in livestock species.

    PubMed

    Habermann, F A; Wuensch, A; Sinowatz, F; Wolf, E

    2007-09-01

    Currently, our knowledge of early mammalian embryogenesis, stem cell differentiation and development is largely based on studies performed in mouse models. However, in important aspects, e.g. the timing of epigenetic reprogramming and embryonic genome activation, livestock species probably reflect far more closely the situation in men and other non-rodent mammals. A major challenge is the fact that in mammals, the development of individual zygotes is highly variable and vulnerable, and the outcome is uncertain. Valid indicators of the highly heterogeneous development and health status, and the actual developmental potential of individual oocytes, zygotes or embryos would be crucially important to tap the full power of holistic transcriptome and proteome analyses. Fluorescent reporter proteins opened new vistas for embryology and stem cell research: they can be used as reporters for the activity of gene promoters or tagged to functional proteins to study their intracellular localization in living cells, tissues and organisms. Fluorescent reporter genes may be used to microscopically observe key processes of early development. Thus, novel information related to developmental potential can be obtained from living embryos before processing them, e.g. for "-omic" studies. This review summarizes the main current reporter gene techniques and gene transfer approaches, which might be suitable for the investigation of early embryogenesis in livestock mammals. The potential of promoter reporter genes is exemplified by a bovine model system for quantitative monitoring of transcriptional reactivation of the so-called pluripotency gene POU5F1 in cloned bovine embryos.

  1. Conference report on the 3rd International Symposium on Lithium Application for Fusion Devices

    DOE PAGESBeta

    Mazzitelli, Guiseppe; Hirooka, Y.; Hu, J. S.; Mirnov, S. V.; Nygren, R.; Shimada, M.; Ono, M.; Tabares, F. L.

    2015-01-14

    The third International Symposium on Lithium Application for Fusion Device (ISLA-2013) was held on 9-11 October 2013 at ENEA Frascati Centre with growing participation and interest from the community working on more general aspect of liquid metal research for fusion energy development. ISLA-2013 has been confirmed to be the largest and the most important meeting dedicated to liquid metal application for the magnetic fusion research. Overall, 45 presentation plus 5 posters were given, representing 28 institutions from 11 countries. The latest experimental results from nine magnetic fusion devices were presented in 16 presentations from NSTX (PPPL, USA), FTU (ENEA, Italy),more » T-11M (Trinity, RF), T-10 (Kurchatov Institute, RF), TJ-II (CIEMAT, Spain), EAST(ASIPP, China), HT-7 (ASIPP, China), RFX (Padova, Italy), KTM (NNC RK, Kazakhstan). Sessions were devoted to the following: (I) lithium in magnetic confinement experiments (facility overviews), (II) lithium in magnetic confinement experiments (topical issues), (III) special session on liquid lithium technology, (IV) lithium laboratory test stands, (V) Lithium theory/modelling/comments, (VI) innovative lithium applications and (VII) special Session on lithium-safety and lithium handling. There was a wide participation from the fusion technology communities, including IFMIF and TBM communities providing productive exchange with the physics oriented magnetic confinement liquid metal research groups. Furthermore, this international workshop will continue on a biennial basis (alternating with the Plasma-Surface Interactions (PSI) Conference) and the next workshop will be held at CIEMAT, Madrid, Spain, in 2015.« less

  2. Bis-three-way junction nanostructure and DNA machineries for ultrasensitive and specific detection of BCR/ABL fusion gene by chemiluminescence imaging.

    PubMed

    Xu, Yongjie; Bian, Xintong; Sang, Ye; Li, Yujian; Li, Dandan; Cheng, Wei; Yin, Yibing; Ju, Huangxian; Ding, Shijia

    2016-01-01

    A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method has been developed for ultrasensitive and specific detection of BCR/ABL fusion gene based on bis-three-way junction (bis-3WJ) nanostructure and cascade DNA machineries. Bis-3WJ probes are designed logically to recognize BCR/ABL fusion gene, which forms the stable bis-3WJ nanostructure for the activation of polymerase/nicking enzyme machineries in cascade, resulting in synthesis of DNAzyme subunits. These DNAzyme subunits can form integrated DNAzyme by self-assembly to catalyze CL substrate, thus providing an amplified signal for the sensing events or outputs for AND logic operation. The imaging method achieved ultrasensitive detection of BCR/ABL fusion gene with a low detection limit down to 23 fM. And this method exhibited wide linear ranges over seven orders of magnitude and excellent discrimination ability toward target. In addition, an acceptable recovery was obtained in complex matrix. It is notable that this biosensing strategy possesses merits of homogenous, isothermal and label-free assay system. Therefore, these merits endow the developed imaging method with a potential tool for CML diagnosis. PMID:27577607

  3. Bis-three-way junction nanostructure and DNA machineries for ultrasensitive and specific detection of BCR/ABL fusion gene by chemiluminescence imaging

    PubMed Central

    Xu, Yongjie; Bian, Xintong; Sang, Ye; Li, Yujian; Li, Dandan; Cheng, Wei; Yin, Yibing; Ju, Huangxian; Ding, Shijia

    2016-01-01

    A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method has been developed for ultrasensitive and specific detection of BCR/ABL fusion gene based on bis-three-way junction (bis-3WJ) nanostructure and cascade DNA machineries. Bis-3WJ probes are designed logically to recognize BCR/ABL fusion gene, which forms the stable bis-3WJ nanostructure for the activation of polymerase/nicking enzyme machineries in cascade, resulting in synthesis of DNAzyme subunits. These DNAzyme subunits can form integrated DNAzyme by self-assembly to catalyze CL substrate, thus providing an amplified signal for the sensing events or outputs for AND logic operation. The imaging method achieved ultrasensitive detection of BCR/ABL fusion gene with a low detection limit down to 23 fM. And this method exhibited wide linear ranges over seven orders of magnitude and excellent discrimination ability toward target. In addition, an acceptable recovery was obtained in complex matrix. It is notable that this biosensing strategy possesses merits of homogenous, isothermal and label-free assay system. Therefore, these merits endow the developed imaging method with a potential tool for CML diagnosis. PMID:27577607

  4. Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes.

    PubMed

    Oka, Masahiro; Mura, Sonoko; Yamada, Kohji; Sangel, Percival; Hirata, Saki; Maehara, Kazumitsu; Kawakami, Koichi; Tachibana, Taro; Ohkawa, Yasuyuki; Kimura, Hiroshi; Yoneda, Yoshihiro

    2016-01-07

    The nucleoporin Nup98 is frequently rearranged to form leukemogenic Nup98-fusion proteins with various partners. However, their function remains largely elusive. Here, we show that Nup98-HoxA9, a fusion between Nup98 and the homeobox transcription factor HoxA9, forms nuclear aggregates that frequently associate with facultative heterochromatin. We demonstrate that stable expression of Nup98-HoxA9 in mouse embryonic stem cells selectively induces the expression of Hox cluster genes. Genome-wide binding site analysis revealed that Nup98-HoxA9 is preferentially targeted and accumulated at Hox cluster regions where the export factor Crm1 is originally prebound. In addition, leptomycin B, an inhibitor of Crm1, disassembled nuclear Nup98-HoxA9 dots, resulting in the loss of chromatin binding of Nup98-HoxA9 and Nup98-HoxA9-mediated activation of Hox genes. Collectively, our results indicate that highly selective targeting of Nup98-fusion proteins to Hox cluster regions via prebound Crm1 induces the formation of higher order chromatin structures that causes aberrant Hox gene regulation.

  5. Detection of EML4-ALK fusion gene in Chinese non-small cell lung cancer by using a sensitive quantitative real-time reverse transcriptase PCR technique.

    PubMed

    Fu, Sha; Wang, Fang; Shao, Qiong; Zhang, Xu; Duan, Li-Ping; Zhang, Xiao; Zhang, Li; Shao, Jian-Yong

    2015-04-01

    Anaplastic lymphoma kinase (ALK) rearrangement is present in approximately 5% of lung adenocarcinoma. Clinical trials on ALK inhibitor phase I to III have shown an interesting disease control rate and acceptable tolerability in ALK rearrangement patients. In clinical application, the precise diagnostic strategy for identifying ALK rearrangements remains to be determined. In this study, ALK rearrangement was screened by using quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR), direct sequencing, 2 fluorescence in situ hybridization (FISH) assays, and immunohistochemistry in 173 lung adenocarcinomas. We identified 18 cases (10.4%) with EML4-ALK fusion-positive by qRT-PCR, and all were positive for EML4-ALK fusion gene validated by direct sequencing. The result was consistent with that of other methods. Furthermore, of the 18 EML4-ALK fusion-positive cases, 16 (9.2%) were positive by using EML4-ALK fusion probe FISH, and 15 (8.7%) were positive by using ALK break-apart probe FISH and immunohistochemistry staining. Of the 18 ALK fusion-positive lung adenocarcinomas, 8 cases (44.4%) were histologically diagnosed as subtypes of cribriform adenocarcinoma, 7 cases (38.9%) as cribriform adenocarcinoma mixed with papillary and/or mucinous pattern, 2 cases (11.1%) as papillary adenocarcinoma, and 1 case (5.6%) as mucinous adenocarcinoma. In the present study, the ALK rearrangement frequency detected by qRT-PCR in Chinese NSCLC patients was higher than that in the western populations. QRT-PCR is a rapid, sensitive technology that could be used as a screening tool for identifying EML4-ALK fusion-positive NSCLC patients who would be sensitive for receiving ALK inhibitor therapy.

  6. Inertial Conference Fusion Semiannual Report October 1999 - March 2000, Volume 1, Number 1

    SciTech Connect

    Hammel, B A

    2000-03-01

    improvements can have important implications for the interpretation of inertial confinement fusion capsule implosions. The fifth article reports on experiments using the OMEGA laser that investigate symmetry control in hohlraums. The experiments explore a control method where different pointings are used for different groups of beams and the beams are staggered in time. This gives a dynamic beam pointing adjustment during the laser pulse. Measurements of the capsule symmetry show agreement with simulations and show the ability to control low-mode drive asymmetries. The sixth article reports on the observation of an intense high-energy proton beam produced by irradiating a thin-foil target with the petawatt laser. This experiment is important for understanding new mechanisms of ion acceleration using high-intensity short-pulse lasers. Proton beams of the type observed here could be of interest for applications ranging from medicine to fast ignition.

  7. Big fusion, little fusion

    NASA Astrophysics Data System (ADS)

    Chen, Frank; ddtuttle

    2016-08-01

    In reply to correspondence from George Scott and Adam Costley about the Physics World focus issue on nuclear energy, and to news of construction delays at ITER, the fusion reactor being built in France.

  8. FINESSE: study of the issues, experiments and facilities for fusion nuclear technology research and development. Interim report. Volume II

    SciTech Connect

    Abdou, M.

    1984-10-01

    The Nuclear Fusion Issues chapter contains a comprehensive list of engineering issues for fusion reactor nuclear components. The list explicitly defines the uncertainties associated with the engineering option of a fusion reactor and addresses the potential consequences resulting from each issue. The next chapter identifies the fusion nuclear technology testing needs up to the engineering demonstration stage. (MOW)

  9. FINESSE: study of the issues, experiments and facilities for fusion nuclear technology research and development. Interim report. Volume I

    SciTech Connect

    Abdou, M.

    1984-10-01

    The following chapters are included in this study: (1) fusion nuclear issues, (2) survey of experimental needs, (3) requirements of the experiments, (4) non-fusion facilities, (5) fusion facilities for nuclear experiments, and (6) fusion research and development scenarios. (MOW)

  10. Development of Plant Gene Vectors for Tissue-Specific Expression Using GFP as a Reporter Gene

    NASA Technical Reports Server (NTRS)

    Jackson, Jacquelyn; Egnin, Marceline; Xue, Qi-Han; Prakash, C. S.

    1997-01-01

    Reporter genes are widely employed in plant molecular biology research to analyze gene expression and to identify promoters. Gus (UidA) is currently the most popular reporter gene but its detection requires a destructive assay. The use of jellyfish green fluorescent protein (GFP) gene from Aequorea Victoria holds promise for noninvasive detection of in vivo gene expression. To study how various plant promoters are expressed in sweet potato (Ipomoea batatas), we are transcriptionally fusing the intron-modified (mGFP) or synthetic (modified for codon-usage) GFP coding regions to these promoters: double cauliflower mosaic virus 35S (CaMV 35S) with AMV translational enhancer, ubiquitin7-intron-ubiquitin coding region (ubi7-intron-UQ) and sporaminA. A few of these vectors have been constructed and introduced into E. coli DH5a and Agrobacterium tumefaciens EHA105. Transient expression studies are underway using protoplast-electroporation and particle bombardment of leaf tissues.

  11. Heavy Ion Fusion Accelerator Research (HIFAR) year-end report, October 1, 1987--March 31, 1988

    SciTech Connect

    Not Available

    1988-06-01

    The basic objective of the Heavy Ion Fusion Accelerator Research (HIFAR) program is to assess the suitability of heavy ion accelerators as igniters for Inertial Confinement Fusion (ICF). A specific accelerator technology, the induction linac, has been studied at Lawrence 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 validation of new accelerator strategies, to cut costs. Key elements to be addressed include: beam quality limits set by transverse and longitudinal beam physics; development of induction accelerating modules, and multiple-beam hardware, at affordable costs; acceleration of multiple beams with current amplification -- both new features in a linac -- without significant dilution of the optical quality of beams; and final bunching, transport, and accurate focusing on a small target.

  12. Inertial confinement fusion quarterly report, April--June 1994. Volume 4, Number 3

    SciTech Connect

    Shaw, M.J.

    1994-06-01

    This issue of the ICF Quarterly contains six articles covering a wide range of activities within the Inertial Confinement Fusion (ICF) Program. It concentrates on target design; theoretical spectral analysis of ICF capsule surfaces; laser fusion experimental methods; and an alternative ICF design, based on ultrafast, ultrapowerful lasers. A key issue for the success of the ICF process is the hydrodynamic stability of the imploding capsule. There are two primary sources of instability growth in the ICF process: (1) asymmetries in the x-ray flux that drive the compression lead to asymmetric in the imploding surface; (2) imperfections on the capsule surface can grow into large perturbations, degrading the capsule performance. In recent years, a great deal of effort, both experimentally and theoretically, has been spent to enhance the Program`s ability to measure, model, and minimize instability growth during an implosion. Four the articles in this issue discuss this subject.

  13. Heavy Ion Fusion Accelerator Research (HIFAR) year-end report, April 1, 1990--September 30, 1990

    SciTech Connect

    Not Available

    1990-12-01

    The basic objective of the Heavy Ion Fusion Accelerator Research (HIFAR) program is to assess the suitability of heavy ion accelerators as igniters for Inertial Confinement Fusion (ICF). A specific accelerator technology, induction acceleration, is being studied at the Lawrence Berkeley Laboratory and at the Lawrence Livermore National Laboratory. 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 validation of new accelerator strategies to cut costs. Key elements to be addressed include: (1) beam quality limits set by transverse and longitudinal beam physics; (2) development of induction accelerating modules, and multiple-beam hardware, at affordable costs; (3) acceleration of multiple beams with current amplification without significant dilution of the optical quality of the beams; (4) final bunching, transport, and accurate focusing on a small target.

  14. Fluid mechanics of fusion lasers. Final report, September 11, 1978-June 5, 1980

    SciTech Connect

    Shwartz, J; Kulkarny, V A; Ausherman, D A; Legner, H H; Sturtevant, B

    1980-01-01

    Flow loop components required to operate continuous-flow, repetitively-pulsed CO/sub 2/ and KrF laser drivers for ICF were identified and their performance requirements were specified. It was found that the laser flow loops can have a major effect on the laser beam quality and overall efficiency. The pressure wave suppressor was identified as the most critical flow loop component. The performance of vented side-wall suppressors was evaluated both analytically and experimentally and found capable of meeting the performance requirements of the CO/sub 2/ and KrF fusion lasers. All other laser flow loop components are essentially similar to those used in conventional, low speed wind tunnels and are therefore well characterized and can be readily incorporated into fusion laser flow systems designs.

  15. Heavy Ion Fusion Accelerator Research (HIFAR) year-end report, April 1--September 30, 1988

    SciTech Connect

    Not Available

    1988-12-01

    The basic objective of the Heavy Ion Fusion Accelerator Research (HIFAR) program is to assess the suitability of heavy ion accelerators as igniters for Inertial Confinement Fusion (ICF). A specific accelerator technology, the induction linac, has been studied at the Lawrence 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 validation of new accelerator strategies, to cut costs. Key elements to be addressed include: beam quality limits set by transverse and longitudinal beam physics; development of induction accelerating modules, and multiple-beam hardware, at affordable costs; acceleration of multiple beams with current amplification --both new features in a linac -- without significant dilution of the optical quality of the beams; final bunching, transport, and accurate focusing on a small target.

  16. Report of the DOE panel on low activation materials for fusion applications

    SciTech Connect

    Conn, R.W.

    1983-06-01

    In February, 1982, the Office of Fusion Energy, DOE, through its Division of Development and Technology, established a Panel to examine materials with attractive radioactivation characteristics for applications in fusion power reactors. Since February, the Panel has met together and in subgroups numerous times. Input from knowledgeable people was elicited via a two day workshop held at UCLA in April, 1982. The agenda, titles of talks, and speakers are given in Appendix II. We present here a synopsis of the Panel's findings based upon both external information provided to us and upon the work and deliberations of the Panel itself. Conclusions and recommendations follow. Background technical information brought together by the Panel is relegated to Appendices III and IV.

  17. Multimodality Imaging of Gene Transfer with a Receptor-Based Reporter Gene

    PubMed Central

    Chen, Ron; Parry, Jesse J.; Akers, Walter J.; Berezin, Mikhail Y.; El Naqa, Issam M.; Achilefu, Samuel; Edwards, W. Barry; Rogers, Buck E.

    2010-01-01

    Gene therapy trials have traditionally used tumor and tissue biopsies for assessing the efficacy of gene transfer. Non-invasive imaging techniques offer a distinct advantage over tissue biopsies in that the magnitude and duration of gene transfer can be monitored repeatedly. Human somatostatin receptor subtype 2 (SSTR2) has been used for the nuclear imaging of gene transfer. To extend this concept, we have developed a somatostatin receptor–enhanced green fluorescent protein fusion construct (SSTR2-EGFP) for nuclear and fluorescent multimodality imaging. Methods An adenovirus containing SSTR2-EGFP (AdSSTR2-EGFP) was constructed and evaluated in vitro and in vivo. SCC-9 human squamous cell carcinoma cells were infected with AdEGFP, AdSSTR2, or AdSSTR2-EGFP for in vitro evaluation by saturation binding, internalization, and fluorescence spectroscopy assays. In vivo biodistribution and nano-SPECT imaging studies were conducted with mice bearing SCC-9 tumor xenografts directly injected with AdSSTR2-EGFP or AdSSTR2 to determine the tumor localization of 111In-diethylenetriaminepentaacetic acid (DTPA)-Tyr3-octreotate. Fluorescence imaging was conducted in vivo with mice receiving intratumoral injections of AdSSTR2, AdSSTR2-EGFP, or AdEGFP as well as ex vivo with tissues extracted from mice. Results The similarity between AdSSTR2-EGFP and wild-type AdSSTR2 was demonstrated in vitro by the saturation binding and internalization assays, and the fluorescence emission spectra of cells infected with AdSSTR2-EGFP was almost identical to the spectra of cells infected with wild-type AdEGFP. Biodistribution studies demonstrated that the tumor uptake of 111In-DTPA-Tyr3-octreotate was not significantly different (P > 0.05) when tumors (n = 5) were injected with AdSSTR2 or AdSSTR2-EGFP but was significantly greater than the uptake in control tumors. Fluorescence was observed in tumors injected with AdSSTR2-EGFP and AdEGFP in vivo and ex vivo but not in tumors injected with AdSSTR2

  18. Helium Find Thaws the Cold Fusion Trail.

    ERIC Educational Resources Information Center

    Pennisi, E.

    1991-01-01

    Reported is a study of cold fusion in which trace amounts of helium, possible evidence of an actual fusion reaction, were found. Research methodology is detailed. The controversy over the validity of experimental results with cold fusion are reviewed. (CW)

  19. Low-density hydrocarbon foams for laser fusion targets: Progress report, 1986

    SciTech Connect

    Chen, C.; Cook, R.C.; Haendler, B.L.; Hair, L.M.; Kong, F.M.; Letts, S.A.

    1987-06-01

    We describe progress made during 1986 in the development of direct-drive hydrocarbon foam targets for laser fusion. The foam materials are polystyrene and resorcinolformaldehyde. The processes for making the foams, their properties, characterization techniques, and the relationships of their properties to target specifications are presented. In the final section, we discuss statistical experimental design techniques that are being used to optimize the foams. 12 refs., 14 figs., 2 tabs.

  20. IFMIF - International Fusion Materials Irradiation Facility Conceptual Design Activity/Interim Report

    SciTech Connect

    Rennich, M.J.

    1995-12-01

    Environmental acceptability, safety, and economic viability win ultimately be the keys to the widespread introduction of fusion power. This will entail the development of radiation- resistant and low- activation materials. These low-activation materials must also survive exposure to damage from neutrons having an energy spectrum peaked near 14 MeV with annual radiation doses in the range of 20 displacements per atom (dpa). Testing of candidate materials, therefore, requires a high-flux source of high energy neutrons. The problem is that there is currently no high-flux source of neutrons in the energy range above a few MeV. The goal, is therefore, to provide an irradiation facility for use by fusion material scientists in the search for low-activation and damage-resistant materials. An accellerator-based neutron source has been established through a number of international studies and workshops` as an essential step for materials development and testing. The mission of the International Fusion Materials Irradiation Facility (IFMIF) is to provide an accelerator-based, deuterium-lithium (D-Li) neutron source to produce high energy neutrons at sufficient intensity and irradiation volume to test samples of candidate materials up to about a full lifetime of anticipated use in fusion energy reactors. would also provide calibration and validation of data from fission reactor and other accelerator-based irradiation tests. It would generate material- specific activation and radiological properties data, and support the analysis of materials for use in safety, maintenance, recycling, decommissioning, and waste disposal systems.

  1. [Aplication of demineralized human bone matrix in the surgical dental fusion treatment. Report of a case].

    PubMed

    Mora-Rincones, Oscar A; Corona-Rodríguez, Julio C; Díaz-Carvajal, Alvaro L; Franco-Carrero, Isabel C

    2008-06-01

    The purpose of this work is to present a surgical alternative in the treatment of the dental fusions through the placement of demineralized human bone matrix (DHBM) (Grafton Putty)*, immediately after the separation and extraction of the fused tooth to the permanent one. The dental fusion is a dental anomaly of union, that consists in the union of two dental germs during development. It could happen at any of the dental germ evolution stages from the dental sheet or from more advanced processes of differentiation. For the clinical treatment, an allograft of DHBM with osteoinductive and osteoconductive properties was used. This had several factors of bone growth, it allowed the gradual growth of a new bone that helped to correct the bone defects post-extraction and to cover the exposed distal wall of the remaining permanent tooth. The clinic evaluation and the periapical and panoramic radiographies images were used for the clinical control. It can be concluded that the surgical separation and the extraction of the tooth with less anatomical likeness to the contralateral and the placement of the DHBM, represent a surgical treatment alternative of the dental fusion.

  2. Inertial confinement fusion. 1995 ICF annual report, October 1994--September 1995

    SciTech Connect

    1996-06-01

    Lawrence Livermore National Laboratory`s (LLNL`s) Inertial Confinement Fusion (ICF) Program is a Department of Energy (DOE) Defense Program research and advanced technology development program focused on the goal of demonstrating thermonuclear fusion ignition and energy gain in the laboratory. During FY 1995, the ICF Program continued to conduct ignition target physics optimization studies and weapons physics experiments in support of the Defense Program`s stockpile stewardship goals. It also continued to develop technologies in support of the performance, cost, and schedule goals of the National Ignition Facility (NIF) Project. The NIF is a key element of the DOE`s Stockpile Stewardship and Management Program. In addition to its primary Defense Program goals, 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 to inertial fusion energy (IFE). Also, ICF technologies have had spin-off applications for industrial and governmental use. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  3. A YAC contig encompassing the XRCC5 (Ku80) DNA repair gene and complementation of defective cells by YAC protoplast fusion

    SciTech Connect

    Blunt, T.; Priestley, A.; Hafezparast, M.; McMillan, T.

    1995-11-20

    The Chinese hamster ovary xrs mutants are sensitive to ionizing radiation, defective in DNA double-strand break rejoining, and unable to carry out V(D)J recombination effectively. Recently, the gene defective in these mutants, XRCC5, has been shown to encode Ku80, a component of the Ku protein and DNA-dependent protein kinase. We present here a YAC contig involving 25 YACs mapping to the region 2q33-q34, which encompasses the XRCC5 gene. Eight new markers for this region of chromosome 2 are identified. YACs encoding the Ku80 gene were transferred to xrs cells by protoplast fusion, and complementation of all the defective phenotypes has been obtained with two YACs. We discuss the advantages and disadvantages of this approach as a strategy for cloning human genes complementing defective rodent cell lines. 44 refs., 2 figs., 4 tabs.

  4. Conserved mechanism of PLAG1 activation in salivary gland tumors with and without chromosome 8q12 abnormalities: identification of SII as a new fusion partner gene.

    PubMed

    Aström, A K; Voz, M L; Kas, K; Röijer, E; Wedell, B; Mandahl, N; Van de Ven, W; Mark, J; Stenman, G

    1999-02-15

    We have previously shown (K. Kas et al, Nat. Genet., 15: 170-174, 1997) that the developmentally regulated zinc finger gene pleomorphic adenoma gene 1 (PLAG1) is the target gene in 8q12 in pleomorphic adenomas of the salivary glands with t(3;8)(p21;q12) translocations. The t(3;8) results in promoter swapping between PLAG1 and the constitutively expressed gene for beta-catenin (CTNNB1), leading to activation of PLAG1 expression and reduced expression of CTNNB1. Here we have studied the expression of PLAG1 by Northern blot analysis in 47 primary benign and malignant human tumors with or without cytogenetic abnormalities of 8q12. Overexpression of PLAG1 was found in 23 tumors (49%). Thirteen of 17 pleomorphic adenomas with a normal karyotype and 5 of 10 with 12q13-15 abnormalities overexpressed PLAG1, which demonstrates that PLAG1 activation is a frequent event in adenomas irrespective of karyotype. In contrast, PLAG1 was overexpressed in only 2 of 11 malignant salivary gland tumors analyzed, which suggests that, at least in salivary gland tumors, PLAG1 activation preferentially occurs in benign tumors. PLAG1 over-expression was also found in three of nine mesenchymal tumors, i.e., in two uterine leiomyomas and one leiomyosarcoma. RNase protection, rapid amplification of 5'-cDNA ends (5'-RACE), and reverse transcription-PCR analyses of five adenomas with a normal karyotype revealed fusion transcripts in three tumors. Nucleotide sequence analysis of these showed that they contained fusions between PLAG1 and CTNNB1 (one case) or PLAG1 and a novel fusion partner gene, i.e., the gene encoding the transcription elongation factor SII (two cases). The fusions occurred in the 5' noncoding region of PLAG1, leading to exchange of regulatory control elements and, as a consequence, activation of PLAG1 gene expression. Because all of the cases had grossly normal karyotypes, the rearrangements must result from cryptic rearrangements. The results suggest that in addition to

  5. TMPRSS2:ERG Gene Fusion Predicts Subsequent Detection of Prostate Cancer in Patients With High-Grade Prostatic Intraepithelial Neoplasia

    PubMed Central

    Park, Kyung; Dalton, James T.; Narayanan, Ramesh; Barbieri, Christopher E.; Hancock, Michael L.; Bostwick, David G.; Steiner, Mitchell S.; Rubin, Mark A.

    2014-01-01

    Purpose High-grade prostatic intraepithelial neoplasia (HGPIN) is considered a precursor lesion of prostate cancer (PCa). The predictive value of ERG gene fusion in HGPIN for PCa was interrogated as a post hoc analysis in the context of a randomized clinical trial. Patients and Methods The GTx Protocol G300104 randomly assigned 1,590 men with biopsy-diagnosed HGPIN to receive toremifene or placebo for 3 years or until a diagnosis of PCa was made on prostate biopsy. As part of this phase III clinical trial, a central pathologist evaluated biopsies of patients with isolated HGPIN at baseline and 12, 24, and 36 months of follow-up. ERG immunohistochemistry was performed on biopsies from 461 patients and evaluated for protein overexpression. Results ERG expression was detected in 11.1% of patients (51 of 461 patients) with isolated HGPIN. In the first year and during the 3-year clinical trial, 14.7% and 36.9% of 461 patients were diagnosed with PCa, respectively. Patients with ERG expression were more likely to develop PCa, with 27 (53%) of 51 ERG-positive and 143 (35%) of 410 ERG-negative patients experiencing progression to PCa (P = .014, Fisher's exact test). ERG expression was not associated with age, baseline PSA, Gleason score, or tumor volume. Conclusion This study underscores the necessity of more stringent follow-up for men with HGPIN that is also positive for ERG overexpression. Clinicians should consider molecular characterization of HGPIN as a means to improve risk stratification. PMID:24297949

  6. The 3;21 translocation in myelodysplasia results in a fusion transcript between the AML1 gene and the gene for EAP, a highly conserved protein associated with the Epstein-Barr virus small RNA EBER 1.

    PubMed Central

    Nucifora, G; Begy, C R; Erickson, P; Drabkin, H A; Rowley, J D

    1993-01-01

    In the 8;21 translocation, the AML1 gene, located at chromosome band 21q22, is translocated to chromosome 8 (q22), where it is fused to the ETO gene and transcribed as a chimeric gene. AML1 is the human homolog of the recently cloned mouse gene pebp2 alpha B, homologous to the DNA binding alpha subunit of the polyoma enhancer factor pebp2. AML1 is also involved in a translocation with chromosome 3 that is seen in patients with therapy-related acute myeloid leukemia and myelodysplastic syndrome and in chronic myelogenous leukemia in blast crisis. We have isolated a fusion cDNA clone from a t(3;21) library derived from a patient with therapy-related myelodysplastic syndrome; this clone contains sequences from AML1 and from EAP, which we have now localized to band 3q26. EAP has previously been characterized as a highly expressed small nuclear protein of 128 residues (EBER 1) associated with Epstein-Barr virus small RNA. The fusion clone contains the DNA binding 5' part of AML1 that is fused to ETO in the t(8;21) and, in addition, at least one other exon. The translocation replaces the last nine codons of AML1 with the last 96 codons of EAP. The fusion does not maintain the correct reading frame of EAP and may not lead to a functional chimeric protein. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 PMID:8395054

  7. Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

    PubMed Central

    Tomazou, Eleni M.; Sheffield, Nathan C.; Schmidl, Christian; Schuster, Michael; Schönegger, Andreas; Datlinger, Paul; Kubicek, Stefan; Bock, Christoph; Kovar, Heinrich

    2015-01-01

    Summary Transcription factor fusion proteins can transform cells by inducing global changes of the transcriptome, often creating a state of oncogene addiction. Here, we investigate the role of epigenetic mechanisms in this process, focusing on Ewing sarcoma cells that are dependent on the EWS-FLI1 fusion protein. We established reference epigenome maps comprising DNA methylation, seven histone marks, open chromatin states, and RNA levels, and we analyzed the epigenome dynamics upon downregulation of the driving oncogene. Reduced EWS-FLI1 expression led to widespread epigenetic changes in promoters, enhancers, and super-enhancers, and we identified histone H3K27 acetylation as the most strongly affected mark. Clustering of epigenetic promoter signatures defined classes of EWS-FLI1-regulated genes that responded differently to low-dose treatment with histone deacetylase inhibitors. Furthermore, we observed strong and opposing enrichment patterns for E2F and AP-1 among EWS-FLI1-correlated and anticorrelated genes. Our data describe extensive genome-wide rewiring of epigenetic cell states driven by an oncogenic fusion protein. PMID:25704812

  8. Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas.

    PubMed

    Specht, Katja; Zhang, Lei; Sung, Yun-Shao; Nucci, Marisa; Dry, Sarah; Vaiyapuri, Sumathi; Richter, Gunther H S; Fletcher, Christopher D M; Antonescu, Cristina R

    2016-04-01

    Small blue round cell tumors (SBRCTs) are a heterogenous group of tumors that are difficult to diagnose because of overlapping morphologic, immunohistochemical, and clinical features. About two-thirds of EWSR1-negative SBRCTs are associated with CIC-DUX4-related fusions, whereas another small subset shows BCOR-CCNB3 X-chromosomal paracentric inversion. Applying paired-end RNA sequencing to an SBRCT index case of a 44-year-old man, we identified a novel BCOR-MAML3 chimeric fusion, which was validated by reverse transcription polymerase chain reaction and fluorescence in situ hybridization techniques. We then screened a total of 75 SBRCTs lacking EWSR1, FUS, SYT, CIC, and BCOR-CCNB3 abnormalities for BCOR break-apart probes by fluorescence in situ hybridization to detect potential recurrent BCOR gene rearrangements outside the typical X-chromosomal inversion. Indeed, 8/75 (11%) SBRCTs showed distinct BCOR gene rearrangements, with 2 cases each showing either a BCOR-MAML3 or the alternative ZC3H7B-BCOR fusion, whereas no fusion partner was detected in the remaining 4 cases. Gene expression of the BCOR-MAML3-positive index case showed a distinct transcriptional profile with upregulation of HOX-gene signature, compared with classic Ewing's sarcoma or CIC-DUX4-positive SBRCTs. The clinicopathologic features of the SBRCTs with alternative BCOR rearrangements were also compared with a group of BCOR-CCNB3 inversion-positive cases, combining 11 from our files with a meta-analysis of 42 published cases. The BCOR-CCNB3-positive tumors occurred preferentially in children and in bone, in contrast to alternative BCOR-rearranged SBRCTs, which presented in young adults, with a variable anatomic distribution. Furthermore, BCOR-rearranged tumors often displayed spindle cell areas, either well defined in intersecting fascicles or blending with the round cell component, which appears distinct from most other fusion-positive SBRCTs and shares histologic overlap with poorly

  9. Molecular machines encoded by bacterially-derived multi-domain gene fusions that potentially synthesize, N-methylate and transfer long chain polyamines in diatoms.

    PubMed

    Michael, Anthony J

    2011-09-01

    Silica glass formation in diatoms requires the biosynthesis of unusual, very long chain polyamines (LCPA) composed of iterated aminopropyl units. Diatoms processively synthesize LCPA, N-methylate the amine groups and transfer concatenated, N-dimethylated aminopropyl groups to silaffin proteins. Here I show that diatom genomes possess signal peptide-containing gene fusions of bacterially-derived polyamine biosynthetic enzymes S-adenosylmethionine decarboxylase (AdoMetDC) and an aminopropyltransferase, sometimes fused to a eukaryotic histone N-methyltransferase domain, that potentially synthesize and N-methylate LCPA. Fusions of similar, alternatively configured domains but with a catalytically dead AdoMetDC and in one case a Tudor domain, may N-dimethylate and transfer multiple aminopropyl unit polyamines onto silaffin proteins.

  10. Inertial confinement fusion target component fabrication and technology development support. Annual report, October 1, 1994--September 30, 1995

    SciTech Connect

    Hoppe, M.

    1996-05-01

    On December 30, 1990, the US Department of Energy entered into a contract with General Atomics (GA) to be the Inertial Confinement Fusion (ICF) Target Component Fabrication and Technology Development Support contractor. This report documents the technical activities of the period October 1, 1994 through September 30, 1995. During this period, GA was assigned 15 tasks in support of the Inertial Confinement Fusion program and its laboratories. A portion of the effort on these tasks included providing direct ``Onsite Support`` at Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), and Sandia National Laboratory Albuquerque (SNLA). The ICF program is anticipating experiments at the National Ignition Facility (NIF) and the OMEGA Upgrade. Both facilities will require capsules containing layered D{sub 2} or deuterium-tritium (D-T) fuel. The authors are part of the National Cryogenic Target Program to create and demonstrate viable ways to generate and characterize cryogenic layers. Progress has been made on ways to both create viable layers and to characterize them. They continued engineering, assembly and testing of equipment for a cryogenic target handling system for University of Rochester`s Laboratory for Laser Energetics (UR/LLE) that will fill, transport, layer, and characterize targets filled with cryogenic fuel, and insert these cryogenic targets into the OMEGA Upgrade target chamber for laser implosion experiments. This report summarizes and documents the technical progress made on these tasks.

  11. Trans-activation function of a 3 prime truncated X gene-cell fusion product from integrated hepatitis B virus DNA in chronic hepatitis tissues

    SciTech Connect

    Takada, Shinako; Koike, Katsuro )

    1990-08-01

    To investigate the expression and transactivation function of the X gene in integrated hepatitis B virus (HBV) DNA from chronic hepatitis tissues, a series of transfectants containing cloned integrated HBV DNAs was made and analyzed for X mRNA expression and trans-activation activity by using a chloramphenicol acetyltransferase assay. Most of the integrated HBV DNAs expressed X mRNA and encoded a product with trans-activation activity in spite of the loss of the 3{prime} end region of the X gene due to integration. From cDNA cloning and sequence analysis of X mRNA transcribed from native or integrated HBV DNA, the X protein was found to be translated from the X open reading frame without splicing. For integrated HBV DNA, transcription was extended to a cellular flanking DNA and an X gene-cell fusion transcript was terminated by using a cellular poly(A) signal. The amino acid sequence deduced from an X-cell fusion transcript indicated truncation of the carboxyl-terminal five amino acids, but the upstream region of seven amino acids conserved among hepadnaviruses was retained in the integrated HBV DNA, suggesting that this conserved region is essential for the transactivation function of the X protein. These findings support the following explanation for hepatocarcinogenesis by HBV DNA integration: the expression of a cellular oncogene(s) is transactivated at the time of chronic infection by the increasing amounts of the integrated HBV gene product(s), such as the X-cell fusion product.

  12. A novel hNIS/tdTomato fusion reporter for visualizing the relationship between the cellular localization of sodium iodide symporter and its iodine uptake function under heat shock treatment.

    PubMed

    Yeom, Chan Joo; Chung, Taemoon; Youn, Hyewon; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key

    2015-01-01

    The function of membrane-localized sodium iodide symporter (NIS) determines the efficacy of radioiodine therapy in thyroid cancer. Here, we describe a dual mode reporter fused with human NIS (hNIS) and a red fluorescent protein named tandem dimeric Tomato (tdTomato) for the in vitro and in vivo imaging of hNIS protein expression, localization, and iodide uptake function. Human cervical epithelial adenocarcinoma cell line (HeLa)-hNIS/tdTomato cells were established by transducing a fusion gene expressing hNIS/tdTomato under the control of a cytomegalovirus promoter. Fluorescence imaging, confocal microscopy, and an 125I uptake assay were performed to validate the integrity of the fusion protein. Actinomycin D and cycloheximide were used to block newly synthesized hNIS proteins. In vivo images were acquired using a gamma camera and a Maestro fluorescence imaging device. The fluorescence intensity of membrane-localized hNIS and 125I uptake both were increased after heat shock. Scintigraphy and fluorescence imaging indicated specific accumulation of the hNIS/tdTomato fusion protein in xenografted tumors, supporting the utility of this system for in vivo monitoring of hNIS expression and activity. We developed a novel hNIS/tdTomato dual mode reporter that enables visualization of the expression, localization, and iodine uptake function of hNIS in vitro and in vivo. PMID:25773964

  13. A novel hNIS/tdTomato fusion reporter for visualizing the relationship between the cellular localization of sodium iodide symporter and its iodine uptake function under heat shock treatment.

    PubMed

    Yeom, Chan Joo; Chung, Taemoon; Youn, Hyewon; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key

    2015-01-01

    The function of membrane-localized sodium iodide symporter (NIS) determines the efficacy of radioiodine therapy in thyroid cancer. Here, we describe a dual mode reporter fused with human NIS (hNIS) and a red fluorescent protein named tandem dimeric Tomato (tdTomato) for the in vitro and in vivo imaging of hNIS protein expression, localization, and iodide uptake function. Human cervical epithelial adenocarcinoma cell line (HeLa)-hNIS/tdTomato cells were established by transducing a fusion gene expressing hNIS/tdTomato under the control of a cytomegalovirus promoter. Fluorescence imaging, confocal microscopy, and an 125I uptake assay were performed to validate the integrity of the fusion protein. Actinomycin D and cycloheximide were used to block newly synthesized hNIS proteins. In vivo images were acquired using a gamma camera and a Maestro fluorescence imaging device. The fluorescence intensity of membrane-localized hNIS and 125I uptake both were increased after heat shock. Scintigraphy and fluorescence imaging indicated specific accumulation of the hNIS/tdTomato fusion protein in xenografted tumors, supporting the utility of this system for in vivo monitoring of hNIS expression and activity. We developed a novel hNIS/tdTomato dual mode reporter that enables visualization of the expression, localization, and iodine uptake function of hNIS in vitro and in vivo.

  14. FDG PET/CT and MR imaging of CD34-negative soft-tissue solitary fibrous tumor with NAB2-STAT6 fusion gene.

    PubMed

    Nishio, Jun; Iwasaki, Hiroshi; Aoki, Mikiko; Nabeshima, Kazuki; Naito, Masatoshi

    2015-02-01

    Extrapleural solitary fibrous tumor (SFT) is an uncommon mesenchymal neoplasm of intermediate biological potential. Herein, we describe the radiological, histological, immunohistochemical and molecular genetic features of an SFT arising in the left thigh of a 55-year-old woman. Magnetic resonance imaging exhibited a well-defined mass with intermediate signal intensity on T1-weighted sequences and heterogeneous high signal intensity on T2-weighted sequences. Contrast-enhanced T1-weighted sequences showed strong homogeneous enhancement of the mass. A prominent vascular pedicle was visible. Integrated positron-emission tomography (PET)/computed tomographic (CT) scan demonstrated a moderate 18F-fluorodeoxyglucose (FDG) uptake (maximum standardized uptake value, 4.45) in the mass. Following an open biopsy, wide excision of the tumor was performed. Histologically, the tumor was composed of a proliferation of spindle cells in a fibrous stroma with focal hyalinization. Thin-walled branching hemangiopericytoma-like vessels were observed. Immunohistochemically, the tumor cells were diffusely positive for signal transducer and activator of transcription 6 (STAT6) but negative for CD34. The MIB-1 labeling index was less than 5%. Subsequent reverse transcriptase-polymerase chain reaction analysis identified a nerve growth factor inducible-A binding protein 2-STAT6 gene fusion. Our case supports the utility of STAT6 immunohistochemistry as an adjunct in the diagnosis of soft-tissue SFT with loss of CD34 positivity. To the best of our knowledge, this is the first report showing the FDG PET/CT findings of soft-tissue SFT.

  15. FDG PET/CT and MR imaging of CD34-negative soft-tissue solitary fibrous tumor with NAB2-STAT6 fusion gene.

    PubMed

    Nishio, Jun; Iwasaki, Hiroshi; Aoki, Mikiko; Nabeshima, Kazuki; Naito, Masatoshi

    2015-02-01

    Extrapleural solitary fibrous tumor (SFT) is an uncommon mesenchymal neoplasm of intermediate biological potential. Herein, we describe the radiological, histological, immunohistochemical and molecular genetic features of an SFT arising in the left thigh of a 55-year-old woman. Magnetic resonance imaging exhibited a well-defined mass with intermediate signal intensity on T1-weighted sequences and heterogeneous high signal intensity on T2-weighted sequences. Contrast-enhanced T1-weighted sequences showed strong homogeneous enhancement of the mass. A prominent vascular pedicle was visible. Integrated positron-emission tomography (PET)/computed tomographic (CT) scan demonstrated a moderate 18F-fluorodeoxyglucose (FDG) uptake (maximum standardized uptake value, 4.45) in the mass. Following an open biopsy, wide excision of the tumor was performed. Histologically, the tumor was composed of a proliferation of spindle cells in a fibrous stroma with focal hyalinization. Thin-walled branching hemangiopericytoma-like vessels were observed. Immunohistochemically, the tumor cells were diffusely positive for signal transducer and activator of transcription 6 (STAT6) but negative for CD34. The MIB-1 labeling index was less than 5%. Subsequent reverse transcriptase-polymerase chain reaction analysis identified a nerve growth factor inducible-A binding protein 2-STAT6 gene fusion. Our case supports the utility of STAT6 immunohistochemistry as an adjunct in the diagnosis of soft-tissue SFT with loss of CD34 positivity. To the best of our knowledge, this is the first report showing the FDG PET/CT findings of soft-tissue SFT. PMID:25667482

  16. Application of β-Lactamase Reporter Fusions as an Indicator of Effector Protein Secretion during Infections with the Obligate Intracellular Pathogen Chlamydia trachomatis

    PubMed Central

    Mueller, Konrad E.; Fields, Kenneth A.

    2015-01-01

    Chlamydia spp. utilize multiple secretion systems, including the type III secretion system (T3SS), to deploy host-interactive effector proteins into infected host cells. Elucidation of secreted proteins has traditionally required ectopic expression in a surrogate T3SS followed by immunolocalization of endogenous candidate effectors to confirm secretion by chlamydiae. The ability to transform Chlamydia and achieve stable expression of recombinant gene products has enabled a more direct assessment of secretion. We adapted TEM-1 β-lactamase as a reporter system for assessment of chlamydial protein secretion. We provide evidence that this system facilitates visualization of secretion in the context of infection. Specifically, our findings provide definitive evidence that C. trachomatis CT695 is secreted during infection. Follow-up indirect immunofluorescence studies confirmed CT695 secretion and indicate that this effector can be secreted at multiple points during the chlamydial developmental cycle. Our results indicate that the BlaM-fusion reporter assay will allow efficacious identification of novel secreted proteins. Moreover, this approach can easily be adapted to enable more sophisticated studies of the secretion process in Chlamydia. PMID:26258949

  17. Spinal cord compression by multistrand cables after solid posterior atlantoaxial fusion. Report of three cases.

    PubMed

    Sudo, Hideki; Abumi, Kuniyoshi; Ito, Manabu; Kotani, Yoshihisa; Minami, Akio

    2002-10-01

    The sublaminar wiring procedure has been commonly used for stabilizing the atlantoaxial complex. Multistrand braided cables were introduced in the early 1990s. In previous biomechanical studies these cables were demonstrated to be superior to monofilament wires in terms of their flexibility, mechanical strength, and fatigue-related characteristics. To the authors' knowledge, they are the first to describe clinically the occurrence of delayed spinal cord compression resulting from multistrand cables after the completion of rigid spinal arthrodesis in the upper cervical spine. Three patients underwent posterior atlantoaxial fusion in which two sublaminar multistrand cables were placed. Between 15 and 48 months postoperatively, they suffered from upper- and lower-extremity numbness as well as gait disturbance. Plain radiography and computerized tomography myelography revealed spinal cord compression caused by the sublaminar cables, although fusion was complete and physiological alignment was maintained at the fused segment. The radiographs obtained immediately after surgery demonstrated that the initial cable placement had been properly performed. The shape of the cable at the initial surgery was oval and then gradually became circular. The anterior arc of the circular shape of the cable in fact led to the spinal cord compression. Considering the mechanism of this late complication, a cable tends to spring open because of its high flexibility and becomes circular shaped even after the complete arthrodesis. When applying multistrand cables for intersegmental fixation at the atlantoaxial complex, delayed complications related to bowing of the cables is possible. PMID:12408393

  18. Heavy Ion Fusion Accelerator Research (HIFAR) half-year report, October 1, 1988--March 31, 1989

    SciTech Connect

    Not Available

    1989-06-01

    The basic objective of the Heavy Ion Fusion Accelerator Research (HIFAR) program is to assess the suitability of heavy ion accelerators as igniters for Inertial Confinement Fusion (ICF). A specific accelerator technology, the induction linac, has been studied at the Lawrence 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 validation of new accelerator strategies, to cut costs. Key elements to be addressed include: beam quality limits set by transverse and longitudinal beam physics; development of induction accelerating modules, and multiple-beam hardware, at affordable costs; acceleration of multiple beams with current amplification --both new features in a linac -- without significant dilution of the optical quality of the beams; and final bunching, transport, and accurate focusing on a small target.

  19. Materials recycle and waste management in fusion power reactors. Progress report for 1982

    SciTech Connect

    Vogler, S.; Jung, J.; Steindler, M.J.; Maya, I.; Levine, H.E.; Peterman, D.D.; Strausburg, S.; Schultz, K.R.

    1983-01-01

    Several components of a STARFIRE fusion reactor have been studied. The breeding ratios were calculated as a function of lithium enrichment and neutron multiplier for systems containing either Li/sub 2/O or LiAlO/sub 2/. The lithium requirements for a fusion economy were also estimated for those cases and the current US resources were found to be adequate. However, competition with other lithium demands in the future emphasizes the need for recovering and reusing lithium. The radioactivities induced in the breeder and the impurities responsible for their formation were determined. The residual radioactivities of several low-activation structural materials were compared with the radioactivity from the prime candidate alloy (PCA) a titanium modified Type 316 stainless steel used in STARFIRE. The impurities responsible for the radioactivity levels were identified. From these radioactive impurity levels it was determined that V15Cr5Ti could meet the requirements for shallow land burial as specified by the Nuclear Regulatory Commission (10CFR61), whereas PCA would require a more restrictive disposal mode, i.e. in a geologic medium. The costs for each of these disposal modes were then estimated.

  20. Dual-modality gene reporter for in vivo imaging.

    PubMed

    Patrick, P Stephen; Hammersley, Jayne; Loizou, Louiza; Kettunen, Mikko I; Rodrigues, Tiago B; Hu, De-En; Tee, Sui-Seng; Hesketh, Robin; Lyons, Scott K; Soloviev, Dmitry; Lewis, David Y; Aime, Silvio; Fulton, Sandra M; Brindle, Kevin M

    2014-01-01

    The ability to track cells and their patterns of gene expression in living organisms can increase our understanding of tissue development and disease. Gene reporters for bioluminescence, fluorescence, radionuclide, and magnetic resonance imaging (MRI) have been described but these suffer variously from limited depth penetration, spatial resolution, and sensitivity. We describe here a gene reporter, based on the organic anion transporting protein Oatp1a1, which mediates uptake of a clinically approved, Gd(3+)-based, hepatotrophic contrast agent (gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid). Cells expressing the reporter showed readily reversible, intense, and positive contrast (up to 7.8-fold signal enhancement) in T1-weighted magnetic resonance images acquired in vivo. The maximum signal enhancement obtained so far is more than double that produced by MRI gene reporters described previously. Exchanging the Gd(3+) ion for the radionuclide, (111)In, also allowed detection by single-photon emission computed tomography, thus combining the spatial resolution of MRI with the sensitivity of radionuclide imaging.

  1. An efficient expression of human growth hormone (hGH) in the milk of transgenic mice using rat beta-casein/hGH fusion genes.

    PubMed

    Lee, C S; Kim, K; Yu, D Y; Lee, K K

    1996-03-01

    In order to produce human growth hormone (hGH) in the milk of transgenic mice, two expression vectors for hGH differing in their 3' flanking sequences were constructed by placing the genomic sequences of hGH gene under the control of the rat beta-casein gene promotor. The 3' flanking sequences of the expression constructs were derived from either the hGH gene (pBCN1GH) or the rat beta-casein gene (pBCN2GH). Transgenic lines bearing pBCN1GH expressed hGH more efficiently than those bearing pBCN2GH in the milk (19-5500 micrograms/mL vs 0.7-2 micrograms/mL). In particular, one of the BCN1GH lines expressed hGH as much as 5500 +/- 620 micrograms/mL. Northern blot analysis showed that the transgene expression was specifically confined to the mammary gland and developmentally regulated like the endogenous mouse beta-casein gene in the mammary gland. However, a low level of nonmammary expression was also detected with more sensitive assay methods. In conclusion, the rat beta-casein/hGH fusion gene could direct an efficient production of hGH in a highly tissue-and stage-specific manner in the transgenic mice and the 3' flanking sequences of hGH gene had an important role for the efficient expression.

  2. Developing a Novel Gene-Delivery Vector System Using the Recombinant Fusion Protein of Pseudomonas Exotoxin A and Hyperthermophilic Archaeal Histone HPhA.

    PubMed

    Deng, Xin; Zhang, Guoli; Zhang, Ling; Feng, Yan; Li, Zehong; Wu, GuangMou; Yue, Yuhuan; Li, Gensong; Cao, Yu; Zhu, Ping

    2015-01-01

    Non-viral gene delivery system with many advantages has a great potential for the future of gene therapy. One inherent obstacle of such approach is the uptake by endocytosis into vesicular compartments. Receptor-mediated gene delivery method holds promise to overcome this obstacle. In this study, we developed a receptor-mediated gene delivery system based on a combination of the Pseudomonas exotoxin A (PE), which has a receptor binding and membrane translocation domain, and the hyperthermophilic archaeal histone (HPhA), which has the DNA binding ability. First, we constructed and expressed the rPE-HPhA fusion protein. We then examined the cytotoxicity and the DNA binding ability of rPE-HPhA. We further assessed the efficiency of transfection of the pEGF-C1 plasmid DNA to CHO cells by the rPE-HPhA system, in comparison to the cationic liposome method. The results showed that the transfection efficiency of rPE-HPhA was higher than that of cationic liposomes. In addition, the rPE-HPhA gene delivery system is non-specific to DNA sequence, topology or targeted cell type. Thus, the rPE-HPhA system can be used for delivering genes of interest into mammalian cells and has great potential to be applied for gene therapy. PMID:26556098

  3. Splenogonadal fusion.

    PubMed

    Tsingoglou, S; Wilkinson, A W

    1976-04-01

    The fusion between splenic tissue and the left gonad or the derivatives of the left mesonephros is a rare congenital anomaly first described in detail by Pommer in 1887/9 and divided into two forms by Putschar and Manion in 1956. In the first or continuous type a cord of splenic or fibrous tissue connects the spleen and the gonadalmesonephric structures. In the second type the fused splenomesonephric structures have lost continuity with the main spleen. An example of the continuous form is presented and the previous reports are briefly reviewed.

  4. High-level expression of a sweet potato sporamin gene promoter: beta-glucuronidase (GUS) fusion gene in the stems of transgenic tobacco plants is conferred by multiple cell type-specific regulatory elements.

    PubMed

    Ohta, S; Hattori, T; Morikami, A; Nakamura, K

    1991-03-01

    Genes coding for sporamin, the most abundant protein of the tuberous root of the sweet potato, are expressed at a high levels in the stems of plantlets cultured axenically on sucrose-containing medium. Their expression is also induced in leaf-petiole explants by high concentrations of sucrose. A fusion gene comprising of the 1 kb 5' upstream region of the gSPO-A1 gene coding for the A-type sporamin and the coding sequence of bacterial beta-glucuronidase (GUS) was introduced into the tobacco genome by Agrobacterium-mediated transformation. Transgenic tobacco plants cultured axenically on sucrose-containing medium expressed GUS activity predominantly in their stems. Histochemical examination of GUS activity using a chromogenic substrate showed a distinct spatial pattern of GUS staining in the stem. Strong GUS activity was detected in the internal phloem of the vascular system and at the node, especially at the base of the axillary bud. Relatively weaker GUS activity was also detected in pith parenchyma. A 5' deletion of the promoter to nucleotide -305, relative to the transcription start site, did not alter significantly the level of GUS activity or the spatial pattern of GUS staining in the stem. However, further deletions to -237 and -192 resulted in a decrease in the level of GUS activity in the stem that occurred simultaneously with the loss of GUS staining in both the internal phloem and at the base of the axillary bud. However, plants with these deletion constructs still exhibited the predominant expression pattern of GUS activity in the stem and GUS staining in the pith parenchyma cells. Deletion to -94 completely abolished the expression of GUS activity. These results indicate that a sequence between -305 and -237 contains a cis-regulatory element(s) that is required for expression of the GUS reporter gene in both the internal phloem and at the base of the axillary bud, while a sequence between -192 and -94 contains a cis-acting element(s) that is required

  5. Fusion reactor systems studies. Progress report for the period November 1, 1996--October 31, 1997, and final report

    SciTech Connect

    El-Guebaly, L.A.; Blanchard, J.P.; Kulcinski, G.L.

    1997-08-01

    During FY97, the University of Wisconsin Fusion Technology Institute personnel have participated in the ARIES-RS and the ARIES-ST projects. The main areas of effort are: (1) neutronics analysis; (2) shielding of components and personnel; (3) neutron wall loading distribution; (4) radiation damage to in-vessel components; (5) components lifetimes; (6) embrittled materials designs issues; (7) stress and structural analysis; (8) activation, LOCA, and safety analysis; (9) support and fabrication of components; (10) vacuum system; and (11) maintenance. Progress made in these areas are summarized.

  6. FES Science Network Requirements - Report of the Fusion Energy Sciences Network Requirements Workshop Conducted March 13 and 14, 2008

    SciTech Connect

    Tierney, Brian; Dart, Eli; Tierney, Brian

    2008-07-10

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In March 2008, ESnet and the Fusion Energy Sciences (FES) Program Office of the DOE Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the FES Program Office. Most sites that conduct data-intensive activities (the Tokamaks at GA and MIT, the supercomputer centers at NERSC and ORNL) show a need for on the order of 10 Gbps of network bandwidth for FES-related work within 5 years. PPPL reported a need for 8 times that (80 Gbps) in that time frame. Estimates for the 5-10 year time period are up to 160 Mbps for large simulations. Bandwidth requirements for ITER range from 10 to 80 Gbps. In terms of science process and collaboration structure, it is clear that the proposed Fusion Simulation Project (FSP) has the potential to significantly impact the data movement patterns and therefore the network requirements for U.S. fusion science. As the FSP is defined over the next two years, these changes will become clearer. Also, there is a clear and present unmet need for better network connectivity between U.S. FES sites and two Asian fusion experiments--the EAST Tokamak in China and the KSTAR Tokamak in South Korea. In addition to achieving its goal of collecting and characterizing the network requirements of the science endeavors funded by the FES Program Office, the workshop emphasized that there is a need for research into better ways of conducting remote

  7. Static and dynamic analyses on the MFTF (Mirror Fusion Test Facility)-B Axicell Vacuum Vessel System: Final report

    SciTech Connect

    Ng, D.S.

    1986-09-01

    The Mirror Fusion Test Facility (MFTF-B) at Lawrence Livermore National Laboratory (LLNL) is a large-scale, tandem-mirror-fusion experiment. MFTF-B comprises many highly interconnected systems, including a magnet array and a vacuum vessel. The vessel, which houses the magnet array, is supported by reinforced concrete piers and steel frames resting on an array of foundations and surrounded by a 7-ft-thick concrete shielding vault. The Pittsburgh-Des Moines (PDM) Corporation, which was awarded the contract to design and construct the vessel, carried out fixed-base static and dynamic analyses of a finite-element model of the axicell vessel and magnet systems, including the simulation of various loading conditions and three postulated earthquake excitations. Meanwhile, LLNL monitored PDM's analyses with modeling studies of its own, and independently evaluated the structural responses of the vessel in order to define design criteria for the interface members and other project equipment. The assumptions underlying the finite-element model and the behavior of the axicell vessel are described in detail in this report, with particular emphasis placed on comparing the LLNL and PDM studies and on analyzing the fixed-base behavior with the soil-structure interaction, which occurs between the vessel and the massive concrete vault wall during a postulated seismic event. The structural members that proved sensitive to the soil effect are also reevaluated.

  8. Inertial Confinement Fusion Quarterly Report: April--June 1993. Volume 3, Number 3

    SciTech Connect

    MacGowan, B.J.; Kotowski, M.; Schleich, D.

    1993-11-01

    This issue of the ICF Quarterly contains six articles describing recent advances in Lawrence Livermore National Laboratory`s inertial confinement fusion (ICF) program. The current emphasis of the ICF program is in support of DOE`s National Ignition Facility (NIF) initiative for demonstrating ignition and gain with a 1-2 MJ glass laser. The articles describe recent Nova experiments and investigations tailored towards enhancing understanding of the key physics and technological issues for the NIF. Titles of the articles are: development of large-aperture KDP crystals; inner-shell photo-ionized X-ray lasers; X-ray radiographic measurements of radiation-driven shock and interface motion in solid density materials; the role of nodule defects in laser-induced damage of multilayer optical coatings; techniques for Mbar to near-Gbar equation-of-state measurements with the Nova laser; parametric instabilities and laser-beam smoothing.

  9. Fusion of a supernumerary tooth to right mandibular second molar: a case report and literature review

    PubMed Central

    Zhu, Min; Liu, Chao; Ren, Shuangshuang; Lin, Zintong; Miao, Leiying; Sun, Weibin

    2015-01-01

    Gemination or fusion is a rare occurrence in the mandibular posterior teeth. The aim of this article is to describe the problems encountered and the strategy employed in treating such cases. A 34 years old patient came with the complaint of spontaneous and radiating pain in the right mandibular posterior region. The tooth in concern was an anomalous ‘double’ second mandibular molar diagnosed as having necrotic pulp with chronic apical abscess of endodontic origin. The present case emphasizes the importance of identifying anatomical anomalies during treatment of fused teeth with supernumerary tooth, and the need for the use of advanced imaging modalities like CBCT which is a critical aid in the diagnosis of such cases. Fused teeth can be managed quite efficiently by an overall combined treatment including both endodontic and periodontal therapy. PMID:26550101

  10. Development of high field superconductors for fusion energy applications. Final report

    SciTech Connect

    Not Available

    1985-09-26

    The purpose of this project was to develop a conductor design and a manufacturing procedure for a composite multifilamentary Nb/sub 3/Sn conductor suitable for winding a magnet for use in a fusion energy power plant. Effort was concentrated on the design of a conductor with tubular niobium filaments in a copper matrix. Bronze in the bores of the filaments would react with the niobium to form Nb/sub 3/Sn on the inside diameter of the niobium tubular filaments during a heat treatment at final size. Four filament geometries were evaluated. The addition of titanium to the bronze was found to increase the current density. The use of a hydrogen atmosphre did not appear to cause any increase in current density. Primary billets were assembled and extruded with five tubular filament designs and for comparison, five rod type filament designs. Billet designs are described.

  11. A Concept Exploration Program in Fast Ignition Inertial Fusion — Final Report

    SciTech Connect

    Stephens, Richarad Burnite; Freeman, Richard R.; Van Woekom, L. D.; Key, M.; MacKinnon, Andrew J.; Wei, Mingsheng

    2014-02-27

    The Fast Ignition (FI) approach to Inertial Confinement Fusion (ICF) holds particular promise for fusion energy because the independently generated compression and ignition pulses allow ignition with less compression, resulting in (potentially) higher gain. Exploiting this concept effectively requires an understanding of the transport of electrons in prototypical geometries and at relevant densities and temperatures. Our consortium, which included General Atomics (GA), The Ohio State University (OSU), the University of California, San Diego (UCSD), University of California, Davis (UC-Davis), and Princeton University under this grant (~$850K/yr) and Lawrence Livermore National Laboratory (LLNL) under a companion grant, won awards in 2000, renewed in 2005, to investigate the physics of electron injection and transport relevant to the FI concept, which is crucial to understand electron transport in integral FI targets. In the last two years we have also been preparing diagnostics and starting to extend the work to electron transport into hot targets. A complementary effort, the Advanced Concept Exploration (ACE) program for Fast Ignition, was funded starting in 2006 to integrate this understanding into ignition schemes specifically suitable for the initial fast ignition attempts on OMEGA and National Ignition Facility (NIF), and during that time these two programs have been managed as a coordinated effort. This result of our 7+ years of effort has been substantial. Utilizing collaborations to access the most capable laser facilities around the world, we have developed an understanding that was summarized in a Fusion Science & Technology 2006, Special Issue on Fast Ignition. The author lists in the 20 articles in that issue are dominated by our group (we are first authors in four of them). Our group has published, or submitted 67 articles, including 1 in Nature, 2 Nature Physics, 10 Physical Review Letters, 8 Review of Scientific Instruments, and has been invited to

  12. Feasibility study of a railgun as a driver for impact fusion: Final report

    SciTech Connect

    Thio. Y.C.

    1986-06-01

    The feasibility of a railgun as a driver for impact fusion is studied through a series of theoretical and experimental investigations. The results of both the theoretical and experimental investigations presented here have helped to identify the potential problems of the railgun launcher to attain velocity in excess of 100 km/s. These include ablation, viscous drag, and secondary arc formation due to either armature dispersion (instability) or restrike. These problems are analyzed and examined experimentally. The behavior of the conventional open-plasma-armature driven railguns have been shown to be quite complex and not easily controllable in the domain of ultrahigh velocity (>6 km/s). Methods to overcome these problems are proposed, analyzed in regards to their technological feasibility, and tested experimentally wherever possible. Techniques for reducing radiative ablation, the concept of a mechanically controlled plasma armature, and the concept of achieving super high augmentation by the technique of trans-augmentation are presented.

  13. Fusion of a supernumerary tooth to right mandibular second molar: a case report and literature review.

    PubMed

    Zhu, Min; Liu, Chao; Ren, Shuangshuang; Lin, Zintong; Miao, Leiying; Sun, Weibin

    2015-01-01

    Gemination or fusion is a rare occurrence in the mandibular posterior teeth. The aim of this article is to describe the problems encountered and the strategy employed in treating such cases. A 34 years old patient came with the complaint of spontaneous and radiating pain in the right mandibular posterior region. The tooth in concern was an anomalous 'double' second mandibular molar diagnosed as having necrotic pulp with chronic apical abscess of endodontic origin. The present case emphasizes the importance of identifying anatomical anomalies during treatment of fused teeth with supernumerary tooth, and the need for the use of advanced imaging modalities like CBCT which is a critical aid in the diagnosis of such cases. Fused teeth can be managed quite efficiently by an overall combined treatment including both endodontic and periodontal therapy. PMID:26550101

  14. Photoacoustic imaging of gene expression using tyrosinase as a reporter gene

    NASA Astrophysics Data System (ADS)

    Paproski, Robert J.; Forbrich, Alexander; Harrison, Tyler; Hitt, Mary; Zemp, Roger J.

    2011-03-01

    Optical reporter genes, such as green fluorescence protein, are powerful research tools that allow visualization of gene expression. We have successfully used tyrosinase as a reporter gene for photoacoustic imaging. Tyrosinase is the key regulatory enzyme in the production of melanin which has a broad optical absorption spectrum. MCF-7 cells were stably transfected with tyrosinase under the control of an inducible promoter. For photoacoustic experiments, MCF-7 cells were resuspended at 108 cells/mL and injected in 700 μm (inner diameter) plastic tubing. Photoacoustic signal of MCF-7 cells expressing tyrosinase were >20-fold greater than those of untransfected MCF-7 cells. Photoacoustic signal of tyrosinaseexpressing MCF-7 cells were approximately 2-fold lesser and greater than those of blood at 576 and 650 nm, respectively, suggesting that photoacoustic signal from blood and tyrosinase-expressing cells can be separated by dualwavelength analysis. Photoacoustic signal from tyrosinase-expressing MCF-7 cells covered by chicken tissue could even be detected at a laser penetration depth of 4 cm, suggesting that tyrosinase can be used to image gene expression in relatively deep tissues. The current data suggests that tyrosinase is a strong reporter gene for photoacoustic imaging.

  15. Fusion of platelet-derived growth receptor {beta} to a novel ets-like gene, tel, in chronic myelomonocytic leukemia with t(5;12) chromosomal translocation

    SciTech Connect

    Golub, T.; Barker, G.; Gilliland, D.G.

    1994-09-01

    Chronic myelomonocytic leukemia (CMML) is a myelodysplastic syndrome characterized by abnormal clonal myeloid proliferation, and by progression to acute myelogenous leukemia (AML). A recently recognized subgroup of CMML has a t(5;12) (q33;p13) balanced translocation. Fluorescence in situ hybridization (FISH) localized the translocation breakpoint near the CSF1 receptor (CSF1R) locus on chromosome 5q. Pulsed-field gel electrophoresis confirmed rearrangements near CSF1R, but involvement of CSF1R itself was excluded. Southern blotting showed a rearrangement within the closely linked PDGF receptor {beta} (PDGFR{beta}) gene. Ribonuclease protection assays localized the translocation breakpoint to nucleotide 1766 in PDGFR{beta} RNA. Anchored PCR was used to identify the chromosome 12 fusion partner, a novel ets-like protein, tel. Tel contains a highly conserved carboxy terminal ets-like DNA-binding domain, and an amino terminal domain with a predicted helix-loop-helix (HLH) secondary structure. The consequence of the t(5;12) translocation is fusion of the tel HLH domain to the PDGFR{beta} transmembrane and tyrosine kinase domains. The tel HLH domain may contribute a dimerization motif which serves to constitutively activate PDGFR{beta} tyrosine kinase activity. The tel-PDGFR{beta} fusion demonstrates the oncogenic potential of PDGFR{beta}, and may provide a paradigm for early events in the pathogenesis of AML.

  16. Quantification of cell fusion events human breast cancer cells and breast epithelial cells using a Cre-LoxP-based double fluorescence reporter system.

    PubMed

    Mohr, Marieke; Tosun, Songül; Arnold, Wolfgang H; Edenhofer, Frank; Zänker, Kurt S; Dittmar, Thomas

    2015-10-01

    The biological phenomenon of cell fusion plays an important role in several physiological processes, like fertilization, placentation, or wound healing/tissue regeneration, as well as pathophysiological processes, such as cancer. Despite this fact, considerably less is still known about the factors and conditions that will induce the merging of two plasma membranes. Inflammation and proliferation has been suggested as a positive trigger for cell fusion, but it remains unclear, which of the factor(s) of the inflamed microenvironment are being involved. To clarify this we developed a reliable assay to quantify the in vitro fusion frequency of cells using a fluorescence double reporter vector (pFDR) containing a LoxP-flanked HcRed/DsRed expression cassette followed by an EGFP expression cassette. Because cell fusion has been implicated in cancer progression four human breast cancer cell lines were stably transfected with a pFDR vector and were co-cultured with the stably Cre-expressing human breast epithelial cell line. Cell fusion is associated with a Cre-mediated recombination resulting in induction of EGFP expression in hybrid cells, which can be quantified by flow cytometry. By testing a panel of different cytokines, chemokines, growth factors and other compounds, including exosomes, under normoxic and hypoxic conditions our data indicate that the proinflammatory cytokine TNF-α together with hypoxia is a strong inducer of cell fusion in human MDA-MB-435 and MDA-MB-231 breast cancer cells.

  17. Multisensor data fusion algorithm development

    SciTech Connect

    Yocky, D.A.; Chadwick, M.D.; Goudy, S.P.; Johnson, D.K.

    1995-12-01

    This report presents a two-year LDRD research effort into multisensor data fusion. We approached the problem by addressing the available types of data, preprocessing that data, and developing fusion algorithms using that data. The report reflects these three distinct areas. First, the possible data sets for fusion are identified. Second, automated registration techniques for imagery data are analyzed. Third, two fusion techniques are presented. The first fusion algorithm is based on the two-dimensional discrete wavelet transform. Using test images, the wavelet algorithm is compared against intensity modulation and intensity-hue-saturation image fusion algorithms that are available in commercial software. The wavelet approach outperforms the other two fusion techniques by preserving spectral/spatial information more precisely. The wavelet fusion algorithm was also applied to Landsat Thematic Mapper and SPOT panchromatic imagery data. The second algorithm is based on a linear-regression technique. We analyzed the technique using the same Landsat and SPOT data.

  18. PSF/SFPQ is a very common gene fusion partner in TFE3 rearrangement-associated perivascular epithelioid cell tumors (PEComas) and melanotic Xp11 translocation renal cancers: clinicopathologic, immunohistochemical, and molecular characteristics suggesting classification as a distinct entity.

    PubMed

    Rao, Qiu; Shen, Qin; Xia, Qiu-yuan; Wang, Zi-yu; Liu, Biao; Shi, Shan-shan; Shi, Qun-li; Yin, Hong-lin; Wu, Bo; Ye, Sheng-bing; Li, Li; Chen, Jie-Yu; Pan, Min-hong; Li, Qing; Li, Rui; Wang, Xuan; Zhang, Ru-song; Yu, Bo; Ma, Heng-hui; Lu, Zhen-feng; Zhou, Xiao-jun

    2015-09-01

    An increasing number of TFE3 rearrangement-associated tumors, such as TFE3 rearrangement-associated perivascular epithelioid cell tumors (PEComas), melanotic Xp11 translocation renal cancers, and melanotic Xp11 neoplasms, have recently been reported. We examined 12 such cases, including 5 TFE3 rearrangement-associated PEComas located in the pancreas, cervix, or pelvis and 7 melanotic Xp11 translocation renal cancers, using clinicopathologic, immunohistochemical, and molecular analyses. All the tumors shared a similar morphology, including a purely nested or sheet-like architecture separated by a delicate vascular network, purely epithelioid cells displaying a clear or granular eosinophilic cytoplasm, a lack of papillary structures and spindle cell or fat components, uniform round or oval nuclei containing small visible nucleoli, and, in most cases (11/12), melanin pigmentation. The levels of mitotic activity and necrosis varied. All 12 cases displayed moderately (2+) or strongly (3+) positive immunoreactivity for TFE3 and cathepsin K. One case labeled focally for HMB45 and Melan-A, whereas the others typically labeled moderately (2+) or strongly (3+) for 1 of these markers. None of the cases were immunoreactive for smooth muscle actin, desmin, CKpan, S100, or PAX8. PSF-TFE3 fusion genes were confirmed by reverse transcription polymerase chain reaction in cases (7/7) in which a novel PSF-TFE3 fusion point was identified. All of the cases displayed TFE3 rearrangement associated with Xp11 translocation. Furthermore, we developed a PSF-TFE3 fusion fluorescence in situ hybridization assay for the detection of the PSF-TFE3 fusion gene and detected it in all 12 cases. Clinical follow-up data were available for 7 patients. Three patients died, and 2 patients (cases 1 and 3) remained alive with no evidence of disease after initial resection. Case 2 experienced recurrence and remained alive with disease. Case 5, a recent case, remained alive with extensive abdominal cavity

  19. RNA Sequencing Identifies Multiple Fusion Transcripts, Differentially Expressed Genes, and Reduced Expression of Immune Function Genes in BRAF (V600E) Mutant vs BRAF Wild-Type Papillary Thyroid Carcinoma

    PubMed Central

    Chindris, Ana-Maria; Asmann, Yan W.; Casler, John D.; Serie, Daniel J.; Reddi, Honey V.; Cradic, Kendall W.; Rivera, Michael; Grebe, Stefan K.; Necela, Brian M.; Eberhardt, Norman L.; Carr, Jennifer M.; McIver, Bryan; Copland, John A.; Aubrey Thompson, E.

    2014-01-01

    Context: The BRAF V600E mutation (BRAF-MUT) confers an aggressive phenotype in papillary thyroid carcinoma, but unidentified additional genomic abnormalities may be required for full phenotypic expression. Objective: RNA sequencing (RNA-Seq) was performed to identify genes differentially expressed between BRAF-MUT and BRAF wild-type (BRAF-WT) tumors and to correlate changes to patient clinical status. Design: BRAF-MUT and BRAF-WT tumors were identified in patients with T1N0 and T2–3N1 tumors evaluated in a referral medical center. Gene expression levels were determined (RNA-Seq) and fusion transcripts were detected. Multiplexed capture/detection and digital counting of mRNA transcripts (nCounter, NanoString Technologies) validated RNA-Seq data for immune system-related