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Sample records for dasatinib inhibits site-specific

  1. Imatinib and Dasatinib Inhibit Hemangiosarcoma and Implicate PDGFR-β and Src in Tumor Growth12

    Science.gov (United States)

    Dickerson, Erin B; Marley, Kevin; Edris, Wade; Tyner, Jeffrey W; Schalk, Vidya; MacDonald, Valerie; Loriaux, Marc; Druker, Brian J; Helfand, Stuart C

    2013-01-01

    Hemangiosarcoma, a natural model of human angiosarcoma, is an aggressive vascular tumor diagnosed commonly in dogs. The documented expression of several receptor tyrosine kinases (RTKs) by these tumors makes them attractive targets for therapeutic intervention using tyrosine kinase inhibitors (TKIs). However, we possess limited knowledge of the effects of TKIs on hemangiosarcoma as well as other soft tissue sarcomas. We report here on the use of the TKIs imatinib and dasatinib in canine hemangiosarcoma and their effects on platelet-derived growth factor receptor β (PDGFR-β) and Src inhibition. Both TKIs reduced cell viability, but dasatinib was markedly more potent in this regard, mediating cytotoxic effects orders of magnitude greater than imatinib. Dasatinib also inhibited the phosphorylation of the shared PDGFR-β target at a concentration approximately 1000 times less than that needed by imatinib and effectively blocked Src phosphorylation. Both inhibitors augmented the response to doxorubicin, suggesting that clinical responses likely will be improved using both drugs in combination; however, dasatinib was significantly (P hemangiosarcoma established that clinically achievable doses of dasatinib may be realized in dogs and provides a means to investigate the effect of TKIs on soft tissue sarcomas in a large animal model. PMID:23544168

  2. Dasatinib synergizes with ATRA to trigger granulocytic differentiation in ATRA resistant acute promyelocytic leukemia cell lines via Lyn inhibition-mediated activation of RAF-1/MEK/ERK.

    Science.gov (United States)

    Ding, Ming; Weng, Xiang-Qin; Sheng, Yan; Wu, Jing; Liang, Cui; Cai, Xun

    2017-10-31

    All-trans retinoic acid (ATRA) resistance has been a critical problem in acute promyelocytic leukemia (APL) relapsed patients. In this study, dasatinib synergized with ATRA to trigger differentiation in ATRA-resistant APL cell lines. The combined treatment activated RAF-1, MEK and ERK as well as enhanced ATRA-promoted up-regulation of the protein level of PU.1, C/EBPβ and C/EBPε. U0126 (MEK specific inhibitor) and sorafenib tosylate (RAF-1 specific inhibitor) suppressed the combined treatment-induced differentiation, ERK phosphorylation and the up-regulation of C/EBPs and PU.1. Sorafenib tosylate also attenuated the MEK activity. However, the combined treatment did not enhance Ras activity and Ras inhibitor neither blocked MEK activation nor inhibited differentiation. Therefore, the combined treatment induced differentiation via Ras independent RAF-1/MEK/ERK. Earlier than RAF-1 activation, dasatinib suppressed Lyn activity, the predominant activated Src family kinase (SFK) and dephosphorylated RAF-1 at S259. Furthermore, SFK inhibitor, PP2 did suppress Lyn activity and mimicked the effect of dasatinib on ATRA-induced differentiation as well as decreased phosphorylation of RAF-1 at S259. Thus, it was suggested that Lyn inhibition might activate RAF-1 by the dephosphorylation of RAF at S259 and lead to differentiation. In conclusion, the combination of dasatinib and ATRA could overcome ATRA resistance through Lyn inhibition-mediated activation of RAF-1/MEK/ERK. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Site-SpecificCu Labeling of the Serine Protease, Active Site Inhibited Factor Seven Azide (FVIIai-N), Using Copper Free Click Chemistry

    DEFF Research Database (Denmark)

    Jeppesen, Troels E; Kristensen, Lotte K; Nielsen, Carsten H

    2018-01-01

    A method for site-specific radiolabeling of the serine protease active site inhibited factor seven (FVIIai) with64Cu has been applied using a biorthogonal click reaction. FVIIai binds to tissue factor (TF), a trans-membrane protein involved in hemostasis, angiogenesis, proliferation, cell migrati...

  4. SGX393 inhibits the CML mutant Bcr-Abl[superscript T315I] and preempts in vitro resistance when combined with nilotinib or dasatinib

    Energy Technology Data Exchange (ETDEWEB)

    O' Hare, Thomas; Eide, Christopher A.; Tyner, Jeffrey W.; Corbin, Amie S.; Wong, Matthew J.; Buchanan, Sean; Holme, Kevin; Jessen, Katayoun A.; Tang, Crystal; Lewis, Hal A.; Romero, Richard D.; Burley, Stephen K.; Deininger, Michael W. (OHSU- Cancer Instit.); (SGX)

    2010-01-12

    Imatinib inhibits Bcr-Abl, the oncogenic tyrosine kinase that causes chronic myeloid leukemia. The second-line inhibitors nilotinib and dasatinib are effective in patients with imatinib resistance resulting from Bcr-Abl kinase domain mutations. Bcr-Abl{sup T315I}, however, is resistant to all Abl kinase inhibitors in clinical use and is emerging as the most frequent cause of salvage therapy failure. SGX393 is a potent inhibitor of native and T315I-mutant Bcr-Abl kinase that blocks the growth of leukemia cell lines and primary hematopoietic cells expressing Bcr-Abl{sup T315I}, with minimal toxicity against Bcr-Abl-negative cell lines or normal bone marrow. A screen for Bcr-Abl mutants emerging in the presence of SGX393 revealed concentration-dependent reduction in the number and range of mutations. Combining SGX393 with nilotinib or dasatinib preempted emergence of resistant subclones, including Bcr-Abl{sup T315I}. These findings suggest that combination of a T315I inhibitor with the current clinically used inhibitors may be useful for reduction of Bcr-Abl mutants in Philadelphia chromosome-positive leukemia.

  5. Fluorescence properties and sequestration of peripheral anionic site specific ligands in bile acid hosts: Effect on acetylcholinesterase inhibition activity.

    Science.gov (United States)

    Islam, Mullah Muhaiminul; Aguan, Kripamoy; Mitra, Sivaprasad

    2016-05-01

    The increase in fluorescence intensity of model acetyl cholinesterase (AChE) inhibitors like propidium iodide (PI) and ethidium bromide (EB) is due to sequestration of the probes in primary micellar aggregates of bile acid (BA) host medium with moderate binding affinity of ca. 10(2)-10(3)M(-1). Multiple regression analysis of solvent dependent fluorescence behavior of PI indicates the decrease in total nonradiative decay rate due to partial shielding of the probe from hydrogen bond donation ability of the aqueous medium in bile acid bound fraction. Both PI and EB affects AChE activity through mixed inhibition and consistent with one site binding model; however, PI (IC50=20±1μM) shows greater inhibition in comparison with EB (IC50=40±3μM) possibly due to stronger interaction with enzyme active site. The potency of AChE inhibition for both the compounds is drastically reduced in the presence of bile acid due to the formation of BA-inhibitor complex and subsequent reduction of active inhibitor fraction in the medium. Although the inhibition mechanism still remains the same, the course of catalytic reaction critically depends on equilibrium binding among several species present in the solution; particularly at low inhibitor concentration. All the kinetic parameters for enzyme inhibition reaction are nicely correlated with the association constant for BA-inhibitor complex formation. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. MDP, a database linking drug response data to genomic information, identifies dasatinib and statins as a combinatorial strategy to inhibit YAP/TAZ in cancer cells.

    Science.gov (United States)

    Taccioli, Cristian; Sorrentino, Giovanni; Zannini, Alessandro; Caroli, Jimmy; Beneventano, Domenico; Anderlucci, Laura; Lolli, Marco; Bicciato, Silvio; Del Sal, Giannino

    2015-11-17

    Targeted anticancer therapies represent the most effective pharmacological strategies in terms of clinical responses. In this context, genetic alteration of several oncogenes represents an optimal predictor of response to targeted therapy. Integration of large-scale molecular and pharmacological data from cancer cell lines promises to be effective in the discovery of new genetic markers of drug sensitivity and of clinically relevant anticancer compounds. To define novel pharmacogenomic dependencies in cancer, we created the Mutations and Drugs Portal (MDP, http://mdp.unimore.it), a web accessible database that combines the cell-based NCI60 screening of more than 50,000 compounds with genomic data extracted from the Cancer Cell Line Encyclopedia and the NCI60 DTP projects. MDP can be queried for drugs active in cancer cell lines carrying mutations in specific cancer genes or for genetic markers associated to sensitivity or resistance to a given compound. As proof of performance, we interrogated MDP to identify both known and novel pharmacogenomics associations and unveiled an unpredicted combination of two FDA-approved compounds, namely statins and Dasatinib, as an effective strategy to potently inhibit YAP/TAZ in cancer cells.

  7. Site-Specific Innovation

    DEFF Research Database (Denmark)

    Reeh, Henrik; Hemmersam, Peter

    2015-01-01

    Currently, cities across the Northern European region are actively redeveloping their former industrial harbours. Indeed, harbours areas are essential in the long-term transition from industrial to information and experience societies; harbours are becoming sites for new businesses and residences...... question is how innovation may contribute to urban life and site-specific qualities....

  8. Degradation of Epidermal Growth Factor Receptor Mediates Dasatinib-Induced Apoptosis in Head and Neck Squamous Cell Carcinoma Cells

    Directory of Open Access Journals (Sweden)

    Yu-Chin Lin

    2012-06-01

    Full Text Available Epidermal growth factor receptor (EGFR is an important oncoprotein that promotes cell growth and proliferation. Dasatinib, a bcr-abl inhibitor, has been approved clinically for the treatment of chronic myeloid leukemia and demonstrated to be effective against solid tumors in vitro through Src inhibition. Here, we disclose that EGFR degradation mediated dasatinib-induced apoptosis in head and neck squamous cell carcinoma (HNSCC cells. HNSCC cells, including Ca9-22, FaDu, HSC3, SAS, SCC-25, and UMSCC1, were treated with dasatinib, and cell viability, apoptosis, and underlying signal transduction were evaluated. Dasatinib exhibited differential sensitivities against HNSCC cells. Growth inhibition and apoptosis were correlated with its inhibition on Akt, Erk, and Bcl-2, irrespective of Src inhibition. Accordingly, we found that down-regulation of EGFR was a determinant of dasatinib sensitivity. Lysosome inhibitor reversed dasatinib-induced EGFR down-regulation, and c-cbl activity was increased by dasatinib, indicating that dasatinib-induced EGFR down-regulation might be through c-cbl-mediated lysosome degradation. Increased EGFR activation by ligand administration rescued cells from dasatinib-induced apoptosis, whereas inhibition of EGFR enhanced its apoptotic effect. Estrogen receptor α (ERα was demonstrated to play a role in Bcl-2 expression, and dasatinib inhibited ERα at the pretranslational level. ERα was associated with EGFR in dasatinib-treated HNSCC cells. Furthermore, the xenograft model showed that dasatinib inhibited HSC3 tumor growth through in vivo down-regulation of EGFR and ERα. In conclusion, degradation of EGFR is a novel mechanism responsible for dasatinib-induced apoptosis in HNSCC cells.

  9. Dasatinib accelerates valproic acid-induced acute myeloid leukemia cell death by regulation of differentiation capacity.

    Directory of Open Access Journals (Sweden)

    Sook-Kyoung Heo

    Full Text Available Dasatinib is a compound developed for chronic myeloid leukemia as a multi-targeted kinase inhibitor against wild-type BCR-ABL and SRC family kinases. Valproic acid (VPA is an anti-epileptic drug that also acts as a class I histone deacetylase inhibitor. The aim of this research was to determine the anti-leukemic effects of dasatinib and VPA in combination and to identify their mechanism of action in acute myeloid leukemia (AML cells. Dasatinib was found to exert potent synergistic inhibitory effects on VPA-treated AML cells in association with G1 phase cell cycle arrest and apoptosis induction involving the cleavage of poly (ADP-ribose polymerase and caspase-3, -7 and -9. Dasatinib/VPA-induced cell death thus occurred via caspase-dependent apoptosis. Moreover, MEK/ERK and p38 MAPK inhibitors efficiently inhibited dasatinib/VPA-induced apoptosis. The combined effect of dasatinib and VPA on the differentiation capacity of AML cells was more powerful than the effect of each drug alone, being sufficiently strong to promote AML cell death through G1 cell cycle arrest and caspase-dependent apoptosis. MEK/ERK and p38 MAPK were found to control dasatinib/VPA-induced apoptosis as upstream regulators, and co-treatment with dasatinib and VPA to contribute to AML cell death through the regulation of differentiation capacity. Taken together, these results indicate that combined dasatinib and VPA treatment has a potential role in anti-leukemic therapy.

  10. Site specific plan

    International Nuclear Information System (INIS)

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. 8 refs., 46 figs., 23 tabs

  11. Dasatinib Modulates Invasive and Migratory Properties of Canine Osteosarcoma and has Therapeutic Potential in Affected Dogs

    Directory of Open Access Journals (Sweden)

    Kevin Marley

    2015-08-01

    Full Text Available BACKGROUND: This investigation sought to elucidate the relationship between hepatocyte growth factor (HGF–induced metastatic behavior and the tyrosine kinase inhibitors (TKIs crizotinib and dasatinib in canine osteosarcoma (OS. Preliminary evidence of an apparent clinical benefit from adjuvant therapy with dasatinib in four dogs is described. METHODS: The inhibitors were assessed for their ability to block phosphorylation of MET; reduce HGF-induced production of matrix metalloproteinase (MMP; and prevent invasion, migration, and cell viability in canine OS cell lines. Oral dasatinib (0.75 mg/kg was tested as an adjuvant therapy in four dogs with OS. RESULTS: Constitutive phosphorylation of MET was detected in two cell lines, and this was unaffected by 20-nM incubation with either dasatinib or crizotinib. Incubation of cell lines with HGF (MET ligand increased cell migration and invasion in both cell lines and increased MMP-9 activity in one. Dasatinib suppressed OS cell viability and HGF-induced invasion and migration, whereas crizotinib reduced migration and MMP-9 production but did not inhibit invasion or viability. CONCLUSIONS: Invasion, migration, and viability of canine OS cell lines are increased by exogenous HGF. HGF induces secretion of different forms of MMP in different cell lines. The HGF-driven increase in viability and metastatic behaviors we observed are more uniformly inhibited by dasatinib. These observations suggest a potential clinical benefit of adjuvant dasatinib treatment for dogs with OS.

  12. Preferential antitumor effect of the Src inhibitor dasatinib associated with a decreased proportion of aldehyde dehydrogenase 1-positive cells in breast cancer cells of the basal B subtype

    Directory of Open Access Journals (Sweden)

    Watanabe Mika

    2010-10-01

    Full Text Available Abstract Background Recent studies have suggested that the Src inhibitor dasatinib preferentially inhibits the growth of breast cancer cells of the basal-like subtype. To clarify this finding and further investigate combined antitumor effects of dasatinib with cytotoxic agents, a panel of breast cancer cell lines of various subtypes was treated with dasatinib and/or chemotherapeutic agents. Methods Seven human breast cancer cell lines were treated with dasatinib and/or seven chemotherapeutic agents. Effects of the treatments on c-Src activation, cell growth, cell cycle, apoptosis and the proportion of aldehyde dehydrogenase (ALDH 1-positive cells were examined. Results The 50%-growth inhibitory concentrations (IC50s of dasatinib were much lower in two basal B cell lines than those in the other cell lines. The IC50s of chemotherapeutic agents were not substantially different among the cell lines. Dasatinib enhanced antitumor activity of etoposide in the basal B cell lines. Dasatinib induced a G1-S blockade with a slight apoptosis, and a combined treatment of dasatinib with etoposide also induced a G1-S blockade in the basal B cell lines. Dasatinib decreased the expression levels of phosphorylated Src in all cell lines. Interestingly, dasatinib significantly decreased the proportion of ALDH1-positive cells in the basal B cell lines but not in the other cell lines. Conclusions The present study indicates that dasatinib preferentially inhibits the growth of breast cancer cells of the basal B subtype associated with a significant loss of putative cancer stem cell population. A combined use of dasatinib with etoposide additively inhibits their growth. Further studies targeting breast cancers of the basal B subtype using dasatinib with cytotoxic agents are warranted.

  13. Comparison of imatinib, dasatinib, nilotinib and INNO-406 in imatinib-resistant cell lines.

    Science.gov (United States)

    Deguchi, Yasuyuki; Kimura, Shinya; Ashihara, Eishi; Niwa, Tomoko; Hodohara, Keiko; Fujiyama, Yoshihide; Maekawa, Taira

    2008-06-01

    We compared the growth-inhibitory effects and inhibition profile of the SRC family kinases (SFKs) of imatinib, dasatinib, nilotinib and INNO-406. Dasatinib exhibited the strongest potency against BCR-ABL with little selectivity over SFKs. Nilotinib exhibited a weaker affinity than the other inhibitors, but was highly specific for ABL and may be useful for the treatment of P-glycoprotein overexpressing leukemic cells. INNO-406 had an intermediate affinity for BCR-ABL between that of dasatinib and nilotinib, and inhibited only SFKs LCK and LYN among SFKs. Both nilotinib and INNO-406 were potent inhibitors of the dasatinib-resistant T315A, F317L and F317V BCR-ABL mutations.

  14. Dasatinib Attenuates Pressure Overload Induced Cardiac Fibrosis in a Murine Transverse Aortic Constriction Model.

    Directory of Open Access Journals (Sweden)

    Sundaravadivel Balasubramanian

    Full Text Available Reactive cardiac fibrosis resulting from chronic pressure overload (PO compromises ventricular function and contributes to congestive heart failure. We explored whether nonreceptor tyrosine kinases (NTKs play a key role in fibrosis by activating cardiac fibroblasts (CFb, and could potentially serve as a target to reduce PO-induced cardiac fibrosis. Our studies were carried out in PO mouse myocardium induced by transverse aortic constriction (TAC. Administration of a tyrosine kinase inhibitor, dasatinib, via an intraperitoneally implanted mini-osmotic pump at 0.44 mg/kg/day reduced PO-induced accumulation of extracellular matrix (ECM proteins and improved left ventricular geometry and function. Furthermore, dasatinib treatment inhibited NTK activation (primarily Pyk2 and Fak and reduced the level of FSP1 positive cells in the PO myocardium. In vitro studies using cultured mouse CFb showed that dasatinib treatment at 50 nM reduced: (i extracellular accumulation of both collagen and fibronectin, (ii both basal and PDGF-stimulated activation of Pyk2, (iii nuclear accumulation of Ki67, SKP2 and histone-H2B and (iv PDGF-stimulated CFb proliferation and migration. However, dasatinib did not affect cardiomyocyte morphologies in either the ventricular tissue after in vivo administration or in isolated cells after in vitro treatment. Mass spectrometric quantification of dasatinib in cultured cells indicated that the uptake of dasatinib by CFb was greater that that taken up by cardiomyocytes. Dasatinib treatment primarily suppressed PDGF but not insulin-stimulated signaling (Erk versus Akt activation in both CFb and cardiomyocytes. These data indicate that dasatinib treatment at lower doses than that used in chemotherapy has the capacity to reduce hypertrophy-associated fibrosis and improve ventricular function.

  15. The tyrosine kinase inhibitor dasatinib induces a marked adipogenic differentiation of human multipotent mesenchymal stromal cells.

    Directory of Open Access Journals (Sweden)

    Adriana Borriello

    Full Text Available BACKGROUND: The introduction of specific BCR-ABL inhibitors in chronic myelogenous leukemia therapy has entirely mutated the prognosis of this hematologic cancer from being a fatal disorder to becoming a chronic disease. Due to the probable long lasting treatment with tyrosine-kinase inhibitors (TKIs, the knowledge of their effects on normal cells is of pivotal importance. DESIGN AND METHODS: We investigated the effects of dasatinib treatment on human bone marrow-derived mesenchymal stromal cells (MSCs. RESULTS: Our findings demonstrate, for the first time, that dasatinib induces MSCs adipocytic differentiation. Particularly, when the TKI is added to the medium inducing osteogenic differentiation, a high MSCs percentage acquires adipocytic morphology and overexpresses adipocytic specific genes, including PPARγ, CEBPα, LPL and SREBP1c. Dasatinib also inhibits the activity of alkaline phosphatase, an osteogenic marker, and remarkably reduces matrix mineralization. The increase of PPARγ is also confirmed at protein level. The component of osteogenic medium required for dasatinib-induced adipogenesis is dexamethasone. Intriguingly, the increase of adipocytic markers is also observed in MSCs treated with dasatinib alone. The TKI effect is phenotype-specific, since fibroblasts do not undergo adipocytic differentiation or PPARγ increase. CONCLUSIONS: Our data demonstrate that dasatinib treatment affects bone marrow MSCs commitment and suggest that TKIs therapy might modify normal phenotypes with potential significant negative consequences.

  16. Dasatinib. En ny tyrosinkinaseinhibitor til behandling af kronisk myeloid leukaemi

    DEFF Research Database (Denmark)

    Bjerrum, Ole Weis; Dufva, Inge Høgh; Stentoft, Jesper

    2008-01-01

    Chronic myeloid leukaemia is characterized by an abnormal tyrosin kinase in the cytoplasm of the clonal cells. The enzyme is derived from a fusion gene on the Philadelphia-chromosome, evolved by a translocation between chromosomes 9 and 22. Understanding the biology of the tyrosin kinase led to t...... to targeted therapy, inhibiting the ATP-binding site by a small molecule--imatinib (Glivec). A novel 2nd generation tyrosin kinase inhibitor--dasatinib (Sprycel)--is now available in cases of insufficient response or intolerance to imatinib. Udgivelsesdato: 2008-Jan-28...

  17. Dasatinib

    Science.gov (United States)

    ... effects.if you are taking antacids, such as aluminum hydroxide/magnesium hydroxide (Maalox), calcium carbonate (Tums), or ... to your pharmacist or contact your local garbage/recycling department to learn about take-back programs in ...

  18. Myeloid Leukemia while on Dasatinib Therapy

    Directory of Open Access Journals (Sweden)

    Monika Conchon

    2010-01-01

    Full Text Available Here we report the case of an 18-year-old woman with chronic myeloid leukemia (CML who became pregnant while undergoing treatment with dasatinib. Before pregnancy, she received imatinib mesylate therapy but could not tolerate the treatment. The regimen was then changed to dasatinib at a dose of 70 mg b.i.d. While she was in hematological remission and on dasatinib therapy, she became pregnant. The unplanned pregnancy was identified after the patient had experienced four weeks of amenorrhea. Because the patient elected to continue the pregnancy to term, dasatinib was stopped immediately. Meanwhile, CML hematological relapse occurred and then she was treated with interferon- (IFN- (9 million IU/day throughout the pregnancy without a complete hematological response. She successfully gave birth to a male baby at 33 weeks by cesarean section delivery with no sequelae or malformations. Although this experience is limited to a single patient, it provides a useful contribution for counselling patients inadvertently exposed to dasatinib during pregnancy.

  19. NORMAL LOAD BEARING BY SITE SPECIFIC CANISTER

    Energy Technology Data Exchange (ETDEWEB)

    NA

    2005-03-23

    The overall purpose of this calculation is to perform a preliminary analysis of the Site Specific Canister/Basket, subject to static gravity loads that include the self weight of the Canister Shell, the Basket, the Spent Nuclear Fuel, the Shield Plug and the related hardware, so that the loads are approximately known for sizing purposes. Based on these loads the stress levels in various components of the Site Specific Canister/Basket are evaluated.

  20. C-kit mutations determine dasatinib mechanism of action in HMC-1 neoplastic mast cells: dasatinib differently regulates PKCδ translocation in HMC-1(560) and HMC-1(560,816) cell lines.

    Science.gov (United States)

    Tobío, Araceli; Alfonso, Amparo; Botana, Luis M

    2015-01-01

    The second generation of tyrosine kinase inhibitors is a group of compounds that inhibit c-kit receptor activity and therefore widely used in the treatment of mastocytosis. In this research, the relationship between the mechanism of action of tyrosine kinase inhibitors and protein kinase C is investigated in HMC-1(560) or HMC-1(560,816) cell lines. From all the tyrosine kinase inhibitors tested, nilotinib is the compound that has the highest cytotoxic effect against HMC-1(560) mast cell line, while midostaurin is the most potent in HMC-1(560,816). Moreover, an increase on histamine release is observed after protein kinase C activation either in HMC-1(560) or HMC-1(560,816) cells. Furthermore, dasatinib increases histamine release in both mast cell lines, which could be related with the secondary reactions previously described in dasatinib-treated patients. Dasatinib also induces Ca(2+)-dependent protein kinase C isoforms translocation from the cytosol to the membrane, whereas protein kinase Cδ is translocated from the cytosol to the nucleus in the HMC-1(560,816) cell line, but not in HMC-1(560) cells. Results obtained demonstrate that dasatinib induces an important cytotoxic effect in both HMC-1 cell lines and differently regulates protein kinase Cδ in HMC-1(560) and HMC-1(560,816) cells. Finally, our results confirm that PKCδ is an essential target for dasatinib.

  1. DOE site-specific threat assessment

    International Nuclear Information System (INIS)

    West, D.J.; Al-Ayat, R.A.; Judd, B.R.

    1985-01-01

    A facility manager faced with the challenges of protecting a nuclear facility against potential threats must consider the likelihood and consequences of such threats, know the capabilities of the facility safeguards and security systems, and make informed decisions about the cost-effectivness of safeguards and security upgrades. To help meet these challenges, the San Francisco Operations Office of the Department of Energy, in conjunction with the Lawrence Livermore Laboratory, has developed a site-specific threat assessment approach and a quantitative model to improve the quality and consistency of site-specific threat assessment and resultant security upgrade decisions at sensitive Department of Energy facilities. 5 figs

  2. Site-Specific Infrared Probes of Proteins

    Science.gov (United States)

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-04-01

    Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

  3. Site-Specific Infrared Probes of Proteins

    Science.gov (United States)

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-01-01

    Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

  4. Prospects for site specific weed management

    DEFF Research Database (Denmark)

    Christensen, Svend; Rasmussen, Jesper; Pedersen, Søren Marcus

    2014-01-01

    Research on Site Specific Weed Management (SSWM) started in the late 80's. Since that moment, considerable research has been conducted on different aspects of SSWM, from fundamental studies on the spatial ecology of weeds to the applied development and testing of new technologies for weed detection...

  5. Increased killing of SCCVII squamous cell carcinoma cells after the combination of Pc 4 photodynamic therapy and dasatinib is associated with enhanced caspase-3 activity and ceramide synthase 1 upregulation

    Science.gov (United States)

    SEPAROVIC, DUSKA; BREEN, PAUL; BOPPANA, NITHIN B.; VAN BUREN, ERIC; JOSEPH, NICHOLAS; KRAVEKA, JACQUELINE M.; RAHMANIYAN, MEHRDAD; LI, LI; GUDZ, TATYANA I.; BIELAWSKA, ALICJA; BAI, AIPING; BIELAWSKI, JACEK; PIERCE, JASON S.; KORBELIK, MLADEN

    2013-01-01

    Photodynamic therapy (PDT) is not always effective as an anticancer treatment, therefore, PDT is combined with other anticancer agents for improved efficacy. The combination of dasatinib and PDT with the silicone phthalocyanine photosensitizer Pc 4 was assessed for increased killing of SCCVII mouse squamous cell carcinoma cells, a preclinical model of head and neck squamous cell carcinoma, using apoptotic markers and colony formation as experimental end-points. Because each of these treatments regulates the metabolism of the sphingolipid ceramide, their effects on mRNA levels of ceramide synthase, a ceramide-producing enzyme, and the sphingolipid profile were determined. PDT + dasatinib induced an additive loss of clonogenicity. Unlike PDT alone or PDT + dasatinib, dasatinib induced zVAD-fmk-dependent cell killing. PDT or dasatinib-induced caspase-3 activation was potentiated after the combination. PDT alone induced mitochondrial depolarization, and the effect was inhibited after the combination. Annexin V+ and propidium iodide+ cells remained at control levels after treatments. In contrast to PDT alone, dasatinib induced upregulation of ceramide synthase 1 mRNA, and the effect was enhanced after the combination. Dasatinib induced a modest increase in C20:1-and C22-ceramide but had no effect on total ceramide levels. PDT increased the levels of 12 individual ceramides and total ceramides, and the addition of dasatinib did not affect these increases. PDT alone decreased substantially sphingosine levels and inhibited the activity of acid ceramidase, an enzyme that converts ceramide to sphingosine. The data suggest that PDT-induced increases in ceramide levels do not correlate with ceramide synthase mRNA levels but rather with inhibition of ceramidase. Cell killing was zVAD-fmk-sensitive after dasatinib but not after either PDT or the combination and enhanced cell killing after the combination correlated with potentiated caspase-3 activation and upregulation of

  6. Growth inhibitory effect of the Src inhibitor dasatinib in combination with anticancer agents on uterine cervical adenocarcinoma cells.

    Science.gov (United States)

    Takiguchi, Eri; Nishimura, Masato; Mineda, Ayuka; Kawakita, Takako; Abe, Akiko; Irahara, Minoru

    2017-11-01

    Uterine cervical adenocarcinoma has a poor clinical prognosis when compared with squamous cell carcinoma. Therefore, the development of new treatment strategies for uterine cervical adenocarcinoma is necessary. Src is a proto-oncogene that is important in cancer progression. Dasatinib is a Src inhibitor that has been reported to be effective when used in combination with anticancer drugs. The present study aimed to confirm Src expression in human cervical adenocarcinoma cell lines and to determine the mechanism underlying the inhibitory effect of dasatinib on Src signaling in vitro . Western blot analysis was performed to investigate Src expression in cervical adenocarcinoma cell lines (HeLa and TCO-2 cells). The cells were cultured for 48 h with the addition of different concentrations of anticancer drugs (paclitaxel or oxaliplatin). Viable cell count was measured using a colorimetric (WST-1) assay. The concentrations of anticancer agents were fixed according to the results obtained, and the same experiments were performed using the drugs in combination with dasatinib at various concentrations to determine the concentrations that significantly affected the number of viable cells. The presence or absence of apoptosis was investigated using a caspase-3/7 assay. Signal transduction in each cell line was examined using western blotting. Src was activated in the two cell lines, and cell proliferation was significantly suppressed by each anticancer drug in combination with 10 µM dasatinib. Caspase-3/7 activity was also increased and Src signaling was suppressed by each anticancer drug in combination with dasatinib. In conclusion, Src is overexpressed in cervical adenocarcinoma cell lines, and dasatinib inhibits intracellular Src signaling and causes apoptosis. The results of the present study suggest that Src may be targeted in novel therapeutic strategies for cervical adenocarcinoma.

  7. Nanoparticles for Site Specific Genome Editing

    Science.gov (United States)

    McNeer, Nicole Ali

    Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to

  8. Site-specific weed control technologies

    DEFF Research Database (Denmark)

    Christensen, Svend; Søgaard, Henning Tangen; Kudsk, Per

    2009-01-01

    Site-specific weed control technologies are defined as machinery or equipment embedded with technologies that detect weeds growing in a crop and, taking into account predefined factors such as economics, takes action to maximise the chances of successfully controlling them. In the article, we...... describe the basic parts of site specific weed control technologies, comprising of weed sensing systems, weed management models and precision weed control implements. A review of state-of-the-art technologies shows that several weed sensing systems and precision implements have been developed over the last...... two decades, though barriers prevent their breakthrough. Most important among these is the lack of a truly robust weed recognition method, owing to mutual shading among plants and limitations in the capacity of highly accurate spraying and weeding apparatuses.   Another barrier is the lack...

  9. Site-Specific PEGylation of Therapeutic Proteins

    Directory of Open Access Journals (Sweden)

    Jonathan K. Dozier

    2015-10-01

    Full Text Available The use of proteins as therapeutics has a long history and is becoming ever more common in modern medicine. While the number of protein-based drugs is growing every year, significant problems still remain with their use. Among these problems are rapid degradation and excretion from patients, thus requiring frequent dosing, which in turn increases the chances for an immunological response as well as increasing the cost of therapy. One of the main strategies to alleviate these problems is to link a polyethylene glycol (PEG group to the protein of interest. This process, called PEGylation, has grown dramatically in recent years resulting in several approved drugs. Installing a single PEG chain at a defined site in a protein is challenging. Recently, there is has been considerable research into various methods for the site-specific PEGylation of proteins. This review seeks to summarize that work and provide background and context for how site-specific PEGylation is performed. After introducing the topic of site-specific PEGylation, recent developments using chemical methods are described. That is followed by a more extensive discussion of bioorthogonal reactions and enzymatic labeling.

  10. Dasatinib in chronic myeloid leukemia: a review

    Directory of Open Access Journals (Sweden)

    Dolly G Aguilera

    2009-03-01

    Full Text Available Dolly G Aguilera1, Apostolia M Tsimberidou21Department of Hematology-Oncology and Stem Cell Transplantation, Children’s Memorial Hospital, Northwestern University, Chicago, IL, USA; 2Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston Texas USAAbstract: Deregulated BCR-ABL tyrosine kinase (TK activity is the molecular marker for chronic myeloid leukemia (CML, which provides an identifiable target for developing therapeutic agents. Imatinib mesylate, a BCR-ABL TK inhibitor, is the frontline therapy for CML. Despite the stunning efficacy of this agent, a small number of patients develop a suboptimal response or resistance to imatinib. In newly diagnosed patients with chronic phase CML, the rate of resistance to imatinib at 4 years was up to 20%, increasing to 70% to 90% for patients in the accelerated/blastic phase. Resistance to imatinib led to the development of novel TK inhibitors such as dasatinib. Several clinical trials have reported more durable complete hematologic and cytogenetic responses with this agent in patients who are resistant or intolerant to imatinib. Dasatinib is well tolerated and has broad efficacy, resulting in durable responses in patients with any BCR-ABL mutation except for T3151 and mutations in codon 317 – most commonly F317L – including mutations that were highly resistant to imatinib, such as L248, Y253, E255, F359, and H396. Dasatinib is recommended for CML in chronic, blastic or accelerated phase that is resistant or intolerant to imatinib. Dasatinib was approved by the FDA at 100 mg once daily as the starting dose in patients with chronic phase CML and at 70 mg twice daily in patients with accelerated or blastic phase CML. Various clinical trial results provided evidence that resistance to one TK inhibitor can be reversed with the use of a different TK inhibitor (TKI. Other second-generation TKIs with activity in CML include nilotinib, bosutinib and

  11. Savannah River Site's Site Specific Plan

    International Nuclear Information System (INIS)

    1991-01-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering

  12. Site specific information in site selection

    International Nuclear Information System (INIS)

    Aeikaes, T.; Hautojaervi, A.

    1998-01-01

    The programme for the siting of a deep repository for final disposal of spent nuclear fuel was started already in 1983 and is carried out today by Posiva Oy which continues the work started by Teollisuuden Voima Oy. The programme aims at site selection by the end of the year 2000. The programme has progressed in successive interim stages with defined goals. After an early phase for site identification, five sites were selected in 1987 for preliminary site characterisation. Three of these were selected and judged to be best suited for the more detailed characterisation in 1992. An additional new site was included into the programme based on a separate feasibility study in the beginning of 1997. Since the year 1983 several safety assessments together with technical plans of the facility have been completed. When approaching the site selection the needs for more detailed consideration of the site specific properties in the safety assessment have been increased. The Finnish regulator STUK has published a proposal for general safety requirements for the final disposal of spent nuclear fuel in Finland. This set of requirements has been projected to be used in conjunction of the decision making by the end 2000. Based on the site evaluation all sites can provide a stable environment and there is evidence that the requirements for the longevity of the canister can be fulfilled at each site. In this manner the four candidate sites do not differ too much from each other. The main difference between the sites is in the salinity of the deep groundwater. The significance of differences in the salinity for the long-term safety cannot be defined yet. The differences may contribute to the discussion of the longevity of the bentonite buffer and also to the modelling of the groundwater flow and transport. The use of the geosphere as a transport barrier is basically culminated on the questions about sparse but fast flow routes and 'how bad channeling can be'. To answer these questions

  13. Taxon- and Site-Specific Melatonin Catabolism

    Directory of Open Access Journals (Sweden)

    Rüdiger Hardeland

    2017-11-01

    Full Text Available Melatonin is catabolized both enzymatically and nonenzymatically. Nonenzymatic processes mediated by free radicals, singlet oxygen, other reactive intermediates such as HOCl and peroxynitrite, or pseudoenzymatic mechanisms are not species- or tissue-specific, but vary considerably in their extent. Higher rates of nonenzymatic melatonin metabolism can be expected upon UV exposure, e.g., in plants and in the human skin. Additionally, melatonin is more strongly nonenzymatically degraded at sites of inflammation. Typical products are several hydroxylated derivatives of melatonin and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK. Most of these products are also formed by enzymatic catalysis. Considerable taxon- and site-specific differences are observed in the main enzymatic routes of catabolism. Formation of 6-hydroxymelatonin by cytochrome P450 subforms are prevailing in vertebrates, predominantly in the liver, but also in the brain. In pineal gland and non-mammalian retina, deacetylation to 5-methoxytryptamine (5-MT plays a certain role. This pathway is quantitatively prevalent in dinoflagellates, in which 5-MT induces cyst formation and is further converted to 5-methoxyindole-3-acetic acid, an end product released to the water. In plants, the major route is catalyzed by melatonin 2-hydroxylase, whose product is tautomerized to 3-acetamidoethyl-3-hydroxy-5-methoxyindolin-2-one (AMIO, which exceeds the levels of melatonin. Formation and properties of various secondary products are discussed.

  14. Statistical and Economic Techniques for Site-specific Nematode Management.

    Science.gov (United States)

    Liu, Zheng; Griffin, Terry; Kirkpatrick, Terrence L

    2014-03-01

    Recent advances in precision agriculture technologies and spatial statistics allow realistic, site-specific estimation of nematode damage to field crops and provide a platform for the site-specific delivery of nematicides within individual fields. This paper reviews the spatial statistical techniques that model correlations among neighboring observations and develop a spatial economic analysis to determine the potential of site-specific nematicide application. The spatial econometric methodology applied in the context of site-specific crop yield response contributes to closing the gap between data analysis and realistic site-specific nematicide recommendations and helps to provide a practical method of site-specifically controlling nematodes.

  15. Statistical and Economic Techniques for Site-specific Nematode Management

    Science.gov (United States)

    Liu, Zheng; Griffin, Terry; Kirkpatrick, Terrence L.

    2014-01-01

    Recent advances in precision agriculture technologies and spatial statistics allow realistic, site-specific estimation of nematode damage to field crops and provide a platform for the site-specific delivery of nematicides within individual fields. This paper reviews the spatial statistical techniques that model correlations among neighboring observations and develop a spatial economic analysis to determine the potential of site-specific nematicide application. The spatial econometric methodology applied in the context of site-specific crop yield response contributes to closing the gap between data analysis and realistic site-specific nematicide recommendations and helps to provide a practical method of site-specifically controlling nematodes. PMID:24643451

  16. [Dasatinib. A novel tyrosine kinase inhibitor for the treatment of chronic myeloid leukaemia

    DEFF Research Database (Denmark)

    Dufva, I.H.; Stentoft, J.; Hasselbalch, H.C.

    2008-01-01

    Chronic myeloid leukaemia is characterized by an abnormal tyrosin kinase in the cytoplasm of the clonal cells. The enzyme is derived from a fusion gene on the Philadelphia-chromosome, evolved by a translocation between chromosomes 9 and 22. Understanding the biology of the tyrosin kinase led to t...... to targeted therapy, inhibiting the ATP-binding site by a small molecule--imatinib (Glivec). A novel 2nd generation tyrosin kinase inhibitor--dasatinib (Sprycel)--is now available in cases of insufficient response or intolerance to imatinib Udgivelsesdato: 2008/1/28...

  17. A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer.

    Directory of Open Access Journals (Sweden)

    Harsh B Pathak

    Full Text Available Molecular targeted therapies have been the focus of recent clinical trials for the treatment of patients with recurrent epithelial ovarian cancer (EOC. The majority have not fared well as monotherapies for improving survival of these patients. Poor bioavailability, lack of predictive biomarkers, and the presence of multiple survival pathways can all diminish the success of a targeted agent. Dasatinib is a tyrosine kinase inhibitor of the Src-family kinases (SFK and in preclinical studies shown to have substantial activity in EOC. However, when evaluated in a phase 2 clinical trial for patients with recurrent or persistent EOC, it was found to have minimal activity. We hypothesized that synthetic lethality screens performed using a cogently designed siRNA library would identify second-site molecular targets that could synergize with SFK inhibition and improve dasatinib efficacy. Using a systematic approach, we performed primary siRNA screening using a library focused on 638 genes corresponding to a network centered on EGFR, HER2, and the SFK-scaffolding proteins BCAR1, NEDD9, and EFS to screen EOC cells in combination with dasatinib. We followed up with validation studies including deconvolution screening, quantitative PCR to confirm effective gene silencing, correlation of gene expression with dasatinib sensitivity, and assessment of the clinical relevance of hits using TCGA ovarian cancer data. A refined list of five candidates (CSNK2A1, DAG1, GRB2, PRKCE, and VAV1 was identified as showing the greatest potential for improving sensitivity to dasatinib in EOC. Of these, CSNK2A1, which codes for the catalytic alpha subunit of protein kinase CK2, was selected for additional evaluation. Synergistic activity of the clinically relevant inhibitor of CK2, CX-4945, with dasatinib in reducing cell proliferation and increasing apoptosis was observed across multiple EOC cell lines. This overall approach to improving drug efficacy can be applied to other

  18. Distinct Dasatinib-Induced Mechanisms of Apoptotic Response and Exosome Release in Imatinib-Resistant Human Chronic Myeloid Leukemia Cells

    Directory of Open Access Journals (Sweden)

    Juan Liu

    2016-04-01

    Full Text Available Although dasatinib is effective in most imatinib mesylate (IMT-resistant chronic myeloid leukemia (CML patients, the underlying mechanism of its effectiveness in eliminating imatinib-resistant cells is only partially understood. This study investigated the effects of dasatinib on signaling mechanisms driving-resistance in imatinib-resistant CML cell line K562 (K562RIMT. Compared with K562 control cells, exsomal release, the phosphoinositide 3-kinase (PI3K/protein kinase B (Akt/ mammalian target of rapamycin (mTOR signaling and autophagic activity were increased significantly in K562RIMT cells and mTOR-independent beclin-1/Vps34 signaling was shown to be involved in exosomal release in these cells. We found that Notch1 activation-mediated reduction of phosphatase and tensin homolog (PTEN was responsible for the increased Akt/mTOR activities in K562RIMT cells and treatment with Notch1 γ-secretase inhibitor prevented activation of Akt/mTOR. In addition, suppression of mTOR activity by rapamycin decreased the level of activity of p70S6K, induced upregulation of p53 and caspase 3, and led to increase of apoptosis in K562RIMT cells. Inhibition of autophagy by spautin-1 or beclin-1 knockdown decreased exosomal release, but did not affect apoptosis in K562RIMT cells. In summary, in K562RIMT cells dasatinib promoted apoptosis through downregulation of Akt/mTOR activities, while preventing exosomal release and inhibiting autophagy by downregulating expression of beclin-1 and Vps34. Our findings reveal distinct dasatinib-induced mechanisms of apoptotic response and exosomal release in imatinib-resistant CML cells.

  19. Dasatinib-induced Seborrheic Dermatitis-like Eruption.

    Science.gov (United States)

    Riahi, Ryan R; Cohen, Philip R

    2017-07-01

    Dasatinib is an oral tyrosine kinase inhibitor approved for imatinib-resistant chronic myelogenous leukemia. It has been investigated in treating other neoplasms, including non-small-cell lung cancer and a subset of melanomas. Seborrheic dermatitis is characterized by erythematous patches or plaques with scaling typically affecting the external ear, glabella, hair-bearing areas of the face, nasolabial fold, and scalp. Antitumor agents are often associated with mucocutaneous side effects, including seborrheic dermatitis. We describe the case of a 79-year-old woman with a history of sinonasal melanoma who developed a seborrheic dermatitis-like eruption while taking dasatinib. We also review the molecular abnormalities associated with melanoma, summarize the mucocutaneous side effects of dasatinib, and list the other antineoplastic agents associated with a seborrheic dermatitis-like eruption.

  20. Appreciating Site-Specific Qualities in Urban Harbours

    DEFF Research Database (Denmark)

    Reeh, Henrik

    2015-01-01

    When “site-specificity” becomes a central value in city and harbor transformation, it soon proves necessary to address the ways in which scholars and professionals actually determine site-specific qualities in urban fabrics and social life. This paper delves into the above questions by means of o...... of site-specificity, even in the traditional harbor settings. Considered with conceptual care, such situations may teach us what it means to “appreciate site-specific qualities”....

  1. Innovation and diffusion of site-specific crop management

    DEFF Research Database (Denmark)

    Pedersen, Søren Marcus; Pedersen, Jørgen Lindgaard

    2004-01-01

    Site-specific crop management or precision farming (PF) is a highly complex management system for site-specific input application of lime, fertilizers and pesticides in arable farming. The Global Positioning System (GPS) is the backbone of the system. To conduct PF several technical systems...

  2. Innovation and Diffusion of Site-specific Crop Management

    DEFF Research Database (Denmark)

    Pedersen, Søren Marcus; Pedersen, Jørgen Lindgaard

    2006-01-01

    Site-specific crop management or precision farming is a highly complex managementsystem for site-specific input application of lime, fertilizers and pesticides in arable farming. The Global Positioning System (GPS)is the backbone of the system. To conduct precision farming several technical systems...

  3. 77 FR 22772 - Environmental Management Site-Specific Advisory Board

    Science.gov (United States)

    2012-04-17

    ... Environmental Management Site-Specific Advisory Board AGENCY: Office of Environmental Management, Department of... Administration, notice is hereby given that the Environmental Management Site-Specific Advisory Board (EM SSAB... recommendations to the Assistant Secretary for Environmental Management (EM) concerning issues affecting the EM...

  4. Site-Specific Chemical Labeling of Long RNA Molecules

    DEFF Research Database (Denmark)

    Jahn, Kasper; Olsen, Eva Maria; Nielsen, Morten Muhlig

    2011-01-01

    Site-specific labeling of RNA molecules is a valuable tool for studying their structure and function. Here, we describe a new site-specific RNA labeling method, which utilizes a DNA-templated chemical reaction to attach a label at a specific internal nucleotide in an RNA molecule. The method...

  5. Recombinant protein hydrazides: application to site-specific protein PEGylation.

    Science.gov (United States)

    Thom, Jennifer; Anderson, David; McGregor, Joanne; Cotton, Graham

    2011-06-15

    Here, we describe a novel method for the site-specific C-terminal PEGylation of recombinant proteins. This general approach exploits chemical cleavage of precursor intein-fusion proteins with hydrazine to directly produce recombinant protein hydrazides. This unique functionality within the protein sequence then facilitates site-specific C-terminal modification by hydrazone-forming ligation reactions. This approach was used to generate folded, site-specifically C-terminal PEGylated IFNalpha2b and IFNbeta1b, which retained excellent antiviral activity, demonstrating the utility of this technology in the PEGylation of therapeutic proteins. As this methodology is straightforward to perform, is compatible with disulfide bonds, and is exclusively selective for the protein C-terminus, it shows great potential as general technology for the site-specific engineering and labeling of recombinant proteins.

  6. Jefferson Proving Ground Site-Specific Sampling Design Plan

    National Research Council Canada - National Science Library

    1992-01-01

    The purpose of this document is to outline field sampling and laboratory analyses that are to be conducted as part of the Jefferson Proving Ground Site-Specific Sampling and Analysis (SSSA) program...

  7. Oxidative stress is involved in Dasatinib-induced apoptosis in rat primary hepatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Tao; Luo, Peihua; Zhu, Hong; Zhao, Yuqin [Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Wu, Honghai; Gai, Renhua; Wu, Youping [Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou 310058 (China); Yang, Bo [Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Yang, Xiaochun, E-mail: yangxiaochun@zju.edu.cn [Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou 310058 (China); He, Qiaojun, E-mail: qiaojunhe@zju.edu.cn [Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou 310058 (China)

    2012-06-15

    Dasatinib, a multitargeted inhibitor of BCR–ABL and SRC kinases, exhibits antitumor activity and extends the survival of patients with chronic myeloid leukemia (CML) and Philadelphia chromosome-positive acute lymphoblastic leukemia (ALL). However, some patients suffer from hepatotoxicity, which occurs through an unknown mechanism. In the present study, we found that Dasatinib could induce hepatotoxicity both in vitro and in vivo. Dasatinib reduced the cell viability of rat primary hepatocytes, induced the release of alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) in vitro, and triggered the ballooning degeneration of hepatocytes in Sprague–Dawley rats in vivo. Apoptotic markers (chromatin condensation, cleaved caspase-3 and cleaved PARP) were detected to indicate that the injury induced by Dasatinib in hepatocytes in vitro was mediated by apoptosis. This result was further validated in vivo using terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assays. Here we found that Dasatinib dramatically increased the level of reactive oxygen species (ROS) in hepatocytes, reduced the intracellular glutathione (GSH) content, attenuated the activity of superoxide dismutase (SOD), generated malondialdehyde (MDA), a product of lipid peroxidation, decreased the mitochondrial membrane potential, and activated nuclear factor erythroid 2-related factor 2 (Nrf2) and mitogen-activated protein kinases (MAPK) related to oxidative stress and survival. These results confirm that oxidative stress plays a pivotal role in Dasatinib-mediated hepatotoxicity. N-acetylcysteine (NAC), a typical antioxidant, can scavenge free radicals, attenuate oxidative stress, and protect hepatocytes against Dasatinib-induced injury. Thus, relieving oxidative stress is a viable strategy for reducing Dasatinib-induced hepatotoxicity. -- Highlights: ►Dasatinib shows potential hepatotoxicity both in vitro and in vivo. ►Apoptosis plays a vital role in Dasatinib

  8. Dasatinib as a treatment for Duchenne muscular dystrophy.

    Science.gov (United States)

    Lipscomb, Leanne; Piggott, Robert W; Emmerson, Tracy; Winder, Steve J

    2016-01-15

    Identification of a systemically acting and universal small molecule therapy for Duchenne muscular dystrophy would be an enormous advance for this condition. Based on evidence gained from studies on mouse genetic models, we have identified tyrosine phosphorylation and degradation of β-dystroglycan as a key event in the aetiology of Duchenne muscular dystrophy. Thus, preventing tyrosine phosphorylation and degradation of β-dystroglycan presents itself as a potential therapeutic strategy. Using the dystrophic sapje zebrafish, we have investigated the use of tyrosine kinase and other inhibitors to treat the dystrophic symptoms in this model of Duchenne muscular dystrophy. Dasatinib, a potent and specific Src tyrosine kinase inhibitor, was found to decrease the levels of β-dystroglycan phosphorylation on tyrosine and to increase the relative levels of non-phosphorylated β-dystroglycan in sapje zebrafish. Furthermore, dasatinib treatment resulted in the improved physical appearance of the sapje zebrafish musculature and increased swimming ability as measured by both duration and distance of swimming of dasatinib-treated fish compared with control animals. These data suggest great promise for pharmacological agents that prevent the phosphorylation of β-dystroglycan on tyrosine and subsequent steps in the degradation pathway as therapeutic targets for the treatment of Duchenne muscular dystrophy. © The Author 2015. Published by Oxford University Press.

  9. Site-specific design optimization of wind turbines

    DEFF Research Database (Denmark)

    Fuglsang, P.; Bak, C.; Schepers, J.G.

    2002-01-01

    This article reports results from a European project, where site characteristics were incorporated into the design process of wind turbines, to enable site-specific design. Two wind turbines of different concept were investigated at six different sites comprising normal flat terrain, offshore......-specific designs showed reductions in cost of energy by up to 15% achieved from an increase in annual energy yield and a reduction in manufacturing costs. The greatest benefits were found at sites with low mean wind speed and low turbulence. Site-specific design was not able to offset the intrinsic economic...

  10. SITE-94. Site specific base data for the performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Geier, J. [ed.] [Clearwater Hardrock Consulting, Monmouth, OR (United States); Tiren, S. [Geosigma AB, Uppsala (Sweden); Dverstorp, B. [Swedish Nuclear Power Inspectorate, Stockholm (Sweden); Glynn, P. [U.S. Geological Survey, Reston, VA (United States)

    1996-06-01

    This report documents the site specific base data that were available, and the utilization of these data within SITE-94. A brief summary is given of SKB`s preliminary site investigations for the Aespoe Hard Rock Laboratory (HRL), which were the main source of site-specific data for SITE-94, and an overview is given of the field methods and instrumentation for the preliminary investigations. A compilation is given of comments concerning the availability and quality of the data for Aespoe, and specific recommendations are given for future site investigations. It was found that the HRL pre-investigations produced a large quantity of data which were, for the most part, of sufficient quality to be valuable for a performance assessment. However, some problems were encountered regarding documentation, procedural consistency, positional information, and storage of the data from the measurements. 77 refs, 4 tabs.

  11. Pinellas Plant FY1990 site specific implementation plan

    International Nuclear Information System (INIS)

    Klein, R.D.

    1990-02-01

    This Site Specific Implementation Plan describes the Corrective Action, Environmental Restoration, and Waste Management activities to be performed at the Pinellas Plant in FY1990 (October 1, 1989 to September 30, 1989). These FY1990 activities are described in the Pinellas Plant FY1991--95 Five-Year Plan. The information used to prepare this plan reflects the best estimate of the project scope, schedules, regulatory, and funding requirements at the time of plan preparation. The Environmental Restoration/Waste Management Five-Year Plan is a dynamic document and will be modified each year; the Site Specific Implementation Plan will, in turn, be modified each year to reflect new findings, information, and knowledge of the various projects. 4 figs., 11 tabs

  12. Drainage filter technologies to mitigate site-specific phosphorus losses

    DEFF Research Database (Denmark)

    Kjærgaard, Charlotte; Heckrath, Goswin Johann; Iversen, Bo Vangsø

    2014-01-01

    of implementing the drainage filter technologies including surface-flow constructed wetlands, subsurface flow constructed wetlands, and drainage well filters (www.supremetech.dk). We will present results on P retention from (i) controlled column experiments with permeable filter substrates, and (ii) a full...... high risks areas of P loss and applying site-specific measures therefore seems a more cost-efficient approach. The Danish Commission for Nature and Agriculture has now called for a shift of paradigm towards targeted mitigation and development of new, cost-efficient technologies to mitigate site......-specific nutrient losses in drainage. The “SUPREME-TECH” project (2010-2015), funded by the Danish Strategic Research Council, aims at providing the scientific basis for developing cost-effective drainage filter technologies to retain P in agricultural drainage waters. The project studies different approaches...

  13. Quantifying site-specific physical heterogeneity within an estuarine seascape

    Science.gov (United States)

    Kennedy, Cristina G.; Mather, Martha E.; Smith, Joseph M.

    2017-01-01

    Quantifying physical heterogeneity is essential for meaningful ecological research and effective resource management. Spatial patterns of multiple, co-occurring physical features are rarely quantified across a seascape because of methodological challenges. Here, we identified approaches that measured total site-specific heterogeneity, an often overlooked aspect of estuarine ecosystems. Specifically, we examined 23 metrics that quantified four types of common physical features: (1) river and creek confluences, (2) bathymetric variation including underwater drop-offs, (3) land features such as islands/sandbars, and (4) major underwater channel networks. Our research at 40 sites throughout Plum Island Estuary (PIE) provided solutions to two problems. The first problem was that individual metrics that measured heterogeneity of a single physical feature showed different regional patterns. We solved this first problem by combining multiple metrics for a single feature using a within-physical feature cluster analysis. With this approach, we identified sites with four different types of confluences and three different types of underwater drop-offs. The second problem was that when multiple physical features co-occurred, new patterns of total site-specific heterogeneity were created across the seascape. This pattern of total heterogeneity has potential ecological relevance to structure-oriented predators. To address this second problem, we identified sites with similar types of total physical heterogeneity using an across-physical feature cluster analysis. Then, we calculated an additive heterogeneity index, which integrated all physical features at a site. Finally, we tested if site-specific additive heterogeneity index values differed for across-physical feature clusters. In PIE, the sites with the highest additive heterogeneity index values were clustered together and corresponded to sites where a fish predator, adult striped bass (Morone saxatilis), aggregated in a

  14. Jefferson Proving Ground Site-Specific Sampling Design Plan.

    Science.gov (United States)

    1992-01-01

    The purpose of this document is to outline field sampling and laboratory analyses that are to be conducted as part of the Jefferson Proving Ground...Site-Specific Sampling and Analysis (SSSA) program. Jefferson Proving Ground (JPG) is a U.S. Army facility located in Madison, Indiana. The SSSA at JPG...will then be analyzed to determine if past activities at Jefferson Proving Ground (JPG) have caused contaminants to enter the groundwater, stream water

  15. Intruder scenarios for site-specific waste classification

    International Nuclear Information System (INIS)

    Kennedy, W.E. Jr.

    1988-01-01

    The US Department of Energy (DOE) is currently revising its low-level radioactive waste (LLW) management requirements and guidelines for waste generated at its facilities that support defense missions. Specifically, draft DOE 5820.2A, Chapter 3, describes the purpose, policy, and requirements necessary for the management of defense LLW. The draft DOE policy calls for DOE LLW operations to be managed to protect the health and safety of the public, preserve the environment, and ensure that no remedial action will be necessary after termination of operations. The requirements and guidelines apply to radioactive wastes but are also intended to apply to mixed hazardous and radioactive wastes as defined in draft DOE 5400.5, Hazardous and Radioactive Mixed Waste. The basic approach used by DOE is to establish overall performance objectives in terms of ground-water protection and public radiation dose limits and to require site-specific performance assessments to determine compliance. As a result of these performance assessments, each site shall develop waste acceptance criteria that define the allowable quantities and concentrations of specific radioisotopes. Additional limitations on waste disposal design, waste form, and waste treatment shall also be developed on a site-specific basis. As a key step in the site-specific performance assessments, an evaluation must be conducted of potential radiation doses to intruders who may inadvertently move onto a closed DOE LLW disposal site after loss of institutional controls must be conducted. This paper describes the types of intruder scenarios that should be considered when performing this step of the site-specific performance assessment

  16. Sustained activation of the AKT/mTOR and MAP kinase pathways mediate resistance to the Src inhibitor, dasatinib, in thyroid cancer.

    Science.gov (United States)

    Mishall, Katie M; Beadnell, Thomas C; Kuenzi, Brent M; Klimczak, Dorothy M; Superti-Furga, Giulio; Rix, Uwe; Schweppe, Rebecca E

    2017-11-28

    New targeted therapies are needed for advanced thyroid cancer. Our lab has shown that Src is a key mediator of tumorigenic processes in thyroid cancer. However, single-agent Src inhibitors have had limited efficacy in solid tumors. In order to more effectively target Src in the clinic, our lab has previously generated four thyroid cancer cell lines that are resistant to dasatinib through gradual dose escalation. We further tested two additional Src inhibitors and shown the dasatinib-resistant (DasRes) cells exhibit cross-resistance to saracatinib, but are sensitive to bosutinib, suggesting that unique off-targets of bosutinib play an important role in mediating sensitivity to bosutinib. To identify the kinases targeted by dasatinib and bosutinib, we utilized an unbiased compound centric chemical proteomics screen. We identified 33 kinases that were enriched in the bosutinib pull down. Using the STRING database to map protein-protein interactions of the unique bosutinib targets, we identified a signaling axis which included mTOR, FAK, and MEK. Inhibition of the mTOR, MEK, and Src/FAK nodes simultaneously was the most effective at reducing cell growth and survival. Overall, these studies have identified key mediators of Src inhibitor resistance, and show that targeting these signaling nodes are necessary for anti-tumor efficacy.

  17. Site-specifically radioiodinated antibody for targeting tumors

    International Nuclear Information System (INIS)

    Rea, D.W.; Ultee, M.E.; Belinka, B.A. Jr.; Coughlin, D.J.; Alvarez, V.L.

    1990-01-01

    Labeling of an antibody site specifically through its carbohydrate regions preserves its antigen-binding activity. Previously site-specific labeling studies have conjugated antibodies with metallic radioisotopes or drugs. We now report site-specific labeling with a new radioiodinated compound, 2-hydroxy-5-iodo-3-methylbenzoyl hydrazide, whose synthesis we described earlier. The compound is reacted with aldehyde groups produced by specific oxidation of the carbohydrate portion of the antibody with sodium m-periodate. Optimized conjugation conditions give good recovery of active antibody containing 10 groups per molecule. The conjugate is stable in solution for at least several weeks at both 4 and -70 degrees C. When injected into nude mice bearing LS174T human cancer xenografts, the conjugate of B72.3 antibody localizes well to tumor tissue, with low uptake by other organs. This biodistribution is similar to that of conjugate prepared by using solid-phase chloramine-T (Iodohead). There are only two significant differences. First, the carbohydrate conjugate is much less susceptible to dehalogenation, and thus shows much less thyroid uptake. Secondly, the biological half-life of the carbohydrate conjugate was about half that of the chloramine-T one. This could be due primarily to lysis of the hydrazine bond through which the antibody is attached to the compound, which would then be excreted rapidly by itself. The new reagent will be especially useful for antibodies which either cannot be labeled by chloramine-T methods, or whose activity is impaired by them

  18. Dasatinib in the treatment of imatinib refractory chronic myeloid leukemia

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Ramchandren

    2009-05-01

    Full Text Available Radhakrishnan Ramchandren, Charles A SchifferDivision of Hematology/Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USAAbstract: The development of imatinib for the treatment of chronic myeloid leukemia (CML has proven to be an example of medical success in the era of targeted therapy. However, imatinib resistance or intolerance occurs in a substantial number of patients. Additionally, patients who have progressed beyond the chronic phase of CML do relatively poorly with imatinib therapy. Mechanisms of imatinib resistance include BCR-ABL point mutations resulting in decreased imatinib binding, as well as mutation-independent causes of resistance such as SRC family kinase dysregulation, BCR-ABL gene amplification, drug influx/efflux mechanisms and other poorly understood processes. The options for therapy in these patients include stem cell transplantation, imatinib dose escalation as well as the use of second-generation tyrosine kinase inhibitors. Dasatinib is a second-generation multi-kinase inhibitor with several theoretical and mechanistic advantages over imatinib. Moreover, several studies have evaluated dasatinib in patients who have progressed on imatinib therapy with encouraging results. Other novel agents such as mTOR inhibitors, bosutinib and INNO 406 have also shown promise in this setting. Although treatment options have increased, the choice of second-line therapy in patients with CML is influenced by concerns surrounding the duration of response as well as toxicity. Consequently, there is no agreed upon optimal second-line agent. This paper reviews the current data and attempts to address these issues. Keywords: chronic myeloid leukemia (CML, dasatinib, imatinib, resistance (imatinib resistance, nilotinib, tyrosine kinase inhibitor

  19. Global phosphotyrosine proteomics identifies PKCδ as a marker of responsiveness to Src inhibition in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Eliot T McKinley

    Full Text Available Sensitive and specific biomarkers of protein kinase inhibition can be leveraged to accelerate drug development studies in oncology by associating early molecular responses with target inhibition. In this study, we utilized unbiased shotgun phosphotyrosine (pY proteomics to discover novel biomarkers of response to dasatinib, a small molecule Src-selective inhibitor, in preclinical models of colorectal cancer (CRC. We performed unbiased mass spectrometry shotgun pY proteomics to reveal the pY proteome of cultured HCT-116 colonic carcinoma cells, and then extended this analysis to HCT-116 xenograft tumors to identify pY biomarkers of dasatinib-responsiveness in vivo. Major dasatinib-responsive pY sites in xenograft tumors included sites on delta-type protein kinase C (PKCδ, CUB-domain-containing protein 1 (CDCP1, Type-II SH2-domain-containing inositol 5-phosphatase (SHIP2, and receptor protein-tyrosine phosphatase alpha (RPTPα. The pY313 site PKCδ was further supported as a relevant biomarker of dasatinib-mediated Src inhibition in HCT-116 xenografts by immunohistochemistry and immunoblotting with a phosphospecific antibody. Reduction of PKCδ pY313 was further correlated with dasatinib-mediated inhibition of Src and diminished growth as spheroids of a panel of human CRC cell lines. These studies reveal PKCδ pY313 as a promising readout of Src inhibition in CRC and potentially other solid tumors and may reflect responsiveness to dasatinib in a subset of colorectal cancers.

  20. Dasatinib, a Src inhibitor, sensitizes liver metastatic colorectal carcinoma to oxaliplatin in tumors with high levels of phospho-Src

    Science.gov (United States)

    Perez, Marco; Lucena-Cacace, Antonio; Marín-Gómez, Luis Miguel; Padillo-Ruiz, Javier; Robles-Frias, Maria Jose; Saez, Carmen; Garcia-Carbonero, Rocio; Carnero, Amancio

    2016-01-01

    Despite the development of new antineoplastic agents for the treatment of colorectal cancer (CRC), oxaliplatin and fluoropyrimidines remain the most commonly employed drugs for the treatment of both early and advanced disease. Intrinsic or acquired resistance is, however, an important limitation to pharmacological therapy, and the development of chemosensitization strategies constitute a major goal with important clinical implications. In the present work, we determined that high levels of activated Src kinase, measured as phospho-Src at the Tyr419 residue in CRC cell lines, can promote colorectal carcinoma cell resistance to oxaliplatin, but not to 5-fluorouracil (5FU), and that inhibition of this protein restores sensitivity to oxaliplatin. Similar results were observed with in vivo patient-derived xenograft (PDX) models that were orthotopically grown in murine livers. In PDX tumor lines derived from human CRC liver metastasis, dasatinib, a Src inhibitor, increases sensitivity to oxaliplatin only in tumors with high p-Src. However, dasatinib did not modify sensitivity to 5FU in any of the models. Our data suggest that chemoresistance induced by p-Src is specific to oxaliplatin, and that p-Src levels can be used to identify patients who may benefit from this combination therapy. These results are relevant for clinicians as they identify a novel biomarker of drug resistance that is suitable to pharmacological manipulation. PMID:27105527

  1. Transforming growth factor β signaling overcomes dasatinib resistance in lung cancer.

    Directory of Open Access Journals (Sweden)

    Edna Gordian

    Full Text Available Lung cancer is the second most common cancer and the leading cause of cancer-related deaths. Despite recent advances in the development of targeted therapies, patients with advanced disease remain incurable, mostly because metastatic non-small cell lung carcinomas (NSCLC eventually become resistant to tyrosine kinase inhibitors (TKIs. Kinase inhibitors have the potential for target promiscuity because the kinase super family is the largest family of druggable genes that binds to a common substrate (ATP. As a result, TKIs often developed for a specific purpose have been found to act on other targets. Drug affinity chromatography has been used to show that dasatinib interacts with the TGFβ type I receptor (TβR-I, a serine-threonine kinase. To determine the potential biological relevance of this association, we studied the combined effects of dasatinib and TGFβ on lung cancer cell lines. We found that dasatinib treatment alone had very little effect; however, when NSCLC cell lines were treated with a combination of TGFβ and dasatinib, apoptosis was induced. Combined TGFβ-1 + dasatinib treatment had no effect on the activity of Smad2 or other non-canonical TGFβ intracellular mediators. Interestingly, combined TGFβ and dasatinib treatment resulted in a transient increase in p-Smad3 (seen after 3 hours. In addition, when NSCLC cells were treated with this combination, the pro-apoptotic protein BIM was up-regulated. Knockdown of the expression of Smad3 using Smad3 siRNA also resulted in a decrease in BIM protein, suggesting that TGFβ-1 + dasatinib-induced apoptosis is mediated by Smad3 regulation of BIM. Dasatinib is only effective in killing EGFR mutant cells, which is shown in only 10% of NSCLCs. Therefore, the observation that wild-type EGFR lung cancers can be manipulated to render them sensitive to killing by dasatinib could have important implications for devising innovative and potentially more efficacious treatment strategies for this

  2. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions

    KAUST Repository

    Walkiewicz, Katarzyna Wiktoria

    2015-06-17

    The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein ‘nanomachines’ to become activated in a site-specific manner.

  3. Dasatinib for the treatment of chronic myeloid leukemia: patient selection and special considerations.

    Science.gov (United States)

    Keskin, Dilek; Sadri, Sevil; Eskazan, Ahmet Emre

    2016-01-01

    Dasatinib is one of the second-generation tyrosine kinase inhibitors used in imatinib resistance and/or intolerance, as well as in the frontline setting in patients with chronic myeloid leukemia-chronic phase, and also in patients with advanced disease. It is also utilized in Philadelphia chromosome-positive acute lymphocytic leukemia. While choosing the appropriate tyrosine kinase inhibitor (ie, dasatinib) for each individual patient, comorbidities and BCR-ABL1 kinase domain mutations should always be taken into consideration, among other things. This review mainly focuses on patient selection prior to dasatinib administration in the treatment of chronic myeloid leukemia.

  4. Optimization under Uncertainty of Site-Specific Turbine Configurations: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Quick, Julian; Dykes, Katherine; Graf, Peter; Zahle, Frederik

    2016-11-01

    Uncertainty affects many aspects of wind energy plant performance and cost. In this study, we explore opportunities for site-specific turbine configuration optimization that accounts for uncertainty in the wind resource. As a demonstration, a simple empirical model for wind plant cost of energy is used in an optimization under uncertainty to examine how different risk appetites affect the optimal selection of a turbine configuration for sites of different wind resource profiles. If there is unusually high uncertainty in the site wind resource, the optimal turbine configuration diverges from the deterministic case and a generally more conservative design is obtained with increasing risk aversion on the part of the designer.

  5. Towards soft robotic devices for site-specific drug delivery.

    Science.gov (United States)

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications.

  6. Temporally-controlled site-specific recombination in zebrafish.

    Directory of Open Access Journals (Sweden)

    Stefan Hans

    Full Text Available Conventional use of the site-specific recombinase Cre is a powerful technology in mouse, but almost absent in other vertebrate model organisms. In zebrafish, Cre-mediated recombination efficiency was previously very low. Here we show that using transposon-mediated transgenesis, Cre is in fact highly efficient in this organism. Furthermore, temporal control of recombination can be achieved by using the ligand-inducible CreER(T2. Site-specific recombination only occurs upon administration of the drug tamoxifen (TAM or its active metabolite, 4-hydroxy-tamoxifen (4-OHT. Cre-mediated recombination is detectable already 4 or 2 hours after administration of TAM or 4-OHT, demonstrating fast recombination kinetics. In addition, low doses of TAM allow mosaic labeling of single cells. Combined, our results show that conditional Cre/lox will be a valuable tool for both, embryonic and adult zebrafish studies. Furthermore, single copy insertion transgenesis of Cre/lox constructs suggest a strategy suitable also for other organisms.

  7. Site-specific calibration of the Hanford personnel neutron dosimeter

    International Nuclear Information System (INIS)

    Endres, A.W.; Brackenbush, L.W.; Baumgartner, W.V.; Rathbone, B.A.

    1994-10-01

    A new personnel dosimetry system, employing a standard Hanford thermoluminescent dosimeter (TLD) and a combination dosimeter with both CR-39 nuclear track and TLD-albedo elements, is being implemented at Hanford. Measurements were made in workplace environments in order to verify the accuracy of the system and establish site-specific factors to account for the differences in dosimeter response between the workplace and calibration laboratory. Neutron measurements were performed using sources at Hanford's Plutonium Finishing Plant under high-scatter conditions to calibrate the new neutron dosimeter design to site-specific neutron spectra. The dosimeter was also calibrated using bare and moderated 252 Cf sources under low-scatter conditions available in the Hanford Calibration Laboratory. Dose equivalent rates in the workplace were calculated from spectrometer measurements using tissue equivalent proportional counter (TEPC) and multisphere spectrometers. The accuracy of the spectrometers was verified by measurements on neutron sources with calibrations directly traceable to the National Institute of Standards and Technology (NIST)

  8. T790M-Selective EGFR-TKI Combined with Dasatinib as an Optimal Strategy for Overcoming EGFR-TKI Resistance in T790M-Positive Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Watanabe, Satomi; Yoshida, Takeshi; Kawakami, Hisato; Takegawa, Naoki; Tanizaki, Junko; Hayashi, Hidetoshi; Takeda, Masayuki; Yonesaka, Kimio; Tsurutani, Junji; Nakagawa, Kazuhiko

    2017-11-01

    T790M mutation-selective EGFR tyrosine kinase inhibitors (EGFR-TKI) have demonstrated clinical benefits in non-small cell lung cancer (NSCLC) patients harboring T790M mutation, which is the major cause of resistance to EGFR-TKI. However, their efficacy is limited, possibly due to the emergence of apoptosis resistance in T790M-positive NSCLC. We previously identified Src family kinases as cooncogenic drivers along with T790M and found that the Src inhibitor dasatinib combined with an irreversible or a preclinical T790M-selective EGFR-TKI enhanced antitumor activity in T790M-positive cells. In the current study, we evaluated the efficacy of dasatinib combined with the clinically relevant T790M-selective EGFR-TKI ASP8273 or osimertinib in EGFR mutation-positive NSCLC with or without T790M mutation. A cell viability assay revealed that dasatinib had synergistic effects with these TKIs in T790M-positive cells and simultaneously inhibited Src, Akt, and Erk, which remained activated upon single-agent treatment. Dasatinib also increased the rate of apoptosis in T790M-positive cells induced by T790M-selective EGFR-TKIs, as determined by the Annexin-V binding assay; this was associated with downregulation of the antiapoptotic Bcl-2 family member Bcl-xL, a finding that was confirmed in mice bearing T790M-positive xenografts. Our results suggest that Bcl-xL plays a key role in the apoptosis resistance of T790M-positive NSCLC, and that dasatinib combined with clinically relevant T790M-selective EGFR-TKIs is potentially effective in overcoming resistance to first-generation EGFR-TKIs in NSCLC patients with acquired T790M. Mol Cancer Ther; 16(11); 2563-71. ©2017 AACR . ©2017 American Association for Cancer Research.

  9. Savannah River Site's Site Specific Plan

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  10. Site specific management in an olive tree plantation

    DEFF Research Database (Denmark)

    Fountas, S.; Aggelopoulou, K.; Bouloulis, C.

    2011-01-01

    . Maps were created as a basis for site-specific management of P, K and lime, and these were applied 15 days after harvest in the winter of 2008. The results indicated considerable spatial variation in yield and soil properties. The soil organic matter content was about 22% greater and the penetration...... resolution). In addition, 91 cores of soil were taken at a depth of 0–30 cm on a 30-m systematic sampling grid corresponding to a density of 10 soil samples per ha. The soil properties measured were penetration resistance, soil texture, organic matter, pH, P, NO3–N, K, Mg, Zn, Mn, Fe, B and Ca contents....... The effect of the method of weed control on the soil condition for post emergence herbicides under no-tillage versus rotary cultivation was evaluated on the basis of soil organic matter content and penetration resistance. The data were analyzed using both descriptive statistics and geostatistical methods...

  11. [Progress on XerCD/dif site-specific recombination].

    Science.gov (United States)

    Tian, De-Qiao; Wang, Yu-Min; Zheng, Tao

    2012-08-01

    In Escherichia coli, 10% to 15% of growing bacteria produce chromosome dimers during DNA replication. These dimers are resolved by XerC and XerD, two chromosome recombinases that target the dif sequence in the replication terminus of chromosome. Phage CTXΦ integrates into vibrio cholerae chromosome in a site-specific manner. However, CTXΦ genome does not encode any recombinase, while recombinase XerC and XerD, which is coded by vibrio cholerae chromosome are required for the integration of CTXΦ into the vibrio cholerae chromosome. The CTXΦ integration site overlaps with the dif site. The wide distribution of XerCD recombinase and dif site among bacteria genome suggests that it may be universal in resolve of chromosome dimers and phage integration. In this article, we reviewed the research progresses on chromosome dimer resolve and phage integration through XerCD/dif site-specific recombination.

  12. Precision agriculture - from mapping to site-specific application

    DEFF Research Database (Denmark)

    Pedersen, Søren Marcus; Lind, Kim Martin Hjorth

    2017-01-01

    -rate application. This chapter also notes that the adoption of several specific variable-rate application technologies have been modest in recent years. However, in contrast the adoption of auto-steering has been significant in the last decade. The last section describes the overall aim of the book and an overview...... of each chapter in the book. Each chapter address a different topic starting with an overview of technologies that are currently available, followed by specific Variable-Rate Technologies such as VRT fertilizer application, VRT pesticide application, site-specific irrigation management, Auto......-steering and Controlled Traffic Systems. Finally, the chapter looks into new developments of autonomous systems with an example of robotic seeding, farm information management in precision agriculture and different methods on the adoption of PA. The last chapter focuses on how PA can fulfil the current policy trends...

  13. Characterization of reference and site specific human acids

    International Nuclear Information System (INIS)

    Kim, J.I.; Buckau, G.

    1988-01-01

    As a part of the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of humic acids have been carried out, as for their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as a reference material, and the humic acid extracted from one of Gorleben groundwaters is also purified to a protonated form and taken as a site specific material. These two humic acids, together with the original Na salt from Aldrich Co., are included for the characterization exercise. The results of characterization provide a basic knowledge that supports the forthcoming study of complexation of humic acids with actinides and fission products in their migration processes in the geosphere. (orig.)

  14. Characterization of reference and site specific humic acids

    International Nuclear Information System (INIS)

    Kim, J.I.; Buckau, G.

    1988-11-01

    As a contribution to the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of selected humic acids have been carried out at TU Muenchen, regarding their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as reference material. Furthermore two humic acids extracted from groundwaters from Gorleben (FRG) and Boom Clay (B) are purified to protonated forms and taken as site specific materials. These three humic acids, together with the original Na salt from Aldrich Co., are included in the present characterization exercise. The results of characterization provide basic knowledge supporting the forthcoming study of complexation of actinides and fission products with humic acid and their migration processes in the geosphere. (orig.)

  15. Activity of dasatinib, a dual SRC/ABL kinase inhibitor, and IPI-504, a heat shock protein 90 inhibitor, against gastrointestinal stromal tumor-associated PDGFRAD842V mutation.

    Science.gov (United States)

    Dewaele, Barbara; Wasag, Bartosz; Cools, Jan; Sciot, Raf; Prenen, Hans; Vandenberghe, Peter; Wozniak, Agnieszka; Schöffski, Patrick; Marynen, Peter; Debiec-Rychter, Maria

    2008-09-15

    Activating mutations in platelet-derived growth factor receptor-alpha (PDGFRA) have been reported in approximately 5% to 10% of patients with gastrointestinal stromal tumors (GIST). Imatinib efficiently inhibits the juxtamembrane PDGFRA mutations, whereas many tyrosine kinase domain activation loop PDGFRA mutations confer primary resistance to imatinib. In this study, we compared the efficacy of second-line tyrosine kinase inhibitors such as dasatinib, sorafenib, and nilotinib against two GIST-related PDGFRA mutants, PDGFRA(D842V) and PDGFRA(DeltaDIM842-844). In addition, we sought to investigate the inhibitory effect of the heat shock protein 90 inhibitor, IPI-504, on these mutants. Primary imatinib-resistant tumor cells and cell lines expressing imatinib-resistant PDGFRA(D842V) or imatinib-sensitive PDGFRA(DeltaDIM842-844) mutants were treated with different concentrations of dasatinib, sorafenib, nilotinib, and IPI-504. The effect of treatment on proliferation, survival, and signaling was determined. All inhibitors tested exhibited a high efficacy toward the PDGFRA(DeltaDIM842-844) mutant. In contrast, ex vivo and in vitro assays revealed that only dasatinib potently inhibited the PDGFRA(D842V) isoform with an IC(50) value of 62 nmol/L. Sorafenib and nilotinib were significantly less efficacious against this mutation, inhibiting the PDGFRA kinase activity at >1,000 and >5,000 nmol/L, and suppressing the proliferation of the cells expressing the PDGFRA(D842V) mutant with an IC(50) value of 239 and 1,310 nmol/L, respectively. IPI-504 treatment potently inhibited PDGFRA kinase activity by inducing the degradation of PDGFRA(D842V) and PDGFRA(DeltaDIM842-844) at 256 and 182 nmol/L, respectively. Treatment with dasatinib or the heat shock protein 90 inhibitor IPI-504 may provide a therapeutic alternative for GIST patients whose tumors carry the imatinib-resistant PDGFRA(D842V) mutant isoform.

  16. Chemical and enzymatic site specific PEGylation of hGH.

    Science.gov (United States)

    da Silva Freitas, Débora; Mero, Anna; Pasut, Gianfranco

    2013-03-20

    Several strategies for site-specific PEGylation have been successfully exploited to conjugate poly(ethylene glycol) (PEG) to pharmaceutical proteins. The advantages sought are those of improving efficacy and increasing the half-life of conjugated proteins while achieving a higher degree of homogeneity. Recombinant human growth hormone (hGH) was thus PEGylated exploiting two site-specific strategies: N-terminal PEGylation using the PEG20 kDa-aldehyde polymer and microbial transglutaminase (mTGase) mediated enzymatic PEGylation using PEG20 kDa-NH2. N-Terminal PEGylation of hGH was carried out by covalent attachment of PEG to the α-amine residue of Phe1 that yielded the monoconjugate PEG-Nter-hGH with a mass of 44152.2 Da, as measured by MALDI-TOF mass spectrometry. The mTGase mediated PEGylation, performed in a water/ethanol solution mixture, allowed a PEG coupling reaction only at the level of hGH Gln141, yielding the single monoconjugate PEG-Gln141-hGH with a mass of 44064.9 Da. Circular dichroism studies showed that both conjugation strategies preserved the native-like secondary structures of hGH. It is vital to maintain the structural integrity of hGH if PEGylated hGH is to be used in therapeutic applications. As expected, the pharmacokinetic profile in rats of PEG-Nter-hGH and PEG-Gln141-hGH revealed a significant increase in systemic exposure with respect to unmodified hGH. The conjugates showed a half-life increase of 4.5-fold with respect to hGH. These results demonstrate that both chemical and enzymatic site-selective PEGylation of hGH generates conjugates with a prolonged half-life.

  17. Site-specific meteorology identification for DOE facility accident analysis

    Energy Technology Data Exchange (ETDEWEB)

    Rabin, S.B.

    1995-09-01

    Currently, chemical dispersion calculations performed for safety analysis of DOE facilities assume a Pasquill D-Stability Class with a 4.5 m/s windspeed. These meteorological conditions are assumed to conservatively address the source term generation mechanism as well as the dispersion mechanism thereby resulting in a net conservative downwind consequence. While choosing this Stability Class / Windspeed combination may result in an overall conservative consequence, the level of conservative can not be quantified. The intent of this paper is to document a methodology which incorporates site-specific meteorology to determine a quantifiable consequence of a chemical release. A five-year meteorological database, appropriate for the facility location, is utilized for these chemical consequence calculations, and is consistent with the approach used for radiological releases. The hourly averages of meteorological conditions have been binned into 21 groups for the chemical consequence calculations. These 21 cases each have a probability of occurrence based on the number of times each case has occurred over the five year sampling period. A code has been developed which automates the running of all the cases with a commercially available air modeling code. The 21 cases are sorted by concentration. A concentration may be selected by the user for a quantified level of conservatism. The methodology presented is intended to improve the technical accuracy and defensability of Chemical Source Term / Dispersion Safety Analysis work. The result improves the quality of safety analyses products without significantly increasing the cost.

  18. The Application of TAPM for Site Specific Wind Energy Forecasting

    Directory of Open Access Journals (Sweden)

    Merlinde Kay

    2016-02-01

    Full Text Available The energy industry uses weather forecasts for determining future electricity demand variations due to the impact of weather, e.g., temperature and precipitation. However, as a greater component of electricity generation comes from intermittent renewable sources such as wind and solar, weather forecasting techniques need to now also focus on predicting renewable energy supply, which means adapting our prediction models to these site specific resources. This work assesses the performance of The Air Pollution Model (TAPM, and demonstrates that significant improvements can be made to only wind speed forecasts from a mesoscale Numerical Weather Prediction (NWP model. For this study, a wind farm site situated in North-west Tasmania, Australia was investigated. I present an analysis of the accuracy of hourly NWP and bias corrected wind speed forecasts over 12 months spanning 2005. This extensive time frame allows an in-depth analysis of various wind speed regimes of importance for wind-farm operation, as well as extreme weather risk scenarios. A further correction is made to the basic bias correction to improve the forecast accuracy further, that makes use of real-time wind-turbine data and a smoothing function to correct for timing-related issues. With full correction applied, a reduction in the error in the magnitude of the wind speed by as much as 50% for “hour ahead” forecasts specific to the wind-farm site has been obtained.

  19. Micro-tattoo guided OCT imaging of site specific inflammation

    Science.gov (United States)

    Phillips, Kevin G.; Choudhury, Niloy; Samatham, Ravikant V.; Singh, Harvinder; Jacques, Steven L.

    2010-02-01

    Epithelial biologists studying human skin diseases such as cancer formation and psoriasis commonly utilize mouse models to characterize the interplay among cells and intracellular signal transduction pathways that result in programmed changes in gene expression and cellular behaviors. The information obtained from animal models is useful only when phenotypic presentations of disease recapitulate those observed in humans. Excision of tissues followed by histochemical analysis is currently the primary means of establishing the morphological presentation. Non invasive imaging of animal models provides an alternate means to characterize tissue morphology associated with the disease of interest in vivo. While useful, the ability to perform in vivo imaging at different time points in the same tissue location has been a challenge. This information is key to understanding site specific changes as the imaged tissue can now be extracted and analyzed for mRNA expression. We present a method employing a micro-tattoo to guide optical coherence tomography (OCT) imaging of ultraviolet induced inflammation over time in the same tissue locations.

  20. Wind turbine generator trends for site-specific tailoring

    Science.gov (United States)

    Jackson, K.; van Dam, C. P.; Yen-Nakafuji, D.

    2005-10-01

    Turbine optimization for specific wind regimes and climate conditions is becoming more common as the market expands into new territories (offshore, low-wind regimes) and as technology matures. Tailoring turbines for specific sites by varying rotor diameter, tower height and power electronics may be a viable technique to make wind energy more economic and less intermittent. By better understanding the wind resource trends and evaluating important wind turbine performance parameters such as specific power (ratio of rated power and rotor swept area), developers and operators can optimize plant output and better anticipate operational impacts. This article presents a methodology to evaluate site-specific wind data for turbine tailoring. Wind characteristics for the Tehachapi wind resource area in California were utilized for this study. These data were used to evaluate the performance of a range of wind turbine configurations. The goal was to analyse the variations in wind power output for the area, assess the changes in these levels with the time of day and season and determine how turbine configuration affects the output. Wind turbine output was compared with California statewide system electrical demand to evaluate the correlation of the wind resource site with local peak demand loads. A comparison of the commercial value of electricity and corresponding wind generation is also presented using a time-dependent valuation methodology. Copyright

  1. Site-specific protein labeling by Sfp phosphopantetheinyl transferase.

    Science.gov (United States)

    Yin, Jun; Lin, Alison J; Golan, David E; Walsh, Christopher T

    2006-01-01

    Sfp phosphopantetheinyl transferase covalently attaches small-molecule probes including biotin and various organic fluorophores to a specific serine residue in the peptidyl carrier protein (PCP) or a short 11-residue peptide tag ybbR through a phosphopantetheinyl linker. We describe here a protocol for site-specific protein labeling by Sfp-catalyzed protein post-translational modification that includes (i) expression and purification of Sfp, (ii) synthesis of small-molecule probe-CoA conjugates, (iii) construction of target protein fusions with PCP or the ybbR tag, (iv) labeling PCP- or ybbR-tagged target protein fusions in cell lysates and on live cell surfaces and (v) imaging fluorophore-labeled cell surface receptors by fluorescence microscopy. To follow this protocol, we advise that you allow 3 d for the expression and purification of Sfp phosphopantetheinyl transferase, 1 d for the synthesis and purification of the small-molecule probe-CoA conjugates as the substrates of Sfp, 3 d for the cloning of target protein genes as fusions to the PCP or the ybbR tag in the appropriate plasmids and another 3 d for transfecting cell lines with the plasmids and the expression of PCP- or ybbR-tagged proteins. Labeling of the PCP- or the ybbR-tagged proteins in cell lysates or on cell surfaces should require only 15-30 min.

  2. The cancer drug Dasatinib increases PGC-1α in adipose tissue but has adverse effects on glucose tolerance in obese mice

    DEFF Research Database (Denmark)

    Sylow, Lykke; Long, Jonathan; Lokurkar, Isha A

    2016-01-01

    Dasatinib (Sprycel) is a tyrosine kinase inhibitor approved for treatment of chronic myeloid leukemia (CML). In this study we identify dasatinib as a potent inducer of PGC-1α mRNA. Dasatinib increased PGC-1α mRNA expression up to 6-fold in 3T3-F442A adipocytes, primary adipocytes, and epididymal...

  3. Site Specific Nutrient Management for Maize on Ultisols Lampung

    Directory of Open Access Journals (Sweden)

    Andarias Makka Murni

    2010-01-01

    Full Text Available Lampung is the third major maize producing province in Indonesia after East Java and Central Java. In Lampungmaize is cultivated mainly in upland areas with ultisols and only some cultivated on paddy field as a secondary cropin the dry season. The average maize yield in Lampung is still 3.4 Mg ha-1 bellow yield potential of 7 - 10 Mg ha-1. Toincrease the productivity of maize through site-specific nutrient management (SSNM, on-farm trials were conductedin five locations in Lampung i.e. four locations in Central Lampung District (Sidowaras, Binjai Ngagung, Watu Agungand Balai Rejo and one location in South Lampung District (Trimulyo, Tegineneng Sub District during the 2004/2005,2005/2006 and 2006/2007 rainy seasons. The experimental setup followed a standard protocol at all sites and includednutrient omission plots (PK, NK, NP to estimate indigenous nutrient supplies, an NPK plot to measure yield responseto fertilizer application, and a farmers’ fertilizer practice (FFP plot in each farmer’s field. An SSNM treatment plot wasincluded in the second and third seasons. Each of the above treatments was paralleled by a plot with improved cropmanagement practice (ICM, i.e. higher planting density, addition of lime, and addition of magnesium. Results showedthat yield response to fertilizer N, P and K application in these sites were: N = 2.3 - 4.1 Mg ha-1; P = 0.6 - 2.0 Mg ha-1;K = 0.3-2.4 Mg ha-1. Attainable yield in the three seasons on average ranged from 7.6 Mg ha-1 to 10.6 Mg ha-1. Yield inthe SSNM treatment (with or without ICM was significantly higher than the FFP indicating great opportunities forfarmers to increase productivity and profitability with improved nutrient and crop management

  4. Improving Site-Specific Radiological Performance Assessments - 13431

    International Nuclear Information System (INIS)

    Tauxe, John; Black, Paul; Catlett, Kate; Lee, Robert; Perona, Ralph; Stockton, Tom; Sully, Mike

    2013-01-01

    An improved approach is presented for conducting complete and defensible radiological site-specific performance assessments (PAs) to support radioactive waste disposal decisions. The basic tenets of PA were initiated some thirty years ago, focusing on geologic disposals and evaluating compliance with regulations. Some of these regulations were inherently probabilistic (i.e., addressing uncertainty in a quantitative fashion), such as the containment requirements of the U.S. Environmental Protection Agency's (EPA's) 40 CFR 191, Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes, Chap. 191.13 [1]. Methods of analysis were developed to meet those requirements, but at their core early PAs used 'conservative' parameter values and modeling approaches. This limited the utility of such PAs to compliance evaluation, and did little to inform decisions about optimizing disposal, closure and long-term monitoring and maintenance, or, in general, maintaining doses 'as low as reasonably achievable' (ALARA). This basic approach to PA development in the United States was employed essentially unchanged through the end of the 20. century, principally by the U.S. Department of Energy (DOE). Performance assessments developed in support of private radioactive waste disposal operations, regulated by the U.S. Nuclear Regulatory Commission (NRC) and its agreement states, were typically not as sophisticated. Discussion of new approaches to PA is timely, since at the time of this writing, the DOE is in the midst of revising its Order 435.1, Radioactive Waste Management [2], and the NRC is revising 10 CFR 61, Licensing Requirements for Land Disposal of Radioactive Waste [3]. Over the previous decade, theoretical developments and improved computational technology have provided the foundation for integrating decision analysis (DA) concepts and objective-focused thinking, plus a Bayesian approach to

  5. 78 FR 46330 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2013-07-31

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... of the Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory.... Highway 160, Pahrump, Nevada 89060. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  6. 78 FR 61348 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2013-10-03

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy. ACTION: Notice..., 2013 of the Environmental Management Site-Specific Advisory Board, Portsmouth (78 FR 56871). This..., Deputy Committee Management Officer. BILLING CODE 6450-01-P ...

  7. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Rohay, Alan C.; Reidel, Steve P.

    2005-02-24

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

  8. Local Delivery Is Critical for Monocyte Chemotactic Protein-1 Mediated Site-Specific Murine Aneurysm Healing

    Directory of Open Access Journals (Sweden)

    Siham Hourani

    2018-03-01

    Full Text Available BackgroundLocal delivery of monocyte chemotactic protein-1 (MCP-1/CCL2 via our drug-eluting coil has been shown to promote intrasaccular aneurysm healing via an inflammatory pathway.ObjectiveIn this study, we validate the importance of local MCP-1 in murine aneurysm healing. Whether systemic, rather than local, delivery of MCP-1 can direct site-specific aneurysm healing has significant translational implications. If systemic MCP-1 is effective, then MCP-1 could be administered as a pill rather than by endovascular procedure. Furthermore, we confirm that MCP-1 is the primary effector in our MCP-1 eluting coil-mediated murine aneurysm healing model.MethodsWe compare aneurysm healing with repeated intraperitoneal MCP-1 versus vehicle injection, in animals with control poly(lactic-co-glycolic acid (PLGA-coated coils. We demonstrate elimination of the MCP-1-associated tissue-healing response by knockout of MCP-1 or CCR2 (MCP-1 receptor and by selectively inhibiting MCP-1 or CCR2. Using immunofluorescent probing, we explore the cell populations found in healed aneurysm tissue following each intervention.ResultsSystemically administered MCP-1 with PLGA coil control does not produce comparable aneurysm healing, as seen with MCP-1 eluting coils. MCP-1-directed aneurysm healing is eliminated by selective inhibition of MCP-1 or CCR2 and in MCP-1-deficient or CCR2-deficient mice. No difference was detected in M2 macrophage and myofibroblast/smooth muscle cell staining with systemic MCP-1 versus vehicle in aneurysm wall, but a significant increase in these cell types was observed with MCP-1 eluting coil implant and attenuated by MCP-1/CCR2 blockade or deficiency.ConclusionWe show that systemic MCP-1 concurrent with PLGA-coated platinum coil implant is not sufficient to produce site-specific aneurysm healing. MCP-1 is a critical, not merely complementary, actor in the aneurysm healing pathway.

  9. Site-specific DNA damage at the GGG sequence by UVA involves acceleration of telomere shortening.

    Science.gov (United States)

    Oikawa, S; Tada-Oikawa, S; Kawanishi, S

    2001-04-17

    Telomere shortening is associated with cellular senescence. We investigated whether UVA, which contributes to photoaging, accelerates telomere shortening in human cultured cells. The terminal restriction fragment (TRF) from WI-38 fibroblasts irradiated with UVA (365-nm light) decreased with increasing irradiation dose. Furthermore, UVA irradiation dose-dependently increased the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in both WI-38 fibroblasts and HL-60 cells. To clarify the mechanism of the acceleration of telomere shortening, we investigated site-specific DNA damage induced by UVA irradiation in the presence of endogenous photosensitizers using (32)P 5'-end-labeled DNA fragments containing the telomeric oligonucleotide (TTAGGG)(4). UVA irradiation with riboflavin induced 8-oxodG formation in the DNA fragments containing telomeric sequence, and Fpg protein treatment led to chain cleavages at the central guanine of 5'-GGG-3' in telomere sequence. The amount of 8-oxodG formation in DNA fragment containing telomere sequence [5'-CGC(TTAGGG)(7)CGC-3'] was approximately 5 times more than that in DNA fragment containing nontelomere sequence [5'-CGC(TGTGAG)(7)CGC-3']. Catalase did not inhibit this oxidative DNA damage, indicating no or little participation of H(2)O(2) in DNA damage. These results indicate that the photoexcited endogenous photosensitizer specifically oxidizes the central guanine of 5'-GGG-3' in telomere sequence to produce 8-oxodG probably through an electron-transfer reaction. It is concluded that the site-specific damage in telomere sequence induced by UVA irradiation may participate in the increase of telomere shortening rate.

  10. First-line treatment for chronic myeloid leukemia: dasatinib, nilotinib, or imatinib

    Directory of Open Access Journals (Sweden)

    Rafiyath Shamudheen

    2010-11-01

    Full Text Available Abstract Imatinib, a tyrosine kinase inhibitor (TKI of BCR-ABL, was the standard first-line therapy for chronic myeloid leukemia (CML for almost 10 years. Dasatinib and nilotinib, two newer drugs with higher potency than imatinib against BCR-ABL and activity against most imatinib-resistant BCR-ABL mutations, have each shown superior efficacy compared with imatinib for first-line treatment of chronic-phase CML in randomized phase 3 trials. With 14 months follow-up time, available data suggest no obvious differences in efficacy between dasatinib and nilotinib. Compared with imatinib, dasatinib is associated with higher rates of pleural effusion and thrombocytopenia, but lower rates of edema, gastrointestinal AEs, musculoskeletal AEs, and rash. Nilotinib is associated with higher rates of dermatologic toxicity, headache, and biochemical abnormalities associated with hepatic and pancreatic toxicity compared with imatinib, but lower rates of edema, gastrointestinal AEs, muscle spasm, and neutropenia. Several studies have shown that poor adherence to imatinib detrimentally affects responses and should be considered in patients with a suboptimal response. The different dosing requirements of dasatinib (once daily with or without food and nilotinib (twice daily with fasting may be an additional factor in selecting frontline agents. This review compares and contrasts the three FDA approved first line TKI agents.

  11. 77 FR 26273 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2012-05-03

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The... CONTACT: Menice Santistevan, Northern New Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road...

  12. 77 FR 47047 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2012-08-07

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal...: Menice Santistevan, Northern New Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road, Santa...

  13. 78 FR 22255 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2013-04-15

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... Committee of the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens' Advisory Board [NNMCAB]). The Federal Advisory Committee Act...

  14. 77 FR 53192 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2012-08-31

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal... CONTACT: Menice Santistevan, Northern New Mexico Citizens' Advisory Board (NNMCAB), 94 Cities of Gold Road...

  15. 76 FR 18540 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2011-04-04

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... Committee of the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens' Advisory Board (NNMCAB). The Federal Advisory Committee Act...

  16. 29 CFR 1926.752 - Site layout, site-specific erection plan and construction sequence.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Site layout, site-specific erection plan and construction... Steel Erection § 1926.752 Site layout, site-specific erection plan and construction sequence. (a... strength or sufficient strength to support the loads imposed during steel erection. (c) Site layout. The...

  17. 76 FR 59393 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-09-26

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Boulevard, Las Vegas, Nevada 89109. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232...

  18. 77 FR 12044 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-02-28

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Charleston Boulevard, Las Vegas, Nevada 89135. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board...

  19. 75 FR 65310 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-10-22

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory..., 755 East Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board...

  20. 78 FR 53135 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2013-08-28

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  1. 75 FR 6370 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-02-09

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory..., 6711 North Buffalo Drive, Las Vegas, Nevada 89131. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board...

  2. 76 FR 10343 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-02-24

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub..., Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  3. 75 FR 48662 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-08-11

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator...

  4. 76 FR 51362 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-08-18

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232...

  5. 78 FR 17192 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2013-03-20

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  6. 76 FR 21878 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-04-19

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub..., Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  7. 78 FR 64932 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2013-10-30

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  8. 76 FR 29229 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-05-20

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Las Vegas, Nevada 89084. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  9. 77 FR 75627 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-12-21

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  10. 77 FR 4027 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-01-26

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232...

  11. 76 FR 80354 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-12-23

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub..., Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  12. 77 FR 49442 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-08-16

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator, 232...

  13. 78 FR 23760 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2013-04-22

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  14. 75 FR 82004 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-12-29

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232...

  15. 77 FR 16021 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-03-19

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub..., Local 4068, 160 West Emery Street, Pahrump, Nevada 89048. FOR FURTHER INFORMATION CONTACT: Denise Rupp...

  16. 75 FR 32930 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-06-10

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory... East Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board...

  17. 77 FR 66962 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-11-08

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub.... Flamingo Road, Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Barbara Ulmer, Board Administrator...

  18. 77 FR 24694 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-04-25

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub..., Las Vegas, Nevada 89119. FOR FURTHER INFORMATION CONTACT: Denise Rupp, Board Administrator, 232 Energy...

  19. 77 FR 39234 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2012-07-02

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub... 160, Pahrump, Nevada 89060. FOR FURTHER INFORMATION CONTACT: Kelly Snyder, Deputy Designated Federal...

  20. 78 FR 14088 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Science.gov (United States)

    2013-03-04

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Savannah River Site... the Environmental Management Site-Specific Advisory Board (EM SSAB), Savannah River Site. The Federal.... ADDRESSES: Westin Savannah Harbor, 1 Resort Drive, Savannah, GA 31421. FOR FURTHER INFORMATION CONTACT...

  1. 78 FR 16260 - Environmental Management Site-Specific Advisory Board, Savannah River Site

    Science.gov (United States)

    2013-03-14

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Savannah River Site... the Environmental Management Site-Specific Advisory Board, Savannah River Site (78 FR 14088). This... Harbor, 1 Resort Drive, Savannah, GA 31421. The new address is Hilton Garden Inn, 1065 Stevens Creek Road...

  2. 75 FR 56527 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Science.gov (United States)

    2010-09-16

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Idaho National... meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Idaho National Laboratory... prior to the meeting. ADDRESSES: Coeur d'Alene Resort, 115 South Second Street, Coeur d'Alene, Idaho...

  3. 77 FR 76475 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2012-12-28

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico... the Environmental Management Site-Specific Advisory Board (EM SSAB), Northern New Mexico. The Federal... Thunder Resort, Caldera A Meeting Room, 20 Buffalo Thunder Trail, Santa Fe, NM 87506. FOR FURTHER...

  4. 75 FR 82002 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-12-29

    ...-82003] [FR Doc No: 2010-32821] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory... announces a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The... the Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  5. 78 FR 4139 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2013-01-18

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and related...

  6. 78 FR 68431 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2013-11-14

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and related...

  7. 75 FR 82003 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-12-29

    ... Doc No: 2010-32813] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Portsmouth. The... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

  8. 78 FR 64208 - Environmental Management Site-Specific Advisory Board Chairs

    Science.gov (United States)

    2013-10-28

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Tuesday, November...

  9. 76 FR 61350 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-10-04

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities. Tentative...

  10. 78 FR 28207 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2013-05-14

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and related...

  11. 78 FR 59012 - Environmental Management Site-Specific Advisory Board Chairs

    Science.gov (United States)

    2013-09-25

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... environmental restoration, waste management, and related activities. Tentative Agenda Topics: Wednesday, October...

  12. 75 FR 8050 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2010-02-23

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and related...

  13. 76 FR 4645 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2011-01-26

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities. Tentative...

  14. 75 FR 6018 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2010-02-05

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... the Board is to make recommendations to DOE-EM and site management in the areas of environmental...

  15. 78 FR 49738 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2013-08-15

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... and site management in the areas of environmental restoration, waste management, and related...

  16. 76 FR 80355 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-12-23

    ...] [FR Doc No: 2011-32913] DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board... a meeting of the Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The... environmental restoration, waste management, and related activities. Tentative Agenda Call to Order...

  17. 78 FR 26635 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2013-05-07

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on May 16, 2013 of the Environmental Management Site-Specific..., Deputy Committee Management Officer. BILLING CODE 6450-01-P ...

  18. 78 FR 20311 - Environmental Management Site-Specific Advisory Board Chairs

    Science.gov (United States)

    2013-04-04

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of Open Webinar. SUMMARY: This notice announces a webinar of the Environmental Management Site-Specific... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management, and...

  19. 75 FR 56526 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-09-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION... Environmental Management Site-Specific Advisory Board (EM SSAB), Portsmouth. The Federal Advisory Committee Act... areas of environmental restoration, waste management and related activities. Tentative Agenda Portsmouth...

  20. 77 FR 64112 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2012-10-18

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site-Specific... management in the areas of environmental restoration, waste management, and related activities. Tentative...

  1. 76 FR 20651 - Environmental Management Site-Specific Advisory Board Chairs

    Science.gov (United States)

    2011-04-13

    ... Environmental Management Site-Specific Advisory Board Chairs AGENCY: Department of Energy. ACTION: Notice of... Environmental Management Site-Specific Advisory Board Chairs (76 FR 17118). This notice announces the...-7711. Issued at Washington, DC, on April 8, 2011. LaTanya R. Butler, Acting Deputy Committee Management...

  2. Site-specific properties and irreversible vegetation changes in semi-arid grazing systems

    NARCIS (Netherlands)

    Rietkerk, M; vandenBosch, F; vandeKoppel, J

    1997-01-01

    There is an urgent need to develop a mechanistic understanding of how site-specific properties can lead to irreversible vegetation changes. We show, by means of a bifurcation analysis of two mathematical models, how site-specific properties determine the resilience of vegetation changes in semi-arid

  3. Site-specific properties and irreversible vegetation changes in semi-arid grazing systems

    NARCIS (Netherlands)

    Rietkerk, M.G.; Bosch, F. van den; Koppel, J. van de

    1997-01-01

    There is an urgent need to develop a mechanistic understanding of how site-specific properties can lead to irreversible vegetation changes. We show, by means of a bifurcation analysis of two mathematica1 models, how site-specific properties determine the resilience of vegetation changes in

  4. FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori.

    Directory of Open Access Journals (Sweden)

    Ding-Pei Long

    Full Text Available A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they have not yet been established for use in the manipulation of the silkworm Bombyx mori genome. In this study, we achieved site-specific excision of a target gene at predefined chromosomal sites in the silkworm using a FLP/FRT site-specific recombination system. We first constructed two stable transgenic target silkworm strains that both contain a single copy of the transgene construct comprising a target gene expression cassette flanked by FRT sites. Using pre-blastoderm microinjection of a FLP recombinase helper expression vector, 32 G3 site-specific recombinant transgenic individuals were isolated from five of 143 broods. The average frequency of FLP recombinase-mediated site-specific excision in the two target strains genome was approximately 3.5%. This study shows that it is feasible to achieve site-specific recombination in silkworms using the FLP/FRT system. We conclude that the FLP/FRT system is a useful tool for genome manipulation in the silkworm. Furthermore, this is the first reported use of the FLP/FRT system for the genetic manipulation of a lepidopteran genome and thus provides a useful reference for the establishment of genome manipulation technologies in other lepidopteran species.

  5. FLP Recombinase-Mediated Site-Specific Recombination in Silkworm, Bombyx mori

    Science.gov (United States)

    Long, Ding-Pei; Zhao, Ai-Chun; Chen, Xue-Jiao; Zhang, Yang; Lu, Wei-Jian; Guo, Qing; Handler, Alfred M.; Xiang, Zhong-Huai

    2012-01-01

    A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they have not yet been established for use in the manipulation of the silkworm Bombyx mori genome. In this study, we achieved site-specific excision of a target gene at predefined chromosomal sites in the silkworm using a FLP/FRT site-specific recombination system. We first constructed two stable transgenic target silkworm strains that both contain a single copy of the transgene construct comprising a target gene expression cassette flanked by FRT sites. Using pre-blastoderm microinjection of a FLP recombinase helper expression vector, 32 G3 site-specific recombinant transgenic individuals were isolated from five of 143 broods. The average frequency of FLP recombinase-mediated site-specific excision in the two target strains genome was approximately 3.5%. This study shows that it is feasible to achieve site-specific recombination in silkworms using the FLP/FRT system. We conclude that the FLP/FRT system is a useful tool for genome manipulation in the silkworm. Furthermore, this is the first reported use of the FLP/FRT system for the genetic manipulation of a lepidopteran genome and thus provides a useful reference for the establishment of genome manipulation technologies in other lepidopteran species. PMID:22768245

  6. Weigh-in-motion (WIM) data for site-specific LRFR bridge load rating.

    Science.gov (United States)

    2011-08-12

    The live load factors in the Load and Resistant Factor Rating (LRFR) Manual are based on load data from Ontario : thought to be representative of traffic volumes nationwide. However, in accordance with the methodology for : developing site-specific l...

  7. Design and integration of components for site specific control of fertilizer application

    NARCIS (Netherlands)

    Bergeijk, van J.

    2001-01-01

    Keywords: Precision Agriculture, Site Specific Agriculture, Global Positioning System, GPS, Fertilizer Application, Information System.

    Spatial and temporal variability in soil, crop and climate characteristics results in non optimal use of fertilizers when the application

  8. Site-specific analysis of geothermal development-data files of prospective sites. Vol. III

    Energy Technology Data Exchange (ETDEWEB)

    Williams, F.; Cohen, A.; Pfundstein, R.; Pond, S.

    1978-02-01

    Development scenarios for 37 hydrothermal and geopressured prospects in the United States were analyzed. This third of three volumes presents site-specific data and sample development schedules for the first plant on line at each of the 37 prospects.

  9. Redox-sensitivity and site-specificity of S- and N- denitrosation in proteins.

    Directory of Open Access Journals (Sweden)

    Frances L Jourd'heuil

    Full Text Available BACKGROUND: S-nitrosation--the formation of S-nitrosothiols (RSNOs at cysteine residues in proteins--is a posttranslational modification involved in signal transduction and nitric oxide (NO transport. Recent studies would also suggest the formation of N-nitrosamines (RNNOs in proteins in vivo, although their biological significance remains obscure. In this study, we characterized a redox-based mechanism by which N-nitroso-tryptophan residues in proteins may be denitrosated. METHODOLOGY/PRINCIPAL FINDINGS: The denitrosation of N-acetyl-nitroso Trp (NANT by glutathione (GSH required molecular oxygen and was inhibited by superoxide dismutase (SOD. Transnitrosation to form S-nitrosoglutathione (GSNO was observed only in the absence of oxygen or presence of SOD. Protein denitrosation by GSH was studied using a set of mutant recombinant human serum albumin (HSA. Trp-214 and Cys-37 were the only two residues nitrosated by NO under aerobic conditions. Nitroso-Trp-214 in HSA was insensitive to denitrosation by GSH or ascorbate while denitrosation at Cys-37 was evident in the presence of GSH but not ascorbate. GSH-dependent denitrosation of Trp-214 was restored in a peptide fragment of helix II containing Trp-214. Finally, incubation of cell lysates with NANT revealed a pattern of protein nitrosation distinct from that observed with GSNO. CONCLUSIONS: We propose that the denitrosation of nitrosated Trp by GSH occurs through homolytic cleavage of nitroso Trp to NO and a Trp aminyl radical, driven by the formation of superoxide derived from the oxidation of GSH to GSSG. Overall, the accessibility of Trp residues to redox-active biomolecules determines the stability of protein-associated nitroso species such that in the case of HSA, N-nitroso-Trp-214 is insensitive to denitrosation by low-molecular-weight antioxidants. Moreover, RNNOs can generate free NO and transfer their NO moiety in an oxygen-dependent fashion, albeit site-specificities appear to differ

  10. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients

    OpenAIRE

    Belstr?m, Daniel; Sembler-M?ller, Maria Lynn; Grande, Maria Anastasia; Kirkby, Nikolai; Cotton, Sean Liam; Paster, Bruce J.; Holmstrup, Palle

    2017-01-01

    OBJECTIVES: The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens.DESIGN: Site specific subgingival plaque samples (n = 54), pooled subgingival plaque samples (n = 18) and stimulated saliva samples (n = 18) were collected from 18 patients with generalized chronic per...

  11. Site-specific and geographical segmental social, environmental and ethical disclosures by the Ghanaian mining sector

    OpenAIRE

    Khalid, Sharif.M; Atkins, Jill; Hennell, Alison

    2014-01-01

    Purpose: This paper explores the extent of site-specific and geographic segmental social, environmental and ethical reporting by mining companies operating in Ghana. We aim to: (i) establish a picture of corporate transparency relating to geographic segmentation of social, environmental and ethical reporting which is specific to operating sites and country of operation, and; (ii) gauge the impact of the introduction of integrated reporting on site-specific social, environmental and ethical re...

  12. Site-specific data confirm arsenic exposure predicted by the U.S. Environmental Protection Agency.

    OpenAIRE

    Walker, S; Griffin, S

    1998-01-01

    The EPA uses an exposure assessment model to estimate daily intake to chemicals of potential concern. At the Anaconda Superfund site in Montana, the EPA exposure assessment model was used to predict total and speciated urinary arsenic concentrations. Predicted concentrations were then compared to concentrations measured in children living near the site. When site-specific information on concentrations of arsenic in soil, interior dust, and diet, site-specific ingestion rates, and arsenic abso...

  13. Lymphocytosis after treatment with dasatinib in chronic myeloid leukemia: Effects on response and toxicity.

    Science.gov (United States)

    Schiffer, Charles A; Cortes, Jorge E; Hochhaus, Andreas; Saglio, Giuseppe; le Coutre, Philipp; Porkka, Kimmo; Mustjoki, Satu; Mohamed, Hesham; Shah, Neil P

    2016-05-01

    The proliferation of clonal cytotoxic T-cells or natural killer cells has been observed after dasatinib treatment in small studies of patients with chronic myeloid leukemia (CML). The incidence of lymphocytosis and its association with response, survival, and side effects were assessed in patients from 3 large clinical trials. Overall, 1402 dasatinib-treated patients with newly diagnosed CML in chronic phase (CML-CP), CML-CP refractory/intolerant to imatinib, or with CML in accelerated or myeloid-blast phase were analyzed. Lymphocytosis developed in 32% to 35% of patients and persisted for >12 months. This was not observed in the patients who received treatment with imatinib. Dasatinib-treated patients in all stages of CML who developed lymphocytosis were more likely to achieve a complete cytogenetic response, and patients who had CML-CP with lymphocytosis were more likely to achieve major and deep molecular responses. Progression-free and overall survival rates were significantly longer in patients with CML-CP who were refractory to or intolerant of imatinib and had lymphocytosis. Pleural effusions developed more commonly in patients with lymphocytosis. Overall, lymphocytosis occurred and persisted in many dasatinib-treated patients in all phases of CML. Its presence was associated with higher response rates, significantly longer response durations, and increased overall survival, suggesting an immunomodulatory effect. Prospective studies are warranted to characterize the functional activity of these cells and to assess whether an immunologic effect against CML is detectable. Cancer 2016;122:1398-1407. © 2016 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. © 2016 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society.

  14. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients.

    Science.gov (United States)

    Belstrøm, Daniel; Sembler-Møller, Maria Lynn; Grande, Maria Anastasia; Kirkby, Nikolai; Cotton, Sean Liam; Paster, Bruce J; Holmstrup, Palle

    2017-01-01

    The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens. Site specific subgingival plaque samples (n = 54), pooled subgingival plaque samples (n = 18) and stimulated saliva samples (n = 18) were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing) and microbial community profiles were compared using Spearman rank correlation coefficient. Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94), compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94) in pooled subgingival samples. Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.

  15. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients.

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    Full Text Available The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens.Site specific subgingival plaque samples (n = 54, pooled subgingival plaque samples (n = 18 and stimulated saliva samples (n = 18 were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing and microbial community profiles were compared using Spearman rank correlation coefficient.Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94, compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94 in pooled subgingival samples.Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.

  16. The Src family kinase inhibitor dasatinib delays pain-related behaviour and conserves bone in a rat model of cancer-induced bone pain

    DEFF Research Database (Denmark)

    Appel, Camilla Kristine; Gallego-Pedersen, Simone; Andersen, Line

    2017-01-01

    -induced bone pain, including cancer growth, osteoclastic bone degradation and nociceptive signalling. Here we investigate the role of dasatinib, an oral Src kinase family and Bcr-Abl tyrosine kinase inhibitor, in an animal model of cancer-induced bone pain. Daily administration of dasatinib (15 mg/kg, p...

  17. Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S -Transferases

    Energy Technology Data Exchange (ETDEWEB)

    Stoddard, Ethan G. [Chemical Biology and Exposure; Killinger, Bryan J. [Chemical Biology and Exposure; Nair, Reji N. [Chemical Biology and Exposure; Sadler, Natalie C. [Chemical Biology and Exposure; Volk, Regan F. [Chemical Biology and Exposure; Purvine, Samuel O. [Chemical Biology and Exposure; Shukla, Anil K. [Chemical Biology and Exposure; Smith, Jordan N. [Chemical Biology and Exposure; Wright, Aaron T. [Chemical Biology and Exposure

    2017-11-01

    Glutathione S-transferases (GSTs) comprise a highly diverse family of phase II drug metabolizing enzymes whose shared function is the conjugation of reduced glutathione to various endo- and xenobiotics. Although the conglomerate activity of these enzymes can be measured by colorimetric assays, measurement of the individual contribution from specific isoforms and their contribution to the detoxification of xenobiotics in complex biological samples has not been possible. For this reason, we have developed two activity-based probes that characterize active glutathione transferases in mammalian tissues. The GST active site is comprised of a glutathione binding “G site” and a distinct substrate binding “H site”. Therefore, we developed (1) a glutathione-based photoaffinity probe (GSH-ABP) to target the “G site”, and (2) a probe designed to mimic a substrate molecule and show “H site” activity (GST-ABP). The GSH-ABP features a photoreactive moiety for UV-induced covalent binding to GSTs and glutathione-binding enzymes. The GST-ABP is a derivative of a known mechanism-based GST inhibitor that binds within the active site and inhibits GST activity. Validation of probe targets and “G” and “H” site specificity was carried out using a series of competitors in liver homogenates. Herein, we present robust tools for the novel characterization of enzyme- and active site-specific GST activity in mammalian model systems.

  18. Dasatinib or imatinib in newly diagnosed chronic-phase chronic myeloid leukemia : 2-year follow-up from a randomized phase 3 trial (DASISION)

    NARCIS (Netherlands)

    Kantarjian, Hagop M.; Shah, Neil P.; Cortes, Jorge E.; Baccarani, Michele; Agarwal, Mohan B.; Soledad Undurraga, Maria; Wang, Jianxiang; Kassack Ipina, Juan Julio; Kim, Dong-Wook; Ogura, Michinori; Pavlovsky, Carolina; Junghanss, Christian; Milone, Jorge H.; Nicolini, Franck E.; Robak, Tadeusz; Van Droogenbroeck, Jan; Vellenga, Edo; Bradley-Garelik, M. Brigid; Zhu, Chao; Hochhaus, Andreas

    2012-01-01

    Dasatinib is a highly potent BCR-ABL inhibitor with established efficacy and safety in imatinib-resistant/-intolerant patients with chronic myeloid leukemia (CML). In the phase 3 DASISION trial, patients with newly diagnosed chronic-phase (CP) CML were randomized to receive dasatinib 100 mg (n =

  19. A method to determine site-specific, anisotropic fracture toughness in biological materials

    International Nuclear Information System (INIS)

    Bechtle, Sabine; Özcoban, Hüseyin; Yilmaz, Ezgi D.; Fett, Theo; Rizzi, Gabriele; Lilleodden, Erica T.; Huber, Norbert; Schreyer, Andreas; Swain, Michael V.; Schneider, Gerold A.

    2012-01-01

    Many biological materials are hierarchically structured, with highly anisotropic structures and properties on several length scales. To characterize the mechanical properties of such materials, detailed testing methods are required that allow precise and site-specific measurements on several length scales. We propose a fracture toughness measurement technique based on notched focused ion beam prepared cantilevers of lower and medium micron size scales. Using this approach, site-specific fracture toughness values in dental enamel were determined. The usefulness and challenges of the method are discussed.

  20. Roles of MinC and MinD in the site-specific septation block mediated by the MinCDE system of Escherichia coli.

    OpenAIRE

    de Boer, P A; Crossley, R E; Rothfield, L I

    1992-01-01

    The proper placement of the cell division site in Escherichia coli requires the site-specific inactivation of potential division sites at the cell poles in a process that requires the coordinate action of the MinC, MinD, and MinE proteins. In the absence of MinE, the coordinate expression of MinC and MinD leads to a general inhibition of cell division. MinE gives topological specificity to the division inhibition process, so that the septation block is restricted to the cell poles. At normal ...

  1. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Sembler-Møller, Maria Lynn; Grande, Maria Anastasia

    2017-01-01

    by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94), compared...

  2. 78 FR 58293 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2013-09-23

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Northern New Mexico...), Northern New Mexico (known locally as the Northern New Mexico Citizens' Advisory Board [NNMCAB]). The... CONTACT: Menice Santistevan, Northern New Mexico Citizens' Advisory Board, 94 Cities of Gold Road, Santa...

  3. 77 FR 20376 - Environmental Management Site-Specific Advisory Board, Northern New Mexico

    Science.gov (United States)

    2012-04-04

    ...:15 p.m. ADDRESSES: Bradbury Science Museum, 15th and Central Avenue, Los Alamos, New Mexico. FOR... Environmental Management Site-Specific Advisory Board, Northern New Mexico AGENCY: Department of Energy. ACTION...-Specific Advisory Board (EM SSAB), Northern New Mexico (known locally as the Northern New Mexico Citizens...

  4. 78 FR 58294 - Environmental Management Site-Specific Advisory Board, Idaho National Laboratory

    Science.gov (United States)

    2013-09-23

    ... management in the areas of environmental restoration, waste management, and related activities. Tentative... Sustainability Transuranic Waste Strategies (Remote-Handled and Contact- Handled) ICP Fiscal Year 2014 Work Plan... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Idaho National...

  5. Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins

    DEFF Research Database (Denmark)

    Lambertsen, L.; Sternberg, Claus; Molin, Søren

    2004-01-01

    the Escherichia coli lac derived promoter, P-A1/04/03, or from the growth-rate-dependent Escherichia coli promoter P-rrnB P1. The mini-Tn7 transposons were inserted and tested in the soil bacterium, Pseudomonas putida KT2440. Successful and site-specific tagging was verified by Southern blots as well as by PCR...

  6. Site Specific Waste Management Instruction for the 116-F-4 soil storage unit

    International Nuclear Information System (INIS)

    Hopkins, G.G.

    1996-08-01

    This Site Specific Waste Management Instruction provides guidance for management of waste generated during the excavation and remediation of soil and debris from the 116-4 soil storage unit located at the Hanford Site in Richland, Washington. This document outlines the waste management practices that will be performed in the field to implement federal, state, and US Department of Energy requirements

  7. 40 CFR 170.232 - Knowledge of labeling and site-specific information.

    Science.gov (United States)

    2010-07-01

    ... of labeling and site-specific information. (a) Knowledge of labeling information. (1) The handler... the handler has access to the product labeling information during handling activities. (b) Knowledge... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Knowledge of labeling and site...

  8. Integrated Decision Support, Sensor Networks and Adaptive Control for Wireless Site-specific Sprinkler Irrigation

    Science.gov (United States)

    The development of site-specific sprinkler irrigation water management systems will be a major factor in future efforts to improve the various efficiencies of water-use and to support a sustainable irrigated environment. The challenge is to develop fully integrated management systems with supporting...

  9. 75 FR 64718 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-10-20

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY...), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of...: Nevada Support Facility, 232 Energy Way, North Las Vegas, Nevada 89030. FOR FURTHER INFORMATION CONTACT...

  10. 76 FR 55370 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-09-07

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770..., 2011; 2 p.m. ADDRESSES: Nevada Site Office, 232 Energy Way, North Las Vegas, Nevada 89030. FOR FURTHER...

  11. 76 FR 50204 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-08-12

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770... 17, 2011, 2 p.m. ADDRESSES: Nevada Site Office, 232 Energy Way, North Las Vegas, Nevada 89030. FOR...

  12. 76 FR 52944 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-08-24

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Advisory Board (EM SSAB), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770..., September 7, 2011; 2 p.m. ADDRESSES: Nevada Site Office, 232 Energy Way, North Las Vegas, Nevada 89030. FOR...

  13. 76 FR 5365 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2011-01-31

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY...), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of.... ADDRESSES: Atomic Testing Museum, 755 East Flamingo Road, North Las Vegas, Nevada 89119. FOR FURTHER...

  14. 75 FR 71677 - Environmental Management Site-Specific Advisory Board, Nevada

    Science.gov (United States)

    2010-11-24

    ... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY...), Nevada. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat. 770) requires that public notice of...: Atomic Testing Museum, 755 East Flamingo Road, North Las Vegas, Nevada 89119. FOR FURTHER INFORMATION...

  15. Probing the unfolding region in a thermolysin-like protease by site-specific immobilization

    NARCIS (Netherlands)

    Mansfeld, J; Vriend, G; Van den Burg, B; Eijsink, VGH; Ulbrich-Hofmann, R

    1999-01-01

    Protein stabilization by immobilization has been proposed to be most effective if the protein is attached to the carrier at that region where unfolding is initiated. To probe this hypothesis, we have studied the effects of site-specific immobilization on the thermal stability of mutants of the

  16. Environmental Restoration Site-Specific Plan for the Portsmouth Gaseous Diffusion Plant, FY 93

    International Nuclear Information System (INIS)

    1993-01-01

    The purpose of this Site-Specific Plan (SSP) is to describe past, present, and future activities undertaken to implement Environmental Restoration and Waste Management goals at the Portsmouth Gaseous Diffusion Plant (PORTS). The SSP is presented in sections emphasizing Environmental Restoration description of activities, resources, and milestones

  17. Creating prescription maps from satellite imagery for site-specific management of cotton root rot

    Science.gov (United States)

    Cotton root rot is a century-old cotton disease that can now be controlled with Topguard Terra Fungicide. However, as this disease tends to occur in the same general areas within fields year after year, site-specific treatment can be more effective and economical. The objective of this study was to ...

  18. 77 FR 2282 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy. ACTION: Notice of... of open meeting announcing a meeting on January 19, 2012, of the Environmental Management Site... Washington, DC, on January 12, 2012. LaTanya R. Butler, Acting Deputy Committee Management Officer. BILLING...

  19. 77 FR 29997 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2012-05-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  20. 75 FR 24686 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-05-05

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  1. 75 FR 65615 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-10-26

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  2. 75 FR 7577 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-02-22

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda: Call to Order...

  3. 77 FR 31837 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-05-30

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... and site management in the areas of environmental restoration, waste management and related activities...

  4. 75 FR 54600 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-09-08

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE) ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  5. 77 FR 2283 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2012-01-17

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  6. 75 FR 19379 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-04-14

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  7. 75 FR 66074 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-10-27

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  8. 76 FR 78909 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2011-12-20

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management, and related activities. Tentative Agenda Call to Order...

  9. 77 FR 37390 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2012-06-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  10. 77 FR 63300 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2012-10-16

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  11. 78 FR 36543 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2013-06-18

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE) ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  12. 75 FR 9404 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-03-02

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  13. 76 FR 57981 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2011-09-19

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  14. 75 FR 51026 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2010-08-18

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  15. 76 FR 36100 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2011-06-21

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy. DOE. ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

  16. 75 FR 61711 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2010-10-06

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  17. 76 FR 48148 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-08-08

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  18. 75 FR 8051 - Environmental Management Site-Specific Advisory Board, Hanford

    Science.gov (United States)

    2010-02-23

    ... Environmental Management Site-Specific Advisory Board, Hanford AGENCY: Department of Energy. ACTION: Notice of open meeting. SUMMARY: This notice announces a combined meeting of the Environmental Management Site... and site management in the areas of environmental restoration, waste management, and related...

  19. 76 FR 5147 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-01-28

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  20. 77 FR 43583 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-07-25

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION: Notice of open meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... management in the areas of environmental restoration, waste management and related activities. Tentative...

  1. 78 FR 10611 - Environmental Management Site-Specific Advisory Board, Portsmouth

    Science.gov (United States)

    2013-02-14

    ... Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY: Department of Energy (DOE). ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the Environmental Management Site... environmental restoration, waste management and related activities. Tentative Agenda Call to Order...

  2. Site-specific glycan-Peptide analysis for determination of N-glycoproteome heterogeneity

    DEFF Research Database (Denmark)

    Parker, Benjamin L; Thaysen-Andersen, Morten; Solis, Nestor

    2013-01-01

    A combined glycomics and glycoproteomics strategy was developed for the site-specific analysis of N-linked glycosylation heterogeneity from a complex mammalian protein mixture. Initially, global characterization of the N-glycome was performed using porous graphitized carbon liquid chromatography-...

  3. Use of GIS-based Site-specific Nitrogen Management for Improving Energy Efficiency

    Science.gov (United States)

    To our knowledge, geographical information system (GIS)-based site-specific nitrogen management (SSNM) techniques have not been used to assess agricultural energy costs and efficiency. This chapter uses SSNM case studies for corn (Zea mays L.) grown in Missouri and cotton (Gossypium hirsutum L.) gro...

  4. Development of Unmanned Aerial Vehicles for Site-Specific Crop Production Management

    Science.gov (United States)

    Unmanned Aerial Vehicles (UAV) have been developed and applied to support the practice of precision agriculture. Compared to piloted aircrafts, an Unmanned Aerial Vehicle can focus on much smaller crop fields with much lower flight altitude than regular airplanes to perform site-specific management ...

  5. Recent advances in covalent, site-specific protein immobilization [version 1; referees

    DEFF Research Database (Denmark)

    Meldal, Morten Peter; Schoffelen, Sanne

    2016-01-01

    The properties of biosensors, biomedical implants, and other materials based on immobilized proteins greatly depend on the method employed to couple the protein molecules to their solid support. Covalent, site-specific immobilization strategies are robust and can provide the level of control...

  6. Summary of some feasibility studies for site-specific solar industrial process heat

    Energy Technology Data Exchange (ETDEWEB)

    None

    1982-01-01

    Some feasibility studies for several different site specific solar industrial process heat applications are summarized. The followng applications are examined. Leather Tanning; Concrete Production: Lumber and Paper Processing; Milk Processing; Molding, Curing or Drying; Automobile Manufacture; and Food Processing and Preparation. For each application, site and process data, system design, and performance and cost estimates are summarized.

  7. 76 FR 31599 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-06-01

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., June 23, 2011, 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  8. 76 FR 11228 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-03-01

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. No. 92-463, 86 Stat..., March 17, 2011; 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  9. 77 FR 51789 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-08-27

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., September 20, 2012, 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  10. 75 FR 37782 - Environmental Management Site-Specific Advisory Board, Paducah, KY

    Science.gov (United States)

    2010-06-30

    ... Environmental Management Site-Specific Advisory Board, Paducah, KY AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., July 15, 2010, 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  11. 77 FR 4799 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-01-31

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., February 16, 2012; 5:30 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive Paducah, Kentucky 42001. FOR...

  12. 77 FR 11516 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2012-02-27

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., March 15, 2012; 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  13. 76 FR 17636 - Environmental Management Site-Specific Advisory Board, Paducah

    Science.gov (United States)

    2011-03-30

    ... Environmental Management Site-Specific Advisory Board, Paducah AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., April 21, 2011; 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  14. 77 FR 20014 - Environmental Management Site-Specific Advisory Board, Paducah, KY

    Science.gov (United States)

    2012-04-03

    ... Environmental Management Site-Specific Advisory Board, Paducah, KY AGENCY: Department of Energy (DOE). ACTION...-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act (Pub. L. 92-463, 86 Stat..., April 26, 2012, 6 p.m. ADDRESSES: Barkley Centre, 111 Memorial Drive, Paducah, Kentucky 42001. FOR...

  15. Hellsgate Big Game Winter Range Wildlife Mitigation Site Specific Management Plan for the Hellsgate Project.

    Energy Technology Data Exchange (ETDEWEB)

    Berger, Matthew T.; Judd, Steven L.

    1999-01-01

    This report contains a detailed site-specific management plan for the Hellsgate Winter Range Wildlife Mitigation Project. The report provides background information about the mitigation process, the review process, mitigation acquisitions, Habitat Evaluation Procedures (HEP) and mitigation crediting, current habitat conditions, desired future habitat conditions, restoration/enhancements efforts and maps.

  16. Site-specific management of cotton root rot using historical remote sensing imagery

    Science.gov (United States)

    Cotton root rot can now be effectively controlled with Topguard Terra Fungicide, but site-specific application of the fungicide can greatly reduce treatment cost as only portions of the field are infested with the disease. The overall goal of this three-year project was to demonstrate how to use his...

  17. Integration of aerial imaging and variable-rate technology for site-specific aerial herbicide application

    Science.gov (United States)

    As remote sensing and variable rate technology are becoming more available for aerial applicators, practical methodologies on effective integration of these technologies are needed for site-specific aerial applications of crop production and protection materials. The objectives of this study were to...

  18. Impairments in site-specific AS160 phosphorylation and effects of exercise training

    DEFF Research Database (Denmark)

    Consitt, Leslie A; Van Meter, Jessica; Newton, Christopher A

    2013-01-01

    The purpose of this study was to determine if site-specific phosphorylation at the level of Akt substrate of 160 kDa (AS160) is altered in skeletal muscle from sedentary humans across a wide range of the adult lifespan (18 to 84 years) and if endurance- and/or strength-oriented exercise training ...

  19. Phage Selection Assisted by Sfp Phosphopantetheinyl Transferase Catalyzed Site-Specific Protein Labeling

    Science.gov (United States)

    Zhao, Bo; Zhang, Keya; Bhuripanyo, Karan; Wang, Yiyang; Zhou, Han; Zhang, Mengnan; Yin, Jun

    2015-01-01

    Summary Phosphopantetheinyl transferases (PPTase) Sfp and AcpS catalyze a highly efficient reaction that conjugates chemical probes of diverse structures to proteins. PPTases have been widely used for site-specific protein labeling and live cell imaging of the target proteins. Here we describe the use of PPTase catalyzed protein labeling in protein engineering by facilitating high throughput phage selection. PMID:25560074

  20. Phage selection assisted by Sfp phosphopantetheinyl transferase-catalyzed site-specific protein labeling.

    Science.gov (United States)

    Zhao, Bo; Zhang, Keya; Bhuripanyo, Karan; Wang, Yiyang; Zhou, Han; Zhang, Mengnan; Yin, Jun

    2015-01-01

    Phosphopantetheinyl transferases (PPTase) Sfp and AcpS catalyze a highly efficient reaction that conjugates chemical probes of diverse structures to proteins. PPTases have been widely used for site-specific protein labeling and live cell imaging of the target proteins. Here we describe the use of PPTase-catalyzed protein labeling in protein engineering by facilitating high-throughput phage selection.

  1. A method for site-specific labeling of multiple protein thiols

    NARCIS (Netherlands)

    Kuiper, Johanna M.; Pluta, Radek; Huibers, Wim H. C.; Fusetti, Fabrizia; Geertsma, Eric R.; Poolman, Bert

    We present a generic method for the site-specific and differential labeling of multiple cysteine residues in one protein. Phenyl arsenic oxide has been employed as a protecting group of two closely spaced thiols, allowing first labeling of a single thiol. Subsequently, the protecting group is

  2. Production of soluble and active microbial transglutaminase in Escherichia coli for site-specific antibody drug conjugation.

    Science.gov (United States)

    Rickert, Mathias; Strop, Pavel; Lui, Victor; Melton-Witt, Jody; Farias, Santiago Esteban; Foletti, Davide; Shelton, David; Pons, Jaume; Rajpal, Arvind

    2016-02-01

    Applications of microbial transglutaminase (mTGase) produced from Streptomyces mobarensis (S. mobarensis) were recently extended from food to pharmaceutical industry. To use mTGase for clinical applications, like generation of site specific antibody drug conjugates, it would be beneficial to manufacture mTGase in Escherichia coli (E. coli). To date, attempts to express recombinant soluble and active S. mobarensis mTGase have been largely unsuccessful. mTGase from S. mobarensis is naturally expressed as proenzyme and stepwise proteolytically processed into its active mature form outside of the bacterial cell. The pro-domain is essential for correct folding of mTGase as well as for inhibiting activity of mTGase inside the cell. Here, we report a genetically modified mTGase that has full activity and can be expressed at high yields in the cytoplasm of E. coli. To achieve this we performed an alanine-scan of the mTGase pro-domain and identified mutants that maintain its chaperone function but destabilize the cleaved pro-domain/mTGase interaction in a temperature dependent fashion. This allows proper folding of mTGase and keeps the enzyme inactive during expression at 20°C, but results in full activity when shifted to 37°C due to loosen domain interactions. The insertion of the 3C protease cleavage site together with pro-domain alanine mutants Tyr14, Ile24, or Asn25 facilitate high yields (30-75 mg/L), and produced an enzyme with activity identical to wild type mTGase from S. mobarensis. Site-specific antibody drug conjugates made with the E .coli produced mTGase demonstrated identical potency in an in vitro cell assay to those made with mTGase from S. mobarensis. © 2015 The Protein Society.

  3. Pediatric phase I trial and pharmacokinetic study of dasatinib: a report from the children's oncology group phase I consortium.

    Science.gov (United States)

    Aplenc, Richard; Blaney, Susan M; Strauss, Lewis C; Balis, Frank M; Shusterman, Suzanne; Ingle, Ashish Mark; Agrawal, Shruti; Sun, Junfeng; Wright, John J; Adamson, Peter C

    2011-03-01

    PURPOSE Dasatinib is an orally available tyrosine kinase inhibitor with low nanomolar activity against SRC family kinases, BCR-ABL, c-KIT, EPHA2, and the PDGF-β receptor. Dasatinib was found to have selective activity in several tumor models in the Pediatric Preclinical Testing Program. PATIENTS AND METHODS A phase I study of dasatinib in pediatric patients with refractory solid tumors or imatinib-refractory, Philadelphia chromosome-positive leukemia was performed. Dose levels of 50, 65, 85, and 110 mg/m²/dose, administered orally twice daily for 28 days, with courses repeated without interruption, were studied. Pharmacokinetic studies were performed with the initial dose. A total of 39 patients (solid tumors, n = 28; chronic myeloid leukemia [CML], n = 9; acute lymphoblastic leukemia, n = 2) were enrolled. No dose-limiting toxicities (DLTs) were observed at the 50, 65, and 85 mg/m² dose levels. At 110 mg/m², two of six patients experienced DLT including grade 2 diarrhea and headache. In children with leukemia, grade 4 hypokalemia (50 mg/m²), grade 3 diarrhea (85 mg/m²), and grade 2 creatinine elevation (50 mg/m²) were observed. DLT in later courses included pleural effusions, hemangiomatosis, and GI hemorrhage. There were three complete cytogenetic responses, three partial cytogenetic responses, and two partial/minimal cytogenetic responses observed in evaluable patients with CML. CONCLUSION Overall, drug disposition and tolerability of dasatinib were similar to those observed in adult patients.

  4. Comparative Fitness Assessment of Anopheles stephensi Transgenic Lines Receptive to Site-Specific Integration

    Science.gov (United States)

    Amenya, Dolphine A.; Bonizzoni, Mariangela; Isaacs, Alison T.; Jasinskiene, Nijole; Chen, Hong; Marinotti, Osvaldo; Yan, Guiyun; James, Anthony A.

    2009-01-01

    Genetically-modified mosquitoes that are unable to transmit pathogens offer opportunities for controlling vector-borne diseases such as malaria and dengue. Site-specific gene recombination technologies are advantageous in the development of these insects because anti-pathogen effector genes can be inserted at integration sites in the genome that cause the least alteration in mosquito fitness. Here we describe Anopheles stephensi transgenic lines containing φC31 attP “docking” sites linked to a fluorescent marker gene. Chromosomal insertion sites were determined and life-table parameters were assessed for transgenic mosquitoes of each line. No significant differences in fitness between the transgenic and non-transgenic mosquitoes were detected in this study. These transgenic lines are suitable for future site-specific integrations of anti-parasite transgenes into the attP sites. PMID:20113372

  5. Site-Specific Integration of Exogenous Genes Using Genome Editing Technologies in Zebrafish

    Directory of Open Access Journals (Sweden)

    Atsuo Kawahara

    2016-05-01

    Full Text Available The zebrafish (Danio rerio is an ideal vertebrate model to investigate the developmental molecular mechanism of organogenesis and regeneration. Recent innovation in genome editing technologies, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs and the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR associated protein 9 (Cas9 system, have allowed researchers to generate diverse genomic modifications in whole animals and in cultured cells. The CRISPR/Cas9 and TALEN techniques frequently induce DNA double-strand breaks (DSBs at the targeted gene, resulting in frameshift-mediated gene disruption. As a useful application of genome editing technology, several groups have recently reported efficient site-specific integration of exogenous genes into targeted genomic loci. In this review, we provide an overview of TALEN- and CRISPR/Cas9-mediated site-specific integration of exogenous genes in zebrafish.

  6. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2018-01-01

    Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien......" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication......-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types....

  7. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation.

    Science.gov (United States)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2018-01-01

    Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types.

  8. Site-specific growth of Au particles on ZnO nanopyramids under ultraviolet illumination

    KAUST Repository

    Yao, Kexin

    2011-01-01

    In this work, wurtzite ZnO nanocrystals with unique "pyramid" morphology were firstly prepared via solvothermal synthesis. It was determined that the ZnO nanopyramids are grown along the polar c-axis with the vertexes pointing to the [001] direction. When the mixture of ZnO nanopyramids and Au precursor (HAuCl4) was exposed to ultraviolet (UV) illumination, Au particles were site-specifically formed on the vertexes of ZnO nanopyramids. The obtained Au/ZnO nanocomposite showed significantly enhanced photocatalytic activity as compared to the bare ZnO nanopyramids. First-principles based calculations well explained the formation of ZnO nanopyramids as well as the site-specific growth of Au, and revealed that during the photocatalysis process the Au particles can accommodate photoelectrons and thus facilitate the charge separation. © 2011 The Royal Society of Chemistry.

  9. Tus-Ter as a tool to study site-specific DNA replication perturbation in eukaryotes.

    Science.gov (United States)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2014-01-01

    The high-affinity binding of the Tus protein to specific 21-bp sequences, called Ter, causes site-specific, and polar, DNA replication fork arrest in E coli. The Tus-Ter complex serves to coordinate DNA replication with chromosome segregation in this organism. A number of recent and ongoing studies have demonstrated that Tus-Ter can be used as a heterologous tool to generate site-specific perturbation of DNA replication when reconstituted in eukaryotes. Here, we review these recent findings and explore the molecular mechanism by which Tus-Ter mediates replication fork (RF) arrest in the budding yeast, S. cerevisiae. We propose that Tus-Ter is a versatile, genetically tractable, and regulatable RF blocking system that can be utilized for disrupting DNA replication in a diverse range of host cells.

  10. Proposed Site-Specific Response Spectra for Surabaya-Madura Bridge

    Directory of Open Access Journals (Sweden)

    Dyah Kusumastuti

    2008-01-01

    Full Text Available This paper presents a site-specific seismic hazard study to determine the recommended seismic design criteria for Suramadu Bridge. The study is performed using probabilistic seismic hazard approach to determine maximum acceleration and response spectra at bedrock and followed by local site effect analysis to determine maximum acceleration and response spectra at ground surface. The probabilistic seismic hazard analysis (PSHA is carried out using 3-dimension (3-D seismic source models (fault source model. Two hazard levels are analysed to represent 150 and 3,300 years return period of ground motion around site location. The local site effect analysis is performed using 1-dimension (1-D shear wave propagation theory to obtain peak ground acceleration and response spectra at ground surface. Finally, the site-specific surface response spectra with 5 percent damping are developed based on the mean plus one standard deviation concept from the result of local site effect analysis.

  11. Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib.

    Science.gov (United States)

    Klammer, Martin; Dybowski, J Nikolaj; Hoffmann, Daniel; Schaab, Christoph

    2015-01-01

    Multivariate biomarkers that can predict the effectiveness of targeted therapy in individual patients are highly desired. Previous biomarker discovery studies have largely focused on the identification of single biomarker signatures, aimed at maximizing prediction accuracy. Here, we present a different approach that identifies multiple biomarkers by simultaneously optimizing their predictive power, number of features, and proximity to the drug target in a protein-protein interaction network. To this end, we incorporated NSGA-II, a fast and elitist multi-objective optimization algorithm that is based on the principle of Pareto optimality, into the biomarker discovery workflow. The method was applied to quantitative phosphoproteome data of 19 non-small cell lung cancer (NSCLC) cell lines from a previous biomarker study. The algorithm successfully identified a total of 77 candidate biomarker signatures predicting response to treatment with dasatinib. Through filtering and similarity clustering, this set was trimmed to four final biomarker signatures, which then were validated on an independent set of breast cancer cell lines. All four candidates reached the same good prediction accuracy (83%) as the originally published biomarker. Although the newly discovered signatures were diverse in their composition and in their size, the central protein of the originally published signature - integrin β4 (ITGB4) - was also present in all four Pareto signatures, confirming its pivotal role in predicting dasatinib response in NSCLC cell lines. In summary, the method presented here allows for a robust and simultaneous identification of multiple multivariate biomarkers that are optimized for prediction performance, size, and relevance.

  12. Site-Specific Waste Management Instruction - 100-DR-1 Group 2 Sites

    International Nuclear Information System (INIS)

    Jackson, R.W.

    1998-01-01

    This site-specific waste management instruction (SSWMI) provides guidance for the management of wastes that may be generated during the excavation and remediation of the 100-DR-1 Group 2 sites. The management of waste generated as a result of these activities will be as directed in this SSWMI. This SSWMI will be revised to incorporate guidance for management of wastes encountered that are not addressed in this SSWMI

  13. DAFS study of site-specific local structure of Mn in manganese ferrite films

    International Nuclear Information System (INIS)

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V.G.

    2006-01-01

    Manganese ferrite (MnFe 2 O 4 ) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency of Mn

  14. Site-specific cancer risk in the Baltic cohort of Chernobyl cleanup workers, 1986-2007.

    Science.gov (United States)

    Rahu, Kaja; Hakulinen, Timo; Smailyte, Giedre; Stengrevics, Aivars; Auvinen, Anssi; Inskip, Peter D; Boice, John D; Rahu, Mati

    2013-09-01

    To assess site-specific cancer risk in the Baltic cohort of Chernobyl cleanup workers, 1986-2007. The Baltic cohort includes 17,040 men from Estonia, Latvia and Lithuania who participated in the environmental cleanup after the accident at the Chernobyl Nuclear Power Station in 1986-1991 and who were followed up for cancer incidence until the end of 2007. Cancer cases diagnosed in the cohort and in the male population of each country were identified from the respective national cancer registers. The proportional incidence ratio (PIR) with 95% confidence interval (CI) was used to estimate the site-specific cancer risk in the cohort. For comparison and as it was possible, the site-specific standardised incidence ratio (SIR) was calculated for the Estonian sub-cohort, which was not feasible for the other countries. Overall, 756 cancer cases were reported during 1986-2007. A higher proportion of thyroid cancers in relation to the male population was found (PIR=2.76; 95%CI 1.63-4.36), especially among those who started their mission shortly after the accident, in April-May 1986 (PIR=6.38; 95%CI 2.34-13.89). Also, an excess of oesophageal cancers was noted (PIR=1.52; 95% CI 1.06-2.11). No increased PIRs for leukaemia or radiation-related cancer sites combined were observed. PIRs and SIRs for the Estonian sub-cohort demonstrated the same site-specific cancer risk pattern. Consistent evidence of an increase in radiation-related cancers in the Baltic cohort was not observed with the possible exception of thyroid cancer, where conclusions are hampered by known medical examination including thyroid screening among cleanup workers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Site-specific cancer risk in the Baltic cohort of Chernobyl cleanup workers, 1986–2007

    Science.gov (United States)

    Rahu, Kaja; Hakulinen, Timo; Smailyte, Giedre; Stengrevics, Aivars; Auvinen, Anssi; Inskip, Peter D.; Boice, John D.; Rahu, Mati

    2013-01-01

    Objective To assess site-specific cancer risk in the Baltic cohort of Chernobyl cleanup workers 1986–2007. Methods The Baltic cohort includes 17,040 men from Estonia, Latvia and Lithuania who participated in the environmental cleanup after the accident at the Chernobyl Nuclear Power Station in 1986–1991, and who were followed for cancer incidence until the end of 2007. Cancer cases diagnosed in the cohort and in the male population of each country were identified from the respective national cancer registers. The proportional incidence ratio (PIR) with 95% confidence interval (CI) was used to estimate the site-specific cancer risk in the cohort. For comparison and as it was possible, the site-specific standardized incidence ratio (SIR) was calculated for the Estonian sub-cohort, which was not feasible for the other countries. Results Overall, 756 cancer cases were reported during 1986–2007. A higher proportion of thyroid cancers in relation to the male population was found (PIR=2.76; 95%CI 1.63–4.36), especially among those who started their mission shortly after the accident, in April–May 1986 (PIR=6.38; 95% CI 2.34–13.89). Also, an excess of oesophageal cancers was noted (PIR=1.52; 95% CI 1.06–2.11). No increased PIRs for leukaemia or radiation-related cancer sites combined were observed. PIRs and SIRs for the Estonian sub-cohort demonstrated the same site-specific cancer risk pattern. Conclusion Consistent evidence of an increase in radiation-related cancers in the Baltic cohort was not observed with the possible exception of thyroid cancer, where conclusions are hampered by known medical examination including thyroid screening among cleanup workers. PMID:23683549

  16. Site specific health and safety plan for drilling in support of in situ redox manipulation

    International Nuclear Information System (INIS)

    Tuttle, B.G.

    1997-02-01

    This document contains the Site Specific Health and Safety Plan for Drilling in support of the In Situ REDOX Manipulation in the 100-HR-3 Operable Unit. Approximately eight wells will be drilled in the 100-D/DR Area using rotary, sonic, or cable tool drilling methods. Split-spoon sampling will be done in conjunction with the drilling. The drilling may be spread out over several months. Included in this document are checklists for health and safety procedures

  17. Protein and Site Specificity of Fucosylation in Liver-Secreted Glycoproteins

    Czech Academy of Sciences Publication Activity Database

    Pompach, Petr; Ashline, David J.; Brnáková, Z.; Benicky, J.; Sanda, M.; Goldman, R.

    2014-01-01

    Roč. 13, č. 12 (2014), s. 5561-5569 ISSN 1535-3893 R&D Projects: GA MŠk LH13051; GA ČR GAP206/12/0503 Grant - others:Charles Univ.(CZ) UNCE_204025/2012 Institutional support: RVO:61388971 Keywords : fucose * glycoproteins * liver * site specificity Subject RIV: CE - Biochemistry Impact factor: 4.245, year: 2014

  18. Site-Specific Multilevel Modeling of Potato Response to Nitrogen Fertilization

    Directory of Open Access Journals (Sweden)

    Serge-Étienne Parent

    2017-12-01

    Full Text Available Technologies of precision agriculture, digital soil maps, and meteorological stations provide a minimum data set to guide precision farming operations. However, determining optimal nutrient requirements for potato (Solanum tuberosum L. crops at subfield scale remains a challenge given specific climatic, edaphic, and managerial conditions. Multilevel modeling can generalize yield response to fertilizer additions using data easily accessible to growers. Our objective was to elaborate a multilevel N fertilizer response model for potato crops using the Mitscherlich equation and a core data set of 93 N fertilizer trials conducted in Québec, Canada. Daily climatic data were collected at 10 × 10 km resolution. Soils were characterized by organic matter content, pH, and texture in the arable layer, and by texture and tools of pedometrics across a gleization-podzolization continuum in subsoil layers. There were five categories of preceding crops and five cultivar maturity orders. The three Mitscherlich parameters (Asymptote, Rate, and Environment were most often site-specific. Sensitivity analysis showed that optimum N dosage increased with non-leguminous high-residue preceding crops, coarser soils, podzolization, drier climatic condition, and late cultivar maturity. The inferential model could guide site-specific N fertilization using an accessible minimum data set to support fertilization decisions. As decision-support system, the model could also provide a range of optimum N doses across a large spectrum of site-specific conditions including climate change.

  19. Site-specific parameter values for the Nuclear Regulatory Commission's food pathway dose model

    International Nuclear Information System (INIS)

    Hamby, D.M.

    1992-01-01

    Routine operations at the Savannah River Site (SRS) in Western South Carolina result in radionuclide releases to the atmosphere and to the Savannah River. The resulting radiation doses to the off-site maximum individual and the off-site population within 80 km of the SRS are estimated on a yearly basis. These estimates are currently generated using dose models prescribed for the commercial nuclear power industry by the Nuclear Regulatory Commission (NRC). The NRC provides default values for dose-model parameters for facilities without resources to develop site-specific values. A survey of land- and water-use characteristics for the Savannah River area has been conducted to determine site-specific values for water recreation, consumption, and agricultural parameters used in the NRC Regulatory Guide 1.109 (1977) dosimetric models. These site parameters include local characteristics of meat, milk, and vegetable production; recreational and commercial activities on the Savannah River; and meat, milk, vegetable, and seafood consumption rates. This paper describes how parameter data were obtained at the Savannah River Site and the impacts of such data on off-site dose. Dose estimates using site-specific parameter values are compared to estimates using the NRC default values

  20. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene-Deoxyadenosine Lesions.

    Science.gov (United States)

    Wickramaratne, Susith; Seiler, Christopher L; Tretyakova, Natalia Y

    2015-06-03

    Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid-phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1,N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen 1,3-butadiene (BD). The resulting oligomers containing site-specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.

  1. Identification of Site-Specific Stroke Biomarker Candidates by Laser Capture Microdissection and Labeled Reference Peptide

    Directory of Open Access Journals (Sweden)

    Tingting Lian

    2015-06-01

    Full Text Available The search to date for accurate protein biomarkers in acute ischemic stroke has taken into consideration the stage and/or the size of infarction, but has not accounted for the site of stroke. In the present study, multiple reaction monitoring using labeled reference peptide (LRP following laser capture microdissection (LCM is used to identify site-specific protein biomarker candidates. In middle cerebral artery occlusion (MCAO rat models, both intact and infarcted brain tissue was collected by LCM, followed by on-film digestion and semi-quantification using triple-quadrupole mass spectrometry. Thirty-four unique peptides were detected for the verification of 12 proteins in both tissue homogenates and LCM-captured samples. Six insoluble proteins, including neurofilament light polypeptide (NEFL, alpha-internexin (INA, microtubule-associated protein 2 (MAP2, myelin basic protein (MBP, myelin proteolipid protein (PLP and 2′,3′-cyclic-nucleotide 3′-phosphodiesterase (CNP, were found to be site-specific. Soluble proteins, such as neuron-specific enolase (NSE and ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1, and some insoluble proteins, including neurofilament heavy polypeptide (NEFH, glial fibrillary acidic protein (GFAP, microtubule-associated protein tau (MAPT and tubulin β-3 chain (TUBB3, were found to be evenly distributed in the brain. Therefore, we conclude that some insoluble protein biomarkers for stroke are site-specific, and would make excellent candidates for the design and analysis of relevant clinical studies in the future.

  2. Comparisons of CAP88PC version 2.0 default parameters to site specific inputs

    International Nuclear Information System (INIS)

    Lehto, M. A.; Courtney, J. C.; Charter, N.; Egan, T.

    2000-01-01

    The effects of varying the input for the CAP88PC Version 2.0 program on the total effective dose equivalents (TEDEs) were determined for hypothetical releases from the Hot Fuel Examination Facility (HFEF) located at the Argonne National Laboratory site on the Idaho National Engineering and Environmental Laboratory (INEEL). Values for site specific meteorological conditions and agricultural production parameters were determined for the 80 km radius surrounding the HFEF. Four nuclides, 3 H, 85 Kr, 129 I, and 137 Cs (with its short lived progeny, 137m Ba) were selected for this study; these are the radioactive materials most likely to be released from HFEF under normal or abnormal operating conditions. Use of site specific meteorological parameters of annual precipitation, average temperature, and the height of the inversion layer decreased the TEDE from 137 Cs- 137m Ba up to 36%; reductions for other nuclides were less than 3%. Use of the site specific agricultural parameters reduced TEDE values between 7% and 49%, depending on the nuclide. Reductions are associated with decreased committed effective dose equivalents (CEDEs) from the ingestion pathway. This is not surprising since the HFEF is located well within the INEEL exclusion area, and the surrounding area closest to the release point is a high desert with limited agricultural diversity. Livestock and milk production are important in some counties at distances greater than 30 km from the HFEF

  3. Direct site-specific immobilization of protein A via aldehyde-hydrazide conjugation.

    Science.gov (United States)

    Zang, Berlin; Ren, Jun; Xu, Li; Jia, Lingyun

    2016-01-01

    Immobilization of affinity ligands on supporting matrices is a key step for the preparation of affinity chromatography resins, and an efficient coupling strategy can significantly improve the validity and cost of the affinity system, especially for systems that employ expensive recombinant proteins or antibodies as affinity ligands. This study described a simple method for obtaining site-specific immobilization of protein A (the ligand) via aldehyde-hydrazide conjugation and its application in antibody purification via protein A chromatography. An aldehyde group was generated at the N-terminus of protein A in vivo by co-expressing a formylglycine-generating enzyme (FGE) and recombinant protein A containing a FGE recognizing sequence (aldehyde tag) in Escherichia coli. The resulting aldehyde allowed direct immobilization of protein A onto the hydrazide-modified agarose matrices under mild condition. We found that 100mM aniline was most effective for catalyzing the coupling reaction, and the recombinant protein A could be coupled with high selectivity, directly from a crude cell extract. The site-specific immobilized protein A showed good capacity for antibody purification. The specificity of the aldehyde-hydrazide reaction not only allowed site-specific immobilization of affinity ligands, but also improved the cost of the process by employing unpurified ligands, a method that might be of great use to industrial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Site-specific estimates of water yield applied in regional acid sensitivity surveys across western Canada

    Directory of Open Access Journals (Sweden)

    Patrick D. SHAW

    2010-08-01

    Full Text Available Runoff or water yield is an important input to the Steady-State Water Chemistry (SSWC model for estimating critical loads of acidity. Herein, we present site-specific water yield estimates for a large number of lakes (779 across three provinces of western Canada (Manitoba, Saskatchewan, and British Columbia using an isotope mass balance (IMB approach. We explore the impact of applying site-specific hydrology as compared to use of regional runoff estimates derived from gridded datasets in assessing critical loads of acidity to these lakes. In general, the average water yield derived from IMB is similar to the long-term average runoff; however, IMB results suggest a much larger range in hydrological settings of the lakes, attributed to spatial heterogeneity in watershed characteristics and landcover. The comparison of critical loads estimates from the two methods suggests that use of average regional runoff data in the SSWC model may overestimate critical loads for the majority of lakes due to systematic skewness in the actual runoff distributions. Implications for use of site-specific hydrology in regional critical loads assessments across western Canada are discussed.

  5. Safe genetic modification of cardiac stem cells using a site-specific integration technique.

    Science.gov (United States)

    Lan, Feng; Liu, Junwei; Narsinh, Kazim H; Hu, Shijun; Han, Leng; Lee, Andrew S; Karow, Marisa; Nguyen, Patricia K; Nag, Divya; Calos, Michele P; Robbins, Robert C; Wu, Joseph C

    2012-09-11

    Human cardiac progenitor cells (hCPCs) are a promising cell source for regenerative repair after myocardial infarction. Exploitation of their full therapeutic potential may require stable genetic modification of the cells ex vivo. Safe genetic engineering of stem cells, using facile methods for site-specific integration of transgenes into known genomic contexts, would significantly enhance the overall safety and efficacy of cellular therapy in a variety of clinical contexts. We used the phiC31 site-specific recombinase to achieve targeted integration of a triple fusion reporter gene into a known chromosomal context in hCPCs and human endothelial cells. Stable expression of the reporter gene from its unique chromosomal integration site resulted in no discernible genomic instability or adverse changes in cell phenotype. Namely, phiC31-modified hCPCs were unchanged in their differentiation propensity, cellular proliferative rate, and global gene expression profile when compared with unaltered control hCPCs. Expression of the triple fusion reporter gene enabled multimodal assessment of cell fate in vitro and in vivo using fluorescence microscopy, bioluminescence imaging, and positron emission tomography. Intramyocardial transplantation of genetically modified hCPCs resulted in significant improvement in myocardial function 2 weeks after cell delivery, as assessed by echocardiography (P=0.002) and MRI (P=0.001). We also demonstrated the feasibility and therapeutic efficacy of genetically modifying differentiated human endothelial cells, which enhanced hind limb perfusion (P<0.05 at day 7 and 14 after transplantation) on laser Doppler imaging. The phiC31 integrase genomic modification system is a safe, efficient tool to enable site-specific integration of reporter transgenes in progenitor and differentiated cell types.

  6. Site-specific data confirm arsenic exposure predicted by the U.S. Environmental Protection Agency.

    Science.gov (United States)

    Walker, S; Griffin, S

    1998-03-01

    The EPA uses an exposure assessment model to estimate daily intake to chemicals of potential concern. At the Anaconda Superfund site in Montana, the EPA exposure assessment model was used to predict total and speciated urinary arsenic concentrations. Predicted concentrations were then compared to concentrations measured in children living near the site. When site-specific information on concentrations of arsenic in soil, interior dust, and diet, site-specific ingestion rates, and arsenic absorption rates were used, measured and predicted urinary arsenic concentrations were in reasonable agreement. The central tendency exposure assessment model successfully described the measured urinary arsenic concentration for the majority of children at the site. The reasonable maximum exposure assessment model successfully identified the uppermost exposed population. While the agreement between measured and predicted urinary arsenic is good, it is not exact. The variables that were identified which influenced agreement included soil and dust sample collection methodology, daily urinary volume, soil ingestion rate, and the ability to define the exposure unit. The concentration of arsenic in food affected agreement between measured and predicted total urinary arsenic, but was not considered when comparing measured and predicted speciated urinary arsenic. Speciated urinary arsenic is the recommended biomarker for recent inorganic arsenic exposure. By using site-specific data in the exposure assessment model, predicted risks from exposure to arsenic were less than predicted risks would have been if the EPA's default values had been used in the exposure assessment model. This difference resulted in reduced magnitude and cost of remediation while still protecting human health.

  7. Simulation of artificial earthquake records compatible with site specific response spectra using time series analysis

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Fadavi Amiri

    2017-11-01

    Full Text Available Time history analysis of infrastructures like dams, bridges and nuclear power plants is one of the fundamental parts of their design process. But there are not sufficient and suitable site specific earthquake records to do such time history analysis; therefore, generation of artificial accelerograms is required for conducting research works in this area.  Using time series analysis, wavelet transforms, artificial neural networks and genetic algorithm, a new method is introduced to produce artificial accelerograms compatible with response spectra for the specified site condition. In the proposed method, first, some recorded accelerograms are selected based on the soil condition at the recording station. The soils in these stations are divided into two groups of soil and rock according to their measured shear wave velocity. These accelerograms are then analyzed using wavelet transform. Next, artificial neural networks ability to produce reverse signal from response spectra is used to produce wavelet coefficients. Furthermore, a genetic algorithm is employed to optimize the network weight and bias matrices by searching in a wide range of values and prevent neural network convergence on local optima. At the end site specific accelerograms are produced. In this paper a number of recorded accelerograms in Iran are employed to test the neural network performances and to demonstrate the effectiveness of the method. It is shown that using synthetic time series analysis, genetic algorithm, neural network and wavelet transform will increase the capabilities of the algorithm and improve its speed and accuracy in generating accelerograms compatible with site specific response spectra for different site conditions.

  8. Spatial Distribution and Site-Specific Spraying of Main Sucking Pests of Elm Trees.

    Science.gov (United States)

    Karimzadeh, R; Iranipour, S

    2017-06-01

    Elm trees are important landscape trees and sucking insects weaken the elm trees and produce large amounts of honeydew. The main objectives of this study were to identify main honeydew-producing pests of elm trees and do site-specific spraying against these pests. To map the spatial distribution of the sucking pests in the large scale, the study area was divided into 40 × 40 m grids and one tree was chosen randomly from each grid (a total of 55 trees). These trees were sampled twice a year in 2011 and 2012. Each sample was a 30-cm branch terminal. Eight samples were taken from each tree in four cardinal directions and two canopy levels. The number of sucking insects and leaves of each sample were counted and recorded. Spatial analysis of the data was carried out using geostatistics. Kriging was used for producing prediction maps. Insecticide application was restricted to the regions with populations higher than threshold. To identify within-tree distribution of the honeydew-producing pests, six and four elm trees were chosen in 2011 and 2012 respectively, and sampled weekly. These trees were sampled as described previously. European elm scale (EES), Gossyparia spuria (Modeer) and two species of aphids were the dominant honeydew-producing pests. The results revealed that the effects of direction, canopy level and their interactions on insect populations were not statistically significant (P < 0.05). Site-specific spraying decreased the amount of insecticides used by ca. 20%, while satisfactory control of the sucking pests and honeydew excretion was obtained. Considering the environmental and economic benefits of site-specific spraying, it is worth doing more complementary works in this area.

  9. Environmental restoration and waste management Site-Specific Plan for the Oak Ridge Reservation

    International Nuclear Information System (INIS)

    1993-01-01

    The United States Department of Energy (DOE) is committed to achieving and maintaining environmental regulatory compliance while responding to public concerns and emphasizing waste minimization. DOE publishes the Environmental Restoration and Waste Management Five-Year Plan (FYP) annually to document its progress towards these goals. The purpose of this Site-Specific Plan (SSP) is to describe the activities undertaken to implement the FYP goals at the DOE Oak Ridge Field Office (DOE/OR) installations and programs specifically for the Oak Ridge Reservation (ORR) and surrounding areas. This SSP addresses activities and goals to be accomplished during FY93 even through the FYP focuses on FY94

  10. Environmental restoration and waste management Site-Specific Plan for the Oak Ridge Reservation. FY 1993

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-15

    The United States Department of Energy (DOE) is committed to achieving and maintaining environmental regulatory compliance while responding to public concerns and emphasizing waste minimization. DOE publishes the Environmental Restoration and Waste Management Five-Year Plan (FYP) annually to document its progress towards these goals. The purpose of this Site-Specific Plan (SSP) is to describe the activities undertaken to implement the FYP goals at the DOE Oak Ridge Field Office (DOE/OR) installations and programs specifically for the Oak Ridge Reservation (ORR) and surrounding areas. This SSP addresses activities and goals to be accomplished during FY93 even through the FYP focuses on FY94.

  11. Site Specific Advisory Board initiative, evaluation survey results supplementary appendix: Summary of individual site results

    International Nuclear Information System (INIS)

    1996-08-01

    This Appendix presents results of the Site-Specific Advisory Board (SSAB) Initiative for each of the 11 sites that participated in the survey. These individual results are a supplement to the June 1996 Summary Report which presented overall survey results. Results are presented in 11 sections, arranged alphabetically by site. Each section includes a series of figures and tables that parallel those presented in the Summary Report. To facilitate comparison, figures are presented both for the individual site and for the overall long survey. The sequence of sections is: Fernald, Hanford, Idaho, Los Alamos, Monticello, Nevada, Pantex, Rocky Flats, St. Louis, Sandia, and Savannah River

  12. Mutagenic replication in human cell extracts of DNA containing site-specific N-2-acetylaminofluorene adducts.

    OpenAIRE

    Thomas, D C; Veaute, X; Kunkel, T A; Fuchs, R P

    1994-01-01

    We have analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of bidirectional replication of double-stranded DNA in a human cell extract. Plasmid vectors were constructed containing the simian virus 40 origin of replication and single AAF adducts at one of three guanines in the Nar I sequence GGCGCC in a lacZ reporter gene. The presence of an AAF adduct diminishes replication efficiency in HeLa cell extracts by 70-80%. Replicati...

  13. Char-recirculation biomass gasification system--a site-specific feasibility study

    International Nuclear Information System (INIS)

    Purdy, K.R.; Kerr, C.P.; Hensley, B.D.

    1991-01-01

    A site-specific feasibility study was conducted for a char-recirculation biomass gasification plant which would dispose of the chippable solid residues of the area sawmills. The plant would receive green hardwood chips and convert them into active charcoal while producing process steam and electrical power. An economic analysis was performed on the basis of not-for-profit operation, marketing crushed active charcoal to a broker at a discounted price, and displacing purchased electric power. Given a market for the active charcoal, the plant was judged to be economically viable

  14. Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations

    Science.gov (United States)

    Petrov, Alexey; Puglisi, Joseph D.

    2010-01-01

    Site-specific labeling of Escherichia coli ribosomes has allowed application of single-molecule fluorescence spectroscopy and force methods to probe the mechanism of translation. To apply these approaches to eukaryotic translation, eukaryotic ribosomes must be specifically labeled with fluorescent labels and molecular handles. Here, we describe preparation and labeling of the small and large yeast ribosomal subunits. Phylogenetically variable hairpin loops in ribosomal RNA are mutated to allow hybridization of oligonucleotides to mutant ribosomes. We demonstrate specific labeling of the ribosomal subunits, and their use in single-molecule fluorescence and force experiments. PMID:20501598

  15. Tus-Ter as a tool to study site-specific DNA replication perturbation in eukaryotes

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2014-01-01

    have demonstrated that Tus-Ter can be used as a heterologous tool to generate site-specific perturbation of DNA replication when reconstituted in eukaryotes. Here, we review these recent findings and explore the molecular mechanism by which Tus-Ter mediates replication fork (RF) arrest in the budding...... yeast, S. cerevisiae. We propose that Tus-Ter is a versatile, genetically tractable, and regulatable RF blocking system that can be utilized for disrupting DNA replication in a diverse range of host cells....

  16. Site-Specific Dual Functionalization of Cysteine Residue in Peptides and Proteins with 2-Azidoacrylates.

    Science.gov (United States)

    Ariyasu, Shinya; Hayashi, Hirohito; Xing, Bengang; Chiba, Shunsuke

    2017-04-19

    Herein, we report use of 2-azidoacrylates to perform site-specific dual functionalization of the cysteine residue of peptides and bovine serum albumin (BSA), a native protein containing one free cysteine residue. The sulfhydryl group of the cysteine residue could be conjugated with 2-azidoacrylates bearing various functionalities, such as fluorescent dyes under physiological aqueous buffer conditions, to afford peptide and protein conjugates anchoring an azide moiety. Successive azide-alkyne cycloaddition enables installation of the second functionality, thus affording dual-functionalized peptide- and protein-based materials.

  17. Site specific analysis of geothermal development-data files of prospective sites. Volume II

    Energy Technology Data Exchange (ETDEWEB)

    Trehan, R.; Cohen, A.; Gupta, J.; Jacobsen, W.; Leigh, J.; True, S.

    1978-08-01

    Development scenarios for 37 hydrothermal and geopressured prospects in the United States were analyzed to assist DOE's Division of Geothermal Energy in mission-oriented planning of geothermal resource development. This second volume of the three-volume series contains the detailed site-specific analyses in terms of technological, economic, and other requirements for meeting the postulated schedules. This presentation should be used in conjunction with Volume III, which contains detailed descriptive data files for each of the 37 prospects. These data files were used for the analyses contained in Volume II and should be useful for other geothermal resource studies. (JGB)

  18. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    Science.gov (United States)

    Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  19. Criteria for compilation of a site-specific thermodynamic database for geochemical speciation calculations

    International Nuclear Information System (INIS)

    Chandratillake, M.; Trivedi, D.P.; Randall, M.G.; Humphreys, P.N.

    1998-01-01

    A methodology has been developed to establish a site-specific database appropriate to geochemical modelling the critical components and the wide range of near field conditions expected in the low level radioactive waste disposal site at Drigg in the UK. Several databases available in the public domain have been compared to select a foundation database. The foundation database was 'trimmed-down' and then customised to suit Drigg applications. The species dominant at Drigg have been identified and the thermodynamic constants of these species have been critically evaluated. The evaluated database has been validated for quality by comparing speciation calculations with plutonium and uranium experimental solubility results. (orig.)

  20. Equilibrium isotope exchange kinetics of native and site-specific mutant forms of E. coli aspartate transcarbamoylase

    International Nuclear Information System (INIS)

    Wedler, F.C.; Hsuanyu, Y.; Kantrowitz, E.R.

    1987-01-01

    Isotope exchange kinetics at equilibrium (EIEK) have been used to probe the kinetic and regulatory mechanisms of native aspartate transcarbamoylase (ATCase) from E. coli at pH 7.0, 30 0 . Substrate saturation patterns were most consistent with a preferred order random kinetic mechanism: C-P prior to L-Asp, C-Asp released before Pi, with the Asp ↔ C-Asp exchange rate 5X faster than C-P ↔ Pi. Computer simulations allow one to fit the EIEK experimental data and to arrive at the best set of kinetic constants for a given enzyme state. These approaches have been applied to modified ATCase. Bound CTP and ATP were observed, respectively, to inhibit and activate differentially Asp ↔ C-Asp, but not C-P ↔ Pi, indicating that these modifiers alter the association-dissociation rates of L-Asp and C-Asp but not of C-P or Pi. Low levels of PALA activated both exchange rates (due to shifting the T-R equilibrium), but higher [PALA] completely blocked both exchanges. The effects of a site-specific mutation of Tyr240 Phe have been similarly probed by EIEK methods. The Phe240 mutant enzyme exhibited kinetic properties markedly different from native ATCase: the data indicate that Phe240 ATCase is much closer to an R-state enzyme than is native enzyme

  1. Site Specific Synthesis and in-situ Immobilization of Fluorescent Silver Nanoclusters on DNA Nanoscaffolds Using Tollens Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Suchetan [Arizona State Univ., Tempe, AZ (United States); Varghese, R. [Arizona State Univ., Tempe, AZ (United States); Deng, Z. [Arizona State Univ., Tempe, AZ (United States); Zhao, Z. [Arizona State Univ., Tempe, AZ (United States); Kumar, A. [Arizona State Univ., Tempe, AZ (United States); Yan, Hao [Arizona State Univ., Tempe, AZ (United States); Liu, Yan [Arizona State Univ., Tempe, AZ (United States)

    2011-04-06

    DNA strands with specific sequences and covalently attached sugar moieties were used for the site-specific incorporation of the sugar units on a DNA origami scaffold. This approach enabled the subsequent site-specific synthesis and in situ immobilization of fluorescent Ag clusters at predefined positions on the DNA nanoscaffold by treatment with the Tollens reagent.

  2. FRY site-specific methylation differentiates pancreatic ductal adenocarcinoma from other adenocarcinomas.

    Science.gov (United States)

    Srisuttee, Ratakorn; Ota, Jun; Muangsub, Tachapol; Keelawat, Somboon; Trirattanachat, Surang; Kitkumthorn, Nakarin; Mutirangura, Apiwat

    2016-06-01

    Adenocarcinoma is a type of cancer that occurs in the glandular cells throughout the body. There are several metastatic adenocarcinoma of unknown primary origin. Currently, there is no highly effective method to differentiate pancreatic ductal adenocarcinoma (PDAC) from other adenocarcinomas. Here, we identified pancreas tissue by site-specific methylation at FRY and found that it can also detect PDAC. The establishment of Combined Bisulphite Restriction Analysis (COBRA) and quantitative real-time PCR techniques of FRY revealed FRY hypermethylation in 21 out of 24 normal pancreatic tissue samples, whereas all other normal tissue samples from thirteen other organs (80 samples) remained totally unmethylated. Similarly in application to PDAC, this marker effectively indicated 25 PDAC among 151 other common adenocarcinomas with values of 100%, 98.7%, 92.6%, and 100% in sensitivity, specificity, positive predictive value and negative predictive value, respectively. In summary, we have demonstrated that this epigenetic site-specific marker has high potential for pancreatic tissue identification and can be applied in PDAC diagnosis. © 2016 APMIS. Published by John Wiley & Sons Ltd.

  3. High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13.

    Science.gov (United States)

    Kretz, Colin A; Tomberg, Kärt; Van Esbroeck, Alexander; Yee, Andrew; Ginsburg, David

    2018-02-12

    We have combined random 6 amino acid substrate phage display with high throughput sequencing to comprehensively define the active site specificity of the serine protease thrombin and the metalloprotease ADAMTS13. The substrate motif for thrombin was determined by >6,700 cleaved peptides, and was highly concordant with previous studies. In contrast, ADAMTS13 cleaved only 96 peptides (out of >10 7 sequences), with no apparent consensus motif. However, when the hexapeptide library was substituted into the P3-P3' interval of VWF73, an exosite-engaging substrate of ADAMTS13, 1670 unique peptides were cleaved. ADAMTS13 exhibited a general preference for aliphatic amino acids throughout the P3-P3' interval, except at P2 where Arg was tolerated. The cleaved peptides assembled into a motif dominated by P3 Leu, and bulky aliphatic residues at P1 and P1'. Overall, the P3-P2' amino acid sequence of von Willebrand Factor appears optimally evolved for ADAMTS13 recognition. These data confirm the critical role of exosite engagement for substrates to gain access to the active site of ADAMTS13, and define the substrate recognition motif for ADAMTS13. Combining substrate phage display with high throughput sequencing is a powerful approach for comprehensively defining the active site specificity of proteases.

  4. Applying Nitrogen Site-Specifically Using Soil Electrical Conductivity Maps and Precision Agriculture Technology

    Directory of Open Access Journals (Sweden)

    E.D. Lund

    2001-01-01

    Full Text Available Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower’s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS-referenced mapping of bulk soil electrical conductivity (EC has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

  5. New developments for the site-specific attachment of protein to surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Camarero, J A

    2005-05-12

    Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

  6. Recent advances in covalent, site-specific protein immobilization [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Morten Meldal

    2016-09-01

    Full Text Available The properties of biosensors, biomedical implants, and other materials based on immobilized proteins greatly depend on the method employed to couple the protein molecules to their solid support. Covalent, site-specific immobilization strategies are robust and can provide the level of control that is desired in this kind of application. Recent advances include the use of enzymes, such as sortase A, to couple proteins in a site-specific manner to materials such as microbeads, glass, and hydrogels. Also, self-labeling tags such as the SNAP-tag can be employed. Last but not least, chemical approaches based on bioorthogonal reactions, like the azide–alkyne cycloaddition, have proven to be powerful tools. The lack of comparative studies and quantitative analysis of these immobilization methods hampers the selection process of the optimal strategy for a given application. However, besides immobilization efficiency, the freedom in selecting the site of conjugation and the size of the conjugation tag and the researcher’s expertise regarding molecular biology and/or chemical techniques will be determining factors in this regard.

  7. Coulomb nanoradiator-mediated, site-specific thrombolytic proton treatment with a traversing pristine Bragg peak

    Science.gov (United States)

    Jeon, Jae-Kun; Han, Sung-Mi; Min, Soon-Ki; Seo, Seung-Jun; Ihm, Kyuwook; Chang, Won-Seok; Kim, Jong-Ki

    2016-11-01

    Traversing proton beam-irradiated, mid/high-Z nanoparticles produce site-specific enhancement of X-ray photon-electron emission via the Coulomb nanoradiator (CNR) effect, resulting in a nano- to micro-scale therapeutic effect at the nanoparticle-uptake target site. Here, we demonstrate the uptake of iron oxide nanoparticles (IONs) and nanoradiator-mediated, site-specific thrombolysis without damaging the vascular endothelium in an arterial thrombosis mouse model. The enhancement of low-energy electron (LEE) emission and reactive oxygen species (ROS) production from traversing proton beam-irradiated IONs was examined. Flow recovery was only observed in CNR-treated mice, and greater than 50% removal of the thrombus was achieved. A 2.5-fold greater reduction in the thrombus-enabled flow recovery was observed in the CNR group compared with that observed in the untreated ION-only and proton-only control groups (p ROS by the proton-irradiated IONs, which suggests chemical degradation of the thrombus without potent emboli.

  8. Determining site-specific background level with geostatistics for remediation of heavy metals in neighborhood soils

    Directory of Open Access Journals (Sweden)

    Tammy M. Milillo

    2017-03-01

    Full Text Available The choice of a relevant, uncontaminated site for the determination of site-specific background concentrations for pollutants is critical for planning remediation of a contaminated site. The guidelines used to arrive at concentration levels vary from state to state, complicating this process. The residential neighborhood of Hickory Woods in Buffalo, NY is an area where heavy metal concentrations and spatial distributions were measured to plan remediation. A novel geostatistics based decision making framework that relies on maps generated from indicator kriging (IK and indicator co-kriging (ICK of samples from the contaminated site itself is shown to be a viable alternative to the traditional method of choosing a reference site for remediation planning. GIS based IK and ICK, and map based analysis are performed on lead and arsenic surface and subsurface datasets to determine site-specific background concentration levels were determined to be 50 μg/g for lead and 10 μg/g for arsenic. With these results, a remediation plan was proposed which identified regions of interest and maps were created to effectively communicate the results to the environmental agencies, residents and other interested parties.

  9. Establishment of monoclonal HCC cell lines with organ site-specific tropisms

    International Nuclear Information System (INIS)

    Wan, Jinliang; Wen, Duo; Dong, Lili; Tang, Jun; Liu, Dongli; Liu, Yang; Tao, Zhonghua; Gao, Dongmei; Sun, Huichuan; Cao, Ya; Fan, Jia; Wu, Weizhong

    2015-01-01

    Organ site-specific metastasis is an ominous feature for most poor-prognostic hepatocellular carcinoma (HCC) patients. Cancer cell lines and animal models are indispensable for investigating the molecular mechanisms of organ specific tropism. However, till now, little is known about the drivers in HCC metastatic tropism, and also no effective way has been developed to block the process of tropistic metastasis. In this study, we established several monoclonal HCC cell lines from HCCLM3-RFP together with their xenograft models, and then analyzed their metastatic potentials and tropisms using in-vitro and in-vivo assays, and finally elucidated the driving forces of HCC tropistic metastases. Six monoclonal cell lines with different organ site-specific tropism were established successfully. SPARC, VCAM1 and ANGPTL4 were found positively correlated with the potentials of lung metastasis, while ITGA1 had a positive relation to lymph node metastasis of enterocoelia. By our powerful platforms, HCC metastatic tropisms in clinic could be easily mimicked and recapitulated for exploring the bilateral interactions between tumor and its microenvironment, elucidating the drivers of HCC metastatic tropisms, and testing anti-cancer effects of newly developed agent in pre-clinical stage. The online version of this article (doi:10.1186/s12885-015-1692-0) contains supplementary material, which is available to authorized users

  10. Environmental Restoration and Waste Management Site-Specific Plan (SSP) for fiscal year 1992 (FY92)

    International Nuclear Information System (INIS)

    1991-09-01

    The FY-92 Site-Specific Plan (FY-92 SSP) for environmental restoration and waste management at the Idaho National Engineering Laboratory (INEL) is designed to provide the reader with easy access to the status of environmental restoration and waste management activities at INEL. The first chapter provides background on INIEL's physical environment, site history and mission, and general information about the site and its facilities. In addition, this chapter discusses the inter-relationships between the Site Specific Plan, the Environmental Restoration and Waste Management Five-Year Plan, the environmental restoration and waste management prioritization systems, and the Activity Data Sheets (ADSs) for environmental restoration and waste management. This discussion should help readers understand what the SSP is and how it fits into the environmental restoration and waste management process at INEL. This understanding should provide the reader with a better context for understanding the discussions in the SSP as well as a better feel for how and what to comment on during the public comment period that will be held from the first of September through the end of October 1991

  11. Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.

    Science.gov (United States)

    Lund, E D; Wolcott, M C; Hanson, G P

    2001-10-16

    Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history.

  12. ADMA/SDMA in Elderly Subjects with Asymptomatic Carotid Atherosclerosis: Values and Site-Specific Association

    Directory of Open Access Journals (Sweden)

    Graziano Riccioni

    2014-04-01

    Full Text Available Asymmetric dimethylarginine (ADMA is an endogenous nitric oxide synthase (NOS inhibitor known as a mediator of endothelial dysfunction and atherosclerosis. Circulating ADMA levels are correlated with cardiovascular risk factors such as hypercholesterolemia, arterial hypertension, diabetes mellitus, hyperhomocysteinemia, age and smoking. We assessed the relationship between ADMA values and site-specific association of asymptomatic carotid atherosclerosis (intima-media thickness (CIMT and plaque in elderly subjects. One hundred and eighty subjects underwent a complete history and physical examination, determination of serum chemistries and ADMA levels, and carotid ultrasound investigation (CUI. All subjects had no acute or chronic symptoms of carotid atherosclerosis. Statistical analyses showed that high plasma levels of ADMA/SDMA were positively correlated to carotid atherosclerosis (CIMT and plaque (p < 0.001, with significant site-specific association. Total cholesterol, low density lipoprotein cholesterol, triglycerides and C-reactive protein plasma concentrations were significantly associated with asymptomatic carotid atherosclerosis (p < 0.001. High serum concentrations of ADMA and SDMA were associated with carotid atherosclerotic lesions as measured by CIMT ad plaque and may represent a new marker of asymptomatic carotid atherosclerosis in elderly subjects.

  13. ADMA/SDMA in Elderly Subjects with Asymptomatic Carotid Atherosclerosis: Values and Site-Specific Association

    Science.gov (United States)

    Riccioni, Graziano; Scotti, Luca; D’Orazio, Nicolantonio; Gallina, Sabina; Speziale, Giuseppe; Speranza, Lorenza; Bucciarelli, Tonino

    2014-01-01

    Asymmetric dimethylarginine (ADMA) is an endogenous nitric oxide synthase (NOS) inhibitor known as a mediator of endothelial dysfunction and atherosclerosis. Circulating ADMA levels are correlated with cardiovascular risk factors such as hypercholesterolemia, arterial hypertension, diabetes mellitus, hyperhomocysteinemia, age and smoking. We assessed the relationship between ADMA values and site-specific association of asymptomatic carotid atherosclerosis (intima-media thickness (CIMT) and plaque) in elderly subjects. One hundred and eighty subjects underwent a complete history and physical examination, determination of serum chemistries and ADMA levels, and carotid ultrasound investigation (CUI). All subjects had no acute or chronic symptoms of carotid atherosclerosis. Statistical analyses showed that high plasma levels of ADMA/SDMA were positively correlated to carotid atherosclerosis (CIMT and plaque) (p < 0.001), with significant site-specific association. Total cholesterol, low density lipoprotein cholesterol, triglycerides and C-reactive protein plasma concentrations were significantly associated with asymptomatic carotid atherosclerosis (p < 0.001). High serum concentrations of ADMA and SDMA were associated with carotid atherosclerotic lesions as measured by CIMT ad plaque and may represent a new marker of asymptomatic carotid atherosclerosis in elderly subjects. PMID:24739810

  14. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  15. Testing the atmospheric dispersion model of CSA N288.1 with site-specific data

    International Nuclear Information System (INIS)

    Chouhan, S.L.; Davis, P.A.

    2001-01-01

    The atmospheric dispersion component of CSA Standard N288. 1, which provides guidelines for calculating derived release limits, has been tested. Long-term average concentrations of tritium in air were predicted using site-specific release rates and meteorological data and compared with measured concentrations at 43 monitoring sites at all CANDU stations in Canada. The predictions correlate well with the observations but were found to be conservative, overestimating by about 50% on average. The model overpredicted 84% of the time, with the highest prediction lying a factor of 5.5 above the corresponding observation. The model underpredicted the remaining 16% of the time, with the lowest prediction about one-half of the corresponding measurement. Possible explanations for this bias are discussed but no single reason appears capable of accounting for the discrepancy. Rather, the tendency to overprediction seems to result from the cumulative effects of a number of small conservatisms in the model. The model predictions were slightly better when site-specific meteorological data were used in the calculations in place of the default data of N288.1. Some large discrepancies between predictions and observations at specific monitoring sites suggest that it is the measurements rather than the model that are at fault. The testing has therefore provided a check on the observations as well as on the model. Recommendations on model use and data collection are made to improve the level of agreement between predictions and observations in the future. (author)

  16. Site-specifically {sup 89}Zr-labeled monoclonal antibodies for ImmunoPET

    Energy Technology Data Exchange (ETDEWEB)

    Tinianow, Jeff N.; Gill, Herman S.; Ogasawara, Annie; Flores, Judith E.; Vanderbilt, Alexander N.; Luis, Elizabeth; Vandlen, Richard; Darwish, Martine; Junutula, Jagath R.; Williams, Simon-P. [Genentech Research and Early Development, Genentech Inc., South San Francisco, CA 94080 (United States); Marik, Jan [Genentech Research and Early Development, Genentech Inc., South San Francisco, CA 94080 (United States)], E-mail: marik.jan@gene.com

    2010-04-15

    Three thiol reactive reagents were developed for the chemoselective conjugation of desferrioxamine (Df) to a monoclonal antibody via engineered cysteine residues (thio-trastuzumab). The in vitro stability and in vivo imaging properties of site-specifically radiolabeled {sup 89}Zr-Df-thio-trastuzumab conjugates were investigated. Methods: The amino group of desferrioxamine B was acylated by bromoacetyl bromide, N-hydroxysuccinimidyl iodoacetate, or N-hydroxysuccinimidyl 4-[N-maleimidomethyl]cyclohexane-1-carboxylate to obtain thiol reactive reagents bromoacetyl-desferrioxamine (Df-Bac), iodoacetyl-desferrioxamine (Df-Iac) and maleimidocyclohexyl-desferrioxamine (Df-Chx-Mal), respectively. Df-Bac and Df-Iac alkylated the free thiol groups of thio-trastuzumab by nucleophilic substitution forming Df-Ac-thio-trastuzumab, while the maleimide reagent Df-Chx-Mal reacted via Michael addition to provide Df-Chx-Mal-thio-trastuzumab. The conjugates were radiolabeled with {sup 89}Zr and evaluated for serum stability, and their positron emission tomography (PET) imaging properties were investigated in a BT474M1 (HER2-positive) breast tumor mouse model. Results: The chemoselective reagents were obtained in 14% (Df-Bac), 53% (Df-Iac) and 45% (Df-Chx-Mal) yields. Site-specific conjugation of Df-Chx-Mal to thio-trastuzumab was complete within 1 h at pH 7.5, while Df-Iac and Df-Bac respectively required 2 and 5 h at pH 9. Each Df modified thio-trastuzumab was chelated with {sup 89}Zr in yields exceeding 75%. {sup 89}Zr-Df-Ac-thio-trastuzumab and {sup 89}Zr-Df-Chx-Mal-thio-trastuzumab were stable in mouse serum and exhibited comparable PET imaging capabilities in a BT474M1 (HER2-positive) breast cancer model reaching 20-25 %ID/g of tumor uptake and a tumor to blood ratio of 6.1-7.1. Conclusions: The new reagents demonstrated good reactivity with engineered thiol groups of trastuzumab and very good chelation properties with {sup 89}Zr. The site-specifically {sup 89}Zr-labeled thio

  17. Differential regulation of the transcriptional activity of the glucocorticoid receptor through site-specific phosphorylation

    Directory of Open Access Journals (Sweden)

    Raj Kumar

    2008-08-01

    Full Text Available Raj Kumar1, William J Calhoun21Division of Gastroenterology; 2Division of Allergy, Pulmonary, Immunology, Critical Care, and Sleep (APICS, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USAAbstract: Post-translational modifications such as phosphorylation are known to play an important role in the gene regulation by the transcription factors including the nuclear hormone receptor superfamily of which the glucocorticoid receptor (GR is a member. Protein phosphorylation often switches cellular activity from one state to another. Like many other transcription factors, the GR is a phosphoprotein, and phosphorylation plays an important role in the regulation of GR activity. Cell signaling pathways that regulate phosphorylation of the GR and its associated proteins are important determinants of GR function under various physiological conditions. While the role of many phosphorylation sites in the GR is still not fully understood, the role of others is clearer. Several aspects of transcription factor function, including DNA binding affinity, interaction of transactivation domains with the transcription initiation complex, and shuttling between the cytoplasmic compartments, have all been linked to site-specific phosphorylation. All major phosphorylation sites in the human GR are located in the N-terminal domain including the major transactivation domain, AF1. Available literature clearly indicates that many of these potential phosphorylation sites are substrates for multiple kinases, suggesting the potential for a very complex regulatory network. Phosphorylated GR interacts favorably with critical coregulatory proteins and subsequently enhances transcriptional activity. In addition, the activities and specificities of coregulators may be subject to similar regulation by phosphorylation. Regulation of the GR activity due to phosphorylation appears to be site-specific and dependent upon specific cell signaling cascade

  18. Site specific passive acoustic detection and densities of humpback whale calls off the coast of California

    Science.gov (United States)

    Helble, Tyler Adam

    Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. Automated methods are needed to aid in the analyses of the recorded data. When a mammal vocalizes in the marine environment, the received signal is a filtered version of the original waveform emitted by the marine mammal. The waveform is reduced in amplitude and distorted due to propagation effects that are influenced by the bathymetry and environment. It is important to account for these effects to determine a site-specific probability of detection for marine mammal calls in a given study area. A knowledge of that probability function over a range of environmental and ocean noise conditions allows vocalization statistics from recordings of single, fixed, omnidirectional sensors to be compared across sensors and at the same sensor over time with less bias and uncertainty in the results than direct comparison of the raw statistics. This dissertation focuses on both the development of new tools needed to automatically detect humpback whale vocalizations from single-fixed omnidirectional sensors as well as the determination of the site-specific probability of detection for monitoring sites off the coast of California. Using these tools, detected humpback calls are "calibrated" for environmental properties using the site-specific probability of detection values, and presented as call densities (calls per square kilometer per time). A two-year monitoring effort using these calibrated call densities reveals important biological and ecological information on migrating humpback whales off the coast of California. Call density trends are compared between the monitoring sites and at the same monitoring site over time. Call densities also are compared to several natural and human-influenced variables including season, time of day, lunar illumination, and ocean noise. The results reveal substantial differences in call densities

  19. Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

    Science.gov (United States)

    Kathrin Hassler, Sibylle; Weiler, Markus; Blume, Theresa

    2018-01-01

    Transpiration is a key process in the hydrological cycle, and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation and evaluation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology and soils, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls.We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites across a 290 km2 catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocity and derived sap flow patterns of these 61 trees, and we determined the importance of the different controls.Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, geology and aspect. For sap flow we included only the stand- and site-specific predictors in the models to ensure variable independence. Of those, geology and aspect were most important. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal

  20. SARC009: Phase 2 study of dasatinib in patients with previously treated, high-grade, advanced sarcoma.

    Science.gov (United States)

    Schuetze, Scott M; Wathen, J Kyle; Lucas, David R; Choy, Edwin; Samuels, Brian L; Staddon, Arthur P; Ganjoo, Kristen N; von Mehren, Margaret; Chow, Warren A; Loeb, David M; Tawbi, Hussein A; Rushing, Daniel A; Patel, Shreyaskumar R; Thomas, Dafydd G; Chugh, Rashmi; Reinke, Denise K; Baker, Laurence H

    2016-03-15

    Dasatinib exhibited activity in preclinical models of sarcoma. The Sarcoma Alliance for Research through Collaboration (SARC) conducted a multicenter, phase 2 trial of dasatinib in patients with advanced sarcoma. Patients received dasatinib twice daily. The primary objective was to estimate the clinical benefit rate (CBR) (complete response or partial response within 6 months or stable disease duration of ≥6 months) with a target of ≥25%. Patients were enrolled into 1 of 7 different cohorts and assessed by imaging every 8 weeks using Choi criteria tumor response and a Bayesian hierarchical design. For each subtype, enrollment was stopped after a minimum of 9 patients were treated if there was a sarcoma (UPS) cohorts fully accrued and 6 of 47 and 8 of 42 evaluable patients, respectively, exhibited clinical benefit. The probability that the CBR was ≥25% in the LMS and UPS cohorts was 0.008 and 0.10, respectively. The median progression-free survival ranged from 0.9 months in patients with rhabdomyosarcoma to 2.2 months in patients with LMS. The median overall survival was 8.6 months. The most frequent adverse events were constitutional, gastrointestinal, and respiratory, and 36% of patients required dose reduction for toxicity. Serious adverse events attributed to therapy occurred in 11% of patients. Dasatinib may have activity in patients with UPS but is inactive as a single agent in the other sarcoma subtypes included herein. The Bayesian design allowed for the early termination of accrual in 5 subtypes because of lack of drug activity. © 2015 American Cancer Society.

  1. OCT-1, ABCB1, and ABCG2 Expression in Imatinib-Resistant Chronic Myeloid Leukemia Treated with Dasatinib or Nilotinib

    OpenAIRE

    Kim, Yeo-Kyeoung; Lee, Seung-Shin; Jeong, Sung-Hoon; Ahn, Jae-Sook; Yang, Deok-Hwan; Lee, Je-Jung; Shin, Myung-Geun; Kim, Hyeoung-Joon

    2014-01-01

    This study explored drug transporter expression levels and their impact on clinical response to imatinib and second-generation tyrosine kinase inhibitors (TKIs) in imatinib- resistant chronic myeloid leukemia (CML). Imatinib-resistant chronic phase CML patients treated with dasatinib (n=10) and nilotinib (n=12) were enrolled. The mRNA expression of the OCT-1, ABCG2, and ABCB1 genes was quantified by using paired bone marrow samples obtained before administering imatinib and at the point of de...

  2. Practical Application of Site-Specific Earthquake Early Warning (EEW) System

    International Nuclear Information System (INIS)

    Kanda, Katsuhisa

    2014-01-01

    The development of an on-site warning system was reported. This system improves the timing of warnings and reduces the number of false alarms by improving the method of estimating the JMA seismic intensity using earthquake early warning system information based on site-specific data. Moreover, the development of an application for practical use in a construction company and an integrated system for realizing system shutdown was also reported. The concept of this system is based on the following. Seismic intensity is not distributed concentrically, and the attenuation relationship cannot explain the distribution of seismic intensity precisely. The standard method of seismic intensity prediction is construed as 'attenuation relationship + soil amplification factor', but this may be improved in the reformulation 'original attenuation relationship for each site + correction factors dependent on the epicenter location and depth' using a seismic intensity database that includes data on recent and historical earthquakes. (authors)

  3. Site-Specific Antioxidative Therapy for Prevention of Atherosclerosis and Cardiovascular Disease

    Directory of Open Access Journals (Sweden)

    Hajime Otani

    2013-01-01

    Full Text Available Oxidative stress has been implicated in pathophysiology of aging and age-associated disease. Antioxidative medicine has become a practice for prevention of atherosclerosis. However, limited success in preventing cardiovascular disease (CVD in individuals with atherosclerosis using general antioxidants has prompted us to develop a novel antioxidative strategy to prevent atherosclerosis. Reducing visceral adipose tissue by calorie restriction (CR and regular endurance exercise represents a causative therapy for ameliorating oxidative stress. Some of the recently emerging drugs used for the treatment of CVD may be assigned as site-specific antioxidants. CR and exercise mimetic agents are the choice for individuals who are difficult to continue CR and exercise. Better understanding of molecular and cellular biology of redox signaling will pave the way for more effective antioxidative medicine for prevention of CVD and prolongation of healthy life span.

  4. Site-specific DNA damage at GGG sequence by oxidative stress may accelerate telomere shortening.

    Science.gov (United States)

    Oikawa, S; Kawanishi, S

    1999-06-25

    Telomere shortening during human aging has been reported to be accelerated by oxidative stress. We investigated the mechanism of telomere shortening by oxidative stress. H2O2 plus Cu(II) caused predominant DNA damage at the 5' site of 5'-GGG-3' in the telomere sequence. Furthermore, H2O2 plus Cu(II) induced 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) formation in telomere sequences more efficiently than that in non-telomere sequences. NO plus O2- efficiently caused base alteration at the 5' site of 5'-GGG-3' in the telomere sequence. It is concluded that the site-specific DNA damage at the GGG sequence by oxidative stress may play an important role in increasing the rate of telomere shortening with aging.

  5. Savannah River Site`s Site Specific Plan. Environmental restoration and waste management, fiscal year 1992

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  6. Generalized theory on the mechanism of site-specific DNA-protein interactions

    Science.gov (United States)

    Niranjani, G.; Murugan, R.

    2016-05-01

    We develop a generalized theoretical framework on the binding of transcription factor proteins (TFs) with specific sites on DNA that takes into account the interplay of various factors regarding overall electrostatic potential at the DNA-protein interface, occurrence of kinetic traps along the DNA sequence, presence of other roadblock protein molecules along DNA and crowded environment, conformational fluctuations in the DNA binding domains (DBDs) of TFs, and the conformational state of the DNA. Starting from a Smolochowski type theoretical framework on site-specific binding of TFs we logically build our model by adding the effects of these factors one by one. Our generalized two-step model suggests that the electrostatic attractive forces present inbetween the positively charged DBDs of TFs and the negatively charged phosphate backbone of DNA, along with the counteracting shielding effects of solvent ions, is the core factor that creates a fluidic type environment at the DNA-protein interface. This in turn facilitates various one-dimensional diffusion (1Dd) processes such as sliding, hopping and intersegmental transfers. These facilitating processes as well as flipping dynamics of conformational states of DBDs of TFs between stationary and mobile states can enhance the 1Dd coefficient on a par with three-dimensional diffusion (3Dd). The random coil conformation of DNA also plays critical roles in enhancing the site-specific association rate. The extent of enhancement over the 3Dd controlled rate seems to be directly proportional to the maximum possible 1Dd length. We show that the overall site-specific binding rate scales with the length of DNA in an asymptotic way. For relaxed DNA, the specific binding rate will be independent of the length of DNA as length increases towards infinity. For condensed DNA as in in vivo conditions, the specific binding rate depends on the length of DNA in a turnover way with a maximum. This maximum rate seems to scale with the

  7. Site-Specific Pre-Swelling-Directed Morphing Structures of Patterned Hydrogels.

    Science.gov (United States)

    Wang, Zhi Jian; Hong, Wei; Wu, Zi Liang; Zheng, Qiang

    2017-12-11

    Morphing materials have promising applications in various fields, yet how to program the self-shaping process for specific configurations remains a challenge. Herein we show a versatile approach to control the buckling of individual domains and thus the outcome configurations of planar-patterned hydrogels. By photolithography, high-swelling disc gels were positioned in a non-swelling gel sheet; the swelling mismatch resulted in out-of-plain buckling of the disc gels. To locally control the buckling direction, masks with holes were used to guide site-specific swelling of the high-swelling gel under the holes, which built a transient through-thickness gradient and thus directed the buckling during the subsequent unmasked swelling process. Therefore, various configurations of an identical patterned hydrogel can be programmed by the pre-swelling step with different masks to encode the buckling directions of separate domains. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Site-specific functionalization of anisotropic nanoparticles: from colloidal atoms to colloidal molecules

    DEFF Research Database (Denmark)

    Li, Fan; Yoo, Won Cheol; Beernink, Molly B

    2009-01-01

    Multipodal nanoparticles (NPs) with controlled tethers are promising principal building blocks, useful for constructing more complex materials, much like atoms are connected into more complex molecules. Here we report colloidal sphere templating as a viable means to create tetrapodal NPs with site......-specific tethers. Amorphous sol-gel materials were molded by the template into shaped NPs that mimic tetravalent atoms but on the length scale of colloids. Synthetic methods were developed to modify only the tips of the tetrapods with a range of possible functional groups to generate anisotropic NPs capable...... are applicable to many compositions regardless of crystal structure, therefore lending themselves to the fabrication of complex assemblies, analogous to those found in the molecular regime....

  9. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry

    Science.gov (United States)

    Zhu, Zhikai; Desaire, Heather

    2015-07-01

    Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.

  10. [Localized aggressive periodontitis: a possible site-specific rather than tooth-specific disease?].

    Science.gov (United States)

    Venezia, E; Abed, Y; Raz, P; Goldstein, M; Schwartz, Z

    2005-04-01

    The diagnosis of localized aggressive periodontitis includes first molar attachment loss as an obligatory criterion. This tooth-specific based diagnosis has never been questioned or tested previously. We present a rare case of aggressive periodontitis that developed during orthodontic treatment, which included extraction of right lower first molar and bodily movement of the second molar to the original first molar site. At the end of the orthodontic therapy, localized periodontal disease was diagnosed at the site of the lower left first molar and the second lower right molar that was now occupying the site of the former first lower molar. The patient's periodontal condition was stabilized, and the bony defects were filled following periodontal treatment. This report shows that bacterial induced aggressive periodontitis developed during orthodontic treatment in a site-specific manner and suggest the hypothesis that localized aggressive periodontitis was targeted to a specific alveolar site rather than a tooth-specific site.

  11. Site-specific labeling of proteins with NMR-active unnatural amino acids

    International Nuclear Information System (INIS)

    Jones, David H.; Cellitti, Susan E.; Hao Xueshi; Zhang Qiong; Jahnz, Michael; Summerer, Daniel; Schultz, Peter G.; Uno, Tetsuo; Geierstanger, Bernhard H.

    2010-01-01

    A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

  12. Tyrosinase-catalyzed site-specific immobilization of engineered C-phycocyanin to surface

    Science.gov (United States)

    Faccio, Greta; Kämpf, Michael M.; Piatti, Chiara; Thöny-Meyer, Linda; Richter, Michael

    2014-06-01

    Enzymatic crosslinking of proteins is often limited by the steric availability of the target residues, as of tyrosyl side chains in the case of tyrosinase. Carrying an N-terminal peptide-tag containing two tyrosine residues, the fluorescent protein C-phycocyanin HisCPC from Synechocystis sp. PCC6803 was crosslinked to fluorescent high-molecular weight forms with tyrosinase. Crosslinking with tyrosinase in the presence of L-tyrosine produced non fluorescent high-molecular weight products. Incubated in the presence of tyrosinase, HisCPC could also be immobilized to amino-modified polystyrene beads thus conferring a blue fluorescence. Crosslinking and immobilization were site-specific as both processes required the presence of the N-terminal peptide in HisCPC.

  13. Precision farming - Technology assessment of site-specific input application in cereals

    DEFF Research Database (Denmark)

    Pedersen, Søren Marcus

    economic and socio-economic analysis. The current status of precision farming in Denmark is as follows: • The technology is primarily applicable for large farm holdings • Economic viability depends on site-specific yield variation • So far, the business economic benefits from most PF-practices are modest...... but it seems possible to obtain a socio-economic benefits from lime, variable rate herbicide and possibly nitrogen application • The technology may improve farm logistics, planning and crop quality (e.g. protein content) - but • The costs of implementing PF-practices are high and • Technical functionality...... several years before the next generation of precision farming systems will be available in practice. Meanwhile, those farmers who already have invested in yield monitors and soil analysis for precision farming should be able to use the current technology in the best possible way....

  14. Site-specific analysis of the cobbly soils at the Grand Junction processing site

    International Nuclear Information System (INIS)

    1992-06-01

    This report describes a recent site-specific analysis to evaluate the necessity of a recommendation to install a slurry trench around the Grand Junction processing site. The following analysis addresses the cobbly nature of the site's radiologically contaminated foundation soil, reassesses the excavation depths based on bulk radionuclide concentrations, and presents data-based arguments that support the elimination of the initially proposed slurry trench. The slurry trench around the processing site was proposed by the Remedial Action Contractor (RAC) to minimize the amount of water encountered during excavation. The initial depths of excavation developed during conceptual design, which indicated the need for a slurry wall, were reexamined as part of this analysis. This reanalysis, based on bulk concentrations of a cobbly subsoil, supports decreasing the original excavation depth, limiting the dewatering quantities to those which can be dissipated by normal construction activities. This eliminates the need for a slurry trench andseparate water treatment prior to permitted discharge

  15. Site-specific programming of the host epithelial transcriptome by the gut microbiota

    DEFF Research Database (Denmark)

    Sommer, Felix; Nookaew, Intawat; Sommer, Nina

    2015-01-01

    BACKGROUND: The intestinal epithelium separates us from the microbiota but also interacts with it and thus affects host immune status and physiology. Previous studies investigated microbiota-induced responses in the gut using intact tissues or unfractionated epithelial cells, thereby limiting....... The microbial impact on host gene expression was highly site specific, as epithelial responses to the microbiota differed between cell fractions. Specific transcriptional regulators were enriched in each fraction. In general, the gut microbiota induced a more rapid response in the colon than in the ileum...... conclusions about regional differences in the epithelium. Here, we sought to investigate microbiota-induced transcriptional responses in specific fractions of intestinal epithelial cells. To this end, we used microarray analysis of laser capture microdissection (LCM)-harvested ileal and colonic tip and crypt...

  16. A site-specific curated database for the microorganisms of activated sludge and anaerobic digesters

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca

    taxonomy, proposes putative names for each genus-level-taxon that can be used as a common vocabulary for all researchers in the field. The online database covers >250 genera found to be abundant and/or important in biological nutrient removal treatment plants, based on extensive in-house surveys with 16S r......) presented here provides a site specific curated taxonomy for abundant and important microorganisms and integrates it into a community knowledge web platform about the microbes in activated sludge (AS) and their associated ADs (www.midasfieldguide.org). The MiDAS taxonomy, a manual curation of the SILVA......RNA gene amplicon sequencing (V1-3 region), including full-scale AS (20 plants, 8 years) and AD systems (36 reactors, 18 plants, 4 years). Surveys also include the Archaea (V3-5 region). The MiDAS field guide is intended as a collaborative platform for researchers and wastewater treatment practitioners...

  17. Testing the atmospheric dispersion model of CSA N288.1 with site-specific data

    CERN Document Server

    Chouhan, S L

    2001-01-01

    The atmospheric dispersion component of CSA Standard N288. 1, which provides guidelines for calculating derived release limits, has been tested. Long-term average concentrations of tritium in air were predicted using site-specific release rates and meteorological data and compared with measured concentrations at 43 monitoring sites at all CANDU stations in Canada. The predictions correlate well with the observations but were found to be conservative, overestimating by about 50% on average. The model overpredicted 84% of the time, with the highest prediction lying a factor of 5.5 above the corresponding observation. The model underpredicted the remaining 16% of the time, with the lowest prediction about one-half of the corresponding measurement. Possible explanations for this bias are discussed but no single reason appears capable of accounting for the discrepancy. Rather, the tendency to overprediction seems to result from the cumulative effects of a number of small conservatisms in the model. The model predi...

  18. Site-specific local structure of Mn in artificial manganese ferrite films

    International Nuclear Information System (INIS)

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Harris, V. G.; Zuo, X.

    2006-01-01

    Diffraction anomalous fine structure (DAFS) spectroscopy has been applied to resolve site-specific Mn local structure in manganese ferrite films grown under nonequilibrium conditions. The DAFS spectra were measured at a number of Bragg reflections in the vicinity of the Mn absorption K edge. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around crystallographically inequivalent Mn sites in the unit cell with nominal octahedral and tetrahedral coordination. The strong preference for Mn to be tetrahedrally coordinated in this compound is not only manifested in the relative site occupancies but also in a strong reduction in coordination number for Mn ions at nominal octahedral sites

  19. Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases

    Directory of Open Access Journals (Sweden)

    Hiroshi Ochiai

    2015-09-01

    Full Text Available Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs associated with human diseases or phenotypes. However, causal relationships between most SNPs and the associated disease have not been established, owing to technical challenges such as unavailability of suitable cell lines. Recently, efficient editing of a single base pair in the genome was achieved using programmable site-specific nucleases. This technique enables experimental confirmation of the causality between SNPs and disease, and is potentially valuable in clinical applications. In this review, I introduce the molecular basis and describe examples of single-base pair editing in human cells. I also discuss the challenges associated with the technique, as well as possible solutions.

  20. Delivery methods for site-specific nucleases: Achieving the full potential of therapeutic gene editing.

    Science.gov (United States)

    Liu, Jia; Shui, Sai-Lan

    2016-12-28

    The advent of site-specific nucleases, particularly CRISPR/Cas9, provides researchers with the unprecedented ability to manipulate genomic sequences. These nucleases are used to create model cell lines, engineer metabolic pathways, produce transgenic animals and plants, perform genome-wide functional screen and, most importantly, treat human diseases that are difficult to tackle by traditional medications. Considerable efforts have been devoted to improving the efficiency and specificity of nucleases for clinical applications. However, safe and efficient delivery methods remain the major obstacle for therapeutic gene editing. In this review, we summarize the recent progress on nuclease delivery methods, highlight their impact on the outcomes of gene editing and discuss the potential of different delivery approaches for therapeutic gene editing. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. On the validity of evolutionary models with site-specific parameters.

    Directory of Open Access Journals (Sweden)

    Konrad Scheffler

    Full Text Available Evolutionary models that make use of site-specific parameters have recently been criticized on the grounds that parameter estimates obtained under such models can be unreliable and lack theoretical guarantees of convergence. We present a simulation study providing empirical evidence that a simple version of the models in question does exhibit sensible convergence behavior and that additional taxa, despite not being independent of each other, lead to improved parameter estimates. Although it would be desirable to have theoretical guarantees of this, we argue that such guarantees would not be sufficient to justify the use of these models in practice. Instead, we emphasize the importance of taking the variance of parameter estimates into account rather than blindly trusting point estimates - this is standardly done by using the models to construct statistical hypothesis tests, which are then validated empirically via simulation studies.

  2. Y-12 site-specific earthquake response analysis and soil liquefaction assessment

    International Nuclear Information System (INIS)

    Ahmed, S.B.; Hunt, R.J.; Manrod, W.E. III.

    1995-01-01

    A site-specific earthquake response analysis and soil liquefaction assessment were performed for the Oak Ridge Y-12 Plant. The main purpose of these studies was to use the results of the analyses for evaluating the safety of the performance category -1, -2, and -3 facilities against the natural phenomena seismic hazards. Earthquake response was determined for seven (7), one dimensional soil columns (Fig. 12) using two horizontal components of the PC-3 design basis 2000-year seismic event. The computer program SHAKE 91 (Ref. 7) was used to calculate the absolute response accelerations on top of ground (soil/weathered shale) and rock outcrop. The SHAKE program has been validated for horizontal response calculations at periods less than 2.0 second at several sites and consequently is widely accepted in the geotechnical earthquake engineering area for site response analysis

  3. Highly Efficient Site-Specific Mutagenesis in Malaria Mosquitoes Using CRISPR

    Directory of Open Access Journals (Sweden)

    Ming Li

    2018-02-01

    Full Text Available Anopheles mosquitoes transmit at least 200 million annual malaria infections worldwide. Despite considerable genomic resources, mechanistic understanding of biological processes in Anopheles has been hampered by a lack of tools for reverse genetics. Here, we report successful application of the CRISPR/Cas9 system for highly efficient, site-specific mutagenesis in the diverse malaria vectors Anopheles albimanus, A. coluzzii, and A. funestus. When guide RNAs (gRNAs and Cas9 protein are injected at high concentration, germline mutations are common and usually biallelic, allowing for the rapid creation of stable mutant lines for reverse genetic analysis. Our protocol should enable researchers to dissect the molecular and cellular basis of anopheline traits critical to successful disease transmission, potentially exposing new targets for malaria control.

  4. Selection of site specific vibration equation by using analytic hierarchy process in a quarry

    International Nuclear Information System (INIS)

    Kalayci, Ulku; Ozer, Umit

    2016-01-01

    This paper presents a new approach for the selection of the most accurate SSVA (Site Specific Vibration Attenuation) equation for blasting processes in a quarry located near settlements in Istanbul, Turkey. In this context, the SSVA equations obtained from the same study area in the literature were considered in terms of distance between the shot points and buildings and the amount of explosive charge. In this purpose, 11 different SSVA equations obtained from the study area in the past 12 years, forecasting capabilities according to designated new conditions, using 102 vibration records as test data obtained from the study area was investigated. In this study, AHP (Analytic Hierarchy Process) was selected as an analysis method in order to determine the most accurate equation among 11 SSAV equations, and the parameters such as year, distance, charge, and r 2 of the equations were used as criteria for AHP. Finally, the most appropriate equation was selected among the existing ones, and the process of selecting according to different target criteria was presented. Furthermore, it was noted that the forecasting results of the selected equation is more accurate than that formed using the test results. - Highlights: • The optimum Site Specific Vibration Attenuation equation for blasting in a quarry located near settlements was determined. • It is indicated that SSVA equations changing over the years don’t give always accurate estimates at changing conditions. • Selection of the blast induced SSVA equation was made using AHP. • Equation selection method was highlighted based on parameters such as charge, distance, and quarry geometry changes (year).

  5. phiC31 integrase-mediated site-specific recombination in barley.

    Directory of Open Access Journals (Sweden)

    Eszter Kapusi

    Full Text Available The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP, which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F(1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity.

  6. Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins.

    Science.gov (United States)

    Steffen, Wojtek; Ko, Fu Chong; Patel, Jigar; Lyamichev, Victor; Albert, Thomas J; Benz, Jörg; Rudolph, Markus G; Bergmann, Frank; Streidl, Thomas; Kratzsch, Peter; Boenitz-Dulat, Mara; Oelschlaegel, Tobias; Schraeml, Michael

    2017-09-22

    Microbial transglutaminases (MTGs) catalyze the formation of Gln-Lys isopeptide bonds and are widely used for the cross-linking of proteins and peptides in food and biotechnological applications ( e.g. to improve the texture of protein-rich foods or in generating antibody-drug conjugates). Currently used MTGs have low substrate specificity, impeding their biotechnological use as enzymes that do not cross-react with nontarget substrates ( i.e. as bio-orthogonal labeling systems). Here, we report the discovery of an MTG from Kutzneria albida (KalbTG), which exhibited no cross-reactivity with known MTG substrates or commonly used target proteins, such as antibodies. KalbTG was produced in Escherichia coli as soluble and active enzyme in the presence of its natural inhibitor ammonium to prevent potentially toxic cross-linking activity. The crystal structure of KalbTG revealed a conserved core similar to other MTGs but very short surface loops, making it the smallest MTG characterized to date. Ultra-dense peptide array technology involving a pool of 1.4 million unique peptides identified specific recognition motifs for KalbTG in these peptides. We determined that the motifs YRYRQ and RYESK are the best Gln and Lys substrates of KalbTG, respectively. By first reacting a bifunctionalized peptide with the more specific KalbTG and in a second step with the less specific MTG from Streptomyces mobaraensis , a successful bio-orthogonal labeling system was demonstrated. Fusing the KalbTG recognition motif to an antibody allowed for site-specific and ratio-controlled labeling using low label excess. Its site specificity, favorable kinetics, ease of use, and cost-effective production render KalbTG an attractive tool for a broad range of applications, including production of therapeutic antibody-drug conjugates. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Site-Specific Difference of Bone Geometry Indices in Hypoparathyroid Patients

    Directory of Open Access Journals (Sweden)

    Hye-Sun Park

    2017-02-01

    Full Text Available BackgroundHypoparathyroid patients often have a higher bone mineral density (BMD than the general population. However, an increase in BMD does not necessarily correlate with a solid bone microstructure. This study aimed to evaluate the bone microstructure of hypoparathyroid patients by using hip structure analysis (HSA.MethodsNinety-five hypoparathyroid patients >20 years old were enrolled and 31 of them had eligible data for analyzing bone geometry parameters using HSA. And among the control data, we extracted sex-, age-, and body mass index-matched three control subjects to each patient. The BMD data were reviewed retrospectively and the bone geometry parameters of the patients were analyzed by HSA.ResultsThe mean Z-scores of hypoparathyroid patients at the lumbar spine, femoral neck, and total hip were above zero (0.63±1.17, 0.48±1.13, and 0.62±1.10, respectively. The differences in bone geometric parameters were site specific. At the femoral neck and intertrochanter, the cross-sectional area (CSA and cortical thickness (C.th were higher, whereas the buckling ratio (BR was lower than in controls. However, those trends were opposite at the femoral shaft; that is, the CSA and C.th were low and the BR was high.ConclusionOur study shows the site-specific effects of hypoparathyroidism on the bone. Differences in bone components, marrow composition, or modeling based bone formation may explain these findings. However, further studies are warranted to investigate the mechanism, and its relation to fracture risk.

  8. Monocytic myeloid-derived suppressor cells as prognostic factor in chronic myeloid leukaemia patients treated with dasatinib.

    Science.gov (United States)

    Giallongo, Cesarina; Parrinello, Nunziatina L; La Cava, Piera; Camiolo, Giuseppina; Romano, Alessandra; Scalia, Marina; Stagno, Fabio; Palumbo, Giuseppe A; Avola, Roberto; Li Volti, Giovanni; Tibullo, Daniele; Di Raimondo, Francesco

    2018-02-01

    Myeloid suppressor cells are a heterogeneous group of myeloid cells that are increased in patients with chronic myeloid leukaemia (CML) inducing T cell tolerance. In this study, we found that therapy with tyrosine kinase inhibitors (TKI) decreased the percentage of granulocytic MDSC, but only patients treated with dasatinib showed a significant reduction in the monocytic subset (M-MDSC). Moreover, a positive correlation was observed between number of persistent M-MDSC and the value of major molecular response in dasatinib-treated patients. Serum and exosomes from patients with CML induced conversion of monocytes from healthy volunteers into immunosuppressive M-MDSC, suggesting a bidirectional crosstalk between CML cells and MDSC. Overall, we identified M-MDSC as prognostic factors in patients treated with dasatinib. It might be of interest to understand whether MDSC may be a candidate predictive markers of relapse risk following TKI discontinuation, suggesting their potential significance as practice of precision medicine. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  9. Annotated Administrative Record Site-Specific Document Index, American Drum & Pallet Co. Removal Site, Memphis, Shelby County, Tennessee

    Science.gov (United States)

    Contains annotated index of site specific documents for the American Drum & Pallet Co. Removal Site in Memphis, Shelby County, Tennessee, January 9, 2008 Region ID: 04 DocID: 10517016, DocDate: 01-09-2008

  10. Fluorine-labeled Dasatinib Nanoformulations as Targeted Molecular Imaging Probes in a PDGFB-driven Murine Glioblastoma Model

    Directory of Open Access Journals (Sweden)

    Miriam Benezra

    2012-12-01

    Full Text Available Dasatinib, a new-generation Src and platelet-derived growth factor receptor (PDGFR inhibitor, is currently under evaluation in high-grade glioma clinical trials. To achieve optimum physicochemical and/or biologic properties, alternative drug delivery vehicles may be needed. We used a novel fluorinated dasatinib derivative (F-SKI249380, in combination with nanocarrier vehicles and metabolic imaging tools (microPET to evaluate drug delivery and uptake in a platelet-derived growth factor B (PDGFB-driven genetically engineered mouse model (GEMM of high-grade glioma. We assessed dasatinib survival benefit on the basis of measured tumor volumes. Using brain tumor cells derived from PDGFB-driven gliomas, dose-dependent uptake and time-dependent inhibitory effects of F-SKI249380 on biologic activity were investigated and compared with the parent drug. PDGFR receptor status and tumor-specific targeting were non-invasively evaluated in vivo using 18F-SKI249380 and 18F-SKI249380-containing micellar and liposomal nanoformulations. A statistically significant survival benefit was found using dasatinib (95 mg/kg versus saline vehicle (P < .001 in tumor volume-matched GEMM pairs. Competitive binding and treatment assays revealed comparable biologic properties for F-SKI249380 and the parent drug. In vivo, Significantly higher tumor uptake was observed for 18F-SKI249380-containing micelle formulations [4.9 percentage of the injected dose per gram tissue (%ID/g; P = .002] compared to control values (1.6%ID/g. Saturation studies using excess cold dasatinib showed marked reduction of tumor uptake values to levels in normal brain (1.5%ID/g, consistent with in vivo binding specificity. Using 18F-SKI249380-containing micelles as radiotracers to estimate therapeutic dosing requirements, we calculated intratumoral drug concentrations (24–60 nM that were comparable to in vitro 50% inhibitory concentration values. 18F-SKI249380 is a PDGFR-selective tracer, which

  11. Scalp simulation - A novel approach to site-specific biomechanical modeling of the skin.

    Science.gov (United States)

    Pittar, N; Winter, T; Falland-Cheung, L; Tong, D; Waddell, J N

    2018-01-01

    This study aimed to determine the hardness of the human scalp in vivo in order to identify an appropriate scalp simulant, from a range of commercially available silicone materials, for force impact assessment. Site-dependent variation in scalp hardness, and the applicability of contemporary skin simulants to the scalp were also considered. A Shore A-type durometer was used to collected hardness data from the scalps of 30 human participants (five males and five females in each of the three age categories: 18-30, 31-40, 41-50) and four commercially available silicones (light, medium, and heavy-bodied PVS, and duplication silicone). One-sample t-tests were used to compare the mean hardness of simulants to that of the scalp. Site-dependent variation in the hardness of the scalp was assessed using a mixed-model repeated measures ANOVA. Mean human scalp hardness derived from participants was 20.6 Durometer Units (DU; SD = 3.4). Analysis revealed only the medium-bodied PVS to be an acceptable scalp simulant when compared to the mean hardness of the human scalp (p = 0.869). Scalp hardness varied significantly anteroposteriorly (with an observable linear trend, p < 0.001), but not mediolaterally (p = 0.271). Comparisons of simulants to site-specific variation in scalp hardness anteroposteriorly found the medium-bodied PVS to be only suitable in the central region of the scalp (p = 0.391). In contrast, the duplication silicone (p = 0.074) and light-bodied PVS (p = 0.147) were only comparable to the posterior region. Contemporary skin simulants fail to accurately represent the scalp in terms of hardness. There is strong support for the use of medium-bodied PVS as a scalp simulant. Human scalp hardness varies significantly anteroposteriorly, but not mediolaterally, corresponding to regional anatomical variation within the scalp. A number of materials were identified as potential simulants for different regions of the scalp when more site-specific simulant research is required

  12. Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins.

    Science.gov (United States)

    Hoffmann, Marcus; Marx, Kristina; Reichl, Udo; Wuhrer, Manfred; Rapp, Erdmann

    2016-02-01

    Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from low-energy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono- and disialylated core-1

  13. Environmental Management Waste Management Facility (EMWMF) Site-Specific Health and Safety Plan, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, N.C. Bechtel Jacobs

    2008-04-21

    The Bechtel Jacobs Company LLC (BJC) policy is to provide a safe and healthy workplace for all employees and subcontractors. The implementation of this policy requires that operations of the Environmental Management Waste Management Facility (EMWMF), located one-half mile west of the U.S. Department of Energy (DOE) Y-12 National Security Complex, be guided by an overall plan and consistent proactive approach to environment, safety and health (ES&H) issues. The BJC governing document for worker safety and health, BJC/OR-1745, 'Worker Safety and Health Program', describes the key elements of the BJC Safety and Industrial Hygiene (IH) programs, which includes the requirement for development and implementation of a site-specific Health and Safety Plan (HASP) where required by regulation (refer also to BJC-EH-1012, 'Development and Approval of Safety and Health Plans'). BJC/OR-1745, 'Worker Safety and Health Program', implements the requirements for worker protection contained in Title 10 Code of Federal Regulations (CFR) Part 851. The EMWMF site-specific HASP requirements identifies safe operating procedures, work controls, personal protective equipment, roles and responsibilities, potential site hazards and control measures, site access requirements, frequency and types of monitoring, site work areas, decontamination procedures, and outlines emergency response actions. This HASP will be available on site for use by all workers, management and supervisors, oversight personnel and visitors. All EMWMF assigned personnel will be briefed on the contents of this HASP and will be required to follow the procedures and protocols as specified. The policies and procedures referenced in this HASP apply to all EMWMF operations activities. In addition the HASP establishes ES&H criteria for the day-to-day activities to prevent or minimize any adverse effect on the environment and personnel safety and health and to meet standards that define acceptable

  14. Inhibition of Src kinase activity attenuates amyloid associated microgliosis in a murine model of Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Dhawan Gunjan

    2012-07-01

    Full Text Available Abstract Background Microglial activation is an important histologic characteristic of the pathology of Alzheimer’s disease (AD. One hypothesis is that amyloid beta (Aβ peptide serves as a specific stimulus for tyrosine kinase-based microglial activation leading to pro-inflammatory changes that contribute to disease. Therefore, inhibiting Aβ stimulation of microglia may prove to be an important therapeutic strategy for AD. Methods Primary murine microglia cultures and the murine microglia cell line, BV2, were used for stimulation with fibrillar Aβ1-42. The non-receptor tyrosine kinase inhibitor, dasatinib, was used to treat the cells to determine whether Src family kinase activity was required for the Aβ stimulated signaling response and subsequent increase in TNFα secretion using Western blot analysis and enzyme-linked immunosorbent assay (ELISA, respectively. A histologic longitudinal analysis was performed using an AD transgenic mouse model, APP/PS1, to determine an age at which microglial protein tyrosine kinase levels increased in order to administer dasatinib via mini osmotic pump diffusion. Effects of dasatinib administration on microglial and astroglial activation, protein phosphotyrosine levels, active Src kinase levels, Aβ plaque deposition, and spatial working memory were assessed via immunohistochemistry, Western blot, and T maze analysis. Results Aβ fibrils stimulated primary murine microglia via a tyrosine kinase pathway involving Src kinase that was attenuated by dasatinib. Dasatinib administration to APP/PS1 mice decreased protein phosphotyrosine, active Src, reactive microglia, and TNFα levels in the hippocampus and temporal cortex. The drug had no effect on GFAP levels, Aβ plaque load, or the related tyrosine kinase, Lyn. These anti-inflammatory changes correlated with improved performance on the T maze test in dasatinib infused animals compared to control animals. Conclusions These data suggest that amyloid

  15. Conservative site-specific and single-copy transgenesis in human LINE-1 elements.

    Science.gov (United States)

    Vijaya Chandra, Shree Harsha; Makhija, Harshyaa; Peter, Sabrina; Myint Wai, Cho Mar; Li, Jinming; Zhu, Jindong; Ren, Zhonglu; D'Alcontres, Martina Stagno; Siau, Jia Wei; Chee, Sharon; Ghadessy, Farid John; Dröge, Peter

    2016-04-07

    Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, term edattH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Site Specific Effect of Tobacco Addiction in Upper Aerodigestive Tract Tumors: A Retrospective Clinicopathological Study

    Directory of Open Access Journals (Sweden)

    Ashok Kumar

    2014-01-01

    Full Text Available An institutional study was carried out in 102 patients to investigate the site specific effect of addictions, that is, tobacco smoking and tobacco chewing (smokeless, both independently and synergistically in development of malignancies in upper aerodigestive tract through retrograde questionnaire. The histopathologically proven cases were interviewed regarding different forms of addictions followed by clinical examination and investigations for grading (according to Modified Broadmann’s method and TNM staging (according to UICC according to the tumor site. Statistical analysis was done by Pearson test. Out of all proven cases of cancers, 29.4% were only tobacco chewers (smokeless, 25.5% were only smokers, 42.2% were having both types of tobacco addictions (smoke and smokeless, and only 2.9% were having no addiction. Out of only tobacco chewers (smokeless, 83.3% were of oral cavity cancers, 6.7% were of oro- and hypopharynx and the rest were of others. Among only smokers, 69.2% cases were of laryngeal and oro- and hypopharynx as compared to 11.5% of oral cavity cancers (nearly 6 times. Tobacco (smokeless chewing is associated with oral cancers whereas tobacco smoking is associated with laryngeal and hypopharyngeal carcinoma. Both smoking and smokeless tobacco act in synergy with each other.

  17. Magnetic norbornene polymer as multiresponsive nanocarrier for site specific cancer therapy.

    Science.gov (United States)

    Rao N, Vijayakameswara; Ganivada, Mutyala Naidu; Sarkar, Santu; Dinda, Himadri; Chatterjee, Koushik; Dalui, Tanmoy; Das Sarma, Jayasri; Shunmugam, Raja

    2014-02-19

    A site-specific, stimuli-responsive nanocarrier has been synthesized by conjugating folate, magnetic particles and doxorubicin to the backbone of norbornene polymer. Monomers, namely, cis-5-norbornene-6-(diethoxyphosphoryl)hexanote (mono 1), norbornene grafted poly(ethyleneglycol)-folate (mono 2), and norbornene derived doxorubicin (mono 3) are carefully designed to demonstrate the smart nanorcarrier capabilities. The synthesis and complete characterization of all three monomers are elaborately discussed. Their copolymerization is done by controlled/living ring-opening metathesis polymerization (ROMP) to get the triblock copolymer PHOS-FOL-DOX. NMR spectroscopy and gel permeation chromatography confirm the formation of the triblock copolymer, while FT-IR spectroscopy, thermogravimetric analysis, along with transmission electron microscope confirm the anchoring of iron particle (Fe3O4) to the PHOS-FOL-DOX. Drug release profile shows the importance of having the hydrazone linker that helps to release the drug exactly at the mild acidic conditions resembling the pH of the cancerous cells. The newly designed nanocarrier shows greater internalization (about 8 times) due to magnetic field. Also, increased intracellular DOX release is observed due to the folate receptor. From these results, it is clear that PHOS-FOL-DOX has the potential to act as a smart nanoreservoir with the magnetic field guidance, folate receptor targeting, and finally pH stimulation.

  18. A Site-Specific Index Based on Weathering Forms Visible in Central Oxford, UK

    Directory of Open Access Journals (Sweden)

    Mary J. Thornbush

    2012-11-01

    Full Text Available The authenticity of much of the stone-work along Queen’s Lane in central Oxford, UK presented an opportunity to produce a photographic survey from which a weathering index could be established. This represents a site-specific approach to devising a weathering form. Because it is photo-based, weathering forms are visible for comparison and classification purposes across disciplines. Limestone pertaining to building ashlar and plinths along this roadway, which mainly belong to Queen’s College, St Edmund Hall, New College, and Hertford College, was classified according to this newly introduced weathering index, the size-extent (S-E index, through consideration of type, size, extent, impact, and trigger. This size- (range and extent-based classification system enables for the assessment of weathering forms of various types, including soiling and decay features as well as those potentially expected in the presence of vegetation and animals. Weathering forms of a range of sizes were present, with a slightly greater abundance of small types (mm-cm in the micro- to mesoscale and more discrete types with a low extent. For this location in central Oxford, chemical weathering was found to be the predominant type of soiling and decay.

  19. Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase.

    Science.gov (United States)

    Nkrumah, Louis J; Muhle, Rebecca A; Moura, Pedro A; Ghosh, Pallavi; Hatfull, Graham F; Jacobs, William R; Fidock, David A

    2006-08-01

    Here we report an efficient, site-specific system of genetic integration into Plasmodium falciparum malaria parasite chromosomes. This is mediated by mycobacteriophage Bxb1 integrase, which catalyzes recombination between an incoming attP and a chromosomal attB site. We developed P. falciparum lines with the attB site integrated into the glutaredoxin-like cg6 gene. Transfection of these attB(+) lines with a dual-plasmid system, expressing a transgene on an attP-containing plasmid together with a drug resistance gene and the integrase on a separate plasmid, produced recombinant parasites within 2 to 4 weeks that were genetically uniform for single-copy plasmid integration. Integrase-mediated recombination resulted in proper targeting of parasite proteins to intra-erythrocytic compartments, including the apicoplast, a plastid-like organelle. Recombinant attB x attP parasites were genetically stable in the absence of drug and were phenotypically homogeneous. This system can be exploited for rapid genetic integration and complementation analyses at any stage of the P. falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms.

  20. Development of a novel DDS for site-specific PEGylated proteins

    Directory of Open Access Journals (Sweden)

    Yoshioka Yasuo

    2011-05-01

    Full Text Available Abstract Because of the shifted focus in life science research from genome analyses to genetic and protein function analyses, we now know functions of numerous proteins. These analyses, including those of newly identified proteins, are expected to contribute to the identification of proteins of therapeutic value in various diseases. Consequently, pharmacoproteomic-based drug discovery and development of protein therapies attracted a great deal of attention in recent years. Clinical applications of most of these proteins are, however, limited because of their unexpectedly low therapeutic effects, resulting from the proteolytic degradation in vivo followed by rapid removal from the circulatory system. Therefore, frequent administration of excessively high dose of a protein is required to observe its therapeutic effect in vivo. This often results in impaired homeostasis in vivo and leads to severe adverse effects. To overcome these problems, we have devised a method for chemical modification of proteins with polyethylene glycol (PEGylation and other water-soluble polymers. In addition, we have established a method for creating functional mutant proteins (muteins with desired properties, and developed a site-specific polymer-conjugation method to further improve their therapeutic potency. In this review, we are introducing our original protein-drug innovation system mentioned above.

  1. Sex- and Site-Specific Normative Data Curves for HR-pQCT.

    Science.gov (United States)

    Burt, Lauren A; Liang, Zhiying; Sajobi, Tolulope T; Hanley, David A; Boyd, Steven K

    2016-11-01

    The purpose of this study was to develop age-, site-, and sex-specific centile curves for common high-resolution peripheral quantitative computed tomography (HR-pQCT) and finite-element (FE) parameters for males and females older than 16 years. Participants (n = 866) from the Calgary cohort of the Canadian Multicentre Osteoporosis Study (CaMos) between the ages of 16 and 98 years were included in this study. Participants' nondominant radius and left tibia were scanned using HR-pQCT. Standard and automated segmentation methods were performed and FE analysis estimated apparent bone strength. Centile curves were generated for males and females at the tibia and radius using the generalized additive models for location, scale, and shape (GAMLSS) package in R. After GAMLSS analysis, age-, sex-, and site-specific centiles (10th, 25th, 50th, 75th, 90th) for total bone mineral density and trabecular number as well as failure load have been calculated. Clinicians and researchers can use these reference curves as a tool to assess bone health and changes in bone quality. © 2016 American Society for Bone and Mineral Research. © 2016 American Society for Bone and Mineral Research.

  2. Design of a soil cutting resistance sensor for application in site-specific tillage.

    Science.gov (United States)

    Agüera, Juan; Carballido, Jacob; Gil, Jesús; Gliever, Chris J; Perez-Ruiz, Manuel

    2013-05-10

    One objective of precision agriculture is to provide accurate information about soil and crop properties to optimize the management of agricultural inputs to meet site-specific needs. This paper describes the development of a sensor equipped with RTK-GPS technology that continuously and efficiently measures soil cutting resistance at various depths while traversing the field. Laboratory and preliminary field tests verified the accuracy of this prototype soil strength sensor. The data obtained using a hand-operated soil cone penetrometer was used to evaluate this field soil compaction depth profile sensor. To date, this sensor has only been tested in one field under one gravimetric water content condition. This field test revealed that the relationships between the soil strength profile sensor (SSPS) cutting force and soil cone index values are assumed to be quadratic for the various depths considered: 0-10, 10-20 and 20-30 cm (r2 = 0.58, 0.45 and 0.54, respectively). Soil resistance contour maps illustrated its practical value. The developed sensor provides accurate, timely and affordable information on soil properties to optimize resources and improve agricultural economy.

  3. Hanford Integrated Planning Process: 1993 Hanford Site-specific science and technology plan

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-01

    This document is the FY 1993 report on Hanford Site-specific science and technology (S&T) needs for cleanup of the Site as developed via the Hanford Integrated Planning Process (HIPP). It identifies cleanup problems that lack demonstrated technology solutions and technologies that require additional development. Recommendations are provided regarding allocation of funding to address Hanford`s highest-priority technology improvement needs, technology development needs, and scientific research needs, all compiled from a Sitewide perspective. In the past, the S&T agenda for Hanford Site cleanup was sometimes driven by scientists and technologists, with minimal input from the ``problem owners`` (i.e., Westinghouse Hanford Company [WHC] staff who are responsible for cleanup activities). At other times, the problem-owners made decisions to proceed with cleanup without adequate scientific and technological inputs. Under both of these scenarios, there was no significant stakeholder involvement in the decision-making process. One of the key objectives of HIPP is to develop an understanding of the integrated S&T requirements to support the cleanup mission, (a) as defined by the needs of the problem owners, the values of the stakeholders, and the technology development expertise that exists at Hanford and elsewhere. This requires a periodic, systematic assessment of these needs and values to appropriately define a comprehensive technology development program and a complementary scientific research program. Basic to our success is a methodology that is defensible from a technical perspective and acceptable to the stakeholders.

  4. Occupational radiation dose assessment for a non site specific spent fuel storage facility

    International Nuclear Information System (INIS)

    Hadley, J.; Eble, R.G. Jr.

    1997-01-01

    To expedite the licensing process of the non site specific Centralized Interim Storage Facility (CISF) the Department of Energy has completed a phase I CISF Topical Safety Analysis Report (TSAR). The TSAR will be used in licensing the phase I CISF if a site is designated. An occupational radiation does assessment of the facility operations is performed as part of the phase I CISF design. The first phase of the CISF has the capability to receive, transfer, and store SNF in dual-purpose cask/canister systems (DPC's). Currently there are five vendor technologies under consideration. The preliminary dose assessment is based on estimated occupational exposures using traditional power plant ISFSI and transport cask handling processes. The second step in the process is to recommend ALARA techniques to reduce potential exposures. A final dose assessment is completed implementing the ALARA techniques and a review is performed to ensure that the design is in compliance with regulatory criteria. The dose assessment and ALARA evaluation are determined using the following input information: Dose estimates from vendor SAR's; ISFSI experience with similar systems; Traditional methods of operations; Expected CISF cask receipt rates; and feasible ALARA techniques. 5 refs., 1 tab

  5. Autoantibodies to myelin basic protein catalyze site-specific degradation of their antigen.

    Science.gov (United States)

    Ponomarenko, Natalia A; Durova, Oxana M; Vorobiev, Ivan I; Belogurov, Alexey A; Kurkova, Inna N; Petrenko, Alexander G; Telegin, Georgy B; Suchkov, Sergey V; Kiselev, Sergey L; Lagarkova, Maria A; Govorun, Vadim M; Serebryakova, Marina V; Avalle, Bérangère; Tornatore, Pete; Karavanov, Alexander; Morse, Herbert C; Thomas, Daniel; Friboulet, Alain; Gabibov, Alexander G

    2006-01-10

    Autoantibody-mediated tissue destruction is among the main features of organ-specific autoimmunity. This report describes "an antibody enzyme" (abzyme) contribution to the site-specific degradation of a neural antigen. We detected proteolytic activity toward myelin basic protein (MBP) in the fraction of antibodies purified from the sera of humans with multiple sclerosis (MS) and mice with induced experimental allergic encephalomyelitis. Chromatography and zymography data demonstrated that the proteolytic activity of this preparation was exclusively associated with the antibodies. No activity was found in the IgG fraction of healthy donors. The human and murine abzymes efficiently cleaved MBP but not other protein substrates tested. The sites of MBP cleavage determined by mass spectrometry were localized within immunodominant regions of MBP. The abzymes could also cleave recombinant substrates containing encephalytogenic MBP(85-101) peptide. An established MS therapeutic Copaxone appeared to be a specific abzyme inhibitor. Thus, the discovered epitope-specific antibody-mediated degradation of MBP suggests a mechanistic explanation of the slow development of neurodegeneration associated with MS.

  6. Site-Specific Covalent Conjugation of Modified mRNA by tRNA Guanine Transglycosylase.

    Science.gov (United States)

    Ehret, Fabian; Zhou, Cun Yu; Alexander, Seth C; Zhang, Dongyang; Devaraj, Neal K

    2018-03-05

    Modified mRNA (mod-mRNA) has recently been widely studied as the form of RNA useful for therapeutic applications due to its high stability and lowered immune response. Herein, we extend the scope of the recently established RNA-TAG (transglycosylation at guanosine) methodology, a novel approach for genetically encoded site-specific labeling of large mRNA transcripts, by employing mod-mRNA as substrate. As a proof of concept, we covalently attached a fluorescent probe to mCherry encoding mod-mRNA transcripts bearing 5-methylcytidine and/or pseudouridine substitutions with high labeling efficiencies. To provide a versatile labeling methodology with a wide range of possible applications, we employed a two-step strategy for functionalization of the mod-mRNA to highlight the therapeutic potential of this new methodology. We envision that this novel and facile labeling methodology of mod-RNA will have great potential in decorating both coding and noncoding therapeutic RNAs with a variety of diagnostic and functional moieties.

  7. Site-specific gene transfer into the rat spinal cord by photomechanical waves

    Science.gov (United States)

    Ando, Takahiro; Sato, Shunichi; Toyooka, Terushige; Uozumi, Yoichi; Nawashiro, Hiroshi; Ashida, Hiroshi; Obara, Minoru

    2011-10-01

    Nonviral, site-specific gene delivery to deep tissue is required for gene therapy of a spinal cord injury. However, an efficient method satisfying these requirements has not been established. This study demonstrates efficient and targeted gene transfer into the spinal cord by using photomechanical waves (PMWs), which were generated by irradiating a black laser absorbing rubber with 532-nm nanosecond Nd:YAG laser pulses. After a solution of plasmid DNA coding for enhanced green fluorescent protein (EGFP) or luciferase was intraparenchymally injected into the spinal cord, PMWs were applied to the target site. In the PMW application group, we observed significant EGFP gene expression in the white matter and remarkably high luciferase activity only in the spinal cord segment exposed to the PMWs. We also assessed hind limb movements 24 h after the application of PMWs based on the Basso-Beattie-Bresnahan (BBB) score to evaluate the noninvasiveness of this method. Locomotor evaluation showed no significant decrease in BBB score under optimum laser irradiation conditions. These findings demonstrated that exogenous genes can be efficiently and site-selectively delivered into the spinal cord by applying PMWs without significant locomotive damage.

  8. Mud crab ecology encourages site-specific approaches to fishery management

    Science.gov (United States)

    Dumas, P.; Léopold, M.; Frotté, L.; Peignon, C.

    2012-01-01

    Little is known about the effects of mud crabs population patterns on their exploitation. We used complementary approaches (experimental, fisher-based) to investigate how small-scale variations in density, size and sex-ratio related to the ecology of S. serrata may impact fishing practices in New Caledonia. Crabs were measured/sexed across 9 stations in contrasted mangrove systems between 2007 and 2009. Stations were described and classified in different kinds of mangrove forests (coastal, riverine, and estuarine); vegetation cover was qualitatively described at station scale. Annual catch was used as an indicator of fishing pressure. Middle-scale environmental factors (oceanic influence, vegetation cover) had significant contributions to crab density (GLM, 84.8% of variance), crab size and sex-ratio (social implications in the Pacific area, where land tenure system and traditional access rights prevent most fishers from freely selecting their harvest zones. This offers a great opportunity to encourage site-specific management of mud crab fisheries.

  9. Development of a site-specific water quality criterion for hexavalent chromium

    International Nuclear Information System (INIS)

    McIntyre, D.O.; Sticko, J.P.; Reash, R.J.

    1995-01-01

    The effluent of treated fly ash from a coal-fired power plant located on the Ohio River periodically exceeds its NPDES acute permit limit for hexavalent chromium of 15 microg/L. The increased levels of hexavalent chromium in the effluent are a recent occurrence which are likely due to changes in coal blends burned in the generating units. Ohio EPA determined the use designation of the receiving stream (Limited Resource Water) was being attained and a one-year biomonitoring program of the effluent detected no acute toxicity to Ceriodaphnia dubia or Daphnia magna. The water-effect ratio (WER) procedure was selected to develop a site-specific criterion maximum concentration for hexavalent chromium for the effluent's receiving stream. WER procedures followed those described in EPA's ''Interim Guidance on Determination and Use of Water-Effect Ratios for Metals'' (1994). Site water used in the WER determinations was undiluted effluent since the receiving stream originates at the discharge point of the outfall. 48-hour acute D. magna and 96-hour acute fathead minnow toxicity tests were selected as the primary and secondary tests, respectively for use in three seasonal WER determinations. The results of the three WER determinations and the status of the regulatory process will be presented

  10. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

    Directory of Open Access Journals (Sweden)

    James I. McDonald

    2016-06-01

    Full Text Available Advances in sequencing technology allow researchers to map genome-wide changes in DNA methylation in development and disease. However, there is a lack of experimental tools to site-specifically manipulate DNA methylation to discern the functional consequences. We developed a CRISPR/Cas9 DNA methyltransferase 3A (DNMT3A fusion to induce DNA methylation at specific loci in the genome. We induced DNA methylation at up to 50% of alleles for targeted CpG dinucleotides. DNA methylation levels peaked within 50 bp of the short guide RNA (sgRNA binding site and between pairs of sgRNAs. We used our approach to target methylation across the entire CpG island at the CDKN2A promoter, three CpG dinucleotides at the ARF promoter, and the CpG island within the Cdkn1a promoter to decrease expression of the target gene. These tools permit mechanistic studies of DNA methylation and its role in guiding molecular processes that determine cellular fate.

  11. Site specific seismic hazard analysis and determination of response spectra of Kolkata for maximum considered earthquake

    Science.gov (United States)

    Shiuly, Amit; Sahu, R. B.; Mandal, Saroj

    2017-06-01

    This paper presents site specific seismic hazard analysis of Kolkata city, former capital of India and present capital of state West Bengal, situated on the world’s largest delta island, Bengal basin. For this purpose, peak ground acceleration (PGA) for a maximum considered earthquake (MCE) at bedrock level has been estimated using an artificial neural network (ANN) based attenuation relationship developed on the basis of synthetic ground motion data for the region. Using the PGA corresponding to the MCE, a spectrum compatible acceleration time history at bedrock level has been generated by using a wavelet based computer program, WAVEGEN. This spectrum compatible time history at bedrock level has been converted to the same at surface level using SHAKE2000 for 144 borehole locations in the study region. Using the predicted values of PGA and PGV at the surface, corresponding contours for the region have been drawn. For the MCE, the PGA at bedrock level of Kolkata city has been obtained as 0.184 g, while that at the surface level varies from 0.22 g to 0.37 g. Finally, Kolkata has been subdivided into eight seismic subzones, and for each subzone a response spectrum equation has been derived using polynomial regression analysis. This will be very helpful for structural and geotechnical engineers to design safe and economical earthquake resistant structures.

  12. Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase.

    Directory of Open Access Journals (Sweden)

    Tao Liu

    Full Text Available Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 63:28:5, in 77 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation in proteins involved in processes related to rhizobial adaptation was also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis, ActR (pH stress and microaerobic adaption, SupA (potassium stress, chaperonin GroEL2 (viability and potentially symbiosis, and ExoP (succinoglycan synthesis and secretion. These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.

  13. Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

    Science.gov (United States)

    Sibert, Bryan S.; Patton, Jeffrey R.

    2012-01-01

    Pseudouridine synthase 1 (Pus1p) is an unusual site-specific modification enzyme in that it can modify a number of positions in tRNAs and can recognize several other types of RNA. No consensus recognition sequence or structure has been identified for Pus1p. Human Pus1p was used to determine which structural or sequence elements of human tRNASer are necessary for pseudouridine (Ψ) formation at position 28 in the anticodon stem-loop (ASL). Some point mutations in the ASL stem of tRNASer had significant effects on the levels of modification and compensatory mutation, to reform the base pair, restored a wild-type level of Ψ formation. Deletion analysis showed that the tRNASer TΨC stem-loop was a determinant for modification in the ASL. A mini-substrate composed of the ASL and TΨC stem-loop exhibited significant Ψ formation at position 28 and a number of mutants were tested. Substantial base pairing in the ASL stem (3 out of 5 bp) is required, but the sequence of the TΨC loop is not required for modification. When all nucleotides in the ASL stem other than U28 were changed in a single mutant, but base pairing was retained, a near wild-type level of modification was observed. PMID:22102571

  14. Site specific plan. [Environmental Restoration and Waste Management, Savannah River Site

    Energy Technology Data Exchange (ETDEWEB)

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. 8 refs., 46 figs., 23 tabs.

  15. Tino Sehgal, site-specifics performances e as instituições da arte

    Directory of Open Access Journals (Sweden)

    Emerson Dionísio Gomes de Oliveira

    Full Text Available O objetivo deste artigo é debater a produção artística de Tino Sehgal enquanto site-specifics performances produzidas em instituições museológicas convencionais. Para tanto, operamos com as noções de sítio e contexto, tomando o museu como componente da obra, e não sua exterioridade. Dois operadores são observados em nossas reflexões. O primeiro é a ativação do público do museu como participante privilegiado da obra, dentro de uma pedagogia museal singular. O segundo é o controle sobre os registros das obras pelo artista, enquanto parte da ação poética e, simultaneamente, ação política debruçada sobre economias simbólicas complexas, pois coloca em evidência a relação entre obras, artistas, discursos mediadores e o público.

  16. Embracing the emerging precision agriculture technologies for site-specific management of yield-limiting factors.

    Science.gov (United States)

    Melakeberhan, H

    2002-09-01

    Precision agriculture (PA) is providing an information revolution using Global Positioning (GPS) and Geographic Information (GIS) systems and Remote Sensing (RS). These technologies allow better decision making in the management of crop yield-limiting biotic and abiotic factors and their interactions on a site-specific (SSM) basis in a wide range of production systems. Characterizing the nature of the problem(s) and public education are among the challenges that scientists, producers, and industry face when adapting PA technologies. To apply SSM, spatio-temporal characteristics of the problem(s) need to be determined and variations within a field demonstrated. Spatio-temporal characteristics of a given pathogen or pest problem may be known but may not be the only or primary cause of the problem. Hence, exact cause-and-effect relationships need to be established by incorporating GIS, GPS, and RS-generated data as well as possible interactions. Exploiting the potential of PA technologies in sustainable ways depends on whether or not we first ask ''Are we doing the right thing?'' (strategic) as opposed to ''Are we doing it right?'' (tactical).

  17. Site-specific earthquake response analysis for Paducah Gaseous Diffusion Plant, Paducah, Kentucky. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Sykora, D.W.; Davis, J.J.

    1993-08-01

    The Paducah Gaseous Diffusion Plant (PGDP), owned by the US Department of Energy (DOE) and operated under contract by Martin Marietta Energy systems, Inc., is located southwest of Paducah, Kentucky. An aerial photograph and an oblique sketch of the plant are shown in Figures 1 and 2, respectively. The fenced portion of the plant consists of 748 acres. This plant was constructed in the 1950`s and is one of only two gaseous diffusion plants in operation in the United States; the other is located near Portsmouth, Ohio. The facilities at PGDP are currently being evaluated for safety in response to natural seismic hazards. Design and evaluation guidelines to evaluate the effects of earthquakes and other natural hazards on DOE facilities follow probabilistic hazard models that have been outlined by Kennedy et al. (1990). Criteria also established by Kennedy et al. (1990) classify diffusion plants as ``moderate hazard`` facilities. The US Army Engineer Waterways Experiment Station (WES) was tasked to calculate the site response using site-specific design earthquake records developed by others and the results of previous geotechnical investigations. In all, six earthquake records at three hazard levels and four individual and one average soil columns were used.

  18. A working group`s conclusion on site specific flow and transport modelling

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, J. [Golder Associates AB (Sweden); Ahokas, H. [Fintact Oy, Helsinki (Finland); Koskinen, L.; Poteri, A. [VTT Energy, Espoo (Finland); Niemi, A. [Royal Inst. of Technology, Stockholm (Sweden). Hydraulic Engineering; Hautojaervi, A. [Posiva Oy, Helsinki (Finland)

    1998-03-01

    This document suggests a strategy plan for groundwater flow and transport modelling to be used in the site specific performance assessment analysis of spent nuclear fuel disposal to be used for the site selection planned by the year 2000. Considering suggested general regulations in Finland, as well as suggested regulations in Sweden and the approach taken in recent safety assessment exercises conducted in these countries, it is clear that in such an analysis, in addition to showing that the proposed repository is safe, there exist needs to strengthen the link between field data, groundwater flow modelling and derivation of safety assessment parameters, and needs to assess uncertainty and variability. The suggested strategy plan builds on an evaluation of different approaches to modelling the groundwater flow in crystalline basement rock, the abundance of data collected in the site investigation programme in Finland, and the modelling methodology developed in the programme so far. It is suggested to model the whole system using nested models, where larger scale models provide the boundary conditions for the smaller ones 62 refs.

  19. Site-specific recombination in the chicken genome using Flipase recombinase-mediated cassette exchange.

    Science.gov (United States)

    Lee, Hong Jo; Lee, Hyung Chul; Kim, Young Min; Hwang, Young Sun; Park, Young Hyun; Park, Tae Sub; Han, Jae Yong

    2016-02-01

    Targeted genome recombination has been applied in diverse research fields and has a wide range of possible applications. In particular, the discovery of specific loci in the genome that support robust and ubiquitous expression of integrated genes and the development of genome-editing technology have facilitated rapid advances in various scientific areas. In this study, we produced transgenic (TG) chickens that can induce recombinase-mediated gene cassette exchange (RMCE), one of the site-specific recombination technologies, and confirmed RMCE in TG chicken-derived cells. As a result, we established TG chicken lines that have, Flipase (Flp) recognition target (FRT) pairs in the chicken genome, mediated by piggyBac transposition. The transgene integration patterns were diverse in each TG chicken line, and the integration diversity resulted in diverse levels of expression of exogenous genes in each tissue of the TG chickens. In addition, the replaced gene cassette was expressed successfully and maintained by RMCE in the FRT predominant loci of TG chicken-derived cells. These results indicate that targeted genome recombination technology with RMCE could be adaptable to TG chicken models and that the technology would be applicable to specific gene regulation by cis-element insertion and customized expression of functional proteins at predicted levels without epigenetic influence. © FASEB.

  20. Design of functionalized cellulosic honeycomb films: site-specific biomolecule modification via "click chemistry".

    Science.gov (United States)

    Xu, William Z; Zhang, Xinyue; Kadla, John F

    2012-02-13

    Value-added materials from naturally abundant polymers such as cellulose are of significant importance. In particular, cellulosic open-framework structures with controlled chemical functionality of the internal surface have great potential in many biosensor applications. Although various cellulose derivatives can form porous honeycomb structured materials, solubility issues and problems with film formation exist. To address this, we have generated robust cellulosic open-framework structures that can be post-functionalized through site-specific modification. Regioselectively modified amphiphilic cellulose azides, 3-O-azidopropoxypoly(ethylene glycol)-2,6-di-O-thexyldimethylsilyl cellulosics, were synthesized, and honeycomb-patterned films were readily produced by the simple breath figures method. Changing the degree of polymerization (DP) of the pendent ethylene glycol (EG(DP)) groups from 22 to 4 increased the corresponding honeycomb film pore diameters from ~1.2 to ~2.6 μm, enabling the potential tuning of pore size. Moreover, these novel azido-functionalized honeycomb films were easily functionalized using Cu(I)-catalyzed alkyne-azide [2 + 3] cycloaddition reaction; biotin was "clicked" onto the azide functionalized cellulosic honeycomb films without any effect to the film structure. These results indicate this system may serve as a platform for the design and development of biosensors.

  1. Site-specific proteolytic degradation of IgG monoclonal antibodies expressed in tobacco plants.

    Science.gov (United States)

    Hehle, Verena K; Lombardi, Raffaele; van Dolleweerd, Craig J; Paul, Mathew J; Di Micco, Patrizio; Morea, Veronica; Benvenuto, Eugenio; Donini, Marcello; Ma, Julian K-C

    2015-02-01

    Plants are promising hosts for the production of monoclonal antibodies (mAbs). However, proteolytic degradation of antibodies produced both in stable transgenic plants and using transient expression systems is still a major issue for efficient high-yield recombinant protein accumulation. In this work, we have performed a detailed study of the degradation profiles of two human IgG1 mAbs produced in plants: an anti-HIV mAb 2G12 and a tumour-targeting mAb H10. Even though they use different light chains (κ and λ, respectively), the fragmentation pattern of both antibodies was similar. The majority of Ig fragments result from proteolytic degradation, but there are only a limited number of plant proteolytic cleavage events in the immunoglobulin light and heavy chains. All of the cleavage sites identified were in the proximity of interdomain regions and occurred at each interdomain site, with the exception of the VL /CL interface in mAb H10 λ light chain. Cleavage site sequences were analysed, and residue patterns characteristic of proteolytic enzymes substrates were identified. The results of this work help to define common degradation events in plant-produced mAbs and raise the possibility of predicting antibody degradation patterns 'a priori' and designing novel stabilization strategies by site-specific mutagenesis. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  2. Site-specific lead exposure from lead pellet ingestion in sentinel mallards

    Science.gov (United States)

    Rocke, T.E.; Brand, C.J.; Mensik, John G.

    1997-01-01

    We monitored lead poisoning from the ingestion of spent lead pellets in sentinel mallards (Anas platyhrynchos) at the Sacramento National Wildlife Refuge (SNWR), Willows, California for 4 years (1986-89) after the conversion to steel shot for waterfowl hunting on refuges in 1986. Sentinel mallards were held in 1.6-ha enclosures in 1 hunted (P8) and 2 non-hunted (T19 and TF) wetlands. We compared site-specific rates of lead exposure, as determined by periodic measurement of blood lead concentrations, and lead poisoning mortality between wetlands with different lead pellet densities, between seasons, and between male and female sentinels. In 1986, the estimated 2-week rate of lead exposure was significantly higher (P 2,000,000 pellets/ha), than in those with lower densities of lead pellets, T19 (18.1%; 173,200 pellets/ha) and TF (0.9%; 15,750 pellets/ha). The probability of mortality from lead poisoning was also significantly higher (P exposure and the probability of lead poisoning mortality in P8 were significantly higher (P exposure or lead poisoning mortality between male and female sentinel mallards. The results of this study demonstrate that in some locations, lead exposure and lead poisoning in waterfowl will continue to occur despite the conversion to steel shot for waterfowl hunting.

  3. Fluorescent site-specific labeling of Escherichia coli expressed proteins with Sfp phosphopantetheinyl transferase.

    Science.gov (United States)

    Zhang, Aihua; Sun, Luo; Buswell, John; Considine, Nancy; Ghosh, Inca; Masharina, Anastasiya; Noren, Christopher; Xu, Ming-Qun

    2011-01-01

    Fluorescent tagging of proteins has become a critical step in optical analysis of protein function in vitro and in living cells. Here we describe a two-tag system for expression and isolation of a protein of interest from Escherichia coli and subsequent site-specific fluorescent labeling with Sfp phosphopantetheinyl transferase (Sfp synthase). In the example presented, adenoviral protein E3-14.7 K (E14.7) was expressed as a tripartite fusion protein with a fluorophore-targeting peptide tag and a chitin-binding domain. This system allows for rapid isolation of the recombinant fusion protein from crude bacterial cell lysate via a single chitin column. Sfp synthase-mediated labeling with fluorophore conjugated to coenzyme A-SH (CoA-SH) resulted in covalent attachment of a fluorescent dye to a specific residue of the peptide tag via a phosphopantetheinyl linker. The fluorescently labeled E14.7 fusion protein was analyzed with a fluorescence imager and subsequently transfected into mammalian cells for imaging with a fluorescence microscope.

  4. Hanford Integrated Planning Process: 1993 Hanford Site-specific science and technology plan

    International Nuclear Information System (INIS)

    1993-12-01

    This document is the FY 1993 report on Hanford Site-specific science and technology (S ampersand T) needs for cleanup of the Site as developed via the Hanford Integrated Planning Process (HIPP). It identifies cleanup problems that lack demonstrated technology solutions and technologies that require additional development. Recommendations are provided regarding allocation of funding to address Hanford's highest-priority technology improvement needs, technology development needs, and scientific research needs, all compiled from a Sitewide perspective. In the past, the S ampersand T agenda for Hanford Site cleanup was sometimes driven by scientists and technologists, with minimal input from the ''problem owners'' (i.e., Westinghouse Hanford Company [WHC] staff who are responsible for cleanup activities). At other times, the problem-owners made decisions to proceed with cleanup without adequate scientific and technological inputs. Under both of these scenarios, there was no significant stakeholder involvement in the decision-making process. One of the key objectives of HIPP is to develop an understanding of the integrated S ampersand T requirements to support the cleanup mission, (a) as defined by the needs of the problem owners, the values of the stakeholders, and the technology development expertise that exists at Hanford and elsewhere. This requires a periodic, systematic assessment of these needs and values to appropriately define a comprehensive technology development program and a complementary scientific research program. Basic to our success is a methodology that is defensible from a technical perspective and acceptable to the stakeholders

  5. Facilitating Site Specific and Citizens Advisory Boards: Running Effective Meetings that Involve Complex Technical Issues

    International Nuclear Information System (INIS)

    Freeman, J.

    2009-01-01

    Environmental cleanup issues at federal sites are more often than not on the agendas of meetings of the Site Specific Advisory Boards (SSABs), also called Citizens Advisory Boards (CABs), that exist at most U.S. Department of Energy (DOE) sites with an Environmental Management (EM) mission. In 1994, when Congress established these committees comprised of local citizens, it enabled community stakeholders to become more directly involved in DOE EM cleanup decisions. This involvement is to help the agency make cost-effective and environmentally sound decisions which lead to faster, safer cleanups. Eight local Boards that fall under the Federal Advisory Committee Act-chartered EM SSAB charter are found in Hanford, Washington; Idaho; Northern New Mexico; Nevada; Oak Ridge, Tennessee; Paducah, Kentucky; Portsmouth, Ohio; and at the Savannah River Site in South Carolina. These boards provide advice and recommendations about EM site-specific issues such as cleanup standards (how clean is clean?), environmental restoration, waste management, the stabilization and disposal of non-stockpile nuclear materials, future land use and long-term stewardship, risk assessment and management, and cleanup science and technology activities. These issues are, by their very nature, loaded with complicated technical terms and strategies, scientific data and interpretations, and long histories of studies and reports. The members of SSABs and CABs rotate on and off the Boards according to defined terms of office, thereby routinely opening the Boards' ranks to new members, many of whom are new to the issues. In addition, members of the public who have access to public comment periods at each Board meeting run up against the same daunting menu of obscure acronyms, scientific terms and notations, and an historical trail which is not always evident except to those involved with the issues over many years. How does a facilitator effectively guide such a group of citizens, each of whom arrives to

  6. Option-4 algorithm for Florida pocket depth probe: reduction in the variance of site-specific probeable crevice depth measurements.

    Science.gov (United States)

    Breen, H J; Rogers, P; Johnson, N W; Slaney, R

    1999-08-01

    Clinical periodontal measurement is plagued by many sources of error which result in aberrant values (outliers). This study sets out to compare probeable crevice depth measurements (PCD) selected by the option-4 algorithm against those recorded with a conventional double-pass method and to quantify any reduction in site-specific PCD variances. A single clinician recorded full-mouth PCD at 1 visit in 32 subjects (mean age 45.5 years) with moderately advanced chronic adult periodontitis. PCD was recorded over 2 passes at 6 sites per tooth with the Florida Pocket Depth Probes, a 3rd generation probe. The option-4 algorithm compared the 1st pass site-specific PCD value (PCD1) to the 2nd pass site-specific PCD value (PCD2) and, if the difference between these values was >1.00 mm, allowed the recording of a maximum of 2 further measurements (3rd and 4th pass measurements PCD3 and PCD4): 4 site-specific measure-meets were considered to be the maximum subject and tissue tolerance. The algorithm selected the 1st 2 measurements whose difference was difference Y) (Y=[(A-B)/A]X 100) and a 75% reduction in the median site-specific variance of PCD1/PCD2.

  7. Joint analysis of site-specific cancer risks for the atomic bomb survivors

    International Nuclear Information System (INIS)

    Pierce, D.A.; Preston, D.L.

    1993-01-01

    Statistical methods are presented for joint analysis of site-specific cancer risks for the atomic-bomb survivors. Previous analyses of these data, aside from those on leukemia, have been made either without regard to cancer type, or separately for types or classes of cancers. Clearly, analyses without regard to cancer type are less than satisfactory. The primary advantages of joint, rather than separate, analyses are that (1) models can be fitted with parameters common to cancer types, which can allow more-precise estimation of effects of interest, (2) significance tests can be used to compare type-specific risks, and (3) a clearer understanding may be obtained of risk-modification factors such as sex, age at exposure, and time since exposure. Joint analysis is straightforward, entailing primarily the incorporation of another factor for cancer type in the usual cross-tabulation of the data for analysis. The use of these methods is illustrated in an analysis of the three categories of cancer studied by the fifth Advisory Committee on the Biological Effects of Ionizing Radiation (BEIR V): digestive, respiratory, and other solid tumors. Based on this analysis, some criticism is made of the BEIR V-preferred models. Since the proposed methods are applicable to models for either relative or absolute risks, some comments on the use of explicit models for the absolute excess risk are also given. Although some of the gains from joint analysis are apparent from the results here, it will be important to use these methods with a more suitable choice of cancer classes and for cancer incidence data in which the diagnoses are more accurate. (author)

  8. Mid-Season High-Resolution Satellite Imagery for Forecasting Site-Specific Corn Yield

    Directory of Open Access Journals (Sweden)

    Nahuel R. Peralta

    2016-10-01

    Full Text Available A timely and accurate crop yield forecast is crucial to make better decisions on crop management, marketing, and storage by assessing ahead and implementing based on expected crop performance. The objective of this study was to investigate the potential of high-resolution satellite imagery data collected at mid-growing season for identification of within-field variability and to forecast corn yield at different sites within a field. A test was conducted on yield monitor data and RapidEye satellite imagery obtained for 22 cornfields located in five different counties (Clay, Dickinson, Rice, Saline, and Washington of Kansas (total of 457 ha. Three basic tests were conducted on the data: (1 spatial dependence on each of the yield and vegetation indices (VIs using Moran’s I test; (2 model selection for the relationship between imagery data and actual yield using ordinary least square regression (OLS and spatial econometric (SPL models; and (3 model validation for yield forecasting purposes. Spatial autocorrelation analysis (Moran’s I test for both yield and VIs (red edge NDVI = NDVIre, normalized difference vegetation index = NDVIr, SRre = red-edge simple ratio, near infrared = NIR and green-NDVI = NDVIG was tested positive and statistically significant for most of the fields (p < 0.05, except for one. Inclusion of spatial adjustment to model improved the model fit on most fields as compared to OLS models, with the spatial adjustment coefficient significant for half of the fields studied. When selected models were used for prediction to validate dataset, a striking similarity (RMSE = 0.02 was obtained between predicted and observed yield within a field. Yield maps could assist implementing more effective site-specific management tools and could be utilized as a proxy of yield monitor data. In summary, high-resolution satellite imagery data can be reasonably used to forecast yield via utilization of models that include spatial adjustment to

  9. Environmental restoration and waste management site-specific plan for Richland Operations Office

    International Nuclear Information System (INIS)

    1991-09-01

    This document was prepared to implement and support the US Department of Energy-Headquarters (DOE-HQ) national plan. The national plan, entitled Environmental Restoration and Waste Management Five-Year Plan (DOE 1990b) (hereinafter referred to as the DOE-HQ Five-Year Plan) is the cornerstone of the US Department of Energy's (DOE) long-term strategy in environmental restoration and waste management. The DOE-HQ Five-Year Plan addresses overall philosophy and environmental and waste-related activities under the responsibilities of the DOE Office of Environmental Restoration and Waste Management. The plan also reaffirms DOE-HQ goals to bring its nuclear sites into environmental compliance in cooperation with its regulators and the public, and to clean up and restore the environment by 2019 (the commitment for the Hanford Site is for one year sooner, or 2018). This document is part of the site-specific plan for the US Department of Energy-Richland Operations Office (DOE-RL). It is the first revision of the original plan, which was dated December 1989 (DOE-RL 1989a). This document is a companion document to the Overview of the Hanford Cleanup Five-Year Plan (DOE-RL 1989d) and The Hanford Site Environmental Restoration and Waste Management Five-Year Plan Activity Data Sheets (DOE-RL 1991). Although there are three documents that make up the complete DOE-RL plan, this detailed information volume was prepared so it could be used as a standalone document. 71 refs., 40 figs., 28 tabs

  10. Comparison of Site-Specific Bone Mineral Densities between Endurance Runners and Sprinters in Adolescent Women

    Directory of Open Access Journals (Sweden)

    Aoi Ikedo

    2016-11-01

    Full Text Available We aimed to compare site-specific bone mineral densities (BMDs between adolescent endurance runners and sprinters and examine the relationship of fat-free mass (FFM and nutrient intake on BMD. In this cross-sectional study, 37 adolescent female endurance runners and sprinters (16.1 ± 0.8 years were recruited. BMD and FFM were assessed by dual-energy X-ray absorptiometry. Nutrient intake and menstrual state were evaluated by questionnaires. After adjusting for covariates, spine and total bone less head (TBLH BMDs were significantly higher in sprinters than endurance runners (TBLH, 1.02 ± 0.05 vs. 0.98 ± 0.06 g/cm2; spine, 0.99 ± 0.06 vs. 0.94 ± 0.06 g/cm2; p < 0.05. There was no significant difference between groups in other sites. The rate of menstrual abnormality was higher in endurance runners compared with sprinters (56.3% vs. 23.8%; p < 0.05. FFM was a significant covariate for BMD on all sites except the spine (p < 0.05. Dietary intake of vitamin D was identified as a significant covariate only for pelvic BMD (p < 0.05. The BMDs of different sites among endurance runners and sprinters were strongly related to FFM. However, the association of FFM with spine BMD cannot be explained by FFM alone. Other factors, including nutrition and/or mechanical loading, may affect the spine BMD.

  11. Human in vivo regional intestinal permeability: quantitation using site-specific drug absorption data.

    Science.gov (United States)

    Sjögren, Erik; Dahlgren, David; Roos, Carl; Lennernäs, Hans

    2015-06-01

    Application of information on regional intestinal permeability has been identified as a key aspect of successful pharmaceutical product development. This study presents the results and evaluation of an approach for the indirect estimation of site-specific in vivo intestinal effective permeability (Peff) in humans. Plasma concentration-time profiles from 15 clinical studies that administered drug solutions to specific intestinal regions were collected and analyzed. The intestinal absorption rate for each drug was acquired by deconvolution, using historical intravenous data as reference, and used with the intestinal surface area and the dose remaining in the lumen to estimate the Peff. Forty-three new Peff values were estimated (15 from the proximal small intestine, 11 from the distal small intestine, and 17 from the large intestine) for 14 active pharmaceutical ingredients representing a wide range of biopharmaceutical properties. A good correlation (r(2) = 0.96, slope = 1.24, intercept = 0.030) was established between these indirect jejunal Peff estimates and jejunal Peff measurements determined directly using the single-pass perfusion double balloon technique. On average, Peff estimates from the distal small intestine and large intestine were 90% and 40%, respectively, of those from the proximal small intestine. These results support the use of the evaluated deconvolution method for indirectly estimating regional intestinal Peff in humans. This study presents the first comprehensive data set of estimated human regional intestinal permeability values for a range of drugs. These biopharmaceutical data can be used to improve the accuracy of gastrointestinal absorption predictions used in drug development decision-making.

  12. Microzonation and site-specific ground motion modelling for Delhi city

    International Nuclear Information System (INIS)

    Parvez, Imtiyaz A.; Vaccari, F.; Panza, G.F.

    2002-11-01

    Delhi - the capital of India - lies on a severe earthquake hazard threats not only from the local earthquakes but also from Himalayan events just 200-250 km apart. The seismic ground motion in a part of Delhi City is computed with a hybrid technique based (on the based) on the modal summation and the finite difference scheme for site-specific strong ground motion modelling. Complete realistic SH and P-SV wave seismograms are computed along two geological cross-sections, (1) North-South, from Inter State Bus Terminal (ISBT) to Sewanagar and (2) East- West, from Tilak Bridge to Punjabi Bagh. Two real earthquake sources of July 15, 1720 (MMI=IX, M=7.4) and August 27, 1960 (M=6.0) have been used in the modelling. The response spectra ratio (RSR), i.e. the response spectra computed from the signals synthesized along the laterally varying section normalized by the response spectra computed from the corresponding signals, synthesized for the bedrock reference regional model, have been determined. As expected, the sedimentary cover causes an increase of the signal amplitude particularly in the radial and transverse components. To further check the site-effects, we reversed the source location to the other side of the cross-section and re-computed the site amplifications. There are only a few sites where a large amplification is invariant with respect to the two source locations considered. The RSR ranges between 5 to 10 in the frequency range from 2.8 to 3.7 Hz, for the radial and transverse components of motion along the NS cross-section. Along the EW cross-section RSR varies between 3.5 to 7.5 in the frequency range from 3.5 to 4.1 Hz. The amplification of the vertical component is large at high frequency (>4 Hz) whereas it is negligible in lower frequency range. (author)

  13. Mutagenic replication in human cell extracts of DNA containing site-specific N-2-acetylaminofluorene adducts.

    Science.gov (United States)

    Thomas, D C; Veaute, X; Kunkel, T A; Fuchs, R P

    1994-08-02

    We have analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of bidirectional replication of double-stranded DNA in a human cell extract. Plasmid vectors were constructed containing the simian virus 40 origin of replication and single AAF adducts at one of three guanines in the Nar I sequence GGCGCC in a lacZ reporter gene. The presence of an AAF adduct diminishes replication efficiency in HeLa cell extracts by 70-80%. Replication product analyses reveal unique termination sites with each damaged vector, suggesting that when the replication fork encounters an AAF adduct, it often stops before incorporation opposite the adduct. We also observed a higher proportion of products representing replication of the undamaged strand compared to the damaged strand. This suggests that the undamaged strand is replicated more readily, either by uncoupling the first fork to encounter the lesion or by replication using the fork arriving from the other direction. Also included among replication products are covalently closed monomer-length molecules resistant to cleavage at the AAF-modified Nar I site. This resistance is characteristic of substrates containing the AAF adduct, suggesting that translesion bypass had occurred. Transformation of Escherichia coli cells with the replicated damaged DNA yielded lacZ alpha revertant frequencies significantly above values obtained with undamaged DNA or with damaged DNA not replicated in vitro. This increase was only seen with the substrate modified at the third guanine position. Analysis of mutant DNA demonstrated the loss of a GC dinucleotide at the Nar I sequence. Generation of this position-dependent AAF-induced frameshift error in a human replication system is consistent with previous observations in E. coli suggesting that, after incorporation of dCMP opposite modified guanine in the third position, realignment of the template-primer occurs to form an intermediate with two

  14. Environmental restoration and waste management site-specific plan for Richland Operations Office. [Contains glossary

    Energy Technology Data Exchange (ETDEWEB)

    1991-09-01

    This document was prepared to implement and support the US Department of Energy-Headquarters (DOE-HQ) national plan. The national plan, entitled Environmental Restoration and Waste Management Five-Year Plan (DOE 1990b) (hereinafter referred to as the DOE-HQ Five-Year Plan) is the cornerstone of the US Department of Energy's (DOE) long-term strategy in environmental restoration and waste management. The DOE-HQ Five-Year Plan addresses overall philosophy and environmental and waste-related activities under the responsibilities of the DOE Office of Environmental Restoration and Waste Management. The plan also reaffirms DOE-HQ goals to bring its nuclear sites into environmental compliance in cooperation with its regulators and the public, and to clean up and restore the environment by 2019 (the commitment for the Hanford Site is for one year sooner, or 2018). This document is part of the site-specific plan for the US Department of Energy-Richland Operations Office (DOE-RL). It is the first revision of the original plan, which was dated December 1989 (DOE-RL 1989a). This document is a companion document to the Overview of the Hanford Cleanup Five-Year Plan (DOE-RL 1989d) and The Hanford Site Environmental Restoration and Waste Management Five-Year Plan Activity Data Sheets (DOE-RL 1991). Although there are three documents that make up the complete DOE-RL plan, this detailed information volume was prepared so it could be used as a standalone document. 71 refs., 40 figs., 28 tabs.

  15. The Xer/dif site-specific recombination system of Campylobacter jejuni.

    Science.gov (United States)

    Leroux, Maxime; Rezoug, Zoulikha; Szatmari, George

    2013-10-01

    Chromosome dimers, which form during the bacterial life cycle, represent a problem that must be solved by the bacterial cell machinery so that chromosome segregation can occur effectively. The Xer/dif site-specific recombination system, utilized by most bacteria, resolves chromosome dimers into monomers using two tyrosine recombinases, XerC and XerD, to perform the recombination reaction at the dif site which consists of 28-30 bp. However, single Xer recombinase systems have been recently discovered in several bacterial species. In Streptococci and Lactococci a single recombinase, XerS, is capable of completing the monomerisation reaction by acting at an atypical dif site called dif SL (31 bp). It was recently shown that a subgroup of ε-proteobacteria including Campylobacter spp. and Helicobacter spp. had a phylogenetically distinct Xer/dif recombination system with only one recombinase (XerH) and an atypical dif motif (difH). In order to biochemically characterize this system in greater detail, Campylobacter jejuni XerH was purified and its DNA-binding activity was characterized. The protein showed specific binding to the complete difH site and to both halves separately. It was also shown to form covalent complexes with difH suicide substrates. In addition, XerH was able to catalyse recombination between two difH sites located on a plasmid in Escherichia coli in vivo. This indicates that this XerH protein performs a similar function as the related XerS protein, but shows significantly different binding characteristics.

  16. Configuration and specifications of an Unmanned Aerial Vehicle (UAV) for early site specific weed management.

    Science.gov (United States)

    Torres-Sánchez, Jorge; López-Granados, Francisca; De Castro, Ana Isabel; Peña-Barragán, José Manuel

    2013-01-01

    A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV). This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM). Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m) were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1) mission planning, 2) UAV flight and image acquisition, and 3) image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index), mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches).

  17. Structural basis for the site-specific incorporation of lysine derivatives into proteins.

    Directory of Open Access Journals (Sweden)

    Veronika Flügel

    Full Text Available Posttranslational modifications (PTMs of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS:tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated ε-N-alkynyl-, ε-N-butyryl-, ε-N-crotonyl- and ε-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance.

  18. Configuration and specifications of an Unmanned Aerial Vehicle (UAV for early site specific weed management.

    Directory of Open Access Journals (Sweden)

    Jorge Torres-Sánchez

    Full Text Available A new aerial platform has risen recently for image acquisition, the Unmanned Aerial Vehicle (UAV. This article describes the technical specifications and configuration of a UAV used to capture remote images for early season site- specific weed management (ESSWM. Image spatial and spectral properties required for weed seedling discrimination were also evaluated. Two different sensors, a still visible camera and a six-band multispectral camera, and three flight altitudes (30, 60 and 100 m were tested over a naturally infested sunflower field. The main phases of the UAV workflow were the following: 1 mission planning, 2 UAV flight and image acquisition, and 3 image pre-processing. Three different aspects were needed to plan the route: flight area, camera specifications and UAV tasks. The pre-processing phase included the correct alignment of the six bands of the multispectral imagery and the orthorectification and mosaicking of the individual images captured in each flight. The image pixel size, area covered by each image and flight timing were very sensitive to flight altitude. At a lower altitude, the UAV captured images of finer spatial resolution, although the number of images needed to cover the whole field may be a limiting factor due to the energy required for a greater flight length and computational requirements for the further mosaicking process. Spectral differences between weeds, crop and bare soil were significant in the vegetation indices studied (Excess Green Index, Normalised Green-Red Difference Index and Normalised Difference Vegetation Index, mainly at a 30 m altitude. However, greater spectral separability was obtained between vegetation and bare soil with the index NDVI. These results suggest that an agreement among spectral and spatial resolutions is needed to optimise the flight mission according to every agronomical objective as affected by the size of the smaller object to be discriminated (weed plants or weed patches.

  19. Inhibition of TGF-β Signaling in Tumor Cells by Small Molecule Src Family Kinase Inhibitors.

    Science.gov (United States)

    Bartscht, Tobias; Rosien, Benjamin; Rades, Dirk; Kaufmann, Roland; Biersack, Harald; Lehnerta, Hendrik; Ungefroren, Hendrik

    2017-01-01

    In a series of studies carried out over the last couple of years in various cell types, it was observed that the experimentally used Src family kinase inhibitors PP1 and PP2 and the clinically used Src/Abl inhibitors AZM475271 and dasatinib are potent inhibitors of TGF-β mediated cellular responses such as Smad and p38 mitogen-activated protein kinase phosphorylation, Smad-dependent transcriptional activation, growth inhibition, epithelial-mesenchymal transition (EMT), and cell motility. While for PP1/PP2 it was demonstrated that these agents directly inhibit the kinase activity of the TGF-β type I receptor activin receptor-like kinase 5, the mechanism of the anti-TGF-β effect of AZM475271 and dasatinib is less clear. In contrast, the anti-TGF-β effect of yet another Src/Abl inhibitor, bosutinib, is more variable with respect to the type of the TGF-β response and the cell type affected, and lacks a clear dose-dependency. In the light of their strong anti-activin receptor-like kinase 5 kinase effect, PP1 and PP2 should not be used when studying the role of c-Src as downstream mediators in TGF-β/activin receptor-like kinase 5 signaling. On the other hand, based upon in vitro findings, it is conceivable that part of the therapeutic effects of AZM475271 and dasatinib seen in preclinical and clinical studies with solid tumors was caused by inhibition of prometastatic TGF-β rather than Src signaling. If AZM475271 and dasatinib can indeed act as dual Src / TGF-β inhibitors in vivo, this may be beneficial for prevention of metastatic disease in more advanced tumor stages. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  20. Site specificity of psoralen-DNA interstrand cross-linking determined by nuclease Bal31 digestion

    DEFF Research Database (Denmark)

    Zhen, W P; Buchardt, O; Nielsen, Henrik

    1986-01-01

    A novel method for determination of psoralen photo-cross-linking sites in double-stranded DNA is described, which is based on a pronounced inhibition of Bal31 exonuclease activity by psoralen-DNA interstrand cross-links. The results using a 51 base pair fragment of plasmid pUC19 and a 346 base pair...

  1. One-year and long-term molecular response to nilotinib and dasatinib for newly diagnosed chronic myeloid leukemia: a matching-adjusted indirect comparison.

    Science.gov (United States)

    Signorovitch, James E; Betts, Keith A; Reichmann, William M; Thomason, Darren; Galebach, Phil; Wu, Eric Q; Chen, Lei; DeAngelo, Daniel J

    2015-02-01

    Nilotinib and dasatinib have shown superior rates of molecular response (MR) compared to imatinib for the treatment of newly diagnosed chronic myeloid leukemia (CML) in chronic phase (CP). This study indirectly compares MR in patients taking nilotinib 300 mg bid with that in those taking dasatinib 100 mg qd by 12 months and through 48 months. Patients in ENESTnd were re-weighted to match published baseline characteristics reported for DASISION using a propensity score model. After matching, differences in rates of major MR (MMR, measured as a 3 log reduction on the International Scale [IS]), MR(4.0) (4 log reduction on IS), and MR(4.5) (4.5 log reduction on IS) relative to imatinib were indirectly compared between nilotinib and dasatinib. Hazard ratios (HRs) were used to indirectly compare MR outcomes between nilotinib and dasatinib through 48 months of follow-up, while rate differences were used to compare progression to AP/BC between nilotinib and dasatinib by 48 months. After matching, rates of MR by 12 months were higher with nilotinib vs dasatinib by 11.7% for MMR (p = 0.045), 8.2% for MR(4.0) (p = 0.029), and 8.5% for MR(4.5) (p < 0.001). Higher rates of MMR (HR = 1.44, p = 0.018) and MR(4.0) (HR = 1.58, p = 0.013) achievement were maintained with nilotinib compared to dasatinib through 48 months of follow-up. No statistically significant differences were observed for MR(4.5) through 48 months or progression to AP/BC by 48 months. LIMITATIONS include comparisons based solely on indirect evidence and HRs for MR(4.0) and MR(4.5) from the DASISION trial being extracted from cumulative incidence curves. This indirect comparison suggests that nilotinib is associated with higher rates of achieving MMR, MR(4.0), and MR(4.5) by 12 months compared to dasatinib for the treatment of newly diagnosed CML-CP. In addition, higher rates of MR achievement with nilotinib were also maintained through 48 months of follow-up.

  2. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    International Nuclear Information System (INIS)

    Falk, Alexander S.; Siemer, Ansgar B.

    2016-01-01

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  3. XerCD-Mediated Site-Specific Recombination Leads to Loss of the 57-Kilobase Gonococcal Genetic Island▿

    OpenAIRE

    Domínguez, Nadia M.; Hackett, Kathleen T.; Dillard, Joseph P.

    2010-01-01

    Most strains of Neisseria gonorrhoeae carry the 57-kb gonococcal genetic island (GGI), as do a few strains of Neisseria meningitidis. The GGI is inserted into the chromosome at the dif site (difA) and is flanked by a partial repeat of the dif site (difB). Since dif is a sequence recognized by the site-specific recombinases XerC and XerD and the GGI shows evidence of horizontal acquisition, we hypothesized that the GGI may be acquired or lost by XerCD-mediated site-specific recombination. We s...

  4. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Falk, Alexander S.; Siemer, Ansgar B., E-mail: asiemer@usc.edu [Keck School of Medicine of USC, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute (United States)

    2016-11-15

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  5. Site-specific equilibrium isotopic fractionation of oxygen, carbon and calcium in apatite

    Science.gov (United States)

    Aufort, Julie; Ségalen, Loïc; Gervais, Christel; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne

    2017-12-01

    results, measurements of site-specific isotopic fractionation properties could improve our understanding and the interpretation of isotopic records in apatites.

  6. Molecular characterization of a complex site-specific radiation-induced DNA double-strand break

    International Nuclear Information System (INIS)

    Datta, K.; Dizdaroglu, M.; Jaruga, P.; Neumann, R.D.; Winters, T.A.

    2003-01-01

    Radiation lethality is a function of radiation-induced DNA double-strand breaks (DSB). Current models propose the lethality of a DSB to be a function of its structural complexity. We present here for the first time a map of damage associated with a site-specific double-strand break produced by decay of 125 I in a plasmid bound by a 125 I-labeled triplex forming oligonucleotide ( 125 I-TFO). The E. coli DNA repair enzymes, endonuclease IV (endo IV), endonuclease III (endo III), and formamidopyrimidine-DNA glycosylase (Fpg), which recognize AP sites, and pyrimidine and purine base damage respectively, were used as probes in this study. 125 I-TFO bound plasmid was incubated with and without DMSO at -80 deg C for 1 month. No significant difference in DSB yield was observed under these conditions. A 32 base pair fragment from the upstream side of the decay site was isolated by restriction digestion and enzymatically probed to identify damage sites. Endo IV treatment of the 5'-end labeled upper strand indicated clustering of AP sites within 3 bases downstream and 7 bases upstream of the targeted base. Also, repeated experiments consistently detected an AP site 4 bases upstream of the 125 Itarget base. This was further supported by complementary results with the 3'-end labeled upper strand. Endo IV analysis of the lower strand also shows clustering of AP sites near the DSB end. Endo III and Fpg probing demonstrated that base damage is also clustered near the targeted break site. DSBs produced in the absence of DMSO displayed a different pattern of enzyme sensitive damage than those produced in the presence of DMSO. Identification of specific base damage types within the restriction fragment containing the DSB end was achieved with GC/MS. Base damage consisted of 8-hydroguanine, 8-hydroxyadenine, and 5-hydroxycytosine. These lesions were observed at relative yields of 8-hydroguanine and 5-hydroxycytosine to 8-hydroxyadenine of 7.4:1 and 4.7:1, respectively, in the absence

  7. Evaluation and interpretation of regional and site-specific hydrochemical data bases for water quality assessment

    Directory of Open Access Journals (Sweden)

    M. G. Hutchins

    1999-01-01

    Full Text Available The spatial distribution of stream water composition, as determined by the Geochemical Baseline Survey of the Environment (G-BASE conducted by the British Geological Survey (BGS can be successfully related under baseflow conditions to bedrock geochemistry. Further consideration of results in conjunction with site-specific monitoring data enables factors controlling both spatial and temporal variability in major element composition to be highlighted and allows the value of the survey to be enhanced. Hence, chemical data (i from streams located on Lower Silurian (Llandovery bedrock at 1 km2 resolution collected as part of the G-BASE survey of Wales and the West Midlands and (ii from catchment monitoring studies located in upland mid-Wales (conducted by Institute of Terrestrial Ecology, have been considered together as an example. Classification of the spatial survey data set in terms of potentially controlling factors was carried out so as to illustrate the level of explanation they could give in terms of observed spatial chemical variability. It was therefore hypothesised that on a geological lithostratigraphic series of limited geochemical contrast, altitude and land-use factors provide better explanation of this variability than others such as lithology at sampling site and stream order. At an individual site, temporal variability was also found to be of considerable significance and, at a monthly time-step, is explicable in terms of factors such as antecedent conditions and seasonality. Data suggest that the degree of this variability may show some relationship with stream order and land-use. Monitoring data from the region also reveal that relationships between stream chemistry and land-use may prove to be strong not only at base flow but also in storm flow conditions. In a wider context, predictions of the sensitivity of stream water to acidification based on classifications of soil and geology are successful on a regional scale. However

  8. Improving 1D Site Specific Velocity Profiles for the Kik-Net Network

    Science.gov (United States)

    Holt, James; Edwards, Benjamin; Pilz, Marco; Fäh, Donat; Rietbrock, Andreas

    2017-04-01

    Ground motion predication equations (GMPEs) form the cornerstone of modern seismic hazard assessments. When produced to a high standard they provide reliable estimates of ground motion/spectral acceleration for a given site and earthquake scenario. This information is crucial for engineers to optimise design and for regulators who enforce legal minimum safe design capacities. Classically, GMPEs were built upon the assumption that variability around the median model could be treated as aleatory. As understanding improved, it was noted that the propagation could be segregated into the response of the average path from the source and the response of the site. This is because the heterogeneity of the near-surface lithology is significantly different from that of the bulk path. It was then suggested that the semi-ergodic approach could be taken if the site response could be determined, moving uncertainty away from aleatory to epistemic. The determination of reliable site-specific response models is therefore becoming increasingly critical for ground motion models used in engineering practice. Today it is common practice to include proxies for site response within the scope of a GMPE, such as Vs30 or site classification, in an effort to reduce the overall uncertainty of the predication at a given site. However, these proxies are not always reliable enough to give confident ground motion estimates, due to the complexity of the near-surface. Other approaches of quantifying the response of the site include detailed numerical simulations (1/2/3D - linear, EQL, non-linear etc.). However, in order to be reliable, they require highly detailed and accurate velocity and, for non-linear analyses, material property models. It is possible to obtain this information through invasive methods, but is expensive, and not feasible for most projects. Here we propose an alternative method to derive reliable velocity profiles (and their uncertainty), calibrated using almost 20 years of

  9. Site-specific relapse pattern of the triple negative tumors in Chinese breast cancer patients

    Directory of Open Access Journals (Sweden)

    Di Genhong

    2009-09-01

    Full Text Available Abstract Background It has been reported that triple negative phenotype is characterized by aggressive clinical history in Western breast cancer patients, however its pattern of metastatic spread had never been reported in the Chinese population. Considering racial disparities, we sought to analyze the spread pattern for different sites of first recurrence in Chinese triple negative breast cancers. Methods A retrospective study of 1662 patients was carried out from a large database of breast cancer patients undergoing surgery between January 1, 2000 and March 31, 2004 at the Cancer Hospital, Fudan University, Shanghai, China. Survival curves were generated using the Kaplan-Meier method and annual relapse hazards were estimated by the hazard function. Results We found a statistically significant difference in relapse-free survival (RFS for locoregional and visceral recurrence (P = 0.007 and P = 0.025, respectively among the triple negative, ERBB2+ and HR+/ERBB2- subgroups in univariate analysis. In the multivariate Cox proportional hazards regression analysis, RFS for either locoregional or visceral relapse in the triple negative category was inferior to that in HR+/ERBB2- patients (P = 0.027 and P = 0.005, respectively, but comparable to that in ERBB2+ women (both P >0.05. Furthermore, the early relapse peak appeared later in the triple negative group than that in the ERBB2+ counterpart for both locoregional and visceral relapse. On the other hand, when compared with triple negative breast cancers, a significantly lower risk of developing bone relapse was discerned for ERBB2+ women (P = 0.048; HR = 0.384, 95% CI 0.148-0.991, with the borderline significance for HR+/ERBB2- breast cancers (P = 0.058; HR = 0.479, 95% CI 0.224-1.025. In terms of bone metastasis, the hazard rate remained higher for the triple negative category than that for the ERBB2+ subtype. Conclusion Based on the site-specific spread pattern in different subgroups, the triple

  10. Site-specific seismic probabilistic tsunami hazard analysis: performances and potential applications

    Science.gov (United States)

    Tonini, Roberto; Volpe, Manuela; Lorito, Stefano; Selva, Jacopo; Orefice, Simone; Graziani, Laura; Brizuela, Beatriz; Smedile, Alessandra; Romano, Fabrizio; De Martini, Paolo Marco; Maramai, Alessandra; Piatanesi, Alessio; Pantosti, Daniela

    2017-04-01

    Seismic Probabilistic Tsunami Hazard Analysis (SPTHA) provides probabilities to exceed different thresholds of tsunami hazard intensity, at a specific site or region and in a given time span, for tsunamis caused by seismic sources. Results obtained by SPTHA (i.e., probabilistic hazard curves and inundation maps) represent a very important input to risk analyses and land use planning. However, the large variability of source parameters implies the definition of a huge number of potential tsunami scenarios, whose omission could lead to a biased analysis. Moreover, tsunami propagation from source to target requires the use of very expensive numerical simulations. At regional scale, the computational cost can be reduced using assumptions on the tsunami modeling (i.e., neglecting non-linear effects, using coarse topo-bathymetric meshes, empirically extrapolating maximum wave heights on the coast). On the other hand, moving to local scale, a much higher resolution is required and such assumptions drop out, since detailed inundation maps require significantly greater computational resources. In this work we apply a multi-step method to perform a site-specific SPTHA which can be summarized in the following steps: i) to perform a regional hazard assessment to account for both the aleatory and epistemic uncertainties of the seismic source, by combining the use of an event tree and an ensemble modeling technique; ii) to apply a filtering procedure which use a cluster analysis to define a significantly reduced number of representative scenarios contributing to the hazard of a specific target site; iii) to perform high resolution numerical simulations only for these representative scenarios and for a subset of near field sources placed in very shallow waters and/or whose coseismic displacements induce ground uplift or subsidence at the target. The method is applied to three target areas in the Mediterranean located around the cities of Milazzo (Italy), Thessaloniki (Greece) and

  11. Dual and multi-stimuli responsive polymeric nanoparticles for programmed site-specific drug delivery.

    Science.gov (United States)

    Cheng, Ru; Meng, Fenghua; Deng, Chao; Klok, Harm-Anton; Zhong, Zhiyuan

    2013-05-01

    In the past decades, polymeric nanoparticles have emerged as a most promising and viable technology platform for targeted and controlled drug delivery. As vehicles, ideal nanoparticles are obliged to possess high drug loading levels, deliver drug to the specific pathological site and/or target cells without drug leakage on the way, while rapidly unload drug at the site of action. To this end, various "intelligent" polymeric nanoparticles that release drugs in response to an internal or external stimulus such as pH, redox, temperature, magnetic and light have been actively pursued. These stimuli-responsive nanoparticles have demonstrated, though to varying degrees, improved in vitro and/or in vivo drug release profiles. In an effort to further improve drug release performances, novel dual and multi-stimuli responsive polymeric nanoparticles that respond to a combination of two or more signals such as pH/temperature, pH/redox, pH/magnetic field, temperature/reduction, double pH, pH and diols, temperature/magnetic field, temperature/enzyme, temperature/pH/redox, temperature/pH/magnetic, pH/redox/magnetic, temperature/redox/guest molecules, and temperature/pH/guest molecules have recently been developed. Notably, these combined responses take place either simultaneously at the pathological site or in a sequential manner from nanoparticle preparation, nanoparticle transporting pathways, to cellular compartments. These dual and multi-stimuli responsive polymeric nanoparticles have shown unprecedented control over drug delivery and release leading to superior in vitro and/or in vivo anti-cancer efficacy. With programmed site-specific drug delivery feature, dual and multi-stimuli responsive nanoparticulate drug formulations have tremendous potential for targeted cancer therapy. In this review paper, we highlight the recent exciting developments in dual and multi-stimuli responsive polymeric nanoparticles for precision drug delivery applications, with a particular focus

  12. Review: A Position Paper on Selenium in Ecotoxicology: A Procedure for Deriving Site-Specific Water Quality Criteria

    Science.gov (United States)

    A. Dennis Lemly

    1997-01-01

    This paper describes a method for deriving site-specific water quality criteria for selenium using a two-step process: (1) gather information on selenium residues and biological effects at the site and in down-gradient systems and (2) examine criteria based on the degree of bioaccumulation, the relationship between mea-sured residues and threshold concentrations for...

  13. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine

    2014-01-01

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tu...

  14. The SSC cycle: a PDCA approach to address site-specific characteristics in a continuous shallow water quality monitoring project.

    Science.gov (United States)

    Miles, Eduardo J

    2008-05-01

    In any water quality-monitoring project there are several critical success factors that must be adequately addressed in order to ensure the implementation and realization of the monitoring objectives. Site selection is one of these critical success factors. The monitoring sites must be selected to comply with the monitoring and data quality objectives. In the real world, ideal monitoring setting conditions are difficult to achieve, and compromises must be made in order to locate the monitoring stations that best represent the environment to be monitored. Site-specific characteristics are all the environmental, logistical and management factors particular to the monitoring site, that could influence the fulfilment of the monitoring and data quality objectives. Therefore, during the site selection process, it is essential to properly consider and evaluate these site-specific characteristics. The SSC cycle was developed with this goal in mind, to assist the monitoring team to systematically address site-specific characteristics. The cycle is a methodology to organize the site-specific characteristics in different categories, and to ensure a comprehensive overview of these characteristics throughout the project life cycle.

  15. Site specific fertilization affects yield, fruit size, quality, and shelf-life of ‘Kent' mango

    Science.gov (United States)

    Site specific fertilization (SSF) defines the type and rate of fertilizer needed for individual orchards. This study presents preliminary results (2010-2011) of a medium term project to quantify the effects of SSF on yield, fruit size, quality, and shelf-life of ‘Kent’ mango. Two orchards are used f...

  16. Site-specific conjugation of single domain antibodies to liposomes enhances photosensitizer uptake and photodynamic therapy efficacy

    NARCIS (Netherlands)

    Broekgaarden, M.; van Vught, R.; Oliveira, S.; Roovers, R. C.; van Bergen En Henegouwen, P. M. P.; Pieters, R. J.; van Gulik, T. M.; Breukink, E.; Heger, M.

    2016-01-01

    Photodynamic therapy for therapy-resistant cancers will greatly benefit from targeted delivery of tumor photosensitizing agents. In this study, a strategy for the site-specific conjugation of single domain antibodies onto liposomes containing the photosensitizer zinc phthalocyanine was developed and

  17. Site-specific conjugation of single domain antibodies to liposomes enhances photosensitizer uptake and photodynamic therapy efficacy.

    Science.gov (United States)

    Broekgaarden, M; van Vught, R; Oliveira, S; Roovers, R C; van Bergen en Henegouwen, P M P; Pieters, R J; Van Gulik, T M; Breukink, E; Heger, M

    2016-03-28

    Photodynamic therapy for therapy-resistant cancers will greatly benefit from targeted delivery of tumor photosensitizing agents. In this study, a strategy for the site-specific conjugation of single domain antibodies onto liposomes containing the photosensitizer zinc phthalocyanine was developed and tested.

  18. Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway

    DEFF Research Database (Denmark)

    Lee, Jae Seong; Beuchert Kallehauge, Thomas; Pedersen, Lasse Ebdrup

    2015-01-01

    gene integration into site-specific loci in CHO cells using CRISPR/Cas9 genome editing system and compatible donor plasmid harboring a gene of interest (GOI) and short homology arms. This strategy has enabled precise insertion of a 3.7-kb gene expression cassette at defined loci in CHO cells following...

  19. GPCC - A weather generator-based statistical downscaling tool for site-specific assessment of climate change impacts

    Science.gov (United States)

    Resolution of climate model outputs are too coarse to be used as direct inputs to impact models for assessing climate change impacts on agricultural production, water resources, and eco-system services at local or site-specific scales. Statistical downscaling approaches are usually used to bridge th...

  20. Development of an unmanned aerial vehicle-based spray system for highly accurate site-specific application

    Science.gov (United States)

    Application of crop production and protection materials is a crucial component in the high productivity of American agriculture. Agricultural chemical application is frequently needed at a specific time and location for accurate site-specific management of crop pests. Piloted aircrafts that carry ...

  1. Site-specific optimisation of the countermeasure structure on rehabilitation of radioactive contaminated territories

    International Nuclear Information System (INIS)

    Yatsalo, B.I.; Okhrimenko, D.V.; Lisyanski, B.G.; Okhrimenko, I.V.; Mirzeabassov, O.A.

    2000-01-01

    The use of 'soft' countermeasures (CMs) (agricultural CMs, some administrative ones, except for relocation/resettlement and some 'strong' measures on restriction of living conditions) allows considering the radiological and economic parameters for assessing their effectiveness. In this case cost-benefit analysis (CBA) or some its modification are used. However, the determination of various radiological and economic parameters (and their combination) is not enough for making final decisions on countermeasure implementation. All radiological, ecological and economic characteristics and other expert knowledge, corresponding standards and regulations should be taken into account, and many of them may not be used very often in analytical methods directly. The approaches to evaluating strong' CMs are based, as a rule, on expert judgements (MAUA, M-Crit). However, in practice they can lead to any result given in advance or to a choice of an weighted solution which does not comply with opinions by most experts due to considerable range of expert opinions and subjective weights for chosen attributes/criteria. Implementation of CMs on rehabilitation of contaminated territories should be based on the radiation protection principles. However, these principles are declared only when realising CMs on rehabilitation of contaminated territories after the Chernobyl accident. In practice some national or departmental standards are used and principles of justification'/'optimisation' are not examined. Taking into consideration a complex character of tasks on CM analysis and comparison of various alternatives it is quite necessary to use up-to-date computer decision support systems (DSSs). One of the systems which is directly intended for site-specific rehabilitation of territories subjected to radioactive contamination after the Chernobyl accident is the PRANA DSS. A key block of PRANA is 'analysis and optimisation of CMs structure'. It is intended for : -determination of territories

  2. Site-specific optimisation of the countermeasure structure on rehabilitation of radioactive contaminated territories

    Energy Technology Data Exchange (ETDEWEB)

    Yatsalo, B.I.; Okhrimenko, D.V.; Lisyanski, B.G.; Okhrimenko, I.V.; Mirzeabassov, O.A. [Obninsk Institute of Nuclear Power Engineering, Obninsk, Kaluga (Russian Federation)

    2000-05-01

    The use of 'soft' countermeasures (CMs) (agricultural CMs, some administrative ones, except for relocation/resettlement and some 'strong' measures on restriction of living conditions) allows considering the radiological and economic parameters for assessing their effectiveness. In this case cost-benefit analysis (CBA) or some its modification are used. However, the determination of various radiological and economic parameters (and their combination) is not enough for making final decisions on countermeasure implementation. All radiological, ecological and economic characteristics and other expert knowledge, corresponding standards and regulations should be taken into account, and many of them may not be used very often in analytical methods directly. The approaches to evaluating strong' CMs are based, as a rule, on expert judgements (MAUA, M-Crit). However, in practice they can lead to any result given in advance or to a choice of an weighted solution which does not comply with opinions by most experts due to considerable range of expert opinions and subjective weights for chosen attributes/criteria. Implementation of CMs on rehabilitation of contaminated territories should be based on the radiation protection principles. However, these principles are declared only when realising CMs on rehabilitation of contaminated territories after the Chernobyl accident. In practice some national or departmental standards are used and principles of justification'/'optimisation' are not examined. Taking into consideration a complex character of tasks on CM analysis and comparison of various alternatives it is quite necessary to use up-to-date computer decision support systems (DSSs). One of the systems which is directly intended for site-specific rehabilitation of territories subjected to radioactive contamination after the Chernobyl accident is the PRANA DSS. A key block of PRANA is 'analysis and optimisation of CMs structure

  3. Detection of Two Types of Weed through Machine Vision System: Improving Site-Specific Spraying

    Directory of Open Access Journals (Sweden)

    S Sabzi

    2018-03-01

    Full Text Available Introduction With increase in world population, one of the approaches to provide food is using site-specific management system or so-called precision farming. In this management system, management of crop production inputs such as fertilizers, lime, herbicides, seed, etc. is done based on farm location features, with the aim of reducing waste, increasing revenues and maintaining environmental quality. Precision farming involves various aspects and is applicable on farm fields at all stages of tillage, planting, and harvesting. Today, in line with precision farming purposes, and to control weeds, pests, and diseases, all the efforts of specialists in precision farming is to reduce the amount of chemical substances in products. Although herbicides improve the quality and quantity of agricultural production, the possibility of applying inappropriately and unreasonably is very high. If the dose is too low, weed control is not performed correctly. Otherwise, If the dosage is too high, herbicides can be toxic for crops, can be transferred to soil and stay in it for a long time, and can penetrate to groundwater. By applying herbicides to variable rate, the potential for significant cost savings and reduced environmental damage to the products and environment will be possible. It is evident that in large-scale modern agriculture, individual management of each plant without using some advanced technologies is not possible. using machine vision systems is one of precision farming techniques to identify weeds. This study aimed to detect three plant such as Centaurea depressa M.B, Malvaneglecta and Potato plant using machine vision system. Materials and Methods In order to train algorithm of designed machine vision system, a platform that moved with the speed of 10.34 was used for shooting of Marfona potato fields. This platform was consisted of a chassis, camera (DFK23GM021,CMOS, 120 f/s, Made in Germany, and a processor system equipped with Matlab 2015

  4. Src Kinase Inhibition Attenuates Morphine Tolerance without Affecting Reinforcement or Psychomotor Stimulation.

    Science.gov (United States)

    Bull, Fiona A; Baptista-Hon, Daniel T; Sneddon, Claire; Wright, Lisa; Walwyn, Wendy; Hales, Tim G

    2017-11-01

    Prolonged opioid administration leads to tolerance characterized by reduced analgesic potency. Pain management is additionally compromised by the hedonic effects of opioids, the cause of their misuse. The multifunctional protein β-arrestin2 regulates the hedonic effects of morphine and participates in tolerance. These actions might reflect µ opioid receptor up-regulation through reduced endocytosis. β-Arrestin2 also recruits kinases to µ receptors. We explored the role of Src kinase in morphine analgesic tolerance, locomotor stimulation, and reinforcement in C57BL/6 mice. Analgesic (tail withdrawal latency; percentage of maximum possible effect, n = 8 to 16), locomotor (distance traveled, n = 7 to 8), and reinforcing (conditioned place preference, n = 7 to 8) effects of morphine were compared in wild-type, µ, µ, and β-arrestin2 mice. The influence of c-Src inhibitors dasatinib (n = 8) and PP2 (n = 12) was examined. Analgesia in morphine-treated wild-type mice exhibited tolerance, declining by day 10 to a median of 62% maximum possible effect (interquartile range, 29 to 92%). Tolerance was absent from mice receiving dasatinib. Tolerance was enhanced in µ mice (34% maximum possible effect; interquartile range, 5 to 52% on day 5); dasatinib attenuated tolerance (100% maximum possible effect; interquartile range, 68 to 100%), as did PP2 (91% maximum possible effect; interquartile range, 78 to 100%). By contrast, c-Src inhibition affected neither morphine-evoked locomotor stimulation nor reinforcement. Remarkably, dasatinib not only attenuated tolerance but also reversed established tolerance in µ mice. The ability of c-Src inhibitors to inhibit tolerance, thereby restoring analgesia, without altering the hedonic effect of morphine, makes c-Src inhibitors promising candidates as adjuncts to opioid analgesics.

  5. Allometric Equations for Estimating Compartment Biomass and Stem Volume in Mature Hybrid Poplars: General or Site-Specific?

    Directory of Open Access Journals (Sweden)

    Julien Fortier

    2017-08-01

    Full Text Available We evaluated the extent to which general or site-specific allometric equations, using diameter at breast height (DBH as a predictor, are more accurate for estimating stem volume, stem biomass, branch biomass, aboveground woody biomass, and coarse root biomass in 14 year-old plantations of Populus canadensis × Populus maximowiczii (clone DN × M-915508 located along an environmental gradient in southern Québec (eastern Canada. The effect of tree size and site on stem wood basic density, moisture content, and proportion of branch biomass was also evaluated. For stem volume, stem biomass, and aboveground biomass, site-specific and general models had comparable fit and accuracy, but lower Akaike’s Information Criterion (AICc values were observed for the general models. For the branch and coarse root biomass, higher fit and accuracy and lower AICc values were observed for the site-specific models. Allometric trajectory changes (plastic allometry across sites were mainly observed for coarse root biomass, branch biomass, and stem volume. On the low fertility site, allocation was increased to coarse roots and decreased to stem volume. Site-specific tradeoffs between tree architecture and stem wood density explained the relatively invariant allometry for the whole aboveground woody biomass across the plantation sites. On the high fertility sites, basic wood density was the lowest and declined as tree DBH increased. At all sites, stem wood moisture content and the proportion of branch biomass increased with DBH. Overall, this study showed that biomass allometry, tree architecture, and biomass quality are a function of both tree size and plantation environment in hybrid poplar. Allometric model selection (site-specific or general should depend on the objective pursued (evaluation of yield, nutrient budget, carbon stocks.

  6. Characterization of site-specific biomechanical properties of human meniscus-Importance of collagen and fluid on mechanical nonlinearities.

    Science.gov (United States)

    Danso, E K; Mäkelä, J T A; Tanska, P; Mononen, M E; Honkanen, J T J; Jurvelin, J S; Töyräs, J; Julkunen, P; Korhonen, R K

    2015-06-01

    Meniscus adapts to joint loads by depth- and site-specific variations in its composition and structure. However, site-specific mechanical characteristics of intact meniscus under compression are poorly known. In particular, mechanical nonlinearities caused by different meniscal constituents (collagen and fluid) are not known. In the current study, in situ indentation testing was conducted to determine site-specific elastic, viscoelastic and poroelastic properties of intact human menisci. Lateral and medial menisci (n=26) were harvested from the left knee joint of 13 human cadavers. Indentation tests, using stress-relaxation and dynamic (sinusoidal) loading protocols, were conducted for menisci at different sites (anterior, middle, posterior, n=78). Sample- and site-specific axisymmetric finite element models with fibril-reinforced poroelastic properties were fitted to the corresponding stress-relaxation curves to determine the mechanical parameters. Elastic moduli, especially the instantaneous and dynamic moduli, showed site-specific variation only in the medial meniscus (pmeniscus. The phase angle showed no statistically significant variation between the sites (p>0.05). The values for the strain-dependent fibril network modulus (nonlinear behaviour of collagen) were significantly different (pmeniscus only between the middle and posterior sites. For the strain-dependent permeability coefficient, only anterior and middle sites showed a significant difference (pmeniscus. This parameter demonstrated a significant difference (pmeniscus shows more site-dependent variation in the mechanical properties as compared to lateral meniscus. In particular, anterior horn of medial meniscus was the stiffest and showed the most nonlinear mechanical behaviour. The nonlinearity was related to both collagen fibrils and fluid. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. An economic analysis of high-dose imatinib, dasatinib, and nilotinib for imatinib-resistant chronic phase chronic myeloid leukemia in China: A CHEERS-compliant article.

    Science.gov (United States)

    Wu, Bin; Liu, Maobai; Li, Te; Lin, Houwen; Zhong, Hua

    2017-07-01

    The aim of the study was to test the cost-effectiveness of dasatinib compared to high-dose imatinib and nilotinib in Chinese patients who were diagnosed with imatinib-resistant chronic myeloid leukemia in the chronic phase (CML-CP). A Markov model combined with clinical effectiveness, utility, and cost data was used. The sensitivity analyses were conducted to determine the robustness of the model outcomes. The impact of patient assistance programs (PAPs) was assessed. Treatment with dasatinib is expected to produce 3.65, 0.59, and 0.15 more quality-adjusted life years (QALYs) in comparison with high-dose imatinib (600 and 800 mg) and nilotinib, respectively. When a PAP was available, dasatinib yielded an incremental cost of $16,417 per QALY compared to imatinib (600 mg) and was cost-saving compared to imatinib (800 mg) and nilotinib. When PAP is available in the Chinese setting, dasatinib is likely to be a cost-effective strategy for patients with CML-CP standard-dose imatinib resistance. The results should be carefully explained due to the assumptions and limitations used in the study.

  8. Safety and efficacy of the combination of pegylated interferon-α2b and dasatinib in newly diagnosed chronic-phase chronic myeloid leukemia patients

    DEFF Research Database (Denmark)

    Hjorth-Hansen, H; Stentoft, J; Richter, J

    2016-01-01

    Dasatinib (DAS) and interferon-α have antileukemic and immunostimulatory effects and induce deep responses in chronic myeloid leukemia (CML). We assigned 40 newly diagnosed chronic-phase CML patients to receive DAS 100 mg o.d. followed by addition of pegylated interferon-α2b (PegIFN) after 3 months...

  9. The Structure of Dasatinib (BNS-354825) Bound to Activated ABL Kinase Domain Elucidates its Inhibitory Activity Against Imatinib-Resistant ABL Mutants

    Energy Technology Data Exchange (ETDEWEB)

    Tokarski,J.; Newitt, J.; Chang, C.; Cheng, J.; Wittekind, M.; Kiefer, S.; Kish, K.; Lee, F.; Borzilerri, R.; et al.

    2006-01-01

    Chronic myeloid leukemia (CML) is caused by the constitutively activated tyrosine kinase breakpoint cluster (BCR)-ABL. Current frontline therapy for CML is imatinib, an inhibitor of BCR-ABL. Although imatinib has a high rate of clinical success in early phase CML, treatment resistance is problematic, particularly in later stages of the disease, and is frequently mediated by mutations in BCR-ABL. Dasatinib (BMS-354825) is a multitargeted tyrosine kinase inhibitor that targets oncogenic pathways and is a more potent inhibitor than imatinib against wild-type BCR-ABL. It has also shown preclinical activity against all but one of the imatinib-resistant BCR-ABL mutants tested to date. Analysis of the crystal structure of dasatinib-bound ABL kinase suggests that the increased binding affinity of dasatinib over imatinib is at least partially due to its ability to recognize multiple states of BCR-ABL. The structure also provides an explanation for the activity of dasatinib against imatinib-resistant BCR-ABL mutants.

  10. A simple reduction-sensitive micelles co-delivery of paclitaxel and dasatinib to overcome tumor multidrug resistance

    Directory of Open Access Journals (Sweden)

    Li J

    2017-11-01

    Full Text Available Jun Li,1,* Ruitong Xu,2,* Xiao Lu,3 Jing He,1 Shidai Jin1 1Department of Medical Oncology, 2Department of General Practice, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 3Department of Medical Oncology, Changshu No 1 People’s Hospital, Changshu, People’s Republic of China *These authors contributed equally to this work Abstract: Multidrug resistance (MDR is one of the major obstacles in successful chemotherapy. The combination of chemotherapy drugs and multidrug-resistant reversing agents for treating MDR tumor is a good strategy to overcome MDR. In this work, we prepared the simple redox-responsive micelles based on mPEG-SS-C18 as a co-delivery system to load the paclitaxel (PTX and dasatinib (DAS for treatment of MCF-7/ADR cells. The co-loaded micelles had a good dispersity and a spherical shape with a uniform size distribution, and they could quickly disassemble and rapidly release drugs under the reduction environment. Compared with MCF-7 cells, the DAS and PTX co-loaded redox-sensitive micelle (SS-PDNPs showed stronger cytotoxicity and a more improving intracellular drug concentration than other drug formulations in MCF-7/ADR cells. In summary, the results suggested that the simple co-delivery micelles of PTX and DAS possessed significant potential to overcome drug resistance in cancer therapy. Keywords: redox responsive, overcoming multidrug resistant, co-delivery, paclitaxel, dasatinib 

  11. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Lyon, David; Young, Clifford

    2017-01-01

    -predictive analyses revealed that lysines residing in disordered regions are preferentially targeted by SUMO, in notable contrast to other widespread lysine modifications. In our data set, we identified 807 SUMOylated peptides that were co-modified by phosphorylation, along with dozens of SUMOylated peptides...... that were co-modified by ubiquitylation, acetylation and methylation. Notably, 9% of the identified SUMOylome occurred proximal to phosphorylation, and numerous SUMOylation sites were found to be fully dependent on prior phosphorylation events. SUMO-proximal phosphorylation occurred primarily in a proline......-directed manner, and inhibition of cyclin-dependent kinases dynamically affected co-modification. Collectively, we present a comprehensive analysis of the SUMOylated proteome, uncovering the structural preferences for SUMO and providing system-wide evidence for a remarkable degree of cross-talk between...

  12. BTK inhibition is a potent approach to block IgE-mediated histamine release in human basophils.

    Science.gov (United States)

    Smiljkovic, D; Blatt, K; Stefanzl, G; Dorofeeva, Y; Skrabs, C; Focke-Tejkl, M; Sperr, W R; Jaeger, U; Valenta, R; Valent, P

    2017-11-01

    Recent data suggest that Bruton's tyrosine kinase (BTK) is an emerging therapeutic target in IgE receptor (IgER)-cross-linked basophils. We examined the effects of four BTK inhibitors (ibrutinib, dasatinib, AVL-292, and CNX-774) on IgE-dependent activation and histamine release in blood basophils obtained from allergic patients (n=11) and nonallergic donors (n=5). In addition, we examined the effects of these drugs on the growth of the human basophil cell line KU812 and the human mast cell line HMC-1. All four BTK blockers were found to inhibit anti-IgE-induced histamine release from basophils in nonallergic subjects and allergen-induced histamine liberation from basophils in allergic donors. Drug effects on allergen-induced histamine release were dose dependent, with IC 50 values ranging between 0.001 and 0.5 μmol/L, and the following rank order of potency: ibrutinib>AVL-292>dasatinib>CNX-774. The basophil-targeting effect of ibrutinib was confirmed by demonstrating that IgE-dependent histamine release in ex vivo blood basophils is largely suppressed in a leukemia patient treated with ibrutinib. Dasatinib and ibrutinib were also found to counteract anti-IgE-induced and allergen-induced upregulation of CD13, CD63, CD164, and CD203c on basophils, whereas AVL-292 and CNX-774 showed no significant effects. Whereas dasatinib and CNX-774 were found to inhibit the growth of HMC-1 cells and KU812 cells, no substantial effects were seen with ibrutinib or AVL-292. BTK-targeting drugs are potent inhibitors of IgE-dependent histamine release in human basophils. The clinical value of BTK inhibition in the context of allergic diseases remains to be determined. © 2017 The Authors. Allergy Published by John Wiley & Sons Ltd.

  13. Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase

    Science.gov (United States)

    Kirchmaier, Stephan; Höckendorf, Burkhard; Möller, Eva Katharina; Bornhorst, Dorothee; Spitz, Francois; Wittbrodt, Joachim

    2013-01-01

    Established transgenesis methods for fish model systems allow efficient genomic integration of transgenes. However, thus far a way of controlling copy number and integration sites has not been available, leading to variable transgene expression caused by position effects. The integration of transgenes at predefined genomic positions enables the direct comparison of different transgenes, thereby improving time and cost efficiency. Here, we report an efficient PhiC31-based site-specific transgenesis system for medaka. This system includes features that allow the pre-selection of successfully targeted integrations early on in the injected generation. Pre-selected embryos transmit the correctly integrated transgene through the germline with high efficiency. The landing site design enables a variety of applications, such as reporter and enhancer switch, in addition to the integration of any insert. Importantly, this allows assaying of enhancer activity in a site-specific manner without requiring germline transmission, thus speeding up large-scale analyses of regulatory elements. PMID:24048591

  14. Site-specific labeling of synthetic peptide using the chemoselective reaction between N-methoxyamino acid and isothiocyanate.

    Science.gov (United States)

    Hara, Toshiaki; Purwati, Euis Maras; Tainosyo, Akira; Kawakami, Toru; Hojo, Hironobu; Aimoto, Saburo

    2015-10-01

    Site-specific labeling of synthetic peptides carrying N-methoxyglycine (MeOGly) by isothiocyanate is demonstrated. A nonapeptide having MeOGly at its N-terminus was synthesized by the solid-phase method and reacted with phenylisothiocyanate under various conditions. In acidic solution, the reaction specifically gave a peptide having phenylthiourea structure at its N-terminus, leaving side chain amino group intact. The synthetic human β-defensin-2 carrying MeOGly at its N-terminus or the side chain amino group of Lys(10) reacted with phenylisothiocyanate or fluorescein isothiocyanate also at the N-methoxyamino group under the same conditions, demonstrating that this method is generally useful for the site-specific labeling of linear synthetic peptides as well as disulfide-containing peptides. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

  15. Immobilization of alkaline phosphatase on magnetic particles by site-specific and covalent cross-linking catalyzed by microbial transglutaminase.

    Science.gov (United States)

    Moriyama, Kousuke; Sung, Kyunga; Goto, Masahiro; Kamiya, Noriho

    2011-06-01

    Bacterial alkaline phosphatase (BAP) was site-specifically and covalently immobilized on magnetic particles (MPs) using the enzymatic reaction of microbial transglutaminase (MTG). Immobilization efficiency was affected by the chemical surface treatment of MPs and immobilized BAP exhibited more than 90% of the initial activity after 10 rounds of recycling. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  16. A Comparative `Bottom Up' Proteomics Strategy for the Site-specific Identification and Quantification of Protein Modifications By Electrophilic Lipids

    OpenAIRE

    Han, Bingnan; Hare, Michael; Wickramasekara, Samanthi; Fang, Yi; Maier, Claudia S.

    2012-01-01

    We report a mass spectrometry-based comparative “bottom up” proteomics approach that combines d0/d4-succinic anhydride labeling with commercially available hydrazine (Hz)-functionalized beads (Affi-gel Hz beads) for detection, identification and relative quantification of site-specific oxylipid modifications in biological matrices. We evaluated and applied this robust and simple method for the quantitative analysis of oxylipid protein conjugates in cardiac mitochondrial proteome samples isola...

  17. Site-specific RNase A activity was dramatically reduced in serum from multiple types of cancer patients.

    Directory of Open Access Journals (Sweden)

    Weiyan Huang

    Full Text Available Potent RNase activities were found in the serum of mammals but the physiological function of the RNases was never well illustrated, largely due to the caveats in methods of RNase activity measurement. None of the existing methods can distinguish between RNases with different target specificities. A systematic study was recently carried out in our lab to investigate the site-specificity of serum RNases on double-stranded RNA substrates, and found that serum RNases cleave double-stranded RNAs predominantly at 5'-U/A-3' and 5'-C/A-3' dinucleotide sites, in a manner closely resembling RNase A. Based on this finding, a FRET assay was developed in the current study to measure this site-specific serum RNase activity in human samples using a double stranded RNA substrate. We demonstrated that the method has a dynamic range of 10(-5 mg/ml- 10(-1 mg/ml using serial dilution of RNase A. The sera of 303 cancer patients were subjected to comparison with 128 healthy controls, and it was found that serum RNase activities visualized with this site-specific double stranded probe were found to be significantly reduced in patients with gastric cancer, liver cancer, pancreatic cancer, esophageal cancer, ovary cancer, cervical cancer, bladder cancer, kidney cancer and lung cancer, while only minor changes were found in breast and colon cancer patients. This is the first report using double stranded RNA as probe to quantify site-specific activities of RNase A in a serum. The results illustrated that RNase A might be further evaluated to determine if it can serve as a new class of biomarkers for certain cancer types.

  18. Site-Specific RNase A Activity Was Dramatically Reduced in Serum from Multiple Types of Cancer Patients

    Science.gov (United States)

    Huang, Weiyan; Zhao, Mei; Wei, Na; Wang, Xiaoxia; Cao, Huqing; Du, Quan; Liang, Zicai

    2014-01-01

    Potent RNase activities were found in the serum of mammals but the physiological function of the RNases was never well illustrated, largely due to the caveats in methods of RNase activity measurement. None of the existing methods can distinguish between RNases with different target specificities. A systematic study was recently carried out in our lab to investigate the site-specificity of serum RNases on double-stranded RNA substrates, and found that serum RNases cleave double-stranded RNAs predominantly at 5′-U/A-3′ and 5′-C/A-3′ dinucleotide sites, in a manner closely resembling RNase A. Based on this finding, a FRET assay was developed in the current study to measure this site-specific serum RNase activity in human samples using a double stranded RNA substrate. We demonstrated that the method has a dynamic range of 10−5 mg/ml- 10−1 mg/ml using serial dilution of RNase A. The sera of 303 cancer patients were subjected to comparison with 128 healthy controls, and it was found that serum RNase activities visualized with this site-specific double stranded probe were found to be significantly reduced in patients with gastric cancer, liver cancer, pancreatic cancer, esophageal cancer, ovary cancer, cervical cancer, bladder cancer, kidney cancer and lung cancer, while only minor changes were found in breast and colon cancer patients. This is the first report using double stranded RNA as probe to quantify site-specific activities of RNase A in a serum. The results illustrated that RNase A might be further evaluated to determine if it can serve as a new class of biomarkers for certain cancer types. PMID:24805924

  19. Site Specific Waste Management Instructions for loading and shipment of category 3 investigation derived waste to ERDF

    International Nuclear Information System (INIS)

    Corriveau, C.E.; Wolf, D.M.

    1996-08-01

    This Site Specific Waste Management Instruction (SSWMI) provides guidance for management of containerized investigation-derived waste being loaded and transported to the Environmental Restoration Disposal Facility. The SSWMI outlines the waste management practices that will be performed in the field to implement federal, state, and US Department of Energy requirements. Additional guidance for waste packaging, marking, labeling and shipping is provided (US DOT rules in 49 CFR have precedence)

  20. Clearing the waters: Evaluating the need for site-specific field fluorescence corrections based on turbidity measurements

    Science.gov (United States)

    Saraceno, John F.; Shanley, James B.; Downing, Bryan D.; Pellerin, Brian A.

    2017-01-01

    In situ fluorescent dissolved organic matter (fDOM) measurements have gained increasing popularity as a proxy for dissolved organic carbon (DOC) concentrations in streams. One challenge to accurate fDOM measurements in many streams is light attenuation due to suspended particles. Downing et al. (2012) evaluated the need for corrections to compensate for particle interference on fDOM measurements using a single sediment standard in a laboratory study. The application of those results to a large river improved unfiltered field fDOM accuracy. We tested the same correction equation in a headwater tropical stream and found that it overcompensated fDOM when turbidity exceeded ∼300 formazin nephelometric units (FNU). Therefore, we developed a site-specific, field-based fDOM correction equation through paired in situ fDOM measurements of filtered and unfiltered streamwater. The site-specific correction increased fDOM accuracy up to a turbidity as high as 700 FNU, the maximum observed in this study. The difference in performance between the laboratory-based correction equation of Downing et al. (2012) and our site-specific, field-based correction equation likely arises from differences in particle size distribution between the sediment standard used in the lab (silt) and that observed in our study (fine to medium sand), particularly during high flows. Therefore, a particle interference correction equation based on a single sediment type may not be ideal when field sediment size is significantly different. Given that field fDOM corrections for particle interference under turbid conditions are a critical component in generating accurate DOC estimates, we describe a way to develop site-specific corrections.

  1. Development of Site-Specific Water Quality Criteria for the Arpa Harbor Wastewater Treatment Plant in Tipalao Bay, Guam

    Science.gov (United States)

    2016-07-01

    statistics and calculation of fD. The standard deviation in measured concentration is provided for those samples analyzed in duplicate. 49 Table...Arithmetic means and standard deviations for Guam site specific criterion and equivalent estimated chronic limits (ECL) generated from WER and BLM...on 29 April 2013. Std. Dev. is standard deviation . 95th % is 95th percentile, 25th % is 25th percentile, Geomean is geometric mean

  2. CRISPR/Cas9-loxP-Mediated Gene Editing as a Novel Site-Specific Genetic Manipulation Tool.

    Science.gov (United States)

    Yang, Fayu; Liu, Changbao; Chen, Ding; Tu, Mengjun; Xie, Haihua; Sun, Huihui; Ge, Xianglian; Tang, Lianchao; Li, Jin; Zheng, Jiayong; Song, Zongming; Qu, Jia; Gu, Feng

    2017-06-16

    Cre-loxP, as one of the site-specific genetic manipulation tools, offers a method to study the spatial and temporal regulation of gene expression/inactivation in order to decipher gene function. CRISPR/Cas9-mediated targeted genome engineering technologies are sparking a new revolution in biological research. Whether the traditional site-specific genetic manipulation tool and CRISPR/Cas9 could be combined to create a novel genetic tool for highly specific gene editing is not clear. Here, we successfully generated a CRISPR/Cas9-loxP system to perform gene editing in human cells, providing the proof of principle that these two technologies can be used together for the first time. We also showed that distinct non-homologous end-joining (NHEJ) patterns from CRISPR/Cas9-mediated gene editing of the targeting sequence locates at the level of plasmids (episomal) and chromosomes. Specially, the CRISPR/Cas9-mediated NHEJ pattern in the nuclear genome favors deletions (64%-68% at the human AAVS1 locus versus 4%-28% plasmid DNA). CRISPR/Cas9-loxP, a novel site-specific genetic manipulation tool, offers a platform for the dissection of gene function and molecular insights into DNA-repair pathways. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  3. Site-specific integration and expression of an anti-malarial gene in transgenic Anopheles gambiae significantly reduces Plasmodium infections.

    Directory of Open Access Journals (Sweden)

    Janet M Meredith

    2011-01-01

    Full Text Available Diseases transmitted by mosquitoes have a devastating impact on global health and this is worsening due to difficulties with existing control measures and climate change. Genetically modified mosquitoes that are refractory to disease transmission are seen as having great potential in the delivery of novel control strategies. Historically the genetic modification of insects has relied upon transposable elements which have many limitations despite their successful use. To circumvent these limitations the Streptomyces phage phiC31 integrase system has been successfully adapted for site-specific transgene integration in insects. Here, we present the first site-specific transformation of Anopheles gambiae, the principal vector of human malaria. Mosquitoes were initially engineered to incorporate the phiC31 targeting site at a defined genomic location. A second phase of genetic modification then achieved site-specific integration of Vida3, a synthetic anti-malarial gene. Expression of Vida3, specifically in the midgut of bloodfed females, offered consistent and significant protection against Plasmodium yoelii nigeriensis, reducing average parasite intensity by 85%. Similar protection was observed against Plasmodium falciparum in some experiments, although protection was inconsistent. In the fight against malaria, it is imperative to establish a broad repertoire of both anti-malarial effector genes and tissue-specific promoters for their expression, enabling those offering maximum effect with minimum fitness cost to be identified. In the future, this technology will allow effective comparisons and informed choices to be made, potentially leading to complete transmission blockade.

  4. The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast.

    Science.gov (United States)

    Larsen, Nicolai B; Sass, Ehud; Suski, Catherine; Mankouri, Hocine W; Hickson, Ian D

    2014-04-07

    Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus, to specific DNA sequences called Ter. Here, we demonstrate that Tus-Ter modules also induce polar RF pausing when engineered into the Saccharomyces cerevisiae genome. This heterologous RF barrier is distinct from a number of previously characterized, protein-mediated, RF pause sites in yeast, as it is neither Tof1-dependent nor counteracted by the Rrm3 helicase. Although the yeast replisome can overcome RF pausing at Tus-Ter modules, this event triggers site-specific homologous recombination that requires the RecQ helicase, Sgs1, for its timely resolution. We propose that Tus-Ter can be utilized as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications.

  5. Site-Specific SERS Assay for Survivin Protein Dimer: From Ensemble Experiments to Correlative Single-Particle Imaging.

    Science.gov (United States)

    Wissler, Jörg; Bäcker, Sandra; Feis, Alessandro; Knauer, Shirley K; Schlücker, Sebastian

    2017-08-01

    An assay for Survivin, a small dimeric protein which functions as modulator of apoptosis and cell division and serves as a promising diagnostic biomarker for different types of cancer, is presented. The assay is based on switching on surface-enhanced Raman scattering (SERS) upon incubation of the Survivin protein dimer with Raman reporter-labeled gold nanoparticles (AuNP). Site-specificity is achieved by complexation of nickel-chelated N-nitrilo-triacetic acid (Ni-NTA) anchors on the particle surface by multiple histidines (His 6 -tag) attached to each C-terminus of the centrosymmetric protein dimer. Correlative single-particle analysis using light sheet laser microscopy enables the simultaneous observation of both elastic and inelastic light scattering from the same sample volume. Thereby, the SERS-inactive AuNP-protein monomers can be directly discriminated from the SERS-active AuNP-protein dimers/oligomers. This information, i.e. the percentage of SERS-active AuNP in colloidal suspension, is not accessible from conventional SERS experiments due to ensemble averaging. The presented correlative single-particle approach paves the way for quantitative site-specific SERS assays in which site-specific protein recognition by small chemical and in particular supramolecular ligands can be tested. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Site-specific probabilistic seismic hazard analyses for the Idaho National Engineering Laboratory. Volume 1: Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-05-01

    This report describes and summarizes a probabilistic evaluation of ground motions for the Idaho National Engineering Laboratory (INEL). The purpose of this evaluation is to provide a basis for updating the seismic design criteria for the INEL. In this study, site-specific seismic hazard curves were developed for seven facility sites as prescribed by DOE Standards 1022-93 and 1023-96. These sites include the: Advanced Test Reactor (ATR); Argonne National Laboratory West (ANL); Idaho Chemical Processing Plant (ICPP or CPP); Power Burst Facility (PBF); Radioactive Waste Management Complex (RWMC); Naval Reactor Facility (NRF); and Test Area North (TAN). The results, probabilistic peak ground accelerations and uniform hazard spectra, contained in this report are not to be used for purposes of seismic design at INEL. A subsequent study will be performed to translate the results of this probabilistic seismic hazard analysis to site-specific seismic design values for the INEL as per the requirements of DOE Standard 1020-94. These site-specific seismic design values will be incorporated into the INEL Architectural and Engineering Standards.

  7. Site-specific probabilistic seismic hazard analyses for the Idaho National Engineering Laboratory. Volume 1: Final report

    International Nuclear Information System (INIS)

    1996-05-01

    This report describes and summarizes a probabilistic evaluation of ground motions for the Idaho National Engineering Laboratory (INEL). The purpose of this evaluation is to provide a basis for updating the seismic design criteria for the INEL. In this study, site-specific seismic hazard curves were developed for seven facility sites as prescribed by DOE Standards 1022-93 and 1023-96. These sites include the: Advanced Test Reactor (ATR); Argonne National Laboratory West (ANL); Idaho Chemical Processing Plant (ICPP or CPP); Power Burst Facility (PBF); Radioactive Waste Management Complex (RWMC); Naval Reactor Facility (NRF); and Test Area North (TAN). The results, probabilistic peak ground accelerations and uniform hazard spectra, contained in this report are not to be used for purposes of seismic design at INEL. A subsequent study will be performed to translate the results of this probabilistic seismic hazard analysis to site-specific seismic design values for the INEL as per the requirements of DOE Standard 1020-94. These site-specific seismic design values will be incorporated into the INEL Architectural and Engineering Standards

  8. Bioavailability of particulate metal to zebra mussels: Biodynamic modelling shows that assimilation efficiencies are site-specific

    Energy Technology Data Exchange (ETDEWEB)

    Bourgeault, Adeline, E-mail: bourgeault@ensil.unilim.fr [Cemagref, Unite de Recherche Hydrosystemes et Bioprocedes, 1 rue Pierre-Gilles de Gennes, 92761 Antony (France); FIRE, FR-3020, 4 place Jussieu, 75005 Paris (France); Gourlay-France, Catherine, E-mail: catherine.gourlay@cemagref.fr [Cemagref, Unite de Recherche Hydrosystemes et Bioprocedes, 1 rue Pierre-Gilles de Gennes, 92761 Antony (France); FIRE, FR-3020, 4 place Jussieu, 75005 Paris (France); Priadi, Cindy, E-mail: cindy.priadi@eng.ui.ac.id [LSCE/IPSL CEA-CNRS-UVSQ, Avenue de la Terrasse, 91198 Gif-sur-Yvette (France); Ayrault, Sophie, E-mail: Sophie.Ayrault@lsce.ipsl.fr [LSCE/IPSL CEA-CNRS-UVSQ, Avenue de la Terrasse, 91198 Gif-sur-Yvette (France); Tusseau-Vuillemin, Marie-Helene, E-mail: Marie-helene.tusseau@ifremer.fr [IFREMER Technopolis 40, 155 rue Jean-Jacques Rousseau, 92138 Issy-Les-Moulineaux (France)

    2011-12-15

    This study investigates the ability of the biodynamic model to predict the trophic bioaccumulation of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni) and zinc (Zn) in a freshwater bivalve. Zebra mussels were transplanted to three sites along the Seine River (France) and collected monthly for 11 months. Measurements of the metal body burdens in mussels were compared with the predictions from the biodynamic model. The exchangeable fraction of metal particles did not account for the bioavailability of particulate metals, since it did not capture the differences between sites. The assimilation efficiency (AE) parameter is necessary to take into account biotic factors influencing particulate metal bioavailability. The biodynamic model, applied with AEs from the literature, overestimated the measured concentrations in zebra mussels, the extent of overestimation being site-specific. Therefore, an original methodology was proposed for in situ AE measurements for each site and metal. - Highlights: > Exchangeable fraction of metal particles did not account for the bioavailability of particulate metals. > Need for site-specific biodynamic parameters. > Field-determined AE provide a good fit between the biodynamic model predictions and bioaccumulation measurements. - The interpretation of metal bioaccumulation in transplanted zebra mussels with biodynamic modelling highlights the need for site-specific assimilation efficiencies of particulate metals.

  9. Nerve Agent Exposure Elicits Site-Specific Changes in Protein Phosphorylation in Mouse Brain

    Science.gov (United States)

    Zhu, Hongwen; O’Brien, Jennifer J.; O’Callaghan, James P.; Miller, Diane B.; Zhang, Qiang; Rana, Minal; Tsui, Tiffany; Peng, Youyi; Tomesch, John; Hendrick, Joseph P.; Wennogle, Lawrence P; Snyder, Gretchen L.

    2010-01-01

    Organophosphorus (OP) compounds cause toxic symptoms, including convulsions, coma, and death, as the result of irreversible inhibition of acetylcholinesterase (AChE). The development of effective treatments to block these effects and attenuate long-term cognitive and motor disabilities that result from OP intoxication is hampered by a limited understanding of the CNS pathways responsible for these actions. We employed a candidate method (called CNSProfile™) to identify changes in the phosphorylation state of key neuronal phosphoproteins evoked by the OP compound, diisopropyl fluorophosphate (DFP). Focused microwave fixation was used to preserve the phosphorylation state of phosphoproteins in brains of DFP-treated mice; hippocampus and striatum were analyzed by immunoblotting with a panel of phospho-specific antibodies. DFP exposure elicited comparable effects on phosphorylation of brain phosphoproteins in both C57BL/6 and FVB mice. DFP treatment significantly altered phosphorylation at regulatory residues on glutamate receptors, including Serine897 (S897) of the NR1 NMDA receptor. NR1 phosphorylation was bi-directionally regulated after DFP in striatum versus hippocampus. NR1 phosphorylation was reduced in striatum, but elevated in hippocampus, compared with controls. DARPP-32 phosphorylation in striatum was selectively increased at the Cdk5 kinase substrate, Threonine75 (T75). Phencynonate hydrochloride, a muscarinic cholinergic antagonist, prevented seizure-like behaviors and the observed changes in phosphorylation induced by DFP. The data reveal region-specific effects of nerve agent exposure on intracellular signaling pathways that correlate with seizure-like behavior and which are reversed by the muscarinic receptor blockade. This approach identifies specific targets for nerve agents, including substrates for Cdk5 kinase, which may be the basis for new anti-convulsant therapies. PMID:20423708

  10. Use of site specific data from Aespoe - preliminary results from the on-going safety analysis SR 97

    International Nuclear Information System (INIS)

    Stroem, A.; Selroos, J.O.; Andersson, Johan

    1998-01-01

    This paper discusses an on-going safety assessment study of SKB as well as the use of field data from Aespoe for obtaining input parameters for flow and radionuclide transport modelling in the geosphere. In the on-going Safety Assessment study SR 97, three individual sites in Sweden are used for exemplifying site specific conditions on overall repository performance. Thus, models capable of reproducing site specific characteristics are utilised. This is primarily obtained by implementing the geologic structural models in suitable conceptual models for groundwater flow on both regional and local scales. The models for flow incorporate observed and/or inferred water conducting features as well as other site-specific characteristics necessary for realistic descriptions of flow at the sites. The flow modelling thus aims at realism; the results obtained for present day conditions should not in any serious aspect conflict with observations at the site. Agreement between observed and modelled entities provides confidence in that a sound understanding of the site is obtained. Aespoe is one of the three sites providing site-specific conditions in SR 97. Transport is subsequently modelled using a stream tube approach where the 'travel times', for non-sorbing species, and discharge locations of a set of one-dimensional stream tubes are obtained from particle tracking in the flow model. The resulting distribution of 'travel times' in a single model realisation reflects the spatial variability and spatial extent of the repository, whereas the ensemble travel time distribution (over several realisations) for a given canister location reflects the uncertainty in travel time. The actual transport paths used in the transport modelling are thus dependent on site specific information such as e.g. existence of water conductive features. Other input parameters to the transport model are based on more generic and/or conservative arguments. However, the goal in a safety assessment

  11. Female site-specific transposase-induced recombination: a high-efficiency method for fine mapping mutations on the X chromosome in Drosophila.

    OpenAIRE

    Marcus, Jeffrey M

    2003-01-01

    P-element transposons in the Drosophila germline mobilize only in the presence of the appropriate transposase enzyme. Sometimes, instead of mobilizing completely, P elements will undergo site-specific recombination with the homologous chromosome. Site-specific recombination is the basis for male recombination mapping, since the male germline does not normally undergo recombination. Site-specific recombination also takes place in females, but this has been difficult to study because of the obs...

  12. Patients with Philadelphia-positive leukemia with Y253H or F359V mutation have a high risk of developing new mutations in the setting of dasatinib resistance.

    Science.gov (United States)

    Jiang, Qian; Qin, Ya-Zhen; Lai, Yue-Yun; Jiang, Hao; Wang, Jing; Huang, Xiao-Jun

    2015-07-01

    The treatment outcome and development of new mutations in patients with imatinib- and/or nilotinib-failure Philadelphia chromosome positive (Ph+) leukemia with highly nilotinib-resistant mutations (Y253H, E255K/V and F359V/C) were assessed on dasatinib therapy. A total of 111 patients with Ph+ leukemia were grouped into three cohorts by baseline BCR-ABL kinase domain mutation status: no mutation (n = 44), non-nilotinib-resistant mutations (n = 26) or nilotinib-resistant mutations (n = 41). The frequencies of hematological, cytogenetic and molecular responses and clinical resistance to dasatinib were similar among the three cohorts during dasatinib therapy. In dasatinib-resistant patients, new mutations were most frequently observed in the cohort with nilotinib-resistant mutations (p = 0.001). Multivariate analysis revealed that advanced disease and harboring Y253H or F359V mutation before dasatinib were independent predictors of developing new mutations. We conclude that patients with Ph+ leukemia with Y253H or F359V mutation have a high likelihood of developing new mutations in the setting of dasatinib resistance.

  13. Prognostic impact of deletions of derivative chromosome 9 in patients with chronic myelogenous leukemia treated with nilotinib or dasatinib.

    Science.gov (United States)

    Quintás-Cardama, Alfonso; Kantarjian, Hagop; Shan, Jianqin; Jabbour, Elias; Abruzzo, Lynne V; Verstovsek, Srdan; Garcia-Manero, Guillermo; O'Brien, Susan; Cortes, Jorge

    2011-11-15

    Deletions of derivative chromosome 9 are a poor prognostic factor in patients with chronic myeloid leukemia (CML) treated with hydroxyurea, interferon, or stem cell transplantation. Imatinib may overcome the adverse prognostic impact of deletions of derivative chromosome 9. A study was undertaken to investigate the prognostic impact of deletions of derivative chromosome 9 in 353 patients with CML receiving the second generation tyrosine kinase inhibitors (TKIs) nilotinib (n = 161) or dasatinib (n = 192). Deletion of derivative chromosome 9 status was determined in 245 (69%). Twenty-eight (11%) patients, 22 in chronic phase, 4 in accelerated phase, and 2 in blast phase, carried deletions of derivative chromosome 9, including 17 receiving nilotinib and 11 receiving dasatinib (P = .47). Overall survival (OS) at 24 months was similar between patients with or without deletions of derivative chromosome 9 (70% vs 71%, P = .76). For patients in chronic phase, no significant differences in overall major cytogenetic response (77% vs 82%, P = .57) or complete cytogenetic response (77% vs 81%, P = .71) rates were observed between patients with or without deletions of derivative chromosome 9. At 24 months, patients with CML in chronic phase without deletions of derivative chromosome 9 had improved event-free survival (EFS) (88% vs 66%, P = .07) and OS (96% vs 82%; P = .08) compared with those carrying deletions of derivative chromosome 9. However, multivariate analysis established second-line versus frontline second generation TKI therapy as the only adverse prognostic factor for EFS and increased bone marrow blast burden and older age as independent adverse prognostic factors for OS. Deletions of derivative chromosome 9 do not appear to be an independent risk factor for survival among patients with CML in chronic phase receiving second generation TKIs. Copyright © 2011 American Cancer Society.

  14. Accounting for both local aquatic community composition and bioavailability in setting site-specific quality standards for zinc.

    Science.gov (United States)

    Peters, Adam; Simpson, Peter; Moccia, Alessandra

    2014-01-01

    Recent years have seen considerable improvement in water quality standards (QS) for metals by taking account of the effect of local water chemistry conditions on their bioavailability. We describe preliminary efforts to further refine water quality standards, by taking account of the composition of the local ecological community (the ultimate protection objective) in addition to bioavailability. Relevance of QS to the local ecological community is critical as it is important to minimise instances where quality classification using QS does not reconcile with a quality classification based on an assessment of the composition of the local ecology (e.g. using benthic macroinvertebrate quality assessment metrics such as River InVertebrate Prediction and Classification System (RIVPACS)), particularly where ecology is assessed to be at good or better status, whilst chemical quality is determined to be failing relevant standards. The alternative approach outlined here describes a method to derive a site-specific species sensitivity distribution (SSD) based on the ecological community which is expected to be present at the site in the absence of anthropogenic pressures (reference conditions). The method combines a conventional laboratory ecotoxicity dataset normalised for bioavailability with field measurements of the response of benthic macroinvertebrate abundance to chemical exposure. Site-specific QSref are then derived from the 5%ile of this SSD. Using this method, site QSref have been derived for zinc in an area impacted by historic mining activities. Application of QSref can result in greater agreement between chemical and ecological metrics of environmental quality compared with the use of either conventional (QScon) or bioavailability-based QS (QSbio). In addition to zinc, the approach is likely to be applicable to other metals and possibly other types of chemical stressors (e.g. pesticides). However, the methodology for deriving site-specific targets requires

  15. Direct toxicity assessment of volatile chlorinated hydrocarbon-contaminated groundwater and derivation of a site-specific guideline.

    Science.gov (United States)

    Hunt, James; Birch, Gavin; Warne, Michael St John; Krassoi, Rick

    2009-04-01

    Groundwater contaminated with a mixture of 14 volatile chlorinated hydrocarbons (VCHs) discharges to an estuarine embayment in Sydney, Australia. A screening-level hazard assessment identified a potential risk to aquatic organisms from surface water contaminated by the groundwater. Direct toxicity assessment of the groundwater was undertaken on 5 indigenous marine species to assess toxicity and derive a site-specific guideline. The testing included acute tests, subchronic tests on early life stages, and a chronic test. Test organisms included a microalga (Nitzschia closterium), an amphipod (Allorchestes compressa), a polychaete worm (Diopatra dentata), and sea urchin (Heliocidaris tuberculata) and oyster larvae (Saccostrea commercialis). Toxicity testing was undertaken in sealed containers to prevent loss of VCHs, and concentrations of VCHs were measured to accurately assess exposure concentrations. No observed effect concentration (NOEC) values varied from 1.56% dilution (1.11 mg total VCHs) to 50% dilution (45.5 mg total VCHs). EC50 values varied from 4.8% dilution (3.77 mg total VCHs) to more than 50% dilution (45.5 mg total VCHs). NOEC data were used to derive species sensitivity distributions (SSDs) and a site-specific guideline. SSDs were derived from Burr type III (including the Pareto) and log-normal distributions. The log-normal distribution represented the best fit, and because the Pareto distribution is a finite threshold model more suited to toxicants with a threshold mode of action, the log-normal SSD and the associated 95% trigger value (TV) of 830 microg/L of total VCHs, was adopted as the site-specific TV for the groundwater.

  16. Massive differential site-specific and species-specific responses of temperate reef fishes to marine reserve protection

    Directory of Open Access Journals (Sweden)

    Tyler D. Eddy

    2014-08-01

    Full Text Available As the field of marine reserve (MR research matures, individual studies and meta-analyses are now able to answer some of the fundamental questions initially posed regarding timelines and trajectories for biological change (often termed recovery, the effect of reserve size, age, and location, and responses to protection as a function of life-history characteristics. Kapiti MR is New Zealand’s fourth oldest MR, established in 1992, and falls into the category of a MR where all sites are not equal in terms of habitat characteristics. We surveyed temperate reef fishes at protected and unprotected sites and compared our data to previous studies at this MR, to quantify changes through time. We employed a before-after-control-impact (BACI approach and compared our results to the commonly employed control–impact (CI or inside/outside analysis. The CI analysis revealed greater abundances and biomasses of reef fish species inside the MR that were not revealed by the BACI analysis. The BACI approach revealed that exploited species of reef fishes increased in biomass by 300%–400% at protected sites. Butterfish (Odax pullus, an exploited herbivorous species, showed pronounced site-specific responses, and increased in abundance by >400% and in biomass by >2 100% in 19 years at protected sites. This study highlights both the importance of site-specific effects and the method of analysis when quantifying MR effects to correctly attribute observed differences among sites to MR effects or to site-specific habitat quality effects.

  17. Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water.

    Science.gov (United States)

    Armstrong, Brandon D; Choi, Jennifer; López, Carlos; Wesener, Darryl A; Hubbell, Wayne; Cavagnero, Silvia; Han, Songi

    2011-04-20

    Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ∼10 Å of a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.

  18. Evaluating Protein Structure and Dynamics Using Co-Solvents, Photochemical Triggers, and Site-Specific Spectroscopic Probes

    Science.gov (United States)

    Abaskharon, Rachel M.

    As ubiquitous and diverse biopolymers, proteins are dynamic molecules that are constantly engaging in inter- and intramolecular interactions responsible for their structure, fold, and function. Because of this, gaining a comprehensive understanding of the factors that control protein conformation and dynamics remains elusive as current experimental techniques often lack the ability to initiate and probe a specific interaction or conformational transition. For this reason, this thesis aims to develop methods to control and monitor protein conformations, conformational transitions, and dynamics in a site-specific manner, as well as to understand how specific and non-specific interactions affect the protein folding energy landscape. First, by using the co-solvent, trifluoroethanol (TFE), we show that the rate at which a peptide folds can be greatly impacted and thus controlled by the excluded volume effect. Secondly, we demonstrate the utility of several light-responsive molecules and reactions as methods to manipulate and investigate protein-folding processes. Using an azobenzene linker as a photo-initiator, we are able to increase the folding rate of a protein system by an order of magnitude by channeling a sub-population through a parallel, faster folding pathway. Additionally, we utilize a tryptophan-mediated electron transfer process to a nearby disulfide bond to strategically unfold a protein molecule with ultraviolet light. We also demonstrate the potential of two ruthenium polypyridyl complexes as ultrafast phototriggers of protein reactions. Finally, we develop several site-specific spectroscopic probes of protein structure and environment. Specifically, we demonstrate that a 13C-labeled aspartic acid residue constitutes a useful site-specific infrared probe for investigating salt-bridges and hydration dynamics of proteins, particularly in proteins containing several acidic amino acids. We also show that a proline-derivative, 4-oxoproline, possesses novel

  19. Site specific waste management instructions for loading and shipment of containerized investigation derived waste to ERDF. Revision 1

    International Nuclear Information System (INIS)

    Corriveau, C.E.; Wolf, D.M.

    1996-08-01

    This Site Specific Waste Management Instruction (SSWMI) provides guidance for management of containerized investigation-derived waste (IDW) being loaded and transported to the Environmental Restoration Disposal Facility (ERDF). Requirements and responsibilities for designating waste, preparing waste profiles, and managing the waste are provided. The SSWMI outlines the waste management practices that will be performed in the field to implement Federal, state, and US Department of Energy (DOE) requirements. Additional guidance for waste packaging, marking, labeling, and shipping, is provided for information; however, the US Department of Transportation (DOT) requirements have precedence

  20. A procedure for estimating site specific derived limits for the discharge of radioactive material to the atmosphere

    CERN Document Server

    Hallam, J; Jones, J A

    1983-01-01

    Generalised Derived Limits (GDLs) for the discharge of radioactive material to the atmosphere are evaluated using parameter values to ensure that the exposure of the critical group is unlikely to be underestimated significantly. Where the discharge is greater than about 5% of the GDL, a more rigorous estimate of the derived limit may be warranted. This report describes a procedure for estimating site specific derived limits for discharges of radioactivity to the atmosphere taking into account the conditions of the release and the location and habits of the exposed population. A worksheet is provided to assist in carrying out the required calculations.

  1. Inversion of Moraxella lacunata type 4 pilin gene sequences by a Neisseria gonorrhoeae site-specific recombinase.

    Science.gov (United States)

    Rozsa, F W; Meyer, T F; Fussenegger, M

    1997-01-01

    A plasmid library of Neisseria gonorrhoeae sequences was screened for the ability to mediate recombinations on a sequence containing the Moraxella lacunata type 4 pilin gene invertible region in Escherichia coli. A plasmid containing the N. gonorrhoeae sequence encoding the putative recombinase (gcr) was identified and sequenced. Plasmids containing gcr were able to mediate site-specific recombinations despite a weak amino acid homology to Piv, the native M. lacunata pilin gene invertase. The gcr gene is present only in pathogenic strains of Neisseria tested; however, in our assays gene knockouts of gcr did not alter the variation of surface features that play a role in the pathogenesis of N. gonorrhoeae. PMID:9079926

  2. Repetitive, Marker-Free, Site-Specific Integration as a Novel Tool for Multiple Chromosomal Integration of DNA

    DEFF Research Database (Denmark)

    Petersen, Kia Vest; Martinussen, Jan; Jensen, Peter Ruhdal

    2013-01-01

    of a minimal bacterial attachment site (attBmin), two mutated loxP sequences (lox66 and lox71) allowing for removal of undesirable vector elements (antibiotic resistance marker), and a counterselection marker (oroP) for selection of loxP recombination on the pKV6 vector. When transformed into L. lactis......We present a tool for repetitive, marker-free, site-specific integration in Lactococcus lactis, in which a nonreplicating plasmid vector (pKV6) carrying a phage attachment site (attP) can be integrated into a bacterial attachment site (attB). The novelty of the tool described here is the inclusion...

  3. Delineation of site-specific management units in a saline region at the Venice Lagoon margin, Italy, using soil reflectance and apparent electrical conductivity

    Science.gov (United States)

    Site-specific crop management utilizes site-specific management units (SSMUs) to apply inputs when, where, and in the amount needed to increase food productivity, optimize resource utilization, increase profitability, and reduce detrimental environmental impacts. It is the objective of this study to...

  4. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    Science.gov (United States)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  5. Maternal Supply of Cas9 to Zygotes Facilitates the Efficient Generation of Site-Specific Mutant Mouse Models

    Science.gov (United States)

    Cebrian-Serrano, Alberto; Zha, Shijun; Hanssen, Lars; Biggs, Daniel; Preece, Christopher

    2017-01-01

    Genome manipulation in the mouse via microinjection of CRISPR/Cas9 site-specific nucleases has allowed the production time for genetically modified mouse models to be significantly reduced. Successful genome manipulation in the mouse has already been reported using Cas9 supplied by microinjection of a DNA construct, in vitro transcribed mRNA and recombinant protein. Recently the use of transgenic strains of mice overexpressing Cas9 has been shown to facilitate site-specific mutagenesis via maternal supply to zygotes and this route may provide an alternative to exogenous supply. We have investigated the feasibility of supplying Cas9 genetically in more detail and for this purpose we report the generation of a transgenic mice which overexpress Cas9 ubiquitously, via a CAG-Cas9 transgene targeted to the Gt(ROSA26)Sor locus. We show that zygotes prepared from female mice harbouring this transgene are sufficiently loaded with maternally contributed Cas9 for efficient production of embryos and mice harbouring indel, genomic deletion and knock-in alleles by microinjection of guide RNAs and templates alone. We compare the mutagenesis rates and efficacy of mutagenesis using this genetic supply with exogenous Cas9 supply by either mRNA or protein microinjection. In general, we report increased generation rates of knock-in alleles and show that the levels of mutagenesis at certain genome target sites are significantly higher and more consistent when Cas9 is supplied genetically relative to exogenous supply. PMID:28081254

  6. Site-specific distribution of claudin-based paracellular channels with roles in biological fluid flow and metabolism.

    Science.gov (United States)

    Tanaka, Hiroo; Tamura, Atsushi; Suzuki, Koya; Tsukita, Sachiko

    2017-10-01

    The claudins are a family of membrane proteins with at least 27 members in humans and mice. The extracellular regions of claudin proteins play essential roles in cell-cell adhesion and the paracellular barrier functions of tight junctions (TJs) in epithelial cell sheets. Furthermore, the extracellular regions of some claudins function as paracellular channels in the paracellular barrier that allow the selective passage of water, ions, and/or small organic solutes across the TJ in the extracellular space. Structural analyses have revealed a common framework of transmembrane, cytoplasmic, and extracellular regions among the claudin-based paracellular barriers and paracellular channels; however, differences in the claudins' extracellular regions, such as their charges and conformations, determine their properties. Among the biological systems that involve fluid flow and metabolism, it is noted that hepatic bile flow, renal Na + reabsorption, and intestinal nutrient absorption are dynamically regulated via site-specific distributions of paracellular channel-forming claudins in tissue. Here, we focus on how site-specific distributions of claudin-2- and claudin-15-based paracellular channels drive their organ-specific functions in the liver, kidney, and intestine. © 2017 New York Academy of Sciences.

  7. Geothermal investment analysis with site-specific applications to Roosevelt Hot Springs and Cove Fort-Sulphurdale, Utah

    Energy Technology Data Exchange (ETDEWEB)

    Cassel, T.A.V.; Edelstein, R.H.; Blair, P.D.

    1978-12-01

    The analysis and modeling of investment behavior in the development of hydrothermal electric power facilities are reported. This investment behavior reflects a degree of sensitivity to public policy alternatives concerning taxation and regulation of the resource and its related energy conversion facilities. The objective of the current research is to provide a realistic and theoretically sound means for estimating the impacts of such public policy alternatives. A stochastic simulation model was developed which offers an efficient means for site-specific investment analysis of private sector firms and investors. The results of the first year of work are discussed including the identification, analysis, quantification and modeling of: a decision tree reflecting the sequence of procedures, timing and stochastic elements of hydrothermal resource development projects; investment requirements, expenses and revenues incurred in the exploration, development and utilization of hydrothermal resources for electric power generation; and multiattribute investment decision criteria of the several types of firms in the geothermal industry. An application of the investment model to specific resource sites in the state of Utah is also described. Site specific data for the Known Geothermal Resource Areas of Roosevelt Hot Springs and Cove Fort-Sulphurdale are given together with hypothesized generation capacity growth rates.

  8. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  9. Quantitative chemoproteomics for site-specific analysis of protein alkylation by 4-hydroxy-2-nonenal in cells.

    Science.gov (United States)

    Yang, Jing; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C

    2015-03-03

    Protein alkylation by 4-hydroxy-2-nonenal (HNE), an endogenous lipid derived electrophile, contributes to stress signaling and cellular toxicity. Although previous work has identified protein targets for HNE alkylation, the sequence specificity of alkylation and dynamics in a cellular context remain largely unexplored. We developed a new quantitative chemoproteomic platform, which uses isotopically tagged, photocleavable azido-biotin reagents to selectively capture and quantify the cellular targets labeled by the alkynyl analogue of HNE (aHNE). Our analyses site-specifically identified and quantified 398 aHNE protein alkylation events (386 cysteine sites and 12 histidine sites) in intact cells. This data set expands by at least an order of magnitude the number of such modification sites previously reported. Although adducts formed by Michael addition are thought to be largely irreversible, we found that most aHNE modifications are lost rapidly in situ. Moreover, aHNE adduct turnover occurs only in intact cells and loss rates are site-selective. This quantitative chemoproteomics platform provides a versatile general approach to map bioorthogonal-chemically engineered post-translational modifications and their cellular dynamics in a site-specific and unbiased manner.

  10. The dock-and-lock method combines recombinant engineering with site-specific covalent conjugation to generate multifunctional structures.

    Science.gov (United States)

    Rossi, Edmund A; Goldenberg, David M; Chang, Chien-Hsing

    2012-03-21

    Advances in recombinant protein technology have facilitated the production of increasingly complex fusion proteins with multivalent, multifunctional designs for use in various in vitro and in vivo applications. In addition, traditional chemical conjugation remains a primary choice for linking proteins with polyethylene glycol (PEG), biotin, fluorescent markers, drugs, and others. More recently, site-specific conjugation of two or more interactive modules has emerged as a valid approach to expand the existing repertoires produced by either recombinant engineering or chemical conjugation alone, thus advancing the range of potential applications. Five such methods, each involving a specific binding event, are highlighted in this review, with a particular focus on the Dock-and-Lock (DNL) method, which exploits the natural interaction between the dimerization and docking domain (DDD) of cAMP-dependent protein kinase (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP). The various enablements of DNL to date include trivalent, tetravalent, pentavalent, and hexavalent antibodies of monospecificity or bispecificity; immnocytokines comprising multiple copies of interferon-alpha (IFNα); and site-specific PEGylation. These achievements attest to the power of the DNL platform technology to develop novel therapeutic and diagnostic agents from both proteins and nonproteins for unmet medical needs.

  11. Site-specific Incorporation of Chemical Fluorescence on Live Enterovirus-71 Virion by Organometallic Palladium Reagent to Monitor Virus Entry.

    Science.gov (United States)

    Lou, Zhiyong; Wang, Yaxin; Liu, Jingwei; Cao, Lin; Wang, Wenjing; Sun, Yuna; Yin, Zheng

    2018-04-06

    Imaging live virus to monitor the viral entry process is essential to understand virus-host interactions during pathogen infection. However, methods for efficient labeling of live viruses, in particular labeling non-enveloped viruses and tracing virus entry processes, remains limited. Recently, labeling using organometallic palladium reagents has provided a highly efficient and a highly selective way to bioconjugate cysteines of virus proteins. Here, the site-specific bioorthogonal labeling mediated by an organometallic palladium reagent on the surface of live enterovirus-71 (EV71) was used to visualize its entry into live cells. In contrast to currently used immunofluorescence and membrane-anchored dyes, this site-specific and quantitative labeling of live EV71 virus allows temporal imaging on a seconds time scale of its entry into host cell membranes with little negative impact on the virulence. This method revealed details of EV71 virus entry and has broad applicability for monitoring virus entry that is difficult to assess using conventional protein labeling approaches. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Long-range chromosome organization in E. coli: a site-specific system isolates the Ter macrodomain.

    Science.gov (United States)

    Thiel, Axel; Valens, Michèle; Vallet-Gely, Isabelle; Espéli, Olivier; Boccard, Frédéric

    2012-01-01

    The organization of the Escherichia coli chromosome into a ring composed of four macrodomains and two less-structured regions influences the segregation of sister chromatids and the mobility of chromosomal DNA. The structuring of the terminus region (Ter) into a macrodomain relies on the interaction of the protein MatP with a 13-bp target called matS repeated 23 times in the 800-kb-long domain. Here, by using a new method that allows the transposition of any chromosomal segment at a defined position on the genetic map, we reveal a site-specific system that restricts to the Ter region a constraining process that reduces DNA mobility and delays loci segregation. Remarkably, the constraining process is regulated during the cell cycle and occurs only when the Ter MD is associated with the division machinery at mid-cell. The change of DNA properties does not rely on the presence of a trans-acting mechanism but rather involves a cis-effect acting at a long distance from the Ter region. Two specific 12-bp sequences located in the flanking Left and Right macrodomains and a newly identified protein designated YfbV conserved with MatP through evolution are required to impede the spreading of the constraining process to the rest of the chromosome. Our results unravel a site-specific system required to restrict to the Ter region the consequences of anchoring the Ter MD to the division machinery.

  13. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system

    Science.gov (United States)

    Karimova, Madina; Abi-Ghanem, Josephine; Berger, Nicolas; Surendranath, Vineeth; Pisabarro, Maria Teresa; Buchholz, Frank

    2013-01-01

    Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the ‘genetic toolbox’ that can be used alone or in combination with other SSRs in heterologous hosts. PMID:23143104

  14. Reaction rate constants of H-abstraction by OH from large ketones: measurements and site-specific rate rules.

    Science.gov (United States)

    Badra, Jihad; Elwardany, Ahmed E; Farooq, Aamir

    2014-06-28

    Reaction rate constants of the reaction of four large ketones with hydroxyl (OH) are investigated behind reflected shock waves using OH laser absorption. The studied ketones are isomers of hexanone and include 2-hexanone, 3-hexanone, 3-methyl-2-pentanone, and 4-methl-2-pentanone. Rate constants are measured under pseudo-first-order kinetics at temperatures ranging from 866 K to 1375 K and pressures near 1.5 atm. The reported high-temperature rate constant measurements are the first direct measurements for these ketones under combustion-relevant conditions. The effects of the position of the carbonyl group (C=O) and methyl (CH3) branching on the overall rate constant with OH are examined. Using previously published data, rate constant expressions covering, low-to-high temperatures, are developed for acetone, 2-butanone, 3-pentanone, and the hexanone isomers studied here. These Arrhenius expressions are used to devise rate rules for H-abstraction from various sites. Specifically, the current scheme is applied with good success to H-abstraction by OH from a series of n-ketones. Finally, general expressions for primary and secondary site-specific H-abstraction by OH from ketones are proposed as follows (the subscript numbers indicate the number of carbon atoms bonded to the next-nearest-neighbor carbon atom, the subscript CO indicates that the abstraction is from a site next to the carbonyl group (C=O), and the prime is used to differentiate different neighboring environments of a methylene group):

  15. 3D site specific sample preparation and analysis of 3D devices (FinFETs) by atom probe tomography.

    Science.gov (United States)

    Kambham, Ajay Kumar; Kumar, Arul; Gilbert, Matthieu; Vandervorst, Wilfried

    2013-09-01

    With the transition from planar to three-dimensional device architectures such as Fin field-effect-transistors (FinFETs), new metrology approaches are required to meet the needs of semiconductor technology. It is important to characterize the 3D-dopant distributions precisely as their extent, positioning relative to gate edges and absolute concentration determine the device performance in great detail. At present the atom probe has shown its ability to analyze dopant distributions in semiconductor and thin insulating materials with sub-nm 3D-resolution and good dopant sensitivity. However, so far most reports have dealt with planar devices or restricted the measurements to 2D test structures which represent only limited challenges in terms of localization and site specific sample preparation. In this paper we will discuss the methodology to extract the dopant distribution from real 3D-devices such as a 3D-FinFET device, requiring the sample preparation to be carried out at a site specific location with a positioning accuracy ∼50 nm. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Site-specific and multielement approach to the determination of liquid-vapor isotope fractionation parameters. The case of alcohols

    International Nuclear Information System (INIS)

    Moussa, I.; Naulet, N.; Martin, M.L.; Martin, G.J.

    1990-01-01

    Isotope fractionation phenomena occurring at the natural abundance level in the course of liquid-vapor transformation have been investigated by using the SNIF-NMR method (site-specific natural isotope fractionation studied by NMR) which has a unique capability of providing simultaneous access to fractionation parameters associated with different molecular isotopomers. This new approach has been combined with the determination of overall carbon and hydrogen fractionation effects by isotope ratio mass spectrometry (IRMS). The results of distillation and evaporation experiments of alcohols performed in technical conditions of practical interest have been analyzed according to the Rayleigh-type model. In order to check the performance of the column, unit fractionation factors were measured beforehand for water and for the hydroxylic sites of methanol and ethanol for which liquid-vapor equilibrium constants were already known. Inverse isotope effects are determined in distillation experiments for the overall carbon isotope ratio and for the site-specific hydrogen isotope ratios associated with the methyl and methylene sites of methanol and ethanol. In contrast, normal isotope effects are produced by distillation for the hydroxylic sites and by evaporation for all the isotopic ratios

  17. pH-sensitive inulin-based nanomicelles for intestinal site-specific and controlled release of celecoxib.

    Science.gov (United States)

    Mandracchia, Delia; Trapani, Adriana; Perteghella, Sara; Sorrenti, Milena; Catenacci, Laura; Torre, Maria Luisa; Trapani, Giuseppe; Tripodo, Giuseppe

    2018-02-01

    Aiming at a site-specific drug release in the lower intestinal tract, this paper deals with the synthesis and physicochemical/biological characterization of pH-sensitive nanomicelles from an inulin (INU) amphiphilic derivative. To allow an intestinal site specific release of the payload, INU-Vitamin E (INVITE) bioconjugates were functionalized with succinic anhydride to provide the system with pH-sensitive groups preventing a premature release of the payload into the stomach. The obtained INVITESA micelles resulted nanosized, with a low critical aggregation concentration and the release studies showed a marked pH-dependent release. The drug loading stabilized the micelles against the acidic hydrolysis. From transport studies on Caco-2 cells, resulted that INVITESA nanomicelles cross the cellular monolayer but are actively re-transported in the secretory (basolateral-apical) direction when loaded in apical side. It suggests that the entrapped drug could not be absorbed before the release from the micelles, enabling so a local release of the active. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

    Energy Technology Data Exchange (ETDEWEB)

    Brauchler, R.; Doetsch, J.; Dietrich, P.; Sauter, M.

    2012-01-10

    In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. The experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.

  19. Recurrent gastrointestinal hemorrhage in treatment with dasatinib in a patient showing SMAD4 mutation with acute lymphoblastic leukemia Philadelphia positive and juvenile polyposis hereditary hemorrhagic telangiectasia syndrome

    Directory of Open Access Journals (Sweden)

    Chiara Sartor

    2013-07-01

    Full Text Available We report a case of a patient affected by juvenile polyposis and hereditary hemorrhagic telangiectasia linked to a SMAD4 mutation who developed acute lymphoblastic leukemia positive for the Philadelphia chromosome translocation and with a complex karyotype. During the treatment with the tyrosine kinase inhibitor dasatinib the patient presented recurrent severe gastrointestinal hemorrhages linked to the genetic background and aggravated by thrombocytopenia.

  20. In vivo tumor angiogenesis imaging with site-specific labeled {sup 99m}Tc-HYNIC-VEGF

    Energy Technology Data Exchange (ETDEWEB)

    Blankenberg, Francis G. [Stanford University, Division of Nuclear Medicine/Department of Radiology and MIPS (Molecular Imaging Program at Stanford), Stanford, CA (United States); Stanford University, Department of Pediatrics, Stanford, CA (United States); Backer, Marina V.; Patel, Vimalkumar; Backer, Joseph M. [SibTech, Inc., Newington, CT (United States); Levashova, Zoia [Stanford University, Division of Nuclear Medicine/Department of Radiology and MIPS (Molecular Imaging Program at Stanford), Stanford, CA (United States)

    2006-07-15

    We recently developed a cysteine-containing peptide tag (C-tag) that allows for site-specific modification of C-tag-containing fusion proteins with a bifunctional chelator, HYNIC (hydrazine nicotinamide)-maleimide. We then constructed and expressed C-tagged vascular endothelial growth factor (VEGF) and labeled it with HYNIC. We wished to test {sup 99m}Tc-HYNIC-C-tagged VEGF ({sup 99m}Tc-HYNIC-VEGF) for the imaging of tumor vasculature before and after antiangiogenic (low continuous dosing, metronomic) and tumoricidal (high-dose) cyclophosphamide treatment. HYNIC-maleimide was reacted with the two thiol groups of C-tagged VEGF without any effect on biologic activity in vitro. {sup 99m}Tc-HYNIC-VEGF was prepared using tin/tricine as an exchange reagent, and injected via the tail vein (200-300 {mu}Ci, 1-2 {mu}g protein) followed by microSPECT imaging 1 h later. Sequencing analysis of HYNIC-containing peptides obtained after digestion confirmed the site-specific labeling of the two accessible thiol groups of C-tagged VEGF. Tumor vascularity was easily visualized with {sup 99m}Tc/VEGF in Balb/c mice with 4T1 murine mammary carcinoma 10 days after implantation into the left axillary fat pad in controls (12.3{+-}5.0 tumor/bkg, n=27) along with its decrease following treatment with high (150 mg/kg q.o.d. x 4; 1.14{+-}0.48 tumor/bkg, n=9) or low (25 mg/kg q.d. x 7; 1.03{+-}0.18 tumor/bkg, n=9) dose cyclophosphamide. Binding specificity was confirmed by observing a 75% decrease in tumor uptake of {sup 99m}Tc/biotin-inactivated VEGF, as compared with {sup 99m}Tc-HYNIC-VEGF. {sup 99m}Tc can be loaded onto C-tagged VEGF in a site-specific fashion without reducing its bioactivity. {sup 99m}Tc-HYNIC-VEGF can be rapidly prepared for the imaging of tumor vasculature and its response to different types of chemotherapy. (orig.)

  1. Site-Specific Hydrogen Isotope Composition of Propane: Mass spectrometric methods, equilibrium temperature dependence, and kinetics of exchange

    Science.gov (United States)

    Xie, H.; Ponton, C.; Kitchen, N.; Lloyd, M. K.; Lawson, M.; Formolo, M. J.; Eiler, J. M.

    2016-12-01

    Intramolecular isotope ordering can constrain temperatures of synthesis, mechanisms of formation, and/or source substrates of organic compounds. Here we explore site-specific hydrogen isotope variations of propane. Statistical thermodynamic models predict that at equilibrium methylene hydrogen (-CH2-) in propane will be 10's of per mil higher in D/H ratio than methyl hydrogen (-CH3) at geologically relevant temperatures, and that this difference is highly temperature dependent ( 0.5-1 ‰/°C). Chemical-kinetic controls on site-specific D/H in propane could constrain the mechanisms, conditions and extents of propane synthesis or destruction. We have developed a method for measuring the difference in D/H ratio between methylene and methyl hydrogen in propane by gas source mass spectrometry. The data were measured using the Thermo Fisher Double Focusing Sector high resolution mass spectrometer (DFS), and involve comparison of the D/H ratios of molecular ion (C3H8+) and the ethyl fragmental ion (C2H5+). We demonstrate the accuracy and precision of this method through analysis of D-labeled and independently analyzed propanes. In the exchange experiments, propane was heated (100-200 oC) either alone or in the presence of D-enriched water (δD=1,1419 ‰ SMOW), with or without one of several potentially catalytic substrates for hours to weeks. Propane was found to exchange hydrogen with water vigorously at 200 °C in the presence of metal catalysts. In the presence of Ni catalyst, methylene hydrogen exchanges 2.5 times faster than methyl hydrogen. Hydrogen exchange in the presence of Pd catalyst is more effective and can equilibrate hydrogen isotope distribution on propane on the order of 7 days. Isotopic exchange in the presence of natural materials have also been tested, but is only measurable in the methylene group at 200 °C. High catalytic activity of Pd permits attainment of a bracketed, time-invariant equilibrium state that we use to calibrate the site-specific

  2. Development of pronuclear injection-based targeted transgenesis in mice through Cre-loxP site-specific recombination.

    Science.gov (United States)

    Ohtsuka, Masato

    2014-01-01

    Microinjection of DNA into the pronuclei of zygotes is the simplest and most widely used method for generating transgenic (Tg) mice. However, it is always associated with random integration of multiple copies of the transgene, resulting in unstable, low, or no transgene expression due to positional effects and/or repeat-induced gene silencing. In addition, random integration sometimes disrupts an endogenous gene that can affect the phenotypes of Tg mice. Our recently developed pronuclear injection-based targeted transgenesis (PITT) method enables the integration of a single-copy transgene into a predetermined genomic locus through Cre-loxP site-specific recombination. The PITT method enables stable and reliable transgene expression in Tg mice and is also applicable for generating knockdown mice. Therefore, the PITT method could represent next-generation transgenesis that overcomes the pitfalls of conventional transgenesis.

  3. CoPc and CoPcF16 on gold: Site-specific charge-transfer processes

    Directory of Open Access Journals (Sweden)

    Fotini Petraki

    2014-04-01

    Full Text Available Interface properties of cobalt(II phthalocyanine (CoPc and cobalt(II hexadecafluoro-phthalocyanine (CoPcF16 to gold are investigated by photo-excited electron spectroscopies (X-ray photoemission spectroscopy (XPS, ultraviolet photoemission spectroscopy (UPS and X-ray excited Auger electron spectroscopy (XAES. It is shown that a bidirectional charge transfer determines the interface energetics for CoPc and CoPcF16 on Au. Combined XPS and XAES measurements allow for the separation of chemical shifts based on different local charges at the considered atom caused by polarization effects. This facilitates a detailed discussion of energetic shifts of core level spectra. The data allow the discussion of site-specific charge-transfer processes.

  4. A rapid method for recombination and site-specific mutagenesis by placing homologous ends on DNA using polymerase chain reaction.

    Science.gov (United States)

    Jones, D H; Howard, B H

    1991-01-01

    We have developed a novel polymerase chain reaction (PCR) method that permits the rapid generation of site-specific mutants and recombinant DNA constructs with a minimum number of steps and primers. DNA segments are modified by using amplifying primers that add homologous ends to the polymerase chain reaction product(s). These homologous ends undergo recombination in vivo following transformation of recA-E. coli strains used routinely in cloning. In vivo circularization of PCR products containing plasmid sequences with a selective marker permits the rapid cloning of the desired mutant or recombinant. In the mutagenesis protocol, 7 of the 12 clones contained the product of interest, and 6 of these clones had no detected error (50% of the clones without detected errors). In each of several recombination protocols, at least 50% of the clones tested contained the insert of interest without detected errors.

  5. Sorption measurements performed under site-specific conditions - Maxey Flats, Kentucky, and West Valley, New York, disposal sites

    International Nuclear Information System (INIS)

    Pietrzak, R.F.; Czyscinski, K.S.; Weiss, A.J.

    1981-01-01

    Sorption coefficients have been determined using site-specific sediments and trench waters, collected from the Maxey Flats, Kentucky, and West Valley, New York, low-level radioactive waste disposal sites. Experimental apparatus and procedures are described to preserve the anoxic character of the liquid phases during experiments. Experiments using anoxic and oxidized trench waters were performed as functions of solution pH, soil/solution ratio, water and soil composition. The lowest sorption was observed with the combination of anoxic waters and untreated soil - the combination most closely resembling the immediate trench environment. For best results in predictive applications, sorption data should be determined under conditions which simulate those in the field as closely as possible. The total radionuclide retention capacity of reducing geochemical environments is the sum of sorption processes on solid phases, as well as precicipation, and coprecipitation reactions involving iron mineral phases

  6. Development of a Site-specific Standard for Selenium in Open Waters of Great Salt Lake, Utah

    Science.gov (United States)

    Moellmer, W. O.; Miller, T.; Ohlendorf, H.; Denbleyker, J.

    2006-12-01

    The Great Salt Lake (GSL) is a unique terminal lake located adjacent to a rapidly growing metropolitan area in the western United States. The open water of the GSL is protected for its current beneficial uses through the application of a narrative criteria clause in the state water quality standards. The Utah Department of Environmental Quality (DEQ) initiated a process in 2004 to develop a site-specific numeric water quality standard for selenium for the open waters of the GSL to balance protection of the GSL's unique ecology and beneficial uses with burgeoning development. The process the DEQ initiated included the formation of a Great Salt Lake Water Quality Steering Committee and a Science Panel to identify the studies required, manage the studies and finally recommend a site-specific standard. Great Salt Lake Water Quality Steering Committee. The DEQ established the GSL Water Quality Steering Committee (Steering Committee) to provide a forum for stakeholders to assist in guiding the process of developing numeric standards for the lake. This group consists of federal and state regulatory agencies, other public entities, conservation organizations, recreation groups, and industrial users of the lake. Great Salt Lake Science Panel. The DEQ established the GSL Science Panel (Science Panel) to advise the DEQ and Steering Committee and provide overall technical direction and review for the program. The Science Panel is composed of 9 members representing federal and state regulatory agencies, industry and academia. The purpose of the panel is to identify data gaps in the literature, design and oversee scientific investigations to fill critical data gaps, and finally recommend a numeric water quality standard to the Steering Committee. Studies Currently Underway. A partnership of researchers—including local and national experts from education and industry—are collaborating with the DEQ, the Steering Committee, and the Science Panel to complete the studies required

  7. Site-specific Pt deposition and etching on electrically and thermally isolated SiO2 micro-disk surfaces

    International Nuclear Information System (INIS)

    Saraf, Laxmikant V

    2010-01-01

    Electrically and thermally isolated surfaces are crucial for improving the detection sensitivity of microelectronic sensors. The site-specific in situ growth of Pt nano-rods on thermally and electrically isolated SiO 2 micro-disks using wet chemical etching and a focused ion/electron dual beam (FIB-SEM) is demonstrated. Fabrication of an array of micro-cavities on top of a micro-disk is also demonstrated. The FIB source is utilized to fabricate through-holes in the micro-disks. Due to the amorphous nature of SiO 2 micro-disks, the Ga implantation possibly modifies through-hole sidewall surface chemistry rather than affecting its transport properties. Some sensor design concepts based on micro-fabrication of SiO 2 micro-disks utilizing thermally and electrically isolated surfaces are discussed from the viewpoint of applications in photonics and bio-sensing.

  8. A novel bench-scale column assay to investigate site-specific nitrification biokinetics in biological rapid sand filters

    DEFF Research Database (Denmark)

    Tatari, Karolina; Smets, Barth F.; Albrechtsen, Hans-Jørgen

    2013-01-01

    A bench-scale assay was developed to obtain site-specific nitrification biokinetic information from biological rapid sand filters employed in groundwater treatment. The experimental set-up uses granular material subsampled from a full-scale filter, packed in a column, and operated with controlled...... and continuous hydraulic and ammonium loading. Flowrates and flow recirculation around the column are chosen to mimic full-scale hydrodynamic conditions, and minimize axial gradients. A reference ammonium loading rate is calculated based on the average loading experienced in the active zone of the full......-scale filter. Effluent concentrations of ammonium are analyzed when the bench-scale column is subject to reference loading, from which removal rates are calculated. Subsequently, removal rates above the reference loading are measured by imposing short-term loading variations. A critical loading rate...

  9. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    2000-01-01

    synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

  10. Bioavailability of particulate metal to zebra mussels: biodynamic modelling shows that assimilation efficiencies are site-specific.

    Science.gov (United States)

    Bourgeault, Adeline; Gourlay-Francé, Catherine; Priadi, Cindy; Ayrault, Sophie; Tusseau-Vuillemin, Marie-Hélène

    2011-12-01

    This study investigates the ability of the biodynamic model to predict the trophic bioaccumulation of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni) and zinc (Zn) in a freshwater bivalve. Zebra mussels were transplanted to three sites along the Seine River (France) and collected monthly for 11 months. Measurements of the metal body burdens in mussels were compared with the predictions from the biodynamic model. The exchangeable fraction of metal particles did not account for the bioavailability of particulate metals, since it did not capture the differences between sites. The assimilation efficiency (AE) parameter is necessary to take into account biotic factors influencing particulate metal bioavailability. The biodynamic model, applied with AEs from the literature, overestimated the measured concentrations in zebra mussels, the extent of overestimation being site-specific. Therefore, an original methodology was proposed for in situ AE measurements for each site and metal. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Site-Specific Transglutaminase-Mediated Conjugation of Interferon α-2b at Glutamine or Lysine Residues.

    Science.gov (United States)

    Spolaore, Barbara; Raboni, Samanta; Satwekar, Abhijeet A; Grigoletto, Antonella; Mero, Anna; Montagner, Isabella Monia; Rosato, Antonio; Pasut, Gianfranco; Fontana, Angelo

    2016-11-16

    Interferon α (IFN α) subtypes are important protein drugs that have been used to treat infectious diseases and cancers. Here, we studied the reactivity of IFN α-2b to microbial transglutaminase (TGase) with the aim of obtaining a site-specific conjugation of this protein drug. Interestingly, TGase allowed the production of two monoderivatized isomers of IFN with high yields. Characterization by mass spectrometry of the two conjugates indicated that they are exclusively modified at the level of Gln101 if the protein is reacted in the presence of an amino-containing ligand (i.e., dansylcadaverine) or at the level of Lys164 if a glutamine-containing molecule is used (i.e., carbobenzoxy-l-glutaminyl-glycine, ZQG). We explained the extraordinary specificity of the TGase-mediated reaction on the basis of the conformational features of IFN. Indeed, among the 10 Lys and 12 Gln residues of the protein, only Gln101 and Lys164 are located in highly flexible protein regions. The TGase-mediated derivatization of IFN was then applied to the production of IFN derivatives conjugated to a 20 kDa polyethylene glycol (PEG), using PEG-NH 2 for Gln101 derivatization and PEG modified with ZQG for Lys164 derivatization. The two mono-PEGylated isomers of IFN were obtained in good yields, purified, and characterized in terms of protein conformation, antiviral activity, and pharmacokinetics. Both conjugates maintained a native-like secondary structure, as indicated by far-UV circular dichroism spectra. Importantly, they disclosed good in vitro antiviral activity retention (about only 1.6- to 1.8-fold lower than that of IFN) and half-lives longer (about 5-fold) than that of IFN after intravenous administration to rats. Overall, these results provide evidence that TGase can be used for the development of site-specific derivatives of IFN α-2b possessing interesting antiviral and pharmacokinetic properties.

  12. Predicting risk of trace element pollution from municipal roads using site-specific soil samples and remotely sensed data.

    Science.gov (United States)

    Reeves, Mari Kathryn; Perdue, Margaret; Munk, Lee Ann; Hagedorn, Birgit

    2018-02-24

    Studies of environmental processes exhibit spatial variation within data sets. The ability to derive predictions of risk from field data is a critical path forward in understanding the data and applying the information to land and resource management. Thanks to recent advances in predictive modeling, open source software, and computing, the power to do this is within grasp. This article provides an example of how we predicted relative trace element pollution risk from roads across a region by combining site specific trace element data in soils with regional land cover and planning information in a predictive model framework. In the Kenai Peninsula of Alaska, we sampled 36 sites (191 soil samples) adjacent to roads for trace elements. We then combined this site specific data with freely-available land cover and urban planning data to derive a predictive model of landscape scale environmental risk. We used six different model algorithms to analyze the dataset, comparing these in terms of their predictive abilities and the variables identified as important. Based on comparable predictive abilities (mean R 2 from 30 to 35% and mean root mean square error from 65 to 68%), we averaged all six model outputs to predict relative levels of trace element deposition in soils-given the road surface, traffic volume, sample distance from the road, land cover category, and impervious surface percentage. Mapped predictions of environmental risk from toxic trace element pollution can show land managers and transportation planners where to prioritize road renewal or maintenance by each road segment's relative environmental and human health risk. Published by Elsevier B.V.

  13. Socioeconomic position, population density and site-specific cancer mortality: A multilevel analysis of Belgian adults, 2001-2011.

    Science.gov (United States)

    Hagedoorn, Paulien; Vandenheede, Hadewijch; Vanthomme, Katrien; Gadeyne, Sylvie

    2018-01-01

    Our study explores the association between individual and neighborhood socioeconomic position (SEP) and all-cancer and site-specific cancer mortality. Data on all Belgian residents are retrieved from a population-based dataset constructed from the 2001 census linked to register data on emigration and mortality for 2001-2011. The study population contains all men and women aged 40 years or older during follow-up. Individual SEP is measured using education, employment status and housing conditions. Neighborhood SEP is measured by a deprivation index (in quintiles). Directly age-standardized mortality rates and multilevel Poisson models are used to estimate the association between individual SEP and neighborhood deprivation and mortality from all-cancer and cancer of the lung, colon and rectum, pancreas, prostate and female breast. The potential confounding role of population density is assessed using multilevel models as well. Our findings show an increase in mortality from all-cancer and site-specific cancer by decreasing level of individual SEP for both men and women. In addition, individuals living in highly deprived neighborhoods experience significantly higher mortality from all-cancer, lung cancer, pancreatic cancer and female colorectal cancer after controlling for individual SEP. Male colorectal and prostate cancer and female breast cancer are not associated with neighborhood deprivation. Population density acts as a confounder for female lung cancer only. Our study indicates that deprivation at both the individual and neighborhood level is associated with all-cancer mortality and mortality from several cancer sites. More research into the role of life-style related and clinical factors is necessary to gain more insight into causal pathway. © 2017 UICC.

  14. Completion of proteomic data sets by Kd measurement using cell-free synthesis of site-specifically labeled proteins.

    Directory of Open Access Journals (Sweden)

    Paul Majkut

    Full Text Available The characterization of phosphotyrosine mediated protein-protein interactions is vital for the interpretation of downstream pathways of transmembrane signaling processes. Currently however, there is a gap between the initial identification and characterization of cellular binding events by proteomic methods and the in vitro generation of quantitative binding information in the form of equilibrium rate constants (Kd values. In this work we present a systematic, accelerated and simplified approach to fill this gap: using cell-free protein synthesis with site-specific labeling for pull-down and microscale thermophoresis (MST we were able to validate interactions and to establish a binding hierarchy based on Kd values as a completion of existing proteomic data sets. As a model system we analyzed SH2-mediated interactions of the human T-cell phosphoprotein ADAP. Putative SH2 domain-containing binding partners were synthesized from a cDNA library using Expression-PCR with site-specific biotinylation in order to analyze their interaction with fluorescently labeled and in vitro phosphorylated ADAP by pull-down. On the basis of the pull-down results, selected SH2's were subjected to MST to determine Kd values. In particular, we could identify an unexpectedly strong binding of ADAP to the previously found binding partner Rasa1 of about 100 nM, while no evidence of interaction was found for the also predicted SH2D1A. Moreover, Kd values between ADAP and its known binding partners SLP-76 and Fyn were determined. Next to expanding data on ADAP suggesting promising candidates for further analysis in vivo, this work marks the first Kd values for phosphotyrosine/SH2 interactions on a phosphoprotein level.

  15. Experimental Study on the Efficacy of Site-Specific PEGylated Human Serum Albumins in Resuscitation From Hemorrhagic Shock.

    Science.gov (United States)

    Song, Xinlei; Zhang, Shu; Cheng, Yanna; Zhao, Ting; Lian, Qianqian; Lu, Lu; Wang, Fengshan

    2016-11-01

    To evaluate the resuscitative efficacy and the effect on reperfusion injury of two site-specific PEGylated human serum albumins modified with linear or branched PEG20kDa, compared with saline, 8% human serum albumin and 25% human serum albumin, in a hemorrhagic shock model. Laboratory. Male Wistar rats. Prospective study. Rats were bled to hemorrhagic hypovolemic shock and resuscitated with different resuscitation fluids. The mean arterial pressure and blood gas variables were measured. Hemorheology analysis was performed to evaluate the influence of resuscitation on RBCs and blood viscosity. The microvascular state was indirectly characterized in terms of monocyte chemotactic protein-1 and endothelial nitric oxide synthase that related to shear stress and vasodilation, respectively. The levels of inflammation-related factors and apoptosis-related proteins were used to evaluate the reperfusion injury in lungs. The results showed that PEGylated human serum albumin could improve the level of mean arterial pressure and blood gas variables more effectively at the end of resuscitation. poly(ethylene glycol) modification was able to increase the viscosity of human serum albumin to the level of effectively enhancing the expression of monocyte chemotactic protein-1 and endothelial nitric oxide synthase, which could promote microvascular perfusion. The hyperosmotic resuscitative agents including both 25% human serum albumin and PEGylated human serum albumins could greatly attenuate lung injury. No significant therapeutic advantages but some disadvantages were found for Y shaped poly(ethylene glycol) modification over linear poly(ethylene glycol) modification, such as causing the decrease of erythrocyte deformability. Linear high molecular weight site-specific PEGylated human serum albumin is recommended to be used as a hyperosmotic resuscitative agent.

  16. Analysis of High Frequency Site-Specific Nitrogen and Oxygen Isotopic Composition of Atmospheric Nitrous Oxide at Mace Head, Ireland

    Science.gov (United States)

    McClellan, M. J.; Harris, E. J.; Olszewski, W.; Ono, S.; Prinn, R. G.

    2014-12-01

    Atmospheric nitrous oxide (N2O) significantly impacts Earth's climate due to its dual role as an inert potent greenhouse gas in the troposphere and as a reactive source of ozone-destroying nitrogen oxides in the stratosphere. However, there remain significant uncertainties in the global budget of this gas. The marked spatial divide in its reactivity means that all stages in the N2O life cycle—emission, transport, and destruction—must be examined to understand the overall effect of N2O on climate. Source and sink processes of N2O lead to varying concentrations of N2O isotopologues (14N14N16O, 14N15N16O, 15N14N16O, and 14N14N18O being measured) due to preferential isotopic production and elimination in different environments. Estimation of source and sink fluxes can be improved by combining isotopically resolved N2O observations with simulations using a chemical transport model with reanalysis meteorology and treatments of isotopic signatures of specific surface sources and stratospheric intrusions. We present the first few months of site-specific nitrogen and oxygen isotopic composition data from the Stheno-TILDAS instrument (Harris et al, 2013) at Mace Head, Ireland and compare these to results from MOZART-4 (Model for Ozone and Related Chemical Tracers, version 4) chemical transport model runs including N2O isotopic fractionation processes and reanalysis meterological fields (NCEP/NCAR, MERRA, and GEOS-5). This study forms the basis for future inverse modeling experiments that will improve the accuracy of isotopically differentiated N2O emission and loss estimates. Ref: Harris, E., D. Nelson, W. Olszewski, M. Zahniser, K. Potter, B. McManus, A. Whitehill, R. Prinn, and S. Ono, Development of a spectroscopic technique for continuous online monitoring of oxygen and site-specific nitrogen isotopic composition of atmospheric nitrous oxide, Analytical Chemistry, 2013; DOI: 10.1021/ac403606u.

  17. Characteristic Tandem Mass Spectral Features Under Various Collision Chemistries for Site-Specific Identification of Protein S-Glutathionylation

    Science.gov (United States)

    Chou, Chi-Chi; Chiang, Bing-Yu; Lin, Jason Ching-Yao; Pan, Kuan-Ting; Lin, Chun-Hung; Khoo, Kay-Hooi

    2015-01-01

    Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.

  18. Direct analysis of site-specific N-glycopeptides of serological proteins in dried blood spot samples.

    Science.gov (United States)

    Choi, Na Young; Hwang, Heeyoun; Ji, Eun Sun; Park, Gun Wook; Lee, Ju Yeon; Lee, Hyun Kyoung; Kim, Jin Young; Yoo, Jong Shin

    2017-08-01

    Dried blood spot (DBS) samples have a number of advantages, especially with respect to ease of collection, transportation, and storage and to reduce biohazard risk. N-glycosylation is a major post-translational modification of proteins in human blood that is related to a variety of biological functions, including metastasis, cell-cell interactions, inflammation, and immunization. Here, we directly analyzed tryptic N-glycopeptides from glycoproteins in DBS samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS) without centrifugation of blood samples, depletion of major proteins, desalting of tryptic peptides, and enrichment of N-glycopeptides. Using this simple method, we identified a total of 41 site-specific N-glycopeptides from 16 glycoproteins in the DBS samples, from immunoglobulin gamma 1 (IgG-1, 10 mg/mL) down to complement component C7 (50 μg/mL). Of these, 32 N-glycopeptides from 14 glycoproteins were consistently quantified over 180 days stored at room temperature. The major abundant glycoproteins in the DBS samples were IgG-1 and IgG-2, which contain nine asialo-fucosylated complex types of 16 different N-glycopeptide isoforms. Sialo-non-fucosylated complex types were primarily detected in the other glycoproteins such as alpha-1-acid glycoprotein 1, 2, alpha-1-antitypsin, alpha-2-macroglobulin, haptoglobin, hemopexin, Ig alpha 1, 2 chain C region, kininogen-1, prothrombin, and serotransferrin. We first report the characterization of site-specific N-glycoproteins in DBS samples by LC-MS/MS with minimal sample preparation.

  19. Site-specific dynamics of CD11b+ and CD103+ dendritic cell accumulations following ozone exposure.

    Science.gov (United States)

    Brand, Jeffrey D; Ballinger, Carol A; Tuggle, Katherine L; Fanucchi, Michelle V; Schwiebert, Lisa M; Postlethwait, Edward M

    2012-12-15

    Pulmonary dendritic cells (DCs) are among the first responders to inhaled environmental stimuli such as ozone (O(3)), which has been shown to activate these cells. O(3) reacts with epithelial lining fluid (ELF) components in an anatomically site-specific manner dictated by O(3) concentration, airway flow patterns, and ELF substrate concentration. Accordingly, the anatomical distribution of ELF reaction products and airway injury are hypothesized to produce selective DC maturation differentially within the airways. To investigate how O(3) affects regional airway DC populations, we utilized a model of O(3)-induced pulmonary inflammation, wherein C57BL/6 mice were exposed to 0.8 ppm O(3) 8 h/day for 1, 3, and 5 days. This model induced mild inflammation and no remarkable epithelial injury. Tracheal, but not more distant airway sites, and mediastinal lymph node (MLN) DC numbers were increased significantly after the third exposure day. The largest increase in each tissue was of the CD103(+) DC phenotype. After 3 days of exposure, fewer DCs expressed CD80, CD40, and CCR7, and, at this same time point, total MLN T cell numbers increased. Together, these data demonstrate that O(3) exposure induced site-specific and phenotype changes in the pulmonary and regional lymph node DC populations. Possibly contributing to ozone-mediated asthma perturbation, the phenotypic changes to DCs within pulmonary regions may alter responses to antigenic stimuli. Decreased costimulatory molecule expression within the MLN suggests induction of tolerance mechanisms; increased tracheal DC number may raise the potential for allergic sensitization and asthmatic exacerbation, thus overcoming O(3)-induced decrements in costimulatory molecule expression.

  20. In vitro dissolution methodology, mini-Gastrointestinal Simulator (mGIS), predicts better in vivo dissolution of a weak base drug, dasatinib.

    Science.gov (United States)

    Tsume, Yasuhiro; Takeuchi, Susumu; Matsui, Kazuki; Amidon, Gregory E; Amidon, Gordon L

    2015-08-30

    USP apparatus I and II are gold standard methodologies for determining the in vitro dissolution profiles of test drugs. However, it is difficult to use in vitro dissolution results to predict in vivo dissolution, particularly the pH-dependent solubility of weak acid and base drugs, because the USP apparatus contains one vessel with a fixed pH for the test drug, limiting insight into in vivo drug dissolution of weak acid and weak base drugs. This discrepancy underscores the need to develop new in vitro dissolution methodology that better predicts in vivo response to assure the therapeutic efficacy and safety of oral drug products. Thus, the development of the in vivo predictive dissolution (IPD) methodology is necessitated. The major goals of in vitro dissolution are to ensure the performance of oral drug products and the support of drug formulation design, including bioequivalence (BE). Orally administered anticancer drugs, such as dasatinib and erlotinib (tyrosine kinase inhibitors), are used to treat various types of cancer. These drugs are weak bases that exhibit pH-dependent and high solubility in the acidic stomach and low solubility in the small intestine (>pH 6.0). Therefore, these drugs supersaturate and/or precipitate when they move from the stomach to the small intestine. Also of importance, gastric acidity for cancer patients may be altered with aging (reduction of gastric fluid secretion) and/or co-administration of acid-reducing agents. These may result in changes to the dissolution profiles of weak base and the reduction of drug absorption and efficacy. In vitro dissolution methodologies that assess the impact of these physiological changes in the GI condition are expected to better predict in vivo dissolution of oral medications for patients and, hence, better assess efficacy, toxicity and safety concerns. The objective of this present study is to determine the initial conditions for a mini-Gastrointestinal Simulator (mGIS) to assess in vivo

  1. Fitness cost implications of phiC31-mediated site-specific integrations in target-site strains of the Mexican fruit fly, Anastrepha ludens (Diptera: Tephritidae)

    Science.gov (United States)

    Site-specific recombination technologies are powerful new tools for the manipulation of genomic DNA in insects that can improve transgenesis strategies such as targeting transgene insertions, allowing transgene cassette exchange and DNA mobilization for transgene stabilization. However, understandin...

  2. Report of the Department of Energy (DOE) Office of Energy Research Review Committee on the site-specific conceptual design of the Superconducting Super Collider

    International Nuclear Information System (INIS)

    1990-09-01

    After it was established in early 1989, the Superconducting Super Collider Laboratory (SSCL) began to prepare a detailed site-specific SSC conceptual design, including cost and schedule estimates. As detailed in the SSC Site-Specific Conceptual Design Report (SCDR), this design builds upon the design in the March 1986 SSC Conceptual Design Report (CDR) and takes into account characteristics of the SSC site, results of continuing magnet R ampersand D, and advances in accelerator design

  3. Site-specific reaction rate constant measurements for various secondary and tertiary H-abstraction by OH radicals

    KAUST Repository

    Badra, Jihad

    2015-02-01

    Reaction rate constants for nine site-specific hydrogen atom (H) abstraction by hydroxyl radicals (OH) have been determined using experimental measurements of the rate constants of Alkane+OH→Products reactions. Seven secondary (S 20, S 21, S 22, S 30, S 31, S 32, and S 33) and two tertiary (T 100 and T 101) site-specific rate constants, where the subscripts refer to the number of carbon atoms (C) connected to the next-nearest-neighbor (N-N-N) C atom, were obtained for a wide temperature range (250-1450K). This was done by measuring the reaction rate constants for H abstraction by OH from a series of carefully selected large branched alkanes. The rate constant of OH with four different alkanes, namely 2,2-dimethyl-pentane, 2,4-dimethyl-pentane, 2,2,4-trimethyl-pentane (iso-octane), and 2,2,4,4-tetramethyl-pentane were measured at high temperatures (822-1367K) using a shock tube and OH absorption diagnostic. Hydroxyl radicals were detected using the narrow-line-width ring-dye laser absorption of the R1(5) transition of OH spectrum near 306.69nm.Previous low-temperature rate constant measurements are added to the current data to generate three-parameter rate expressions that successfully represent the available direct measurements over a wide temperature range (250-1450. K). Similarly, literature values of the low-temperature rate constants for the reaction of OH with seven normal and branched alkanes are combined with the recently measured high-temperature rate constants from our group [1]. Subsequent to that, site-specific rate constants for abstractions from various types of secondary and tertiary H atoms by OH radicals are derived and have the following modified Arrhenius expressions:. S20=8.49×10-17T1.52exp(73.4K/T)cm3molecule-1s-1(250-1450K) S21=1.07×10-15T1.07exp(208.3K/T)cm3molecule-1s-1(296-1440K) S22=2.88×10-13T0.41exp(-291.5K/T)cm3molecule-1s-1(272-1311K) S30=3.35×10-18T1.97exp(323.1K/T)cm3molecule-1s-1(250-1366K) S31=1.60×10-18T2.0exp(500.0K/T)cm3

  4. Controlled cobalt doping in the spinel structure of magnetosome magnetite: New evidences from element- and site-specific XMCD analyses

    Science.gov (United States)

    Pan, Y.; LI, J.; Menguy, N.; Arrio, M. A.; Sainctavit, P.; Juhin, A.; Wang, Y.; Chen, H.; Bunau, O.; Otero, E.; Ohresser, P.

    2016-12-01

    Controlled cobalt doping in the spinel structure of magnetosome magnetite: New evidences from element- and site-specific XMCD analyses Jinhua Li1,2*, Nicolas Menguy2,3, Marie-Anne Arrio3, Philippe Sainctavit3,4, Amélie Juhin3, Yinzhao Wang1,2, Haitao Chen5, Oana Bunau3, Edwige Otero4, Philippe Ohresser4, Yongxin Pan1,21Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China. 2France-China Biomineralization and Nano-structures Laboratory, Chinese Academy of Sciences, Beijing 100029, China. 3IMPMC, CNRS UMR 7590, Sorbonne Universités, MNHN, UPMC, IRD UMR 206, 75005 Paris, France. 4Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France. 5Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China *To whom correspondence may be addressed. Email: lijinhua@mail.iggcas.ac.cnThe biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. However, the coordination chemistry and magnetism of such metal-doped magnetosomes still remains largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe2+ ions by Co2+ ions in octahedral (Oh) sites of magnetite. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study this study indicates a biologically controlled process on cobalt doping and magnetic alteration by MTB system

  5. Site-specific keloid fibroblasts alter the behaviour of normal skin and normal scar fibroblasts through paracrine signalling.

    Directory of Open Access Journals (Sweden)

    Kevin J Ashcroft

    Full Text Available Keloid disease (KD is an abnormal cutaneous fibroproliferative disorder of unknown aetiopathogenesis. Keloid fibroblasts (KF are implicated as mediators of elevated extracellular matrix deposition. Aberrant secretory behaviour by KF relative to normal skin fibroblasts (NF may influence the disease state. To date, no previous reports exist on the ability of site-specific KF to induce fibrotic-like phenotypic changes in NF or normal scar fibroblasts (NS by paracrine mechanisms. Therefore, the aim of this study was to investigate the influence of conditioned media from site-specific KF on the cellular and molecular behaviour of both NF and NS enabled by paracrine mechanisms. Conditioned media was collected from cultured primary fibroblasts during a proliferative log phase of growth including: NF, NS, peri-lesional keloid fibroblasts (PKF and intra-lesional keloid fibroblasts (IKF. Conditioned media was used to grow NF, NS, PKF and IKF cells over 240 hrs. Cellular behavior was monitored through real time cell analysis (RTCA, proliferation rates and migration in a scratch wound assay. Fibrosis-associated marker expression was determined at both protein and gene level. PKF conditioned media treatment of both NF and NS elicited enhanced cell proliferation, spreading and viability as measured in real time over 240 hrs versus control conditioned media. Following PKF and IKF media treatments up to 240 hrs, both NF and NS showed significantly elevated proliferation rates (p<0.03 and migration in a scratch wound assay (p<0.04. Concomitant up-regulation of collagen I, fibronectin, α-SMA, PAI-1, TGF-β and CTGF (p<0.03 protein expression were also observed. Corresponding qRT-PCR analysis supported these findings (P<0.03. In all cases, conditioned media from growing marginal PKF elicited the strongest effects. In conclusion, primary NF and NS cells treated with PKF or IKF conditioned media exhibit enhanced expression of fibrosis-associated molecular markers

  6. Reaction rate constants of H-abstraction by OH from large ketones: Measurements and site-specific rate rules

    KAUST Repository

    Badra, Jihad

    2014-01-01

    Reaction rate constants of the reaction of four large ketones with hydroxyl (OH) are investigated behind reflected shock waves using OH laser absorption. The studied ketones are isomers of hexanone and include 2-hexanone, 3-hexanone, 3-methyl-2-pentanone, and 4-methl-2-pentanone. Rate constants are measured under pseudo-first-order kinetics at temperatures ranging from 866 K to 1375 K and pressures near 1.5 atm. The reported high-temperature rate constant measurements are the first direct measurements for these ketones under combustion-relevant conditions. The effects of the position of the carbonyl group (CO) and methyl (CH3) branching on the overall rate constant with OH are examined. Using previously published data, rate constant expressions covering, low-to-high temperatures, are developed for acetone, 2-butanone, 3-pentanone, and the hexanone isomers studied here. These Arrhenius expressions are used to devise rate rules for H-abstraction from various sites. Specifically, the current scheme is applied with good success to H-abstraction by OH from a series of n-ketones. Finally, general expressions for primary and secondary site-specific H-abstraction by OH from ketones are proposed as follows (the subscript numbers indicate the number of carbon atoms bonded to the next-nearest-neighbor carbon atom, the subscript CO indicates that the abstraction is from a site next to the carbonyl group (CO), and the prime is used to differentiate different neighboring environments of a methylene group):P1,CO = 7.38 × 10-14 exp(-274 K/T) + 9.17 × 10-12 exp(-2499 K/T) (285-1355 K)S10,CO = 1.20 × 10-11 exp(-2046 K/T) + 2.20 × 10-13 exp(160 K/T) (222-1464 K)S11,CO = 4.50 × 10-11 exp(-3000 K/T) + 8.50 × 10-15 exp(1440 K/T) (248-1302 K)S11′,CO = 3.80 × 10-11 exp(-2500 K/T) + 8.50 × 10-15 exp(1550 K/T) (263-1370 K)S 21,CO = 5.00 × 10-11 exp(-2500 K/T) + 4.00 × 10-13 exp(775 K/T) (297-1376 K) © 2014 the Partner Organisations.

  7. Site-specific assessments of the abundance of three inshore dolphin species to inform conservation and management

    Directory of Open Access Journals (Sweden)

    Alexander Mark Brown

    2016-02-01

    Full Text Available Assessing the abundance of wildlife populations is essential to their effective conservation and management. Concerns have been raised over the vulnerability of tropical inshore dolphins in waters off northern Australia to anthropogenic impacts on local populations, yet a lack of abundance data precludes assessment of their conservation status and the management of threats. Using small vessels as cost-effective research platforms, photo-identification surveys and capture-recapture models were applied to provide the first quantitative abundance data for Australian snubfin (Orcaella heinsohni, Australian humpback (Sousa sahulensis, and Indo-Pacific bottlenose dolphins (Tursiops aduncus at five sites in the Kimberley region of north-western Australia. The abundance of each species was highly variable between different sites, likely reflecting species-specific habitat preferences. Within the c. 130 km2 study sites, the estimated abundance of most species was ≤ 60 individuals (excluding calves, and fewer than 20 humpback dolphins were identified at each site in any one 3-5 week sampling period. However, larger estimates of c. 130 snubfin and c. 160 bottlenose dolphins were obtained at two different sites. Several local populations showed evidence of site fidelity, particularly snubfin dolphins. By implementing a standardized, multi-site approach, data on local populations were provided within a broader, regional context, and indicated that each species is patchily distributed in the region. This highlights the need for site-specific baseline data collection using appropriate survey techniques to quantitatively assess the potential impacts of threatening activities to local populations. These findings further illustrate the need to gain a greater understanding of known and potential threats to inshore dolphin populations, their relative impacts, and to mitigate where necessary. In particular, the level of interactions with inshore gillnet fisheries

  8. Site-specific advantages in skeletal geometry and strength at the proximal femur and forearm in young female gymnasts.

    Science.gov (United States)

    Dowthwaite, Jodi N; Rosenbaum, Paula F; Scerpella, Tamara A

    2012-05-01

    We evaluated site-specific skeletal adaptation to loading during growth, comparing radius (RAD) and femoral neck (FN) DXA scans in young female gymnasts (GYM) and non-gymnasts (NON). Subjects from an ongoing longitudinal study (8-26yr old) underwent annual DXA scans (proximal femur, forearm, total body) and anthropometry, completing maturity and physical activity questionnaires. This cross-sectional analysis used the most recent data meeting the following criteria: gynecological age ≤2.5yr post-menarche; and GYM annual mean gymnastic exposure ≥5.0h/wk in the prior year. Bone geometric and strength indices were derived from scans for 173 subjects (8-17yr old) via hip structural analysis (femoral narrow neck, NN) and similar radius formulae (1/3 and Ultradistal (UD)). Maturity was coded as M1 (Tanner I breast), M2 (pre-menarche, ≥Tanner II breast) or M3 (post-menarche). ANOVA and chi square compared descriptive data. Two factor ANCOVA adjusted for age, height, total body non-bone lean mass and percent body fat; significance was tested for main effects and interactions between gymnastic exposure and maturity. At the distal radius, GYM means were significantly greater than NON means for all variables (pproximal femur, GYM exhibited narrower periosteal and endosteal dimensions, but greater indices of cortical thickness, BMC, aBMD and section modulus, with lower buckling ratio (pradius BMC, width, endosteal diameter, cortical cross-sectional area, and section modulus (GYM advantages primarily post-menarche); and 3) UD radius BMC and axial compressive strength (GYM advantages were larger with greater maturity, greatest post-menarche). Maturity-specific comparisons suggested site-specific skeletal adaptation to loading during growth, with greater advantages at the radius versus the proximal femur. At the radius, GYM advantages included greater bone width, cortical cross-sectional area and cortical thickness; in contrast, at the femoral neck, GYM bone tissue cross

  9. Evaluation of site-specific factors influencing heavy metal contents in the topsoil of vegetated infiltration swales

    International Nuclear Information System (INIS)

    Horstmeyer, Nils; Huber, Maximilian; Drewes, Jörg E.; Helmreich, Brigitte

    2016-01-01

    Stormwater runoff of traffic areas is usually polluted by organic and inorganic substances and must be treated prior to discharge into groundwater. One widely used treatment method is infiltrating the runoff over the topsoil of vegetated swales. The aim of this study was to evaluate the factors influencing the heavy metal contents in such topsoil layers of vegetated infiltration swales near highways, roads, and parking lots. In total, 262 topsoil samples were taken from 35 sampling sites, which varied in age, traffic volume, road design, driving style, and site-specific conditions. In the evaluation of all soil samples, the median heavy metal values of cadmium, chromium, copper, lead, and zinc were yielding 0.36 (mean: 1.21) mg/kg DM, 37.0 (mean: 44.5) mg/kg DM, 28.0 (mean: 61.5) mg/kg DM, 27.0 (mean: 71.9) mg/kg DM, and 120 (mean: 257) mg/kg DM, respectively. The main purpose was to evaluate the site-specific data (i.e., surrounding land use characteristics, traffic area site data, and operational characteristics). In general, heavy metal contents increased with increasing traffic volumes. However, other factors also had a notable impact. Factors such as road design (e.g., curves, crossings, and roundabouts) and grade of congestion significantly influenced the heavy metal contents. High heavy metal contents were detected for stop-and-go areas, roundabouts, crossings, and sites with traffic lights, signs, and guardrails. Findings of this study can be used to identify highly polluted traffic areas and to verify or improve standards regarding the treatment of runoff from traffic areas. - Highlights: • Correlation of contents with traffic volume, road design, and stop-and-go traffic • Increased heavy metal contents at stop-and-go sites, roundabouts, and crossings • Different soil contents and behavior of cadmium, chromium, copper, lead, and zinc • Identification of factors influencing the variability of zinc in topsoil samples

  10. DEVELOPING SITE-SPECIFIC DERIVED CONCENTRATION GUIDELINE LEVELS FOR MULTIPLE MEDIA AT THE CONNECTICUT YANKEE HADDAM NECK PLANT

    International Nuclear Information System (INIS)

    Taylor, S.W.; Smith, L.C.; Carr, R.K.; Carson, A.; Darois, E.

    2003-01-01

    As part of the license termination process, site-specific Derived Concentration Guideline Levels for the Haddam Neck Plant site are developed for soil, groundwater, concrete left standing, and concrete demolished that satisfy the radiological criteria for unrestricted use as defined in 10 CFR 20.1402. Background information on the license termination process and characteristics of the Haddam Neck Plant site are presented. The dose models and associated resident farmer and building occupancy scenarios, applicable pathways, and critical groups developed to establish the Derived Concentration Guideline Levels are described. A parameter assignment process is introduced wherein general population values are used to establish behavioral and metabolic parameters representative of an average member of the critical group, while the uncertainty associated with important physical parameters is considered. A key element of the parameter assignment process is the use of sensitivity analysis to identify the dose sensitive physical parameters and to ensure that such parameters are assigned conservative values. Structuring the parameter assignment process, completing the formal sensitivity analyses, and assigning conservative values to the sensitive physical parameters in a consistent way establishes a calculation framework that lead to Derived Concentration Guideline Levels with a uniform level of conservatism across all media and all radionuclides

  11. Assessing Optimal Flight Parameters for Generating Accurate Multispectral Orthomosaicks by UAV to Support Site-Specific Crop Management

    Directory of Open Access Journals (Sweden)

    Francisco-Javier Mesas-Carrascosa

    2015-09-01

    Full Text Available This article describes the technical specifications and configuration of a multirotor unmanned aerial vehicle (UAV to acquire remote images using a six-band multispectral sensor. Several flight missions were programmed as follows: three flight altitudes (60, 80 and 100 m, two flight modes (stop and cruising modes and two ground control point (GCP settings were considered to analyze the influence of these parameters on the spatial resolution and spectral discrimination of multispectral orthomosaicked images obtained using Pix4Dmapper. Moreover, it is also necessary to consider the area to be covered or the flight duration according to any flight mission programmed. The effect of the combination of all these parameters on the spatial resolution and spectral discrimination of the orthomosaicks is presented. Spectral discrimination has been evaluated for a specific agronomical purpose: to use the UAV remote images for the detection of bare soil and vegetation (crop and weeds for in-season site-specific weed management. These results show that a balance between spatial resolution and spectral discrimination is needed to optimize the mission planning and image processing to achieve   every agronomic objective. In this way, users do not have to sacrifice flying at low altitudes to cover the whole area of interest completely.

  12. A comparative 'bottom up' proteomics strategy for the site-specific identification and quantification of protein modifications by electrophilic lipids.

    Science.gov (United States)

    Han, Bingnan; Hare, Michael; Wickramasekara, Samanthi; Fang, Yi; Maier, Claudia S

    2012-10-22

    We report a mass spectrometry-based comparative "bottom up" proteomics approach that combines d(0)/d(4)-succinic anhydride labeling with commercially available hydrazine (Hz)-functionalized beads (Affi-gel Hz beads) for detection, identification and relative quantification of site-specific oxylipid modifications in biological matrices. We evaluated and applied this robust and simple method for the quantitative analysis of oxylipid protein conjugates in cardiac mitochondrial proteome samples isolated from 3- and 24-month-old rat hearts. The use of d(0)/d(4)-succinic anhydride labeling, Hz-bead based affinity enrichment, nanoLC fractionation and MALDI-ToF/ToF tandem mass spectrometry yielded relative quantification of oxylipid conjugates with residue-specific modification information. Conjugation of acrolein (ACR), 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-noneal (ONE) to cysteine, histidine and lysine residues were identified. HHE conjugates were the predominant subset of Michael-type adducts detected in this study. The HHE conjugates showed higher levels in mitochondrial preparations from young heart congruent with previous findings by others that the n-3/n-6 PUFA ratio is higher in young heart mitochondrial membranes. Although this study focuses on protein adducts of reactive oxylipids, the method might be equally applicable to protein carbonyl modifications caused by metal catalyzed oxidation reactions. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. A Comparative `Bottom Up' Proteomics Strategy for the Site-specific Identification and Quantification of Protein Modifications By Electrophilic Lipids

    Science.gov (United States)

    Han, Bingnan; Hare, Michael; Wickramasekara, Samanthi; Fang, Yi; Maier, Claudia S.

    2012-01-01

    We report a mass spectrometry-based comparative “bottom up” proteomics approach that combines d0/d4-succinic anhydride labeling with commercially available hydrazine (Hz)-functionalized beads (Affi-gel Hz beads) for detection, identification and relative quantification of site-specific oxylipid modifications in biological matrices. We evaluated and applied this robust and simple method for the quantitative analysis of oxylipid protein conjugates in cardiac mitochondrial proteome samples isolated from 3- and 24-month-old rat hearts. The use of d0/d4-succinic anhydride labeling, Hz-bead based affinity enrichment, nanoLC fractionation and MALDI-ToF/ToF tandem mass spectrometry yielded relative quantification of oxylipid conjugates with residue-specific modification information. Conjugation of acrolein (ACR), 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-noneal (ONE) to cysteine, histidine and lysine residues were identified. HHE conjugates were the predominant subset of Michael-type adducts detected in this study. The HHE conjugates showed higher levels in mitochondrial preparations from young heart congruent with previous findings by others that the n-3/n-6 PUFA ratio is higher in young heart mitochondrial membranes. Although this study focuses on protein adducts of reactive oxylipids the method might be equally applicable to protein carbonyl modifications caused by metal catalyzed oxidation reactions. PMID:22842153

  14. Instrumentation of Molecular Imaging on Site-Specific Targeting Fluorescent Peptide for Early Detection of Breast Cancer

    Science.gov (United States)

    Yu, Ping; Ma, Lixin

    2012-02-01

    In this work we developed two biomedical imaging techniques for early detection of breast cancer. Both image modalities provide molecular imaging capability to probe site-specific targeting dyes. The first technique, heterodyne CCD fluorescence mediated tomography, is a non-invasive biomedical imaging that uses fluorescent photons from the targeted dye on the tumor cells inside human breast tissue. The technique detects a large volume of tissue (20 cm) with a moderate resolution (1 mm) and provides the high sensitivity. The second technique, dual-band spectral-domain optical coherence tomography, is a high-resolution tissue imaging modality. It uses a low coherence interferometer to detect coherent photons hidden in the incoherent background. Due to the coherence detection, a high resolution (20 microns) is possible. We have finished prototype imaging systems for the development of both image modalities and performed imaging experiments on tumor tissues. The spectroscopic/tomographic images show contrasts of dense tumor tissues and tumor necrotic regions. In order to correlate the findings from our results, a diffusion-weighted magnetic resonance imaging (MRI) of the tumors was performed using a small animal 7-Telsa MRI and demonstrated excellent agreement.

  15. Dietary fat and fiber interactively modulate apoptosis and mitochondrial bioenergetic profiles in mouse colon in a site-specific manner.

    Science.gov (United States)

    Fan, Yang-Yi; Vaz, Frederic M; Chapkin, Robert S

    2017-07-01

    We have demonstrated that the combination of bioactive components generated by fish oil (containing n-3 polyunsaturated fatty acids) and fermentable fiber (leading to butyrate production) act coordinately to protect against colon cancer. This is, in part, the result of an enhancement of apoptosis at the base of the crypt across all stages (initiation, promotion, and progression) of colon tumorigenesis. As mitochondria are key organelles capable of regulating the intrinsic apoptotic pathway and mediating programmed cell death, we investigated the effects of diet on mitochondrial function by measuring mucosal cardiolipin composition, mitochondrial respiratory parameters, and apoptosis in isolated crypts from the proximal and distal colon. C57BL/6 mice (n=15/treatment) were fed one of two dietary fats (corn oil and fish oil) and two fibers (pectin and cellulose) for 4 weeks in a 2×2 factorial design. In general, diet modulated apoptosis and the mucosal bioenergetic profiles in a site-specific manner. The fish/pectin diet promoted a more proapoptotic phenotype - for example, increased proton leak (Pinteraction=0.002) - compared with corn/cellulose (control) only in the proximal colon. With respect to the composition of cardiolipin, a unique phospholipid localized to the mitochondrial inner membrane where it mediates energy metabolism, fish oil feeding indirectly influenced its molecular species with a combined carbon number of C68 or greater, suggesting compensatory regulation. These data indicate that dietary fat and fiber can interactively modulate the mitochondrial metabolic profile and thereby potentially modulate apoptosis and subsequent colon cancer risk.

  16. Integrated use of biomarkers and bioaccumulation data in Zebra mussel (Dreissena polymorpha) for site-specific quality assessment.

    Science.gov (United States)

    Binelli, A; Ricciardi, F; Riva, C; Provini, A

    2006-01-01

    One of the useful biological tools for environmental management is the measurement of biomarkers whose changes are related to the exposure to chemicals or environmental stress. Since these responses might vary with different contaminants or depending on the pollutant concentration reached in the organism, the support of bioaccumulation data is needed to prevent false conclusions. In this study, several persistent organic pollutants -- 23 polychlorinated biphenyl (PCB) congeners, 11 polycyclic aromatic hydrocarbons (PAHs), six dichlorodiphenyltricholroethane (DDT) relatives, hexachlorobenzene (HCB), chlorpyrifos and its oxidized metabolite -- and some herbicides (lindane and the isomers alpha, beta, delta; terbutilazine; alachlor; metolachlor) were measured in the soft tissues of the freshwater mollusc Zebra mussel (Dreissena polymorpha) from 25 sampling sites in the Italian portions of the sub-alpine great lakes along with the measure of ethoxyresorufin dealkylation (EROD) and acetylcholinesterase (AChE) activity. The linkage between bioaccumulation and biomarker data allowed us to create site-specific environmental quality indexes towards man-made chemicals. This classification highlighted three different degrees of xenobiotic contamination of the Italian sub-alpine great lakes: a high water quality in Lake Lugano with negligible pollutant levels and no effects on enzyme activities, an homogeneous poor quality for Lakes Garda, Iseo and Como, and the presence of some xenobiotic point-sources in Lake Maggiore, whose ecological status could be jeopardized, also due to the heavy DDT contamination revealed since 1996.

  17. Site-specific activation of dopamine and serotonin transmission by aniracetam in the mesocorticolimbic pathway of rats.

    Science.gov (United States)

    Nakamura, K; Shirane, M; Koshikawa, N

    2001-04-06

    The effects of aniracetam on extracellular levels of dopamine (DA), serotonin (5-HT) and their metabolites were examined in five brain regions in freely moving stroke-prone spontaneously hypertensive rats (SHRSP) using in vivo microdialysis. Basal DA release in SHRSP was uniformly lower in all regions tested than that in age-matched control Wistar Kyoto rats. 3,4-Dihydroxyphenylacetic acid and homovanillic acid levels were altered in the basolateral amygdala, dorsal hippocampus and prefrontal cortex of SHRSP. While basal 5-HT release decreased in the striatum and increased in the basolateral amygdala, there was no associated change in 5-hydroxyindoleacetic acid levels. Systemic administration of aniracetam to SHRSP enhanced both DA and 5-HT release with partly associated change in their metabolite levels in the prefrontal cortex, basolateral amygdala and dorsal hippocampus, but not in the striatum and nucleus accumbens shell, in a dose-dependent manner (30 and/or 100 mg/kg p.o.). Microinjection (1 and 10 ng) of aniracetam or its metabolites (N-anisoyl-GABA and 2-pyrrolidinone) into the nucleus accumbens shell produced no turning behavior. These findings indicate that SHRSP have a dopaminergic hypofunction throughout the brain and that aniracetam elicits a site-specific activation in mesocorticolimbic dopaminergic and serotonergic pathways in SHRSP, possibly via nicotinic acetylcholine receptors in the ventral tegmental area and raphe nuclei. The physiological roles in the aniracetam-sensitive brain regions may closely link with their clinical efficacy towards emotional disturbances appearing after cerebral infarction.

  18. RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells.

    Science.gov (United States)

    Suzuki, Takahiro; Shimizu, Yuri; Furuhata, Erina; Maeda, Shiori; Kishima, Mami; Nishimura, Hajime; Enomoto, Saaya; Hayashizaki, Yoshihide; Suzuki, Harukazu

    2017-09-12

    RUNX1 is an essential master transcription factor in hematopoietic development and plays important roles in immune functions. Although the gene regulatory mechanism of RUNX1 has been characterized extensively, the epigenetic role of RUNX1 remains unclear. Here, we demonstrate that RUNX1 contributes DNA demethylation in a binding site-directed manner in human hematopoietic cells. Overexpression analysis of RUNX1 showed the RUNX1-binding site-directed DNA demethylation. The RUNX1-mediated DNA demethylation was also observed in DNA replication-arrested cells, suggesting an involvement of active demethylation mechanism. Coimmunoprecipitation in hematopoietic cells showed physical interactions between RUNX1 and DNA demethylation machinery enzymes TET2, TET3, TDG, and GADD45. Further chromatin immunoprecipitation sequencing revealed colocalization of RUNX1 and TET2 in the same genomic regions, indicating recruitment of DNA demethylation machinery by RUNX1. Finally, methylome analysis revealed significant overrepresentation of RUNX1-binding sites at demethylated regions during hematopoietic development. Collectively, the present data provide evidence that RUNX1 contributes site specificity of DNA demethylation by recruitment of TET and other demethylation-related enzymes to its binding sites in hematopoietic cells.

  19. Characterization of Site-Specific Glycosylation in Influenza A Virus Hemagglutinin Produced by Spodoptera frugiperda Insect Cell Line.

    Science.gov (United States)

    Liu, Yan-Jun; Wu, Shiaw-Lin; Love, Kerry R; Hancock, William S

    2017-10-17

    Influenza hemagglutinin is a surface glycoprotein related to virus invasion and host immune system response. Understanding site specific glycosylation of hemagglutinin will increase our knowledge about virus evolution and can improve the design and quality of vaccines. In our study, we used glycoproteomic analysis based on multienzyme digestion followed by LC tandem MS analysis to determine the glycosylation of Influenza hemagglutinin (H1/A/California/04/2009) using the following steps: PNGaseF treatment combined with trypsin or pepsin digestion was used to determine the glycosites and glycan occupancy. Three enzymes, trypsin, AspN, and pepsin, were used separately to generate suitable glycopeptides for online LC tandem MS analysis. The glycan structure of a given glycopeptide was determined by collision-induced dissociation MS/MS fragmentation, and the peptide backbone information was provided by collision-induced dissociation (CID)-MS3 fragmentation. With this approach, 100% sequence coverage of the hemagglutinin sample was obtained. Six glycosylation sites fitting the sequon N-X-S/T were successfully confirmed, and the glycan heterogeneity as well as the ratios of glycoforms were determined at each site.

  20. Active site specificity profiling datasets of matrix metalloproteinases (MMPs 1, 2, 3, 7, 8, 9, 12, 13 and 14

    Directory of Open Access Journals (Sweden)

    Ulrich Eckhard

    2016-06-01

    Full Text Available The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015 [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number http://www.ebi.ac.uk/pride/archive/projects/PXD002265.

  1. Site-specific mutagenesis in Enterobacter agglomerans: construction of nif B mutants and analysis of the gene's structure and function.

    Science.gov (United States)

    Siddavattam, D; Nickles, A; Herterich, S; Steibl, H D; Kreutzer, R; Klingmüller, W

    1995-12-15

    A novel technique was developed which may be generally well suited to the site-specific construction of mutations in Enterobacter agglomerans. The method is based on the observation that E. agglomerans can be cured of a plasmid of the incompatibility group IncQ by cultivation on citrate-containing medium. To test the applicability of this technique, we inserted a kanamycin cassette into the cloned nifB gene, transferred it into E. agglomerans, and selected for recombinants in which the wild-type nifB was replaced by the mutated gene by growing transformants on citrate medium with kanamycin. The nifB- mutants with the kanamycin cassette inserted in either orientation showed a nif- phenotype. Further, we determined the nucleotide sequence of nifB. A typical sigma 54-dependent promoter and a consensus NifA binding site were found upstream of nifB. Activation of this promoter by both heterologous and homologous NifA proteins was observed in vivo. The predicted amino acid sequence of the NifB protein showed strong similarity to the NifB sequences of other diazotrophic bacteria. The typical clustering of cysteine residues at the N-terminal end indicates its involvement in Fe-Mo cofactor biosynthesis.

  2. Surface magnetic contribution in zinc ferrite thin films studied by element- and site-specific XMCD hysteresis-loops

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza Zélis, P.; Pasquevich, G.A. [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Departamento de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Salcedo Rodríguez, K.L.; Sánchez, F.H. [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina); Rodríguez Torres, C.E., E-mail: torres@fisica.unlp.edu.ar [IFLP-CCT-La Plata-CONICET and Departamento de Física, Facultad de Ciencias Exactas, C. C. 67, Universidad Nacional de La Plata, 1900 La Plata (Argentina)

    2016-12-01

    Element- and site-specific magnetic hysteresis-loops measurements on a zinc ferrite (ZnFe{sub 2}O{sub 4}) thin film were performed by X-ray magnetic circular dichroism. Results show that iron in octahedral and tetrahedral sites of spinel structure are coupled antiferromagnetically between them, and when magnetic field is applied the magnetic moment of the ion located at octahedral sites aligns along the field direction. The magnetic measurements reveal a distinctive response of the surface with in-plane anisotropy and an effective anisotropy constant value of 12.6 kJ/m{sup 3}. This effective anisotropy is due to the combining effects of demagnetizing field and, volume and surface magnetic anisotropies K{sub V} =3.1 kJ/m{sup 3} and K{sub S} =16 μJ/m{sup 2}. - Highlights: • Surface magnetic response in ZnFe{sub 2}O{sub 4} film (thickness t ∼57 nm) by XMCD is studied. • Measurements of magnetic moment vs. applied field cycles via XMCD are presented. • Fe{sup 3+} at A- and B-sites are coupled antiferromagnetically between them. • A distinctive response of the surface with in-plane magnetic anisotropy is determined. • Volume and surface magnetic anisotropy are determined: 3.1 kJ/m{sup 3} and 16 μJ/m{sup 2}.

  3. In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Stuckey, Samantha; Mukherjee, Kuntal; Storici, Francesca

    2011-01-01

    Delitto perfetto is a site-specific in vivo mutagenesis system that has been developed to generate changes at will in the genome of the yeast Saccharomyces cerevisiae. Using this technique, it is possible to rapidly and efficiently engineer yeast strains without requiring several intermediate steps as it functions in only two steps, both of which rely on homologous recombination to drive the changes to the target DNA region. The first step involves the insertion of a cassette containing two markers at or near the locus to be altered. The second step involves complete removal of this cassette with oligonucleotides and/or other genetic material and transfer of the expected genetic modification(s) to the chosen DNA locus. Here we provide a detailed protocol of the delitto perfetto approach and present examples of the most common and useful applications for in vivo mutagenesis to generate base substitutions, deletions, insertions, as well as for precise in vivo assembly and integration of multiple genetic elements, or gene collage.

  4. The three-dimensional microstructure of trabecular bone: Analysis of site-specific variation in the human jaw bone

    International Nuclear Information System (INIS)

    Kim, Jo Eun; Yi, Won Jin; Heo, Min Suk; Lee, Sam Sun; Choi, Soon Chul; Huh, Kyung Hoe; Shin, Jae Myung; Oh, Sung Ook

    2013-01-01

    This study was performed to analyze human maxillary and mandibular trabecular bone using the data acquired from micro-computed tomography (micro-CT), and to characterize the site-specific microstructures of trabeculae. Sixty-nine cylindrical bone specimens were prepared from the mandible and maxilla. They were divided into 5 groups by region: the anterior maxilla, posterior maxilla, anterior mandible, posterior mandible, and mandibular condyle. After the specimens were scanned using a micro-CT system, three-dimensional microstructural parameters such as the percent bone volume, bone specific surface, trabecular thickness, trabecular separation, trabecular number, structure model index, and degrees of anisotropy were analyzed. Among the regions other than the condylar area, the anterior mandibular region showed the highest trabecular thickness and the lowest value for the bone specific surface. On the other hand, the posterior maxilla region showed the lowest trabecular thickness and the highest value for the bone specific surface. The degree of anisotropy was lowest at the anterior mandible. The condyle showed thinner trabeculae with a more anisotropic arrangement than the other mandibular regions. There were microstructural differences between the regions of the maxilla and mandible. These results suggested that different mechanisms of external force might exist at each site.

  5. The three-dimensional microstructure of trabecular bone: Analysis of site-specific variation in the human jaw bone

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jo Eun; Yi, Won Jin; Heo, Min Suk; Lee, Sam Sun; Choi, Soon Chul; Huh, Kyung Hoe [Dept. of Oral and Maxillofacial Radiology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul (Korea, Republic of); Shin, Jae Myung [Dept. of Oral and Maxillofacial Surgery, Ilsan Paik Hospital, Inje University College of Medicine, Goyang (Korea, Republic of); Oh, Sung Ook [A Plus Dental Clinic, Seoul (Korea, Republic of)

    2013-12-15

    This study was performed to analyze human maxillary and mandibular trabecular bone using the data acquired from micro-computed tomography (micro-CT), and to characterize the site-specific microstructures of trabeculae. Sixty-nine cylindrical bone specimens were prepared from the mandible and maxilla. They were divided into 5 groups by region: the anterior maxilla, posterior maxilla, anterior mandible, posterior mandible, and mandibular condyle. After the specimens were scanned using a micro-CT system, three-dimensional microstructural parameters such as the percent bone volume, bone specific surface, trabecular thickness, trabecular separation, trabecular number, structure model index, and degrees of anisotropy were analyzed. Among the regions other than the condylar area, the anterior mandibular region showed the highest trabecular thickness and the lowest value for the bone specific surface. On the other hand, the posterior maxilla region showed the lowest trabecular thickness and the highest value for the bone specific surface. The degree of anisotropy was lowest at the anterior mandible. The condyle showed thinner trabeculae with a more anisotropic arrangement than the other mandibular regions. There were microstructural differences between the regions of the maxilla and mandible. These results suggested that different mechanisms of external force might exist at each site.

  6. Site-specific modification of genome with cell-permeable Cre fusion protein in preimplantation mouse embryo

    International Nuclear Information System (INIS)

    Kim, Kyoungmi; Kim, Hwain; Lee, Daekee

    2009-01-01

    Site-specific recombination (SSR) by Cre recombinase and its target sequence, loxP, is a valuable tool in genetic analysis of gene function. Recently, several studies reported successful application of Cre fusion protein containing protein transduction peptide for inducing gene modification in various mammalian cells including ES cell as well as in the whole animal. In this study, we show that a short incubation of preimplantation mouse embryos with purified cell-permeable Cre fusion protein results in efficient SSR. X-Gal staining of preimplantation embryos, heterozygous for Gtrosa26 tm1Sor , revealed that treatment of 1-cell or 2-cell embryos with 3 μM of Cre fusion protein for 2 h leads to Cre-mediated excision in 70-85% of embryos. We have examined the effect of the concentration of the Cre fusion protein and the duration of the treatment on embryonic development, established a condition for full term development and survival to adulthood, and demonstrated the germ line transmission of excised Gtrosa26 allele. Potential applications and advantages of the highly efficient technique described here are discussed.

  7. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    International Nuclear Information System (INIS)

    Sibirtsev, Yu.T.; Konechnyi, A.A.; Rasskazov, V.A.

    1986-01-01

    An acid site-specific endonuclease has been detected in mature sea urchin eggs and cells of embryos at early stages of differentiation. Fractionation with ammonium sulfate, followed by chromatography on columns with DEAE, phosphocellulose, and hydroxyapatite resulted in an 18,000-fold purification. The molecular weight of the enzyme was determined at ∼ 29,000, the optimum pH 5.5. The activity of the enzyme does not depend on divalent metal ions, EDTA, ATP, and tRNA, but it is modulated to a substantial degree by NaCl. The maximum rate of cleavage of the DNA supercoil (form I) is observed at 100 mM NaCl. Increasing the NaCl concentration to 350 mM only slightly lowers the rate of cleavage of form I, yielding form II, but entirely suppresses the accumulation of form III. Restriction analysis of the products of enzymatic hydrolysis of Co1E1 and pBR322 DNA showed that at the early stages of hydrolysis the enzyme exhibits pronounced specificity for definite sites, the number of which is 12 for Co1 E1 DNA and 8 sites for pBR322 DNA

  8. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.

    Science.gov (United States)

    Bendl, Jaroslav; Stourac, Jan; Sebestova, Eva; Vavra, Ondrej; Musil, Milos; Brezovsky, Jan; Damborsky, Jiri

    2016-07-08

    HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins' stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein's structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Genetic Code Expansion- and Click Chemistry-Based Site-Specific Protein Labeling for Intracellular DNA-PAINT Imaging.

    Science.gov (United States)

    Nikić-Spiegel, Ivana

    2018-01-01

    Super-resolution microscopy allows imaging of cellular structures at nanometer resolution. This comes with a demand for small labels which can be attached directly to the structures of interest. In the context of protein labeling, one way to achieve this is by using genetic code expansion (GCE) and click chemistry. With GCE, small labeling handles in the form of noncanonical amino acids (ncAAs) are site-specifically introduced into a target protein. In a subsequent step, these amino acids can be directly labeled with small organic dyes by click chemistry reactions. Click chemistry labeling can also be combined with other methods, such as DNA-PAINT in which a "clickable" oligonucleotide is first attached to the ncAA-bearing target protein and then labeled with complementary fluorescent oligonucleotides. This protocol will cover both aspects: I describe (1) how to encode ncAAs and perform intracellular click chemistry-based labeling with an improved GCE system for eukaryotic cells and (2) how to combine click chemistry-based labeling with DNA-PAINT super-resolution imaging. As an example, I show click-PAINT imaging of vimentin and low-abundance nuclear protein, nucleoporin 153.

  10. Quantifying DNA double-strand breaks induced by site-specific endonucleases in living cells by ligation-mediated purification.

    Science.gov (United States)

    Chailleux, Catherine; Aymard, François; Caron, Pierre; Daburon, Virginie; Courilleau, Céline; Canitrot, Yvan; Legube, Gaëlle; Trouche, Didier

    2014-03-01

    Recent advances in our understanding of the management and repair of DNA double-strand breaks (DSBs) rely on the study of targeted DSBs that have been induced in living cells by the controlled activity of site-specific endonucleases, usually recombinant restriction enzymes. Here we describe a protocol for quantifying these endonuclease-induced DSBs; this quantification is essential to an interpretation of how DSBs are managed and repaired. A biotinylated double-stranded oligonucleotide is ligated to enzyme-cleaved genomic DNA, allowing the purification of the cleaved DNA on streptavidin beads. The extent of cleavage is then quantified either by quantitative PCR (qPCR) at a given site or at multiple sites by genome-wide techniques (e.g., microarrays or high-throughput sequencing). This technique, named ligation-mediated purification, can be performed in 2 d. It is more accurate and sensitive than existing alternative methods, and it is compatible with genome-wide analysis. It allows the amount of endonuclease-mediated breaks to be precisely compared between two conditions or across the genome, thereby giving insight into the influence of a given factor or of various chromatin contexts on local repair parameters.

  11. A molecular switch sensor for detection of PRSS1 genotype based on site-specific DNA cleavage of restriction endonuclease.

    Science.gov (United States)

    Liu, Qicai; Gao, Feng; Weng, Shaohuang; Peng, Huaping; Lin, Liqing; Zhao, Chengfei; Lin, Xinhua

    2015-01-01

    PRSS1 mutations or polymorphism in the peripheral blood of patients can be used as susceptible molecular markers to pancreatic cancer. A sensor for selective electrochemical detection of PRSS1 genotypes was developed based on site-specific DNA cleavage of restriction endonuclease EcoRI. A mercapto-modified hairpin probe was immobilized on a gold electrode. The probe's neck can be cleaved by EcoRI in the absence of rs10273639 C/C of PRSS1 genotype, but it cannot be cleaved in the presence of T/T. The difference in quantity of electric charge was monitored by biosensors before and after enzymatic cleavage. Electrochemical signals are generated by differential pulse voltammetry interrogation of methylene blue (MB) that quantitatively binds to surface-confined hairpin probe via electrostatic interactions. The results suggested this method had a good specificity in distinguishing PRSS1 genotypes. There was a good linear relationship between the charge and the logarithmic function of PRSS1 rs10273639 T/T type DNA concentration (current=120.6303+8.8512log C, R=0.9942). The detection limit was estimated at 0.5 fM. The molecular switch sensor has several advantages, and it is possible to qualitatively, quantitatively, and noninvasively detect PRSS1 genotypes in the blood of patients with pancreatic cancer. © 2015 by the Association of Clinical Scientists, Inc.

  12. Identification of the active site serine in pancreatic cholesterol esterase by chemical modification and site-specific mutagenesis.

    Science.gov (United States)

    DiPersio, L P; Fontaine, R N; Hui, D Y

    1990-10-05

    Chemical modification and site-specific mutagenesis approaches were used in this study to identify the active site serine residue of pancreatic cholesterol esterase. In the first approach, purified porcine pancreatic cholesterol esterase was covalently modified by incubation with [3H]diisopropylfluorophosphate (DFP). The radiolabeled cholesterol esterase was digested with CNBr, and the peptides were separated by high performance liquid chromatography. A single 3H-containing peptide was obtained for sequence determination. The results revealed the binding of DFP to a serine residue within the serine esterase homologous domain of the protein. Furthermore, the DFP-labeled serine was shown to correspond to serine residue 194 of rat cholesterol esterase (Kissel, J. A., Fontaine, R. N., Turck, C. W., Brockman, H. L., and Hui, D. Y. (1989) Biochim. Biophys. Acta 1006, 227-236). The codon for serine 194 in rat cholesterol esterase cDNA was then mutagenized to ACT or GCT to yield mutagenized cholesterol esterase with either threonine or alanine, instead of serine, at position 194. Expression of the mutagenized cDNA in COS-1 cells demonstrated that substitution of serine 194 with threonine or alanine abolished enzyme activity in hydrolyzing the water-soluble substrate, p-nitrophenyl butyrate, and the lipid substrates cholesteryl [14C]oleate and [14C] lysophosphatidylcholine. These studies definitively identified serine 194 in the catalytic site of pancreatic cholesterol esterase.

  13. Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Udo; Albers, Boris J.; Liebmann, Marcus; Schwendemann, Todd C.; Baykara, Mehmet Z.; Heyde, Markus; Salmeron, Miquel; Altman, Eric I.; Schwarz, Udo D.

    2008-02-27

    The authors present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1 pm could successfully be resolved. In addition, lateral drifts rates of below 15 pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

  14. Site-Specific Measurement of Water Dynamics in the Substrate Pocket of Ketosteroid Isomerase Using Time-Resolved Vibrational Spectroscopy

    Science.gov (United States)

    Jha, Santosh Kumar; Ji, Minbiao; Gaffney, Kelly J.; Boxer, Steven G.

    2012-01-01

    Little is known about the reorganization capacity of water molecules at the active sites of enzymes and how this couples to the catalytic reaction. Here, we study the dynamics of water molecules at the active site of a highly proficient enzyme, Δ5-3-ketosteroid isomerase (KSI), during a light-activated mimic of its catalytic cycle. Photo-excitation of a nitrile containing photo-acid, coumarin183 (C183), mimics the change in charge density that occurs at the active site of KSI during the first step of the catalytic reaction. The nitrile of C183 is exposed to water when bound to the KSI active site, and we used time-resolved vibrational spectroscopy as a site-specific probe to study the solvation dynamics of water molecules in the vicinity of the nitrile. We observed that water molecules at the active site of KSI are highly rigid, during the light-activated catalytic cycle, compared to the solvation dynamics observed in bulk water. Based upon this result we hypothesize that rigid water dipoles at the active site might help in the maintenance of the pre-organized electrostatic environment required for efficient catalysis. The results also demonstrate the utility of nitrile probes in measuring the dynamics of local (H-bonded) water molecules in contrast to the commonly used fluorescence methods which measure the average behavior of primary and subsequent spheres of solvation. PMID:22931297

  15. Site-specific electron-induced cross-linking of ortho-carborane to form semiconducting boron carbide

    Science.gov (United States)

    Pasquale, Frank L.; Kelber, Jeffry A.

    2012-01-01

    Semiconducting boron carbide (B10C2Hx) films have been formed by bombardment of condensed ortho-carborane (closo-1,2-dicarbadodecaborane) multilayers on polycrystalline copper substrates by 200 eV electrons under ultra-high vacuum conditions. The film formation process was characterized by X-ray and ultraviolet photoelectron spectroscopies. Electron bombardment results in the cross-linking of the icosahedral units. The cross-linking is accompanied by a shift in the B(1s) binding energy indicating site-specific cross-linking between two boron sites on adjacent carborane icosahedra. An additional shift in valence band binding energies attributed to the surface photovoltage effect is indicative of the formation of a p-type semiconductor. This is the first report of B10C2Hx formation by electron bombardment of condensed films, and the data indicate that this method is a viable route towards formation of ultra-thin films of tailored composition and cross-linkages for emerging nanoelectronics and sensor applications.

  16. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

    Science.gov (United States)

    Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

    2015-01-01

    Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

  17. A site-specific and multi-element isotopic approach to origin inference of sugars in foods and beverages

    International Nuclear Information System (INIS)

    Martin, M.L.; Martin, G.J.; Guillou, C.

    1991-01-01

    A strategy is presented for the characterization of sugars according to their botanical origin. The samples fermented in standardized conditions can be described in the multi-dimensional space of the overall carbon isotope ratio of ethanol measured by isotope ratio mass spectrometry (IRMS) and of the specific hydrogen isotope parameters of the methyl and methylene sites derived from nuclear magnetic resonance investigation of site-specific natural isotope fractionation (SNIF-NMR method). In the comparison of natural juices, the deuterium and oxygen-18 parameters of water extracted from the juice and from the end fermentation medium also contain information on the origin of the product. The isotopic effects of the concentration processes leading to concentrated juices, musts and syrups can be estimated and taken into account in interpreting the data. The classification power of this multi-element and multi-site approach is illustrated by discriminant analyses involving selected isotopic variables associated with pineapple, apple and barley sugars, compared to beet and cane sugars which are common sources of enrichment. The ability of the method to detect adulteration by exogenous sugars is improved when environmental conditions can be taken into account. (authors)

  18. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.

    Science.gov (United States)

    Bloom, Jesse D

    2017-01-17

    Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. I describe a new approach that uses a null model based on experimental measurements of a gene's site-specific amino-acid preferences generated by deep mutational scanning in the lab. This null model makes it possible to identify both diversifying selection for repeated amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual protein sites, approaches like the one here can improve our ability to identify many interesting forms of selection in natural sequences. This article was reviewed by Sebastian Maurer-Stroh, Olivier Tenaillon, and Tal Pupko. All three reviewers are members of the Biology Direct editorial board.

  19. Eubacterial SpoVG homologs constitute a new family of site-specific DNA-binding proteins.

    Directory of Open Access Journals (Sweden)

    Brandon L Jutras

    Full Text Available A site-specific DNA-binding protein was purified from Borrelia burgdorferi cytoplasmic extracts, and determined to be a member of the highly conserved SpoVG family. This is the first time a function has been attributed to any of these ubiquitous bacterial proteins. Further investigations into SpoVG orthologues indicated that the Staphylococcus aureus protein also binds DNA, but interacts preferentially with a distinct nucleic acid sequence. Site-directed mutagenesis and domain swapping between the S. aureus and B. burgdorferi proteins identified that a 6-residue stretch of the SpoVG α-helix contributes to DNA sequence specificity. Two additional, highly conserved amino acid residues on an adjacent β-sheet are essential for DNA-binding, apparently by contacts with the DNA phosphate backbone. Results of these studies thus identified a novel family of bacterial DNA-binding proteins, developed a model of SpoVG-DNA interactions, and provide direction for future functional studies on these wide-spread proteins.

  20. Site-Specific Modification Using the 2′-Methoxyethyl Group Improves the Specificity and Activity of siRNAs

    Directory of Open Access Journals (Sweden)

    Xinyun Song

    2017-12-01

    Full Text Available Rapid progress has been made toward small interfering RNA (siRNA-based therapy for human disorders, but rationally optimizing siRNAs for high specificity and potent silencing remains a challenge. In this study, we explored the effect of chemical modification at the cleavage site of siRNAs. We found that modifications at positions 9 and 10 markedly reduced the silencing potency of the unmodified strand of siRNAs but were well tolerated by the modified strand. Intriguingly, addition of the 2′-methoxyethyl (MOE group at the cleavage site improved both the specificity and silencing activity of siRNAs by facilitating the oriented RNA-induced silencing complex (RISC loading of the modified strand. Furthermore, we combined MOE modifications at positions 9 and 10 of one strand together with 2′-O-methylation (OMe at position 14 of the other strand and found a synergistic effect that improved the specificity of siRNAs. The surprisingly beneficial effect of the combined modification was validated using siRNA-targeting endogenous gene intercellular adhesion molecule 1 (ICAM1. We found that the combined modifications eliminated its off-target effects. In conclusion, we established effective strategies to optimize siRNAs using site-specific MOE modifications. The findings may allow the creation of superior siRNAs for therapy in terms of activity and specificity.